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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.

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... Detailed overviews of the temporal trends, applications and integration of the various types of molecular markers can be found in Schlötterer (2004) Genetic composition has been assessed for thousands of species globally with increasingly high-resolution population-level genetic data sets available at decreasing costs (Vranckx et al., 2012;Romiguier et al., 2014;Lawrence et al., 2019). Although the changing technology and limited number of systematic monitoring programs does pose problems for spatiotemporal comparisons (see Sections III.1 on obtaining genetic data and V.2 on scale and standardization), recent studies are identifying gaps in genetic marker data availability (Miraldo et al., 2016) and are jointly analyzing genetic summaries obtained across different species, studies and markers using standardization and normalization procedures [e.g. De Kort et al. (2021) for amplified fragment length polymorphism (AFLP)/microsatellites]. Further, hundreds of species now have had their genomes sequenced and assembled, which makes developing genetic markers and interpreting genetic data more efficient in these and related species (e.g. ...
... Most archived genetic data cannot be operationalized yet. Typically, less than 10% of sequences are georeferenced, and most cannot be geolocated based on text descriptions (Gratton et al., 2017;Miraldo et al., 2016;Toczydlowski et al., 2021). For example, Theodoridis et al. (2020) examined mammal mitochondrial genetic diversity globally, comprising >150,000 mitochondrial DNA sequences from BOLD and GenBank. ...
... The first category of macrogenetic studies involves integrating data sets from multiple species (tens to thousands) spanning large geographic scales (thousands of square kilometres to global coverage) with extensive environmental databases to identify spatial trends or patterns in EBVs (reviewed in Leigh et al., 2021). A study may test for correlations between genetic diversity and macro-ecological correlates such as latitude (Miraldo et al., 2016), assorted environmental variables (Manel et al., 2020), anthropogenic impact (Millette et al., 2020;Schmidt et al., 2020), species diversity (Theodoridis et al., 2020), or life-history traits (De Kort et al., 2021). Such studies may generate multispecies genetic data from scratch (e.g. ...
Article
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Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (Ne). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.
... In recent decades, owning to public databases of a large number of DNA sequences, it become feasible to analyze the global GD pattern based on multiple taxa. After a pioneer study on the global GD patterns of terrestrial vertebrates (Miraldo et al., 2016), many studies on GD patterns at the global scale have emerged for mammals and amphibians (Gratton et al., 2017), fishes (Manel et al., 2020), insects and plants (Millette et al., 2019). These studies applied gene markers of either neutral genes, such as Cytochrome b (Cyt b) and Cytochrome Oxidase I (COI), or functional genes, such as major histocompatibility complex genes (MHC II) (Li et al., 2021). ...
... These studies applied gene markers of either neutral genes, such as Cytochrome b (Cyt b) and Cytochrome Oxidase I (COI), or functional genes, such as major histocompatibility complex genes (MHC II) (Li et al., 2021). However, most of these studies focused on macro-scaled ranges, e.g., at a country or continent level (Miraldo et al., 2016;Millette et al., 2019;Hu et al., 2021;Schmidt and Garroway, 2021). Research efforts at smaller regional scales and/or at species divergence centres are rather scarce Deng et al., 2019;Yu et al., 2019). ...
... There is no strong linear correlation between the GD parameters and the three geographical variables (latitude, longitude, and elevation). Whereas a poleward decrease of GD has been identified (Miraldo et al., 2016), our result indicates that patterns observed at a global scale may not apply to local scales, especially in the complicated topographical areas of the MSC (Lei, 2012;Rahbek et al., 2019b). ...
Article
Genetic diversity is one of the three dimensions of biodiversity and fundamental to various life forms on the Earth. Understanding the distribution pattern of genetic diversity and its driving forces has been an important topic in ecology, biogeography and conservation biology since the last decade. We investigated the genetic diversity pattern of passerine birds in the Mountains of Southwest China, a global biodiversity hotspot with the highest species richness of birds in the entire Eurasia, and explored the influencing forces of environmental variables on genetic diversity. We compiled 1189 Cytochrome b sequences of 27 passerine species from 152 geographic sites, covering the range of Mountains of Southwest China and its adjoining areas. We generated genetic diversity distribution maps using a grid-cell method based on nucleotide diversity and haplotype diversity indices. We further analyzed the variation pattern of the two indices along latitudinal, longitudinal, and elevational gradients. The correlations between the two indices and environmental variables were also evaluated. The nucleotide diversity hotspots were mostly located in the southern Hengduan Mountains, while for haplotype diversity, three hotspots were detected: the southeast edge of the Qinghai-Tibetan Plateau, the southern Hengduan Mountains and the Qinling Mountains. There was no monotonic increasing or decreasing pattern in nucleotide diversity or haplotype diversity along latitudinal, longitudinal or elevational gradients except for altitudinal range. Correlation and model selection analyses detected multiple environmental variables in driving genetic diversity patterns, including temperature, precipitation, vegetation, human influence, longitude and altitude range. Similar to the pattern of species richness, the nucleotide diversity pattern of passerine birds in the Mountains of Southwest China presents a decreasing trend from southwest to northeast, while the haplotype diversity pattern is more likely decreased from west to east. Our results indicate that the distribution pattern of genetic diversity may be derived from the complex topography and diverse microclimates in the Mountains of Southwest China.
... We calculated nucleotide diversity (Tajima, 1993) as our IGD metric (e.g., Miraldo et al., 2016). Nucleotide diversity is the average number of nucleotide differences per site between two randomly chosen sequences from the same population and can be corrected for sequence length. ...
... To map the distribution of IGD across the Patagonian steppe, we calculated the average nucleotide diversity for each species contained in each grid cell. Then, we averaged the nucleotide diversity of species within each cell, following Miraldo et al. (2016), to estimate the genetic diversity of the cell (IGD t ). Although in some cases the estimated Π for each species within a cell was based on different regions of the plastid DNA, the uniparental inheritance of the chloroplast DNA without recombination in angiosperms and the relatively similar mutation rates among the intergenic spacers used in phylogeographic studies make this a typical procedure in comparative phylogeography (e.g., Alsos et al., 2005). ...
... Although in some cases the estimated Π for each species within a cell was based on different regions of the plastid DNA, the uniparental inheritance of the chloroplast DNA without recombination in angiosperms and the relatively similar mutation rates among the intergenic spacers used in phylogeographic studies make this a typical procedure in comparative phylogeography (e.g., Alsos et al., 2005). Similar approaches were also applied in animals (Miraldo et al., 2016;Schmidt et al., 2020). Finally, each grid cell was classified based on IGD quartiles as: low-IGD t (lower quartile, Q1), mid-IGD t (Q2 containing the median), and high-IGD t (upper quartile, Q3). ...
Article
Intraspecific genetic diversity (IGD), the fundamental dimension of biodiversity, is scarcely considered in the context of anthropogenic impact at regional and global scales. Here, encouraged by the knowledge about the effect of past climate changes that shaped IGD at the community level, we evaluated how current land use and future climate changes may erode mechanisms underlying genetic diversity and species richness of the native flora of the Patagonian steppe, a cold desert that covers 827,446 km² in the southern cone of South America. About 36% of the Patagonian steppe could serve as Anthropocene refugia, with only 1.8% being protected areas at present. Moreover, 63% of the areas with the highest species richness and endemism, and 37% with the highest genetic diversity are outside the refugia areas. Human-driven changes threaten plant biodiversity mainly in northern Patagonia. We provide the first broad assessment of climate change and land-use effects on IGD for the Patagonian steppe. The conservation of the detected high genetic diversity and species-rich areas with moderate land use and projected low climate anomaly should be prioritized, whereas high-risk areas, those for which a high climatic anomaly is projected, deserve monitoring and mitigation policies. This approach which includes IGD as a biodiversity metric may be useful for other endangered ecoregions in the world, with promising results for biodiversity conservation.
... Moreover, the amount of genetic variation distributed among populations is integrally tied to their resilience and adaptability to environmental change (Barrett & Schluter, 2007;Charlesworth & Charlesworth, 1987;Keller & Waller, 2002;Savolainen, Lascoux, & Merilä, 2013;Schindler, Armstrong, & Reed, 2015). Efforts to map genetic variation globally have shown mixed responses to anthropogenic impacts among broad categories of animal taxa (Millette et al., 2020;Miraldo et al., 2016). However, none evaluated the relative importance of historic versus contemporary land use in driving contemporary spatial patterns of genetic diversity, so it is uncertain to what extent land use legacies (Foster et al., 2003) have shaped patterns of modern-day genetic variation. ...
... The COI locus is commonly used to study broad patterns of genetic diversity over large spatial and temporal scales (Millette et al., 2020;Miraldo et al., 2016), often being the only locus with sufficient data for macroecological studies (though improvements in public sequence archives will create opportunity for multi-locus or genome-wide analyses e.g. Millette et al., 2021). ...
... We note that there has been some discussion about the suitability of this approach for grouping sequences spatially, and that comparison of distances among sequences between demes were substantially larger that distances among sequences within demes, confirming that there was no 'daisy chaining' effect in our data ( Fig. S1) . We estimated nucleotide diversity, the average number of variable sites in each pair of sequences, from aligned COI sequences within each deme that possessed at least 2 sequences using equation 2 of Miraldo et al. (2016): ...
