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An Anthropocene map of genetic diversity
Abstract
The Anthropocene is witnessing a loss of biodiversity, with well-documented declines in the diversity of ecosystems and species. For intraspecific genetic diversity, however, we lack even basic knowledge on its global distribution. We georeferenced 92,801 mitochondrial sequences for >4500 species of terrestrial mammals and amphibians, and found that genetic diversity is 27% higher in the tropics than in nontropical regions. Overall, habitats that are more affected by humans hold less genetic diversity than wilder regions, although results for mammals are sensitive to choice of genetic locus. Our study associates geographic coordinates with publicly available genetic sequences at a massive scale, yielding an opportunity to investigate both the drivers of this component of biodiversity and the genetic consequences of the anthropogenic modification of nature.
... In both native and invasive species, geographical and environmental changes contribute to genetic divergence in spite of some differences in the life history, reproductive mode and genome characteristics (Bock et al. 2015, Mounger et al. 2021. Therefore, similar geographical patterns of genetic diversity may eventually emerge between native and invasive species (Avise et al. 1987, Avise 1992, Miraldo et al. 2016. ...
... Latitude is one of the most predictive factors of biodiversity gradients (Gaston 2000). A variety of studies ranging from the tropics to the poles have demonstrated species diversity and total genetic diversity across species at both neutral and functional loci tend to decrease with increasing latitude (Adams and Hadly 2013, Miraldo et al. 2016. However, intraspecific genetic diversity tends to increase with latitude (Lawrence and Fraser 2020), implying a negative correlation between species-specific diversity and associated species diversity along latitudinal gradients. ...
... Lower latitudes have been reported to have higher species diversity (Schluter andPennell 2017, Guo et al. 2021) and total genetic diversity across animal species (Adams and Hadly 2013, Miraldo et al. 2016) than higher latitudes. However, this latitudinal gradient of biodiversity may result from shorter generation times, higher mutation rates and higher metabolic rates under higher temperature in animals living at the lower latitudes (Rohde 1992, Allen et al. 2006, Lawrence and Fraser 2020, while plants may have different characteristics. ...
Within‐species genetic diversity is shaped by multiple evolutionary forces within the confines of geography, and has cascading effects on the biodiversity of other taxa and levels. Invasive species are often initially limited in genetic diversity but still respond rapidly to their new range, possibly through ‘pre‐adapted' genotypes or multiple sources of genetic diversity, but little is known about how their genetic structure differs from that of native species and how it alters the genetic‐species diversity relationship. Here, we selected a widespread native species Phragmites australis and its co‐occurring invasive competitor Spartina alterniflora as our model plant species. We investigated the genetic structure of P. australis using two chloroplast fragments and ten nuclear microsatellites in 13 populations along the Chinese coastal wetlands. We discovered a distinct geographical differentiation, showing that the northern and southern populations harbored unique genotypes. We also found a significant increase in genetic diversity (allelic richness and expected heterozygosity) from south to north. Combined with previous studies of S. alterniflora , the Mantel tests revealed a significant correlation of genetic distances between P. australis and S. alterniflora even when controlling for geographic distance, suggesting that the invasive species S. alterniflora might exhibit a phylogeographic pattern similar to that of the native species to some extent. Furthermore, our results suggest that the S. alterniflora invasion has altered the relationship between the genetic diversity of the dominant native plant and the associated species richness of soil nematodes. The reason for the alteration of genetic‐species diversity relationship might be that the biological invasion weakens the environmental impact on both levels of biodiversity. Our findings contribute to understanding the latitudinal patterns of intraspecific genetic diversity in widespread species. This work on the genetic diversity analysis of native species also provides significant implications for the invasion stage and ecological consequences of biological invasions.
... Class III macrogenetic studies, as defined by Leigh et al. 19 , summarize the geographic distribution of intraspecific genetic variation of a taxonomic group across broad geographic scales and use data from large numbers of species aggregated from public repositories. Typically used to find correlated environmental variables that predict this critical component of biodiversity 19,20 , previous class III macrogenetic studies have focused on vertebrate groups, uncovering links between global patterns in intraspecific mitochondrial genetic diversity, species richness, and phylogenetic diversity 21,22 , while documenting latitudinal gradients [23][24][25] . They have provided mixed support for the influence of human disturbance on mitochondrial genetic diversity 21,23,26,27 , and suggest that climate stability 21,27 and species' range sizes 20,28 affect intraspecific mitochondrial genetic diversity on a global scale. ...
... Typically used to find correlated environmental variables that predict this critical component of biodiversity 19,20 , previous class III macrogenetic studies have focused on vertebrate groups, uncovering links between global patterns in intraspecific mitochondrial genetic diversity, species richness, and phylogenetic diversity 21,22 , while documenting latitudinal gradients [23][24][25] . They have provided mixed support for the influence of human disturbance on mitochondrial genetic diversity 21,23,26,27 , and suggest that climate stability 21,27 and species' range sizes 20,28 affect intraspecific mitochondrial genetic diversity on a global scale. ...
... The lack of a latitudinal gradient in GDM and the presence of one in GDE peaking in the subtropics also contrasts with recent macrogenetic studies of vertebrates, all of which find a negative latitudinal gradient of GDM and related metrics peaking in the tropics and declining poleward, including for mammals 20 , amphibians 23 , and fishes 22 . Why would GDE be lower in areas like the wet tropics where the species diversities of most insect groups reach their peaks 87,88 ? ...
Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth’s biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.
... Existing surveys of IGD are often limited in their geographic and/or taxonomic scope (e.g., Barrow et al., 2021) due to challenges associated with assembling and analyzing large data sets. The most comprehensive surveys to date, which sampled ~4,500 species of terrestrial vertebrates (Miraldo et al., 2016) and ~5,400 fish (Manel et al., 2020), found evidence that species in tropical areas contain higher levels of IGD than nontropical species. While these investigations did not include a wide range of taxonomic groups or explore the potential historical causes of the observed pattern, they suggest that a latitudinal gradient in IGD may be present, mirroring the wellknown species richness latitudinal gradient (Gaston, 2000;Willig et al., 2003). ...
... Here, we explore both questions by collecting genetic data from more than 38,000 species across the tree of life using the phylogatR database (Pelletier et al., 2021), which uses metadata records to associate DNA sequence accessions from databases such as NCBI GenBank and Barcode of Life Database (BOLD) to natural history and locality data stored in Global Biodiversity Information Facility (GBIF). An expansive quality control protocol was implemented because repurposed data can contain a variety of errors including incorrect taxonomic assignment, incorrect alignment, or artifactual insertions/deletions in the gene sequence (Miraldo et al., 2016;Sidlauskas et al., 2010). After using a stringent set of filters (see Supplementary Materials and Supplementary Figure S1), our data set contained a total of 1,048,698 unique DNA sequences from 38,134 species (28,656 insects, 6,959 vertebrates, 1,559 arachnids, and 960 plants: Supplementary Table S1). ...
... Nucleotide diversity (π) was calculated to describe patterns of intraspecific genetic diversity. Although other statistics such as the number of haplotypes and haplotype diversity are also used to describe patterns of genetic diversity within species, they are not suitable for many of the sequences retrieved from opensource repositories because many sequences are uploaded to GenBank as unique haplotypes per locality and/or have different lengths, precluding a reliable estimation of those genetic diversity measures (Miraldo et al., 2016). As a result, we choose to describe the patterns of genetic diversity using π, defined as the average number of polymorphic sites in pairwise sequence comparison following Nei and Li (1979) and presented in Equation 1: ...
Intraspecific genetic diversity is a key aspect of biodiversity. Quaternary climatic change and glaciation influenced intraspecific genetic diversity by promoting range shifts and population size change. However, the extent to which glaciation affected genetic diversity on a global scale is not well established. Here we quantify nucleotide diversity, a common metric of intraspecific genetic diversity, in more than 38,000 plant and animal species using georeferenced DNA sequences from millions of samples. Results demonstrate that tropical species contain significantly more intraspecific genetic diversity than nontropical species. To explore potential evolutionary processes that may have contributed to this pattern, we calculated summary statistics that measure population demographic change and detected significant correlations between these statistics and latitude. We find that nontropical species are more likely to deviate from neutral expectations, indicating that they have historically experienced dramatic fluctuations in population size likely associated with Pleistocene glacial cycles. By analyzing the most comprehensive data set to date, our results imply that Quaternary climate perturbations may be more important as a process driving the latitudinal gradient in species richness than previously appreciated.
... We considered several variables describing environmental change between LGM and present: climate anomalies, temporal habitat (vegetation) stability and topographic heterogeneity. Additionally, we included human footprint to account for human-mediated effects on genetic diversity (Miraldo et al., 2016). ...
... Nucleotide diversity showed negative, albeit weak, relationship with human footprint, suggesting a negative impact of present-day human impacts on intraspecific diversity, partially agreeing with a global analysis of amphibian genetic diversity (Miraldo et al., 2016). Nevertheless, the occurrence of broad-scale relationships between genetic diversity and human impacts remains controversial (Millette et al., 2020). ...
... This stresses the importance of climatically stable areas for both the persistence of intraspecific diversity, and the occurrence of micro-endemic species of very high conservation priority (IUCN, 2022). Obtaining broad-scale, generalizable information on the distribution of intraspecific diversity requires merging a large amount of data, that allow covering multiple species across a large number of sites (Miraldo et al., 2016;Millette et al., 2020). However, the integration of data collected by several authors for diverse aims can be challenging because of multiple processes, including complex spatial patterns, methodological differences among studies, and subjective choices performed during data integration (Gratton et al., 2017b). ...
Biodiversity is a multifaceted concept, and conservation actions must consider all levels of biodiversity. Spatial prioritization of conservation efforts usually targets species diversity, while consideration of intraspecific genetic diversity is frequently hampered by the lack of data. Here, we combined genetic data (mtDNA) from multiple amphibian species and measures of environmental stability to i) identify the overall drivers of present-day intraspecific genetic diversity (nucleotide diversity and phylogenetic originality); ii) define priority areas for the conservation of genetic diversity, and iii) assess the surrogacy value of species diversity for genetic diversity in Italy and nearby areas. We tested for potential environmental predictors of genetic diversity and originality by fitting spatially-explicit Bayesian mixed models, and used species-specific predictions to generate spatial prioritizations of intraspecific genetic diversity. Present-day phylogenetic originality was positively correlated with climate and habitat stability since the Last Glacial Maximum (pseudo-R2: 0.61), while the same set of predictors had limited explanatory power for nucleotide diversity (pseudo-R2: 0.15). The spatial pattern of originality remarkably matched previously identified refugial areas for plants, as well as the distribution of some micro-endemic species. Prioritizations targeting phylogenetic originality showed that high conservation performance might be achieved with relatively low effort. However, the surrogacy between genetic and species-diversity was limited, implying that larger efforts would be needed to preserve genetic diversity while taking species diversity into account. Our study provides an example of how spatially-explicit approaches allow prioritization of conservation efforts accounting for both species and intraspecific genetic diversity, thus improving the long-term conservation of biodiversity.
... Understanding the distribution of genetic diversity is important for providing insights on the spatial distribution of biodiversity, with implications for conservation planning (De Kort et al., 2021;Lawrence & Fraser, 2020;Leigh et al., 2021;Nielsen et al., 2022;Theodoridis et al., 2020). As a growing field, 'macrogenetics' -the study of genetic diversity at broad scales (Blanchet et al., 2017) -thus far has revealed that genetic diversity spatial patterns are weaker, loci specific (e.g., neutral microsatellites vs. adaptive genes), taxa-specific or in contrast to species diversity (Adams & Hadly, 2013;Habrich et al., 2021;Manel et al., 2020;Millette et al., 2020;Miraldo et al., 2016;Schmidt et al., 2022;Theodoridis et al., 2020;Yiming et al., 2021). The environmental factors that structure spatial patterns of macrogenetics remain of interest and are likely complex and interactive (De Kort et al., 2021). ...
