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Are Q(ST)-F(ST) comparisons for natural populations meaningful?

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Abstract

Comparisons between putatively neutral genetic differentiation amongst populations, F(ST), and quantitative genetic variation, Q(ST), are increasingly being used to test for natural selection. However, we find that approximately half of the comparisons that use only data from wild populations confound phenotypic and genetic variation. We urge the use of a clear distinction between narrow-sense Q(ST), which can be meaningfully compared with F(ST), and phenotypic divergence measured between populations, P(ST), which is inadequate for comparisons in the wild. We also point out that an unbiased estimate of Q(ST) can be found using the so-called 'animal model' of quantitative genetics.

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... A measure that has been proposed as a potential proxy for Q ST is the P ST , or phenotypic divergence in a trait across populations (Brommer, 2011, Leinonen et al., 2006, Leinonen et al., 2013. However, P ST results should be interpreted with caution (Pujol et al., 2008). This is because P ST might be biased by the inherent influence of environmental effects, nonadditive genetic variances, and genotype by environment interactions (Brommer, 2011, Leinonen et al., 2006. ...
... In a similar fashion as the comparison Q ST vs F ST , the comparison P ST vs F ST has been used in several studies in order to detect selection (reviewed by Brommer, 2011). However, the interpretation of these results should be carried out with caution, as P ST could include environmental and nonadditive genetic effects (Pujol et al., 2008). The fact that our P ST estimates were greater than Q ST corroborates that P ST vs F ST comparisons should be avoided as a general method to study local adaptation, as also suggested by Pujol et al. (2008). ...
... However, the interpretation of these results should be carried out with caution, as P ST could include environmental and nonadditive genetic effects (Pujol et al., 2008). The fact that our P ST estimates were greater than Q ST corroborates that P ST vs F ST comparisons should be avoided as a general method to study local adaptation, as also suggested by Pujol et al. (2008). Then, the use of P ST as a proxy for Q ST can only be justified when between and within population estimates of additive genetic variation are available or can be reliably inferred by different approaches (Brommer, 2011;Cohen and Dor, 2018;Gentili et al., 2018;Monzón-Arguëllo et al., 2014). ...
Article
The rough periwinkle Littorina saxatilis is characterised for showing shell phenotypic variation associated to environmental clines and this is found in parallel across shores. In order to disentangle the additive genetic effects and the environmental factors involved in this variation, we analysed natural populations subjected to a gradient in wave exposure and crab predation in 3 different Rias (primary estuaries) from Galicia (NW Spain). In addition to previously described “Crab” and “Wave” ecotypes, we studied a new phenotype (“Crab+”) associated to the most sheltered habitats of the gradient. We obtained estimates of heritability and Qst (between population genetic differentiation) in embryos and Pst (between population phenotypic differentiation) in adults for shell morphology traits. Heritability estimates were close to one for shell size and relative shell aperture, suggesting a low impact of environmental factors in embryos. Estimates of Qst between ecotypes were significant and typically much higher than published Fst estimates from neutral markers, indicating a role for selection on shaping additive genetic variation. Estimates of Pst between ecotypes for adults were substantially larger than embryos´ Qst, suggesting also a role of phenotypic plasticity in ecotype differentiation. Our results suggest that Pst vs Fst comparisons should be taken with caution because they might not reflect real additive genetic effects, but Pst vs Qst comparisons could shed light into the role of phenotypic plasticity.
... Varying environmental conditions affecting different whelk populations can create an inequality of c and h 2 (Saether et al. 2007, Pujol et al. 2008, Brommer 2011. Therefore the sensitivity of PST comparisons (Paper III&IV) with the neutral expectation of genetic drift and migration, was evaluated by using a selection of simulated values of c/h 2 (from 0.2 to 2.0, as in Brommer (2011)). ...
... A common garden experiment was designed in order to study the interaction of environmental and genetic effects on the shell morphology of the common whelk (Paper IV), both on a fine-(within Breiðafjörður) and large-scale (across the North Atlantic). Common garden experiments allow us to control for possible environmental effects on morphological variation in animal population (Pascoal et al. 2012, Villemereuil et al. 2015 by rearing individuals from the same species or population from the egg/larval stage in a controlled environment and estimate genetic components and partition of genetic variance among groups (Saether et al. 2007, Pujol et al. 2008, Brommer 2011, Villemereuil et al. 2015. If the genetic effect on the morphological characteristics is independent of the environment, individuals from different areas will maintain their distinct morphology during the experiment, whereas if the characteristics are the result of plastic responses to the environment, the organisms will have similar genetic components and partition of genetic variance among groups (Saether et al. 2007, Pujol et al. 2008, Brommer 2011, Villemereuil et al. 2015. ...
... Common garden experiments allow us to control for possible environmental effects on morphological variation in animal population (Pascoal et al. 2012, Villemereuil et al. 2015 by rearing individuals from the same species or population from the egg/larval stage in a controlled environment and estimate genetic components and partition of genetic variance among groups (Saether et al. 2007, Pujol et al. 2008, Brommer 2011, Villemereuil et al. 2015. If the genetic effect on the morphological characteristics is independent of the environment, individuals from different areas will maintain their distinct morphology during the experiment, whereas if the characteristics are the result of plastic responses to the environment, the organisms will have similar genetic components and partition of genetic variance among groups (Saether et al. 2007, Pujol et al. 2008, Brommer 2011, Villemereuil et al. 2015. Egg-masses and juveniles (after hatching) were reared in 4-liter buckets with aerated seawater at 3-6° C (Smith and Thatje 2012) at Hólar University and cohorts of potential siblings (i.e. ...
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Variation in morphology of shelled marine gastropods across small spatial scales may reflect restricted population connectivity, resulting in evolutionary or plastic responses to environmental heterogeneity. Species delimitation of shelled gastropods is often based solely on shell characteristics; therefore, morphological variation can lead to taxonomic confusion and inaccurate estimates of species diversity. A comprehensive delimitation approach based on both phenotypic and genotypic information is needed in the face of such taxonomic uncertainty. The common whelk Buccinum undatum, a subtidal gastropod ubiquitous in the North Atlantic, exhibits considerable spatial variation in shell morphology and color. The purpose of the current project was to perform a comprehensive analysis of phenotypic differentiation across the whelk’s distribution and compare with a revised analysis of molecular genetic differentiation among the populations. Phylogenetic reconstruction revealed monophyletic Eastern and Western North Atlantic whelk lineages, which diverged early in the Pleistocene glaciation (~2.1 Mya). Species screening indices indicated cryptic speciation as a result of allopatric divergence. Genetic distances between populations from the two continents were similar to or greater than interspecific genetic distances across several North Pacific and North Atlantic Buccinum species. Morphological differentiation in whelk populations across the North Atlantic reflected this genetic split. Concordant with observed genetic differentiation, Canadian and Icelandic whelk reared in a common garden experiment revealed consistent morphological differences between juveniles from the two continents. Finally, analysis of fine-scaled phenotypic variation of common whelk in Breiðafjörður, Iceland, revealed that shell color diversity, shape and proportion of striped individuals were all related to depth.
... The population structure based on components of phenotypic variance was quantifi ed by P ST (Brommer, 2011;Pujol et al., 2008), estimated according to the expression: ...
... The P ST -F ST comparison showed that the among-fruit differentiation for the two wing traits was higher than expected under a neutral model. Despite the potential pitfalls of using P ST as an approximation of Q ST (Pujol et al., 2008), the differences in P ST estimates among different quantitative traits also support the hypothesis that wing traits might be a response to environmental challenges yielding different outcomes in different fruits. The effects of the host on wing morphology have been recorded in cactophylic species of Drosophila (Robertson, 1987;Soto et al., 2010) as well as in several tephritid species (Navarro-Campos et al., 2011;Gómez Cendra et al., 2016;Pieterse et al., 2017). ...
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In some regions of Argentina and Brazil, the South American fruit fly Anastrepha fraterculus (Wied.) (Diptera: Tephritidae) causes significant damage to crops. An efficient integrated management program requires knowledge of pest population dynamics, dispersion patterns, sexual and oviposition behaviour, and adaptive landscape. The present study combined simple sequence repeat (SSR) molecular markers and morphometric datasets in order to analyse the population structure and infer the oviposition resource use strategy of the females. Infested guava fruits were collected from nine wild trees in Tucumán, Argentina, and a total of 140 adult A. fraterculus were recovered. These were then measured for six morphometric traits and 89 of them were genotyped for eight SSR loci. Genetic variability estimates were high (expected heterozygosity = 0.71, allelic richness = 12.5), with 8 to 20 alleles per locus. According to Wright's F-statistics estimates, the highest proportion (83%) of genetic variation occurred within individuals while variance between and within fruits were similar (≈ 8.5%). Analysis of the cryptic genetic structure based on SSR using different approaches, namely discriminant analysis of principal components (DAPC) and sparse non-negative matrix factorization (SNMF), yielded results consistent with the occurrence of two clusters with virtually no admixture. Average kinship between individuals which had emerged from the same fruit (0.07) was lower than that expected for full-sib families. Univariate and multivariate analyses of phenotypic data showed 54-66% of variance among individuals within fruits and 34-46% among fruits. The comparison between phenotypic (PST) and molecular (FST) differentiation identified wing width and length as possible target of positive selection. The average kinship and high genetic variation within fruits, together with the highly significant genetic differentiation among fruits, supports the hypothesis that each fruit was colonised by about three ovipositing females. The results also indicate that females were able to disperse widely from the emergence site before mating and starting oviposition activity.
... An adjustment for h 2 and c is necessary for B. undatum because the species exhibits late sexual maturity (~5 years), internal fertilization and a long lifespan, which are not ideal characteristics for the detailed common garden studies needed to estimate genetic components affecting shell traits and the partition of genetic variance among groups (Q ST ) (Magnúsdóttir, 2010;Mariani et al., 2012). Different B. undatum populations are likely to be subjected to different environmental conditions that can create an inequality of c and h 2 (Saether et al., 2007;Pujol et al., 2008;Brommer, 2011;Magnúsdóttir et al., 2018), thus the sensitivity of P ST comparisons with the neutral expectation of genetic drift and migration, based on microsatellites (Pálsson et al., 2014) and COI (Magnúsdóttir et al., 2019), was evaluated by performing a selection of simulated values of c/h 2 (from 0.2 to 2.0, as described by Brommer (2011)) for the phenotypic divergence between Canada, the Eastern North Atlantic and Greenland. The F ST for both microsatellites and COI was estimated based on Weir & Cockerham (1984). ...
... Assessment of P ST vs. F ST for such a phenotypically variable species as B. undatum appears to be more sensitive over shorter distances/ more similar environments, as described by Mariani et al. (2012), than when comparisons are made on a larger scale/in variable environments, such as in the present study. This might be attributable to the inequality of additive genetic effects (c) and heritability (h 2 ) across phenotypically plastic populations (Saether et al., 2007;Pujol et al., 2008;Brommer, 2011). Moreover, genetic differences could be caused by drift over such a long time, whereas selection pressure would tend to constrain the shape (Johannesson, 2015;Gemmell et al., 2018). ...
Article
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The variation in shelled marine gastropod morphology across small spatial scales can reflect restricted population connectivity, resulting in evolution or plastic responses to environmental heterogeneity. The common whelk, Buccinum undatum, is a subtidal gastropod, ubiquitous in the North Atlantic, that exhibits considerable spatial variation in shell morphology and colour. Given that species delimitation in shelled marine gastropods is often based on shell characteristics, such morphological variation can lead to taxonomic confusion. Phylogeographical analysis based on mitochondrial DNA and microsatellites suggested cryptic species composed of Western and Eastern North Atlantic common whelk populations, the separation of which dates to the onset of the Pleistocene glaciation ~2.1 Mya. Divergence within the Eastern North Atlantic is more recent and characterized by isolation by distance. In the present study, phenotypic variation in shell morphology across the North Atlantic range is analysed and compared with molecular divergence. The morphological variation of B. undatum populations reflected the pattern observed for the molecular markers only for certain comparisons of populations and might, in other cases, reflect larger constraints on the morphological variation and, possibly, the impact of environmental influences.
... with σ 2 G(among) being the variance between species/ populations and σ 2 G(within) the variance within species/ populations (Raeymaekers et al., 2007;Pujol et al., 2008). P ST values which are magnitude higher genetic differentiation at neutral genetic markers (F ST values) can be a signature of selection (Raeymaekers et al., 2007;Brommer, 2011). ...
... The P ST value (0.48) for stomatal density in the present study was considerably higher than the mean genetic differentiation values between Q. petraea and Q. robur observed at eight microsatellite loci (F ST = 0.030). Higher differentiation at phenotypic traits than at putatively neutral nuclear microsatellites suggests that these traits are under divergent selection and involved in local adaptation (e.g., Conner & Hartl, 2004;Pujol et al., 2008;Whitlock, 2008;Brommer, 2011). P ST is generally higher than neutral genetic differentiation, implying that natural selection overcomes ongoing gene flow to maintain morphological differences (Leinonen et al., 2013). ...
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Abstract: This study examined variation of stomatal density in two populations of Quercus petraea (Matt.) Liebl. and two populations of Q. robur L. from northwestern Turkey. Stomatal density was determined in fully expanded and dried leaf samples that were collected from trees under natural conditions. Stomatal densities of Q. petraea and Q. robur varied from 186 to 459 per mm2 (mean value: 333 stomata per mm2 ) and from 397 to 826 per mm2 (mean value: 517 stomata per mm2 ), respectively. Significant differences in stomatal density were found between these two oak species in Turkey as well as between populations within species. Strong and significant negative correlations were observed between stomatal density and leaf length within each species and across the species. While in Central Europe Q. petraea occurs in drier environments than Q. robur, in the present study Q. robur populations grow in more arid environments and have smaller leaves and a higher stomatal density than Q. petraea. Stomatal density had negative correla- tions with each of the other leaf characters apart from sinus width. In addition, the interspecific PST value (0.48) for stomatal density was relatively high compared to the mean genetic differentiation calculated at eight microsatellite loci (FST = 0.030), suggesting different local adaptations of populations. Further studies that include additional populations will be necessary to associate genetic variation at candidate genes with phenotypic and environmental variation.