Article
Recent declines in once‐common species are triggering concern that an environmental crisis point has been reached. Yet, the lack of long abundance time series data for most species can make it difficult to attribute these changes to anthropogenic causes, and to separate them from normal cycles. Genetic diversity, on the other hand, is sensitive to past and recent environmental changes, and reflects a measure of a populations’ potential to adapt to future stressors. Here, we consider whether patterns of genetic diversity among aquatic insects can be linked to historical and recent patterns of land use change. We collated mitochondrial cytochrome c oxidase subunit I (COI) variation for >700 aquatic insect species across the United States, where patterns of agricultural expansion and intensification have been documented since the 1800s. We found that genetic diversity was lowest in regions where cropland was historically (pre‐1950) most extensive, suggesting a legacy of past environmental harm. Genetic diversity further declined where cropland has since expanded, even after accounting for climate and sampling effects. Notably though, genetic diversity also appeared to rebound where cropland has diminished. Our study suggests that genetic diversity at the community level can be a powerful tool to infer potential population declines and rebounds over longer time spans than is typically possible with ecological data. For the aquatic insects that we considered, patterns of land use many decades ago appear to have left long‐lasting damage to genetic diversity that could threaten evolutionary responses to rapid global change.
... Understanding the distribution of genetic diversity is 44 important for providing insights on the spatial distribution of biodiversity as a whole, with 45 implications for conservation planning (De Kort et al., 2021;Lawrence & Fraser, 2020;Leigh et 46 al., 2021;Theodoridis et al., 2020). Although still in its infancy, 'macrogenetics'the study of 47 genetic diversity across different taxa at broad scalesthus far has not revealed patterns as 48 widespread or as obvious across latitudes as those found in species diversity (Adams & Hadly, 49 2013;Manel et al., 2020;Millette et al., 2020;Miraldo et al., 2016;Theodoridis et al., 2020). 50 ...
... Future works should aim to investigate such within-group variation, as we were unable to 367 account for variability at or below the genus level due to significant loss of data. nuclear PGD is less clear than species diversity or previously used mitochondrial DNA data 370 (Miraldo et al., 2016). Distinctively, our results indicate that temperature variability, along with 371 mean temperature, might be one of the main driving factors affecting PGD. ...
... A latitudinal gradient would appear when assessing individual species, 395 but when looking across all species, latitudes considered low for one species may be considered 396 high for another. Thus the latitudinal gradient is less pronounced across Classes (De Kort et al., 397 2021;Millette et al., 2020;Miraldo et al., 2016;Schluter & Pennell, 2017), particularly when 398 accounting for species identity (De Kort et al., 2021;Gratton et al., 2017). This could also 399 explain why we found little evidence for the "classic" latitudinal gradient across species. ...
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Relative to species diversity gradients, the broad scale distribution of population-specific genetic diversity (PGD) across taxa remains understudied. We used nuclear DNA data collected from 6285 vertebrate populations across the Americas to assess the role environmental variables play in structuring the spatial/latitudinal distribution of PGD, a key component of adaptive potential in the face of environmental change. Our results provide key evidence for taxa-specific responses and that temperature variability in addition to mean temperature may be a primary driver of PGD. Additionally, we found some positive influence of precipitation, productivity, and elevation on PGD; identified trends were dependent on the metric of PGD. In contrast to the classic negative relationship between species diversity and latitude, we report either a positive or taxa-dependent relationship between PGD and latitude, depending on the metric of PGD. The inconsistent latitudinal gradient in different metrics of PGD may be due to opposing processes diminishing patterns across latitudes that operate on different timescales, as well as the flattening of large-scale genetic gradients when assessing across species versus within species. Our study highlights the nuance required to assess broad patterns in genetic diversity, and the need for developing balanced conservation strategies that ensure population, species, and community persistence.
... Broad-scale patterns of population genetic biodiversity across species have only recently begun to be mapped thanks to the accumulation of open data in public repositories. We are still in the early stages of understanding the links between microevolutionary processes and macroecological patterns (Manel et al., 2020;Miraldo et al., 2016;Schmidt, Dray, & Garroway, 2022;Theodoridis et al., 2020). ...
... Although we did not detect clear latitudinal or longitudinal gradients in nuclear genetic diversity across North America, previous findings suggest mitochondrial genetic diversity in amphibians and other ectotherms varies latitudinally and mirrors species richness patterns (Manel et al., 2020;Miraldo et al., 2016). Miraldo et al. (2016 found that amphibian mitochondrial genetic diversity in North America was highest in the species-rich southeastern United ...
... Although we did not detect clear latitudinal or longitudinal gradients in nuclear genetic diversity across North America, previous findings suggest mitochondrial genetic diversity in amphibians and other ectotherms varies latitudinally and mirrors species richness patterns (Manel et al., 2020;Miraldo et al., 2016). Miraldo et al. (2016 found that amphibian mitochondrial genetic diversity in North America was highest in the species-rich southeastern United ...
Article
Ecological limits on population sizes and the number of species a region can sustain are thought to simultaneously produce spatial patterns in population genetic diversity and species richness due to the effects of random drift operating in parallel across population and community levels. Here, we test the extent to which resource‐based environmental limits jointly determine these patterns of biodiversity in amphibians. North America. Amphibians. We repurposed open, raw microsatellite data from 19 species sampled at 554 sites in North America and mapped nuclear genetic diversity at the continental scale. We then tested whether ecological limits defined by resource availability and environmental heterogeneity could simultaneously shape biogeographic patterns in genetic diversity and species richness with structural equation modelling. Spatial patterns of population genetic diversity run opposite patterns of species richness and genetic differentiation. However, while measures of resource availability and niche heterogeneity predict 89% of the variation in species richness, these landscape metrics were poor predictors of genetic diversity. Although heterogeneity appears to be an important driver of genetic and species biodiversity patterns in amphibians, variation in genetic diversity both within and across species makes it difficult to infer general processes producing spatial patterns of amphibian genetic diversity. This result differs from those found in endotherms and may be due to the considerable life history variation found across amphibians.
... Unfortunately, datasets covering simultaneously intra-and interspecific diversity patterns within a taxon above the genus level remain rare and highly incomplete (e.g., [2][3][4][5]). It is difficult to obtain a broader picture of the diversity and phylogeny of, say, a family-level taxon across its whole distribution range, sampling all genera, species and the intraspecific diversity. ...
... Comprehensive and reliable information about diversity and its distribution is only obtained by a dense and geographically balanced sampling of populations. Data can be often repurposed from earlier studies, but utilization of published data is often difficult: they may be published in a summarized form [8] and they are often not appropriately georeferenced (e.g., [2,9]. Moreover, the sampling may be spatially and taxonomically biased depending on the goals of the original studies and filling the gaps in coverage then promises a diminished chance of discovery, which may lower the motivation to do such work. ...
Article
Full-text available
Sequences of mitochondrial genes revolutionized the understanding of animal diversity and continue to be an important tool in biodiversity research. In the tribe Helicini, a prominent group of the western Palaearctic land snail fauna, mitochondrial data accumulating since the 2000s helped to newly delimit genera, inform species-level taxonomy and reconstruct past range dynamics. We combined the published data with own unpublished sequences and provide a detailed overview of what they revealed about the diversity of the group. The delimitation of Helix is revised by placing Helix godetiana back in the genus and new synonymies are suggested within the genera Codringtonia and Helix. The spatial distribution of intraspecific mitochondrial lineages of several species is shown for the first time. Comparisons between species reveal considerable variation in distribution patterns of intraspecific lineages, from broad postglacial distributions to regions with a fine-scale pattern of allopatric lineage replacement. To provide a baseline for further research and information for anyone re-using the data, we thoroughly discuss the gaps in the current dataset, focusing on both taxonomic and geographic coverage. Thanks to the wealth of data already amassed and the relative ease with which they can be obtained, mitochondrial sequences remain an important source of information on intraspecific diversity over large areas and taxa.
... If true, we should be able to infer processes underlying biodiversity patterns at both genetic and species levels by attempting to understand their common causes. The accumulation of open molecular genetic data now allows us to tackle these types of questions by repurposing and synthesizing publicly archived raw data (e.g., Leigh et al. 2021;Miraldo et al. 2016;Manel et al. 2020;Schmidt et al. 2020a;Theodoridis et al. 2020;Schmidt and Garroway 2021). ...
... Notably, the negative correlation we find between spatial patterns of species richness and nuclear genetic diversity runs opposite the relatively consistent positive correlations found between species richness and mitochondrial genetic diversity gradients (Martin and McKay 2004;Adams and Hadly 2012;Miraldo et al. 2016;Manel et al. 2020;Theodoridis et al. 2020). Mitochondrial DNA has several idiosyncrasies associated with the specific biology of mitochondria that distinguish it from genetic diversity measured with neutral nuclear DNA (Schmidt and Garroway 2021a). ...
Article
The processes that give rise to species richness gradients are not well understood, but may be linked to resource-based limits on the number of species a region can support. Ecological limits placed on regional species richness should also affect population demography, suggesting that these processes could also generate genetic diversity gradients. If true, we might better understand how broad-scale biodiversity patterns are formed by identifying the common causes of genetic diversity and species richness. We develop a hypothetical framework based on the consequences of regional variation in ecological limits set by resource availability and heterogeneity to simultaneously explain spatial patterns of species richness and neutral genetic diversity. Repurposing raw genotypic data spanning 38 mammal species sampled across 801 sites in North America, we show that estimates of genome-wide genetic diversity and species richness share spatial structure. Notably, species richness hotspots tend to harbor lower levels of within-species genetic variation. A structural equation model encompassing eco-evolutionary processes related to resource availability, habitat heterogeneity, and contemporary human disturbance supports the spatial patterns we detect. These results suggest broad-scale patterns of species richness and genetic diversity could both partly be caused by intraspecific demographic and evolutionary processes acting simultaneously across species. This article is protected by copyright. All rights reserved
... Gaither et al., 2013;Lawrence et al., 2019;Selkoe et al., 2014;Sexton et al., 2014), or retrieving existing data from sequence repositories (e.g. Miraldo et al., 2016) using automated data retrieval (e.g. custom scripts: Barrow et al., 2020;SequinR: Charif & Lobry, 2007;rentrez: Winter, 2017), followed by georeferencing, quality control and analysis (e.g. ...
