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An Anthropocene map of genetic diversity
Abstract
The Anthropocene is witnessing a loss of biodiversity, with well-documented declines in the diversity of ecosystems and species. For intraspecific genetic diversity, however, we lack even basic knowledge on its global distribution. We georeferenced 92,801 mitochondrial sequences for >4500 species of terrestrial mammals and amphibians, and found that genetic diversity is 27% higher in the tropics than in nontropical regions. Overall, habitats that are more affected by humans hold less genetic diversity than wilder regions, although results for mammals are sensitive to choice of genetic locus. Our study associates geographic coordinates with publicly available genetic sequences at a massive scale, yielding an opportunity to investigate both the drivers of this component of biodiversity and the genetic consequences of the anthropogenic modification of nature.
... Therefore, mapping the spatial patterns of genetic diversity, and identifying hotspots of genetic diversity for multiple taxa (Hewitt, 2004(Hewitt, , 2011Hampe and Petit, 2005) would provide valuable information to identify priority areas promoting the long-term conservation of biodiversity in an evolutionary perspective (i.e., adding a temporal and dynamic dimension to the area-based conservation approach). The last two decades have seen a substantial increase in the availability of genetic data, and a few attempts to map the spatial patterns of genetic diversity have been made (e.g., Miraldo et al., 2016;Blanchet et al., 2017;Carvalho et al., 2017;Kling et al., 2019;Mazel et al., 2018;Dapporto et al., 2022;French et al., 2023;Schmidt et al., 2024). Yet, these studies identified patterns of genetic diversity over global or regional scales, relying on genetic information mainly coming from mitochondrial genes, which is by far the most available genetic marker (Schmidt and Garroway, 2021). ...
... Nucleotide diversity (π) is the average number of nucleotide differences per site between two randomly chosen sequences from the same population (Tajima, 1993). Nucleotide diversity has been chosen because it is less sensitive to the variation of sequence length among the different studies, and because it was widely used to map mitochondrial genetic diversity (Miraldo et al., 2016). If available, the estimators were directly imported from the study; if not, allelic richness was estimated using the diveRsity R package (Keenan et al., 2013), while nucleotide diversity was estimated using DNASP 5.10 (Librado and Rozas, 2009). ...
... In fact, although motivated by the wider availability of mitochondrial data in public database, using maps of genetic diversity based on mitochondrial data (see e.g. Miraldo et al., 2016;Dapporto et al., 2022;French et al., 2023) could lead policymakers to address conservation initiatives on worthless areas and/or populations (Mazel et al., 2018;Schultz et al., 2024), dispersing the efforts and the scanty investments on biodiversity conservation. On this novel perspective, we suggest dismissing the use of mitochondrial genetic data in conservation biology, as it looks unreliable at biological relevant scale, and to promote novel, region-wide assessment of genome-wide patterns of genetic variation. ...
... The use of data science techniques has allowed biodiversity studies to expand their geographic and taxonomic focus to explore broader patterns of evolution, which can be difficult to assess using traditional meta-analysis methods [21]. Macrogenetics, a relatively new field that merges biodiversity data with genetic data [22,23], has been used to explore how human impacts influence levels of intraspecific genetic diversity [24,25], to study past and future climate refugia [26,27], and to quantify latitudinal biodiversity gradients [28][29][30][31]. Macrogenetic methods, particularly in combination with predictive modeling, can be used to inform conservation policies by identifying species, taxonomic groups, or geographic areas in need of further investigation [32,33]. ...
... In addition, while mitochondrial data can be suitable for preliminary assessments of species diversity [77], these assessments should be considered in tandem with other species information and relevant data when describing species boundaries. However, with recent advances in technology rapidly increasing the quantity of publicly accessible genetic and geographic datasets, these data offer a cost effective and efficient way to explore large-scale patterns and predictors of intraspecific genetic variation (e.g., [24,29,78]). Our results suggest that there are undescribed genetic lineages that may warrant further investigation distributed within Caudata. ...
... This is particularly important when dealing with clades suspected of harboring high levels of cryptic diversity. For example, Miraldo et al. [24] generated the first global map of genetic diversity within species of mammals and amphibians. One of their main conclusions was that amphibians displayed lower levels of genetic variation in areas with higher human impact. ...
The geographic distribution of genetic variation within a species reveals information about its evolutionary history, including responses to historical climate change and dispersal ability across various habitat types. We combine genetic data from salamander species with geographic, climatic, and life history data collected from open-source online repositories to develop a machine learning model designed to identify the traits that are most predictive of unrecognized genetic lineages. We find evidence of hidden diversity distributed throughout the clade Caudata that is largely the result of variation in climatic variables. We highlight some of the difficulties in using machine-learning models on open-source data that are often messy and potentially taxonomically and geographically biased.
... The study of broad-scale geographic patterns of genetic variation, taxonomic and phylogenetic diversity, and speciation rate have provided insights into eco-evolutionary processes forming latitudinal diversity gradients (LDG) in many taxa (Manel et al., 2020;Miraldo et al., 2016;Rabosky et al., 2018;Theodoridis et al., 2020). LDGs have been extensively studied and shown to be consistent across most localities, scales, habitats and taxonomic groups, yet the evolutionary and ecological causes of this pattern are still poorly understood (Mittelbach et al., 2007). ...
... We used a publicly available genetic dataset of the cytochrome C oxidase subunit I (COI) gene. Mitochondrial loci have long been used for exploring correlations between species and genetic diversity in global-scale macrogenetic studies (Leigh et al., 2021;Manel et al., 2020;Miraldo et al., 2016;Theodoridis et al., 2020), and despite the limitations associated with using a single gene, this is currently the best way to conduct large-scale biodiversity studies of largely unexplored taxonomic groups. ...
... Considering that the intensity of sampling, both in terms of the number of molecular clusters per cell and the number of sequences in each molecular cluster, varied substantially among cells, we also evaluated the impact of this variation. In that sense, we ran sensitivity tests following Miraldo et al. (2016) ( Figure S3). Molecular clusters with 10 or more sequences and only cells with three or more molecular clusters were retained for further analysis. ...
Knowledge of global patterns of genetic diversity is essential for biodiversity conservation as this parameter describes the ability of a species to respond to environmental changes. Ichneumonoids parasitoid wasps are among the few taxa showing an anomalous latitudinal diversity gradient.
