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ESTIMATING F-STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
... It has long been hypothesised that Strongyloides in people and in dogs may be the same parasite, and thus that people may be zoonotically infected by dogs (9). This has been hypothesised because of the morphological similarity of Strongyloides from people and dogs, and because of case reports of people in non-Strongyloides endemic regions having acquired S. stercoralis infections, apparently from dogs (10,11). ...
... To investigate the genetic relationship between iL3s from people and dogs we calculated the pairwise fixation index (FST) values among all samples using VCFtools after (10). We made three pairwise comparisons: (i) Dog-Dog, (ii) Human-Human, (iii) Human-Dog. ...
Gut nematode worms are important parasites of people and other animals. The parasitic nematode Strongyloides stercoralis infects an estimated 600 million people worldwide, and is one of the soil-transmitted helminthiases, a WHO-defined neglected tropical disease. It has long been suggested that human S. stercoralis infection may be a zoonosis from dogs. We investigated this by whole genome sequence analysis of S. stercoralis from sympatric human and dog populations in Asia. We find that human- and dog-derived S. stercoralis have genetically distinct nuclear genomes, but we also find evidence of rare cross infection. Analysis of the S. stercoralis mitochondrial genome reveals evidence of historical introgression between human- and dog-derived parasites. Based on these data we suggest that S. stercoralis was originally a parasite of canids, that began to infect humans when people domesticated dogs, since when human- and dog-derived parasites have differentiated, but have not become separate species.
Significance Statement
Nematode worms infect approximately a quarter of the world’s human population; Strongyloides stercoralis infects some 600 million people. It has been suggested that S. stercoralis in people and dogs is the same parasite, such that some human infection is acquired zoonotically from dogs. It is important to understand the source of human Strongyloides infection to be able to control it and the harm that it causes. Our population genomic analyses of human- and dog-derived S. stercoralis in Asia show that these parasites are distinct, but also reveal rare cross infection events. Our results are consistent with S. stercoralis ancestrally being a parasite of dogs that began infecting people when dogs became domesticated.
... The degree of genetic differentiation of P. tomentosa was analyzed at different scales using Wright's Fstatistics, such as the parameters F IS (the inbreeding coe cient), F IT , and F ST , which are widely used to estimate the genetic structure of a population [25]. The F IS was used to evaluate the degree of inbreeding in each population. ...
... To evaluate the differences in and extent of genetic differentiation between and within populations of P. tomentosa, Wright's F-statistic and gene ow (Nm) were evaluated with GenAlEx v.6.5 [53,54], while an analysis of molecular variance (AMOVA) was conducted with Arlequin v.3.5.2.2 software [25,56,57]. The Nm between populations was calculated from the F ST value, with the following formula: Nm = (1 − F ST ) / 4 × F ST . ...
Background Prunus tomentosa Thunb. is a fruit tree native to China and has a wide natural distribution range. The germplasm resources are found in the six geographical regions of China and comprises a variety of ecological types. However, little is known about genetic diversity and population structure, with its abundant genetic information. nuclear simple sequence repeat markers, with biparentally inherited characteristics, is powerful for evaluating the genetic diversity of population. And P. tomentosa is an important and excellent plant material, with high adaptability to almost all soil types and climatic conditions. So the research contributed to not only proposing scientific conservation strategies of P. tomentosa but also developing P. tomentosa germplasm to breed novel cherry cultivar. Results A total of 822 germplasms from 40 populations were used for assessing the genetic diversity and population structure of P. tomentosa . The indicators of genetic diversity showed high values, including observable heterozygosity (0.546), expected heterozygosity (0.819), Shannon’s information index ( I = 1.951), polymorphism information content (0.799). The populations displaying the greatest diversity—Gan-XlM, Shaan-HM, and Gan-ZhC. In addition, extensive genetic differentiation was detected. The genetic differentiation coefficient ( F ST ) values calculated from heterozygosity and analysis of molecular variance were greater than 0.15. Gene flow was relatively stable (number of migrants [ Nm ] = 1.065). Mantel test analysis showed that there was a significant correlation ( R ² = 0.065, P < 0.05) between the genetic distance and the geographical distance of the populations. Integrated cluster, structure, and principal component analysis indicated that the 40 populations were clustered into a Northwest Group and a Northeast Group. However, the Chuan-Aba, Xin-TKS, and Xin-ALR populations were clearly differentiated. Conclusions The P. tomentosa populations showed high or moderate polymorphism. The genetic differentiation within each population was higher than that between populations. There was a significant correlation between the genetic distance and the geographical distance. Based on genetic diversity and population differentiation levers, the most diverse populations - Gan-XlM, Shaan-HS, and Gan-PL from Gansu and Shaanxi provinces, should first be protected and applied to the innovation of cherry germplasm, followed by significantly differentiated populations, including Chuan-Aba, Ning-HlM, and Gan-PL.
... Quantitative genetic approach: P ST -F ST approach P ST -F ST approach detects signal of selection for each trait by comparing phenotypic differentiation (P ST , Leinonen et al., 2008) with neutral genetic differentiation (F ST , Weir & Cockerham, 1984) overall populations. This phenotype-genotype comparison has three possible outcomes: (1) P ST = F ST , indicating that neutral processes (e.g. ...
... P ST and F ST were inferred from our set of 6 populations, and are therefore called 'global'. We estimated global F ST values for each locus individually and over all loci following Weir & Cockerham (1984) and using the R package heirfstat (Goudet, 2005). To calculate the global P ST for each of the phenotypic traits, we extracted the variance components (between and within populations) and their confidence intervals (CIs) from the posterior distribution of a Bayesian generalized linear mixed model with the population effect set as a random effect (Bertrand et al., 2016;Seeholzer & Brumfield, 2018). ...
Adaptive radiation in Ophrys orchids leads to complex floral phenotypes that vary in scent, color and shape.
Using a novel pipeline to quantify these phenotypes, we investigated trait divergence at early stages of speciation in six populations of Ophrys aveyronensis experiencing recent allopatry. By integrating different genetic/genomic techniques, we investigated: variation and integration of floral components (scent, color and shape); phenotypes and genomic regions under divergent selection; and the genomic bases of trait variation.
We identified a large genomic island of divergence, likely associated with phenotypic variation in particular in floral odor. We detected potential divergent selection on macular color, while stabilizing selection was suspected on floral morphology and for several volatile olfactive compounds. We also identified candidate genes involved in anthocyanin and in steroid biosynthesis pathways associated with standing genetic variation in color and odor.
This study sheds light on early differentiation in Ophrys, revealing patterns that often become invisible over time, that is the geographic mosaic of traits under selection and the early appearance of strong genomic divergence. It also supports a crucial genomic region for future investigation and highlights the value of a multifaceted approach in unraveling speciation within taxa with large genomes.
... The extent of genetic differentiation among populations was assessed by comparing pairwise F ST values (Weir and Cockerham 1984) across all loci, using the package 'hierfstat' ver. 0.5-10 (Goudet 2005) in R. A global F ST value for the region across all loci and populations was calculated with the package 'polysat', and its significant difference from zero was assessed using 1000 permutations. ...
Ecological processes maintaining landscape genetic variation and metacommunity structure in natural landscapes have traditionally been studied in isolation. Their integrated study may inform on whether major ecological processes affect species or landscapes differently, yielding a more cohesive understanding of the spatial organization of biodiversity. Here, we investigated the relative importance of spatial and environmental drivers on cladoceran metacommunity structure and the landscape genetic structure of its most widespread member, Daphnia magna , in soda pans of the Seewinkel region in Austria, covering the entire habitat network. These temporary pans exhibit strong environmental gradients, with wind serving as a key dispersal agent among them. Our study shows both parallels and divergences in the relative impacts of environmental sorting and spatial connectivity on landscape genetic versus metacommunity structure. The metacommunity primarily reflects environmental structuring, while spatial signals dominate in the D. magna metapopulation. The weaker environmental signal in Daphnia suggests that environmental gradients are not a key driver of landscape genetic structure in neutral markers. Prevailing wind direction was an important driver both in metacommunity and landscape genetic structure. This suggests its pivotal role across the two levels of ecological organization via determining connectivity among pans, thereby affecting dispersal and colonization rates, influencing both local species and genetic composition.
... Null alleles were checked using MICROCHECKER (Van Oosterhout et al. 2004). Weir and Cockerham's FIS (Weir and Cockerham 1984) was calculated for each population using the FSTAT version 2.9.3.2 (Goudet 1995). Allelic richness (An), a standardized measure of the number of alleles per locus independent of the sample size, was also calculated by FSTAT. ...
The IUCN classifies two-endemic fishes of the Western Ghats in Peninsular India: Nilgiri mystus Hemibagrus punctatus is critically endangered, and Yellow catfish Horabagrus brachysoma is vulnerable. These are threatened by habitat degradation, excess fishing, and dam construction. ICAR-NBFGR, the premier research organisation in India for fish conservation, aims to conserve these two species through captive propagation, stock identification, and stock-specific ranching programs. The information on this species’ genetic diversity and population structure is crucial for the successful rehabilitation of the species. Microsatellite markers are considered suitable markers for genetic stock structure analyses. An attempt was made to identify microsatellite markers in H. brachysoma (n = 27) and H. punctatus (n = 31) using Illumina Sequencing technology. The preliminary studies show that markers are efficient enough to differentiate the genetic stocks of these conservation-important species across their range of natural distribution. Three genetic stocks are identified in H. brachysoma and two in H.punctatus using the developed markers.
... Genetic divergence among populations was assessed with F ST (Weir and Cockerham, 1984). By AMOVA, the hierarchical partition of genetic diversity was assessed using ARLEQUIN (Excoffier et al., 2005). ...
The genetic integrity of fish populations has been continuously threatened due to various anthropogenic actions, particularly restocking programs. These losses in genetic diversity present erosion of global biodiversity. The genetic status of Hypophthalmichthys molitrix in the Indus River was assessed by using microsatellite markers. For the purpose, samples were collected from five selective Indus River sites, and DNA extraction was done by proteinase-K and standard phenol/chloroform DNA isolation method. Genomic DNA was PCR amplified by Labeo rohita cross-species amplification of H. molitrix. The results showed a low-to-moderate level of genetic diversity. The number of alleles on each locus ranging from 2.0 to 6.0, with an average of 3.48 was observed at various loci. The average observed and expected heterozygosities ranged from 0.664 to 0.76 and 0.631 to 0.664, respectively. For all tested loci, population combinations showed significant deviation (p<0.05) from HWE. The AMOVA indicated that most of the variation lied within individuals in populations of H. molitrix. Based on Nei's genetic distance, UPGMA dendrogram was constructed that resulted in two clusters: one cluster consisted of JB and CB while other consisted of GG, GB and TB. The findings of this research will be useful for restoring, conservation and monitoring the natural aquatic fish species in Pakistan.
... Weir and Cockerham (1984) 57 FST was calculated for every SNP using VCFtools version 0.1.14 54 between 282 monogyne samples and 388 polygyne samples, where the social form was defined based on the distribution of kinship score within the nest. ...
Supergenes are non-recombining chromosomal regions that code for complex polymorphic traits. With the advance of population genomics, studies in diverse organisms revealed supergenes associated with a myriad of complex traits, ranging from morphology to sexual behavior, from butterfly wing patterns to floral morphs. Two supergenes have been described on non-homologous social chromosomes in two ant lineages, Solenopsis and Formica, that diverged more than 90 million years ago. In both lineages, the supergene is associated with social polymorphism, where some colonies are headed by a single queen (monogyne) while others harbor multiple queens (polygyne). We discovered a new supergene associated with similar social polymorphism in the desert ant Cataglyphis niger. Although Cataglyphis is more closely related to Formica than to Solenopsis, the social chromosome in C. niger is homologous to the Solenopsis social chromosome, with conservation of synteny in gene content as well as gene order. Therefore, this is an ancient chromosome dating back to the common ancestor of Solenopsis and Cataglyphis, at least 90 million years ago. Previous work dated the Solenopsis supergene to be only one million years old, therefore, we propose that the two supergenes have evolved independently in the two diverged lineages on this ancient social chromosome. We surveyed hymenopteran genomes to discover a bee chromosome homologous to the ants social chromosome. The conservation of the gene set on these homologous chromosomes in ants and bees suggests that this chromosome plays an important role in social behavior across social Hymenoptera. We hypothesize that the conserved gene set in the social chromosome was repeatedly used as a pre-adapted toolkit for the evolution of social traits in general and specifically in the evolution of polygyne social structure in ants.