... For example, a meta-analysis of marine fishes using 140 species and >11,000 microsatellite loci found that allelic richness was 12% lower in over-harvested populations (Pinsky & Palumbi, 2014). Similarly, mitochondrial analysis of >90,000 sequences from >4500 species found that habitats experiencing a greater scale of human impact hold less genetic diversity (Miraldo et al., 2016), but no such pattern was found in a later study of >175,000 mitochondrial sequences and >17,000 species (Millette et al., 2020). These findings suggest that the factors potentially impacting 'evolvability' (i.e. ...
Article
We consider the opportunities and challenges comparative phylogeography (CP) faces in the genomic age to determine: (1) how we can maximise the potential of big CP analyses to advance biogeographic and macroevolutionary theory; and (2) what we can, and will struggle, to achieve using CP approaches in this era of genomics. World‐wide. All. We review the literature to discuss the future of CP ‐ particularly examining CP insights enabled by genomics that may not be possible for single species and/or few molecular markers. We focus on how geography and species' natural histories interact to yield congruent and incongruent patterns of neutral and adaptive processes in the context of both historical and recent rapid evolution. We also consider how CP genomic data are being stored, accessed, and shared. With the widespread availability of genomic data, the shift from a single‐ to a multi‐locus perspective is resulting in detailed historical inferences and an improved statistical rigour in phylogeography. However, the time and effort required for collecting co‐distributed species and accruing species‐specific ecological knowledge continue to be limiting factors. Bioinformatic skills and user‐friendly analytical tools, alongside the computational infrastructure required for big data, can also be limiting. Over the last ~35 years, there has been much progress in understanding how intraspecific genetic variation is geographically distributed. The next major steps in CP will be to incorporate evolutionary processes and community perspectives to account for patterns and responses among co‐distributed species and across temporal scales, including those related to anthropogenic change. However, the full potential of CP will only be realised if we employ robust study designs within a sound comparative framework. We advocate that phylogeographers adopt such consistent approaches to enhance future comparisons to present‐day findings.
... All nonavian reptile groups (the tuatara, squamates, turtles and crocodilians) are collectively termed 'reptiles' here, even though they do not form a monophyletic group. It should be noted that while amphibians, birds and mammals have traditionally been used as model groups for studies of macroecological patterns and analyses of global gradients of genetic diversity (Jetz et al., 2012;Miraldo et al., 2016), reptiles are becoming included in global-level comparisons only recently as their distribution data have not been available for long (Roll et al., 2017;Roll et al., 2021). ...
... It must, however, be noted that tropical biomes suffer from a general shortage of records and genetic samples (Hughes et al., 2021). Combined with the fact that lowland Amazonia harbours some of the highest levels of within-species genetic diversity (Miraldo et al., 2016) it may be that the large ranges are in fact composed of ranges of species that remain cryptic for the time being and are yet to be uncovered once samples from across this vast and diverse ecosystem become available (Funk et al., 2012). ...
Article
Full-text available
Resolving the tree of life is among the greatest challenges for modern biology, yet genetic data for many species are lacking to infer their position in the tree with confidence. In fact, little is known about what the missing species are and where to look for them. I identify main hotspots that host the most unsampled vertebrate species and test the hypothesis that local diversity determines the degree of sampling effort. Global. Terrestrial vertebrates (amphibians, birds, mammals, reptiles). I use published distributional data and search DNA sequence repositories to identify taxa with no genetic data available. I map spatial patterns of the unsampled diversity and sampling effort to test the effect of species richness on sampling completeness. I examine the dependence of country‐level sampling completeness on the country's socio‐economic development. About 24% of living terrestrial vertebrate species have no genetic data available. The Andes, Central Africa and the Malay Archipelago are the most unsampled. Sampling effort is highest in North America, continental South‐East Asia and Amazonia. In contrast, Central Africa, the Horn of Africa, Malay Archipelago and Andes are consistently the least sampled regions. Regions of low diversity are better sampled than biodiversity hotspots. The most unsampled species are in the tropics. I pinpoint several key regions that are least represented in the tree of life and where sampling should be prioritized. Country's wealth seems to be an informative proxy for its sampling completeness.
... These populations include terrestrial (46.6%), marine (21.9%), freshwater (14.1%), amphibious (9.7%), and diadromous (7.7%) populations of fungi (<2% of unique species), chromists (<2%), plants (23%), and animals (73%; Fig. 1). CaliPopGen includes population level data with broader taxonomic coverage than recent, more global compilations, which have focused on freshwater and marine fishes 15 , mammals 16 , mammals and amphibians 17 , vertebrates 18 , and birds, fishes, insects and mammals 19 . Its focus at the regional (state) level is unique. ...
... Molecular markers in our database include RFLPs, AFLPs, allozymes and isozymes, microsatellites, mitochondrial, and other nuclear markers, whereas previously published datasets frequently focussed on one or a few loci (e.g. [15][16][17]19 ) or single marker types (e.g. 18 ,). ...
Article
Full-text available
CaliPopGen is a database of population genetic data for native and naturalized eukaryotic species in California, USA. It summarizes the published literature (1985–2020) for 5,453 unique populations with genetic data from more than 187,394 individuals and 448 species (513 species plus subspecies) across molecular markers including allozymes, RFLPs, mtDNA, microsatellites, nDNA, and SNPs. Terrestrial habitats accounted for the majority (46.4%) of the genetic data. Taxonomic groups with the greatest representation were Magnoliophyta (20.31%), Insecta (13.4%), and Actinopterygii (12.85%). CaliPopGen also reports life-history data for most included species to enable analyses of the drivers of genetic diversity across the state. The large number of populations and wide taxonomic breadth will facilitate explorations of ecological patterns and processes across the varied geography of California. CaliPopGen covers all terrestrial and marine ecoregions of California and has a greater density of species and georeferenced populations than any previously published population genetic database. It is thus uniquely suited to inform conservation management at the regional and state levels across taxonomic groups.
... It is an integral component of biodiversity, and can alter community dynamics and ecosystem functioning through its influence on processes such as nutrient cycling and trophic cascades (Des Roches et al., 2018;Raffard et al., 2019). Intraspecific genetic diversity has been heavily influenced by human activities (Miraldo et al., 2016;Mimura et al., 2017), with a conservative estimate of 5.4-6.5% loss within populations of wild organisms since the industrial revolution (Leigh et al., 2019). Despite its widely acknowledged importance and continuing decline, intraspecific genetic diversity is often a neglected aspect of biodiversity conservation (Mimura et al., 2017). ...
Article
1. Intraspecific genetic diversity provides the evolutionary potential to adapt to changing environments and 'hotspots' of high intraspecific diversity are recognized as key targets for conservation. 2. In southwestern Australia, intraspecific genetic diversity for mesic taxa is not uniformly distributed. Many species comprise highly divergent lineages with unique haplotypes resulting from contraction to refugia during historical arid cycles. Sampling strategies in studies of the region's unique and ancient freshwater fauna have often focused on broad distributional range, making it difficult to determine boundaries between lineages and the location of genetic hotspots. 3. This study explored the spatial distribution of intraspecific genetic diversity in the threatened freshwater mussel, Westralunio carteri. Mitochondrial DNA sequences for 164 specimens, sampled from all basins within the distribution of the species, were used to describe lineage boundaries and the location of hotspots, and to reconstruct historical demographics. 4. There was strong evidence for three subregions of genetic diversity based on the largely non-overlapping distributions of three evolutionarily significant units. Spatial and demographic analyses suggest that these evolutionarily significant units persisted through past arid cycles in separate refugia. The majority of haplotypes were unique to a single location, indicating limited connectivity among populations in recent times. Hotspots were identified throughout the region. Most notably, a significant hotspot in the southwestern corner probably arose through the overlap of lineages in historical refugia. 5. Conservation assessments often focus on the species as a whole, even though sublineages, hotspots and the threats faced are not evenly distributed across the species range. This paper highlights that effective conservation of spatially structured taxa requires targeted management of multiple genetic units. Given the importance of formal taxonomic description for conservation listings, further investigation of the potential for species delimitation within W. carteri is required. K E Y W O R D S
... Rapid climate change driven by human activities is one of the leading causes of global biodiversity loss in this new millennium (Thomas et al., 2004). Therefore, understanding how species will respond to future climate change and predicting their extinction risks are crucial if conservation biologists are to implement conservation efforts to protect threatened species (Brook et al., 2008;Cronk, 2016;Miraldo et al., 2016;Scheffers et al., 2016;Urban, 2015). To avoid climatedriven extinction, species must (a) escape to suitable climatic conditions, (b) acclimate via phenotypic plasticity, or (c) adapt via natural selection based on standing genetic variation and/or new mutations. ...
Article
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Habitat loss induced by climate warming is a major threat to biodiversity, particularly to threatened species. Understanding the genetic diversity and distributional responses to climate change of threatened species are critical to facilitate their conservation and management. Cupressus gigantea, a rare conifer found in the eastern Qinghai‐Tibet Plateau (QTP) at 3,000 to 3,600 m.a.s.l., is famous for its largest specimen, the King Cypress, which is >55 m tall. Here, we obtained transcriptome data from 96 samples of 10 populations covering its whole distribution and used these data to characterize genetic diversity, identify conservation units, and elucidate genomic vulnerability to future climate change. After filtering, we identified 145,336, 26,103, and 2,833 single nucleotide polymorphisms in the whole, putatively neutral, and putatively adaptive datasets, respectively. Based on the whole and putatively neutral datasets, we found that populations from the Yalu Tsangpo River (YTR) and Nyang River (NR) catchments could be defined as separate management units (MUs), due to distinct genetic clusters and demographic histories. Results of gradient forest models suggested that all populations of C. gigantea might be at risk due to the high expected rate of climate change, and the NR MU had a higher risk than the YTR MU. This study deepens our understanding of the complex evolutionary history and population structure of threatened tree species in extreme environments, such as dry river valleys above 3000 m.a.s.l. in the QTP, and provides insights into their susceptibility to global climate change and potential for adaptive responses.