Using the largest georeferenced molecular dataset for this group, we used a macrogenetics approach to examine latitudinal patterns and predictors of intraspecific genetic diversity. We calculated the mean nucleotide diversity of mitochondrial DNA barcode sequences at three geographic levels: grid cells, latitudinal bands and climatic zones.
Nucleotide diversity values were consistently higher at northern temperate latitudes, peaking at 50°. We found a positive but weak relationship between intraspecific diversity and the latitude, between intra‐ and interspecific diversity, and a positive effect of the temperature range.
Examining the spatial relationship between different levels of biodiversity and its drivers is particularly relevant considering climate change and its impact on species distribution. Yet, in insects, it has been challenging to integrate ecological, evolutionary and geographical components when analysing the processes leading to species richness gradients.
... Latitudinal trends in different aspects of biodiversity have been found or proposed for a variety of organisms (11,20,(25)(26)(27)(28). The "southern richness-northern purity" hypothesis states that, in temperate areas of the Northern Hemisphere that were partly covered by ice sheets during the glacial maxima, the IGV is inversely correlated with latitude. ...
... Because of these phenomena, there is contrasting evidence about the correlation between the patterns exposed by nuclear DNA and mtDNA (6,59). Nevertheless, macrogenetic studies based on mtDNA revealed large-scale patterns in IGV (11,26,60,61), and, up to now, there is no alternative marker to COI with sufficient data available to carry out comparative analyses at broad taxonomic and spatial scope (11,25,59,60). We hope that the availability of sequencing data obtained from next-generation sequencing on a large number of species will allow, in the near future, for the provision of more refined data to replicate similar studies based on multiple nuclear markers (6). ...
... The latitudinal trend of IGV was assessed using a band-wise method following Miraldo et al. (26) and Dincă et al. (30) (fig. S1C). ...
The interplay between geographic barriers and climatic oscillations over the past 2.6 million years structured genetic variation at the continental scale. The genetic legacy of the Quaternary ice ages (GLQ) hypothesis outlines this phenomenon for Europe, but a comprehensive data-driven assessment is lacking. Using innovative genetic landscape methods, we model the GLQ in the West Palearctic based on 31,653 Cytochrome c oxidase subunit 1 (COI) sequences from 494 butterfly species and three functional traits. Seven distinct bioregions with varying levels of genetic endemicity emerge, revealing a latitudinal gradient in variation that confirms the “southern richness, northern purity” hypothesis. Through shift from case studies to a comparative approach, we objectively identify the main glacial refugia, colonization routes, and barriers to dispersal. Our findings offer a quantitative model of the GLQ across Europe, North Africa, and neighboring Asia, with broader applicability to other taxa and potentially scalable to encompass life on Earth.
... Similarly, elucidating the processes that generate genetic diversity helps create a common ground for evolutionary biology and community ecology around topics of diversity and patterns of speciation. Despite this importance, the general patterns of genetic diversity across species remain poorly understood at global scales (De Kort et al., 2021;Manel et al., 2020;Miraldo et al., 2016). ...
... Much of our knowledge on intraspecific genetic diversity, including local and regional estimates in various taxa, has only been collected in recent decades. Macrogenetic studies have compiled these data to better understand global distributions of genetic diversity (Figuerola-Ferrando et al., 2023;Miraldo et al., 2016). Large knowledge gaps still exist, however, as the strength and direction of latitudinal gradients in genetic diversity appear to vary across taxa and ecological systems (De Kort et al., 2021). ...
... While previous studies have also found latitudinal gradients in mitochondrial genetic diversity, the methods frequently employed by these studies have come under recent criticism (Gratton et al., 2017;Paz-Vinas et al., 2021). Most earlier macrogenetic studies, especially those investigating patterns in mitochondrial diversity, collected genetic data from shared public resources (e.g., GenBank), pooled sequences into predefined grid cells or latitudinal bands, calculated diversity at the species level, and then averaged species estimates together (Manel et al., 2020;Miraldo et al., 2016;Theodoridis et al., 2020). While informative, studies of this design often struggle to TA B L E 1 Mitochondrial DNA (π and H d ) model results for latitude and longitude. ...
Genetic diversity is a fundamental component of biodiversity. Examination of global patterns of genetic diversity can help highlight mechanisms underlying species diversity, though a recurring challenge has been that patterns may vary by molecular marker. Here, we compiled 6862 observations of genetic diversity from 492 species of marine fish and tested among hypotheses for diversity gradients: the founder effect hypothesis, the kinetic energy hypothesis, and the productivity‐diversity hypothesis. We fit generalized linear mixed effect models (GLMMs) and explored the extent to which various macroecological drivers (latitude, longitude, temperature (SST), and chlorophyll‐a concentration) explained variation in genetic diversity. We found that mitochondrial genetic diversity followed geographic gradients similar to those of species diversity, being highest near the Equator, particularly in the Coral Triangle, while nuclear genetic diversity did not follow clear geographic patterns. Despite these differences, all genetic diversity metrics were correlated with chlorophyll‐a concentration, while mitochondrial diversity was also positively associated with SST. Our results provide support for the kinetic energy hypothesis, which predicts that elevated mutation rates at higher temperatures increase mitochondrial but not necessarily nuclear diversity, and the productivity‐diversity hypothesis, which posits that resource‐rich regions support larger populations with greater genetic diversity. Overall, these findings reveal how environmental variables can influence mutation rates and genetic drift in the ocean, caution against using mitochondrial macrogenetic patterns as proxies for whole‐genome diversity, and aid in defining global gradients of genetic diversity.
... In fact, this approach offers significant advantages over traditional morphology-based identification methods by being rapid, accurate and standardized. In addition, molecular analyses can provide a unique advantage by revealing patterns of regional genetic divergence, allowing for biodiversity comparisons at broader geographic and taxonomic scales (33)(34)(35)(36). In this context, nuclear DNA is generally preferred when the goal is to provide a comprehensive representation of Intraspecific Genetic Variation (IGV), especially considering neutral markers. ...
... The accelerated lineage sorting rate of COI can result in fact in oversimplified evolutionary relationships, potentially overlooking crucial details in population histories (38). However, the gap between maximum intraspecific and minimum interspecific distances has been employed for species delimitation in various animal groups, including insects (33)(34)(35). This method has proven effective in resolving cryptic species complexes, uncovering genetic divergence patterns and contributing to the exploration of biodiversity in phylogeography studies (39). ...