... Together, these effects could result in higher GD P at more productive latitudes and lower elevations, such as those within 20° of the Equator (Figure 1). GD P has been infrequently studied in past macrogenetic works relative to studies based on repurposed individual-based sequence data from mitochondrial DNA (Millette et al., 2020;Miraldo et al., 2016;Theodoridis et al., 2020;Theodoridis et al., 2021;vs. De Kort et al., 2021;Schmidt et al., 2020;Yiming et al., 2021). ...
... De Kort et al., 2021;Schmidt et al., 2020;Yiming et al., 2021). Individual-based mitochondrial DNA studies found some support for a decrease in genetic diversity away from the Equator across species and taxonomic differences (e.g., stronger trends in mammals) (Adams & Hadly, 2013;Gratton et al., 2017;Martin & Mckay, 2004;Millette et al., 2020;Miraldo et al., 2016;Yiming et al., 2021). However, inconsistencies between archiving practices in mitochondrial DNA repositories have resulted in biased measures of genetic diversity when repurposed for macrogenetic research Paz-Vinas et al., 2021 e.g., 'high' or 'low' latitude groups) (Adams & Hadly, 2013;Martin & Mckay, 2004;Millette et al., 2020). ...
The broad scale distribution of population-specific genetic diversity (GDP) across taxa remains understudied relative to species diversity gradients, despite its relevance for systematic conservation planning. We used nuclear DNA data collected from 3678 vertebrate populations across the Americas to assess the role of environmental and spatial variables in structuring the distribution of GDP, a key component of adaptive potential in the face of environmental change. We specifically assessed non-linear trends for a metric of GD P, expected heterozygosity (HE), and found more evidence for spatial hotspots and cold spots in HE rather than a strict pattern with latitude. We also detected inconsistent relationships between HE and environmental variables, where only 11 of 30 environmental comparisons among taxa groups were statistically significant at the .05 level, and the shape of significant trends differed substantially across vertebrate groups. Only one of six taxonomic groups, freshwater fishes, consistently showed significant relationships between HE and most (four of five) environmental variables. The remaining groups had statistically significant relationships for either two (amphibians, reptiles), one (birds, mammals), or no variables (anadromous fishes). Our study highlights gaps in the theoretical foundation upon which macrogenetic predictions have been made thus far in the literature, as well as the nuances for assessing broad patterns in GDP among vertebrate groups. Overall, our results suggest a disconnect between patterns of species and genetic diversity, and underscores that large-scale factors affecting genetic diversity may not be the same factors as those shaping taxonomic diversity. Thus, careful spatial and taxonomic-specific considerations are needed for applying macrogenetics to conservation planning.
... 11 Because ecosystems are inherently dynamic, there is some debate over the utility and appropriateness of integrity for conservation in the scientific literature 12 ; however, integrity is widely recognized in political and legal frameworks as essential to describing the condition or quality of an ecosystem, as opposed to simple and insufficient indicators of extent or quantity. 6,10,13 Ecologists have demonstrated the utility of integrity under the accelerating impacts of climate change, noting that assessments incorporating integrity can reveal biological consequences of changes occurring and what actions may be working in response. 13 Mounting scientific evidence underscores the role of integrity in reducing the risks of natural hazards, 14 protecting critical freshwater resources, 15 providing climate refugia for biodiversity, 16,17 and benefiting human health 18 (Figure 1; Table S1). ...
... 6,10,13 Ecologists have demonstrated the utility of integrity under the accelerating impacts of climate change, noting that assessments incorporating integrity can reveal biological consequences of changes occurring and what actions may be working in response. 13 Mounting scientific evidence underscores the role of integrity in reducing the risks of natural hazards, 14 protecting critical freshwater resources, 15 providing climate refugia for biodiversity, 16,17 and benefiting human health 18 (Figure 1; Table S1). ...
... Indeed, anticipated ecosystem, biodiversity, and human population shifts under climate change necessitate the use of integrity indicators to determine the drivers of changes in integrity and the best actions for remediation. 13 It may be increasingly important to acknowledge that future climatic conditions at a given site may inhibit it from achieving its historical reference state due to unavoidable ecological change, but climate analogues, knowledge of ecosystem dynamics and state changes, and integrity indicators that span a variety of ecosystem types can help contextualize observed changes in integrity. 79 They can also serve to guide management recommendations and interventions and avoid restoration to a historic reference state when difficult, impossible, impractical, or undesirable. ...
... Similarly, elucidating the processes that generate genetic diversity helps create a common ground for evolutionary biology and community ecology around topics of diversity and patterns of speciation (Vellend & Geber 2005). Despite this importance, the general patterns of genetic diversity across species remains poorly understood at global scales (de Kort et al. 2021;Manel et al. 2020;Messmer et al. 2012;Miraldo et al. 2016). Efforts to understand such trends are vital for identifying the factors creating and maintaining biodiversity and for pinpointing high priority areas and taxa for conservation. ...
... Much of our knowledge on intraspecific genetic diversity, including local and regional estimates in various taxa, has only been collected in recent decades. Recent studies compiled these data to construct broad-scale geographic patterns in order to better understand global distributions of genetic diversity (Li et al. 2021;Manel et al. 2020;Miraldo et al. 2016). For example, Martin & McKay (2004) revealed greater genetic divergence among vertebrate populations at lower latitudes, while Schmidt et al. (2022) found that environmental heterogeneity was an important predictor of genetic diversity in North American mammals. ...
... Previous studies have found latitudinal gradients in mitochondrial genetic diversity, mirroring our results here (Manel et al. 2020;Miraldo et al. 2016). However, the methods and statistical analyses frequently employed by these studies have come under recent criticism (Gratton et al. 2017, Paz-Vinas et al. 2021. ...
Genetic diversity is a fundamental component of biodiversity and the medium for speciation events. Examination of global patterns of genetic diversity can help highlight mechanisms underlying species diversity. Here, we compiled 6862 observations of genetic diversity from 492 species of marine fish globally, assessed their associations with macroecological drivers, and tested among three hypotheses for diversity gradients: the founder effect hypothesis, the kinetic energy hypothesis, and the productivity-richness hypothesis. We found that mitochondrial genetic diversity follows latitudinal and longitudinal gradients similar to those of species diversity, being highest near the equator, particularly in the Coral Triangle, while nuclear genetic diversity did not follow clear geographic patterns. Despite these differences, all genetic diversity metrics were positively correlated with chlorophyll, while mitochondrial diversity was also positively associated with sea surface temperature. These findings provide support for the kinetic energy hypothesis, which predicts that elevated metabolic and mutation rates at higher temperatures should increase mitochondrial diversity, and the productivity-richness hypothesis, which posits that resource-rich regions support larger populations with greater genetic diversity. Overall, these findings reveal how environmental controls on mutation and drift in the ocean combine to establish global gradients of genetic diversity within species, and in turn, community assemblages.
... E : Species traits -median body mass of mammalian species (Santini et al., 2017) . F : Genetic composition -Average genetic diversity within mammalian and amphibian species within each grid cell (Miraldo et al., 2016) . and boreal forests (0.5 billion tons per year). ...
... .2F; Miraldo et al., 2016). Other regions with high genetic diversity include the subtropical parts of South Africa for mammals and the eastern coast of Japan for amphibians. ...
... Island populations in the survey tended to have lost more genetic diversity than mainland populations: those from Mauritius and the Seychelles have lost an average of 49% of their genetic diversity (Leigh et al., 2018). Support for a general humancaused decline comes from a map showing that withinspecies genetic diversity of amphibians and mammals tends to be lower in areas with greater human influences, especially urban areas, other settlements, and croplands (Miraldo et al., 2016; see Figure 2 .2 .2F in Section 2.2.3.1). ...
... Compared to the ecological dimensions of biodiversity loss, our understanding of the global distribution and the extent of human-induced evolutionary changes and genetic diversity loss is less developed [12,25]. This is unfortunate because genetic variation is the raw material enabling species to robustly adapt to a changing world [25]. ...
... Compared to the ecological dimensions of biodiversity loss, our understanding of the global distribution and the extent of human-induced evolutionary changes and genetic diversity loss is less developed [12,25]. This is unfortunate because genetic variation is the raw material enabling species to robustly adapt to a changing world [25]. Despite the growing recognition of this dimension of biodiversity, predictions in evolutionary science and applications face many challenges similar to ecologically oriented disciplines [26][27][28]. ...
Ecological and evolutionary predictions are being increasingly employed to inform decision-makers confronted with intensifying pressures menacing life on Earth. For these efforts to effectively guide conservation actions, knowing the limit of predictability is pivotal. In this study, we provide realistic expectations about the enterprise of predicting changes in ecological and evolutionary observations through time. We begin with an intuitive explanation of predictability (that is, the extent to which predictions are possible) employing an easy-to-use metric, predictive power PP(t). To illustrate the challenge of forecasting, we then show that among insects, birds, fishes, and mammals (i) 50% of the populations are predictable at most one year in advance, and (ii) the median one-year-ahead predictive power corresponds to a sobering prediction R^2 of approximately 20%. Nonetheless, predictability is not an immutable property of ecological systems. For example, different harvesting strategies can impact the predictability of exploited populations to varying degrees. Moreover, considering multivariate time series, incorporating explanatory variables or accounting for time trends (environmental forcing) can enhance predictability. To effectively address the urgent challenge of biodiversity loss, researchers and practitioners must be aware of the predictive information within the available data and explore efficient ways to leverage this information for environmental stewardship.
... Global-scale studies either investigate the biogeographic correlates of variation in cross-species average of genetic diversity between spatial grid cells or use species as analytical units to additionally understand the life history correlates of variation in genetic diversity. Analyses at the level of spatial grid cells show that mitochondrial genetic diversity of well-studied taxa decreases with latitude, indicating a relationship between latitude and evolutionary rate or stability (Gratton et al., 2017;Manel et al., 2020;Miraldo et al., 2016). Species-level global comparisons of nuclear genetic diversity reveal taxon-specific drivers of genetic diversity in animals, influenced by life-history strategy, environment, range size and position of the population within the range extent (De Kort et al., 2021). ...
... beetles -Fujisawa et al., 2015;salamanders-Barrow et al., 2021;amphibians andmolluscs-De Kort et al., 2021. Grid-level studies: amphibians-Gratton et al., 2017;Miraldo et al., 2016;mammals-Millette et al., 2020;Theodoridis et al., 2020), mirroring the latitudinal gradient in species diversity (Mittelbach et al., 2007). The mechanisms shaping latitudinal patterns in genetic diversity are thought to be congruent with those driving species diversity, related to climatic stability, longer evolutionary history, larger area with higher productivity and higher temperature resulting in high rates of molecular evolution at low latitudes (Fine, 2015). ...
Aim
To investigate the drivers of intra‐specific genetic diversity in centipedes, a group of ancient predatory soil arthropods.
Location
Asia, Australasia and Europe.
Time Period
Present.
Major Taxa Studied
Centipedes (Class: Chilopoda).
Methods
We assembled a database of 1245 mitochondrial cytochrome c oxidase subunit I sequences representing 128 centipede species from all five orders of Chilopoda. This sequence dataset was used to estimate genetic diversity for centipede species and compare its distribution with estimates from other arthropod groups. We studied the variation in centipede genetic diversity with species traits and biogeography using a beta regression framework, controlling for the effect of shared evolutionary history within a family.