... This work is arguably most needed in biodiversity hotspots, the regions of the world that are richest in diversity while simultaneously most at risk due to human activities (Myers et al., 2000;Zachos & Habel, 2011). Not only are these regions some of the richest in biodiversity on our planet, but undescribed biodiversity-especially species and genetic diversity-is often concentrated in these regions (Hamilton et al., 2010;Miraldo et al., 2016;Mora et al., 2011). ...
Article
Taxon‐specific characteristics and extrinsic climatic and geological forces may both shape population differentiation and speciation. In geographically and taxonomically focused investigations, differentiation may occur synchronously as species respond to the same external conditions. Conversely, when evolution is investigated in taxa with largely varying traits, population differentiation and speciation is complex and shaped by interactions of Earth’s template and species‐specific traits. As such, it is important to characterize evolutionary histories broadly across the tree of life, especially in geographic regions that are exceptionally diverse and under pressures from human activities such as in biodiversity hotspots. Here, using whole‐genome sequencing data, we characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six species, populations on either side of the GRV exhibited significant but varying levels of genetic differentiation. Species’ dispersal ability was negatively correlated with levels of population differentiation. Isolation with migration models indicated varied patterns of population differentiation and connectivity among populations of the focal species. We found that demographic histories—estimated for each individual—varied by both species and population but were consistent between individuals of the same species and sampling region. We found that genomic diversity varied by half an order of magnitude across species, and that this variation could largely be explained by the harmonic mean of effective population size over the past 200,000 years. Overall, we found that even in highly dispersive species like birds, the GRV acts as a substantial biogeographic barrier.
... However, automated georeferencing algorithms may be a viable tool to improve sequence attribution geographically (Miraldo et al., 2016). When splits apply to allopatric populations, the latitude/longitude of the sample origin solves name application. ...
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Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequence data from around the globe, facilitating biodiversity research. However, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have led to widespread scientific name changes. Taxonomic instability, or “splits, lumps, and shuffles”, present logistical challenges to large-scale biodiversity research because species or populations may be listed under different names in different data sources, or because different species or populations may be listed under previous names. Consequently, distributional and trait data are often difficult to link directly to DNA sequence data without extensive and time consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize all avian names in use in NCBI GenBank, a primary source of genetic data, to a widely-used and regularly-updated avian taxonomy: eBird/Clements. Of 14,341 avian species or subspecies names used by GenBank, 11,031 names directly matched an eBird/Clements name, which were linked to over 6 million nucleotide sequences. For the remaining unique avian names in GenBank, we used Avibase’s taxonomic concepts, taxonomic descriptions in Cornell’s Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names were linked to over 600,000 nucleotide sequences, approximately 9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under two or more GenBank names. Our avian GenBank naming reconciliation is open source and available at GitHub, where it can be updated to correspond with future annual eBird/Clements taxonomic updates. LAY SUMMARY – 23% of avian names on GenBank do not match eBird/Clements, a widely-used standardized avian taxonomy – 600,000 nucleotide sequences on GenBank are associated with names that do not match eBird/Clements – 10% of eBird/Clements names have nucleotide sequences listed under multiple GenBank names – We provide an open source taxonomic reconciliation to mitigate difficulties associated with non-standardized name use for GenBank data
... 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). ...
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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.
... Although many groups of organisms are widely distributed in tropical regions, the detailed pattern of variation in species (Costa and Magnusson 2010)-including spatial, genetic, and morphological variation-and their genetic structure have recently been documented, corresponding to several independent evolutionary units (Ribas et al. 2012;Schultz et al. 2017). Genetic diversity of terrestrial mammals and amphibians is 27% higher in tropical areas, and disturbed habitats have less genetic diversity compared to undisturbed areas (Miraldo et al. 2016). Well-sampled molecular phylogenies have recently been developed to reveal the evolution of tropical biota (Dexter et al. 2017;Eiserhardt et al. 2017). ...
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Scientists have not been able to estimate, to the nearest order of magnitude, the number of species in the Amazon. Although the Amazon includes one of the largest forests in the world, it is also one of the least known biologically. Documenting its biodiversity is challenging because of its immense size, heterogeneity, and limited access. Based on current knowledge, the Amazon exhibits the highest density of species as well as the highest number of threatened species (many of them endemics) for vascular and non-vascular plants, fish, amphibians, birds, and mammals. Deeper knowledge of bio- diversity patterns is still lacking, and the spatial turnover of species assemblages at different scales remains poorly understood. In the Amazon, we can also find some outstanding examples of animal behavior. For example, many fish migrate over long distances, and some of them perform the longest known migrations in freshwaters of the world, traveling the entire length of the Amazon Basin in a round trip migration of~12,000 km. It is also important to consider that plant–animal interactions and trophic interactions are central ecological processes in Amazonian forests. Disruptions of these interactions can alter forest community composition over the long-term. Functional diversity, in- cluding intra- and inter-specific variation, has recently attracted the attention of scientists, and it is evident that it contributes to community and ecosystem resilience to perturbations including climate change. There is still much to learn about Amazon biodiversity, species assemblages, and ecological interactions. There are spatial and taxonomic biases in the data (including many unexplored loca- tions and lesser-known taxonomic groups), which affect our understanding of biodiversity patterns in the Amazon. The chapter highlights the need for more basic and applied research to improve our knowledge of biodiversity patterns across the region. This information is critical for understanding the impacts of human activities and informing conservation and restoration actions.
... Importantly, if genetic diversity patterns were simply averaged across all species, as is commonly undertaken in comparative phylogeography studies (Miraldo et al., 2016;Selkoe et al., 2016), no geographic patterns would have been evident. This is best exemplified by comparing the maps of genetic diversity within each major cluster ( Figure 3c) with those for all species combined (cluster 20: Figure S4). ...
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Aim While in recent years, there have been considerable advances in discerning spatial genetic patterns within species, the task of identifying common patterns across species is still challenging. Approaches using new data from co-sampled species permit rigorous statistical analysis but are often limited to a small number of species. Meta-analyses of published data can encompass a much broader range of species, but are usually restricted by uneven data properties. There is a need for new approaches that bring greater statistical rigour to meta-analyses and are also able to discern more than a single spatial pattern among species. We propose a new approach for comparative multi-species meta-analyses of published population genetic data that address many existing limitations. Innovation The proposed “genogeographic clustering” technique takes a three-stage approach: (i) use common genetic metrics to gain location-specific measures across the sampled range of each species; (ii) for each species, determine the spatial genetic pattern by fitting a smooth “genogeographic” trend curve to the genetic data; and (iii) quantitatively cluster species according to their similarity in spatial pattern. We apply this technique to 21 species of intertidal invertebrate from the New Zealand coastline, to resolve common spatial patterns from disparate profiles of genetic diversity. Main conclusions The genogeographic curves are shown to successfully capture the known spatial patterns within each intertidal species and readily permit statistical comparison of those patterns, regardless of sampling and marker inconsistencies. The species clustering technique is shown to discern groups of species that clearly share spatial patterns within groups but differ significantly among groups. Genogeographic species clustering provides a novel approach to discerning multiple common spatial patterns of diversity among a large number of species. It will permit more rigorous comparative studies from diverse published data and can be easily extended to a wide variety of alternative measures of genetic diversity or divergence.
... Despite the lack of studies investigating the combined effect of life-history traits and environmental factors on genetic diversity at the local scale of the population, various quantitative reviews focused on both life-history traits and spatial factors to understand genetic diversity across populations that is at the global scale of species or metapopulation (Schoville et al. 2012;Romiguier et al. 2014;Miraldo et al. 2016;Manel et al. 2020). In particular, these studies demonstrated that the genetic diversity is lower for long-lived or low-fecundity species than for short-lived or high-fecundity species. ...
Article
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Genetic diversity at population scale, depends on species life-history traits, population dynamics and local and global environmental factors. We first investigate the effect of life-history traits on the neutral genetic diversity of a single population using a deterministic mathematical model. When the population is stable, we show that semelparous species with precocious maturation and iteroparous species with delayed maturation exhibit higher diversity because their life history traits tend to balance the lifetimes of non reproductive individuals (juveniles) and adults which reproduce. Then, we extend our model to a metapopulation to investigate the additional effect of dispersal on diversity. We show that dispersal may truly modify the local effect of life history on diversity. As a result, the diversity at the global scale of the metapopulation differ from the local diversity which is only described through local life history traits of the populations. In particular, dispersal usually promotes diversity at the global metapopulation scale.
... La biodiversité est actuellement menacée par les activités d'une espèce en particulier : l'espèce humaine ( Figure 1) (Díaz et al., 2019 ;Dirzo et Raven, 2003 ;Duraiappah et al., 2005 ;Ceballos et al., 2015 ;Pereira et al., 2012 ;Sala et al., 2000 ;Vitousek et al., 1997). En effet, les activités humaines sont responsables du déclin et de la disparition de nombreuses espèces (Ceballos et al., 2015 ;Díaz et al., 2019 ;Dirzo et al., 2014) et elles bouleversent les patrons de diversités spécifique et génétique (DiBattista, 2008 ;Garner et al., 2005 ;Miraldo et al., 2016) 1 . Alors que la pollution des milieux (Penuelas et al., 2013) et le changement climatique (Bellard et al., 2012) modifient entre autres les aires de distribution potentielle des espèces, l'introduction d'espèces exotiques invasives bouleverse les interactions entre espèces (Vitousek et al., 1996). ...