... Nevertheless, insufficient or undisclosed metadata poses a significant challenge, leading to the exclusion of a substantial portion of genetic datasets. Previous studies have reported that 40-73% of potentially suitable data are ultimately excluded due to inadequate metadata (31,33,34,47). The Genomic Standards Consortium has established the Minimum Information about any Sequence (MIxS) standards, which outline the essential metadata requirements for genetic sequence data (48). ...
Insect decline has become a growing concern in recent years, with studies showing alarming declines in populations of several taxa. Our knowledge about genetic spatial patterns and evolutionary history of insects still exhibits significant gaps hindering our ability to effectively conserve and manage insect populations and species. Genetic data may provide valuable insights into the diversity and the evolutionary relationships of insects’ species and populations. Public repositories, such as GenBank and BOLD, containing vast archives of genetic data with associated metadata, offer an irreplaceable resource for researchers contributing to our understanding of species diversity, population structure and evolutionary relationships. However, there are some issues in using these data, as they are often scattered and may lack accuracy due to inconsistent sampling protocols and incomplete information. In this paper we describe a curated georeferenced database of genetic data collected in GenBank and BOLD, for insects listed in the International Union for Conservation of Nature (IUCN) Italian Red Lists (dragonflies, bees, saproxylic beetles and butterflies). After querying these repositories, we performed quality control and data standardization steps. We created a dataset containing approximately 33 000 mitochondrial sequences and associated metadata about taxonomy, collection localities, geographic coordinates and IUCN Red List status for 1466 species across the four insect lists. We describe the current state of geographical metadata in queried repositories for species listed under different conservation status in the Italian Red Lists to quantify data gaps posing barriers to prioritization of conservation actions. Our curated dataset is available for data repurposing and analysis, enabling researchers to conduct comparative studies. We emphasize the importance of filling knowledge gaps in insect diversity and distribution and highlight the potential of this dataset for promoting other research fields like phylogeography, macrogenetics and conservation strategies. Our database can be downloaded through the Zenodo repository in SQL format.
Database URL: https://zenodo.org/records/8375181
... In both native and invasive species, geographical and environmental changes contribute to genetic divergence in spite of some differences in the life history, reproductive mode and genome characteristics (Bock et al. 2015, Mounger et al. 2021. Therefore, similar geographical patterns of genetic diversity may eventually emerge between native and invasive species (Avise et al. 1987, Avise 1992, Miraldo et al. 2016. ...
... Latitude is one of the most predictive factors of biodiversity gradients (Gaston 2000). A variety of studies ranging from the tropics to the poles have demonstrated species diversity and total genetic diversity across species at both neutral and functional loci tend to decrease with increasing latitude (Adams and Hadly 2013, Miraldo et al. 2016. However, intraspecific genetic diversity tends to increase with latitude (Lawrence and Fraser 2020), implying a negative correlation between species-specific diversity and associated species diversity along latitudinal gradients. ...
... Lower latitudes have been reported to have higher species diversity (Schluter andPennell 2017, Guo et al. 2021) and total genetic diversity across animal species (Adams and Hadly 2013, Miraldo et al. 2016) than higher latitudes. However, this latitudinal gradient of biodiversity may result from shorter generation times, higher mutation rates and higher metabolic rates under higher temperature in animals living at the lower latitudes (Rohde 1992, Allen et al. 2006, Lawrence and Fraser 2020, while plants may have different characteristics. ...
Within‐species genetic diversity is shaped by multiple evolutionary forces within the confines of geography, and has cascading effects on the biodiversity of other taxa and levels. Invasive species are often initially limited in genetic diversity but still respond rapidly to their new range, possibly through ‘pre‐adapted' genotypes or multiple sources of genetic diversity, but little is known about how their genetic structure differs from that of native species and how it alters the genetic‐species diversity relationship. Here, we selected a widespread native species Phragmites australis and its co‐occurring invasive competitor Spartina alterniflora as our model plant species. We investigated the genetic structure of P. australis using two chloroplast fragments and ten nuclear microsatellites in 13 populations along the Chinese coastal wetlands. We discovered a distinct geographical differentiation, showing that the northern and southern populations harbored unique genotypes. We also found a significant increase in genetic diversity (allelic richness and expected heterozygosity) from south to north. Combined with previous studies of S. alterniflora , the Mantel tests revealed a significant correlation of genetic distances between P. australis and S. alterniflora even when controlling for geographic distance, suggesting that the invasive species S. alterniflora might exhibit a phylogeographic pattern similar to that of the native species to some extent. Furthermore, our results suggest that the S. alterniflora invasion has altered the relationship between the genetic diversity of the dominant native plant and the associated species richness of soil nematodes. The reason for the alteration of genetic‐species diversity relationship might be that the biological invasion weakens the environmental impact on both levels of biodiversity. Our findings contribute to understanding the latitudinal patterns of intraspecific genetic diversity in widespread species. This work on the genetic diversity analysis of native species also provides significant implications for the invasion stage and ecological consequences of biological invasions.
... Compared to the ecological dimensions of biodiversity loss, our understanding of genetic diversity loss is less developed [12,24]. This is unfortunate because genetic variation is the raw material enabling species to robustly adapt to a changing world [24]. ...
... Compared to the ecological dimensions of biodiversity loss, our understanding of genetic diversity loss is less developed [12,24]. This is unfortunate because genetic variation is the raw material enabling species to robustly adapt to a changing world [24]. Despite the growing recognition of this dimension of biodiversity, predictions in evolutionary science face many challenges similar to ecology [25][26][27]. ...
Ecological and evolutionary predictions are being increasingly employed to inform decision-makers confronted with intensifying pressures on biodiversity. For these efforts to effectively guide conservation actions, knowing the limit of predictability is pivotal. In this study, we provide realistic expectations for the enterprise of predicting changes in ecological and evolutionary observations through time. We begin with an intuitive explanation of predictability (the extent to which predictions are possible) employing an easy-to-use metric, predictive power PP(t). To illustrate the challenge of forecasting, we then show that among insects, birds, fishes and mammals, (i) 50% of the populations are predictable at most 1 year in advance and (ii) the median 1-year-ahead predictive power corresponds to a prediction R ² of only 20%. Predictability is not an immutable property of ecological systems. For example, different harvesting strategies can impact the predictability of exploited populations to varying degrees. Moreover, incorporating explanatory variables, accounting for time trends and considering multivariate time series can enhance predictability. To effectively address the challenge of biodiversity loss, researchers and practitioners must be aware of the information within the available data that can be used for prediction and explore efficient ways to leverage this knowledge for environmental stewardship.