... Under controlled conditions, phenotypic differences should be entirely due to additive genetic effects, so c/h 2 = 1 and P ST is equivalent to Q ST , and analogous to Q ST for a given quantitative trait (Wright, 1950). In wild populations, h 2 and c are usually difficult to estimate (Brommer, 2011) and nonadditive genetic effects such as selection can strongly influence the estimation of P ST (Brommer, 2011;Brommer, Hanski, Kekkonen, & Väisänen, 2014;Leinonen, Cano, Mäkinen, & Merilä, 2006;Pujol, Wilson, Ross, & Pannell, 2008). Consequently, we used a sequence of 100 values of c/h 2 between zero and two (Brommer, 2011). ...
... Since most documented phenotypic traits are affected by environmental conditions, at least some fraction of variation in bill size could be due to phenotypic plasticity. To measure the exact contribution of the additive genetic differentiation to bill size, it would be essential to calculate Q ST under common garden conditions (Pujol et al., 2008). ...
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Abstract Despite the enormous advances in genetics, links between phenotypes and genotypes have been made for only a few nonmodel organisms. However, such links can be essential to understand mechanisms of ecological speciation. The Costa Rican endemic Mangrove Warbler subspecies provides an excellent subject to study differentiation with gene flow, as it is distributed along a strong precipitation gradient on the Pacific coast with no strong geographic barriers to isolate populations. Mangrove Warbler populations could be subject to divergent selection driven by precipitation, which influences soil salinity levels, which in turn influences forest structure and food resources. We used single nucleotide polymorphisms (SNPs) and morphological traits to examine the balance between neutral genetic and phenotypic divergence to determine whether selection has acted on traits and genes with functions related to specific environmental variables. We present evidence showing: (a) associations between environmental variables and SNPs, identifying candidate genes related to bill morphology (BMP) and osmoregulation, (b) absence of population genetic structure in neutrally evolving markers, (c) divergence in bill size across the precipitation gradient, and (d) strong phenotypic differentiation (PST) which largely exceeds neutral genetic differentiation (FST) in bill size. Our results indicate an important role for salinity, forest structure, and resource availability in maintaining phenotypic divergence of Mangrove Warblers through natural selection. Our findings add to the growing body of literature identifying the processes involved in phenotypic differentiation along environmental gradients in the face of gene flow.
... P ST estimates in the previous studies were made on traits measured in natural populations. Thus the observed variation between and within populations could include environmental effects, genotype x environment interactions, and non-additive genetic effects, which can inflate the estimated variances [70]. Since the populations in our study were grown in a common environment, most of the environmental effects on variance estimates were likely cancelled out, resulting in a decreased estimate of between population variance. ...
... Non-adaptive phenotypic plasticity has indeed been observed in alpine plant populations (e.g. [70]). However, to evaluate the (non) adaptive character of plasticity in F. rubra, it is necessary to relate the degree of plasticity of each individual to an estimate of its fitness [9,10,78], which is a complicated task in clonal grasses. ...
Article
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Species response to climate change is influenced by predictable (selective) and unpredictable (random) evolutionary processes. To understand how climate change will affect present day species, it is necessary to assess their adaptive potential and distinguish it from the effects of random processes. This will allow predicting how different genotypes will respond to forecasted environmental change. Space for time substitution experiments are an elegant way to test the response of present day populations to climate variation in real time. Here we assess neutral and putatively adaptive variation in 11 populations of Festuca rubra situated along crossed gradients of temperature and moisture using molecular markers and pheno-typic measurements, respectively. By comparing population differentiation in putatively neutral molecular markers and phenotypic traits (Q ST-F ST comparisons), we show the existence of adaptive differentiation in phenotypic traits and their plasticity across the climatic gradient. The observed patterns of differentiation are due to the high genotypic and phenotypic differentiation of the populations from the coldest (and wettest) environment. Finally, we observe statistically significant covariation between markers and phenotypic traits, which is likely caused by isolation by adaptation. These results contribute to a better understanding of the current adaptation and evolutionary potential to face climate change of a widespread species. They can also be extrapolated to understand how the studied populations will adjust to upcoming climate change without going through the lengthy process of phenotyping.
... Structure of epigenetic population variation. We measured epigenetic divergence by computing P st , the phenotypic differentiation between populations (Pujol et al., 2008;Edelaar et al., 2011;Leinonen et al., 2013), for methylation and expression sites across the genome. This measure is analogous to F st (Weir and Cockerham, 1984), varies from 0 to 1, and estimates population differentiation for quantitative traits. ...
... P st is a measure of the proportion of variance explained by between-population divergence. It is the phenotypic analog of the population genetics parameter F st (Leinonen et al., 2013;Pujol et al., 2008). For a single probe, P st was calculated as: σ 2 b /(σ 2 b + 2σ 2 w ), where σ 2 b is the between population variance and σ 2 w is the average within population variance. ...
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DNA methylation is an epigenetic modification, influenced by both genetic and environmental variation, that can affect transcription and many organismal phenotypes. Although patterns of DNA methylation have been shown to differ between human populations, it remains to be determined whether epigenetic diversity mirrors the patterns observed for DNA polymorphisms or gene expression levels. We measured DNA methylation at 480,000 sites in 34 individuals from five diverse human populations in the Human Genome Diversity Panel, and analyzed these together with single nucleotide polymorphisms (SNPs) and gene expression data. We found greater population-specificity of DNA methylation than of mRNA levels, which may be driven by the greater genetic control of methylation. This study provides insights into gene expression and its epigenetic regulation across populations and offers a deeper understanding of worldwide patterns of epigenetic diversity in humans.
... However, such tests have been applied for only a few species, and additional approaches have had to be developed to approximate Q ST from the phenotypic variation observed in natural populations, an estimate called P ST (Storz, 2002). Despite different limitations of these proxies (Pujol et al., 2008;Brommer, 2011), F ST -P ST comparisons do provide evidence that natural selection contributes more to phenotypic differentiation than genetic drift (Ojeda et al., 2016) or phenotypic plasticity (Chin & Sillett, 2016). These tests can also guide the further refinement of research hypotheses and the design of field experiments to test them (Leinonen et al., 2008). ...
... where, σ 2 B and σ 2 W , are, respectively, the betweenand within-population phenotypic variance, h 2 is the heritability of the trait (not available) and c is a constant ascertaining the partitioning of additive genetic effects across populations (also not available); c determines the proportion of phenotypic differentiation that can be accounted for by differences in the distribution of additive genetic variation among localities or by phenotypic plasticity and non-additive effects (Pujol et al., 2008). ...
Article
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Interacting stochastic and selective forces drive population and species divergence. Such interaction may generate contrasting clines between genetic and phenotypic factors, which can be related to either geographical or environmental variation depending on the predominant evolutionary force (which in its turn is partly determined by population size). Here, we investigated whether the morphological and genetic differentiation across a species complex in Abies in central Mexico fits isolation by distance (IBD) or isolation-by-adaptation (IBA) frameworks. This complex includes two species (A. religiosa and A. flinckii) with discernible morphological and environmental differences and dissimilar range sizes. After comparing variation at nuclear SSR loci and diagnostic morphological traits of needles with the climate variables contributing to ecological differentiation, we found that the widely distributed A. religiosa has more genetic diversity and is morphologically more heterogeneous than the geographically restricted A. flinckii. Morphological differentiation at three physiologically important traits (needle thickness, number of stomata rows and location of the resin duct) is significantly correlated with geography in A. flinckii (indicative of IBD), but is significantly associated with climate variation in A. religiosa (suggesting IBA). In agreement with quantitative genetics theory, PST (phenotypic differentiation)-G’ST (genetic differentiation) comparisons indicate contrasting contributions of putatively adaptive (A. religiosa) and stochastic (A. flinckii) factors to the morphological differentiation of species related to their population size. The integration of such quantitative genetic/evolutionary aspects may reinforce species descriptions and help in disentangling resilient taxonomic discordance.
... In order to detect selection and rule out other causes as an explanation for the differentiation of phenotypic traits, it is necessary to compare the observed differentiation with neutral differentiation expected under random genetic drift. Although this has been attempted by contrasting neutral genetic (F ST ) and quantitative trait (Q ST ) differentiation (Brommer, 2011;Østbye, Naesje, Bernatchez, Sandlund, & Hindar, 2005;Ozerov et al., 2015;Whitlock, 2008), assessing the interplay between environmental and genetic causes of differentiation has been problematic as F ST /Q ST comparison does not allow for detection of interactions between phenotypes, genotypes, and the environment (Pujol, Wilson, Ross, & Pannell, 2008). Therefore, it is often challenging to disentangle whether the observed differentiation in phenotypic traits is a response to natural selection or simply just a plastic response to environmental differences, especially when the number of populations is small and they are subject to strong random genetic drift (Brommer, 2011;Leinonen, McCairns, O'Hara, & Merilä, 2013;Ovaskainen, Karhunen, Zheng, Arias, & Merilä, 2011;Pujol et al., 2008). ...
... Although this has been attempted by contrasting neutral genetic (F ST ) and quantitative trait (Q ST ) differentiation (Brommer, 2011;Østbye, Naesje, Bernatchez, Sandlund, & Hindar, 2005;Ozerov et al., 2015;Whitlock, 2008), assessing the interplay between environmental and genetic causes of differentiation has been problematic as F ST /Q ST comparison does not allow for detection of interactions between phenotypes, genotypes, and the environment (Pujol, Wilson, Ross, & Pannell, 2008). Therefore, it is often challenging to disentangle whether the observed differentiation in phenotypic traits is a response to natural selection or simply just a plastic response to environmental differences, especially when the number of populations is small and they are subject to strong random genetic drift (Brommer, 2011;Leinonen, McCairns, O'Hara, & Merilä, 2013;Ovaskainen, Karhunen, Zheng, Arias, & Merilä, 2011;Pujol et al., 2008). However, recent efforts in coupling quantitative and population genetic theory have created realistic models (Ovaskainen et al., 2011) and tools (R package "driftsel," Karhunen, Merilä, Leinonen, Cano, & Ovaskainen, 2013), for this exercise. ...
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Adaptive radiation is the evolution of ecological and phenotypical diversity. It arises via ecological opportunity that promotes the exploration of underutilized or novel niches mediating specialization and reproductive isolation. The assumed precondition for rapid local adaptation is diversifying natural selection, but random genetic drift could also be a major driver of this process. We used 27 populations of European whitefish (Coregonus lavaretus) from nine lakes distributed in three neighboring subarctic watercourses in northern Fennoscandia as a model to test the importance of random drift versus diversifying natural selection for parallel evolution of adaptive phenotypic traits. We contrasted variation for two key adaptive phenotypic traits correlated with resource utilization of polymorphic fish; the number of gill rakers and the total length of fish, with the posterior distribution of neutral genetic differentiation from 13 microsatellite loci, to test whether the observed phenotypic divergence could be achieved by random genetic drift alone. Our results show that both traits have been under diversifying selection and that the evolution of these morphs has been driven by isolation through habitat adaptations. We conclude that diversifying selection acting on gill raker number and body size has played a significant role in the ongoing adaptive radiation of European whitefish morphs in this region.
... There are important caveats to this however, for instance when using phenotypic variation as a proxy for quantitative genetic variation (Pujol et al., 2008), or when "isolation by adaptation" scenarios are plausible (e.g., Funk et al., 2011;Nosil et al., 2008). Nonetheless, molecular genetic data provide an important opportunity to nuance expectations of phenotypic structuring among populations hypothesised to have undergone parallel evolution. ...
... Two caveats to this method should be noted: first, it assumes that to a first approximation genome-wide F ST measures neutral differentiation (i.e., from drift and gene flow); second, since we are modelling phenotypic variation in wild caught fish rather than in a commongarden experiment, any contributions to population divergence from phenotypic plasticity are likely to be partitioned into V Pop . S (Pujol et al., 2008 2.4.5 | Genotype-phenotype association mapping from pool-seq data ...
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Parallel evolution, in which independent populations evolve along similar phenotypic trajectories, offers insights into the repeatability of adaptive evolution. Here, we revisit a classic example of parallelism, that of repeated evolution of brighter males in the Trinidadian guppy (Poecilia reticulata). In guppies, colonisation of low predation habitats is associated with emergence of ‘more colourful’ phenotypes since predator‐induced viability selection for crypsis weakens while sexual selection by female preference for conspicuousness remains strong. Our study differs from previous investigations in three respects. First, we adopt a multivariate phenotyping approach to characterise parallelism in multi‐trait space. Second, we use ecologically‐relevant colour traits defined by the visual systems of the two selective agents (i.e. guppy, predatory cichlid). Third, we estimate population genetic structure to test for adaptive (parallel) evolution against a model of neutral phenotypic divergence. We find strong phenotypic differentiation that is inconsistent with a neutral model but very limited support for the predicted pattern of greater conspicuousness at low predation. Effects of predation regime on each trait were in the expected direction, but weak, largely non‐significant, and explained little among‐population variation. In multi‐trait space, phenotypic trajectories of lineages colonising low from high predation regimes were not parallel. Our results are consistent with reduced predation risk facilitating adaptive differentiation, potentially by female choice, but suggest that this proceeds in independent directions of multi‐trait space across lineages. Pool‐sequencing data also revealed SNPs showing greater differentiation than expected under neutrality, among which some are found in genes contributing to colour pattern variation, presenting opportunities for future genetic study.
... Estimating variance components, heritability, and robustness of calyx color P ST − A major critique of P ST using data only from natural populations is that it confounds phenotypic and genetic variation, especially in the case of a phenotypically plastic trait ( Pujol et al., 2008 ). Further, most experiments that use P ST do not estimate heritability, but take a value from the literature and perform a subsequent sensitivity analysis. ...
... Th is P ST -based analysis is robust to previous criticisms concerning studies that involve phenotypic traits with signifi cant plasticity and environmental induction ( Pujol et al., 2008 ;Whitlock, 2008 ). Specifi cally, because our estimates of heritability and genetic variance come from a reciprocal transplant experiment on the off spring of members of the populations in the present study as well as the general European range of S. vulgaris ( Berardi, 2014 ), and because the referenced experimental gardens are located in the area of the populations in the current study, our estimates should be robust and with minimal infl ation of P ST due to environmental eff ects. ...