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La connectivité écologique des habitats est nécessaire aux processus écologiques assurant le maintien de la biodiversité. Des méthodes ont donc été développées pour la modéliser afin de comprendre précisément son influence et d’orienter les mesures de conservation de la biodiversité. Parmi ces méthodes, les graphes paysagers modélisent un réseau d’habitat sous la forme d’un ensemble de taches d’habitat (noeuds) reliées par des chemins de dispersion potentiels (liens). La validité écologique de ces outils nécessitait néanmoins d’être évaluée à l’aide de données reflétant les réponses biologiques des populations à la connectivité de leurs habitats. Les données génétiques permettent cette validation car la structure génétique des populations dépend notamment des flux génétiques entre leurs taches d’habitat. La structure génétique peut également être modélisée par un graphe génétique dont les noeuds correspondent à des populations et dont les liens sont pondérés par le degré de différenciation génétique entre populations. L’objectif de cette thèse était d’utiliser conjointement des graphes génétiques et paysagers pour (i) évaluer la validité écologique des graphes paysagers et (ii) améliorer notre compréhension de la relation entre connectivité et structure génétique. Après avoir identifié les méthodes de construction et d’analyse des graphes génétiques les plus adaptées à chaque contexte et développé un outil informatique permettant l’utilisation conjointe des graphes génétiques et paysagers, nous les avons comparés dans le cadre de deux études empiriques. Elles ont permis (i) d’évaluer l’influence respective des différentes composantes de la connectivité des habitats sur la diversité et la différenciation génétiques et (ii) de confirmer la validité écologique des graphes paysagers. Nous avons ensuite montré que l’intégration de variables associées à la fois aux noeuds et aux liens de ces deux types de graphes améliorait l’estimation de l’influence des éléments du paysage sur la connectivité. Les méthodes développées dans cette thèse pourraient trouver d’autres applications dans ce champ d’étude comme dans d’autres. Nous espérons que les résultats de cette thèse et l’outil informatique développé y contribueront.
... Over recent decades, species extinctions and reductions in population abundance have attracted much attention (Ceballos et al., 2015;Dirzo et al., 2014;Seibold et al., 2019;van Klink et al., 2020). Loss of genetic diversity within species though has received much less consideration, arguably because it is more difficult to observe (Gauthier et al., 2020;Hoban et al., 2020;Miraldo et al., 2016). Species with small and isolated populations are prone to losses of genetic diversity through drift, and are vulnerable to inbreeding depression, both of which can increase extinction risk (Barnosky et al., 2011;Frankham, 1995;Spielman et al., 2004). ...
Article
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Biodiversity is currently declining at the global scale. Apart from species declines and lowered abundances, the loss of genetic diversity is equally concerning as it may undermine fitness and the potential to adapt to future environmental change. We compared genetic diversity of historical and recent Alpine populations of two butterfly species, Lycaena helle and L. hippothoe, over a period of about 10 years. Using microsatellite markers, we found no changes over time in L. helle, while genetic diversity decreased, and differentiation increased in L. hippothoe. Lycaena helle inhabits peat bogs and wetland fallows with populations being strongly isolated, while L. hippothoe used to occur in population networks on hay meadows, with the latter being strongly exposed to agricultural intensification. We conclude that currently L. hippothoe populations are strongly declining due to changes in land use, resulting in genetic erosion potentially due to the collapse of population networks. Stable genetic diversity was found in the glacial relict species Lycaena helle. Decreased genetic diversity was found in the grassland butterfly Lycaena hippothoe. We conclude that land use intensification may reduce genetic diversity over a period of only 10 years.
... Eupithecia manniaria-(c) Austria, Lengberg, 13.V.1986, slide CREA-0200; (d) Italy, Santa Maria, 6.IV.2016, slide CREA-0168 TA B L E 4 Measurements (in mm, means ± SD) of male and female genitalia in the Eupithecia conterminata complex of Europe of "southern richness and northern purity" (e.g., Hewitt, 1996), also recovered for European butterflies in a recent study . Furthermore, our data are in line with repeated observations from recent years demonstrating that the taxonomic richness of southern areas is correlated with high genetic diversity (de Kort et al., 2021;Miraldo et al., 2016;Pelletier & Carstens, 2018;Yiming et al., 2021). ...
Article
en The Barcode Index Numbers (BINs) are operational species units based on patterns of COI divergences that in most cases correspond to species. It has been repeatedly observed that more than one BIN can be found under the same species name particularly when large geographic scales are considered. One such case concerns Eupithecia conterminata, a species widespread in North European countries and restricted to mountainous regions in the rest of the continent, for which five BINs are found in Europe. In order to solve the question concerning the taxonomic status of these BINs and European populations, we employed an integrated approach by combining classical morphological traits (genitalia and wing markings) with those of molecular data, the latter involving both mitochondrial and nuclear genes. This approach allowed us to recognize two valid species in Europe, E. conterminata, currently known only in Fennoscandia, Baltic countries and Russia, and Eupithecia manniaria sp. rev., with distribution covering Central and South European countries. We furthermore synonymized Eupithecia pindosata syn. nov. from Greece with E. manniaria. The European range of these species and their mitochondrial diversity appear to be coherent with biogeographical histories of their foodplants Picea abies and Abies species. Astratta it I Barcode Index Number (BINs) sono unità tassonomiche operative basate sui pattern di divergenza del COI che in molti casi corrispondono ad una specie. È stato ripetutamente osservato che più di un BIN può essere trovato sotto uno stesso nome, soprattutto quando vengono considerate ampie scale geografiche. Uno di questi casi riguarda Eupithecia conterminata, diffusa nei paesi dell’Europa settentrionale e limitata alle regioni montuose nel resto del continente, per la quale in Europa sono stati trovati cinque BIN. Per chiarire lo status tassonomico di questi BIN e delle popolazioni europee, in questo lavoro abbiamo usato un approccio integrato che ha combinato caratteri morfologici classici (struttura dei genitali e pattern alare) con dati molecolari, gli ultimi riguardanti sia geni mitocondriali che nucleari. Questo approccio ci ha permesso di confermare la presenza di due specie in Europa, E. conterminata, attualmente conosciuta solo per Fennoscandia, paesi baltici e Russia, e E. manniaria sp. rev. nota per l’Europa centro-meridionale. Inoltre, abbiamo posto in sinonimia E. pindosata syn. nov. della Grecia con E. manniaria. La distribuzione europea di queste specie e la loro diversità mitocondriale sembra essere coerente con la storia biogeografica delle loro piante nutrici, Picea abies e diverse specie di Abies.
... Molecular data already frequently contribute towards creating biodiversity inventories (Taberlet et al. 2018, Ruppert et al. 2019) and rapid biodiversity assessments at local scales (eDNA and meta-barcoding, Yu et al. 2012, McClenaghan et al. 2020 including baseline flora and fauna identification (Hofreiter et al. 2001). They are also routinely employed for overcoming sampling gaps in cryptic taxa and remote areas (Barratt et al. 2017, Lentendu et al. 2018, Ritter et al. 2019a, understanding gene-environment interactions (Ritter et al. 2018, Zinger et al. 2019, species interaction (Doliwa et al. 2021, Ritter et al. 2021 and cross-taxonomic analyses of genetic diversity and population structure (Miraldo et al. 2016, Gratton et al. 2017, Theodoridis et al. 2020. Recent applications have highlighted the use of molecular data for biodiversity monitoring (Flanagan et al. 2018, Hunter et al. 2018) and the response to stressors and conservation measures (Beermann et al. 2018, Zizka et al. 2020a, with a number of programs instigated by several stakeholders to monitor genetic diversity (e.g. ...
Article
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Due to increasing human transformation of virtually all habitats on Earth, setting global priorities for conservation is essential. The emerging disciplines of macroecology and macroevolution (MEE) can provide a global perspective and information for such prioritization but remain relatively separated from conservation prioritization, partly because MEE researchers are unaware of the requirements for effective conservation prioritization and existing approaches implementing these. Indeed, existing approaches for conservation prioritization at large scale are scattered across literature. Here, we systematically review this literature and provide a guideline for researchers in MEE as to which of approaches might be suitable for their needs. From >11 000 scientific publications, we identified 134 methods suitable for commonly used MEE data and geographic scale. Furthermore, we use a ‘trait matrix' to identify families of similar approaches and to design a guideline to select the most suitable method, given a user‐defined set of data and analysis scope. The guidelines are freely available via the conserveR R‐package (<https://github.com/azizka/conserveR>). Finally, we used our review to identify increasing scalability, continuous monitoring and the integration of molecular, remote sensing and animal movement data as key areas for future impacts of MEE in conservation prioritization. We anticipate that our review can serve as a guide to MEE researchers interested in linking their data to conservation as well as for conservation scientists interested in using MEE approaches.
... This could enable mechanistic models projected forward-in-time such as discussed in section II.3.6. The production of new genomic datasets across entire ecosystems should further help create maps of genetic diversity at high resolution to track losses (Parks et al., 2013;Miraldo et al., 2016;Li et al., 2021). ...
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More species than ever before are at risk of extinction due to anthropogenic habitat loss and climate change. But even species that are not threatened have seen reductions in their populations and geographic ranges, likely impacting their genetic diversity. Although preserving genetic diversity is a key conservation target to maintain the adaptability of species, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. By bridging biodiversity and population genetics theories, we introduce the first mathematical framework to understand the loss of naturally occurring DNA mutations within a species--what we call genetic diversity extinction. Analyzing genome-wide variation data of 10,126 geo-tagged individuals from 19 plant and animal species, we show that genome-wide diversity follows a power law with geographic area, which can predict genetic diversity decay in simulated spatial extinctions. Given pre-21st century values of ecosystem transformations, we estimate that over 10% of genetic diversity may be extinct, already surpassing the United Nations targets for genetic preservation. These estimated losses could rapidly increase with advancing climate change and habitat destruction, highlighting the need for new forecasting tools that assist in the rapid implementation of policies to protect genetic resources.