... Anthropogenic disturbance also affects host genetics 28 . Habitat fragmentation, for example, increases inbreeding and decreases gene flow, leading to reduced genetic variation within fragmented populations 29,30 . ...
... Fragmentation and changes to pathogen pressure are expected to shape host genetics 28,64 . We found high genome-wide genetic diversity (SNPs) in spiny rats from continuous forests compared to lower diversity on forested islands and forest fragments embedded in an agricultural matrix. ...
Anthropogenic disturbance may increase the emergence of zoonoses. Especially generalists that cope with disturbance and live in close contact with humans and livestock may become reservoirs of zoonotic pathogens. Yet, whether anthropogenic disturbance modifies host-pathogen co-evolutionary relationships in generalists is unknown. We assessed pathogen diversity, neutral genome-wide diversity (SNPs) and adaptive MHC class II diversity in a rodent generalist inhabiting three lowland rainforest landscapes with varying anthropogenic disturbance, and determined which MHC alleles co-occurred more frequently with 13 gastrointestinal nematodes, blood trypanosomes, and four viruses. Pathogen-specific selection pressures varied between landscapes. Genome-wide diversity declined with the degree of disturbance, while MHC diversity was only reduced in the most disturbed landscape. Furthermore, pristine forest landscapes had more functional important MHC–pathogen associations when compared to disturbed forests. We show co-evolutionary links between host and pathogens impoverished in human-disturbed landscapes. This underscores that parasite-mediated selection might change even in generalist species following human disturbance which in turn may facilitate host switching and the emergence of zoonoses.
... Ochoa-Ochoa et al., 2020). Global genetic diversity patterns also appear to follow a latitudinal gradient in amphibians (Miraldo et al., 2016), but less is known about the predictors of intraspecific genetic variation. In a study of Nearctic amphibian species, the most important predictors of genetic diversity were taxonomic family, number of sequences, and for salamander species (N = 98), those at more northern latitudes had lower genetic diversity (Barrow et al., 2021). ...
... Although latitude was not a significant predictor of π, analysing mean latitude with π and geographical range size revealed that amphibians near the equator have larger ranges, and diversity increases near the equator and slowly decreases towards higher latitudes (Appendix S4). This pattern of genetic diversity forms a plateau around the equator, a pattern noted by Pereira (2016) in his perspective about a global study mapping amphibian genetic diversity by Miraldo et al. (2016). Higher environmental and climatic heterogeneity may lead to diversification dynamics with higher speciation and lower extinction rates supporting rapid evolution in the Neotropics (Brown, 2014). ...
Aim
Intraspecific genetic variation is key for adaptation and survival in changing environments and is known to be influenced by many factors, including population size, dispersal and life‐history traits. We investigated genetic variation within Neotropical amphibian species to provide insights into how natural history traits, phylogenetic relatedness, climatic and geographic characteristics can explain intraspecific genetic diversity.
Location
Neotropics.
Taxon
Amphibians.
Methods
We assembled data sets using open‐access databases for natural history traits, genetic sequences, phylogenetic trees, climatic and geographic data. For each species, we calculated overall nucleotide diversity ( π ) and tested for isolation by distance (IBD) and isolation by environment (IBE). We then identified predictors of π , IBD and IBE using random forest (RF) regression or RF classification. We also fitted phylogenetic generalized linear mixed models (PGLMMs) to predict π , IBD and IBE.
Results
We compiled 4052 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2477 sequences from 176 species that were not linked to occurrence data. RF regressions and PGLMMs were congruent in identifying range size and precipitation ( σ ) as the most important predictors of π , influencing it positively. RF classification and PGLMMs identified minimum elevation as an important predictor of IBD; most species without IBD tended to occur at higher elevations. Maximum latitude and precipitation ( σ ) were the best predictors of IBE, and most species without IBE occur at lower latitudes and in areas with more variable precipitation.
Main Conclusions
This study identified predictors of genetic variation in Neotropical amphibians using both machine learning and phylogenetic methods. This approach was valuable to determine which predictors were congruent between methods. We found that species with small ranges or living in zones with less variable precipitation tended to have low genetic diversity. We also showed that Western Mesoamerica, Andes and Atlantic Forest biogeographic units harbour high diversity across many species that should be prioritized for protection. These results could play a key role in the development of conservation strategies for Neotropical amphibians.
... Compared to the ecological dimensions of biodiversity loss, our understanding of the global distribution and the extent of human-induced evolutionary changes and genetic diversity loss is less developed [12,25]. This is unfortunate because genetic variation is the raw material enabling species to robustly adapt to a changing world [25]. ...
... Compared to the ecological dimensions of biodiversity loss, our understanding of the global distribution and the extent of human-induced evolutionary changes and genetic diversity loss is less developed [12,25]. This is unfortunate because genetic variation is the raw material enabling species to robustly adapt to a changing world [25]. Despite the growing recognition of this dimension of biodiversity, predictions in evolutionary science and applications face many challenges similar to ecologically oriented disciplines [26][27][28]. ...
Ecological and evolutionary predictions are being increasingly employed to inform decision-makers confronted with intensifying pressures menacing life on Earth. For these efforts to effectively guide conservation actions, knowing the limit of predictability is pivotal. In this study, we provide realistic expectations about the enterprise of predicting changes in ecological and evolutionary observations through time. We begin with an intuitive explanation of predictability (that is, the extent to which predictions are possible) employing an easy-to-use metric, predictive power PP(t). To illustrate the challenge of forecasting, we then show that among insects, birds, fishes, and mammals (i) 50% of the populations are predictable at most one year in advance, and (ii) the median one-year-ahead predictive power corresponds to a sobering prediction R^2 of approximately 20%. Nonetheless, predictability is not an immutable property of ecological systems. For example, different harvesting strategies can impact the predictability of exploited populations to varying degrees. Moreover, considering multivariate time series, incorporating explanatory variables or accounting for time trends (environmental forcing) can enhance predictability. To effectively address the urgent challenge of biodiversity loss, researchers and practitioners must be aware of the predictive information within the available data and explore efficient ways to leverage this information for environmental stewardship.
... Assessments of the genetic diversity of wild species have become increasingly comprehensive (Rhie et al., 2021). While assessments of the risk of loss and geographic distribution of genetic diversity are in their infancy (Miraldo et al., 2016), increasing attention is now being paid to practical monitoring of genetic diversity (Hoban et al., 2021). Genetic diversity between species, known as phylogenetic diversity, is also important, and more and more evidence from both fossils and molecular studies means that it is increasingly possible to establish dates of species divergence to construct a time tree of life (Hedges & Kumar, 2009). ...