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Premise of study: Environmental heterogeneity over a species range can lead to divergent selection among populations, leading to phenotypic differences. The plant flavonoid pathway controls key reproductive and defense-related traits and responds to selection and environmental stressors, allowing for hypotheses about phenotypic divergence across environmental gradients. We hypothesized that with increasing elevation, more flavonoids would be produced as a response to increased UV radiation and that plants would be better defended against herbivores. Methods: We measured floral color, flavonoids, and herbivory in natural populations of Silene vulgaris (Caryophyllaceae) along elevational transects in the French Alps. We correlated phenotypes with environmental variables and calculated genotypic divergence (FST) to compare with phenotypic divergence (PST). Key results: We found significant phenotypic variation in S. vulgaris along elevational gradients. Strong positive correlations were observed between floral color, leaf non-anthocyanidin flavonoid concentration, and elevation. Floral anthocyanin and leaf non-anthocyanidin flavonoid phenotypes negatively covaried with temperature and precipitation seasonality. Comparisons of PST to FST provided evidence for stabilizing selection on floral color among transects and divergent selection along the elevational gradient. Conclusions: Flavonoid production increases along elevational gradients in S. vulgaris, with clinal variation in calyx anthocyanins and increasing leaf non-anthocyanin flavonoid concentrations. Despite the photoprotective and antiherbivore properties of some flavonoids, flavonoid production in flowers and leaves was correlated with population microclimatic variables: temperature and precipitation. Taken together, the results suggest that different flavonoid groups are targeted by selection in different tissues and provide evidence for divergent patterns of selection for flavonoids between high and low elevations.
... Several caveats about the use of P ST as an approach to Q ST are well known: non-additive genetic variance (epistasis or dominance effects), maternal effects or environmental factors and genotypeenvironment interaction, can lead to a distorted picture of additive genetic variation when studying only phenotypic variation in natural conditions (Pujol et al., 2008;Brommer, 2011;Leinonen et al., 2013). Nonetheless, here we used a common garden approach, where individuals from different populations were raised and analyzed under the same environmental conditions, which allow us to control some of these unwanted effects. ...
... Thus, P ST estimates depend on the ratio . Since these parameters are extremely changing to obtain in the wild and usually unknown (Pujol et al., 2008), we considered a set of values to calculate P ST (Brommer, 2011). We constructed several matrices for the P ST values obtained for different values of ...
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Del mismo modo que la temperatura y los efectos del cambo climático varían con en el espacio y en el tiempo, esta tesis doctoral se centra en conocer la variación en los límites térmicos fisiológicos a diferentes escalas espacio-temporales así como caracterizar el ambiente térmico al que actualmente se encuentran expuestos las poblaciones y especies de anfibios analizadas. Ello nos permitirá, en primer lugar, aportar información básica para tratar de predecir las consecuencias del calentamiento global, y en segundo lugar, poner a prueba algunas hipótesis macrofisiológicas recientes. Así, los capítulos 1, 2 y 3 se centran en la variabilidad espacial de los límites de tolerancia térmicos en anfibios (a lo largo de gradientes altitudinales y latitudinales). Dado que existe cierta controversia acerca del grado de variación encontrada entre poblaciones de la misma especie y entre especies distintas, los capítulos 1 y 3 adoptan un enfoque interespecífico mientras que el capítulo 2 se ocupa de analizar la variabilidad intraspecífica encontrada para una serie de poblaciones de Rana temporaria a lo largo de un gradiente climático altitudinal. Los capítulos 4, 5 y 6 se centran en analizar el cambio en los límites de tolerancia en el tiempo ya sea a través de procesos de aclimatación (capítulos 4 y 5) o el cambio en las tolerancias térmicas en diferentes estadios de desarrollo (capítulo 6). En el capítulo 1: “Testing the climate variability hypothesis in thermal tolerance limits of tropical and temperate tadpoles”, analizamos la variación latitudinal en los CTmax/CTmin de 47 sp. de anfibios, durante su etapa larvaria, comparando dos comunidades procedentes de Brasil (Bahía) y la Península Ibérica y el Norte de África. En este trabajo ponemos a prueba la hipótesis de variabilidad climática en renacuajos, analizando además la relevancia de la información térmica a escalas micro y macroclimáticas como predictores de estos parámetros fundamentales de las curvas de performance de los ectotermos. En el capítulo 2: “Can breeding phenology and plasticity prevent local adaptation in thermal tolerance?”, estudiamos la variación altitudinal de los límites de tolerancia térmica en once poblaciones de Rana temporaria, al tiempo que caracterizamos su ambiente térmico teniendo en cuenta la fenología de la especie, y discutimos acerca de los aspectos que pueden estar afectando al grado de diferenciación en las tolerancias térmicas mostrado entre las poblaciones, así como si esta diferenciación puede responder a procesos de adaptación local. En el capítulo 3: “Altitudinal variation of the critical thermal limits in 20 species of tadpoles in the tropical Andes”, realizamos una comparación altitudinal interespecífica en los límites térmicos de 20 especies de anuros andinos , durente su etapa larvaria, y una valoración preliminar del riesgo de extinción de estas especies, basándonos en las estimas de su tolerancia al calentamiento. Del mismo modo que en el capítulo 1, comprobaremos además como la hipótesis de variabilidad climática puede explicar los resultados obtenidos. La segunda parte de la tesis trata de los efectos sobre las tolerancias térmicas de la variación temporal, mediante cambios en las temperaturas de aclimatación y el estadio de desarrollo ontogénico: En el capítulo 4: “Acclimation of critical thermal limits in temperate and tropical tadpoles”, analizamos las supuestas diferencias en el potencial de aclimatación de anfibios tropicales y templados, sometidos a temperaturas constantes en el laboratorio (hipótesis de Brattstrom, Brattstrom (1968)). En el capítulo 5: “The effect of constant vs fluctuating acclimation on critical thermal limits in three temperate tadpoles”, comparamos los efectos que la aclimatación puede tener sobre las tolerancia térmica de tres especies de anfibios de la Península Ibérica cuando se usan a) unas temperaturas de aclimatación constantes, o b) simulando unas condiciones similares a las que pueden ocurrir en la naturaleza, mediante el empleo de aclimataciones con temperaturas diarias fluctuantes. En el capítulo 6: “Ontogenetic shifts in thermal tolerances in temperate anurans. Does metamorphosis impose a thermal constraint that may affect vulnerability to global warming?”, analizamos los cambios que tienen lugar a lo largo del desarrollo ontogenético (larvas, metamórficos y juveniles) en la tolerancia térmica de los individuos de seis especies de anuros procedentes de Marruecos y la Península Ibérica.
... Quantitative data were collected from each plant, as indicated by Pujol et al. (2008) and Sahli et al. (2008), for accurate and unbiased estimation of the genetic variance among the subpopulations. Of 3000 seeds sown, 2461 seedlings emerged and were evaluated, representing all 150 open-pollinated families. ...
... Thus, directional selection would cause minimum differences in the allele frequencies of several loci, rendering the quantitative variance lower than the molecular variance among the subpopulations. The robustness of the results was discussed based on the characteristics of the experiment conducted in a greenhouse (Pujol et al. 2008) and on the model used to calculate Q ST -F ST (Whitlock and Guillaume 2009) and F ST via microsatellites (Edelaar and Björklund 2011). ...
Article
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Knowing how microevolutionary processes, such as genetic drift and natural selection, shape variation in adaptive traits is strategic for conservation measures. One way to estimate local adaptation is to compare divergences in quantitative traits (QST) and neutral loci (FST). Therefore, we have assessed the pattern of phenotypic and molecular genetic divergence among natural subpopulations of the fruit tree Eugenia dysenterica DC. A provenance and progeny test was performed to assess the quantitative traits of the subpopulations collected in a wide distribution area of the species in the Brazilian Cerrado. The sampled environments are in a biodiversity hotspot with heterogeneous soil and climate conditions. By associating quantitative trait variation in initial seedling development with neutral microsatellite marker variation, we tested the local adaptation of the traits by the QST–FST contrast. Genetic drift was prevalent in the phenotypic differentiation among the subpopulations, although the traits seedling emergence time and root green mass, which are relevant for adaptation to the Cerrado climate, showed signs of uniform selection. Our results suggest that E. dysenterica has a spatial genetic structure divided into two large groups, separated by a line that divides the Cerrado biome in a southwestern to northeastern direction. This structure must be taken into account for managing E. dysenterica genetic resources both for conservation and breeding purposes.
... Most of the variation in phenotypic traits was greater than the neutral genetic differentiation (P ST > F ST ), suggesting that phenotypic variation cannot be explained by genetic drift alone, but at least partially derives from natural selection. However, since the validity of the approximation of Q ST by P ST has been largely criticized 55 , the results should be interpreted cautiously. Contrary to Q ST , which measures additive genetic differentiation under common garden conditions 56 , P ST is calculated from phenotypic data alone, and thus it cannot distinguish between the contribution of plasticity and genetic evolution to the observed variation. ...
Article
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Studying patterns of phenotypic variation among populations can shed light on the drivers of evolutionary processes. The house sparrow (Passer domesticus) is one of the world's most ubiquitous bird species, as well as a successful invader. We investigated phenotypic variation in house sparrow populations across a climatic gradient and in relation to a possible scenario of an invasion. We measured variation in morphological, coloration, and behavioral traits (exploratory behavior and neophobia) and compared it to the neutral genetic variation. We found that sparrows were larger and darker in northern latitudes, in accordance with Bergmann's and Gloger's biogeographic rules. Morphology and behavior mostly differed between the southernmost populations and the other regions, supporting the possibility of an invasion. Genetic differentiation was low and diversity levels were similar across populations, indicating high gene flow. Nevertheless, the southernmost and northern populations differed genetically to some extent. Furthermore, genetic differentiation (F ST) was lower in comparison to phenotypic variation (P ST), indicating that the phenotypic variation is shaped by directional selection or by phenotypic plasticity. This study expands our knowledge on evolutionary mechanisms and biological invasions.
... The disadvantage of this approach is that PST includes the non-additive genetic variance resulting from environmental factors and genotype by environment interactions. If this is not taken into account, PST may overestimate the amount of additive genetic variance (Pujol et al. 2008). One would expect that, in the wild, environmental effects play a larger role in determining phenotypic variance across populations than within populations. ...
Article
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Genital morphology in animals with internal fertilization is considered to be among the fastest evolving traits. Sexual selection is often proposed as the main driver of genital diversification but the exact selection mechanisms involved are usually unclear. In addition, the mechanisms operating may differ even between pairs of sibling species. We investigated patterns of male genital variation within and between natural populations of the cactophilic fly Drosophila koepferae ranging its entire geographic distribution and compared them with those previously observed in its sibling species, D. buzzatii. Using both mtDNA and nDNA markers we found that genital shape variation in D. koepferae is more restricted than expected for neutral evolution, suggesting the predominance of stabilizing selection. We also detected dissimilar patterns of divergence between populations of D. koepferae that were allopatric and sympatric with D. buzzatii. The constrained evolution inferred for D. koepferae’s genitalia clearly contrasts with the rapid divergence and higher morphological disparity observed in the populations of D. buzzatii. Finally, different possible scenarios of male genital evolution in each species and within the radiation of D. buzzatii cluster are discussed.
... If the observed phenotypic divergence is larger than the neutral genetic divergence, it can be concluded that the observed phenotypic divergence is not only produced by genetic drift; however, this only suggests that the observed phenotypic divergence is larger than that expected due to random effects, and does not demonstrate that the observed phenotypic divergence is produced by genetic divergence. Therefore, this method cannot exclude the possibility that the observed phenotypic divergence is produced by phenotypic plasticity (Pujol et al. 2008). ...
Article
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Transplant and common garden experiments have been used in studies on local adaptation, but are difficult to be conducted for large animals with long life span. A previous study on the southern Japanese islands demonstrated that relative limb lengths of sika deer (Cervus nippon) were short on islands with steep slopes. We hypothesized that this morphological variation was evidence for local adaptation, and tested this hypothesis by comparing phenotypic divergence with neutral genetic divergence among eight populations of the sika deer in the southern Japanese islands. Divergence patterns differed between the phenotypic and neutral genetic features. Genetic similarity was high among individuals on Kyushu (OI, KGS, and KGK). Individuals on Tanegashima (TN) and Yakushima (YK) also constituted a group, whereas individuals on Tsushima (TS), Wakamatsujima (WM), and Kuchinoerabujima (KE) formed a genetically distinct group. Phenotypic data indicated that individuals from TS, OI, KGS, and KGK exhibited similarity, whereas individuals on YK formed an isolated group that was separated from the other populations. The degree of phenotypic divergence was larger than that of neutral genetic divergence between TN and YK. These results suggest that divergent selection worked between two of the eight island populations (TN and YK). The morphological trait of captive-bred individuals from TN and YK, which had never experienced their original environments, retained their original morphological features. By combining the results of multiple analyses, we found that the difference in relative limb length between the two populations was consistent with local adaptation hypothesis, although conclusive results were not obtained for the other populations.
... For more difficult to study species, evidence of local adaptation to environmental gradients stems from comparisons between the extent of trait variation and neutral genetic differentiation (PST-FST comparisons) (Leinonen et al. 2006). While these results are best interpreted with caution because the genetic architecture of traits varies across populations and environments (Brommer 2011;Parsons et al. 2016;Pujol et al. 2008), many marine species demonstrate variation in quantitative traits that exceed expectations given genetic drift alone. These putatively non-neutral patterns often correlate with environmental gradients, suggesting clinal adaptation (Defaveri & Merila 2013;Flanagan et al. 2016;Ledoux et al. 2015;Mariani et al. 2012). ...
Chapter
Biologists hoping to understand the population genetics and evolution of marine organisms face a common challenge. Clear boundaries that define populations, shape gene flow, and drive natural selection are not apparent when looking across a featureless seascape. Instead, many marine species are broadly and continuously distributed across gradients in environmental variables such as pH, temperature, and salinity. Clinal adaptation to these environmental gradients is rampant among marine species and occurs across a broad range of demographic contexts. This chapter describes how the recent application of population genomics tools is beginning to reveal the genetic basis of clinal adaptation to environmental gradients in the sea. First, the chapter outlines the demographic and alternative selective scenarios that produce clinal variation in allele frequency and may result in spurious identification of adaptive genetic variants. Once these pitfalls are considered, the chapter briefly overviews population genomic techniques for identifying adaptive variants. Then, relevant and recent empirical studies are reviewed to draw generalizations about the genetic basis of clinal adaptation in the marine environment. Finally, future directions for the field are outlined, emphasizing an increased integration of the phenotype and genetic architecture in analyses of clinal adaptation and highlighting the potential of new tools such as machine learning and polygenic analysis.