Results
A wide variation in genetic diversity across centipede species (0–0.1713) falls towards the higher end of values among arthropods. Overall, 27.57% of the variation in mitochondrial COI genetic diversity in centipedes was explained by a combination of predictors related to life history and biogeography. Genetic diversity decreased with body size and latitudinal position of sampled localities, was greater in species showing maternal care and increased with geographic distance among conspecifics.
Main Conclusions
Centipedes fall towards the higher end of genetic diversity among arthropods, which may be related to their long evolutionary history and low dispersal ability. In centipedes, the negative association of body size with genetic diversity may be mediated by its influence on local abundance or the influence of ecological strategy on long‐term population history. Species with maternal care had higher genetic diversity, which goes against expectations and needs further scrutiny. Hemispheric differences in genetic diversity can be due to historic climatic stability and lower seasonality in the southern hemisphere. Overall, we find that despite the differences in mean genetic diversity among animals, similar processes related to life‐history strategy and biogeography are associated with the variation within them.
... How much we don't know and where knowledge gaps are, should be described concomitantly when conservation evaluation is performed (e.g. Ignorance maps; Rocchini et al., 2011;Miraldo et al., 2016;Tessarolo et al., 2021). A strategy to consider ignorance could start by acknowledging in advance that our knowledge is taxonomically and spatially biased (Meyer et al., 2016). ...
... In conservation assessments, it should be a priority to analyze how, when and from where our taxonomic and spatial data comes to reduce not only the deficits but also their biases (e.g., Miraldo et al., 2016). By doing so, we could start to understand how much of our perception of species' exposure to human-driven changes can be affected by knowledge shortfalls and their interplay (Hortal et al., 2015). ...
Only a small fraction of the species on Earth is known (Linnean shortfall), while geographic ranges of already described species are poorly documented (Wallacean shortfall). While the effect of both shortfalls in conservation assessments has been analyzed and discussed individually, it is still unclear how these knowledge shortfalls interplay affect our perception of species' exposure to human-driven changes. To asses this, by simulating virtual species in a geographically-fragmented ecoregion, we raised hypothetical scenarios of taxonomical and/or geographical knowledge accumulation through time. We described how such accumulation affects our perception of species' exposure to climate and land-use changes. We found that filling both Wallacean and Linnean shortfalls separately, could generate contrasting perceptions on the potential response of species to a given threat. Moreover, the filling of both gaps together would increase or decrease our risk perception depending, exclusively, on the trend of taxonomic changes. These findings highlight a clear but poorly considered interplay between Linnean and Wallacean shortfalls. Trends on basic knowledge accumulation for a given taxon, especially its taxonomic stability, will determine the degree and direction of our biases in estimating its exposure to human threats. Robust assessments of taxonomic effort and geographic ignorance are essential in conservation assessments. There is also a pressing need to bridge the gap between taxonomic and biogeographic efforts, taking into account the interplay between geographic and taxonomic knowledge deficits, to achieve accurate conservation assessments and resource allocations.
... Here, we investigated the predictors of the GD in crabs (Brachyura) at the species scale by compiling the most comprehensive genetic data set (cytochrome c oxidase subunit I-COI) to date (Blanchet et al., 2017). The use of the COI gene was motivated because of its thousands of publicly available sequences (Porter & Hajibabaei, 2018) that are being used to investigate the predictors of GD in other taxa (Blanchet et al., 2017;Manel et al., 2020;Miraldo et al., 2016;Theodoridis et al., 2020). Additionally, we focused on the mtDNA because of its broad and confirmed applicability in barcoding, eDNA, metabarcoding, phylogenetic and phylogeographic studies (Collins et al., 2018;Hebert et al., 2003;Lefébure et al., 2006;Mantelatto et al., 2020;Silva et al., 2011;Timm & Bracken-Grissom, 2015). ...
... We provide insights on the association between ecological and lifehistory traits with crabs' GD and contribute with taxon-specific results to the field investigating the predictors of GD. Our work takes advantage of publicly available COI sequence data to investigate the predictors of GD following the tendency of recent approaches (Manel et al., 2020;Miraldo et al., 2016;Theodoridis et al., 2020) but focusing on an invertebrate group. Using eight life-history and demographic traits, we support the hypothesis that population size fluctuation is the most crucial factor predicting GD, but other life-history traits might also play a role (Kort et al., 2021;Romiguier et al., 2014). ...
Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analysed across 150 species (16 992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.
... Assessing global patterns of indigenous peoples' land (89) Assessing the global distribution and diversity of plants, mammals, and amphibians (e.g. [90][91][92][93] Assessing global genetic diversity (94) The first map was produced by Ellis & Ramankutty (51) in 2008 ...
As anthropogenic transformation of Earth's ecology accelerates, and its impacts on the sustainability of humanity and the rest of nature become more obvious, geographers and other researchers are leveraging an abundance of spatial data to map how industrialization is transforming the biosphere. This review examines the methodologies used to create such maps and how they have enhanced our understanding of how societies can abate biodiversity loss, mitigate climate change, and achieve global sustainability goals. Although there have been great advances over the past two decades in mapping industrial transformations of ecology across the planet, the field is still in its infancy. We outline future research directions to better understand anthropogenic transformation of the biosphere and the utility of integrating global maps of socioeconomic, ecological, biodiversity, and climate data to explore and inform potential pathways of human-driven social-ecological change.
... Estudos de meta-análise indicam reduções signifi cativas na diversidade genética de várias espécies após a revolução industrial e demais eventos associados a perda ou degradação dos hábitats (Leigh et al. 2019, Miraldo et al. 2016. O avanço em metodologias e abordagens levou ao avanço de ferramentas estatísticas e modelos matemáticos. ...
... Estudos de meta-análise indicam reduções signifi cativas na diversidade genética de várias espécies após a revolução industrial e demais eventos associados a perda ou degradação dos hábitats (Leigh et al. 2019, Miraldo et al. 2016. O avanço em metodologias e abordagens levou ao avanço de ferramentas estatísticas e modelos matemáticos. ...
Este livro representa uma exploração profunda e fascinante da biologia da conservação, campo acadêmico que surgiu em resposta à crescente crise da biodiversidade. Ele combina diversas disciplinas, incluindo ecologia, genética, fisiologia e gestão ambiental para enfrentar os desafios únicos da conservação de uma espécie aquática endêmica ancestral. O livro destaca as espécies endêmicas Isoëtes cangae e Isoëtes serracarajensis, ambas descobertas nos campos rupestres ferruginosos da Floresta Nacional de Carajás. Os lagos aqui abordados são rasos, mas biodiversos, e apresentam características oligotróficas, o que é incomum e, por isso, é habitat de I. cangae. A distribuição limitada de I. cangae a torna uma espécie muito interessante do ponto de vista ecológico e botânico, motivando uma parceria entre o Instituto de Biodiversidade e Sustentabilidade (NUPEM–UFRJ), o Instituto Tecnológico Vale (ITVDS) e a Vale S.A. para conservá-la. O livro discute a abordagem interdisciplinar necessária para conservar essas espécies e seus ecossistemas, incluindo pesquisas que vão desde a identificação e busca pelas espécies, o desenvolvimento de técnicas de propagação e cultivo em larga escala, a determinação da estrutura genética de suas populações a testes em campo para verificação de adequabilidade de habitat. Destinado a estudantes, pesquisadores e entusiastas da ecologia, este livro é um guia indispensável para compreender a importância da conservação da biodiversidade e as estratégias para alcançá-la. Ele oferece uma visão única e valiosa sobre a complexidade e a beleza do mundo natural, bem como a necessidade urgente de protegê-lo. Finalmente, as informações geradas são parte fundamental para auxílio em gestão pública de áreas destinadas ao manejo e ao uso sustentável de recursos naturais.
... The first theories mainly focused on macro-organisms, which were easier to study through direct observation. Several extensive works revealed clear patterns in the distribution of animals and plants around the globe related to the origin and the history of organisms (Finlay, 2002) and reported an increasing species diversity towards the tropics for several taxonomic groups (Hillebrand & Azovsky, 2001, Miraldo et al., 2016, Schluter & Pennell, 2017, De Kort et al., 2021. In islands, usually lower diversity and higher endemism were observed and were related to their geographic isolation and organism dispersal limitation (Kier et al., 2009;MacArthur & Wilson, 1967). ...
The distribution of microorganisms has long been assumed to be cosmopolitan and primarily controlled by the environment, but recent studies suggest that microbes may also exhibit strong biogeographical patterns driven by dispersal limitation. Past attempts to study the global biogeography of freshwater diatoms have always encountered the great difficulty of collecting taxonomically harmonized large‐scale data. However, developments in molecular techniques and DNA metabarcoding provide a unique opportunity to overcome these limitations and to disclose diatom biodiversity at an unprecedented scale and resolution. Here, we assembled DNA metabarcoding data of freshwater benthic diatom communities sampled in seven geographic regions across the world to investigate how diatom diversity varies along latitude and to assess the proportion of genetic variants of these microorganisms which are exclusive or shared across regions. We observed significant differences in assemblages among climate zones and found that genetic richness is not affected by latitude, but by an island effect. The genetic resolution directly impacts the proportion of variants shared across regions; however, the majority of taxa remained specific to a single geographic region. Freshwater diatoms disperse over long distances and across oceans but at rates that allow the appearance of local genetic variants and the regionalization of assemblages. Future work should focus on putting these diversity dynamics into a temporal context, an approach that should be possible by bringing together new sequencing techniques and phylogeography.
... The study of broad-scale geographic patterns of genetic variation, taxonomic and 24 phylogenetic diversity, and speciation rate have provided insights into eco-evolutionary 25 processes forming latitudinal diversity gradients (LDG) in many taxa [1][2][3][4] . LDGs have been 26 extensively studied and shown to be consistent across most localities, scales, habitats, 27 and taxonomic groups, yet the evolutionary and ecological causes of this pattern are still 28 poorly understood 5 . ...
Parasitoid wasps are among the shortlist of taxa showing an anomalous latitudinal diversity gradient. Using the largest georeferenced molecular dataset, we used a macrogenetics approach to explore the spatial relationship between intra- and interspecific levels of diversity and potential environmental variables influencing the anomalous diversity pattern. Nucleotide diversity values were consistently higher at temperate latitudes, peaking at 50 degrees. We found a positive but weak relationship between intraspecific diversity and the latitude, between intra- and interspecific diversity, and a significant positive effect of the temperature range. Examining the spatial relationship between these levels of biodiversity and its drivers is particularly relevant considering climate change and its impact on species distribution. Yet, in insects, it has been challenging to integrate ecological, evolutionary, and geographical components when analyzing the processes leading to species richness gradients. Our study demonstrates how macrogenetics analyses of large-scale patterns of diversity provide insights into potential causes.
... Anthrome maps based on this system of classification have been used widely in teaching, research, and conservation (e.g. Chapin III et al., 2012;Martin et al., 2014;Merritts et al., 2014;National Geographic Society, 2014;Quinn et al., 2014;Miraldo et al., 2016;Gibson & Quinn, 2017;Dinerstein et al., 2017;Smith et al., 2019). ...
Anthromes, or anthropogenic biomes, characterize the globally significant ecological patterns shaped by sustained direct human interactions with ecosystems, including agriculture, urbanization, and other land uses. The emergence of anthromes has literally paved the way for the Anthropocene, and now cover more than three quarters of Earth’s ice-free land surface, including dense settlements, villages, croplands, rangelands, and cultured lands; wildlands untransformed by agriculture and settlements cover the remaining area.