"This report comprises two parts. Part I, the bulk of the report, assesses the relationships between nature conservation and agriculture in our globalised world, drawing from data, publications, and expertise from IUCN and beyond. Chapter 1 provides definitions and framing of ‘agriculture’, ‘nature’, and associated terms. Chapter 2 uses both synthesis of the evidence and empirical analysis to explore how agriculture affects nature. Chapter 3, conversely, explores the impacts that nature, mediated by ecosystem services and disservices, has on agriculture. Drawing from these, Chapter 4 harnesses integrated assessment modelling to examine the prospects for simultaneous achievement of global goals for both agriculture and conservation. Chapter 5 then examines a range of realistic policy scenarios currently under discussion in the agriculture and conservation sectors and beyond. Chapter 6 concludes with key messages emerging from the report. Finally, Part II documents four key indicators of nature and conservation, drawing in part from data based on IUCN standards for countries across the world."
... Despite the importance of the within-species genetic element, few data sets are available to assess it (Figure 3). Metrics of genetic diversity within wild mammal and amphibian species (47) complement research on metrics of genetic diversity within domesticated species by the Food and Agriculture Organisation of the United Nations (48). In the GBF monitoring framework, the proportion of populations within each species with an effective population size of more than 500 individuals has been adopted as a headline indicator. ...
Biodiversity metrics are increasingly in demand for informing government, business, and civil society decisions. However, it is not always clear to end users how these metrics differ or for what purpose they are best suited. We seek to answer these questions using a database of 573 biodiversity-related metrics, indicators, indices, and layers, which address aspects of genetic diversity, species, and ecosystems. We provide examples of indicators and their uses within the state–pressure–response–benefits framework that is widely used in conservation science. Considering complementarity across this framework, we recommend a small number of metrics considered most pertinent for use in decision-making by governments and businesses. We conclude by highlighting five future directions: increasing the importance of national metrics, ensuring wider uptake of business metrics, agreeing on a minimum set of metrics for government and business use, automating metric calculation through use of technology, and generating sustainable funding for metric production.
... Historical climate disturbances and frequent human activity have caused many species that were once widespread with continuous distributions to become small, fragmented populations [1]. High levels of inbreeding continually occur in these populations, leading to the accumulation of deleterious mutations and low species adaptability, ultimately increasing the risk of extinction [2,3]. ...
Background
Advanced whole-genome sequencing techniques enable covering nearly all genome nucleotide variations and thus can provide deep insights into protecting endangered species. However, the use of genomic data to make conservation strategies is still rare, particularly for endangered plants. Here we performed comprehensive conservation genomic analysis for Malania oleifera, an endangered tree species with a high amount of nervonic acid. We used whole-genome resequencing data of 165 samples, covering 16 populations across the entire distribution range, to investigate the formation reasons of its extremely small population sizes and to evaluate the possible genomic offsets and changes of ecology niche suitability under future climate change.
Results
Although M. oleifera maintains relatively high genetic diversity among endangered woody plants (θπ = 3.87 × 10−3), high levels of inbreeding have been observed, which have reduced genetic diversity in 3 populations (JM, NP, and BM2) and caused the accumulation of deleterious mutations. Repeated bottleneck events, recent inbreeding (∼490 years ago), and anthropogenic disturbance to wild habitats have aggravated the fragmentation of M. oleifera and made it endangered. Due to the significant effect of higher average annual temperature, populations distributed in low altitude exhibit a greater genomic offset. Furthermore, ecological niche modeling shows the suitable habitats for M. oleifera will decrease by 71.15% and 98.79% in 2100 under scenarios SSP126 and SSP585, respectively.
Conclusions
The basic realizations concerning the threats to M. oleifera provide scientific foundation for defining management and adaptive units, as well as prioritizing populations for genetic rescue. Meanwhile, we highlight the importance of integrating genomic offset and ecological niche modeling to make targeted conservation actions under future climate change. Overall, our study provides a paradigm for genomics-directed conservation.
... Rapid environmental change poses a significant concern for the persistence of wildlife populations because of the loss of genetic diversity and adaptive potential (Pauls et al. 2013, Miraldo et al. 2016, Leigh et al. 2019. Levels of genetic variation differ among populations and species and can be influenced by many factors, including historical events, geographic features, and life history and ecological traits (Avise 2000, Leffler et al. 2012, Ellegren and Galtier 2016. ...
In nature, small populations are often of concern because of limited genetic diversity, which underlies adaptive potential in the face of environmental change. Assessing patterns of genetic variation within co-distributed species sampled across varied landscapes can therefore illuminate their capacity to persist over time. We sequenced new genome-wide sequence data (double-digest restriction site-associated DNA sequencing) for four frog species (Anaxyrus terrestris, Hyla cinerea, Hyla squirella, and Rana sphenocephala) sampled from two barrier islands and the adjacent mainland of northern Florida. We calculated genomic diversity metrics and analysed spatial patterns of genomic variation for each species. We found higher genomic diversity within mainland individuals compared to island individuals for all species, suggesting a consistent effect of small island area on diversity across species. Three species (all but A. terrestris) showed significant signatures of isolation by distance, and some clustering analyses indicated separation of island and mainland individuals within species. We identified subtle differences in the strength of these patterns among species, with the strongest genetic differentiation observed in R. sphenocephala. Finally, we found evidence of recent migration between island and mainland populations for all species, which likely explains the limited genetic structure observed and contributes to the persistence of these small populations.
... Retrospective georeferencing is often needed in such situations (for example, refs. 28,45,79), but this often relies on inference (for example, coordinates derived from place names) leaving substantial room for error or lost resolution. We therefore encourage authors to enrich metadata in their old data archives. ...
Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.
... Human activities have impacted all ecosystems on our planet, reducing their biodiversity and, consequently, their ability to maintain ecological functions and provide benefits to society (Haddad et al. 2015;Newbold et al. 2015;Miraldo et al. 2016). The Brazilian seasonally dry tropical forest called Caatinga is one of the most threatened biomes in the country due to the poorly planned use of its resources, especially concerning the removal of native vegetation (Santana and Souto 2006). ...