... where r 2 B is the phenotypic variance between populations, r 2 W is the phenotypic variance within populations, h 2 is the heritability of the trait, and the scalar c is the proportion of the total phenotypic divergence between populations due to the partitioning of additive genetic variance between populations. Put simply, c measures the degree to which phenotypic differences between populations are caused by between-population genetic differences rather than phenotypic plasticity in response to environmental differences or nonadditive genetic variance (Pujol, Wilson, Ross, & Pannell, 2008). Thus, the accuracy with which P ST approximates Q ST rests on the value of c/h 2 . ...
Article
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During the process of ecological speciation, reproductive isolation results from divergent natural selection and leads to a positive correlation between genetic divergence and adaptive phenotypic divergence, i.e. isolation-by-adaptation (IBA). In natural populations, phenotypic differentiation is often autocorrelated with geographic distance, making IBA difficult to distinguish from the neutral expectation of isolation-by-distance (IBD). We examined these two alternatives in a dramatic case of clinal phenotypic variation in an Andean songbird, the Line-cheeked Spinetail (Cranioleuca antisiensis). At its geographic extremes, this species shows a near three-fold difference in body mass (11.5 to 31.0 g) with marked plumage differences. We analyzed phenotypic, environmental, and genetic data (5,154 SNPs) from 172 individuals and 19 populations sampled along its linear distribution in the Andes. We found that body mass was tightly correlated with environmental temperature, consistent with local adaptation as per Bergmann's Rule. Using a PST-FST analysis, we found additional support for natural selection driving body mass differentiation, but these results could also be explained by environment-mediated phenotypic plasticity. When we assessed the relative support for patterns of IBA and IBD using variance partitioning, we found that IBD was the best explanation for genetic differentiation along the cline. Adaptive phenotypic or environmental divergence can reduce gene flow, a pattern interpreted as evidence of ecological speciation's role in diversification. Our results provide a counterexample to this interpretation. Despite conditions conducive to ecological speciation, our results suggest that dramatic size and environmental differentiation within C. antisiensis are not limiting gene flow.
... P st is a measure of the proportion of variance explained by between-population divergence. It is the phenotypic analog of the population genetics parameter F st 27,29 . For a single probe, P st was calculated as σ 2 b /(σ 2 b + 2σ 2 w ), where σ 2 b is the between population variance and σ 2 w is the average within population variance. ...
Article
DNA methylation is an epigenetic modification, influenced by both genetic and environmental variation, that plays a key role in transcriptional regulation and many organismal phenotypes. Although patterns of DNA methylation have been shown to differ between human populations, it remains to be determined how epigenetic diversity relates to the patterns of genetic and gene expression variation at a global scale. Here we measured DNA methylation at 485,000 CpG sites in five diverse human populations, and analysed these data together with genome-wide genotype and gene expression data. We found that population-specific DNA methylation mirrors genetic variation, and has greater local genetic control than mRNA levels. We estimated the rate of epigenetic divergence between populations, which indicates far greater evolutionary stability of DNA methylation in humans than has been observed in plants. This study provides a deeper understanding of worldwide patterns of human epigenetic diversity, as well as initial estimates of the rate of epigenetic divergence in recent human evolution. DNA methylation patterns are studied in five diverse human populations. The evolutionary stability of DNA methylation in humans is found to be much greater than that observed previously in plants.
... They also vary with the method being used (e.g., sibship similarity vs animal models for V A ). Estimates are therefore associated with a unique set of conditions and cannot be generalized to other populations. Comparisons between multiple populations can still be achieved but require pedigree connections to quantify the effect of shared genes in different environments [17], or controlled conditions to homogenize environmental effects [18]. ...
Article
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Although there are many examples of contemporary directional selection, evidence for responses to selection that match predictions are often missing in quantitative genetic studies of wild populations. This is despite the presence of genetic variation and selection pressures - theoretical prerequisites for the response to selection. This conundrum can be explained by statistical issues with accurate parameter estimation, and by biological mechanisms that interfere with the response to selection. These biological mechanisms can accelerate or constrain this response. These mechanisms are generally studied independently but might act simultaneously. We therefore integrated these mechanisms to explore their potential combined effect. This has implications for explaining the apparent evolutionary stasis of wild populations and the conservation of wildlife.
... For each population pair, pairwise P ST values were calculated for each trait (and for an average P ST ), using the following formula: PST = cσ 2 B /(cσ 2 B + 2h 2 σ 2 W ). In this formula, σ 2 B and σ 2 W are the between-population and within-population variance components for a trait, respectively; h 2 expresses the heritability (the proportion of phenotypic variance that is due to additive genetic effects); the scalar c expresses the proportion of the total variance that is presumed to be due to additive genetic variance across populations (Brommer, 2011;Leinonen et al., 2013). The problems of using P ST as an approximation of Q ST are well known in the literature and mainly caused by the difficulty of performing an accurate estimation of the parameters c (proportion of the total variance) and h 2 (heritability) in the wild, for a set of traits ( Pujol et al., 2008). Consequently, Brommer (2011) recommended assessing the strength of P ST -F ST comparisons exploring the variation range of c and h 2 values, where c ≤ h 2 and ( 0 < c/h 2 ≤ 1). ...
Article
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Background Due to habitat loss and fragmentation, numerous forest species are subject to severe population decline. Investigating variation in genetic diversity, phenotypic plasticity and local adaptation should be a prerequisite for implementing conservation actions. This study aimed to explore these aspects in ten fragmented populations of Physospermum cornubiense in view of translocation measures across its Italian range. Methods For each population we collected environmental data on landscape (habitat size, quality and fragmentation) and local conditions (slope, presence of alien species, incidence of the herbivorous insect Metcalfa pruinosa and soil parameters). We measured vegetative and reproductive traits in the field and analysed the genetic population structure using ISSR markers (STRUCTURE and AMOVA). We then estimated the neutral (F ST ) and quantitative (P ST ) genetic differentiation of populations. Results The populations exhibited moderate phenotypic variation. Population size (range: 16–655 individuals), number of flowering adults (range: 3–420 individuals) and inflorescence size (range: 5.0–8.4 cm) were positively related to Mg soil content. Populations’ gene diversity was moderate (Nei-H = 0.071–0.1316); STRUCTURE analysis identified five different clusters and three main geographic groups: upper, lower, and Apennine/Western Po plain. Fragmentation did not have an influence on the local adaptation of populations, which for all measured traits showed P ST < F ST , indicating convergent selection. Discussion The variation of phenotypic traits across sites was attributed to plastic response rather than local adaptation. Plant translocation from suitable source populations to endangered ones should particularly take into account provenance according to identified genetic clusters and specific soil factors.
... The widespread presence of epigenetic marks in natural populations, thus, poses a challenge for researchers aiming to infer quantitative genetic parameters or estimate population divergence in quantitative traits. While it is well known that phenotypic plasticity can cause similarities between individuals that are not based upon genetic resemblance (Pujol et al. 2008), the same can also hold true for epigenetic inheritance of traits. The authors review the development of breeding designs and analyses that aim to partition epigenetic variance from total genetic variance, but also highlight that epigenetic modulations can still affect the remaining quantitative genetic parameters. ...
... Implications of phenotypic plasticity shaping P ST and Q ST Although it is generally understood that P ST is a bad surrogate for Q ST in Q ST -F ST comparisons (Falconer and Mackay, 1996;Pujol et al., 2008;Brommer, 2011), understanding the relationship between P ST and Q ST can help us understand how plasticity affects population differentiation in the wild. Our models allow to take a closer look at this important question. ...
Article
Several evolutionary processes shape the genetic and phenotypic differentiation of populations. Among them, the joint effects of gene flow, selection and phenotypic plasticity are poorly known, especially when trying to understand how maladaptive plasticity affects population divergence. We extended a quantitative genetic model of Hendry et al. (2001) to describe these joint effects on phenotypic and additive genetic divergence between two populations, and their phenotypic and genetic differentiation (PST and QST). With individual-based simulations, we tested our model predictions and further modeled allelic differentiation at neutral (FST) and adaptive (FSTQ) loci. While adaptive phenotypic plasticity allows for large phenotypic divergence and differentiation despite high gene flow, maladaptive plasticity promotes genetic divergence and generates countergradient variation, under extensive migration with phenotypic differences sometimes opposed to genetic differences. Maladaptive plasticity can also promote adaptive phenotypic divergence by reducing the effective gene flow. Overall, plasticity decouples genetic from phenotypic differences between populations, and blurs the correlation between phenotypic divergence and local adaptation. By deriving models of population differentiation for three different life cycles, we further describe the effect of a species’ ecology on evolution in structured populations.
... Pairwise comparisons between populations were performed with Tukey´s HSD post hoc test at the 5% significance level. Quantitative trait differentiation [15] among populations was estimated for all traits as QST = , with G among being the variance among populations and G withing the variance within populations [17,18]. QST describes the genetic differentiation at traits among provenances in the common garden trial in which the environmental variance is minimized. ...
Article
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Differences in growth traits among twelve populations across the 􀀌􀀞􀀑􀀛􀀏􀀞􀀜􀀁􀀗􀀍􀀏􀀛􀀍􀀘􀀝􀀓􀀑􀀛􀀍 subsp. 􀀜􀀡􀀜􀀂 􀀚􀀔􀀛􀀑􀀘􀀜􀀔􀀜 (ispir oak) distribution range in Turkey were investigated in a common garden seedling trial. The study revealed considerable variation in growth traits across the studied ispir oak populations. The highest values of growth traits were determined in populations of the eastern part of Turkey. Shoot height showed highly significant correlations with environmental variables of populations. The high genetic differentiation at phenotypic traits (QST) in the seedling common garden experiment suggested an important role of these traits in local adaptation. In this regard, it would be beneficial to use local provenance planting stock for woodland production, habitat conservation and restoration.
... Finally, environmental differences between groups are important sources of between-group trait differences. Environmental differences and associated differences in the effect of geneenvironment interactions can act in concert with or in opposition to any genetic differences that influence a trait, leading to between-group trait differences that are larger or smaller than would be expected on the basis of neutral genetic differences alone (Pujol et al. 2008). ...
Article
Models that examine genetic differences between populations alongside a genotype–phenotype map can provide insight about phenotypic variation among groups. We generalize a simple model of a completely heritable, additive, selectively neutral quantitative trait to examine the relationship between single-locus genetic differentiation and phenotypic differentiation on quantitative traits. In agreement with similar efforts using different models, we show that the expected degree to which two groups differ on a neutral quantitative trait is not strongly affected by the number of genetic loci that influence the trait: neutral trait differences are expected to have a magnitude comparable to the genetic differences at a single neutral locus. We discuss this result with respect to population differences in disease phenotypes, arguing that although neutral genetic differences between populations can contribute to specific differences between populations in health outcomes, systematic patterns of difference that run in the same direction for many genetically independent health conditions are unlikely to be explained by neutral genetic differentiation.
... La estructura poblacional basada en componentes de varianza fenotípica fue cuantificada por el coeficiente PST (Brommer, 2011;Pujol et al., 2008), estimada según la Expresión 6: ...
Thesis
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Anastrepha fraterculus, la mosca sudamericana de la fruta, es una importante especie plaga. Utiliza frutas de árboles silvestres y comerciales como sitios de alimentación y cría, acelerando el proceso de descomposición de los frutos. El conocimiento de su dinámica poblacional es de especial interés para la ecología, la biología evolutiva y los programas de manejo. La genética del paisaje combina la genética de poblaciones, la ecología del paisaje y la geoestadística y utiliza marcadores moleculares para cuantificar formalmente la distribución de la variación genética, estimar indirectamente parámetros biológicos y demográficos como la endogamia y la capacidad de dispersión o detectar discontinuidades a pequeña escala en la distribución de las subpoblaciones. En el presente estudio se combinaron datos fenotípicos, genotípicos y espaciales, en el marco de la genética del paisaje, para descubrir la estructura genética espacial (SGS) y los procesos demográficos de una población local de A. fraterculus en la ecorregión de las Yungas, en Argentina. Se analizaron ocho loci de repetición de secuencia simple (SSR) y seis rasgos morfométricos en los individuos obtenidos, considerando los niveles jerárquicos: árbol / fruto / individuo. El análisis paralelo de la variación de rasgos moleculares y múltiples marcadores morfológicos es relevante porque estos últimos se asocian frecuentemente con diferentes componentes del valor adaptativo (fitness), como el éxito en el apareamiento, la tasa de desarrollo y la capacidad de dispersión. El presente trabajo mostró la existencia de una dinámica metapoblacional, con una estructura críptica interna revelada por el análisis bayesiano. Se detectaron 3 grupos o clusters separados espacialmente. Las estimaciones de variabilidad genética fueron altas (He = 0,72, RA = 4,39) y la estructuración genética dentro de los clusters se atribuyó a los árboles de procedencia de las moscas. Los análisis multivariados de los datos fenotípicos mostraron que en promedio el 52,81% de la varianza se explica por el nivel de árbol, seguido por el 28,37% entre individuos. El análisis espacial de los rasgos morfológicos reveló una autocorrelación negativa en todos los casos. SGS y el aislamiento por distancia basado en SSR no mostraron una autocorrelación significativa para coancestría molecular. La comparación entre la diferenciación fenotípica (PST) y molecular (FST) identificó una selección positiva entre moscas a nivel del fruto para todos los rasgos. En cuanto al flujo génico entre subpoblaciones, resultó elevado, con una capacidad de dispersión estimada de al menos 10 km. El tamaño efectivo (Ne) máximo de la metapoblación se estimó en unas 800 moscas y dentro de las subpoblaciones (clusters) el Ne se asoció con los niveles de deriva genética experimentada por los linajes fundadores. La dinámica de la metapoblación cambiaría a lo largo del tiempo debido a la estacionalidad de las actividades de repoblación y de disponibilidad de recursos. La información sobre la estrategia de colonización y la estructura interna revelada en esta tesis puede ser útil para el diseño de una estrategia de manejo integrado. Estos datos podrían ser incorporados en planes de manejo de A. fraterculus en Argentina, lo cual aumentaría su eficiencia y disminuiría el uso de pesticidas.