... In the next part, we will use the diploid SNP dataset generated above to calculate FST estimates among the INV and ST individuals for each inversion using the method of Weir & Cockerham [75] as implemented in VCFtools. The fixation index FST summarizes genetic structure and is scaled between zero (no differentiation) and one (complete differentiation). ...
Chromosomal inversions are structural mutations resulting in the reversal of the gene order along the corresponding genomic region. Due to their influence on recombination patterns, they can have a major influence on genetic variation and the evolutionary process. Accordingly, inversions can act as supergenes that keep together co-adapted gene complexes that form the genetic basis of many complex phenotypes in diverse organisms. In this book chapter, I will present an analysis pipeline to investigate the influence of two common cosmopolitan inversion, In(2L)t and In(3R)Payne, on genome-wide genetic variation and differentiation in worldwide populations of the vinegar fly Drosophila melanogaster. We will use single-individual and pooled resequencing data in combination with population genomics analysis tools to explore the impact of these two inversions on genetic variation, population structure, and clinal variation in natural populations.
... where π S is the average proportion of pairwise differences between haplotypes within a subpopulation and π B is the average proportion of pairwise differences between haplotypes from different subpopulations [30; the same quantity is estimated by ref. [31] θ; see ref. [32]. F ST can also be defined in terms of the standardized variance in allele frequencies among subpopulations, or in terms of mean coalescence times for alleles within subpopulations versus the whole population [33]. ...
Background selection, by which selection on deleterious alleles reduces diversity at linked neutral sites, influences patterns of total neutral diversity, π T , and genetic differentiation, F ST , in structured populations. The theory of background selection may be split into two regimes: the background selection regime , where selection pressures are strong and mutation rates are sufficiently low such that deleterious alleles are at a deterministic mutation-selection balance, and the interference selection regime , where selection pressures are weak and mutation rates are sufficiently high that deleterious alleles accumulate and interfere with another, leading to selective interference. Previous work has quantified the effects of background selection on π T and F ST only for deleterious alleles in the background selection regime . Furthermore, there is evidence to suggest that migration reduces the effects of background selection on F ST , but this has not been fully explained. Here, we derive novel theory to predict the effects of migration on background selection experienced by a subpopulation and extend previous theory from the interference selection regime to make predictions in an island model. Using simulations, we show that this theory best predicts F ST and π T . Moreover, we demonstrate that background selection may generate minimal increases in F ST under sufficiently high migration rates, because migration reduces correlated effects on fitness over generations within subpopulations. However, we show that background selection may still cause substantial reductions in π T , particularly for metapopulations with a larger effective population size. Our work further extends the theory of background selection into structured populations, and suggests that background selection will minimally confound locus-to-locus F ST scans.
... The gene flow between predefined groups was further assessed using the R package Hierfstat 62 for the calculation of pairwise population fixation index (F ST ) under the WC model 63 . Lower F ST values indicate the vivid exchange of animals and hence gene flow between examined farms while high values correspond to genetic isolation. ...
Cyprus, facing climate change and desertification, has Europe’s second highest population growth. Halloumi cheese’s Protected Designation of Origin status boosted goat and sheep milk demand. Optimizing primary sector production is key to balancing food production and environmental sustainability. The present study aims to explore the genetic diversity and population structure of Cyprus Chios sheep, as well as the impact of existing breeding nuclei on the breed’s gene pool. Two breeding nuclei aiming to preserve genetic diversity and boost local milk production and four private farms were sampled. Genome-wide data using Illumina 50 K arrays were generated, analyzing over 1000 animals from six farms. At least three distinct genetic groups were identified, two of which are represented by the nuclei’s distinct genetic profiles and a third was found in private farms. Calculated metrics indicate a negative correlation of gene flow with geographic distance in case of the Eastern nucleus. Presented results support recent, though limited inbreeding (mean FROH=0.046), compared to other commercial breeds. Estimated effective population size reveals a stabilizing trend to a relatively high number (Ne ~ 200) which indicates relatively high diversity that allows further genetic improvement. Revealed genomic diversity highlights the necessity of such exploration before effectively implementing genomic evaluation programs.
... Nucleotide diversity (Pi) per site, inbreeding coefficient (F), Hardy-Weinberg equilibrium and fixation index per site (F st , Weir and Cockerham 1984) were computed with VCFtools (Danecek et al. 2011) using the --site-pi, --het, --hardy and --weir-fst-pop functions, respectively. The Pi per site as calculated with VCFtools is equivalent to the expected heterozygosity. ...
Maize (Zea mays ssp. mays L.) landraces are traditional American crops with high genetic variability that conform a source of original alleles for conventional maize breeding. Northern Argentina, one the southernmost regions of traditional maize cultivation in the Americas, harbours around 57 races traditionally grown in two regions with contrasting environmental conditions, namely, the Andean mountains in the Northwest and the tropical grasslands and Atlantic Forest in the Northeast. These races encounter diverse threats to their genetic diversity and persistence in their regions of origin, with climate change standing out as one of the major challenges. In this work, we use genome‐wide SNPs derived from ddRADseq to study the genetic diversity of individuals representing the five groups previously described for this area. This allowed us to distinguish two clearly differentiated gene pools, the highland northwestern maize (HNWA) and the floury northeastern maize (FNEA). Subsequently, we employed essential biodiversity variables at the genetic level, as proposed by the Group on Earth Observations Biodiversity Observation Network (GEO BON), to evaluate the conservation status of these two groups. This assessment encompassed genetic diversity (Pi), inbreeding coefficient (F) and effective population size (Ne). FNEA showed low Ne values and high F values, while HNWA showed low Ne values and low Pi values, indicating that further genetic erosion is imminent for these landraces. Outlier detection methods allowed identification of putative adaptive genomic regions, consistent with previously reported flowering‐time loci and chromosomal regions displaying introgression from the teosinte Zea mays ssp. mexicana. Finally, species distribution models were obtained for two future climate scenarios, showing a notable reduction in the potential planting area of HNWA and a shift in the cultivation areas of FNEA. These results suggest that maize landraces from Northern Argentina may be unable to cope with climate change. Therefore, active conservation policies are advisable.
... The genetic divergence among populations of Labeo species was assessed by calculating the FST values for all pairwise comparisons between sample locations, using the method proposed by Weir and Cockerham (1984). The statistical significance of the FST estimations was evaluated through the implementation of 10,000 permutations. ...
... Unbiased Weir and Cockerham F ST [34] and Nei's genetic distances [35] between populations were estimated with StAMMP v. 1.6.3 ...
Background: The genetic diversity of a population defines its ability to adapt to episodic and fluctuating environmental changes. For species of agricultural value, available genetic diversity also determines their breeding potential and remains fundamental to the development of practices that maintain health and productivity. In this study, we used whole-genome resequencing to investigate genetic diversity within and between naturalized and captively reared populations of Pacific oysters from the US Pacific coast. The analyses included individuals from preserved samples dating to 1998 and 2004, two contemporary naturalized populations, and one domesticated population. Results: Despite high overall heterozygosity, there was extremely low but significant genetic divergence between populations, indicative of high gene flow. The captive population, which was reared for over 25 years was the most genetically distinct population and exhibited reduced nucleotide diversity, attributable to inbreeding. Individuals from populations that were separated both geographically and temporally did not show detectable genetic differences, illustrating the consequences of human intervention in the form translocation of animals between farms, hatcheries and natural settings. Fifty-nine significant F ST outlier sites were identified, the majority of which were present in high proportions of the captive population individuals, and which are possibly associated with domestication. Conclusion: Pacific oysters in the US Pacific coast harbor high genetic heterozygosity which obscures weak population structure. Differences between these Pacific oyster populations could be leveraged for breeding and might be a source of adaptation to new environments.
... We estimated the among-population genomic differentiation (F ST ) by using the whole-genome pool-sequences of B. incana from Frachon et al. (2023). Pairwise F ST values between populations (Weir and Cockerham, 1984) were calculated using the poolfstat package in R v. 4.2.2 (Gautier et al., 2022). Then, to disentangle the main factors (environment vs geographic distance) explaining the variation in genomic differentiation among the 15 populations, we tested whether an isolation by resistance (IBR) model better predicted the observed patterns of genetic differentiation between population pairs compared to a null model of isolation by distance (IBD; Wright, 1943) which only accounts for geographic distance. ...
... Overall and pairwise F ST values (Weir and Cockerham 1984) were estimated with the R package hierfstat v0.5-11 (Goudet 2005) both among geographic regions and among genetic clusters as identified by STRUCTURE. F ST values were considered significant if the 95% confidence interval obtained from 1000 bootstrap iterations did not include zero. ...
Quantifying connectivity between endangered or threatened marine populations is critical information for management and conservation, especially where abundance and productivity differ among such populations. Spatial patterns of such connectivity depend not only on extrinsic factors such as oceanography and bathymetry but also on intrinsic species‐specific factors such as life history, demography and the location of glacial refugia. Nevertheless, population structure is often inferred from related or ecologically similar species. For example, the population structure in most rockfish species ( Sebastes spp.) in the Salish Sea and the US West Coast is currently inferred from genetic data of three species that are known to hybridise in Puget Sound. Here, we determined the population structure and connectivity in five Puget Sound Rockfish species (Black [ Sebastes melanops ], Yellowtail [ S. flavidus ], Redstripe [ S. proriger ], Greenstriped [ S. elongatus ], and Puget Sound Rockfish [ S. emphaeus ]) from over 12,000 restriction‐site associated DNA sequencing (RADseq) loci. We found species‐specific patterns of genetic differentiation, attributable to both extrinsic and intrinsic factors. Specifically, Black and Puget Sound rockfishes showed no genetic differentiation; Yellowtail and Greenstriped rockfishes were structured according to known geographic barriers; and Redstripe Rockfish revealed evidence for temporal genetic differentiation, suggesting irregular recruitment influences population structure. Only Yellowtail Rockfish followed the federal DPS boundaries generally assumed for rockfish, further emphasizing the importance of species‐specific management for the effective recovery and management of these rockfish populations and of marine species in general.
... Genetic differentiation among populations was assessed using the global Fixation Index (F ST ) [41,42], which considers information from all loci equally. To compute pairwise F ST values between populations, we calculated the site frequency spectrum of each population in ANGSD (doSAF) and then used the RealSFS module [35] to determine the two-dimensional SFS and calculate pairwise weighted global F ST values based on 50-kb overlapping windows, with a step size of 25 kb. ...
Background
Ticks are crucial vectors of a wide range of pathogens, posing significant threats to human and animal health globally. Understanding the genetic basis of tick biology and host–parasite interactions is essential for developing effective control programs. This study investigates the fine-scale genetic structure of Hyalomma marginatum Koch, 1844, the primary vector of Crimean-Congo hemorrhagic fever (CCHF) in Türkiye. Despite its significant public health importance, information regarding its population structure and genetic diversity is quite limited.
Methods
We used restriction site-associated DNA sequencing (RAD-Seq) to obtain genome-wide sequence data from 10 tick populations in Türkiye, collected from regions with low, moderate, and high incidence rates of CCHF. Based on these data, we determined population structure and diversity of populations using principal component analysis (PCA) and admixture analysis. Furthermore, we calculated pairwise FST and utilized discriminant analysis of principal components (DAPC) to understand genetic differentiation between populations.