Umbu (Spondias tuberosa Arruda) is an endemic fruit tree restricted to the Brazilian seasonally dry tropical forest called Caatinga. This study aimed to evaluate the structure and genomic diversity of umbu trees from seven locations in the Caatinga biome, distributed among four Brazilian states. Using genotyping-by-sequencing (GBS), a total of 5,336 SNPs were obtained, of which 250 showed outlier behavior. Therefore, 5,086 neutral SNPs were used for population structure and genetic diversity analyses. Both discriminant analysis of principal components (DAPC) and neighbor-joining cluster analyses classified the accessions into four groups, with a genetic structure observed among groups, disagreeing with our initial hypothesis of low genetic structure between locations. Isolation by distance (r² = 0.974; p = 0.0015) was detected. Moderate to high levels of genetic diversity were found, with the average observed heterozygosity (HO = 0.221) higher than the expected heterozygosity (HE = 0.199) and with negative inbreeding coefficient (FIS) values. Most genetic variation was found within locations, although high diversity between locations (22.1%) was observed. The results obtained are important for understanding the levels and distribution of genetic variation, suggesting that most locations are priorities for conservation actions, contributing with different alleles to the species' gene pool in Brazil.
... ;https://doi.org/10.1101https://doi.org/10. /2024 3 richness (Pianka, 1966;Willig et al., 2003) and more recently in functional diversity (Schumm et al., 2019), genetic diversity (Miraldo et al., 2016), and biotic interactions (Roslin et al., 2017). ...
The writings of naturalists from two centuries past are brimming with accounts of the stark differences in the kinds and numbers of organisms encountered during the day and night and between the tropical and temperate zones. However, only recently have ecologists begun to systematically describe and explain the geographic variation in the diel activities of species on Earth. Examining data from 60 insect communities globally, I find that the partitioning of total species richness across three diel activity periods tracks the latitudinal gradient. In general, the proportions of diurnal and nocturnal species are highest among tropical communities and decline poleward, while cathemeral activity characterises over half of all species in communities at high latitudes. These latitudinal trends in diel partitioning at the community level broadly reflect recently documented patterns in the global distributions of vertebrate species using different activity periods. I outline six hypotheses that may account for a latitudinal gradient in the diel partitioning of species richness.
... Effective area-based protection from destructive human activities is key to halting biodiversity loss, and provides significant climate mitigation and adaption 1,187-189 ; yet, the majority of areas harbouring high levels of biodiversity and carbon globally remain unprotected 190 . Intact ecosystems are of particular importance: despite having higher levels of biodiversity 191,192 , as well as carbon capture and storage capacities compared to degraded equivalents 193 , only a tenth of the 3% of terrestrial ecosystems estimated to remain faunally intact are formally protected 194 . Intact areas urgently require formal protection [195][196][197] ; however, a large proportion of ecosystems altered by humans also need protection. ...
Headlines:
(1) Biodiversity loss and climate change are two of the biggest and most urgent threats facing human society worldwide.
(2) Human activities drive both crises, but the crises also fuel one another.
(3) Although many solutions benefitting biodiversity can significantly
contribute to climate action, and vice versa, the two are often governed by separate policy instruments.
(4) An integrated approach is necessary to prioritise and implement solutions that deliver benefits for climate and nature simultaneously.
(5) Creating a sustainable future where people and the planet can thrive will require large-scale restoration of degraded ecosystems, protection of existing habitats and reduction of demand for natural resources, supported by policy measures that address the primary socioeconomic drivers.
... Human activities have impacted all ecosystems on our planet, reducing their biodiversity and, consequently, their ability to maintain ecological functions and provide bene ts to society (Haddad et al. 2015;Newbold et al. 2015;Miraldo et al. 2016). The Brazilian seasonally dry tropical forest called Caatinga is one of the most threatened biomes in the country due to the poorly planned use of its resources, especially concerning the removal of native vegetation (Santana and Souto 2006). ...
Umbu ( Spondias tuberosa Arruda) is an endemic fruit tree restricted to the Brazilian seasonally dry tropical forest called Caatinga. This study aimed to evaluate the structure and genomic diversity of umbu trees from seven locations in the Caatinga biome, distributed among four Brazilian states. Using genotyping-by-sequencing (GBS), a total of 5,336 SNPs were obtained, of which 250 showed outlier behavior. Therefore, 5,086 neutral SNPs were used for population structure and genetic diversity analyses. Both discriminant analysis of principal components (DAPC) and neighbor-joining cluster analyses classified the accessions into four groups, with a genetic structure observed among groups, disagreeing with our initial hypothesis of low genetic structure between locations. Isolation by distance (r ² = 0.974; p = 0.0015) was detected. Moderate to high levels of genetic diversity were found, with the average observed heterozygosity ( H O = 0.221) higher than the expected heterozygosity ( H E = 0.199) and with negative inbreeding coefficient ( F IS ) values. Most genetic variation was found within locations, although high diversity between locations (22.1%) was observed. The results obtained are important for understanding the levels and distribution of genetic variation, suggesting that most locations are priorities for conservation actions, contributing with different alleles to the species' gene pool in Brazil.
... 2 Genetic diversity encompasses the diverse gene pool represented in a population that enables it to respond to changing environments and pressures. 3,4 Populations with rich genetic diversity commonly have greater evolutionary potential when facing environmental changes and are therefore less prone to extinction than populations with relatively lower genetic diversity. 5,6 Rich genetic diversity is also crucial for maintaining the stability and functional diversity of ecosystems, which connects genetic diversity with ecosystem service functions. ...
Genetic diversity represents the fundamental basis of biological variation within species, and is therefore the ultimate representation of biodiversity. Despite that all forms of diversity being defined by genomic differences, genetic diversity has received relatively less attention compared with species and ecosystem diversity. Here, we review recent literature and conclude that progress in understanding genetic diversity of seed plants, is strongly associated with advances in sequencing technology. We here present case studies to illustrate the application of genetic diversity for tracing crop domestication and delimiting species boundaries. Understanding genetic diversity is particularly critical for the field of conservation biology, and there is a clear shift to population‐level genetic studies to understand rare species. We then document additional factors that potentially influence genetic diversity, including climate change, habitat fragmentation, and species invasion. Finally, we identify current research limitations and propose directions for future studies. We highlight the need to develop broad‐scale genetic diversity knowledge, combined with other aspects of diversity to improve biodiversity conservation outcomes. We conclude that populating global databases with genomic‐scale sequence data for all species is an urgent and achievable goal now.
... Anthropogenic factors are important drivers of the evolutionary history of species and populations (Miraldo et al. 2016;Queirós et al. 2020). Among them landscape changes, such as habitat loss and fragmentation, connectivity impairment and population isolation have led to decrease in species abundance and limited gene flow (Kvie et al. 2019). ...