... Together, these pieces of evidence suggest that selection acting on a few traits could overcome the effects of drift associated with the low observed effective population sizes and high inbreeding in this species. Because populations inhabiting the Cerrado are submitted to seasonal variation of precipitation, such specific traits could be seen as preliminary candidates for local adaptation (see Pujol et al. 2008), but still demand further investigation to confirm their importance. ...
Article
Both genetic drift and divergent selection are predicted to be drivers of population differentiation across patchy habitats, but the extent to which these forces act on natural populations to shape traits is strongly affected by species’ ecological features. In this study, we infer the genomic structure of Pitcairnia lanuginosa, a widespread herbaceous perennial plant with a patchy distribution. We sampled populations in the Brazilian Cerrado and the Central Andean Yungas and discovered and genotyped SNP markers using double-digest restriction-site associated DNA sequencing. In addition, we analyzed ecophysiological traits obtained from a common garden experiment and compared patterns of phenotypic and genetic divergence (PST–FST comparisons) in a subset of populations from the Cerrado. Our results from molecular analyses pointed to extremely low genetic diversity and a remarkable population differentiation, supporting a major role of genetic drift. Approximately 0.3% of genotyped SNPs were flagged as differentiation outliers by at least two distinct methods, and Bayesian generalized linear mixed models revealed a signature of isolation by environment in addition to isolation by distance for high-differentiation outlier SNPs among the Cerrado populations. PST–FST comparisons suggested divergent selection on two ecophysiological traits linked to drought tolerance. We showed that these traits vary among populations, although without any particular macro-spatial pattern, suggesting local adaptation to differences in micro-habitats. Our study shows that selection might be a relevant force, particularly for traits involved in drought stress, even for populations experiencing strong drift, which improves our knowledge on eco-evolutionary processes acting on non-continuously distributed species.
... Selection has also been inferred through comparisons of additive genetic variance of expression (Q ST ) with sequence divergence in neutral molecular markers (F ST ) across populations 44 . However, while Q ST :F ST approaches have been successfully applied to gene expression variation in a few instances [45][46][47][48][49] , accurately estimating the additive genetic basis of gene expression level can be challenging 50 , and there is a tendency for dominance variance to bias Q ST estimates, potentially leading to incorrect inferences of neutrality 44 . ...
Article
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A substantial amount of phenotypic diversity results from changes in gene expression levels and patterns. Understanding how the transcriptome evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of gene expression evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene expression are subject to biases that can lead to false signatures of selection. Here, we first outline the main approaches for describing expression evolution and their inherent biases. Next, we bridge the gap between the fields of phylogenetic comparative methods and transcriptomics to reinforce the main pitfalls of inferring selection on expression patterns and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of transcriptional variation and identifying major, unanswered questions in disentangling how selection acts on the transcriptome.
... In our study of black-fronted terns, we obtained a critical c/h 2 value for weight of 0.252, which is in between those of the other studies. Hence, although our results from the P ST -F ST comparison are suggestive of natural selection along the latitudinal gradient of the South Island, they do not rule out phenotypic plasticity due to environmental, epistatic or dominance effects (Pujol, Wilson, Ross, & Pannell, 2008;Whitlock, 1999). ...
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Aim To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black‐fronted tern (Chlidonias albostriatus), a specialist of the spatially and temporally dynamic environments of braided rivers. Location New Zealand. Methods We used a three‐pronged approach based on 17 microsatellites, two mitochondrial loci (cytochrome b/control region) and phenotypic data (head‐bill length, bill depth, wing length, weight). We determined large‐scale genetic structure throughout the whole breeding range (approx. 150,000 km²), calculated genetic divergence of breeding colonies and tested for isolation‐by‐distance between colonies. We investigated the level of fine‐scale genetic structure based on spatial autocorrelation analyses and assessed the presence of a body size cline based on phenotypic data. Lastly, we compared phenotypic divergence (PST) and the level of divergence by genetic drift (FST) among breeding colonies to test for underlying mechanisms of population differentiation. Results Nuclear and mitochondrial DNA showed that across their range black‐fronted terns were effectively panmictic, with low genetic divergence between breeding colonies overall and no isolation‐by‐distance. However, at fine geographical scales black‐fronted terns accrued significant genetic structure for distances up to 75 km, primarily driven by males, indicating more frequent female dispersal. Furthermore, a phenotypic cline in accordance with Bergmann's rule was evident. PST exceeded FST in three traits, suggestive of local adaptation. Main conclusions Significant fine‐scale structure can be present in highly mobile, specialist species while not affecting spatial structures at larger scales. Hence, methodologies applied to both whole landscapes and local scales are important to appropriately estimate connectivity in dynamic metapopulations and investigate the processes behind connectivity. Conservation management will need to include protecting currently uninhabited patches to facilitate natural colonization of suitable habitat. For black‐fronted terns, managing whole catchments throughout the entire breeding range would be preferable to managing single patches.
... When the magnitude of phenotypic differentiation among populations surpasses genetic differentiation at adaptively neutral loci, it is likely that divergent natural selection has took place (Q ST > F ST ;Spitze 1993;Schluter 2000;Pujol et al. 2008). Here, we estimated the genetic differentiation between two populations of D. stramonium at microsatellite loci and phenotypic differentiation in the concentration Table 4. Asterisks indicate statistically significant differences. ...
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It is thought that natural selection exerted by herbivores on plants has promoted the evolution of plant traits that function as defence. However, such selective pressures may vary spatially differentiating populations in plant defence phenotypes. Yet, to ascertain the role of natural selection on phenotypic differentiation between populations, it is necessary to discard other evolutionary processes like genetic drift. Evolutionary biologists have designed approaches to determine whether population differentiation has been produced by natural selection in contrast to random processes as a null hypothesis. To accomplish this, we compare the magnitude of differentiation among populations in plant defence against herbivores (selection) and in neutral loci (genetic drift). Our study system is the plant Datura stramonium, whose anti-herbivore defence includes tropane alkaloids and foliar trichomes, and its specialized herbivorous insects. We selected two geographically close natural populations of D. stramonium in Central Mexico and estimated, under controlled conditions, population differentiation at neutral loci (microsatellites) and defence traits (concentration of tropane alkaloids and leaf trichome density). Results indicate very low genetic differentiation at neutral loci between populations but strong and significant phenotypic differentiation in putative defence traits. The average values of tropane alkaloids and leaf trichome density were higher in Ticumán than in Teotihuacán. Twelve out of 21 individual tropane alkaloids were significantly more abundant in plants from Ticumán, and the relative proportion of three of them contrasted markedly. Thus, results point that differentiation between populations of D. stramonium results from natural selection on defence traits.
... Using the neutral SNPs from the genome-wide SNP panel, F ST value for genetic divergence was calculated. F ST result between the high-and low-altitude population was 0.007484551, showing a very low degree of genetic divergence due to the altitude (Pujol et al., 2008). Using F ST value, we further derived a value of 33.152 with Nm, using the equation provided by Wright (1951) that Nm = (1 -Fst)/(4Fst). ...
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As an important functional organ of plants, leaves alter their shapes in response to a changing environment. The variation of leaf shape has long been an important evolutionary and developmental force in plants. Despite an increasing amount of investigations into the genetic controls of leaf morphology, few have systematically studied the genetic architecture controlling shape differences among distinct altitudes. Altitude denotes a comprehensive complex of environmental factors affecting plant growth in many aspects, e.g., UV-light radiation, temperature, and humidity. To reveal how plants alter ecological adaptation to altitude through genes, we used Populus szechuanica var. tibetica growing on the Qinghai-Tibetan plateau. FST between the low- and high- altitude population was 0.00748, QST for leaf width, length and area were 0.00924, 0.1108, 0.00964 respectively. With the Elliptic Fourier-based morphometric model, association study of leaf shape was allowed, the dissection of the pleiotropic expression of genes mediating altitude-derived leaf shape variation was performed. For high and low altitudes, 130 and 131 significant single-nucleotide polymorphisms (SNPs) were identified. QTLs that affected leaf axis length and leaf width were expressed in both-altitude population, while QTLs regulating “leaf tip” and “leaf base” were expressed in low-altitude population. Pkinase and PRR2 were common significant genes in both types of populations. Auxin-related and differentiation-related genes included PIN1, CDK-like, and CAK1AT at high altitude, whereas they included NAP5, PIN-LIKES, and SCL1 at low altitude. The presence of Stress-antifung gene, CIPK3 and CRPK1 in high-altitude population suggested an interaction between genes and harsh environment in mediating leaf shape, while the senescence repression-related genes (EIN2 and JMJ18) and JMT in jasmonic acid pathway in low-altitude population suggested their crucial roles in ecological adaptability. These data provide new information that strengthens the understanding of genetic control with respect to leaf shape and constitute an entirely novel perspective regarding leaf adaptation and development in plants.
... It is worth noticing that statistical significance of Q ST versus F ST is diversified with different statistical power and robustness (P-value from the literature). For the sake of clarity, P ST estimates were discarded because they do not control for the effect of the environment (Pujol et al. 2008;Brommer 2011); most were therefore located above the 1: Indeed, under uniform selection, negative covariance between genes effects (which may be seen as linkage disequilibrium, a nonrandom association of genes) builds up, decreasing the between-population variance to levels lower than those predicted on the basis of gene flow alone (Kremer & Le Corre 2012). It is also worth noting that a Q ST < F ST pattern may occur under diversifying selection (Le . ...
Thesis
Force est de constater que les dépérissements forestiers augmentent. Ces observations vont de pairs avec l’accroissement des événements climatiques extrêmes. Aussi dans ce contexte, il est nécessaire d’identifier de nouveaux caractères de resistance à la sécheresse. La résistance à la cavitation est actuellement le meilleur marqueur de la survie d’une espèce à la sécheresse. Cette thèse avait deux objectifs : (i) comprendre le mécanisme de propagation de la cavitation dans le xylème chez les gymnospermes. (ii) Quantifier la variation phénotypique intraspécifique de ce caractère chez Pinus pinaster La variation intraspécifique peut être décomposé en de la variation en variation génétique, de la variation environnemental et de l’interaction des deux (plasticité phénotypique). La démarché a été la suivante (i) une étude interspécifique de la résistance à la cavitation a été couplé à des mesures micro-anatomiques. (ii) Pour le volet intraspécifique, nous avons phénotypé 6 populations dans deux test de populations-descendances, ainsi qu’en population naturelles in situ. La propagation de l’embolie chez les Pinaceae et les ex-Taxodiaceae pourrait être due au passage du germe d’air (rupture capillaire) à travers des nanopores dans le torus. En effet, la pression de rupture d’un ménisque air-sève est corrélée à l’entrée de l’air dans le xylème. Alors que la variation interspécifique est grande, la résistance à la cavitation varie faiblement au sein d’une espèce. Ainsi les populations provenant de climat contrasté ne présentent pas ou peu de différence génétique (en test de provenance) ou en populations naturelles in situ. Ce caractère présente une plasticité phénotypique mais faible comparée à celle de la croissance en hauteur par exemple. La comparaison entre la variation génétique entre populations et la variation des marqueurs neutres entre ces mêmes populations montrent que la variation de ce caractère semble réduite par l’architecture génétique sous-jacente. La resistance à la cavitation est vraisemblablement un trait canalisé.
... The population structure based on components of phenotypic variance was quantified by P ST (Brommer 2011;Pujol et al. 2008), estimated according to the expression: ...
Article
Anastrepha fraterculus (Wiedmann) is an important American pest species. Knowledge of its population dynamics is of particular interest for ecology, evolutionary biology, and management programs. In the present study, phenotypic, genotypic, and spatial data were combined, within the frame of landscape genetics, to uncover the spatial population genetic structure (SGS) and demographic processes of an Argentinian local population from the Yungas ecoregion. Eight simple sequence repeats (SSR) loci and six morphometric traits were analysed considering the hierarchical levels: tree/fruit/individual. Genetic variability estimates were high (H E = 0.72, R A = 4.39). Multivariate analyses of phenotypic data showed that in average 52.81% of variance is explained by the tree level, followed by between individuals 28.37%. Spatial analysis of morphological traits revealed a negative autocorrelation in all cases. SGS analysis and isolation by distance based on SSR showed no significant autocorrelation for molecular coancestry. The comparison between phenotypic (PST) and molecular (FST) differentiation identified positive selection in different fruits for all traits. Bayesian analysis revealed a cryptic structure within the population, with three clusters spatially separated. The results of this study showed a metapopulation dynamics. The genetic background of the components of this metapopulation is expected to change through time due to seasonality, repopulation activities, and high gene flow, with an estimated dispersal ability of at least 10 km. Effective population size (Ne) of the metapopulation was estimated in around 800 flies, and within subpopulations (clusters) Ne was associated with the levels of genetic drift experienced by the founding lineages.
... It was not possible to estimate Q ST because we have no knowledge of the relatedness between trees in the wild populations. The variance in phenotypic values within and among populations was assessed via P ST (Pujol et al., 2008;Brommer, 2011), a surrogate of Q ST defined by: ...
Article
Economically and ecologically important quantitative traits of Acacia aroma are related to life history and the size and shape of fruits and leaves. Substantial variation is observed for these traits in natural populations, suggesting a possible genetic basis that could be useful for selection programmes. Our objective was to detect signals of selection on 12 phenotypic traits in 170 individuals belonging to seven populations of A. aroma in the Chaco Region of Argentina. Phenotypic traits were compared with molecular markers assessed in the same populations. Here, we search for signatures of natural selection by comparing quantitative trait variation to neutral genetic variation through the PST–FST test. We further test for differences among populations for the 12 phenotypic traits, an association of phenotypic variation with environmental variables and geographical distance, and we compare the power of discrimination between the phenotypic and AFLP datasets. The PST–FST test suggested directional selection for tree height and stabilizing selection for the remaining traits. Analyses of variance showed significant differentiation for eight phenotypic traits. These results suggest selecting among provenances as a management strategy to improve tree height (which showed divergent selection), whereas significant genetic gain for the other traits might be obtained by selection within provenances.
... is not justified for this study because we did not measure phenotype in a common garden, and the genetic basis of colour pattern in red-eyed treefrogs is unknown (Pujol et al., 2008). ...