... The resulting population bottleneck further reduced the adaptive potential and functional diversity of species, and poses dangers and difficulties in the recovery of populations under natural conditions. Many wild animals and plants are facing an unprecedented survival crisis [3][4][5][6][7]. ...
Understanding in the evolutionary processes, endangered mechanisms, and adaptive evolution history are key scientific issues in conservation biology. During the past decades, advances in high-throughput sequencing and multi-disciplinary crossover have triggered the development of conservation genomics, which refers to the use of new genomic technologies and genomic information in solving the existing problems in conservation biology. Conservation genomics mainly focuses on the endangered mechanism and conservation strategies aiming at protection of survivability and diversity of endangered species. Application of conservation genomics into the study of endanger plant species has provided innovated protection concept for biologists and promoted the development of population-based conservation strategies. This chapter summarizes the studies of population genomics for agronomically and commercially important plants threatened and endangered, discusses the advantages of conservation genomics for the analysis of genetic diversity, inferences about the history of population dynamics, evaluation of natural forces on wild plant populations, and the establishment of effective conservation strategies. This chapter also presents the development trends in genomics for the conservation of endangered plant species.
... The Darwinian shortfall was generally more pronounced in megadiverse countries with the lowest per capita GDP, often in Africa, Asia, and South America. This highlights the biased amount of phylogenetic information and studies focused on the evolutionary history of species from the Nearctic and Palearctic regions, even when considering the large difference in species richness among regions (Culumber et al., 2019;Miraldo et al., 2016). In general, these patterns reflect the concentration of biodiversity researchers in North America and Europe (Tydecks et al., 2018) and the low investment in less economically developed countries to maintain biodiversity institutions and research (Paknia et al., 2015). ...
Knowledge shortfalls of the evolutionary history of bony fishes hamper phylogenetically informed conservation approaches. To direct future research efforts and phylogenetically based conservation actions, we calculated Darwinian shortfalls for taxonomic clades (genus, family and order-level) and countries, as well as derived a phylogenetic based prioritization metric for bony fishes. We built a synthesis phylogeny for 32,870 bony fishes using a global backbone phylogeny and inserting absent species by their taxonomic hierarchies (supertree approach). Then, we quantified knowledge shortfalls as the sum of inserted branch lengths divided by the total sum of branch lengths. The Darwinian shortfall was generally higher in diverse clades and countries with the lowest gross domestic product per capita and higher number of species and proportion of freshwater species. Clades and countries with the highest deficits should be prioritized for future research efforts, such as the Gymnotiformes from Brazil. By weighing species' evolutionary distinctiveness and vulnerability, we highlighted species that should be prioritized for best conserving the fish tree of life. Our study provides an open-data framework for prioritizing future efforts toward advancing biodiversity knowledge and conservation.
... This study found that altitude had an impact on viral populations and that humidity represented by precipitation had a negative effect on viral diversity. Microbial diversity and function can be in uenced by latitude, temperature, and geochemical characteristics [73,74]. For example, Gao et al. (2022) found that latitude and annual average rainfall may affect virus quantity and function, becoming major driving forces of virus diversity and functional composition [57]. ...
Background
Bats (Chiroptera) are major sources of epidemics. To understand the dynamics of diseases, it is crucial to study the dynamics of microorganisms in the environment and the relationship between microorganisms and bats. In this study, we investigated the soil virus communities in bat caves using viral metagenomic sequencing technology. We further explored host–pathogen interactions with regard to the effects of the environment by combining analyses of microorganisms (viruses and bacteria) and immune genes (major histocompatibility complex, MHC) of the main resident species (Rhinolophus ferrumequinum) in the bat caves.
Results
A total of 31 families of viruses were identified. Significant differences were observed in alpha diversity, beta diversity, and the relative abundances of soil virus families, indicating their habitat specificity in bat caves. Zoonotic risk viruses were also found, and the composition of viruses in bat caves was similar to the distribution of virus families of R. ferrumequinum in a previous study. Second, the alpha diversity of both viruses and bacteria was significantly negatively correlated with precipitation of the wettest month. The relative abundances of viral and bacterial families were correlated with MHC allele frequencies. Moreover, a structural equation model further revealed that the precipitation of the coldest quarter significantly negatively affected virus diversity, which in turn significantly negatively affected the MHC allele frequencies in R. ferrumequinum. The MHC allele frequencies were negatively affected by bacterial alpha diversity.
Conclusions
The results of the present study suggest that the polymorphism of the MHC class I gene of R. ferrumequinum is driven by environmental pathogen selection pressure and that environmental climate affects the host immune genes by regulating the diversity of microorganisms. This study is the first to demonstrate the diversity of virus communities in bat caves, and thus has significance for protecting bat habitats from human disturbance and in preventing zoonotic diseases.
... The monitoring and maintenance of genetic diversity is essential for the conservation of the species [9,10], especially in habitats that are more affected by humans [11]. As low levels of variance and genetic homogeneity within local populations may promote genetic degradation, fertility reduction, and the spread of infectious diseases in populations [12,13], genetic studies of fallow deer are carried out worldwide to decipher the population's structure and health [14][15][16]. ...
The fallow deer (Dama dama) represents significant game management value globally, and human activities are significantly impacting the species. Besides the positive effects, these activities can threaten its existence, health, and value. The aim of the authors was to develop a tetranucleotide microsatellite panel that could be clearly interpreted and used for genetic testing of fallow deer. Such a panel did not exist until now and could be particularly useful in the field of conservation genetics and forensics. A total of 99 tetrameric microsatellites, originally designed for related deer species, were tested on 20 fallow deer individuals from five Hungarian sampling areas. Original and newly designed primers were used to amplify the microsatellite regions using previously published or optimized PCR protocols. The lengths and sequences of specific amplicons were detected using capillary electrophoresis, and the rate of polymorphism was determined. Altogether, 80 markers provided PCR products of adequate quality and quantity. Among them, 15 markers proved to be polymorphic (2–5 alleles/locus), and 14 tetrameric markers were selected for further analysis. Statistical calculations showed that the selected polymorphic microsatellites can potentially enable key individualization in many areas of wildlife and population genetics, thus protecting the species.
... Biodiversity is facing an unprecedented crisis and substantial efforts should be made in favor of the conservation of natural populations [1,2]. However, the realization of conservation goals requires a thorough knowledge about the functioning of the biological systems of interest [3]. ...
Biodiversity is facing an unprecedented crisis and substantial efforts are needed to conserve natural populations, especially in river ecosystems. The use of molecular tools to guide conservation practices in rivers has grown in popularity over the last decades, but the amount of precision and/or biological information that would be gained by switching from the traditional short tandem repeats (STRs) to the increasingly used single nucleotide polymorphisms (SNPs) is still debated. Here, we compared the usefulness of STRs and SNPs to study spatial patterns of genetic variability in two freshwater fish species (Phoxinus dragarum and Gobio occitaniae) in southern France. SNPs were obtained from a pool-seq procedure and mapped to new genome assemblies. They provided much more precise estimates of genetic diversity and genetic differentiation than STRs, but both markers allowed the detection of very similar genetic structures in each species, which could be useful for delineating conservation units. While both markers provided similar outcomes, there were two discrepancies in genetic structures that could, nonetheless, be explained by unrecorded stocking events. Overall, we demonstrated that SNPs are not unconditionally superior to STRs in the context of large-scale riverscape genetic conservation, and that the choice of marker should primarily be based on research questions and resources available.
... In this way, life-history traits (e.g., longevity; Azizan & Paradis, 2021) and biogeographic factors (e.g., core versus periphery of species distribution ranges) were identified as important drivers underlying macroscale genetic patterns in terrestrial plants and animals (De Kort et al., 2021). The impact of latitude was shown to vary among taxa (Lawrence & Fraser, 2020;Millette et al., 2020;Miraldo et al., 2016), contrasting with the prevalence of the latitudinal gradient in terrestrial species richness (Gaston, 2000). Moreover, echoing the contrasted links between genetic diversity in one particular species and diversity of the associated community at regional scale (e.g., Vellend & Geber, 2005), a positive species-genetic diversity correlation (SGDC) was reported by some macrogenetic studies (e.g., Manel et al., 2020;Theodoridis et al., 2020) but not by others (e.g., Lawrence & Fraser, 2020). ...
Aim
Intraspecific genetic diversity is one of the pillars of biodiversity, supporting the resilience and evolutionary potential of populations. Yet, our knowledge regarding the patterns of genetic diversity at macroecological scales, so‐called macrogenetic patterns, remains scarce, particularly in marine species. Marine habitat‐forming (MHF) species are key species in some of the most diverse but also most impacted marine ecosystems, such as coral reefs and marine forests. We characterize the patterns and drivers of genetic diversity in MHF species and provide a macrogenetic baseline, which can be used for conservation planning and for future genetic monitoring programmes.
Location
Global.
Time period
Contemporary.
Major taxa studied
Bryozoans, hexacorals, hydrozoans, octocorals, seagrasses, seaweeds, sponges.
Methods
We analysed a database including genetic diversity estimates based on microsatellites in more than 9,000 georeferenced populations from 140 species, which belong to seven animal and plant taxa. Focusing on expected heterozygosity, we used generalized additive models to test the effect of latitude, taxon, and conservation status. We tested the correlation between the species richness and the genetic diversity.
Results
We reveal a significant but complex biogeographic pattern characterized by a bimodal latitudinal trend influenced by taxonomy. We also report a positive species genetic diversity correlation at the scale of the ecoregions. The difference in genetic diversity between protected and unprotected areas was not significant.
Main conclusions
The contrasting results between MHF animals and plants suggest that the latitudinal genetic diversity patterns observed in MHF species are idiosyncratic, as reported in terrestrial species. Our results support the existence of shared drivers between genetic and species diversities, which remain to be formally identified. Concerning, these macrogenetic patterns are not aligned from the existing network of marine protected areas. Providing the first macrogenetic baseline in MHF species, this study echoes the call regarding the need to consider genetic diversity in biodiversity assessments and management.
... Habitat association and organismal traits gained attention for their association in the adaptive and evolutionary potential of the species (Romiguier et al. 2014;Miraldo et al. 2016;Harvey et al. 2017). Many evolutionary studies have demonstrated the host associations which are generally conserved across phylogenies as they are efficiently associated with a particular host, and it is difficult to be associated with new habitat (Goto et al. 2012). ...
The reef-associated palaemonid shrimp fauna of Indian waters, especially in island ecosystems, is one of the least studied. During explorations at Lakshadweep Islands, Cuapetes elegans (Paulson 1875), C. grandis (Stimpson 1857) and a new species, Cuapetes purushothamani sp. nov., were recorded and illustrated based on the specimens collected from dead coral and rocky shore regions of eastern lagoon of Agatti Island (0.5–1.0 m), Lakshadweep, India. The new species shows close relation with C. elegans, possessing distinctive characteristics as indicated: rostrum extends as far as antennal scale, arrangement of ventral teeth below the wide edentulous dorsal part of rostrum, long dorsal spines of telson, a fewer number of segments in antennal flagellum, fingers of first chelated leg slightly longer than palm, chela of second cheliped longer than combined length of merus and carpus with inflated palm. In addition, the partial sequences of mitochondrial genes cytochrome c oxidase I (COI), 16S and nuclear Histone 3 (H3) gene were generated and compared with other available species of Cuapetes. The phylogenetic analyses strongly supported our new discovery, Cuapetes purushothamani sp. nov., which possesses a close relationship with C. elegans by having high interspecific genetic divergences (COI: 19.2–19.9%; 16S: 12–12.8%; H3: 3.1–3.9%).
http://zoobank.org/urn:lsid:zoobank.org:pub:1B5C9228-9D9F-430E-BF11-C6DC7510DF1B
... Human activities have impacted most ecosystems on a global scale [84][85][86]. Ecosystem restoration, defined as the process of assisting the recovery of ecosystems that have been degraded [87] has become a tool to overcome human pressures on the structure and function of ecosystems. Under ecosystem degradation, the ability of ecosystems to maintain ecological functions and provide benefits to society declines [86,88]. ...