... The distinction of our models is evidenced by the fact that it depicts the best possible areas for conservation of T. govanianum not only by considering climate and habitat suitability, but also taking into account the impact of human activities and focussing on precise zone for reintroduction within a suitable predicted habitat. The transition from healthy ecosystems to highly modified ones acts as chief predictor for the species facing growing extinction risk (Di Marco et al. 2018), and this transition decreases the viability of species populations by impacting their genetic diversity (Miraldo et al. 2016). Venter et al. 2016 argued an increase of 9% in the global human footprint over a period of 16 years (1993)(1994)(1995)(1996)(1997)(1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009) with only 3% of terrestrial land free from human pressures, thereby necessitating enhanced conservation strategies. ...
Article
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Climate change, land-use changes and other anthropogenic pressures are globally the major drivers of biodiversity decline with profound implications, especially for the fragile Himalayan ecosystems. These drivers, if factored into the biodiversity conservation models, significantly improve their reliability and help a great deal prioritise habitats for better management. Here we focussed on an important medicinal plant species (Trillium govanianum), endemic to Himalayan region that is beset with the twin challenge of climate change and growing human footprint. We predicted the current and future projection of the distribution range of this species using SDM tool ‘MaxEnt’ supplemented with ‘Zonation’ software and ‘human pressure index’. Decrease in the potential geographic range of T. govanianum, with a narrow room for conservation due to anthropogenic pressures in the predicted suitable habitats, was clearly revealed from our results. We identified the precise zones within the predicted suitable habitats under the future climatic scenarios (2050 and 2070) for priority conservation to endure the impact of climate change and growing human pressures. These results hold considerable promise in designing the effective conservation strategies for the target species. In the context of post 2020 biodiversity outlook, we advocate augmenting the species distribution models with human footprint index, zonation analysis and the climate change scenarios, to realistically meet the desired conservation targets.
... However, the drivers of intraspecific variation across species have largely been tested in isolation, and most of the few studies that compared multiple drivers of genetic diversity did so at spatial scales too large to be informative for conservation (Manel et al., 2020;Wyborn & Evans, 2021). Multi-species comparisons in particular have immense power to detect patterns in the spatio-temporal variation of genetic diversity at global scales (De Kort et al., 2021), although patterns tend to differ between regions and systems (Gratton et al., 2017;Manel et al., 2020;Miraldo et al., 2016). Inferences from multi-species studies may be limited by various factors including uneven sampling strategies, comparisons across taxa with different marker types or divergent evolutionary dynamics, but are likely to still resolve broad-scale patterns even where some species may have vastly different population genetic patterns (Page & Hughes, 2014;Wright et al., 2015). ...
Article
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Aim Intraspecific genetic variation is a key component of biodiversity, with higher diversity indicating greater resilience and population substructuring suggesting unique evolutionary histories. Comparative approaches, in which intraspecific genetic variation is assessed across multiple species, are powerful tools to identify evolutionary hotspots, but are still rarely applied at spatial scales relevant to conservation planning. Here, we use comparative phylogeography to understand patterns and potential drivers of genetic variation within a biodiversity and ocean warming hotspot. Location The South African coastline, Indian/Atlantic Oceans. Methods A literature search was conducted to obtain mitochondrial DNA cytochrome oxidase c subunit I and cytochrome b sequence data for 17 marine fish and invertebrate species. From these data, we compared averages of haplotype and nucleotide diversity, and within‐region ΦST between four biogeographic provinces in the region. Mixed linear models tested whether environmental variability, habitat preference, or geographic location significantly influence genetic variation. Results Average diversity values differed between haplotype and nucleotide diversity, but both broadly displayed highest diversity levels within the South‐West bioregion, which is also a region of high levels of within‐region ΦST. Range in sea surface temperatures (SSTs) was the only significant fixed‐effect term in the haplotype diversity mixed linear models. Mean SST, stability in SSTs since the Mid‐Holocene and position within the species' geographic distribution all had no significant effect on genetic variation. Main conclusions Along this coastline characterized by high environmental heterogeneity, we find that variation in temperature is a prominent source of intraspecific variation. Genetic diversity differs between bioregions, but does not display higher levels within the core of each species’ range when assessed across multiple species. With elevated levels of genetic diversity, the South‐West region of the South African coast is highlighted as a conservation priority area, representing both high genetic diversity and differentiation across taxa.
... Large spatial-scale patterns of interspecific diversity have been widely studied, such as the distribution of species diversity across latitudinal ranges (Gaston, 2000). It has been shown further that intraspecific diversity follows the same global patterns as interspecific diversity, with higher diversity in the tropics and a decrease towards the poles (Miraldo et al., 2016;Manel et al., 2020, but see de Kort et al., 2021. At more local scales (i.e. ...
Article
Intraspecific genetic diversity is heterogeneously distributed in natural landscapes and often forms repeatable spatial patterns. For instance, in rivers, genetic diversity increases towards downstream areas, whereas genetic differentiation increases in isolated upstream areas. Nonetheless, these patterns can be modified by human‐induced perturbations, and documenting the extent to which human activities alter these natural patterns is important for conservation. Among the human pressures that affect freshwater biodiversity, stocking natural populations with captive‐bred strains is a common practice worldwide that can strongly alter the genetic integrity of wild populations. The main objectives of this study were to document the spatial distribution of captive‐bred ancestry in brown trout (Salmo trutta) populations from four French basins having been stocked according to different practices, and to quantify for each basin the effect of captive‐bred ancestry on the spatial distribution of genetic diversity and differentiation. The four basins were sampled along their upstream–downstream gradient, and a total of 1,686 individuals were genotyped at 192 single nucleotide polymorphism loci. For all basins, individuals with a strong assignment to the captive strain were mostly found in upper reaches, although the average proportion of captive‐bred ancestry varied strikingly among rivers (from 1.9 to 58.7%). Although spatial patterns of genetic differentiation were not affected by introgression and showed an expected increase with increasing distances from the river mouth in all basins, there was evidence that the classical pattern of downstream increase in genetic diversity was reversed when considering highly introgressed populations. These findings demonstrate that the stocking of captive‐bred strains can strongly modify natural spatial patterns of diversity, even when stocking occurred many generations ago and has now ended. The study illustrates the major impacts of humans on intraspecific biodiversity patterns, and emphasizes the importance of conservation plans that take into account this artificial distribution of genetic diversity.
... The viral taxonomic and functional richness in our study follows the latitudinal diversity gradient paradigm that suggests higher biodiversity in the tropics with a decrease toward the poles (Fig. 2a). While in general agreement with the diversity patterns of other domains of life 43,44 , more samples from a wider range of latitudes should be analysed to verify this result. The overall effect of latitude on viral taxonomic and functional richness in the AMD sediments may be primarily attributable to the variations in prokaryotic richness (Fig. 3). ...
Article
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Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments. The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage sediments sampled across Southern China, showing the predominant effects of prokaryotic communities and the influence of environmental variables on viral taxonomy and function.
... The database includes primary population genetic information for 5,453 populations of 448 species from four main marker types. In comparison to other macrogenetic databases(Lawrence et al. 2019;Manel et al. 2020;Millette et al. 2020;Miraldo et al. 2016; ...
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A recently published macrogenetic dataset of California’s flora and fauna, CaliPopGen, comprehensively summarizes population genetic research published between 1985-2020. Integrating these genetic data into the requisite “best available science” upon which conservation professionals rely should facilitate the prioritization of populations based on genetic health. We evaluate the extent to which the CaliPopGen Dataset provides genetic diversity estimates that are 1) unbiased, 2) sufficient in quantity, 3) cover entire species’ ranges, and 4) include potentially adaptive loci. We identified genetic diversity estimates for 4,462 spatially-referenced populations of 432 species, confirming California’s rich published history of population genetics research. Most recent studies used microsatellites markers, which have uniquely high levels of variation, and estimates of all genetic metrics varied significantly across marker types. Most studies used less than 10 loci for inferences, rendering parameter estimates potentially unreliable, and covered small spatial extents that include only a fraction of the studied species’ California distribution (median 16.3%). In contrast, the ongoing California Conservation Genomics Project (CCGP) aims to cover the full geographical and environmental breadth of each species’ occupied habitats, and uses a consistent approach based on whole-genome data. However, the CCGP will sequence only 12% of the number of individuals, and covers only about half the evolutionary diversity, of the CaliPopGen Database. There is clearly a place in the evaluation of the genetic health of California for both approaches going forward, especially if differences among studies can be minimized, and overlap emphasized. A complementary use of both datasets is warranted to inform optimal conservation decision-making.
... were used to calculate genetic diversity. The genetic diversity of each species was defined and calculated following Mirado et al. [43]. ...
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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.
... Although many groups of organisms are widely distributed in tropical regions, the detailed pattern of variation in species (Costa and Magnusson 2010)-including spatial, genetic, and morphological variation-and their genetic structure have recently been documented, corresponding to several independent evolutionary units (Ribas et al. 2012;Schultz et al. 2017). Genetic diversity of terrestrial mammals and amphibians is 27% higher in tropical areas, and disturbed habitats have less genetic diversity compared to undisturbed areas (Miraldo et al. 2016). Well-sampled molecular phylogenies have recently been developed to reveal the evolution of tropical biota (Dexter et al. 2017;Eiserhardt et al. 2017). ...
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This Report provides a comprehensive, objective, open, transparent, systematic, and rigorous scientific assessment of the state of the Amazon’s ecosystems, current trends, and their implications for the long-term well-being of the region, as well as opportunities and policy relevant options for conservation and sustainable development.
... Genomics models and concepts are widely applied for biodiversity sustenance, from ideal seed selection for preservation to assessing the degree of impact at community-level effects. The concept of population genomics has provided valuable information on population size, demographic history, ability of the populations to evolve and adapt to the changing environment, etc. (Miraldo et al. 2016;Hu et al. 2020Hu et al. , 2021Hohenlohe et al. 2021). They have been able to successfully develop large sets of markers that increase the ability to detect and quantify low levels of hybridization or admixture. ...