Article
Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of color-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg color patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple color-pattern morphs. To explore possible causes of this variation, we generated a SNP dataset to analyze population genetic structure, measure genetic diversity, and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness correspond with individual measures of color pattern along the coast, including testing for the role of hybridization in geographic regions where orange and purple phenotypic groups co-occur. We found no evidence that color-pattern polymorphism in the transition zone arose through recent hybridization. Instead, a strong pattern of genetic isolation by distance (IBD) indicates that color-pattern variation was either retained through other processes such as ancestral color polymorphisms or ancient secondary contact, or else it was generated by novel mutations. We found that phenotype changes along the Pacific coast more than would be expected based on genetic divergence and geographic distance alone. Combined, our results suggest the possibility of selective pressures acting on color pattern at a small geographic scale.
... Second, we ran models including only random factors within each temperature to get variance components and Q ST estimates specific for each temperature treatment. As our data were obtained from a common garden experiment, the environmental source of phenotypic variance, which can bias Q ST estimates, was excluded (Pujol, Wilson, Ross, & Pannell, 2008). A potential limitation in our study was that it used only full-sib data from F1 offspring and the Q ST estimates were broad sense estimates of genetic variance and may therefore be influenced by nonadditive genetic and maternal sources of variance (Goudet & Büchi, 2006;Merilä & Crnokrak, 2001;Whitlock, 1999). ...
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While adaptive divergence along environmental gradients has repeatedly been demonstrated, the role of postglacial colonization routes in determining phenotypic variation along gradients has received little attention. Here we used a hierarchical QST‐FST approach to separate the roles of adaptive and neutral processes in shaping phenotypic variation in moor frog (Rana arvalis) larval life‐histories along a 1700 km latitudinal gradient across northern Europe. This species has colonized Scandinavia via two routes with a contact zone in northern Sweden. By using neutral SNP and common garden phenotypic data from 13 populations at two temperatures, we showed that most of the variation along the gradient occurred between the two colonizing lineages. We found little phenotypic divergence within the lineages, however, all phenotypic traits were strongly diverged between the southern and northern colonization routes, with higher growth and development rates and larger body size in the north. The QST estimates between the colonization routes were four times higher than FST, indicating a prominent role for natural selection. QST within the colonization routes did not generally differ from FST, but we found temperature‐dependent adaptive divergence close to the contact zone. These results indicate that lineage‐specific variation can account for much of the adaptive divergence along a latitudinal gradient. This article is protected by copyright. All rights reserved.
... Although several caveats are associated with this method (Edelaar et al. 2011), it is widely used to evaluate natural selection (e.g., Gömöry et al. 2015;Bertrand et al. 2016;López et al. 2020). In particular, under common garden conditions, it is possible to overcome the main criticism to the method (Pujol et al. 2008) as phenotypic differences are expected to be entirely due to genetic effects. ...
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The resistance of different genotypes to abiotic stress may be due to genetic effects and/or to phenotypic plasticity allowing them to acclimate to variable conditions. The contribution of one or the other mechanism determines different strategies with implications for the species conservation and adaptive management. In this study, the ecophysiological response to drought of Nothofagus pumilio provenance sites (humid, mesic and xeric) from contrasting precipitation regimes was evaluated in a common garden trial. Seedlings were submitted to progressive drought by withdrawing irrigation (control vs water deficit). Assuming a genetic base determined by selection pressures, populations from more xeric sites are expected to show higher resistance to drought, e. g., higher resistance to xylem cavitation and safety margin, stronger stomatal control and osmotic adjustment. Vulnerability to cavitation curves were performed, and the percentage loss of conductivity (P12, P50, P88 and slope) was obtained. The water potential at turgor loss point (TLP) and the osmotic potential at full turgor (π100) were calculated from pressure–volume curves. The humid site showed a significantly higher P50 value than the mesic and the xeric sites. Pre-dawn water potential differed between the provenances from xeric and mesic conditions under severe water deficit. Natural selection was inferred from the comparison of differentiation at neutral markers and phenotypic traits (FST vs. PST), with signals of adaptive variation (PST > FST) for stomatal density, specific leaf area, TLP, π100 and stomatal conductance. Results suggest a differential adaptive capacity to drought of N. pumilio provenance sites that could be evidencing local adaptation to their home environment.
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The differential response of marine populations to climate change remains poorly understood. Here, we combine common garden thermotolerance experiments in aquaria and population genetics to disentangle the factors driving the population response to thermal stress in a temperate habitat-forming species: the octocoral Paramuricea clavata. Using eight populations separated from tens of meters to hundreds of kilometers, which were differentially impacted by recent mortality events, we identify 25 °C as a critical thermal threshold. After one week of exposure at this temperature, seven of the eight populations were affected by tissue necrosis and after 30 days of exposure at this temperature, the mean % of affected colonies increased gradually from 3 to 97%. We then demonstrate the weak relation between the observed differential phenotypic responses and the local temperature regimes experienced by each population. A significant correlation was observed between these responses and the extent of genetic drift impacting each population. Local adaptation may thus be hindered by genetic drift, which seems to be the main driver of the differential response. Accordingly, conservation measures should promote connectivity and control density erosion in order to limit the impact of genetic drift on marine populations facing climate change.
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The integration of genetic information with ecological and phenotypic data constitutes an effective approach to gain insight into the mechanisms determining interpopulation variability and the evolutionary processes underlying local adaptation and incipient speciation. Here, we use the Pyrenean Morales grasshopper (Chorthippus saulcyi moralesi) as study system to (i) analyze the relative role of genetic drift and selection on range-wide patterns of phenotypic differentiation and (ii) identify the potential selective agents (environment, elevation) responsible for variation. We also test the hypothesis that (iii) the development of dispersal-related traits is associated with different parameters related to population persistence/turnover, including habitat suitability stability over the last 120 000 years, distance to the species distribution core, and population genetic variability. Our results indicate that selection shaped phenotypic differentiation across all the studied morphological traits (body size, forewing length and shape). Subsequent analyses revealed that among-population differentiation in forewing length was significantly explained by a temperature gradient, suggesting an adaptive response to thermoregulation or flight performance under contrasting temperature regimes. We found support for our hypothesis predicting a positive association between the distance to the species distribution core and the development of dispersal-related morphology, which suggests increased dispersal capability in populations located at range edges that, in turn, exhibit lower levels of genetic variability. Overall, our results indicate that range-wide patterns of phenotypic variation are partially explained by adaptation in response to local environmental conditions and differences in habitat persistence between core and peripheral populations.
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Adaptive evolution enhances the fitness of populations via the natural selection of genetic variants. Phenotypic plasticity may also increase fitness but it can be neutral or even maladaptive. In natural environments, water and light are factors that generate plastic responses of plants. The purpose of this study was to analyze the adaptive phenotypic plasticity and the genetic differentiation of wild Capsicum annuum populations in northwest Mexico. 20 families from each population were subject to water-light treatments, assessing nine traits. Significant plastic responses as well as interaction of treatments by populations and treatments by families within populations were detected for almost all traits. Differences among and within populations had a genetic basis. Population trait means were not correlated to latitude. Phenotypic differentiation may be the result of different regimes of natural selection in each population (and non-clinal) or due to genetic drift. Variation in magnitude and patterns of multivariate norms of reaction was detected, pointing a potential to produce large phenotypic responses. Multivariate norms of reaction differentiated populations and treatments effects separately. Water and light drove patterns of multivariate responses, allowing to clarify the effect of each factor. Intensities of selection gradients of foliar traits were larger than vegetative traits. Magnitudes of selection differed among populations and treatments. Selection magnitudes decreased as resource availability increased and correlated negatively to population plasticity. Opposed patterns of linear selection suggested a trade-off between leaf area and specific leaf area. Results suggested that natural selection is relevant in the determination of phenotypic responses of wild Capsicum annuum in northwest Mexico.
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Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 804 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting expression quantitative trait locus (eQTL). Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection.
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Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci-a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other systems. In particular, there is an opportunity to develop new methods that leverage datasets with genomic data and common garden trait measurements to systematically detect the quantitative traits important for adaptation. Here, we develop methods that do just this, using principal components of the relatedness matrix to detect excess divergence consistent with polygenic adaptation, and using a conditional test to control for confounding effects due to population structure. We apply these methods to inbred maize lines from the United States Department of Agriculture germplasm pool and maize landraces from Europe. Ultimately, these methods can be applied to additional domesticated and wild species to give us a broader picture of the specific traits that contribute to adaptation and the overall importance of polygenic adaptation in shaping quantitative trait variation.
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The water hyacinth grasshopper Cornops aquaticum (Bruner 1906) constitutes an appropriate model to assess phenotypic and karyotypic variability in the context of differentiation and adaptation of insect populations because it occurs over a wide latitudinal range. This study represents a general analysis of phenotype, karyotype and molecular variation in native populations of C. aquaticum in South America. This is also relevant because this insect is considered a promising biological control agent of water hyacinth, a native South American aquatic plant but a pest in South Africa. Along Paraná and Uruguay River Basins, body size correlated negatively with latitude, and positively so with temperature and rainfall in both sexes. To test whether the chromosomal and phenotypic patterns were adaptive, we compared them with neutral microsatellite loci variation in populations from the medium and lower course of the Paraná River. Firstly, the lack of pairwise association between karyotype and phenotype distance matrixes with that of neutral loci suggested non-neutrality. Secondly, phenotypic differentiation for all morphometric traits ( P ST ) was significantly larger than molecular differentiation ( F ST ), indicating a prevailing divergence selection effect on the observed phenotypic patterns. Finally, the phenotypic and genotypic spatial structures – inferred from Bayesian approaches – were discordant: neutral genetic structure clustered together most populations except for the two southernmost, downstream ones, whereas phenotypic spatial structure groups together all the deltaic populations and singles out the two northernmost ones. The results suggest directional selection leading to higher centric fusion frequencies in the downstream populations and favouring morphometric optimal differences in relation to the environment.
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In order to elucidate the role of evolutionary forces in shaping the variation of quantitative traits in Senegalia gilliesii we evaluate seven phenotypic traits in three Argentinean populations, two of them sharing environmental and vegetation type conditions, and a third one ecologically differentiated from the former. The phenotypic traits were compared with molecular markers. Here, we search for signatures of selection by means of the comparison PST-FST . We assessed if the averages of the seven phenotypic traits were different among populations by means of ANOVA and we performed discriminant analysis of principal components (DAPC) for both morphological and molecular data. The ANOVA showed significant results only for two traits. For all foliar traits and two spine traits, the PST-FST comparison suggested the occurrence of stabilizing selection. The DAPC obtained from AFLP data showed three well defined groups of populations; when the same analysis was conducted with morphological data the scatterplot showed high overlapping among individuals and could not separate the populations. Overall, our findings suggest a prominent role of stabilizing selection in all foliar traits and stipular spine length. These results could be extrapolated to other tropical and subtropical acacias. Further studies are needed to analyse the mechanisms underlying genetic differentiation in natural populations of S. gilliesii, find its relationship with eco-geographical variables.
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Hymenaea stigonocarpa (Mart. Ex Hayne), popularly known as jatobá-do-cerrado, is a fruit tree widely distributed in the Brazilian Savanna, has multiple uses and is a promising genetic resource. This study aimed to physically characterize fruits and seeds of H. stigonocarpa, as well as to estimate the phenotypic variability at three hierarchical levels: populations, mother trees within populations, and fruits/seeds within mother trees. Fruits from six mother trees were sampled from each of the 25 natural populations found in the Brazilian Savanna. The morphometric characterization of 742 fruits was carried out by evaluating 10 quantitative traits in fruits and seeds. In addition, comparative analyses were performed between the average values of H. stigonocarpa and the botanical variety H. stigonocarpa var. brevipetiolata. Significant phenotypic variations were noticed at all hierarchical levels. A high phenotypic differentiation among the populations was observed for quantitative traits (fruit mass and size, pulp mass and seed mass), being higher when H. stigonocarpa var. brevipetiolata was included in the analysis.
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Quercus vulcanica, an endemic species with scattered distribution, and Q. frainetto are naturally distributed in Turkey. Although they have been reported as closely related species, Q. vulcanica differs from Q. frainetto in the longer petioles and the leaves evenly distributed along the shoots. Knowledge of the amount and distribution of genetic variation in the species and potential hybridization with related species is crucial for the conservation of the species. Therefore, the aims of the study were to analyze leaf morphological and stomatal variation, and to assess patterns of genetic variation at 3 gSSR and 17 expressed sequence tag (EST)-SSR markers within and between four Q. vulcanica and two Q. frainetto populations sampled from Turkey. Based on canonical discriminant and principal component analyses, petiole length, petiole ratio and number of lobes mainly accounted for the discrimination between Q. vulcanica and Q. frainetto. The means of stomatal densities for Q. vulcanica and Q. frainetto were 810 and 862 stomata per mm², respectively. The mean genetic differentiation between Q. frainetto and Q. vulcanica at 20 microsatellite loci was very low (FST = 0.047). Two loci, 2P24 (FST = 0.119, P = 0.003) and PIE102 (FST = 0.127, P < 0.000), showed comparatively high interspecific differentiation and were identified as outlier loci. Genetic assignment analyses and discriminant analyses based on phenotypic traits assigned most individuals to the one or the other species. Further studies including more populations and genome-wide markers are necessary to assess the level of adaptive genetic variation and potential introgression between Q. vulcanica and other related species.
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Phenotypic divergence among natural populations can be explained by natural selection or by neutral processes such as drift. Many examples in the literature compare putatively neutral (FST) and quantitative genetic (QST) differentiation in multiple populations to assess their evolutionary signature and identify candidate traits involved with local adaptation. Investigating these signatures in closely related or recently diversified species has the potential to shed light on the divergence processes acting at the interspecific level. Here, we conducted this comparison in two subspecies of snapdragon plants (eight populations of Antirrhinum majus pseudomajus and five populations of A. m. striatum) in a common garden experiment. We also tested whether altitude was involved with population phenotypic divergence. Our results identified candidate phenological and morphological traits involved with local adaptation. Most of these traits were identified in one subspecies but not the other. Phenotypic divergence increased with altitude for a few biomass‐related traits, but only in A. m. striatum. These traits therefore potentially reflect A. m. striatum adaptation to altitude. Our findings imply that adaptive processes potentially differ at the scale of A. majus subspecies.