Wild species living in captivity are subject to loss of genetic diversity, inbreeding depression, and differentiation among populations. Only very few species have been under human care for centuries but have not been selectively bred, have free-ranging movements most of the time, and retain porous barriers to gene flow between wild and captive populations. Such captive populations are expected to retain high levels of genetic diversity and anthropogenic factors should result in a limited genetic differentiation from wild populations. Asian elephants have been trained and used by humans for at least 4000 years as war animals, mounts of kings and draught animals. In Myanmar and Laos, elephants are still being used for hauling timber in the forest while retaining traditional management practices including seasonal release, free mating and movement. However, habitat fragmentation, isolation and reduced gene flows are threatening both semi-captive and wild pools. We genotyped 167 semi-captive elephants from Laos and Myanmar using a panel of 11 microsatellite loci to estimate the genetic diversity and population structure. We found that elephants of both countries presented high levels of genetic diversity and a low degree of inbreeding, if any. This agrees with the expected high level of genetic diversity in semi-captive populations. We found a weak differentiation along a geographical gradient from southern Laos to northern Myanmar but no differentiation between wild-caught and captive-born pools. The potential value for conservation of a large population of semi-captive elephants has been recognized but the conservation community has yet to fully explore the potential role semi-captive elephants could play in maintaining gene flows.
... Our knowledge regarding comprehensive genetic diversity studies remains insufficient. To date, most performed studies focused on terrestrial species [6][7][8][9][10] , with only several performed in the marine realm [11][12][13] . ...
Genetic diversity, a fundamental aspect of biodiversity, greatly influences the ecological and evolutionary characteristics of populations and species. Compiling genetic data is crucial as the initial step in comprehending and applying genetic resources; however, regional collating work is still insufficient, especially in marine ecosystems. Here, by conducting a thorough literature search and quality-control procedures, we provide a dataset of genetic diversity studies on marine species in the China Seas. The final dataset comprised a total of 746 studies (encompassing 840 data sets and 3658 populations) across 343 species from 1998 to 2022. For each data set, information including publication year, publication language, studied species, belonged taxonomic group, applied molecular markers, and sampling strategies (number of populations, total number of individuals, etc.) was collated to analyse the scope, strengths, and omissions of these works. This dataset offers a comprehensive overview of genetic diversity studies in the China Seas, which may help to adjust future research focuses, promote conservation and macrogenetics studies in this region, and also facilitate regional cooperation.
... Such inconsistency may be more pronounced for metrics compared across communities from different taxonomic groups or habitat types [7][8][9]11,12 , given the high variability we found even within approximately the same system, that is, invertebrates sampled from the river bottom following similar methodologies. Community metrics other than those we examined may provide more consistent insight into anthropogenic change, such as observed:expected richness 56 , genetic diversity, functional diversity or trait composition [57][58][59] . However, responses in these types of metrics can be similarly variable across communities 10,18 . ...
Humans impact terrestrial, marine and freshwater ecosystems, yet many broad-scale studies have found no systematic, negative biodiversity changes (for example, decreasing abundance or taxon richness). Here we show that mixed biodiversity responses may arise because community metrics show variable responses to anthropogenic impacts across broad spatial scales. We first quantified temporal trends in anthropogenic impacts for 1,365 riverine invertebrate communities from 23 European countries, based on similarity to least-impacted reference communities. Reference comparisons provide necessary, but often missing, baselines for evaluating whether communities are negatively impacted or have improved (less or more similar, respectively). We then determined whether changing impacts were consistently reflected in metrics of community abundance, taxon richness, evenness and composition. Invertebrate communities improved, that is, became more similar to reference conditions, from 1992 until the 2010s, after which improvements plateaued. Improvements were generally reflected by higher taxon richness, providing evidence that certain community metrics can broadly indicate anthropogenic impacts. However, richness responses were highly variable among sites, and we found no consistent responses in community abundance, evenness or composition. These findings suggest that, without sufficient data and careful metric selection, many common community metrics cannot reliably reflect anthropogenic impacts, helping explain the prevalence of mixed biodiversity trends.
... The resulting urgent need for expanded monitoring of PGD motivates the development of globally implementable indicators of genetic diversity [6][7][8][9] , some of which are included in the recently adopted CBD Kunming-Montreal Global Biodiversity Framework 3,10 . But while ongoing anthropogenic loss of PGD is being documented [11][12][13] , efforts to detect climate change effects on PGD are taxonomically and geographically limited 14,15 and are absent from international biodiversity agreements. Populations in extreme climatic conditions, such as those near trailing climatic niche margins, are particularly relevant to species' potential for adaptation to a changing climate 16 . ...
Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species’ joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern
European countries. This need could be met in part by expanding the European Union’s Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity.
... However, an increasing number of researches demonstrate that intraspecific genetic differentiation occurs in habitats devoid of physical barriers (Mattingsdal et al. 2020). Intraspecific genetic divergence can illuminate the initial stages of new speciation (Bowen et al. 2016;Miraldo et al. 2016), and adaptation to diverse environments are major forces reshaping genetic variation (Mattingsdal et al. 2020;Pratt et al. 2022). Advancements in marine genomics offer an unprecedented opportunity to understand how these species adapt to environmental changes in the marine ecosystem (Oppen and Coleman 2022; Johannesson et al. 2023). ...
Understanding the genetic composition and regional adaptation of marine species under environmental heterogeneity and fishing pressure is crucial for responsible management. In order to understand the genetic diversity and adaptability of yellowfin seabream (Acanthopagrus latus) along southern China coast, this study was conducted a seascape genome analysis on yellowfin seabream from the ecologically diverse coast, spanning over 1600 km. A total of 92 yellowfin seabream individuals from 15 sites were performed whole-genome resequencing, and 4,383,564 high-quality single nucleotide polymorphisms (SNPs) were called. By conducting a genotype-environment association analysis, 29,951 adaptive and 4,328,299 neutral SNPs were identified. The yellowfin seabream exhibited two distinct population structures, despite high gene flow between sites. The seascape genome analysis revealed that genetic structure was influenced by a variety of factors including salinity gradients, habitat distance, and ocean currents. The frequency of allelic variation at the candidate loci changed with the salinity gradient. Annotation of these loci revealed that most of the genes are associated with osmoregulation, such as kcnab2a, kcnk5a, and slc47a1. These genes are significantly enriched in pathways associated with ion transport including G protein-coupled receptor activity, transmembrane signaling receptor activity, and transporter activity. Overall, our findings provide insights into how seascape heterogeneity affects adaptive evolution, while providing important information for regional management in yellowfin seabream populations.