Results
PCA and admixture analysis indicated minimal genetic structure between populations, but we detected notable genetic differentiation and high genetic diversity from regions with high CCHF rates. Furthermore, our DAPC identified 31 significant single-nucleotide polymorphisms (SNPs) associated with regions with high CCHF incidence, with 25 SNPs located near genes involved in critical biological functions such as nucleic acid binding, transmembrane transport, and proteolysis. These findings suggest that genetic variations in these regions may confer adaptive advantages in environments with high pathogen loads.
Conclusions
This study provides the first comprehensive analysis of H. marginatum genetic diversity in Türkiye, revealing significant differentiation in populations from CCHF-endemic regions. These results underscore the importance of considering fine-scale genetic diversity to fully understand the drivers of genetic variation in ticks and their implications for vectorial capacity.
Graphical Abstract
... Two metrics of population genetic differentiation, Weir and Cockerham's (1984) F ST (θ) of Wright's F-statistics and D JOST (Jost 2008), were estimated using 'diveRsity' (Keenan et al. 2013b). D JOST is metric of differentiation that is independent of the level of gene diversity (Jost 2008;Alcala and Rosenberg 2019), and thus is regarded as a better measure of genetic differentiation between samples for multi-allelic microsatellite markers (Prodöhl et al. 2019). ...
Untangling the patterns and proximate drivers of intraspecific genetic and phenotypic structuring informs our understanding of the evolutionary processes shaping diversity. This study investigated morphological and genetic structuring of brown trout (Salmo trutta L.) populations across varying spatial scales in a single, complex, dendritic river catchment and examined the potential natural and anthropogenic environmental features driving this structuring. Morphometric and hierarchical genetic structuring analyses of fish from 22 sampling sites in the River Foyle catchment, Ireland (~ 4500km²) identified 19 morphologically distinct groups and 15 genetically distinct populations, separated by river distances ranging from 0.4 km to 188 km. Isolation by Distance was the main factor shaping both genetic and morphological divergence, indicating that strong philopatry is one of the major drivers of the observed population structuring in this system. However, both natural and anthropogenic environmental variables also explained pairwise genetic and morphological differences between sampling sites. Thus, the pairwise differences in the area of woodland in the upstream catchment, water phosphorus concentration, biological oxygen demand, catchment slope, urban area in upstream catchment, altitude, site specific percentage of canopy cover and dissolved oxygen concentration in the river channel were correlated with genetic divergence. The pairwise differences in the concentration of suspended solids, the extent of bankside overhang, the composition of bedrock, boulder and cobble substrates, watercourse width, catchment slope and site altitude were correlated with between-site morphological differences. We hypothesise that local differential selection pressures comprising both natural environmental variation and variation resulting from anthropogenic effects, in combination with strong philopatry and random genetic processes drive the clearly defined genetic and phenotypic patterns described here.
... F-statistics (F ST , F IT , and F IS ) which are measures used to summarize population structure (Mughal and DeGiorgio 2022;Weir and Cockerham 1984) were assessed, as well as, N m which corresponds to the effective number of migrants, a complementary value of F-Statistics. Those indexes allow to understand the extent of genetic flow and differentiation, of M. calimaensis (Fig. 1), there are no significant biogeographical barriers; therefore, the evaluated localities were not initially considered distinct geographical populations. ...
This study aims to comprehend the factors that influence local endemism in Magnolia calimaensis, a tree species inhabiting the rain forests of Buenaventura in Colombia, classified as critically endangered with an estimated population of fewer than 100 individuals. A total of 38 individuals were collected from the Bajo Calima and Bahía Málaga localities. Subsequently, microsatellite marker analysis of the species’ genetic diversity and structure were conducted. Nine microsatellites from other tropical Magnolia species amplified in this system, with only seven being variable and functional. The results revealed diminished levels of genetic diversity and notable indices of inbreeding for both populations (He: 0.30 / F: 0.63 for Bajo Calima and He: 0.31 / F: 0.22 for Bahía Málaga). Furthermore, F-Statistics indicate high genetic differentiation between populations (FST=0.42) and low migration (Nm=0.34). Despite the continuity of the rain forests inhabited by the species and the availability of dispersion vectors, the results suggest that its restricted distribution is not related to the landscape. We hypothesize that gene flow and broader distribution are constrained by the species’ reproductive biology. Frequent geitonogamy and self-pollination in Magnolia, along with the potential impact of Lepidoptera parasites damaging floral structures during critical developmental stages, may play a significant role. Future studies should aim to investigate these factors in detail. The genetic results emphasize the urgent need to implement genetic restoration strategies to preserve and ensure the perpetuity of known populations of M. calimaensis.
... Mean pairwise F ST(Weir and Cockerham 1984) computed over loci between all pairs of populations (arlsumstat v. 3.5.2, Excoffier and Lischer 2010). ...
Halyomorpha halys is a polyphagous insect pest, which was first found outside its native regions in 1996, and since then it has rapidly spread worldwide causing damage to agriculture. Investigating the genetic diversity among H. halys populations is essential to understand the colonization history out of its native areas. Analyses based on mtDNA indicate multiple invasions from Asia to European and American continents, as well as serial invasions within invaded countries, but the colonization dynamics are still debated. Recently, genome-wide data (ddRAD) have been published to investigate the genomic structure of H. halys, proposing China as a putative source of multiple serial invasion events to Europe and the Americas. In this study we re-analyze published ddRAD sequences from worldwide populations of H. halys to better elucidate the colonization process. We assessed the genetic diversity in native populations identifying genetic differentiation between populations in China. Furthermore, we observed a complex pattern of population structure in the invaded countries, that may have originated from the occurrence of multiple independent colonization waves through time, from sub-populations present in the native range to Europe and the Americas. We tested alternative colonization hypotheses through Approximate Bayesian Computation comparison of demographic scenarios. Our results support multiple waves of migration from East China to invaded territories and the occurrence of European and American bridgehead effects. These results underline the importance of demographic inference through genome-wide data to investigate biological invasions, whose knowledge become fundamental to establish new strategies of management and control of invasive species.
... To choose a comprehensive set of diagnostic markers for the SNP assay, we employed a two-step selection process. First, we calculated pairwise measures of F ST (Weir and Cockerham 1984) between genetically distinct honey bee lineages using VCFtools v0.1.17 (Danecek et al. 2011). ...
Hybrid populations of Africanized honey bees (scutellata‐hybrids), notable for their defensive behaviour, have spread rapidly throughout South and North America since their unintentional introduction. Although their migration has slowed, the large‐scale trade and movement of honey bee queens and colonies raise concern over the accidental importation of scutellata‐hybrids to previously unoccupied areas. Therefore, developing an accurate and robust assay to detect scutellata‐hybrids is an important first step toward mitigating risk. Here, we used an extensive population genomic dataset to assess the genomic composition of Apis mellifera native populations and patterns of genetic admixture in North and South American commercial honey bees. We used this dataset to develop a SNP assay, where 80 markers, combined with machine learning classification, can accurately differentiate between scutellata‐hybrids and non‐scutellata‐hybrid commercial colonies. The assay was validated on 1263 individuals from colonies located in Canada, the United States, Australia and Brazil. Notably, we demonstrate that using a reduced SNP set of as few as 10 loci can still provide accurate results.
... The Fis values provide insights into the breeding dynamics within these populations: positive Fis values suggest inbreeding, while negative values indicate outbreeding. For instance, the XS population demonstrated outbreeding dynamics,while NS and ZS demonstrated inbreeding dynamics [46]. ...
Background
Outbreaks of the coral predator Crown-of-Thorns Starfish (CoTS) pose a severe threat to coral reefs in the Indo-Pacific Ocean. In 2018, the South China Sea (SCS) experienced significant CoTS outbreaks, leading to extensive coral mortality across the Xisha, Zhongsha, Dongsha, and Nansha Islands, severely impacting the coral reef ecosystem.
Results
To explore the origins of these outbreaks, we conducted a comprehensive genomic analysis using data from genomic single nucleotide polymorphism sites (SNPs) and mitochondrial haplotypes. Our analysis reveals that CoTS populations in the SCS, which exhibit moderate genetic diversity and may have undergone positive selection or population expansion. There was limited genetic differentiation among CoTS populations from XS, ZS, and NS groups. Especially between the XS and ZS groups, there was almost no genetic differentiation. The populations from XS, ZS, and NS groups have strong genetic connections with populations in Vietnam and the Philippines. There was high gene flow from Vietnam to the Xisha Islands and from the Philippines to the Nansha Islands, suggesting that the CoTS populations in these regions primarily originate from these neighboring countries.
Conclusion
The comprehensive analyses of SNP and mitochondrial genomes have provided valuable insights into the population genetics of CoTS. This research has generated significant genomic resources and facilitated important studies on the genetics of the CoTS species. By identifying potential source populations and understanding the genetic basis of their spread, managers can develop more effective conservation strategies to protect vulnerable coral reef ecosystems in the SCS.
... Fourth, we estimated genetic divergence between populations by calculating pairwise FST values (Weir & Cockerham, 1984) with the R package StAMPP v.1.6.3 (Pembleton et al., 2013). We tested statistical significance with 95% confidence intervals constructed using 10,000 permutations. ...
Studies of biogeographic processes have often centred islands as model systems, yet questions remain about the role of Pleistocene sea-level fluctuations in shaping islands' biodiversity. One novel, potentially informative model system is the Lord Howe Island Group of Australia. Despite the World Heritage status of this archipelago, almost nothing is known of the biogeographic origins, evolutionary distinctiveness or genetic diversity of the ecological communities across its 28 islands. In this study, we focused on the cockroach Panesthia lata , an ecologically specialized invertebrate with one of the broadest recorded distributions of any LHIG species. To investigate the influence of Pleistocene sea-level fluctuations on LHIG fauna, we explored the phylogeography of P. lata using single-nucleotide polymorphisms and complete mitochondrial genomes. Our analyses reveal that the lineage on the permanently isolated islet Ball's Pyramid is highly divergent from the remaining populations, while those on the episodically connected Lord Howe, Roach and Blackburn Islands experienced gene flow during the last glacial period. These results offer the first evidence that Pleistocene land bridges allowed for overland migration across the archipelago. Further, although P. lata was believed to have been locally extirpated by rodents on Lord Howe Island, we discovered two surviving, relict populations. We also detected high levels of inbreeding in all populations, emphasizing the need for ongoing conservation management. Finally, the combination of shallow genetic structure and low diversity suggests that genetic rescue from another island may be a viable strategy to conserve the Lord Howe Island population of P. lata , as well as other species that have been similarly impacted by rodents.
... (Rochette et al., 2019). StAMPP software (Pembleton et al., 2013) was used to calculate pairwise fixation indices (F ST ) following Weir-Cockerham method (Weir & Cockerham, 1984). False discovery rate was set at 10% using Benjamini-Hochberg procedure (Benjamini & Hochberg, 1995), with 95% CI estimated using 1000 bootstraps. ...
As native genetic resources of Nile tilapia populations face numerous anthropogenic and natural disturbances, we aimed to identify populations worthy of conservation management to facilitate the natural evolutionary trajectory of this species. Here, we used the ddRAD-seq approach for population genomic analysis and delineation of conservation units (CUs). In total, 209 fin-clip samples from nine wild populations in Ethiopia were subjected to ddRAD-seq, producing 121,149 high-quality SNPs that were used for downstream analyses. Genetic diversity metrics revealed low-to-moderate levels of within-population genetic variation, with population pairwise FST analysis indicating significant genetic differentiation between populations from the Nile River Basin and those from the Ethiopian Rift Valley lakes. Genetic clustering analyses suggested the presence of 3–4 genetic groups. A combined outlier loci detection approach identified thousands of putative SNPs under selection, with enrichment analysis revealing genes and pathways associated with environmental response, metabolism, growth, and reproduction. Moreover, recently outlined workflows for CU delineation have identified three CUs that are of interest for conservation and aquaculture applications.