Ecological restoration has recognized explicitly the recovery of ecosystem functions. The emphasis on ecosystem functions in restoration efforts can be defined as functional restoration. Functional restoration, i.e., rehabilitation of ecosystem functions, is particularly applicable to highly degraded landscapes such as desertified areas, where restoration to the original state is impossible. This review paper produced a general conceptual model of the fundamental processes that regulate ecosystem functions in water-limited ecosystems. The Israeli Negev Desert was used as a case study to test the model results in the field. We developed general guiding principles for functional restoration of degraded landscapes that integrate functional restoration methods and include four successive steps: (1) identifying the fundamental processes that regulate ecosystem functions in alternative states; (2) detecting drivers leading to degraded states; (3) functional restoration: changing the state of the degraded landscape; and (4) monitoring the impact of the restoration effort and assessing its success in terms of ecosystem services. Our case study, the Negev, provided us with insights on how to reverse desertification in water-limited systems by restoring source–sink networks as a subset of functional restoration. The four suggested steps of functional restoration are essential for ecosystem recovery in the Anthropocene.
... Habitats with greater anthropogenic pressures are generally less genetically diverse than those that are less disturbed (Miraldo et al. 2016), with coastal regions being particularly prone to high levels of disturbance from anthropogenic activities and environmental change (Azuz-Adeath and Yañez-Arancibia 2019; Holligan and Reiners 1992;Suchanek 1994). Coastal regions that are geographically isolated or ecologically marginal are often the most at risk of biodiversity losses at all scales (Buonomo et al. 2018;Johannesson and André 2006), yet often lack crucial intraspecific genetic diversity due to sequential founder events (Eckert et al. 2008). ...
Biodiversity represents the variability within and between ecosystems, species and individuals and is critical for ecosystem functioning. The most basic element of biodiversity is genetic diversity. Genetic diversity is important in defining a species adaptive potential, yet is still a largely neglected aspect of biodiversity. Moreover, traditional taxonomically recognized species often conflict with evolutionary or ecologically relevant units, whilst the ecological significance of intraspecific variants are also often overlooked. Within this thesis, I assess the genetic diversity of two variant forms of the perennial, marine, brown alga Fucus vesiculosus (Fucaceae, Phaeophyceae) and their potential ecological differences within the Baltic Sea. Special focus lies on determining the processes forming and maintaining populations of the free-living form are and how this influences their genetic diversity.
This thesis consists of four papers bridging genetics and ecology at varying spatial scales. Papers I & II use molecular techniques to determine the spatial genetic structure over long and short temporal scales. I determine that the Baltic Sea free-living Fucus should continue to be taxonomically classified as F. vesiculosus, yet free-living populations are markedly different from their attached counterparts. In particular, clonality plays a major role in forming and maintaining populations yet is nearly entirely absent from the attached form. This reliance on clonality significantly reduces the genetic diversity of the free-living form, nevertheless the genetic diversity can still be considered relativity high. Papers III & IV examine the potential ecological significance of the free-living form. Paper III describes the heterogeneity of the free-living form’s phenotype in terms of morphological traits. Free-living thalli are polymorphous with phenotypic complexity varying at the population and individual level. Consequently, I conclude that free-living mats of F. vesiculosus form highly complex canopies similar to those of the attached form. Paper IV provides biodiversity estimates for the associated faunal community. The paper confirms the ecological significance of free-living F. vesiculosus as a habitat forming species comparable to the attached form.
The four papers included in this thesis highlight the heterogeneous nature of the free-living form of F. vesiculosus. Thus for Baltic Sea F. vesiculosus, it is imperative that management strategies are tailored throughout the varying scales of biodiversity, including that of the intraspecific variation within and between the two forms.
... Functional diversity measures the combination of species traits that are associated with adaptations to the environment and species' roles in ecological processes 26 , and communities with higher functional alpha diversity provide a wider range of ecological functions 27,28 . Phylogenetic diversity measures the diversity of evolutionary lineages [29][30][31] , which represents species' evolutionary history as well as their potential adaptability to environmental changes [32][33][34][35][36] . Since these different facets of diversity can idiosyncratically respond to disturbances 14,37,38 , consideration of taxonomic, functional and phylogenetic diversity might provide complementary insights into the effect of land-use change on species communities, but they are rarely included together in assessments of biotic homogenization. ...
Loss of natural habitat due to land-use change is one of the major threats to biodiversity worldwide. It not only affects the diversity of local species communities (alpha diversity) but can also lead to large-scale homogenization of community composition (reduced beta diversity) and loss of regional diversity (gamma diversity), but these effects are still rarely investigated. We assessed the impact of land-use change on taxonomic, functional and phylogenetic diversity of amphibians in Rwanda, both on the local (community-level) and regional scale (country-wide). Alpha diversity in local communities was higher in farmland than in natural habitats; however, species turnover among farmland sites was much lower than among natural sites, resulting in highly homogenized communities and reduced taxonomic, functional and phylogenetic gamma diversity in farmland across Rwanda. Amphibians found in farmland were mostly disturbance-tolerant species that are widespread in eastern Africa and beyond. In contrast, most of the regionally endemic frog species that make this region a continent-wide hotspot of amphibian diversity were found only in the natural habitats. Ongoing habitat conversion might result in further homogenization of amphibian communities across sub-Saharan Africa and the loss of regional endemism, unique evolutionary lineages, and multifunctionality.
... Local or global extinctions of species in turn threaten the ecosystems upon which the quality of human lives depend (Brauman et al. 2020;Des Roches et al. 2021). Concerningly, genetic diversity, like all levels of biodiversity, is declining rapidly during the Anthropocene across the tree of life (Pinsky & Palumbi 2014;Miraldo et al. 2016;Leigh et al. 2019;Exposito-Alonso et al. 2022). This article is protected by copyright. ...
Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome‐scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a “distributed datathon” to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and from direct communication with authors. Starting with 848 candidate genomic datasets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 datasets (N = 440 datasets comprising 45,105 individuals from 762 species in 17 phyla). Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declined significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever. This article is protected by copyright. All rights reserved
... Current conservation efforts, which are usually focused on species, overlook intraspecific variation and its corresponding ecological effects (Angelini et al., 2011;Power et al., 1996). However, variation within species is particularly subject to human impacts through declines in population genetic diversity and local extirpation (Miraldo et al., 2016;Moran et al., 2016;Palkovacs et al., 2012). In fact, current extinction rates of populations are orders of magnitude greater than extinction rates of species (Ceballos et al., 2015;Leclère et al., 2020). ...
Patterns of resource use observed at the species level emerge from the way individuals exploit the range of available resources. Hence, accounting for interindividual differences in resource use, such as pollinator use by plants, is essential to advance our understanding of community assembly and persistence. By using finely resolved data on plant–pollinator interactions, we evaluated how interindividual plant variation in pollinator use scales up to affect community structure and dynamics. All co‐occurring plant species comprised specialists interacting with proper subsets of pollinators that visited generalists, and differences in interaction patterns were driven by among‐individual trait variation. Furthermore, the nested structure and feasibility of plant–pollinator communities were maximised at higher levels of interindividual plant variation in traits and pollinator use. Our study sheds light on how pervasive properties of community structure arise from individual‐level processes and contributes to elucidate the importance of preserving intraspecific variation in traits and resource use within populations. Accounting for interindividual differences in resource use, such as pollinator use by plants, is essential to advance our understanding of community assembly and persistence. This study sheds light on how pervasive properties of mutualistic communities' structure and dynamics arise from individual‐level processes, and contributes to elucidate the importance of preserving intraspecific variation in traits and resource use within populations.
... Genetic diversity and evolutionary process can be presented and analyzed by different kinds of genetic data such as sequences of genes and genomes. As the most widely used genetic data, sequence data can help identify species and infer the relationship among biological groups (Tautz et al., 2002;Hebert et al., 2003;Alamouti et al., 2011), and together with species distributions, can provide important information for quantifying the geographical distribution of genetic variation within and among species and the evolution process of current biodiversity patterns (Ma et al., 2012;Miraldo et al., 2016;Toczydlowski et al., 2021). Large scale geographic data analysis provides an effective way to understand the extensive impact of geographic, geological and climatic changes on species distribution (Guralnick and Hill, 2009;Pope et al., 2015;Pelletier et al., 2022). ...
The biogeography field benefits more and more from the growth and application of genetic data such as nucleotide sequences and whole genomes. It has been perceived by scientists that genetic data may be imbalanced among different geographical regions and taxonomic groups. However, the lack of empirical evidence prevents the understanding of current data volume and distribution of genetic data. Based on the construction of a dataset including records for 365 millions of nucleotide sequences of Animalia, Plantae, and Fungi kingdoms, 6 millions of COI sequences of insects, 77 thousands of COI sequences of mammals, 220 thousands of rbcl sequences of Magnoliopsida, and 44 thousands of ITS sequences of Dothideomycetes, here we present evidence on geographical and taxonomical imbalance of the genetic data, identify major gaps and inappropriate practices in the production, application and sharing of genetic data. We then discuss our perspectives on how to fill up gaps and improve the quantity and quality of genetic data.
... Allozymes (Li et al., 2010), microsatellites (Gu et al., 2013), mitochondrial and nuclear loci (Wang et al., 2017) have been used in conservation genetic researches. For example, mitochondrial DNA has been used to evaluate the global genetic diversity pattern of terrestrial amphibians and mammals (Miraldo et al., 2016). Microsatellites have been used to identify the conservation units of the Blue Eared Pheasant (Crossoptilon auritum; Gu et al., 2013). ...
Evaluating the genetic status of threatened species is an essential task in conservation genetics. However, the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate genetic diversity at the whole genomic level. Next generation sequencing can meet this demand, but high quality samples such as blood or muscle tissues are required. However, it is difficult to collect such samples from threatened species because sampling work may impact their health. Therefore, it is essential to design a workflow to evaluate the whole genomic status of threatened species using non-destructive sampling. Even though the non-destructive sampling has been used in traditional barcoding technique, the barcoding technique can not evaluate the whole genomic status. Brown Eared Pheasant (Crossoptilon mantchuricum) is an endangered species, with captive populations maintained in Taiyuan Zoo, China, and Europe. However, the genetic diversity, inbreeding pattern, and mutation load of these two populations are unclear. To uncover the genetic status of these two captive populations, we applied 2b-RAD technology to evaluate the genomic status of these populations using feathers as samples. The feathers could be collected by non-destructive sampling. The results indicate that the Taiyuan Zoo population has a lower genetic diversity and higher inbreeding coefficient than the European population. The Taiyuan Zoo population has lethal mutations when homozygous. The current project uses a non-destructive sampling technique to evaluate the whole genomic status of the two captive populations, providing a paradigm for conservation genetics, which will facilitate the development of conservation biology.
... Given the longevity of these trees, generations considered to be parental still have showed genes with potential to boost the levels of observed heterozygosity in this work (Caballero et al. 2019;Carvalho et al. 2010). Our results suggest that the presence of individuals of these species has preceded the processes of fragmentation and loss of habitat in the regions they are located (Newbold et al. 2015;Miraldo et al. 2016). ...