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Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.
... 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, Pendleton, Shapiro, & Palkovacs, 2021). Concerningly, genetic diversity, like all levels of biodiversity, is declining rapidly during the Anthropocene across the tree of life (Leigh, Hendry, Vázquez-Domínguez, & Friesen, 2019;Miraldo et al., 2016;Pinsky & Palumbi, 2014). ...
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Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic diversity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a "distributed datathon" to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 492 contained samples from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 82% of these 492 datasets (N = 401 BioProjects comprising 42,104 individuals or BioSamples). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the samples were taken was the most easily found; information about sampling permits was the most challenging to locate. 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 discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines 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 observable metadata decay, 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 forever.
... Genetic diversity is one of the three levels of biodiversity that the International Union for Conservation of Nature (IUCN) recommends for planetary environmental conservation (McNeely et al. 1990;Newton et al. 1999;Verma 2016). It has been demonstrated that genetic variability is essential for species to respond to environmental fluctuations such like changing climate, habitats, and biotic interactions such as new or altered diseases (Reed et al. 2002;Miraldo et al. 2016). The importance of genetic diversity in sustaining ecosystem resilience and functionality (Schaberg et al. 2008;Roger et al. 2012), as well as species diversity (Vellend and Geber 2005) cannot be overstated. ...
Article
Conservation of biodiversity entails not just the preservation of specific taxa, but also genetic diversity. Despite the fact that molecular data appear to be crucial for freshwater fish conservation management, the information about genetic diversity of the genus Luciobarbus Heckel, 1843 populations in Morocco is still very rare. Accordingly, this study’s main purpose was to present genetic and biogeographic information of nine Luciobarbus species out of 15 Luciobarbus species native to Morocco. Sequencing of the complete cytochrome b gene (1140 bp) confirmed the presence of two evolutionary lineages of Luciobarbus in Morocco and displayed low to high level of genetic diversity within Luciobarbus populations. Populations with the largest size had the highest level of genetic diversity, according to our findings. Moreover, the “star-like” shape of the haplotype networks along with low and insignificant value of the Harpending raggedness index supported the hypothesis of population expansion in Luciobarbus populations. Nevertheless, additional investigations should ideally be undertaken separately for each species in order to untangle genetic diversity trends.
... For instance, empirical studies have found that populations of small animals with high fecundity and short longevity, large geographic ranges and long-distance dispersal harbour relatively high genetic diversity (Eo et al., 2011;Romiguier et al., 2014;Doyle et al., 2015;Dalongeville et al., 2016), whereas other studies could not validate this life-history related genetic diversity pattern (Mitton and Lewis, 1989;Vachon et al., 2018). Despite the lack of studies investigating the combined effect of life-history traits and environmental factors on genetic diversity at the local scale of the population, various quantitative reviews focused on both life-history traits and spatial factors to understand genetic diversity across populations that is at the global scale of species or metapopulation (Schoville et al., 2012;Romiguier et al., 2014;Miraldo et al., 2016;Manel et al., 2020). In particular, these studies demonstrated that the genetic diversity is lower for long-lived or low-fecundity species than for short-lived or highfecundity species. ...
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Genetic diversity at population scale, depends on species life-history traits, population dynamics and local and global environmental factors. We first investigate the effect of life-history traits on the neutral genetic diversity of a single population using a deterministic mathematical model. When the population is stable, we show that semelparous species with precocious maturation and iteroparous species with delayed maturation exhibit higher diversity because their life history traits tend to balance the lifetimes of non reproductive individuals (juveniles) and adults which reproduce. Then, we extend our model to a metapopulation to investigate the additional effect of dispersal on diversity. We show that dispersal may truly modify the local effect of life history on diversity. As a result, the diversity at the global scale of the metapopulation differ from the local diversity which is only described through local life history traits of the populations. In particular, dispersal usually promotes diversity at the global metapopulation scale.
... In addition to the species richness, multiple biodiversity facets could be extracted from eDNA data to understand the complex ecosystem processes. 17 While sequence diversity and taxonomic diversity refer to diversity of interspecific genetic variants 18 and species richness, functional diversity refers to the diversity of traits represented by the local community. 19 From the local to landscape, the α diversity describes the richness background within the local environment, and the β diversity refers to the degree of change in community composition, or the degree of community differentiation, 20 which are driven by the complex gradient or pattern of the environment. ...
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Ecological qualities and resources in coasts are threatened by various human activities, such as pollution and fishery. Impact evaluation of environmental stressors over a wide coastal stretch has been limited due to lack of efficient and standardizable biodiversity monitoring and assessment tools. Integrating environmental DNA (eDNA) and ecological traits, a holistic approach was developed to assess the impact of pollution and aquaculture on fish biodiversity in Chinese coastal areas. Taking the Yalujiang Estuary (YLJK) from the Yellow Sea and the Nan'ao Island Area (NAO) from the South China Sea as cases, the performance of the eDNA biomonitoring workflow was validated. First, the eDNA results of 22 sampling sites reached more than 85% of the asymptotes of species or ASVs in each area. A total of 115 fish species in both areas were detected and NAO was 1.8 times richer than YLJK using eDNA and the fish eDNA composition was consistent with the historical data. eDNA recovered distinct variations of fish sequence, taxonomic and functional diversity, and the corresponding trends following the offshore distance between the two areas. Fish sequence diversity was decreased primarily by estuarine pollution factors (chemical oxygen demand and zinc) in the YLJK. Compared with no breeding areas, lower fish sequence diversity was in breeding areas in the NAO. By integrating ecological traits, the eDNA approach offers promising opportunities for future fish biodiversity monitoring and assessment in national and global coastal environments.
... species, ecosystem, gene and cultural diversity) of biodiversity and has been extensively investigated in recent decades for different taxonomic groups and different geographic regions of the world (Gaston & Spicer, 2013). Despite that genetic diversity is often considered as the most fundamental dimension of biodiversity (May et al., 1994), it receives less attention and only a few studies considered genetic diversity mapping (Ellegren & Galtier, 2016;Manel et al., 2020;Miraldo et al., 2016). Knowing the distribution of genetic diversity is essential for the conservation of biodiversity at all its levels from genes to ecosystems (Dalongeville et al., 2022;Ellegren & Galtier, 2016;Gaston & Spicer, 2013;Hu et al., 2021;Manel et al., 2020;Thompson et al., 2021). ...
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Aim The Irano‐Anatolian biodiversity hotspot is among the least‐known biodiversity hotspots on earth. In this study, we aim to map the richness and genetic divergence of lizards in the biodiversity hotspot and its surrounding areas and identify the most important determinants of the richness and genetic divergence patterns. Location Iran and Turkey (Irano‐Anatolian biodiversity hotspot). Methods Here, we mapped the distribution of 211 lizard species in Iran and Turkey using existing occurrence data and generated the first genetic divergence pattern map of the lizard species in the two countries to identify areas of high species diversity and genetic divergence in the Irano‐Anatolian biodiversity hotspot. We also identified determinants of lizard richness and genetic divergence patterns. Results Results showed that the Zagros Mountains, Central Iranian Plateau and the northern Persian Gulf have the highest lizard richness. The Zagros Mountains, Central Iranian Plateau, the northern Persian Gulf and the regions around the Lut Desert and Jazmourian Plain have the highest total genetic divergence in Iran. Alborz and Kopet Dag mountains and south western parts of Turkey have the highest average genetic divergence. The annual temperature was the most important predictor of lizard richness, and temperature change velocity was the most influential determinant of genetic divergence pattern. Much to our surprise, species diversity and most areas with high genetic divergence are located outside of Irano‐Anatolian biodiversity hotspot. Main conclusions This study showed that lizard richness and genetic divergence patterns are associated with current and past climate. In particular, this study highlights the legacy of past climate changes on lizard genetic divergence distribution patterns. We showed that most of the species‐rich and genetically diverse regions are located outside of the biodiversity hotspot. So conservation efforts that are concentrated inside the biodiversity hotspot may not benefit lizard biodiversity conservation. Thus, future studies and conservation programs on the biodiversity hotspot should also consider its surrounding areas.
... 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. ...
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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. 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. 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.
... A general trend in latitudinal studies of genetic variation is the loss of genetic variability towards the poles (e.g. Adams and Hadly 2012;Miraldo et al. 2016;Smith et al. 2017). In the northern hemisphere, populations of many species become smaller and more fragmented with increasing latitude (e.g. ...
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Genetic variation is often lower at high latitudes, which may compromise the adaptability and hence survival of organisms. Here we show that genetic variability is negatively correlated with northern latitude in European green toads (Bufotes viridis). The result holds true for both putatively neutral microsatellite variation and supposedly adaptive MHC Class IIB variation. In particular, our findings have bearing on the conservation status of this species in Sweden, on the northern limit of its distribution where local populations are small and fragmented. These genetically impoverished populations are closely related to other populations found around the Baltic Sea basin. The low neutral and adaptive variation in these fringe populations compared to population at central ranges confirms a pattern shared across all other amphibians so far studied. In Sweden, the situation of green toads is of concern as the remaining populations may not have the evolutionary potential to cope with present and future environmental challenges.
Article
Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequences from around the globe. Yet, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have required widespread scientific name changes. Taxonomic instability, colloquially “splits, lumps, and shuffles'', presents logistical challenges to large-scale biodiversity research because (1) the same species or sets of populations may be listed under different names in different data sources, or (2) the same name may apply to different sets of populations representing different taxonomic concepts. Consequently, distributional and trait data are often difficult to link directly to primary DNA sequence data without extensive and time-consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize avian taxon names in use in NCBI GenBank, a primary source of genetic data, to a widely used and regularly updated avian taxonomy: eBird/Clements. Of 14,341 avian species/ subspecies names in GenBank, 11,031 directly matched an eBird/Clements; these link to over 6 million nucleotide sequences. For the remaining unmatched avian names in GenBank, we used Avibase’s system of taxonomic concepts, taxonomic descriptions in Cornell’s Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names linked to over 600,000 nucleotide sequences, ~9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under 2 or more GenBank names. Our taxonomic reconciliation is a first step towards rigorous and open-source curation of avian GenBank sequences and is available at GitHub, where it can be updated to correspond to future annual eBird/Clements taxonomic updates.