... Weighted F ST values between the sexes were calculated in 100-kb overlapping windows with 10-kb steps using Weir and Cockerham (1984) estimator based on SNP datasets with VCFtools. A changepoint package (Killick and Eckley 2014) was used to detect regions where the F ST values change significantly, in order to detect candidate SLRs (He et al. 2021). ...
The evolution of sex chromosomes can involve recombination suppression sometimes involving structural changes, such as inversions, allowing subsequent rearrangements, including inversions and gene transpositions. In the two major genus Salix clades, Salix and Vetrix, almost all species are dioecious, and sex-linked regions have evolved on chromosome 7 and 15, with either male or female heterogamety. We used chromosome conformation capture (Hi-C) and PacBio HiFi (high-fidelity) reads to assemble chromosome-level, gap-free X and Y chromosomes from both clades, S. triandra (15XY system), a basal species in the Vetrix clade, and the Salix clade species S. mesnyi (7XY system). Combining these with other available genome assemblies, we found inversions within the sex-linked regions, which are likely to be pericentromeric and probably recombined rarely in the ancestral species, before sexlinkage evolved. The Y-linked regions in all 15XY and 7XY species include partial duplicates containing exon 1 of an ARR17-like gene similar to male-determining factors in other Salicaceae species. We also found duplicates of a Y-specific gene, which we named MSF. The derived Salix clade 7XY chromosome systems appear to have evolved when these two genes transposed from the 15Y to the 7Y. Additionally, the 7Y chromosomes in S. dunnii and S. chaenomeloides probably evolved from the ancestral 7X of the Salix clade, involving a similar transposition, and loss of the ancestral 7Y. We suggest that pericentromeric regions that recombine infrequently may facilitate the evolution of sex linkage.
... To assess genetic differentiation further, pairwise fixation indices (F ST ) (Weir & Cockerham, 1984) were calculated for Recent versus English red grouse using the [--fst] function in PLINK (v1.9) (Purcell et al., 2007). F ST is a measure of population differentiation ranging from 0 to 1, with 0 being the most similar and 1 being the most differentiated. ...
A debate in conservation genomics centers on whether to conserve small, fragmented populations independently or blend them through translocations from larger populations. Translocations of red grouse (Lagopus scotica) from Great Britain to supplement the Irish population have been suggested. We incorporate a variety of genetic datasets to address this. We used genome wide data from 23 contemporary and historic red grouse from Great Britain and Ireland. We also investigate microsatellite data, sequence candidate pigmentation genes, and assess phenotypic color variation. Genomic data indicate higher inbreeding in Irish grouse relative to an English population and significant divergence for genomic (FST = 0.095) and microsatellite (FST = 0.03) markers. Contemporary Ne was seven times smaller in the Irish population compared to the English. We identified divergent regions linked to pigmentation, immune response, and food intake. We show phenotypic differences in plumage color and sequence divergence among coding regions in the melanin pathway including MC1R (FST from genomic data of 0.3). The two populations thus appear locally adapted and this divergence between the source and target population when used for conservation translocations can swamp locally adapted alleles and/or introduce maladapted genotypes, leading to outbreeding depression. While it is important to avoid inbreeding by sustaining larger populations, our research emphasizes the need for practitioners to consider population divergence and local adaptation. We advocate against translocations between Ireland and Britain as a conservation strategy in this particular case and underscore the importance of prioritizing local populations where possible.
... Wright's Fixation Index (FST) The unbiased fixation index (Theta) estimator proposed by Weir and Cockerham was calculated to detect signatures of selection [3,26], in R version 4.2.3 (http://www.r-project.org/, accessed on 16 March 2023). ...
Domestication and selection significantly changed phenotypic traits in modern domestic animals. To identify the genomic regions associated with prolificacy in this study, 837 ewes from three Iranian indigenous sheep breeds, consisting of Baluchi, Lori-Bakhtiari, and Zandi uniparous breeds, and one Greek highly prolific dairy sheep, namely Chios, were genotyped using OvineSNP50K arrays. Statistical tests were then performed using different and complementary methods based on either site frequency (FST) and haplotype (hapFLK) between populations, followed by a pathway analysis of the genes contained in the selected regions. The results revealed that for the top 0.01 percentile of the obtained FST values, 16 genomic regions on chromosomes 2, 3, 4, 7, 8, 9, 13, 14, 16, 18, 19, and 20, and for hapFLK values, 3 regions located on chromosomes 3, 7, and 13, were under selection. A bioinformatic analysis of these genomic regions showed that these loci overlapped with potential candidate genes associated with prolificacy in sheep including GNAQ, COL5A2, COL3A1, HECW1, FBN1, COMMD3, RYR1, CCL28, SERPINA14, and HSPA2. These regions also overlapped with some quantitative trait loci (QTLs) linked to prolificacy traits, milk yield, and body weight. These findings suggest that future research could further link these genomic regions to prolificacy traits in sheep.
... To obtain a quantitative measure of genetic differentiation between the guanaco populations, the fixation index Fst was estimated using the --fst command in Plink with the dataset pruned for LD. We estimated Fst values per SNP based on the method described by Weir and Cockerham (1984) and calculated a weighted average of Fst values per SNP between population pairs. As a first scan of the isolation-by-distance effect, we measured on Google Earth the minimal distance (km) between the pair of closer locations within each defined population and performed a linear regression using Fst values as a function of distance. ...
The South American fauna has endured challenges such as illegal hunting, cattle expansion, climate change, and landscape fragmentation. Despite ongoing conservation efforts that aim to address these issues, genetic diversity remains overlooked. We genotyped 126 Lama guanicoe individuals from an area of 2 million km2 in Patagonia and Cuyo using the 60K SNPs Axiom-Camelids, and we assessed population viability through genetic diversity, inbreeding, and population size. We then explored population connectivities through network analyses, genetic differentiation, and Bayesian approaches. Our findings reveal six genetic clusters: Cuyo, Somuncura, North Patagonia, Central Patagonia, South Patagonia, and Tierra del Fuego Island (TDFI). Cuyo and TDFI guanacos differed from others due to isolation-by-distance and geographical barriers, respectively. Cuyo exhibited the highest degree of allele conservation, but TDFI faced heightened vulnerability due to isolation and increased homozygosity. Sharp bottlenecks in Cuyo and North Patagonia coincided with the expansion of sheep farming, while bottlenecks in the other populations occurred during the Little Ice Age. North Patagonia acted as a probable contact zone, facilitating mixing of the Cuyo, Somuncura, and Central Patagonia populations. The Central and South Patagonian populations presented the highest gene flow. Thus, genomic advances help to define distinct conservation units (genetic stocks) to guide management practices and decisions.
... PCA and clustering analyses were performed using the SNP-only dataset 1. Principal component analysis was conducted using Plink based on the variance-standardized relationship matrix. We calculated Weir and Cockerham's F ST [40], d XY , and π [41] in non-overlapping 10 kb windows with pixy [42] using the all-sites dataset 1. We estimated individual admixture proportions with the likelihood model-based program ADMIXTURE 1.3.0 ...
Alternative reproductive tactics are discrete, intrasexual differences in reproductive behaviour within a population. In some cases, these complex phenotypes are determined by autosomal supergenes or sex chromosomes—both of which exhibit reduced recombination and thus enable the linked inheritance of co‐adapted alleles from multiple loci. Most alternative reproductive tactics in amphibians are plastic (and reversible), environmentally determined and lacking morphological differentiation, but a striking exception is found in the two‐lined salamander ( Eurycea bislineata ) species complex. In some populations, two distinct male phenotypes coexist: ‘searching’ males have mental glands, protruding premaxillary teeth and elongate cirri used in terrestrial courtship, while ‘guarding’ males lack these traits and instead have hypertrophied jaw musculature used in mate guarding at aquatic nesting sites. These tactics differ in many morphological and behavioural phenotypes, but their proximate cause has not yet been described. Here, we generated genome‐wide SNP data from > 130 Eurycea cf. wilderae collected from Highlands Biological Station. We provide evidence for an XY sex determination and for a Y‐linked polymorphism underlying alternative reproductive tactics in this population. We then develop and validate a PCR‐based genotyping assay and apply it to characterise the sex ratio and relative frequency of male tactics from a sample of larvae. Our results add to the growing body of literature exploring the importance of supergenes and sex chromosomes in complex intraspecific polymorphisms, and we highlight opportunities for future work to continue exploring the genomic architecture of these traits.
Since the rapid spread and establishment of Africanized honey bee populations in South America, Africanized bees have persisted as the dominant strain. Remarkably, Chile has remained free of Africanized bee populations, making the country a valuable exporter of mated queens. Given Chile’s pivotal role in the apiculture industry, monitoring the genetic makeup of its honey bee colonies is crucial, yet documentation has been limited to a few studies. Here, we evaluate the ancestral composition of honey bees across eleven different regions in Chile. We find that Chilean honey bees have low levels of admixture, which is markedly lower relative to commercial colonies located internationally. The genetic ancestry of Chilean honey bees is primarily of Eastern European origin, with low levels of Western European ancestry. Finally, we detect a significant relationship between geography and genetic ancestry, suggesting regional adaptations that warrant further investigation.
Despite identifying genes regulating the coat colour in Western pig breeds, the genetic basis of the coat colour in Chinese indigenous pigs is still not understood due to the diversity of indigenous breeds and their genetic differences from exotic pigs. In this study, 215 Wuzhishan pigs with three coat colour patterns (white, black, and black-back/white-belly) were used to conduct a genome-wide association analysis. We found that genes responsible for the coat colour in the Wuzhishan breed are located on chromosome 8. Ninety-seven genome-wide significant SNPs are related to the animal’s coat colour. Using a haplotype-sharing analysis, we narrowed the potential candidate region to a 10.1 Mb interval encompassing only one gene, RAPGEF2, which participates in the regulation of melanogenesis. Two additional candidate genes, PDGFRA and KIT, are located within 1 Mb of the genome-wide significant SNPs. Gene ontology analysis and literature mining suggest that these candidate genes are associated with the animal’s coat colour. mRNA expression results revealed that RAPGEF2 and PDGFRA had significantly higher expressions in black pigs than in white pigs and higher expressions in black skin than in white skin from the same black-back/white-belly pigs. These results suggest that RAPGEF2 and PDGFRA are potential candidate genes regulating the coat colour in Wuzhishan pigs. Interestingly, mutations of KIT (a gene duplication and a G to A substitution at the splicing site in intron 17) were detected in white Wuzhishan pigs but not in black-back/white-belly or black pigs, suggesting a close genetic relationship between white Wuzhishan pigs and Western white pig breeds. In summary, these results indicate that the expression of RAPGEF2 and PDGFRA may cause the coat colour variation by influencing the deposition of melanin, while the mutation of KIT causes the white coat colour. Our results may provide a theoretical basis for the breeding of white coat colour Wuzhishan pigs, and shed light on the complex genetic background of coat colour variations in indigenous Chinese pig breeds.
This study aimed to characterize the genetic diversity and morphological traits of 32 populations of Phaseolus coccineus collected from the Aniene Valley. Quantitative seed trait analyses revealed that Mandolone accessions exhibited significantly higher seed weights and dimensions compared to Fagiolone accessions. Specifically, Mandolone accessions showed an average weight of 189.48 g per 100 seeds, with seed heights and lengths averaging 14.38 mm and 23.84 mm, respectively. In contrast, Fagiolone accessions had an average seed weight of 174.13 g, with seed heights and lengths of 13.95 mm and 22.58 mm, respectively. Molecular analysis, conducted using 9 poly-morphic SSR loci, identified 53 alleles across 320 genotypes, with a mean expected heterozygosity (He) of 0.695. This indicated that there was high genetic variability within the Aniene Valley populations. The genetic diversity analysis revealed two genetic clusters corresponding to the Mando-lone and Fagiolone landraces. This was supported by UPGMA, PCoA, and STRUCTURE analyses. This study highlights the need to conserve the genetic diversity within these landraces and provides a basis for the development of conservation strategies for P. coccineus germplasms in the singular ecological context of the Aniene Valley.