Understanding populational genetic diversity is crucial for making proper decisions about conservation and sustainable species management. In this work, we overviewed the conservation genetics of economically exploited tree species that are vulnerable to extinction in the Atlantic Forest of Brazil. For this, data on genetic parameters from research on 10 species of evergreen trees dwelling in that environment were compiled. Genetic variability differences between young and adults were assessed when data were available for both stages. Very low values observed for the probability of identity (PI) suggested that the SSR markers used had sufficient statistical power to consistently evaluate genetic variability of the populations. An innovative analytical approach using linear mixed-effect models revealed an integrated influence of the number of individuals sampled per population and the number of SSR markers on the output of the genetic estimators assessed. A large number of different alleles (NA) were observed in four out of the 10 species, indicating these populations may still hold unique and rare alleles. HO was smaller than HE for all but one of the studied species, suggesting higher numbers of homozygotes than expected. Comparison of data between ontogenic stages suggested that the time frame of habitat loss and fragmentation was not yet sufficient to cause significant loss of genetic diversity and differentiate populations. Our findings are discussed considering that intensity and duration of selective lodging and economic exploitation appear to be crucial for the underlying ecological patterns and for the definition of proper diversity conservation strategies.
... As a consequence, community-level genetic data are accumulating in massive online repositories (e.g., GenBank; https://www.ncbi.nlm.nih.gov/genbank), such that it is becoming increasingly possible to study intraspecific genetic variation across multiple communities from regional to global scales (i.e., "macrogenetics"; Leigh et al., 2021;Miraldo et al., 2016). One focus, therefore, is to encourage development of models that will provide an explicit biogeographical context (Edwards et al., 2022) for macrogenetic studies by integrating community-scale intraspecific genetic variation into mechanistic models to understand and predict how biodiversity accumulates across spatial scales and levels of organization. ...
Background
MacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on predicting patterns of species richness, abundance distributions, trait data and/or phylogenies. The distribution of genetic variation across species within a community is an emerging pattern that contains signatures of past population histories, which might provide an historical lens for the study of contemporary communities. As intraspecific genetic diversity data become increasingly available at the scale of entire communities, there is an opportunity to integrate microevolutionary processes into our models, moving towards development of a genetic theory of island biogeography.
Motivation/goal
We aim to promote the development of process‐based biodiversity models that predict community genetic diversity patterns together with other community‐scale patterns. To this end, we review models of ecological, microevolutionary and macroevolutionary processes that are best suited to the creation of unified models, and the patterns that these predict. We then discuss ongoing and potential future efforts to unify models operating at different organizational levels, with the goal of predicting multidimensional community‐scale data including a genetic component.
Main conclusions
Our review of the literature shows that despite recent efforts, further methodological developments are needed, not only to incorporate the genetic component into existing island biogeography models, but also to unify processes across scales of biological organization. To catalyse these developments, we outline two potential ways forward, adopting either a top‐down or a bottom‐up approach. Finally, we highlight key ecological and evolutionary questions that might be addressed by unified models including a genetic component and establish hypotheses about how processes across scales might impact patterns of community genetic diversity.
... were used to calculate genetic diversity. The genetic diversity of each species was defined and calculated following Mirado et al. [43]. ...
Marine biodiversity plays important roles in ocean ecosystem services and has substantial economic value. Species diversity (SR), genetic diversity (GD) and phylogenetic diversity (PD), which reflect the number, evolutionary potential and evolutionary history of species in ecosystem functioning, are three important dimensions of biodiversity. Marine protected areas (MPAs) have been demonstrated as an effective area-based tool for protecting marine biodiversity, but only 2.8% of the ocean has been fully protected. It is urgent to identify global conservation priority areas and percentage of the ocean across multiple dimensions of biodiversity based on Post-2020 Global Biodiversity Framework. Here, we investigate the spatial distribution of marine genetic and phylogenetic diversity using 80 075 mitochondrial DNA barcode sequences from 4 316 species and a newly constructed phylogenetic tree of 8 166 species. We identify that the Central Indo-Pacific Ocean, Central Pacific Ocean and Western Indian Ocean harbour high levels of biodiversity across three dimensions of biodiversity, which could be designated as conservation priority areas. We also find that strategically protecting approximately 22% of the ocean would allow us to reach the target of conserving approximately 95% of currently known taxonomic, genetic and phylogenetic diversity. Our study provides insights into the spatial distribution pattern of multiple marine diversities and the findings would help to design comprehensive conservation schemes for global marine biodiversity.
In this chapter, we discuss other patterns that can be obtained from assemblages from a macroecological perspective, expanding the reasoning of the previous chapter on species richness. We discuss the phylogenetic and functional estimates of diversity, rebuilding the concept of diversity beyond richness and improving our understanding of processes underlying broad-scale patterns. We can compare patterns in PD and FD by considering phylogenies as backbones for comparative analyses of trait diversification or as surrogates for diversity. We then show macroecological patterns comparing distinct assemblages (β-diversity), using different approaches, and discuss the relationship between metrics and scale issues. Several methodological advances have been made in partitioning β-diversity into nestedness (richness-derived) and turnover components and expanding the concept to incorporate phylogenetic and functional dimensions. Nevertheless, there are also interesting applications of the distinct approaches used to evaluate β-diversity to evaluate continuous geographic patterns of dissimilarity among assemblages (distance-decay similarity) and establish regionalization schemes.
In ecology and evolution, genetic and genomic data are commonly collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, such data are typically used only once by the data-generating authors. The repurposing of genetic and genomic datasets remains uncommon because it is often difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new research field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible, they could be reused for many additional purposes, far beyond their initial intended impact. In this review, we outline the main challenges with existing genetic and genomic data archives, factors underlying the challenges, and current best practices for archiving genetic and genomic data. Recognising that this is a longstanding issue due to an absence of formal data management training within the research field of ecology and evolution, we highlight key steps that universities, funding bodies, and scientific publishers could take to ensure timely change towards good data archiving.
This planetary boundaries framework update finds that six of the nine boundaries are transgressed, suggesting that Earth is now well outside of the safe operating space for humanity. Ocean acidification is close to being breached, while aerosol loading regionally exceeds the boundary. Stratospheric ozone levels have slightly recovered. The transgression level has increased for all boundaries earlier identified as overstepped. As primary production drives Earth system biosphere functions, human appropriation of net primary production is proposed as a control variable for functional biosphere integrity. This boundary is also transgressed. Earth system modeling of different levels of the transgression of the climate and land system change boundaries illustrates that these anthropogenic impacts on Earth system must be considered in a systemic context.
Genetic biodiversity is rapidly gaining attention in global conservation policy. However, for almost all species, conservation relevant, population-level genetic data are lacking, limiting the extent to which genetic diversity can be used for conservation policy and decision-making. Macrogenetics is an emerging discipline that explores the patterns and processes underlying population genetic composition at broad taxonomic and spatial scales by aggregating and reanalyzing thousands of published genetic datasets. Here we argue that focusing macrogenetic tools on conservation needs, or conservation macrogenetics, will enhance decision-making for conservation practice and fill key data gaps for global policy. Conservation macrogenetics provides an empirical basis for better understanding the complexity and resilience of biological systems and, thus, how anthropogenic drivers and policy decisions affect biodiversity.
Human activities have placed significant pressure on the terrestrial biosphere, leading to ecosystem degradation and carbon losses. However, the full impact of these activities on terrestrial biomass carbon remains unexplored. In this study, we examined changes in global human footprint (HFP) and human-induced aboveground biomass carbon (AGBC) losses from 2000 to 2018. Our findings show an increasing trend in HFP globally, resulting in the conversion of wilderness areas to highly modified regions. These changes have altered global biomes' habitats, particularly in tropical and subtropical regions. We also found accelerated AGBC loss driven by HFP expansion, with a total loss of 19.99 ± 0.196 PgC from 2000 to 2018, especially in tropical regions. Additionally, AGBC is more vulnerable in the Global South than in the Global North. Human activities threaten natural habitats, resulting in increasing AGBC loss even in strictly protected areas. Therefore, scientifically guided planning of future human activities is crucial to protect half of Earth through mitigation and adaptation under future risks of climate change and global urbanization.
Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in the breeding area predicted by environmental niche modeling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Among other factors, the demise of ecosystem-engineering megafauna which maintained open habitats may have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.
Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of ‘speciation-by-extinction’ in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.
The Balkan Peninsula acted as a refugium for many steppic species during the Pleistocene, resulting in a high genetic variability, which, in some cases, presents a northward decreasing latitudinal gradient. In the present study, we investigate the genetic diversity of the European ground squirrel (Spermophilus citellus) in its Balkan distribution, sampled comprehensively across its entire distribution in Greece (133 samples from 21 localities). These samples are compared with others from Serbia (54 samples from eight localities) and the available published data from its range in Europe (124 sequences from GenBank). Our results show that the genetic diversity of the Greek and Serbian populations is not correlated with a latitudinal gradient. However, when the entire European range is considered, the model that best fits the genetic variation of the species is based on the ‘centre–periphery’ hypothesis. The founder (centre) populations of the species were most probably situated in south-eastern Bulgaria and European Turkey and underwent rapid expansion post-glacially, during the Holocene, both northwards (Central Europe) and southwards (Greece), as revealed by the decreased genetic diversity and phylogeographical inference analysis in these marginal regions. These results indicate a particular phylogeographical history of a European species and set a baseline for conservation management in its southern populations.
Addressing climate change and biodiversity loss will be the defining ecological, political, and humanitarian challenge of our time. Alarmingly, policymakers face a narrowing window of opportunity to prevent the worst impacts, necessitating complex decisions about which land to set aside for biodiversity preservation. Yet, our ability to make these decisions is hindered by our limited capacity to predict how species will respond to synergistic drivers of extinction risk. We argue that a rapid integration of biogeography and behavioral ecology can meet these challenges because of the distinct, yet complementary levels of biological organization they address, scaling from individuals to populations, and from species and communities to continental biotas. This union of disciplines will advance efforts to predict biodiversity's responses to climate change and habitat loss through a deeper understanding of how biotic interactions and other behaviors modulate extinction risk, and how responses of individuals and populations impact the communities in which they are embedded. Fostering a rapid mobilization of expertise across behavioral ecology and biogeography is a critical step toward slowing biodiversity loss.
Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for two mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; four individuals and 6,820-44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (Phylogenetically Independent Contrasts: R 2 = 0.31, p = 0.007) and GBS diversity (R 2 = 0.21; p = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across species' ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups.
The effects of anthropogenic climate change on biodiversity have been recognized on every continent, ocean, and across different taxonomic groups. Here, we study the range dynamics and demography of a cosmopolitan species: the deer mouse, Peromyscus maniculatus. We generated a multilocus SNP dataset using the ddRADseq protocol for 218 individuals across the geographic range within three western North American lineages of this species group. We evaluated population structure using several methods and explored the correlation between geographic and genetic distances. We modeled the demographic history using a site frequency spectrum approach and used a machine learning algorithm to infer current and past (Last Glacial Maximum; LGM) environmental suitability. Lastly, we explored the origin of population expansion for the identified lineages. The genome-wide SNP dataset was able to identify three regionally distinct groups- 1) P. m. gambelii (southern California); 2) P. keeni (Pacific Northwest); 3) P. m. sonoriensis (a broad population spanning the Pacific Northwest through central California and across the Rocky Mountains into the Great Plains). Demographic analysis indicated the splits between the three populations occurred within the last 500 thousand years, with one very recent (late Holocene) split. Ecological niche models for each of these lineages predicted suitable environment present throughout their known ranges for current conditions, and a severe reduction of northern habitat in the past. The deer mouse has responded to past climate changes by expanding its range during interglacial periods and contracting its range during glacial periods leading to strong population differentiation. But lower magnitude climate change or other processes within the Holocene interglacial period led to population differentiation as well, which is likely still ongoing today given the substantial anthropogenic climate change and other landscape transformations caused by humans during the Anthropocene. By understanding the historical processes that led to the contemporary geographic distribution of biodiversity, we can determine the relative importance of different factors that shape biodiversity, now and into the future.