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L’adaptation d’un champignon pathogène à son milieu, ainsi que l’évolution et la structuration des populations qui en découlent, sont fortement influencés par ses traits d’histoire de vie qui conditionnent sa fitness. C’est ce que nous avons illustré chez Melampsora larici-populina, l’agent de la rouille du peuplier. Ainsi, nous avons mis en évidence que le volume des spores du champignon évolue de manière répétable au cours des épidémies annuelles dans la vallée de la Durance, et ce sous l’effet de la sélection naturelle, signe que ce trait intervient directement dans le processus adaptatif du champignon. Par conséquent, les contraintes génétiques conditionnant le potentiel adaptatif du champignon en lien avec les traits d’histoire de vie ont été étudiées en laboratoire, au sein d’une descendance S1 issue de l’autofécondation d’une souche de référence. Les résultats obtenus suggèrent que M. larici-populina présente un potentiel adaptatif élevé. Enfin, une carte génétique à haute résolution du champignon, comprenant 18 chromosomes, a été construite afin d’étudier le déterminisme génétique de ces traits d'histoire de vie. Un locus de virulence ainsi que des QTL intervenant dans l’expression de la taille des lésions ont pu être détectés et positionnés avec précision sur cette carte. Ce travail a mis en évidence le rôle des traits quantitatifs dans l’adaptation et la structuration des populations de M. larici-populina en réponse aux pressions de sélection du milieu, en lui conférant un potentiel adaptatif élevée, essence de l’adaptation des organismes. Il ouvre également de nombreuses perspectives de recherche visant à identifier les bases génétiques de l’adaptation de ce champignon pathogène à son hôte, éléments indispensables à l’élaboration de stratégies de lutte durables
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The analysis of quantitative genetic variation is fundamental to conservation biology, as the majority of traits related to individual survival and adaptation to the environment are typically quantitative. The main objective of conservation biology is to guarantee the long-term survival of populations or species at the brink of extinction. Most efforts are devoted to maintain the largest possible fitness and evolutionary potential of populations by avoiding inbreeding depression, genetic drift, and adaptation to captivity. Quantitative genetics provides the main theoretical and empirical framework to develop conservation programs to address these issues.
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Rules are presented for assigning coefficients to the genetic group portion(s) of the mixed model equations after transformation to solve directly for total genetic value (group plus animal solutions) simultaneously for sires and cows using an animal model. Inclusion of all known relationships seems to reduce the need for groups to account for genetic selection and genetic trend. Migration of animals into a population, however, results in a need for grouping to account for genetic merit of the migrants. Selection of parents on which records are not available also creates a need for grouping. Group solutions represent the average genetic merit of phantom (unidentified, or represented by only one descendant) animals selected to be parents that do not have records available. Groups can be crossclassified with time and the genetic path of selection. The total genetic value for every animal includes a function of genetic groups. The function of genetic groups is specific for each individual animal and depends on the number of generations to the base phantom ancestors and on the genetic groups to which those phantom ancestors are assigned. The group coefficients presented account for genetic selection that cannot be defined by known genetic relationships.
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Abstract Population density cycles influence phenotypic evolution through both density-dependent selection during periods of high density and through enhanced genetic drift during periods of low density. We investigated the response of different phenotypic traits to the same density cycles in a population of the yellow-necked mouse, Apodemus flavicollis, from Białowieza National Park in Poland. We examined nonmetric skull traits, skull and mandible size, skull and mandible shape, and transferrin allele frequencies. We found that all of the traits changed significantly over the seven-year study period. The greatest changes in nonmetric traits and mandible size occurred during periods of increasing density, and the magnitude of changes in skull and mandible shape was correlated with the magnitude of density changes. Frequencies of transferrin alleles changed the most when population density was in decline. Changes among the five phenotypic traits were generally uncorrelated with one another, except for skull and mandible shape. Nonmetric traits were selectively neutral when assessed with QST/FST analysis, whereas mandible size, mandible shape, and skull shape showed evidence of fairly strong selection. Selection on skull size was weak or nonexistent. We discuss how different assumptions about the genetic components of variance affect QST estimates when phenotypic variances are substituted for genetic ones. We also found that change in mandible size, mandible shape, skull size, and skull shape were greater than expected under a neutral model given reasonable assumptions about heritability and effective population size.
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Quantitative genetic analyses for body size and for life history characters within and among populations of Daphnia obtusa reveal substantial genetic variance at both hierarchical levels for all traits measured. Simultaneous allozymic analysis on the same population samples indicate a moderate degree of differentiation: GST = 0.28. No associations between electrophoretic genotype and phenotypic characters were found, providing support for the null hypothesis that the allozymic variants are effectively neutral. Therefore, GST can be used as the null hypothesis that neutral phenotypic evolution within populations led to the observed differentiation for the quantitative traits, which I call QST. The results of this study provide evidence that natural selection has promoted diversification for body size among populations, and has impeded diversification for relative fitness. Analyses of population differentiation for clutch size, age at reproduction, and growth rate indicate that neutral phenotypic evolution cannot be excluded as the cause.
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The importance of directional selection relative to neutral evolution may be determined by comparing quantitative genetic variation in phenotype (Q(ST)) to variation at neutral molecular markers (F(ST)). Quantitative divergence between salmonid life history types is often considerable, but ontogenetic changes in the significance of major sources of genetic variance during post-hatch development suggest that selective differentiation varies by developmental stage. In this study, we tested the hypothesis that maternal genetic differentiation between anadromous and resident brook charr (Salvelinus fontinalis Mitchill) populations for early quantitative traits (embryonic size/growth, survival, egg number and developmental time) would be greater than neutral genetic differentiation, but that the maternal genetic basis for differentiation would be higher for pre-resorption traits than post-resorption traits. Quantitative genetic divergence between anadromous (seawater migratory) and resident Laval River (Québec) brook charr based on maternal genetic variance was high (Q(ST) > 0.4) for embryonic length, yolk sac volume, embryonic growth rate and time to first response to feeding relative to neutral genetic differentiation [F(ST) = 0.153 (0.071-0.214)], with anadromous females having positive genetic coefficients for all of the above characters. However, Q(ST) was essentially zero for all traits post-resorption of the yolk sac. Our results indicate that the observed divergence between resident and anadromous brook charr has been driven by directional selection, and may therefore be adaptive. Moreover, they provide among the first evidence that the relative importance of selective differentiation may be highly context-specific, and varies by genetic contributions to phenotype by parental sex at specific points in offspring ontogeny. This in turn suggests that interpretations of Q(ST)-F(ST) comparisons may be improved by considering the structure of quantitative genetic architecture by age category and the sex of the parent used in estimation.
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Although conservation biology has long focused on population dynamics and genetics, phenotypic plasticity is likely to play a significant role in population viability. Here, an investigation is made into the relative contribution of genetic diversity and phenotypic plasticity to the phenotypic variation in natural populations of Ranunculus nodiflorus, a rare annual plant inhabiting temporary puddles in the Fontainebleau forest (Paris region, France) and exhibiting metapopulation dynamics. The genetic diversity and phenotypic plasticity of quantitative traits (morphological and fitness components) were measured in five populations, using a combination of field measurements, common garden experiments and genotyping at microsatellite loci. It is shown that populations exhibit almost undetectable genetic diversity at molecular markers, and that the variation in quantitative traits observed among populations is due to a high level of phenotypic plasticity. Despite the lack of genetic diversity, the natural population of R. nodiflorus exhibits large population sizes and does not appear threatened by extinction; this may be attributable to large phenotypic plasticity, enabling the production of numerous seeds under a wide range of environmental conditions. Efficient conservation of the populations can only be based on habitat management, to favour the maintenance of microenvironmental variation and the resulting strong phenotypic plasticity. In contrast, classical actions aiming to improve genetic diversity are useless in the present case.
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The phenotypic variance is assumed to be greater in a more heterogeneous environment. The validity of this assumption is important for microevolutionists to extrapolate results from the laboratory to field environments. We subjected clutches of eggs from common snapping turtles (Chelydra serpentina) to a split-family design to evaluate the variability in incubation time and four size traits of neonates from eggs incubated in the laboratory and those left in situ. Mean size measurements were similar between the laboratory and the field, but incubation time was systematically longer in the field. We found no tendency among clutches for hatchlings resulting from eggs incubated in laboratory or field environments to demonstrate greater variability. Also contrary to expectation, clutches that experienced greater thermal variation in the field did not exhibit greater variation in phenotypic traits. Consequently, extrapolating results from the laboratory to the field may not always be problematic for microevolutionary analyses.
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Author Summary Genetic variation in quantitative or complex traits can be partitioned into many components due to additive, dominance, and interaction effects of genes. The most important is the additive genetic variance because it determines most of the correlation of relatives and the opportunities for genetic change by natural or artificial selection. From reviews of the literature and presentation of a summary analysis of human twin data, we show that a high proportion, typically over half, of the total genetic variance is additive. This is surprising as there are many potential interactions of gene effects within and between loci, some revealed in recent QTL analyses. We demonstrate that under the standard model of neutral mutation, which leads to a U-shaped distribution of gene frequencies with most near 0 or 1, a high proportion of additive variance would be expected regardless of the amount of dominance or epistasis at the individual loci. We also show that the model is compatible with observations in populations undergoing selection and results of QTL analyses on F2 populations.
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The genetic correlation is a central parameter of quantitative genetics, providing a measure of the rate at which traits respond to indirect selection (i.e., selection that does not act upon the traits under study, but some other trait with which they have genes in common). In this paper, I review the pattern of variation among four combinations of traits: life history × life history (L × L), morphological × morphological (M × M), life history × morphological (L × M), and behavioral × behavioral (B × B). A few other combinations were investigated, but insufficient data were obtained for separate analysis. A total of 1798 correlations, distributed over 51 different animal and plant species, were analyzed. The analysis was conducted at two levels: first by dividing the data set solely by trait combination, and second by blocking the data by trait combination and species. Because selection will tend to fix alleles that show positive correlations with fitness traits faster than those that are negative and because the latter are expected to arise more frequently by mutation, correlations between life-history traits are predicted to be more often negative than those between morphological traits. This prediction was supported, with the ranking in decreasing proportion of negative correlations being: L × L > L × M > B × B > M × M. The mean magnitude of the genetic correlation shows little variation among morphological and life-history combinations, and the distribution of values is remarkably flat. However, the estimated standard errors and the coefficient of variation (SE/rG ) are large, making it difficult to separate biological factors influencing the pattern of dispersion from experimental error. Analysis of the phenotypic and genetic correlations suggest that for the combinations M × M and L × M, but not L × L or B × B, the phenotypic correlation is an adequate estimate of the genetic correlation.
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Abstract Comparisons of estimates of genetic differentiation at molecular markers (FST) and at quantitative traits (QST) are a means of inferring the level and heterogeneity of selection in natural populations. However, such comparisons are questionable because they require that the influence of drift and selection on QST be detectable over possible background influences of environmental or nonadditive genetic effects on QST-values. Here we test this using an experimental evolution approach in metapopulations of Arabidopsis thaliana experiencing different levels of drift and selection heterogeneity. We estimated the intensity and heterogeneity of selection on morphological and phe-nological traits via selection differentials. We demonstrate that QST-values increased with increasing selection heterogeneity when genetic drift was limited. The effect of selection on QST was thus detectable despite significant genotype-by-environment interactions that most probably biased the estimates of genetic differentiation. Although they cannot be used as a direct validation of the conclusions of prior studies, our results strongly support both the relevance of QST as an estimator of genetic differentiation and the role of local selection in shaping the genetic differentiation of natural populations.
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The genetic correlation is a central parameter of quantitative genetics, providing a measure of the rate at which traits respond to indirect selection (i.e., selection that does not act upon the traits under study, but some other trait with which they have genes in common). In this paper, I review the pattern of variation among four combinations of traits: life history x life history (L x L), morphological x morphological (M x M), life history x morphological (L x M), and behavioral x behavioral (B x B). A few other combinations were investigated, but insufficient data were obtained for separate analysis. A total of 1798 correlations, distributed over 51 different animal and plant species, were analyzed. The analysis was conducted at two levels: first by dividing the data set solely by trait combination, and second by blocking the data by trait combination and species. Because selection will tend to fix alleles that show positive correlations with fitness traits faster than those that are negative and because the latter are expected to arise more frequently by mutation, correlations between life-history traits are predicted to be more often negative than those between morphological traits. This prediction was supported, with the ranking in decreasing proportion of negative correlations being: L x L > L x M > B x B > M x M. The mean magnitude of the genetic correlation shows little variation among morphological and life-history combinations, and the distribution of values is remarkably flat. However, the estimated standard errors and the coefficient of variation (SE/r(G)) are large, making it difficult to separate biological factors influencing the pattern of dispersion from experimental error. Analysis of the phenotypic and genetic correlations suggest that for the combinations M x M and L x M, but not L x L or B x B, the phenotypic correlation is an adequate estimate of the genetic correlation.
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This paper presents a perspective of how inferred relatedness, based on genetic marker data such as microsatellites or amplified fragment length polymorphisms (AFLPs), can be used to demonstrate quantitative genetic variation in natural populations. Variation at two levels is considered: among pairs of individuals within populations, and among pairs of subpopulations within a population. In the former, inferred pairwise relatedness, combined with trait measures, allow estimates of heritability ‘in the wild’. In the latter, estimates of QST are obtained, in the absence of known heritabilities, via estimates of pairwise FST. Estimators of relatedness based on the ‘Kronecker operator’ are given. Both methods require actual variation of relationship, a rarely studied aspect of population structure, and not necessarily present. Some conditions for appropriate population structures in the wild are identified, in part through a review of recent studies.
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Quantitative trait divergence and variability among 12 greenfinch populations across continental Europe was examined and compared to divergence in neutral genetic markers (allozymes). The added among locality variance component for 16 skeletal traits was large (mean 28%, range 4–48%) equalling a divergence of up to three SD units. The divergence in quantitative traits (Qst = 0.04-0.48) greatly exceeded that in alloymes (FST= 0.01-0.07), indicating the differentiation in quantitative traits to be larger than expected by mutation and drift alone. This conclusion was consistent also with results from the multivariate approach of Rogers & Harpending. However, genetic and morphometric distances between populations were positively correlated, even when controlling for the geographic distance separating pairs of populations. In concordance with Bergmann's rule, most traits were strongly and positively correlated with latitude, indicating latitudinally ordered genetic or/and environmental effects. However, the correlation between lower mandible width and latitude was strongly negative, demonstrating an inverse relationship between beak size and body size across the populations. These results are interpreted to reflect the re-colonization of history of northern Europe (genetic and geographic distances correlated) which has been paralleled by selection acting on quantitative traits (QST>FST)- In particular, the counter-gradient variation in beak width, a functionally important trait, is suggestive of an adaptive basis for quantitative trait divergence.