Objectives: The aim of this study was to investigate the genomic structure of the cattle breeds selected for meat and milk production and to identify selection signatures between them. Methods: A total of 391 animals genotyped at 41,258 SNPs and belonging to nine breeds were considered: Angus (N = 62), Charolais (46), Hereford (31), Limousin (44), and Piedmontese (24), clustered in the Meat group, and Brown Swiss (42), Holstein (63), Jersey (49), and Montbéliarde (30), clustered in the Milk group. The population stratification was analyzed by principal component analysis (PCA), whereas selection signatures were identified by univariate (Wright fixation index, FST) and multivariate (canonical discriminant analysis, CDA) approaches. Markers with FST values larger than three standard deviations from the chromosomal mean were considered interesting. Attention was focused on markers selected by both techniques. Results: A total of 10 SNPs located on seven different chromosomes (7, 10, 14, 16, 17, 18, and 24) were identified. Close to these SNPs (±250 kb), 165 QTL and 51 genes were found. The QTL were grouped in 45 different terms, of which three were significant (Bonferroni correction < 0.05): milk fat content, tenderness score, and length of productive life. Moreover, genes mainly associated with milk production, immunity and environmental adaptation, and reproduction were mapped close to the common SNPs. Conclusions: The results of the present study suggest that the combined use of univariate and multivariate approaches can help to better identify selection signatures due to directional selection.
The radiation of cichlid species in the East African Great Lakes is remarkable and rapid. The population genetics of two deep-water Cyphotilapia species along the east coast of Lake Tanganyika from Burundi to southern Tanzania was determined using ddRAD-seq. A combination of ADMIX-TURE, PCA, genome polarization, and 2D site frequency spectrum analyses confirmed the presence of two species, C. frontosa in the north and C. gibberosa in the south, as documented in other studies. We also found evidence of a potential hybrid zone connecting the two species at a sharp genetic cline centered in the middle of the lake and apparent introgression in both directions, but predominantly from 'gibberosa' into 'frontosa'. The highest proportion of introgressed 'gibberosa' ancestry was present in the southernmost populations of C. frontosa collected near Karilani Island and Cape Kabogo. At the intra-specific level, there was support for between 1 and 3 populations of C. frontosa, whereas the results indicated only a single homogeneous population of C. gibberosa. The presence of different morphs in the lake despite the low levels of heterozygosity suggests that a small number of loci may be involved in the morphological variation and/or that there is a more complex interplay between genetics and the environment in different locations. Key Contribution: This study focused on the genetics of Cyphotilapia based on nine samples along the east coast of Lake Tanganyika. The study confirmed the presence of two species, with Cyphotilapia frontosa in the north of the lake and C. gibberosa in the south of the lake. There was evidence of potentially three populations present for C. frontosa but no evidence was found of separate populations in C. gibberosa. In the central region of the lake, we found evidence of introgression between the two species with a greater degree of gene flow from C. gibberosa to C. frontosa.
Red fox, Vulpes vulpes , is a globally distributed species characterized by its high adaptability to diverse habitats and a broad range of food resources. This remarkable adaptability has allowed the red fox to thrive in various environments, from urban areas to remote wilderness. In this study, we used a set of microsatellite markers for the comparative genetic analysis of red fox populations from two countries. We included populations from the Eastern Alps and the northern Dinaric Mountains in Slovenia, as well as the Central Dinaric Mountains in Bosnia and Herzegovina. We successfully isolated DNA and genotyped 118 red fox samples. Our analyses, which included Bayesian clustering techniques, revealed a weak genetic differentiation among the studied populations. However, it is noteworthy that statistically significant differences in estimates of genetic differentiation were only apparent when comparing the populations between the two countries. Further spatial genetic clustering analyses provided additional insights, unveiling a differentiation into four genetic clusters. These clusters comprised two distinct groups in Bosnia and Herzegovina and two in Slovenia. This pattern of differentiation suggests that isolation by distance is a key factor influencing the genetic structure of the red fox in this studied region. Additionally, our findings highlighted that populations from the Alps and northern Dinaric Mountains exhibit higher genetic diversity and observed heterozygosity compared to their counterparts in the Central Dinaric Mountains. The genetic diversity is also notable when compared to other European red fox populations. Studying genetic diversity is crucial for the resilience and adaptability of populations, ensuring their survival amid environmental changes and human-induced pressures.
The genetic structure and diversity of eight indigenous sheep breeds - Sidaoun, Rembi, Hamra, D’men, Ouled Djellal, Sardi, Berguia and Daraa- were identified by analyzing ten microsatellite loci in 183 unrelated individuals. Parameters such as allele diversity, observed heterozygosity, expected heterozygosity, unbiased expected heterozygosity, and genetic distance have been calculated. Additionally, wright F-statistics values (FIS, FIT and FST) were determined. The average number of alleles per locus was also estimated. Within these breeds, the mean number of alleles ranged from 12.60 in D’men to 17.80 in Ouled Djellal. Mean expected heterozygosity (He) varied between 0.83 in Sidaoun and 0.91 in Ouled Djellal. Inbreeding coefficient for all microsatellites is low, with a negative FIS = -0.014 ranging from -0.057 for INRA063 to 0.018 in McM42. The FST (mean genetic differentiation) value was found to be 0.062, indicating that only 6.2% of total genetic diversity is attributed to genetic differentiation among populations, while 93.8% of total genetic variance results from differentiation within each population. A phylogenetic tree based on genetic distance revealed three distinct groups: D'men/ Sidaoun, Ouled Djellal/ Rembi/ Berguia, and Sardi/ Daraa. However, the Hamra sheep breed appeared in a separate cluster. This study has provided important information on the genetic resources of Hamra, Rembi, D'men, and Sidaoun sheep that justifies priority conservation measures. Our results confirm that the microsatellite markers used in this study are sufficiently polymorphic and can be successfully used to study the genetic diversity of Algerian sheep populations.
In recent years, research has gradually uncovered the mechanisms of animal adaptation to hypoxic conditions in different altitude environments, particularly at the genomic level. However, past genomic studies on high-altitude adaptation have often not delved deeply into the differences between varying altitude levels. This study conducted whole-genome sequencing on 60 Tibetan sheep (Medium Altitude Group (MA): 20 Tao sheep (TS) at 2887 m, High Altitude Group (HA): 20 OuLa sheep (OL) at 3501 m, and Ultra-High Altitude Group (UA): 20 AWang sheep (AW) at 4643 m) from different regions of the Tibetan Plateau in China to assess their responses under varying conditions. Population genetic structure analysis revealed that the three groups are genetically independent, but the TS and OL groups have experienced gene flow with other northern Chinese sheep due to geographical factors. Selection signal analysis identified FGF10, MMP14, SLC25A51, NDUFB8, ALAS1, PRMT1, PRMT5, and HIF1AN as genes associated with ultra-high-altitude hypoxia adaptation, while HMOX2, SEMA4G, SLC16A2, SLC22A17, and BCL2L2 were linked to high-altitude hypoxia adaptation. Functional analysis showed that ultra-high-altitude adaptation genes tend to influence physiological mechanisms directly affecting oxygen uptake, such as lung development, angiogenesis, and red blood cell formation. In contrast, high-altitude adaptation genes are more inclined to regulate mitochondrial DNA replication, iron homeostasis, and calcium signaling pathways to maintain cellular function. Additionally, the functions of shared genes further support the adaptive capacity of Tibetan sheep across a broad geographic range, indicating that these genes offer significant selective advantages in coping with oxygen scarcity. In summary, this study not only reveals the genetic basis of Tibetan sheep adaptation to different altitudinal conditions but also highlights the differences in gene regulation between ultra-high- and high-altitude adaptations. These findings offer new insights into the adaptive evolution of animals in extreme environments and provide a reference for exploring adaptation mechanisms in other species under hypoxic conditions.
Understanding the genetic basis of porcine mental health (PMH)-related traits in intensive pig farming systems may promote genetic improvement animal welfare enhancement. However, investigations on this topic have been limited to a retrospective focus, and phenotypes have been difficult to elucidate due to an unknown genetic basis. Intensively farmed pigs, such as those of the Duroc, Landrace, and Yorkshire breeds, have undergone prolonged selection pressure in intensive farming systems. This has potentially subjected genes related to mental health in these pigs to positive selection. To identify genes undergoing positive selection under intensive farming conditions, we employed multiple selection signature detection approaches. Specifically, we integrated disease gene annotations from three human gene–disease association databases (Disease, DisGeNET, and MalaCards) to pinpoint genes potentially associated with pig mental health, revealing a total of 254 candidate genes related to PMH. In-depth functional analyses revealed that candidate PMH genes were significantly overrepresented in signaling-related pathways (e.g., the dopaminergic synapse, neuroactive ligand‒receptor interaction, and calcium signaling pathways) or Gene Ontology terms (e.g., dendritic tree and synapse). These candidate PMH genes were expressed at high levels in the porcine brain regions such as the hippocampus, amygdala, and hypothalamus, and the cell type in which they were significantly enriched was neurons in the hippocampus. Moreover, they potentially affect pork meat quality traits. Our findings make a significant contribution to elucidating the genetic basis of PMH, facilitating genetic improvements for the welfare of pigs and establishing pigs as valuable animal models for gaining insights into human psychiatric disorders.
Piangua, Anadara tuberculosa, is an economically important mollusk for the human population living on the Colombian Pacific Coast. In the last years, the demand and exploitation of this mollusk have increased, putting it at risk to the point of being endangered. This research aimed to identify the genetic diversity and population structure of piangua in two localities on the Pacific Coast of Colombia. We assembled a chromosome-level genome using PacBio-Hifi and Arima sequencing. We obtained 274 scaffolds with an N50 of 45.42 Mbp, a total size of 953 Mbp, and a completeness of 91% based on BUSCO scores. The transposable elements accounted for 30.29% of the genome, and 24,317 genes were annotated. Genome-guided variant calling for 89 samples using DArT sequencing data delivered 4,825 bi-allelic SNPs, which supported genetic diversity and population structure analyses. Data showed that the piangua populations in the two localities were under expansion events more than 100k years ago. However, results also showed a reduction in genetic diversity, as evidenced by the loss of heterozygosity, which may be caused by high levels of inbreeding, probably due to a recent overexploitation. Furthermore, although we evidenced gene flow between the two localities, there is also a subtle geographical population structure between the two localities and among mangroves in one of the localities. This is the first study in Colombia that provides relevant genetic information on piangua to lay the foundations for conservation strategies.
Worldwide, humans have strongly altered river networks. Key changes resulted in modified hydromorphology, poor habitat quality and availability, migration barriers, and pollution. Restoration measures aim at mitigating anthropogenic stressors and at restoring connectivity, but the biological success of these measures is not guaranteed. Analyzing genetic diversity and metapopulation structure of target species in the river network with genetic markers can help to understand recolonization processes and to identify persisting gene flow barriers. Here, we studied the population genetic structure of the two pollution‐tolerant detritivorous isopod species, Asellus aquaticus and Proasellus coxalis, in the former heavily degraded and polluted, but now mostly restored Emscher catchment in Germany. For both species, we analyzed mitochondrial cytochrome c oxidase I (COI) gene sequences and nuclear genome‐wide single nucleotide polymorphism (SNP) data. Surprisingly, we found a strong metapopulation structure for both species with several isolated populations on a small‐scale of few kilometers, but a still high genetic diversity, especially in the COI gene. For both taxa, potentially cryptic species are known, but our SNP data showed that the mitochondrial lineages represent only one species, each, in the study area. This highlights the importance of integrating high‐resolution nuclear markers into species identification because species diversity may otherwise be overestimated. While we could identify some migration barriers and find indications for passive dispersal by birds or humans, these factors could not fully explain the local metapopulation structure, suggesting that also other drivers, such as isolation by adaptation, priority effects, or biotic interactions, play a role in shaping the population genetic structure.