Genetic diversity provides the long-term capacity of species, communities, and the biosphere to persist under change [...]
Natural climate change and recent anthropogenic activities have largely contributed to habitat loss and fragmentation across the world, leading to 70% of worldwide remaining forests to be within 1 km of forest edges (Haddad et al., 2015). Ecological studies have shown that edge-effect influences ecological communities, species richness and abundance across many taxa, contributing to worldwide decline in biodiversity. Since edge-effect reduces species abundance and connectivity, it is also expected to negatively influence species genetic variation. In fact, previous theoretical studies had showed that populations closer to the edges of a finite stepping-stone model tends to have shorter coalescence times, and therefore, lower genetic diversity, than central populations. However, predicting the impact of edge effect on local genetic diversity remains challenging in realistic and more complex habitat fragments, where the additive effect of multiple edges is expected to take place. In the present study we explore the genetic consequence of habitat loss at the scale of a habitat fragment (patch-scale), looking at the interplay between patch-size and edge-effect on spatial genetic diversity. We propose a statistical approach to estimate edge-impacted effective population size from habitat cover information and use this measure to predict spatial genetic diversity in both equilibrium and non-equilibrium populations. We address these questions using spatially-explicit simulations and propose a spatially-explicit analytical framework able to model spatio-temporal changes in genetic diversity due to edge-effect and habitat loss.
This package provides tools to assess the association between two spatial processes. Currently, three methodologies are implemented: An adapted t-test to perform hypothesis testing about the independence between the processes, a suitable nonparametric correlation coefficient, and the codispersion coefficient. SpatialPack gives methods to complement methodologies that are available in geoR for one spatial process. With contributions of Francisco Cuevas and Diego Mancilla.
Human activity is leaving a pervasive and persistent signature on Earth. Vigorous debate continues about whether this warrants recognition as a new geologic time unit known as the Anthropocene. We review anthropogenic markers of functional changes in the Earth system through the stratigraphic record. The appearance of manufactured materials in sediments, including aluminum, plastics, and concrete, coincides with global spikes in fallout radionuclides and particulates from fossil fuel combustion. Carbon, nitrogen, and phosphorus cycles have been substantially modified over the past century. Rates of sea-level rise and the extent of human perturbation of the climate system exceed Late Holocene changes. Biotic changes include species invasions worldwide and accelerating rates of extinction. These combined signals render the Anthropocene stratigraphically distinct from the Holocene and earlier epochs. Copyright
The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes
that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus
on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific
advances over the past 5 years. Several of the boundaries now have a two-tier approach, reflecting the importance of cross-scale
interactions and the regional-level heterogeneity of the processes that underpin the boundaries. Two core boundaries—climate
change and biosphere integrity—have been identified, each of which has the potential on its own to drive the Earth system
into a new state should they be substantially and persistently transgressed.
The integration of species distributions and evolutionary relationships is one of the most rapidly moving research fields today and has led to considerable advances in our understanding of the processes underlying biogeographical patterns. Here, we develop a set of metrics, the specific overrepresentation score ( SOS ) and the geographic node divergence ( GND ) score, which together combine ecological and evolutionary patterns into a single framework and avoids many of the problems that characterize community phylogenetic methods in current use.
This approach goes through each node in the phylogeny and compares the distributions of descendant clades to a null model. The method employs a balanced null model, is independent of phylogeny size, and allows an intuitive visualization of the results.
We demonstrate how this novel implementation can be used to generate hypotheses for biogeographical patterns with case studies on two groups with well‐described biogeographical histories: a local‐scale community data set of hummingbirds in the North Andes, and a large‐scale data set of the distribution of all species of New World flycatchers. The node‐based analysis of these two groups generates a set of intuitively interpretable patterns that are consistent with current biogeographical knowledge.
Importantly, the results are statistically tractable, opening many possibilities for their use in analyses of evolutionary, historical and spatial patterns of species diversity. The method is implemented as an upcoming R package nodiv , which makes it accessible and easy to use.
We live amid a global wave of anthropogenically driven biodiversity loss: species and population extirpations and, critically,
declines in local species abundance. Particularly, human impacts on animal biodiversity are an under-recognized form of global
environmental change. Among terrestrial vertebrates, 322 species have become extinct since 1500, and populations of the remaining
species show 25% average decline in abundance. Invertebrate patterns are equally dire: 67% of monitored populations show 45%
mean abundance decline. Such animal declines will cascade onto ecosystem functioning and human well-being. Much remains unknown
about this “Anthropocene defaunation”; these knowledge gaps hinder our capacity to predict and limit defaunation impacts.
Clearly, however, defaunation is both a pervasive component of the planet’s sixth mass extinction and also a major driver
of global ecological change.
The class of beta regression models is commonly used by practitioners to model variables that assume values in the standard unit interval (0,1). It is based on the assumption that the dependent variable is beta-distributed and that its mean is related to a set of regressors through a linear predictor with unknown coefficients and a link function. The model also includes a precision parameter which may be constant or depend on a (potentially different) set of regressors through a link function as well. This approach naturally incorporates features such as heteroskedasticity or skewness which are commonly observed in data taking values in the standard unit interval, such as rates or proportions. This paper describes the betareg package which provides the class of beta regressions in the R system for statistical computing. The underlying theory is briefly outlined, the implementation discussed and illustrated in various replication exercises.
Reducing the rate of biodiversity loss and averting dangerous biodiversity change are international goals, reasserted by the Aichi Targets for 2020 by Parties to the United Nations (UN) Convention on Biological Diversity (CBD) after failure to meet the 2010 target ( 1, 2). However, there is no global, harmonized observation system for delivering regular, timely data on biodiversity change ( 3). With the first plenary meeting of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) soon under way, partners from the Group on Earth Observations Biodiversity Observation Network (GEO BON) ( 4) are developing—and seeking consensus around—Essential Biodiversity Variables (EBVs) that could form the basis of monitoring programs worldwide.
It has been proposed that inbreeding contributes to the decline and
eventual extinction of small and isolated populations,. There is ample
evidence of fitness reduction due to inbreeding (inbreeding depression)
in captivity and from a few experimental, and observational field
studies,, but no field studies on natural populations have been
conducted to test the proposed effect on extinction. It has been argued
that in natural populations the impact of inbreeding depression on
population survival will be insignificant in comparison to that of
demographic and environmental stochasticity,. We have now studied the
effect of inbreeding on local extinction in a large metapopulation of
the Glanville fritillary butterfly (Melitaea cinxia). We found that
extinction risk increased significantly with decreasing heterozygosity,
an indication of inbreeding, even after accounting for the effects of
the relevant ecological factors. Larval survival, adult longevity and
egg-hatching rate were found to be adversely affected by inbreeding and
appear to be the fitness components underlying the relationship between
inbreeding and extinction. To our knowledge, this is the first
demonstration of an effect of inbreeding on the extinction of natural
populations. Our results are particularly relevant to the increasing
number of species with small local populations due to habitat loss and
fragmentation.
Aim To map and characterize anthropogenic transformation of the terrestrial biosphere before and during the Industrial Revolution, from 1700 to 2000.
Location Global.
Methods Anthropogenic biomes (anthromes) were mapped for 1700, 1800, 1900 and 2000 using a rule‐based anthrome classification model applied to gridded global data for human population density and land use. Anthropogenic transformation of terrestrial biomes was then characterized by map comparisons at century intervals.
Results In 1700, nearly half of the terrestrial biosphere was wild, without human settlements or substantial land use. Most of the remainder was in a seminatural state (45%) having only minor use for agriculture and settlements. By 2000, the opposite was true, with the majority of the biosphere in agricultural and settled anthromes, less than 20% seminatural and only a quarter left wild. Anthropogenic transformation of the biosphere during the Industrial Revolution resulted about equally from land‐use expansion into wildlands and intensification of land use within seminatural anthromes. Transformation pathways differed strongly between biomes and regions, with some remaining mostly wild but with the majority almost completely transformed into rangelands, croplands and villages. In the process of transforming almost 39% of earth's total ice‐free surface into agricultural land and settlements, an additional 37% of global land without such use has become embedded within agricultural and settled anthromes.
Main conclusions Between 1700 and 2000, the terrestrial biosphere made the critical transition from mostly wild to mostly anthropogenic, passing the 50% mark early in the 20th century. At present, and ever more in the future, the form and process of terrestrial ecosystems in most biomes will be predominantly anthropogenic, the product of land use and other direct human interactions with ecosystems. Ecological research and conservation efforts in all but a few biomes would benefit from a primary focus on the novel remnant, recovering and managed ecosystems embedded within used lands.
In many large-scale conservation or ecological problems where experiments are intractable or unethical, regression methods are used to attempt to gauge the impact of a set of nominally independent variables (X) upon a dependent variable (Y). Workers often want to assert that a given X has a major influence on Y, and so, by using this indirection to infer a probable causal relationship. There are two difficulties apart from the demonstrability issue itself: (1) multiple regression is plagued by collinear relationships in X; and (2) any regression is designed to produce a function that in some way minimizes the overall difference between the observed and predicted Ys, which does not necessarily equate to determining probable influence in a multivariate setting. Problem (1) may be explored by comparing two avenues, one in which a single best regression model is sought and the other where all possible regression models are considered contemporaneously. It is suggested that if the two approaches do not agree upon which of the independent variables are likely to be significant, then the deductions must be subject to doubt.
Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.Contact:
peter@biomatters.com
We introduce glmulti, an R package for automated model selection and multi-model inference with glm and related functions. From a list of explanatory variables, the pro- vided function glmulti builds all possible unique models involving these variables and, optionally, their pairwise interactions. Restrictions can be specied for candidate models, by excluding specic terms, enforcing marginality, or controlling model complexity. Mod- els are tted with standard R functions like glm. The n best models and their support (e.g., (Q)AIC, (Q)AICc, or BIC) are returned, allowing model selection and multi-model inference through standard R functions. The package is optimized for large candidate sets by avoiding memory limitation, facilitating parallelization and providing, in addition to exhaustive screening, a compiled genetic algorithm method. This article brie y presents the statistical framework and introduces the package, with applications to simulated and real data.
Marine ecosystems are centrally important to the biology of the planet, yet a comprehensive understanding of how anthropogenic
climate change is affecting them has been poorly developed. Recent studies indicate that rapidly rising greenhouse gas concentrations
are driving ocean systems toward conditions not seen for millions of years, with an associated risk of fundamental and irreversible
ecological transformation. The impacts of anthropogenic climate change so far include decreased ocean productivity, altered
food web dynamics, reduced abundance of habitat-forming species, shifting species distributions, and a greater incidence of
disease. Although there is considerable uncertainty about the spatial and temporal details, climate change is clearly and
fundamentally altering ocean ecosystems. Further change will continue to create enormous challenges and costs for societies
worldwide, particularly those in developing countries.