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The comparison of the degree of differentiation in neutral marker loci and genes coding quantitative traits with standardized and equivalent measures of genetic differentiation (FST and QST, respectively) can provide insights into two important but seldom explored questions in evolutionary genetics: (i) what is the relative importance of random genetic drift and directional natural selection as causes of population differentiation in quantitative traits, and (ii) does the degree of divergence in neutral marker loci predict the degree of divergence in genes coding quantitative traits? Examination of data from 18 independent studies of plants and animals using both standard statistical and meta-analytical methods revealed a number of interesting points. First, the degree of differentiation in quantitative traits (QST) typically exceeds that observed in neutral marker genes (FST), suggesting a prominent role for natural selection in accounting for patterns of quantitative trait differentiation among contemporary populations. Second, the FST – QST difference is more pronounced for allozyme markers and morphological traits, than for other kinds of molecular markers and life-history traits. Third, very few studies reveal situations were QST < FST, suggesting that selection pressures, and hence optimal phenotypes, in different populations of the same species are unlikely to be often similar. Fourth, there is a strong correlation between QST and FST indices across the different studies for allozyme (r=0.81), microsatellite (r=0.87) and combined (r=0.75) marker data, suggesting that the degree of genetic differentiation in neutral marker loci is closely predictive of the degree of differentiation in loci coding quantitative traits. However, these interpretations are subject to a number of assumptions about the data and methods used to derive the estimates of population differentiation in the two sets of traits.
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Molecular markers appear to be poor indicators of heritable variation in adaptive traits. Direct comparison of population structure in markers with that in traits is made possible by the measure Qst, which partitions quantitative genetic variation in a manner analogous to Fst for single gene markers. A survey of the literature reveals that mean Qst is typically larger than and poorly correlated with mean Fst across 29 species. Within species, Qst varies widely among traits; traits experiencing the strongest local selection pressures are expected to be the most divergent from molecular Fst. Thus, Qst will be particularly relevant to conservation efforts where preserving extant adaptation to local environments is an important goal. Recent theoretical and simulation studies suggest however that Fst is a better predictor of the pattern of allelic differentiation at quantitative trait loci (QTLs) than is Qst in random mating populations, in which case allelic variation at QTLs might be better assessed by molecular markers than will extant variation in the traits themselves.
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Clinal variation in quantitative traits is often attributed to the effects of spatially varying selection. However, identical patterns can be produced by the interplay between purely stochastic processes (i.e. drift in combination with spatially restricted gene flow). One means of distinguishing between adaptive and nonadaptive causes of geographical variation is to compare relative levels of between-population divergence in quantitative traits and neutral DNA markers. Such comparisons can be used to test whether levels of trait divergence attributable to additive genetic effects (as measured by QST) exceed null expectations based on the level of divergence at neutral marker loci (as measured by FST). The purpose of this study was to use an approach based on 'QST vs. FST' contrasts to test for evidence of diversifying selection on body size of an Indian fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae). Specifically, relative levels of between-population divergence in body size and microsatellite DNA markers were compared to assess whether the observed pattern of clinal size variation could be explained by a neutral model of isolation by distance. QST for body size was calculated using unbiased estimators of within- and between-population variance of principal component scores. The association between body size variation and geographical/environmental distance was tested using pairwise and partial matrix correspondence tests (MCTs). Independent variables (representing causal hypotheses) were constructed as between-locality distance matrices. The effects of neutral genetic divergence were assessed by including a matrix of pairwise FST as an independent variable. Partial MCTs revealed highly significant associations between phenotypic divergence (QST) and both geographical and environmental distance, even when the effects of neutral genetic divergence (FST) were partialled out. Results of the tests confirmed that migration-drift equilibrium is not a sufficient explanation for the latitudinal pattern of clinal size variation in C. sphinx. The geographical patterning of pairwise QST is most likely attributable to spatially varying selection and/or the direct influence of latitudinally ordered environmental effects.
Article
In this study, we investigate the relative role of historical factors and evolutionary forces in promoting population differentiation in a new case of sympatric dwarf and normal ecotypes of the rainbow smelt (Osmerus mordax Mitchill) in Lac Saint-Jean (Québec, Canada). Our first objective was to test the hypothesis that the evolution of sympatric smelt ecotypes in Lac Saint-Jean has been contingent upon the secondary contact between two evolutionary lineages in postglacial times. Secondly, the QST method was applied to test the null hypothesis that the extent of phenotypic differences relative to that of neutral marker variation would be similar in comparisons involving populations within and among ecotypes. Thirdly, we applied a quantitative-genetic method as an exploratory assessment as to whether the amount of gene flow observed between populations could affect divergence in adaptive traits under specific conditions. This study revealed a unique situation of dwarf and normal smelt ecotypes that are, respectively, characterized by selmiparous and iteroparous life histories and the occurrence in each of two genetically distinct populations that synchronously use the same spawning habitat in two tributaries. Historical contingency has apparently played little role in the origin of these populations. In contrast, an important role of divergent natural selection in driving their phenotypic divergence was suggested. While divergent selection has apparently been strong enough to maintain phenotypic differentiation in the face of migration, this study suggests that gene flow has been sufficiently important to modulate the extent of adaptive differentiation being achieved between ecotypes, unless the extent of stabilizing selection acting on smelt ecotypes is much more pronounced than usually reported in natural populations.
Article
Comparisons of estimates of genetic differentiation at molecular markers (F(ST)) and at quantitative traits (Q(ST)) are a means of inferring the level and heterogeneity of selection in natural populations. However, such comparisons are questionable because they require that the influence of drift and selection on Q(ST) be detectable over possible background influences of environmental or nonadditive genetic effects on Q(ST)-values. Here we test this using an experimental evolution approach in metapopulations of Arabidopsis thaliana experiencing different levels of drift and selection heterogeneity. We estimated the intensity and heterogeneity of selection on morphological and phenological traits via selection differentials. We demonstrate that Q(ST)-values increased with increasing selection heterogeneity when genetic drift was limited. The effect of selection on Q(ST) was thus detectable despite significant genotype-by-environment interactions that most probably biased the estimates of genetic differentiation. Although they cannot be used as a direct validation of the conclusions of prior studies, our results strongly support both the relevance of Q(ST) as an estimator of genetic differentiation and the role of local selection in shaping the genetic differentiation of natural populations.
Article
Combining morphological and genetic analysis, we compared patterns of diversification within and between morphs among sympatric European whitefish (Coregonus lavaretus L.) populations in Lake Femund, Norway. Seven external populations, from potential colonization routes into Lake Femund were included. We found that deep-, shallow-, river- and bay spawning populations are distinct morphs in Lake Femund. Within morphs, populations range from being similar genetically (Fst=0-0.005) among deep-spawning populations to being highly differentiated (Fst=0.153) between bay-spawning populations. Between morphs, genetic differences ranged from a low (Fst=0.008-0.022) between deep- and shallow-spawning populations to high difference (Fst=0.125-0.143) between shallow- and bay-spawning populations. A higher proportion of molecular variance was seen among (3.9%) than within morphs (2.8%). The adaptive gene combinations behind the four morphs seem to have originated within the lake, although the lake could have been colonized from more than one source population.
Article
Many morphological and life-history traits show phenotypic plasticity that can be described by reaction norms, but few studies have attempted individual-level analyses of reaction norms in the wild. We analyzed variation in individual reaction norms between laying date and three climatic variables (local temperature, local rainfall, and North Atlantic Oscillation) of 1126 female collared flycatchers (Ficedula albicollis) with a restricted maximum likehood linear mixed model approach using random-effect best linear unbiased predictor estimates for the elevation (i.e., expected laying date in the average environment) and slope (i.e., adjustment in laying date as a function of environment) of females' reaction norms. Variation in laying date was best explained by local temperature, and individual females differed in both the elevation and the slope of their laying date-temperature reaction norms. As revealed by animal model analyses, there was weak evidence for additive genetic variance of elevation (h2 +/- SE = 0.09 +/- 0.09), whereas there was no evidence for heritability of slope (h2 +/- SE = 0.00 +/- 0.01). Selection analysis, using a female's lifetime production of fledglings or recruits as an estimate of her fitness, revealed significant selection for a lower phenotypic value and breeding value for elevation (i.e., earlier laying date at the average temperature). There was selection for steeper phenotypic values of slope (i.e., greater plasticity in the adjustment of laying date to temperature), but no significant selection on the breeding values of slope. Although these results suggest that phenotypic laying date is influenced by additive genetic factors, as well as by an interaction with the environment, selection on plasticity would not produce an evolutionary response.
Article
The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where additional effort is required. I suggest that some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions. Other issues, such as the costs of plasticity are currently at the forefront of research in this field, and are likely to be areas of major future development.
Article
Detecting the action of selection in natural populations can be achieved using the QST-FST comparison that relies on the estimation of FST with neutral markers, and QST using quantitative traits potentially under selection. QST higher than FST suggests the action of directional selection and thus potential local adaptation. In this article, we apply the QST-FST comparison to four populations of the hermaphroditic freshwater snail Radix balthica located in a floodplain habitat. In contrast to most studies published so far, we did not detect evidence of directional selection for local optima for any of the traits we measured: QST calculated using three different methods was never higher than FST. A strong inbreeding depression was also detected, indicating that outcrossing is probably predominant over selfing in the studied populations. Our results suggest that in this floodplain habitat, local adaptation of R. balthica populations may be hindered by genetic drift, and possibly altered by uneven gene flow linked to flood frequency.
Article
Comparisons of neutral marker and quantitative trait divergence can provide important insights into the relative roles of natural selection and neutral genetic drift in population differentiation. We investigated phenotypic and genetic differentiation among Fennoscandian threespine stickleback (Gasterosteus aculeatus) populations, and found that the highest degree of differentiation occurred between sea and freshwater habitats. Within habitats, morphological divergence was highest among the different freshwater populations. Pairwise phenotypic and neutral genetic distances among populations were positively correlated, suggesting that genetic drift may have contributed to the morphological differentiation among habitats. On the other hand, the degree of phenotypic differentiation (PST) clearly surpassed the neutral expectation set by FST, suggesting a predominant role for natural selection over genetic drift as an explanation for the observed differentiation. However, separate PST/FST comparisons by habitats revealed that body shape divergence between lake and marine populations, and even among marine populations, can be strongly influenced by natural selection. On the other hand, genetic drift can play an important role in the differentiation among lake populations.
Article
Population density cycles influence phenotypic evolution through both density-dependent selection during periods of high density and through enhanced genetic drift during periods of low density. We investigated the response of different phenotypic traits to the same density cycles in a population of the yellow-necked mouse, Apodemus flavicollis, from Białowieza National Park in Poland. We examined nonmetric skull traits, skull and mandible size, skull and mandible shape, and transferrin allele frequencies. We found that all of the traits changed significantly over the seven-year study period. The greatest changes in nonmetric traits and mandible size occurred during periods of increasing density, and the magnitude of changes in skull and mandible shape was correlated with the magnitude of density changes. Frequencies of transferrin alleles changed the most when population density was in decline. Changes among the five phenotypic traits were generally uncorrelated with one another, except for skull and mandible shape. Nonmetric traits were selectively neutral when assessed with Q(ST)/F(ST) analysis, whereas mandible size, mandible shape, and skull shape showed evidence of fairly strong selection. Selection on skull size was weak or nonexistent. We discuss how different assumptions about the genetic components of variance affect Q(ST) estimates when phenotypic variances are substituted for genetic ones. We also found that change in mandible size, mandible shape, skull size, and skull shape were greater than expected under a neutral model given reasonable assumptions about heritability and effective population size.
Article
Three measures of divergence, estimated at nine putatively neutral microsatellite markers, 14 quantitative traits, and seven quantitative trait loci (QTL) were compared in eight populations of the three-spined stickleback (Gasterosteus aculeatus L.) living in the Scheldt river basin (Belgium). Lowland estuarine and polder populations were polymorphic for the number of lateral plates, whereas upland freshwater populations were low-plated. The number of short gill rakers and the length of dorsal and pelvic spines gradually declined along a coastal-inland gradient. Plate number, short gill rakers and spine length showed moderate to strong signals of divergent selection between lowland and upland populations in comparison between P(ST) (a phenotypic alternative for Q(ST)) and neutral F(ST). However, such comparisons rely on the unrealistic assumption that phenotypic variance equals additive genetic variance, and that nonadditive genetic effects and environmental effects can be minimized. In order to verify this assumption and to confirm the phenotypic signals of divergence, we tested for divergent selection at the underlying QTL. For plate number, strong genetic evidence for divergent selection between lowland and upland populations was obtained based on an intron marker of the Eda gene, of which the genotype was highly congruent with plate morph. Genetic evidence for divergent selection on short gill rakers was limited to some population pairs where F(ST) at only one of two QTL was detected as an outlier, although F(ST) at both loci correlated significantly with P(ST). No genetic confirmation was obtained for divergent selection on dorsal spine length, as no outlier F(ST)s were detected at dorsal spine QTL, and no significant correlations with P(ST) were observed.
Article
Evolutionary theory is primarily concerned with genetic processes, yet empirical testing of this theory often involves data collected on phenotypes. To make this tenable, the implicit assumption is often made that phenotypic patterns are good predictors of genetic patterns; an assumption that coined the phenotypic gambit. Although this assumption has been validated for traits with high heritability, such as morphology, its generality for traits with low heritabilities, such as life-history and behavioural traits, remains controversial. Using a large-scale cross-fostering experiment, we were able to measure genetic, common environmental and phenotypic correlations between four colour traits and two skeletal traits in a wild population of passerine birds, the blue tit (Parus caeruleus). Colour traits had little heritable variation but common environment effects were found to be important; skeletal traits showed the opposite pattern. Positive correlations because of a shared natal environment were found between all traits, obscuring negative genetic correlations between some colour and skeletal traits. Consequently, phenotypic patterns were poor surrogates for genetic patterns and we suggest that this may be common if trade-offs or substantial parental effects exist. For this group of traits, the phenotypic gambit cannot be made and we suggest caution when inferring genetic patterns from phenotypic data, especially for behavioural and life-history traits.