The earlier vertion of AncestryPainter is a Perl program to display the ancestry composition of numerous individuals using a rounded graph. Motivated by the requests of users in practical applications, we updated AncestryPainter to version 2.0 by coding in an R package and improving the layout, providing more options and compatible statistical functions for graphing. Apart from improving visualization functions per se in this update, we added an extra graphing module to visualize genetic distance through radial bars of varying lengths surrounding a core. Notably, AncestryPainter 2.0 implements a method admixture history graph (AHG) to infer the admixture sequence of multiple ancestry populations, and allows for multiple pie charts at the center of the graph to display the ancestry composition of more than one target population. We validated the six AHG metrics using both simulated and real data and implemented a Pearson coefficient-based metric with the best performance in AncestryPainter 2.0. Furthermore, a statistical module to merge ancestry proportion matrices. AncestryPainter 2.0 is freely available at https://github.com/Shuhua-Group/AncestryPainterV2 and https://pog.fudan.edu.cn/#/Software.
Coadaptation of mitochondrial and nuclear genes is essential for proper cellular function. When populations become isolated, theory predicts that they should maintain mito‐nuclear coadaptation in each population, even as they diverge in genotype. Mito‐nuclear incompatibilities may therefore arise when individuals from populations with divergent co‐evolved mito‐nuclear gene sets are re‐united and hybridise, contributing to selection against inter‐population hybrids and, potentially, to speciation. Here, we explored genetic divergence and gene flow between populations of a stingless bee (Tetragonula hockingsi) that have highly divergent mitogenomes. We identified three distinct populations across the species' 2500 km range on the east coast of Queensland (Australia): ‘Cape York’, ‘Northern’, and ‘Southern’. The mitogenomes of each population showed > 12% pairwise nucleotide divergence from each other, and > 7% pairwise amino acid divergence. Based on nuclear SNPs from reduced representation sequencing, we identified at least two zones of gene flow between populations: a narrow natural zone between Northern and Southern populations (coinciding with a biogeographic barrier, the Burdekin Gap), and an artificial zone at the southern edge of the species' distribution, where Cape York, Northern, and Southern mito‐lineages have been brought together in recent decades due to beekeeping. In the artificial hybrid zone, we also confirmed that males of all three mito‐lineages were attracted to the mating aggregations of Southern queens, consistent with inter‐population hybridisation. Populations of T. hockingsi thus appear to be in the ‘grey zone’ of the speciation continuum, having strong genetic differentiation but incomplete reproductive isolation. Among the nuclear SNPs most differentiated between Northern and Southern populations, several were associated with genes involved in mitochondrial function, consistent with populations having co‐diverged mito‐nuclear gene sets. Our observations suggest that coadapted sets of mitochondrial and nuclear genes unique to each population of T. hockingsi may play a role in maintaining population boundaries, though more study is needed to confirm the fitness costs of mito‐nuclear incompatibilities in hybrid individuals.
The evolution of sex chromosomes can involve recombination suppression sometimes involving structural changes, such as inversions, allowing subsequent rearrangements, including inversions and gene transpositions. In the two major genus Salix clades, Salix and Vetrix, almost all species are dioecious, and sex-linked regions have evolved on chromosome 7 and 15, with either male or female heterogamety. We used chromosome conformation capture (Hi-C) and PacBio HiFi (high-fidelity) reads to assemble chromosome-level, gap-free X and Y chromosomes from both clades, S. triandra (15XY system), a basal species in the Vetrix clade, and the Salix clade species S. mesnyi (7XY system). Combining these with other available genome assemblies, we found inversions within the sex-linked regions, which are likely to be pericentromeric and probably recombined rarely in the ancestral species, before sex-linkage evolved. The Y-linked regions in all 15XY and 7XY species include partial duplicates containing exon 1 of an ARR17-like gene similar to male-determining factors in other Salicaceae species. We also found duplicates of a Y-specific gene, which we named MSF. The derived Salix clade 7XY chromosome systems appear to have evolved when these two genes transposed from the 15Y to the 7Y. Additionally, the 7Y chromosomes in S. dunnii and S. chaenomeloides probably evolved from the ancestral 7X of the Salix clade, involving a similar transposition, and loss of the ancestral 7Y. We suggest that pericentromeric regions that recombine infrequently may facilitate the evolution of sex-linkage.
Invasive species with native ranges spanning strong environmental gradients are well suited for examining the roles of selection and population history in rapid adaptation to new habitats, providing insight into potential evolutionary responses to climate change. The Atlantic oyster drill ( Urosalpinx cinerea ) is a marine snail whose native range spans the strongest coastal latitudinal temperature gradient in the world, with invasive populations established on the US Pacific coast. Here, we leverage this system using genome‐wide SNPs and environmental data to examine invasion history and identify genotype–environment associations indicative of local adaptation across the native range, and then assess evidence for allelic frequency shifts that would signal rapid adaptation within invasive populations. We demonstrate strong genetic structuring among native regions which aligns with life history expectations, identifying southern New England as the source of invasive populations. Then, we identify putatively thermally adaptive loci across the native range but find no evidence of allele frequency shifts in invasive populations that suggest rapid adaptation to new environments. Our results indicate that while these loci may underpin local thermal adaptation in their native range, selection is relaxed in invasive populations, perhaps due to complex polygenic architecture underlying thermal traits and/or standing capacity for phenotypic plasticity. Given the prolific invasion of Urosalpinx , our study suggests population success in new environments is influenced by factors other than selection on standing genetic variation that underlies local adaptation in the native range and highlights the importance of considering population history and environmental selection pressures when evaluating adaptive capacity.
We conducted an electrophoretic study of enzyme polymorphisms, using pectoral muscle biopsy, in a linear series of four song dialect populations of White-crowned Sparrows in central, coastal, California. Variation is described at eight loci among nine sampling locations in the four dialects. Statistical analyses showed significant heterogeneity among samples within dialects in five of 32 possible tests over all eight loci. Differences between dialects were over twice as great with 18 of 48 possible tests giving statistical significance. Analysis by F-statistics revealed average inbreeding coefficients of FST = .042, FIS = -.006, and FIT = .034. These values suggest that the observed genetic differentiation among dialects is caused primarily by restricted gene flow between dialects, with little or no influence caused by consanguineous mating within dialects. The overall average genetic distance between dialects is 0.009 with adjacent dialects being more similar than dialects farther apart. In a between-dialect comparison, there was a significant regression of genetic distance on geographic distance. In a between-samples, within-dialect comparison, genetic distance was not significantly correlated with geographic distance. Therefore, genetic differentiation is not explained by isolation-by-distance but is interpreted as a consequence of song dialects. The genetic distance values are in the same range as described by others for subspecies, semispecies, and sibling species of birds.
Patterns and levels of genetic variation were studied in five bristlecone pine (Pinus longaeva) populations in the eastern Great Basin. Fourteen enzyme loci were examined using horizontal starch gel electrophoresis. Low but significant levels of genetic variation were observed among populations. No patterns of decreasing genetic identity were observed with an increase in geographic separation. In contrast, levels of genetic variation within populations were high. All populations were polymorphic for the same 11 loci. Levels of heterozygosity were effectively the same in all populations with a mean heterozygosity of 0.327 Genetic identity between altitudinal zones within populations was effectively the same as that between populations. Analyses were also done to determine if there were deviations in expected genotype frequencies. All but two of the loci deviated significantly from expectations in at least one population. A cp-4 had consistent excesses of heterozygotes while Gdh-3, Lap-8 and Got-5 have consistent deficiences. All other polymorphic loci deviated from the expected in both directions. The low interpopulation variation and the high intrapopulation variation, along with paleoecological data, argue for the continuity of bristlecone pine throughout much of the Great Basin during the last full glacial. The maintenance of high levels of variation from that time until the present are a result of several factors which would appear to include: (1) high outcrossing rates; (2) maintenance of large population sizes; (3) production of large numbers of seeds; (4) microhabitat adaptation in a spatially and temporally heterogeneous environment.
A variety of hypotheses regarding the relationship of recombination system to population genetic structure were tested with allozymic variation data for three biotically sympatric and closely related annuals in the genus Oenothera, each with a different recombination system. The autogamous O. mexicana is apparently monomorphic, uniform both within and among populations, displaying no detectable heterozygosity. Both the outcrossing O. grandis and the clonal O. laciniata have low levels of gene diversity (5% and 7%, respectively). The outcrosser's populations generally are close to Hardy-Weinberg expectations, while those of the clonal species tend to deviate strongly. Although the levels of species-wide variation are about the same for O. grandis and O. laciniata, the latter shows a significant paucity of variation within populations and a significant wealth of between-population variation when compared to the former. The population genetic correlates of the recombination system described here and elsewhere for species of Oenothera generally are in accord with the expectations of population genetics theory.
Thomomys bottae pocket gophers are characterized by high between population heterogeneity in allele frequencies yet may retain very high levels of within population variability (individual heterozygosity). The mechanisms which might be responsible for these two, somewhat conflicting observations have been explored by examining the extent of local population structuring and resulting variability levels in pocket gopher populations at Hastings Natural History Reservation in Carmel Valley, California. The specific components which can affect either or both of these parameters and which were examined in this study included: (1) extent of inbreeding (consanguineous matings); (2) the dispersion patterns of adults within fields in relation to breeding patterns; (3) the sex ratio of adults in breeding units; (4) the variance in male reproductive effort based on paternity determination of litters from pregnant females; and (5) the effect of local experimental population extirpations on resulting structuring. Pocket gopher populations were found to be composed of small numbers of individuals, usually significantly skewed in sex ratio in favor of females among breeding adults, and with high variance in male reproductive success. Inbreeding did not appear to be a significant component in the level of population structuring observed. These parameters combine to produce small genetically effective population units, with measured Ne ranging from 12 to 26, which can generate extensive between population genetic heterogeneity despite a moderate level of intergroup dispersal. The experimental population extinctions in some fields demonstrated that, while recolonization can produce some homogenizing effects across fields, extensive heterogeneity can be reinstated after a single generation of breeding when such is confined to the small numbers of individuals characterizing the breeding units at Hastings Reservation. Despite the momentary small Ne, empirical evidence shows that individual heterozygosity levels can remain high and within population variability thus appears to be a balance between small population size generating between population differentiation and effective dispersal maintaining individual heterozygosity.
The genetic structure of the black-tailed prairie dog (Cynomys ludovicianus) was studied by an electrophoretic analysis of four polymorphic blood proteins and by pedigree analysis. Only one probable case of close inbreeding (father-daughter) was observed in a three-year period; the average inbreeding coefficient was less than that expected if matings were at random. The evidence for nonrandom mating was consistent with behavioral observations taken at the main study colony. In nine of 11 instances, polymorphic loci exhibited an excess of heterozygotes (that is, negative fixation indices). The existence of locus-specific differences among fixation indices suggested that some factor in addition to the avoidance of close inbreeding was causing the excess of heterozygotes. Two possible explanations for this result are selective differences among genotypes and sex-related allele frequency differences. Additional evidence for outbreeding in the black-tailed prairie dog is (a) the relatively high heterozygosity within colonies, (b) the relatively low genetic heterogeneity among colonies and (c) the high rate of male migration among colonies.