Using two genetic approaches and seven different plant systems, we present findings from a meta-analysis examining the strength of the effects of plant genetic introgression and genotypic diversity across individual, community and ecosystem levels with the goal of synthesizing the patterns to date. We found that (i) the strength of plant genetic effects can be quite high; however, the overall strength of genetic effects on most response variables declined as the levels of organization increased. (ii) Plant genetic effects varied such that introgression had a greater impact on individual phenotypes than extended effects on arthropods or microbes/fungi. By contrast, the greatest effects of genotypic diversity were on arthropods. (iii) Plant genetic effects were greater on above-ground versus below-ground processes, but there was no difference between terrestrial and aquatic environments. (iv) The strength of the effects of intraspecific genotypic diversity tended to be weaker than interspecific genetic introgression. (v) Although genetic effects generally decline across levels of organization, in some cases they do not, suggesting that specific organisms and/or processes may respond more than others to underlying genetic variation. Because patterns in the overall impacts of introgression and genotypic diversity were generally consistent across diverse study systems and consistent with theoretical expectations, these results provide generality for understanding the extended consequences of plant genetic variation across levels of organization, with evolutionary implications.
The mitochondrial DNA of plant and animal cells is a transcriptionally active genome that traces its origins to a symbiotic infection of eucaryotic cells by bacterial progenitors. As prescribed by the Serial Endosymbiosis Theory, symbiotic organelles have gradually transferred their genes to the eucaryotic genome, producing a functional interaction of nuclear and mitochondrial genes in organelle function. We report here a recent remarkable transposition of 7.9 kb of a typically 17.0-kb mitochondrial genome to a specific nuclear chromosomal position in the domestic cat. The intergrated segment has subsequently become amplified 38-76 times and now occurs as a tandem repeat macrosatellite with multiple-length alleles resolved by pulse-field gel electrophoresis (PFGE) segregating in cat populations. Sequence determination of the nuclear mitochondrial DNA segment, Numt, revealed a d(CA)-rich 8-bp motif [ACACACGT] repeated imperfectly five times at the deletion junction that is a likely target for recombination. The extent and pattern of sequence divergence of Numt genes from the cytoplasmic mtDNA homologues plus the occurrence of Numt in other species of the family Felidae allowed an estimate for the origins of Numt at 1.8-2.0 million years ago in an ancestor of four modern species in the genus Felis. Numt genes do not function in cats; rather, the locus combines properties of nuclear minisatellites and pseudogenes. These observations provide an empirical glimpse of historic genomic events that may parallel the accommodation of organelles in eucaryotes.
There is controversy concerning the role of genetic factors in species extinctions. Many authors have asserted that species are usually driven to extinction before genetic factors have time to impact them, but few studies have seriously addressed this issue. If this assertion is true, there will be little difference in genetic diversity between threatened and taxonomically related nonthreatened species. We compared average heterozygosities in 170 threatened taxa with those in taxonomically related nonthreatened taxa in a comprehensive metaanalysis. Heterozygosity was lower in threatened taxa in 77% of comparisons, a highly significant departure from the predictions of the no genetic impact hypothesis. Heterozygosity was on average 35% lower (median 40%) in threatened taxa than in related nonthreatened ones. These differences in heterozygosity indicate lowered evolutionary potential, compromised reproductive fitness, and elevated extinction risk in the wild. Independent evidence from stochastic computer projections has demonstrated that inbreeding depression elevates extinction risk for threatened species in natural habitats when all other threatening processes are included in the models. Thus, most taxa are not driven to extinction before genetic factors affect them adversely.
DNA techniques, analytical methods and palaeoclimatic studies are greatly advancing our knowledge of the global distribution of genetic diversity, and how it evolved. Such phylogeographic studies are reviewed from Arctic, Temperate and Tropical regions, seeking commonalities of cause in the resulting genetic patterns. The genetic diversity is differently patterned within and among regions and biomes, and is related to their histories of climatic changes. This has major implications for conservation science.
Uncorrectable skew and heteroscedasticity are among the "lemons" of psychological data, yet many important variables naturally exhibit these properties. For scales with a lower and upper bound, a suitable candidate for models is the beta distribution, which is very flexible and models skew quite well. The authors present maximum-likelihood regression models assuming that the dependent variable is conditionally beta distributed rather than Gaussian. The approach models both means (location) and variances (dispersion) with their own distinct sets of predictors (continuous and/or categorical), thereby modeling heteroscedasticity. The location sub-model link function is the logit and thereby analogous to logistic regression, whereas the dispersion sub-model is log linear. Real examples show that these models handle the independent observations case readily. The article discusses comparisons between beta regression and alternative techniques, model selection and interpretation, practical estimation, and software.
Species-energy theory indicates that recent climate warming should have driven increases in species richness in cool and species-poor parts of the Northern Hemisphere. We confirm that the average species richness of British butterflies has increased since 1970-82, but much more slowly than predicted from changes of climate: on average, only one-third of the predicted increase has taken place. The resultant species assemblages are increasingly dominated by generalist species that were able to respond quickly. The time lag is confirmed by the successful introduction of many species to climatically suitable areas beyond their ranges. Our results imply that it may be decades or centuries before the species richness and composition of biological communities adjusts to the current climate.
Theory predicts, and recent empirical studies have shown, that the diversity of plant species determines the diversity of
associated herbivores and mediates ecosystem processes, such as aboveground net primary productivity (ANPP). However, an often-overlooked
component of plant diversity, namely population genotypic diversity, may also have wide-ranging effects on community structure
and ecosystem processes. We showed experimentally that increasing population genotypic diversity in a dominant old-field plant
species, Solidago altissima, determined arthropod diversity and community structure and increased ANPP. The effects of genotypic diversity on arthropod
diversity and ANPP were comparable to the effects of plant species diversity measured in other studies.
Global conservation strategies commonly assume that different taxonomic groups show congruent geographical patterns of diversity, and that the distribution of extinction-prone species in one group can therefore act as a surrogate for vulnerable species in other groups when conservation decisions are being made. The validity of these assumptions remains unclear, however, because previous tests have been limited in both geographical and taxonomic extent. Here we use a database on the global distribution of 19,349 living bird, mammal and amphibian species to show that, although the distribution of overall species richness is very similar among these groups, congruence in the distribution of rare and threatened species is markedly lower. Congruence is especially low among the very rarest species. Cross-taxon congruence is also highly scale dependent, being particularly low at the finer spatial resolutions relevant to real protected areas. 'Hotspots' of rarity and threat are therefore largely non-overlapping across groups, as are areas chosen to maximize species complementarity. Overall, our results indicate that 'silver-bullet' conservation strategies alone will not deliver efficient conservation solutions. Instead, priority areas for biodiversity conservation must be based on high-resolution data from multiple taxa.
A phylogeny and timescale derived from analyses of multilocus nuclear DNA sequences for Holarctic genera of plethodontid salamanders reveal them to be an old radiation whose common ancestor diverged from sister taxa in the late Jurassic and underwent rapid diversification during the late Cretaceous. A North American origin of plethodontids was followed by a continental-wide diversification, not necessarily centered only in the Appalachian region. The colonization of Eurasia by plethodontids most likely occurred once, by dispersal during the late Cretaceous. Subsequent diversification in Asia led to the origin of Hydromantes and Karsenia, with the former then dispersing both to Europe and back to North America. Salamanders underwent rapid episodes of diversification and dispersal that coincided with major global warming events during the late Cretaceous and again during the Paleocene–Eocene thermal optimum. The major clades of plethodontids were established during these episodes, contemporaneously with similar phenomena in angiosperms, arthropods, birds, and mammals. Periods of global warming may have promoted diversification and both inter- and transcontinental dispersal in northern hemisphere salamanders by making available terrain that shortened dispersal routes and offered new opportunities for adaptive and vicariant evolution.
• historical biogeography
• paleogeography
• Plethodontidae dispersal
• salamander phylogeny
• phylogeny
Recent studies have generated an explosion of phylogenetic and biogeographic data and have provided new tools to investigate the processes driving large-scale gradients in species diversity. Fossils and phylogenetic studies of plants and animals demonstrate that tropical regions are the source for almost all groups of organisms, and these groups are composed of a mixture of ancient and recently derived lineages. These findings are consistent with the hypothesis that the large extent of tropical environments during the past 10-50 million years, together with greater climatic stability, has promoted speciation and reduced extinction rates. Energy availability appears to only indirectly contribute to global patterns of species diversity, especially considering how some marine diversity gradients can be completely decoupled from temperature and productivity gradients. Instead, climate stability and time-integrated area together determine the baselines of both terrestrial and marine global diversity patterns. Biotic interactions likely augment diversification and coexistence in the tropics.
Current predictions of extinction risks from climate change vary widely depending on the specific assumptions and geographic and taxonomic focus of each study. I synthesized published studies in order to estimate a global mean extinction rate and determine which factors contribute the greatest uncertainty to climate change-induced extinction risks. Results suggest that extinction risks will accelerate with future global temperatures, threatening up to one in six species under current policies. Extinction risks were highest in South America, Australia, and New Zealand, and risks did not vary by taxonomic group. Realistic assumptions about extinction debt and dispersal capacity substantially increased extinction risks. We urgently need to adopt strategies that limit further climate change if we are to avoid an acceleration of global extinctions.
Copyright © 2015, American Association for the Advancement of Science.
Clifford, Richardson, and Hemon (1989, Biometrics 45, 123-134) presented modified tests of association between two spatially autocorrelated processes, for lattice and non-lattice data. These tests are built on the sample covariance and on the sample correlation coefficient; they require the estimation of an effective sample size that takes into account the spatial structure of both processes. Clifford et al. developed their method on the basis of an approximation of the variance of the sample correlation coefficient and assessed it by Monte Carlo simulations for lattice and non-lattice networks of moderate to large size. In the present paper, the variance of the sample covariance is computed for a finite number of locations, under the multinormality assumption, and the mathematical derivation of the definition of effective sample size is given. The theoretically expected number of degrees of freedom for the modified t test with renewed modifications is compared with that computed on the basis of equation (2.9) of Clifford et al. (1989). The largest differences are observed for small numbers of locations and high autocorrelation, in particular when the latter is present with opposite sign in the two processes. Basic references that were missing in Clifford et al. (1989) are given and inherent ambiguities are discussed.
We established replicated experimental populations of the annual plant Clarkia pulchella to evaluate the existence of a causal relationship between loss of genetic variation and population survival probability. Two treatments differing in the relatedness of the founders, and thus in the genetic effective population size (Ne), were maintained as isolated populations in a natural environment. After three generations, the low Ne treatment had significantly lower germination and survival rates than did the high Ne treatment. These lower germination and survival rates led to decreased mean fitness in the low Ne populations: estimated mean fitness in the low Ne populations was only 21% of the estimated mean fitness in the high Ne populations. This inbreeding depression led to a reduction in population survival: at the conclusion of the experiment, 75% of the high Ne populations were still extant, whereas only 31% of the low Ne populations had survived. Decreased genetic effective population size, which leads to both inbreeding and the loss of alleles by genetic drift, increased the probability of population extinction over that expected from demographic and environmental stochasticity alone. This demonstrates that the genetic effective population size can strongly affect the probability of population persistence.
As climates change across already stressed ecosystems, there is no doubt that species will be affected, but to what extent
and which will be most vulnerable remain uncertain. The fossil record suggests that most species persisted through past climate
change, whereas forecasts of future impacts predict large-scale range reduction and extinction. Many species have altered
range limits and phenotypes through 20th-century climate change, but responses are highly variable. The proximate causes of
species decline relative to resilience remain largely obscure; however, recent examples of climate-associated species decline
can help guide current management in parallel with ongoing research.