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Sequencing data—genomics, transcriptomics, epigenomics, proteomics, and metabolomics—have revolutionized biological research, enabling a more detailed study of processes, ranging from subcellular to evolutionary, that drive biological organization. These processes, collectively, are responsible for generating patterns of phenotypic variation and can operate over dramatically different timescales (milliseconds to billions of years). While researchers often study phenotypic variation at specific levels of biological organization to isolate processes operating at that particular scale, the varying types of sequence data, or ‘omics, can also provide complementary inferences to link molecular and phenotypic variation to produce an integrated view of evolutionary biology, ranging from molecular pathways to speciation. We briefly describe how ‘omics has been used across biological levels and then demonstrate the utility of integrating different types of sequencing data across multiple biological levels within the same study to better understand biological phenomena. However, single time point studies cannot evaluate the temporal dynamics of these biological processes. Therefore, we put forward temporal ‘omics as a framework that can better enable researchers to study the temporal dynamics of target processes. Temporal ‘omics is not infallible, as the temporal sampling regime directly impacts inferential ability. Thus, we also discuss the role the temporal sampling regime plays in deriving inferences about the environmental conditions driving biological processes and provide examples that demonstrate the impact of the sampling regime on biological inference. Finally, we forecast the future of temporal ‘omics by highlighting current methodological advancements that will enable temporal ‘omics to be extended across species and timescales. We extend this discussion to using temporal multi-omics to integrate across the biological hierarchy to evaluate and link the temporal dynamics of processes that generate phenotypic variation.
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A large body of research across science and humanities has come to deal with diversity, which, as a scientific concept, has proved immensely relevant in helping researchers understand anything from ecosystems and natural habitats to cities and culture. Here, we develop a first method to quantify and map urban diversity. Our article begins with a concrete example through which we demonstrate how to apply a basic version of our method to create a diversity map for a given urban area. This map is easy to interpret and can be used to accurately locate the most diverse centers of urban activity. We then go on to show how our basic method can be expanded to quantify many different types of urban diversity, and how it can be used to create regional and global diversity maps. Such diversity maps are relevant in both studying diversity and modeling the dynamics of diversification in urban environments. We conclude the article by making a bridge to other scientific disciplines, and by proposing six key steps that may serve as a foundation for a general framework for the evaluation and mapping of diversity across all fields of science.
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Patterns of genetic diversity within species contain information about the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta‐analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time‐consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready‐to‐analyze sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR: large meta‐analyses of thousands of species that can address classic questions in evolutionary biology and ecology, and student‐ or citizen‐ science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web‐based tools that enable these data to be recycled and reanalyzed and increase accessibility to big data for research labs and classroom instructors with limited computational expertise and resources.
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The ongoing biodiversity crisis is causing rapid species losses faster than taxonomists' capacity to describe new species. Integrative taxonomic approaches need robust taxonomic baseline data to correctly describe and conserve global species diversity, in which genetic data are one of the pillars. However, despite their broad use throughout the biological sciences, the quality of genetic data within public repositories is still not guaranteed. Here, we curated GenBank Cytochrome‐b records of Aves, a well‐known taxon undergoing continuous taxonomic changes, and provide a curated database to aid taxonomic and conservation efforts. After curation of 54 114 records, the database represents 50 280 sequences from 6867 species (63% of current bird biodiversity), with a per‐genus median of two species (50% interquartile ranges of 1–4) and three sequences (1–9). Overall, 4469 bird species have ≥ 2 sequences representing 91.7% and 97.5% of currently known families and orders, respectively. We flagged 1336 erroneous records (2.5% of Aves Cytochrome‐b records) in need of taxonomic curation (71%) or removal, 45% of which lack any voucher information preventing a proper taxonomic assignation. Compared to Amphibia, a group for which a similar analysis was recently published, Aves records have a five‐fold higher prevalence of errors caused by contamination, sequencing errors or diverging mutation pattern. We provide a species‐level taxonomic update for 839 GenBank records, including changes at the genus (76), family (21), and order (16) levels. Scientific conclusions from the manuscripts that ever used those data might be compromised. A further concern is the current availability of GenBank records previously identified as erroneous in published manuscripts, demonstrating the need for improved communication between NCBI and the community. We call for caution when utilizing GenBank records without curation of retrieved data, despite new improvements.
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Taxon-specific characteristics and extrinsic climatic and geological forces may both shape population differentiation and speciation. In geographically and taxonomically focused investigations, differentiation may occur synchronously as species respond to the same external conditions. Conversely, when evolution is investigated in taxa with largely varying traits, population differentiation and speciation is complex and shaped by interactions of Earth’s template and species-specific traits. As such, it is important to characterize evolutionary histories broadly across the tree of life, especially in geographic regions that are exceptionally diverse and under pressures from human activities such as in biodiversity hotspots. Here, using whole-genome sequencing data, we characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six species, populations on either side of the GRV exhibited significant but varying levels of genetic differentiation. Species’ dispersal ability was negatively correlated with levels of population differentiation. Isolation with migration models indicated varied patterns of population differentiation and connectivity among populations of the focal species. We found that demographic histories—estimated for each individual—varied by both species and population but were consistent between individuals of the same species and sampling region. We found that genomic diversity varied by half an order of magnitude across species, and that this variation could largely be explained by the harmonic mean of effective population size over the past 200,000 years. Overall, we found that even in highly dispersive species like birds, the GRV acts as a substantial biogeographic barrier.
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1. Microbes play an essential role in soil biogeochemical processes and maintenance of soil nutrients, but not all microbial taxa contribute equally, and their functions in soil nutrient cycling and microbial network stability are unclear in arid fertigation agricultural ecosystems. 2. In this study, a 4‐year field experiment was conducted in an irrigation district in China using three levels of irrigation [high (400 mm), medium (300 mm), and low (200 mm)] and two levels of fertilization [high (600 kg/ha P2O5 + 300 kg/ha urea) and low (300 kg/ha P2O5 + 150 kg/ha urea)] to reveal the ecological roles of core and noncore taxa in maintaining soil nutrient cycling and their associations with microbial network stability. 3. Our results showed that combining medium irrigation with low fertilization resulted in higher levels of soil organic C, inorganic N, available P, multinutrient cycling, and noncore bacterial diversity compared with the other treatments. Soils supporting a higher diversity of noncore bacterial taxa had a high soil multinutrient cycling index, while soils harbouring highly diverse core taxa exhibited a more stable bacterial network. The soil multinutrient cycling index was also significantly positively related to the subnetwork modularity of noncore taxa. Moreover, noncore taxa could serve as diverse pools that turn into core taxa in response to changes in the external environment. Acinetobacter, Flavobacterium, Gemmatimonas, and Salinimicrobium, which belong to the noncore taxa, were involved in soil C and N cycling in the arid agricultural ecosystem. 4. Synthesis and applications Our results suggest that soil microbiota contribute differently to ecosystem functions. Changes in soil nutrient cycling were more closely related to variations in noncore taxa, while bacterial network stability was more associated with core taxa. Our study emphasized the role of noncore microbiota, which has been neglected in previous studies. Furthermore, our findings suggested that combining medium irrigation with low fertilization is effective for enhancing soil nutrients and bacterial diversity, providing guidance for managing arid agricultural ecosystems.
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The genetic diversity of populations plays a crucial role in ensuring species and ecosystem resilience to threats such as climate change and habitat degradation. Despite this recognized importance of genetic diversity, and its relevance to the Convention on Biological Diversity and the United Nations Sustainable Development Goals, it remains difficult to observe and synthesize genetic data at a national scale. The “Ira Moana—Genes of the Sea—Project” ( https://sites.massey.ac.nz/iramoana/ ) has worked to improve stewardship of genetic data for Aotearoa New Zealand’s (NZ) marine organisms to facilitate marine genetic biodiversity observation, research, and conservation. The Ira Moana Project has established interoperable data infrastructures and tools that help researchers follow international best-practice (including the FAIR Principles for Data Stewardship and CARE Principles for Indigenous Data Governance) and contribute to a national genetic data resource. Where possible, the Project has employed existing infrastructures (such as the Genomic Observatories Metadatabase, GEOME) to allow interoperability with similar research activities, but has also innovated to accommodate the national interests of NZ. The Ira Moana Project has an inclusive model, and through presentations, workshops, and datathons, it has provided training, education, and opportunities for collaboration among NZ researchers. Here, we outline the motivations for the Ira Moana Project, describe the Project activities and outcomes, and plans for future development. As a timely response to national and international pressures on genetic biodiversity research, it is hoped that the Ira Moana Project will facilitate NZ researchers, communities, and conservation practitioners to navigate this crucial period, and provide tangible solutions nationally and globally.
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Should wilderness be understood as primarily untrammeled or primarily natural? In this paper, we examine the conceptual and philosophical roots of untrammeled and natural in the context of the 1964 Wilderness Act and show how in some situations tension can arise between them, leading to a stewardship dilemma and subsequent debate over the future conservation role of wilderness. After showing that this debate is ultimately rooted in a false dichotomy, we offer a conceptual framework that presents managers with the tools necessary to shepherd the wilderness idea through the changing environmental realities of the Anthropocene, and continue to allow wilderness to be both a cornerstone and touchstone for conservation in the 21st century.
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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.
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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
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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.
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