The apportionment of genetic variation within and among populations of Desmodium nudiflorum (L) DC was determined. Allozyme frequencies within populations conform to Hardy-Weinberg expectations and no population substructure was detected. Within populations FST values average 0.015 and are not significant. Most of the genetic diversity within a population, 75%, is due to differences between individuals rather than differences between subpopulations. In contrast, there is significant genetic differentiation between populations. Standardized genetic variances average 0.165 Each population contains a unique set of polymorphic loci; loci which are polymorphic in more than one population have significant differences in gene frequencies. A large portion of the genetic diversity of the species, 47.4%, is not represented within individual populations. Genetic distances between populations average 0.014 and are independent of geographical distance. The genetic structure of D. nudiflorum is most similar to a random patchwork.
An electrophoretic survey of 22 loci in the Rhytidoponera impressa group revealed seven variant loci. Gene frequencies and average heterozygosity have been estimated for 35 populations (five species) occurring in tracts of mesic forest (mostly rainforest and wet sclerophyll) along the east coast of Australia. Estimated heterozygosity (Ĥ) per population varies from .000 to .072 (mean .036 ± .003 SE). This is consistent with low values reported for other species of Hymenoptera, and contrasts with higher levels of allozyme variability reported in most diploid insects. However the evidence supporting the hypothesis that haplodiploidy is responsible for the reduced variation is still weak. Local populations show no evidence of inbreeding, insofar as there are no detectable departures from panmixia (FIS ≈ 0). When considered over all loci, most populations are only moderately differentiated, the mean genetic distance (Nei's measure, D) between conspecific populations being 0.015 ± 0.001 SE (N = 219 comparisons). Nevertheless, there is marked heterogeneity of gene frequencies at the segregating loci. Mean estimates of FST (based on four loci) in Rhytidoponera confusa (.294) and chalybaea (.380) are larger than FST values reported for most outbreeding species. Divergent gene frequencies may be a reflection of both stochastic processes (founder effect and a high sampling variance) and selection, since contemporary population sizes appear to be quite high. These findings are consistent with theoretical expectations of rapid population differentiation under haplodiploidy, although the habitat requirements of the impressa group are also conducive to population divergence. The mean genetic distance between all interspecific populations is 0.136 ± 0.005 SE (N = 376). Genetic distance data suggest the possibility that two species (impressa and enigmatica) are recently derived from divergent populations of a third, paraphyletic species (chalybaea). The occurrence of sibling species in the Rhytidoponera impressa group is paralleled by numerous other examples in the Hymenoptera, and lends support to the notion that speciation is a potentially rapid process in this group of insects.
Protein polymorphism was analyzed in 10 populations of Oe. organensis at 15 loci. Only Mdh was polymorphic; and it displayed only two alleles. Gene frequencies at this locus were analyzed for plant and seed collections made in 1972 and 1975. Interpopulation gene frequency heterogeneity was small; FST for adults and seeds were 0.14 and 0.09, respectively. In 9 of the 10 populations collected in 1975, heterozygote deficiency relative to Hardy-Weinberg expectations (F) was less in the seed crop than in the adult plants. Estimates of random outcrossing (t) were close to 1 for most populations. Treating populations and years collectively, t = .88. The species as a whole behaves nearly as a panmictic unit, with Mdh variation rather evenly distributed. This interpretation is in accord with that proposed by Emerson (1939) based upon S-gene polymorphism.
Allozyme variation was compared in selfing and outcrossing populations of Gilia achilleifolia. A group of selfing populations in the northern part of the distribution and a group of outcrossing populations in the southern part of the distribution contained similar amounts of genetic variation; however, individual selfing populations contained less genetic variation than individual outcrossing populations. Most of this difference was in number of alleles per locus and percent loci polymorphic per population. Selfing populations had higher heterozygote frequencies than expected based on knowledge of their outcrossing rate. Evidence is presented that suggests some of the heterozygosity excess is the result of selection. As selfing and outcrossing populations fall into distinct geographical groups, it was possible to study the apportionment of genetic diversity within each group. The among population component of genetic diversity in the selfing group was larger than that of the outcrossing group. In general, the relationship between breeding system and amount and structuring of genetic variation in G. achilleifolia agrees with theoretical considerations and with comparisons that have been made interspecifically in several plant genera.
Research on the jackknife technique since its introduction by Quenouille and Tukey is reviewed. Both its role in bias reduction and in robust interval estimation are treated. Some speculations and suggestions about future research are made. The bibliography attempts to include all published work on jackknife methodology.
Genetic variation for seven variable loci was analyzed for prairie dogs within and between populations in eastern New Mexico. Significant genetic differentiation was found for prairie dogs from populations in close proximity (5-15 km) as well as for those from distant parts of their range. The degree of local differentiation was greater than that among regions separated by major geographical barriers. The patterns of genetic similarities between prairie dogs from different populations were not in agreement with proposed taxonomic classifications. Significant heterogeneity of allele frequencies was found for prairie dogs from different wards (portions of a population separated by unsuitable habitat) within a population, as well as for those from different coteries (harem groups) within the wards. The social behavior of prairie dogs has resulted in genetic differentiation over very small distances and rapid inbreeding and genetic drift within the social groups. The mechanisms and consequences for sustaining such fine scale subdivision are discussed.
Electrophoretic variation was examined at 38 loci in the milkfish, Chanos chanos. Samples were collected from 14 locations across the Pacific Ocean from the Philippines to Hawaii. Average heterozygosity per locus was 0.075 ± 0.011, an above average value for heterozygosity with respect to previously investigated fish species. From 16 to 23% of the loci were considered polymorphic and the average number of alleles per locus was 1.45 ± 0.08. No latitudinal changes in genic variation were found; instead, levels of genic variation increased slightly with increasing distance from the Philippine region. The Hawaii samples had a noticeable loss of variation at the polymorphic loci. The magnitude of interpopulation divergence was extremely low, even between samples separated by up to 10,000 km. The average genetic distance (Nei, 1978) was 0 002 and the mean FST (Wright, 1965) was 0.041. FST values were calculated for other marine fishes and compared here. Considerable population divergence at four polymorphic loci was seen between the samples taken in Hawaii. This is in agreement with earlier work on eye lens proteins of milkfish (Smith, 1978). Explanations for this relatively abrupt change are discussed. The possibility that gene flow between the samples is reduced due to the presence of local oceanic gyres is emphasized. Patterns of geographic variation in allele frequency were assessed by (1) genetic distance analysis, (2) by grouping samples according to their potential for gene flow (viz., oceanic circulation patterns and number/proximity of neighboring islands) and then by testing, locus by locus, the allele frequency variation within and between the groups, and (3) by examining the data for latitudinal variation. The first two techniques yielded the same results; distinctive groups or samples were the eight Philippine samples, the four samples taken from across the equatorial Pacific Ocean, and the two samples from Hawaii. Significant regressions for allele frequency on latitude were seen at the Est-2 locus for two negatively correlated alleles across all the samples and within the Philippine samples. Although one of the most unequivocal results of this study was the uniqueness of the Hawaiian samples, it is interesting to note how similar they were with all the other samples, even though separated by 1,700 km from the nearest sample and 10,000 km from the Philippines. Other recent and different approaches to this problem suggest that the phenomenon of high genetic similarity among oceanic populations of marine organisms may be common. Oceanic conditions that affect gene flow among localities necessarily play a large role in determining the magnitude of population differentiation in marine organisms.
Genic diversity and the organization of genetic variability in pitch pine were examined in 11 populations across the species range. Pitch pine is genetically variable; 76.2% of the loci studied were polymorphic and the average individual heterozygosity was 14.6%, but this is less than that exhibited by several other woody species. The contrast may reflect differences among species in their evolutionary history, or may be an artifact relating to the choice of enzyme systems analyzed. Only a small percent of the observed genic diversity in pitch pine appears to be interpopulation, the remainder is due to differences between individuals within populations, in agreement with results for other tree species. Analysis of F-statistics indicates that populations of pitch pine simulate panmixis with an F̄IS of 0.009. Populations are only weakly differentiated, and genetic and geographic distance are only weakly correlated. Central populations seem to be more variable than those near the species border. An isolated population at the northern extreme of the species range has a heterozygosity of 11.7%, compared to the species average of 13.8% and an average of 15.0% for central populations from New Jersey. The dwarf forest populations of the New Jersey Pine Plains are essentially identical in genic constitution to tall forest of the New Jersey Pine Barrens, at least for the allozyme loci we sampled. Whatever factors are responsible for the dwarf stature of these populations, they have not resulted in detectable changes in allozyme frequencies among populations. In general, results of allozyme analysis are not in agreement with previously reported patterns for morphological and growth traits, emphasizing the need to sample several types of loci to adequately understand the genetic structure of populations.
Genetic subdivision has been examined in island populations of the ants Formica fusca and F. exsecta, and in continuous populations of F sanguinea and F. transkaucasica. The estimates of genetic differentiation are based on the distribution of cMDH genotypes in the populations. The sample-size corrected values of FST* among the island populations were .074 in fusca and .090 in exsecta (12 islands within the total area of 3 x 5 km). Using the island model of population structure, these values correspond to migration rates m = .015-.03 in fusca and .11 in exsecta. The estimates of Nem, 3.0 and 2.1, indicate important allele frequency differentiation among the islands. The structure of the continuous populations was analyzed both in a core population in which all the nests were examined, and in a larger area which was sampled using a grid pattern (the areas examined are 150 x 1,000 m in transkaucasica, and 2.5 x 2.5 km in sanguinea). The sample-size corrected standarized allele frequency variance among the study plots in the grid was FST* = .072 in transkaucasica and .046 in sanguinea. Using Wright's model of isolation by distance, the neighborhood sizes are estimated to be 50 < NN < 100 in both species. The estimate of sanguinea is affected by a slight excess of heterozygotes and a high autocorrelation between neighboring nests. Although the present results should be considered only as tentative (due to the use of only one locus), they suggest important microdifferentiation within Formica populations.
Genetic variation in both chromosomal and allozyme features has been summarized for the pocket gopher, Thomomys bottae. The former data supplement those presented earlier (Patton, 1972); the latter are based on the examination of 23 presumptive gene loci for 825 individuals from 50 populations. The salient points of the study are as follows: (1) Inter and intrapopulation variability in both karyotype and allozyme pattern are extreme. Populations may differ by as many as 19 cytologically detectable features, all apparently involving whole-arm constitutive heterochromatin additions/deletions. These do not impose any known meiotic load in heterozygotes. Divergence in allozyme frequencies between populations on a macrogeographic scale is quite high. Indeed, the average T. bottae population pair shares only 79 percent overall similarity (range 63 to 98 percent, based on Rogers' [1972] S-value. The geographic pattern is one of strong regionally delineated units which, while somewhat internally uniform, abut and interbreed with adjacent regional units. There is a high degree of concordance between the allozyme and chromosomal geographic patterns. (2) Most populations of T. bottae are quite variable genically, the average being polymorphic for 33 percent of the loci examined (range, 13 to 57 percent). Additionally, the average individual is heterozygous at 9.3 percent of its loci (range, 3.0 to 16.9 percent). Thus, the species is not only considerably more variable than its relative T. 'talpoides' complex (Nevo et al., 1974) but it is also more variable than the average rodent. (3) The most satisfying explanation for the generally high level of genic variability involves the lack of severe bottlenecking in a given population's history and the degree of gene flow between populations. A significant correlation was found between overall variability and both population density and degree of population geographic connectedness. The latter is reflected in an extremely strong, inverse relationship between pair-wise genic similarity (S-value) and ecogeographic distance between populations occupying relatively continuous habitat types, even over extensive geographic distances. This suggests that gene flow plays a major role in geographic structuring, despite the apparent low vagility typical of fossorial rodents. (4) The data presented here do not support the concept of homozygosity as an adaptive strategy in response to the uniform subterranean environment of fossorial rodents (e.g., Nevo et al., 1974). Instead, a model is developed which identifies historical impact of population range changes on the degree of bottlenecking and the development of reproductive isolation resulting from fixation of chromosomal rearrangements between populations as key elements to explain the level of observed variability in Thomomys species. (5) Divergence in structural gene loci as assayed by electrophoretic techniques is relatively unrelated to the attainment of reproductive isolation in pocket gophers (and probably other organisms as well, see Gottlieb, 1976; Avise, 1976). Rather, speciation events are strongly correlated with chromosomal rearrangements of the type which may cause severe meiotic imbalances in heterozygotes. This is substantiated by the fact that T. umbrinus populations, which differ from T. bottae by several translocations and are reproductively isolated (Patton, 1973), share closer genic similarity to some geographic segments of T. bottae than the latter do among themselves.
Thirty geographic samples of the monarch butterfly, Danaus plexippus L., were collected in the summer and fall of 1973, 1974, and 1975, in the eastern-central U.S. and Canada. Using Wright's F-statistics and electrophoretic alleles at six enzyme-loci as genetic markers, an analysis of the genetic structure of the population as a whole was carried out. It was assumed a priori that the monarch population undergoes changes in population structure during the spring repopulation of the northern range, the relatively sedentary summer buildup in population size, and lastly the fall migration to the Gulf states and Mexico. These changes should be detectable in the genetic structure. In non-migratory collections, common alleles at several loci show statistically significant allele frequency variation among collections (FST > 0). The sexes differ persistently in allele frequency at two of the loci (Got and Ndh). Among-sample variances are reduced in the migratory collections, and none of the alleles show significant differentiation (FST = 0). Thus, migration swamps genetic differentiation generated prior to, and during, the less vagile summer period. Inbreeding coefficients FIS) computed for each of the individual samples show persistent heterozygote excesses at three loci (Ndh, Got, and Mdh, FIS
The organization of genetic variability in the pitcher plant, Sarracenia purpurea L., was examined. Particular attention was given to the Cranberry Island population which was founded by a single specimen in 1912. Ten additional populations were also sampled for genetic variability at ten genetic loci. S. purpurea has a moderate level of genetic variability; half of the loci are polymorphic and heterozygosity per individual is 9.5%. Genetic diversity in the species was apportioned into within and between population components. The within population component is .67, indicating a substantial portion of the genetic diversity in the species is not represented within individual populations. Analysis of allele frequencies by chi-square and F statistics also indicate substantial levels of differentiation between populations. Gene frequencies and identity values show no correlation with geographical distance; however, heterozygosity and mean number of alleles per locus are significantly higher in the eastern populations. The Cranberry Island population exhibits reduced genetic variability relative to the species as a whole. Only one polymorphic locus was found, and heterozygosity per individual is 50% below the species mean. However, several other populations also exhibit low levels of genetic variability relative to the species. Founder effect and genetic drift may account as well for the loss of variability in these isolated populations.
This study was designed to obtain a direct measure of gene flow in free-living populations of house mice, Mus musculus. Ten wild-caught females that were homozygous for the Hbbs hemoglobin allele were introduced in January, 1976, into two populations on the Rossway Poultry Farm in Dutchess Co., New York where resident mice (N = 155) lacked this allele. Six of the ten introduced females were recaptured and all were pregnant. The allele spread through one coop at a rate predicted by the recapture distances of resident mice. Many carriers of the allele remained near an introduced female, their putative mother. About half of the female carriers became pregnant. The frequency of the introduced allele rose from an estimated 0.11 at the time of the introduction to 0.15 at the time the coop was cleaned out 10 months later. At the end of 2.5 yr the frequency of the introduced allele was 0.02. Within a generation or two of the introduction the allele appeared in two other coops in which no introductions occurred. In two of these other coops, carriers of the introduced allele appeared which had first been trapped in a coop where females were originally introduced. Less than one percent of the mice were known to move between coops. Of the 12 male and three female mice that emigrated from their original coops, over half were caught only once in their original coop. There was a high turnover of mice in all coops. Nearly half the mice caught in any month were missing from the sample in the next month. In most coops, females remained in residence longer than males. In the Rossway study, the gradual progression of the allele through the coop population suggests that gene flow occurs through the breeding of adjacent neighbors. Long-range gene flow between coops occurred within two generations of the introduction. Population differentiation, when it occurs, does so through isolation by distance. Gene flow between coops occurs at a rate sufficient to prevent genetic drift. In a second introduction of four females homozygous for the Hbbs allele on the Shields farm, Dutchess Co., New York, in June, 1977, the allele also became established in the populations. One introduced female, recaptured in September, 1977, had ten recent placental scars. One year after this introduction, the gene frequency of the introduced allele was 0.03.
Allozyme variation was assessed by horizontal starch-gel electrophoresis among 13 samples representing three chromosome races (2n = 32, 2n = 34, and 2n = 36) of Sceloporus grammicus. The data were used to evaluate levels of genetic variability and divergence within and among these cytotypes, and the degree of genetic subdivision across all population samples. Little allozymic divergence was apparent among populations of the three cytotypes with most samples sharing the common electromorphs Two cases of divergence within cytotypes were evident. Two geographically proximal, 2n = 32 samples were fixed for alternate electromorphs at Ldh-1. Additionally a geographically isolated sample of the 2n = 36 cytotype from the Sierra de Tamaulipas was strongly differentiated at Est-1 and Ldh-1, and was genetically the most distinct sample among all cytotypes. The overall pattern of genetic variation suggests that the chromosomal differences between cytotypes do not reduce gene flow among cytotypes to any appreciable extent. Allopatric isolation appears to be more effective than chromosomal rearrangement in promoting or maintaining genetic divergence among these samples. Allozymic parameters for these cytotypes do not suggest functionally subdivided population structures and are inconsistent with stasipatric speciation and chromosomal transilience models. Among-sample genetic distances are low and the Fst value is one of the lowest reported for vertebrate populations. These values are more consistent with an hypothesis of relatively unrestricted gene flow. High and homogenous levels of heterozygosity among these cytotypes suggest that the derived forms (2n = 34 and 2n = 36) have not originated by recent population bottlenecks and prolonged inbreeding.
This study compares electrophoretic estimates of genetic structure with theoretical predictions based on demographic data. Electromorph frequencies at four loci show insignificant microgeographic differentiation among five farm colonies of house sparrows in eastern Kansas (average FST = 0076). Using estimates of interfarm dispersal and effective population size based on banding and breeding biology data from a prior study of the same population, a theoretical FST value is calculated from equations of the stepping stone model of genetic structure. The theoretical value (.0136) does not differ significantly from the mean FST estimated from electrophoretic data. Thus, the negligible amount of microgeographic genetic differentiation is consistent with expectation.
Two new indices are presented for the measurement of distances between populations on the basis of attribute data. The intermediate variables used to obtain these indices help to analyse attribute data in almost all the ways in which quantitative data could be analysed. The advantages and disadvantages of these and other indices are discussed.
The amount and organization of genetic variation was studied in three annual species of Phlox: P. drummondii and P. roemariana are cross-fertilizing, and P. cuspidata is partially self-fertilizing. These species are confined to central and southern Texas, and are common elements of the spring flora forming large discontinuous populations. The phloxes are pollinated by lepidopterans and have no special mechanisms for long distance seed dispersal. Twenty loci were analyzed using gel electrophoresis. Phlox cuspidata is polymorphic at 20% of the loci, as are each of the outbreeders. Two or three alleles occur at these loci. The inbreeder has less genetic diversity and distributes it more between populations than do the outbreeders. Mean heterozygosity is 0.8% in P. cuspidata, 5.2% in P. drummondii, and 4.6% in P. roemariana. All species display a heterozygote deficiency relative to random mating expectations; FIS in the selfer is 0.67 vs. about 0.40 in the outcrossers. Heterozygote deficiency in all species ostensibly is due principally to the Wahlund effect and to consanguineous mating. If the species is treated as the potential unit of panmixis, FIT is only 10% greater than FIS in P. cuspidata, and 20% greater in P. drummondii and P. roemariana. The selfer shows significantly greater gene frequency heterogeneity between populations than do the outbreeders; FST averages 0.41 in P. cuspidata, and 0.20 in P. roemariana and P. drummondii. Statistical tests based upon Gabriel connected-graphs were used to determine whether the distribution of genetic diversity within species and gene frequencies departed from a random pattern. Significant deviations are present in P. drummondii, but are absent in the other species. Differences between central and marginal populations are not apparent. The genetic distances associated with various stages of evolutionary divergence were estimated. The D for populations is about 0.014. In P. drummondii the distance between populations is 0.020, but the distance between subspecies is even less, 0.006. Cultivars of P. drummondii have a D of 0.06. The genetic distance between the closely related P. drummondii and P. cuspidata is 0.18. Species in different subsections are much more divergent. The genetic distances between P. roemariana, and P. drummondii and P. cuspidata are 0.35 and 0.53, respectively. The degree of cross-incompatibility between population systems is positively correlated with genetic distance. Very weak barriers are present between subspecies, moderate barriers between cultivars and between closely related species, and insurmountable barriers between distantly related species.
Research on the jackknife technique since its introduction by Quenouille and Tukey is reviewed. Both its role in bias reduction and in robust interval estimation are treated. Some speculations and suggestions about future research are made. The bibliography attempts to include all published work on jackknife methodology.
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Kidney and skeletal muscle samples from 734 moose (Alces alces) from 18 localities in Scandinavia were analyzed electrophoretically for 16 enzymes presumably representing 23 structural loci. Polymorphism was observed at five loci coding for malate dehydrogenase, peptidase, phosphoglucose isomerase, phosphoglucomutase, and phosphomannose isomerase, respectively. The fraction of polymorphic loci ranged from 4.3 to 13.0 percent, and average heterozygosities varied between 0.006 and 0.047, with a mean of 0.020. The allele frequency distributions indicate significant spatial heterogeneity. Approximately 10% of the total genetic variation is attributable to differences between localities. These results do not conform with those of other electrophoretic studies on moose that report striking genetic homogeneity, even between intercontinental subspecies. We conclude that those studies were based on too few loci, individuals, or samples to provide an adequate picture of the variability pattern in this large mammal.
Population structure in the freshwater sunfish Lepomis macrochirus was analyzed by examining genotypes at three polymorphic loci in 2,560 individuals representing 64 localities distributed evenly among eight reservoirs and two drainages in the southeastern United States. There is no evidence of inbreeding within localities, but allele frequencies among localites within a reservoir are often heterogeneous; mean standardized variance (FST) for localities of a reservoir was 0.029, consistent across loci. This magnitude of differentiation is slight, far less than for snail populations within cities or house mice on adjacent farms, and occurs despite the immense sizes of the reservoirs sampled (up to 100,000 acres and 1,200 shoreline miles). It seems realistic to regard a reservoir population as a quasi-panmictic assemblage of local populations between which differentiation is minimal and only weakly oriented to distance of geographic separation. Variances in allele frequencies among reservoirs within a drainage are much greater (F̄ST = 0.392), accounting for nearly 90 percent of the total variance observed in the study. Adjacent reservoirs are more similar in allele frequency than are those farther apart. A roughly parallel allelic cline among reservoirs of the two drainages may reflect preexisting heterogeneity among the founding populations in the linear river habitat. Allele frequencies in these reservoirs have not changed significantly during five years of observation. The adaptive significance, if any, of the alternative allelic states is unknown. Furthermore, contemporaneous processes affecting population structure, whether deterministic or stochastic, must act upon a preexisting structure derived from a unique set of historical developments which are seldom known for any species. Thus by hard criteria, definitive statements about the causal processes responsible for population structure are only rarely warranted, even in case studies such as the bluegill where the empirical results appear straightforward.