... Assessing global patterns of indigenous peoples' land (89) Assessing the global distribution and diversity of plants, mammals, and amphibians (e.g. [90][91][92][93] Assessing global genetic diversity (94) The first map was produced by Ellis & Ramankutty (51) in 2008 ...
As anthropogenic transformation of Earth's ecology accelerates, and its impacts on the sustainability of humanity and the rest of nature become more obvious, geographers and other researchers are leveraging an abundance of spatial data to map how industrialization is transforming the biosphere. This review examines the methodologies used to create such maps and how they have enhanced our understanding of how societies can abate biodiversity loss, mitigate climate change, and achieve global sustainability goals. Although there have been great advances over the past two decades in mapping industrial transformations of ecology across the planet, the field is still in its infancy. We outline future research directions to better understand anthropogenic transformation of the biosphere and the utility of integrating global maps of socioeconomic, ecological, biodiversity, and climate data to explore and inform potential pathways of human-driven social-ecological change.
... Estudos de meta-análise indicam reduções signifi cativas na diversidade genética de várias espécies após a revolução industrial e demais eventos associados a perda ou degradação dos hábitats (Leigh et al. 2019, Miraldo et al. 2016. O avanço em metodologias e abordagens levou ao avanço de ferramentas estatísticas e modelos matemáticos. ...
... Estudos de meta-análise indicam reduções signifi cativas na diversidade genética de várias espécies após a revolução industrial e demais eventos associados a perda ou degradação dos hábitats (Leigh et al. 2019, Miraldo et al. 2016. O avanço em metodologias e abordagens levou ao avanço de ferramentas estatísticas e modelos matemáticos. ...
Este livro representa uma exploração profunda e fascinante da biologia da conservação, campo acadêmico que surgiu em resposta à crescente crise da biodiversidade. Ele combina diversas disciplinas, incluindo ecologia, genética, fisiologia e gestão ambiental para enfrentar os desafios únicos da conservação de uma espécie aquática endêmica ancestral. O livro destaca as espécies endêmicas Isoëtes cangae e Isoëtes serracarajensis, ambas descobertas nos campos rupestres ferruginosos da Floresta Nacional de Carajás. Os lagos aqui abordados são rasos, mas biodiversos, e apresentam características oligotróficas, o que é incomum e, por isso, é habitat de I. cangae. A distribuição limitada de I. cangae a torna uma espécie muito interessante do ponto de vista ecológico e botânico, motivando uma parceria entre o Instituto de Biodiversidade e Sustentabilidade (NUPEM–UFRJ), o Instituto Tecnológico Vale (ITVDS) e a Vale S.A. para conservá-la. O livro discute a abordagem interdisciplinar necessária para conservar essas espécies e seus ecossistemas, incluindo pesquisas que vão desde a identificação e busca pelas espécies, o desenvolvimento de técnicas de propagação e cultivo em larga escala, a determinação da estrutura genética de suas populações a testes em campo para verificação de adequabilidade de habitat. Destinado a estudantes, pesquisadores e entusiastas da ecologia, este livro é um guia indispensável para compreender a importância da conservação da biodiversidade e as estratégias para alcançá-la. Ele oferece uma visão única e valiosa sobre a complexidade e a beleza do mundo natural, bem como a necessidade urgente de protegê-lo. Finalmente, as informações geradas são parte fundamental para auxílio em gestão pública de áreas destinadas ao manejo e ao uso sustentável de recursos naturais.
... The first theories mainly focused on macro-organisms, which were easier to study through direct observation. Several extensive works revealed clear patterns in the distribution of animals and plants around the globe related to the origin and the history of organisms (Finlay, 2002) and reported an increasing species diversity towards the tropics for several taxonomic groups (Hillebrand & Azovsky, 2001, Miraldo et al., 2016, Schluter & Pennell, 2017, De Kort et al., 2021. In islands, usually lower diversity and higher endemism were observed and were related to their geographic isolation and organism dispersal limitation (Kier et al., 2009;MacArthur & Wilson, 1967). ...
The distribution of microorganisms has long been assumed to be cosmopolitan and primarily controlled by the environment, but recent studies suggest that microbes may also exhibit strong biogeographical patterns driven by dispersal limitation. Past attempts to study the global biogeography of freshwater diatoms have always encountered the great difficulty of collecting taxonomically harmonized large‐scale data. However, developments in molecular techniques and DNA metabarcoding provide a unique opportunity to overcome these limitations and to disclose diatom biodiversity at an unprecedented scale and resolution. Here, we assembled DNA metabarcoding data of freshwater benthic diatom communities sampled in seven geographic regions across the world to investigate how diatom diversity varies along latitude and to assess the proportion of genetic variants of these microorganisms which are exclusive or shared across regions. We observed significant differences in assemblages among climate zones and found that genetic richness is not affected by latitude, but by an island effect. The genetic resolution directly impacts the proportion of variants shared across regions; however, the majority of taxa remained specific to a single geographic region. Freshwater diatoms disperse over long distances and across oceans but at rates that allow the appearance of local genetic variants and the regionalization of assemblages. Future work should focus on putting these diversity dynamics into a temporal context, an approach that should be possible by bringing together new sequencing techniques and phylogeography.
... The study of broad-scale geographic patterns of genetic variation, taxonomic and 24 phylogenetic diversity, and speciation rate have provided insights into eco-evolutionary 25 processes forming latitudinal diversity gradients (LDG) in many taxa [1][2][3][4] . LDGs have been 26 extensively studied and shown to be consistent across most localities, scales, habitats, 27 and taxonomic groups, yet the evolutionary and ecological causes of this pattern are still 28 poorly understood 5 . ...
Parasitoid wasps are among the shortlist of taxa showing an anomalous latitudinal diversity gradient. Using the largest georeferenced molecular dataset, we used a macrogenetics approach to explore the spatial relationship between intra- and interspecific levels of diversity and potential environmental variables influencing the anomalous diversity pattern. Nucleotide diversity values were consistently higher at temperate latitudes, peaking at 50 degrees. We found a positive but weak relationship between intraspecific diversity and the latitude, between intra- and interspecific diversity, and a significant positive effect of the temperature range. Examining the spatial relationship between these levels of biodiversity and its drivers is particularly relevant considering climate change and its impact on species distribution. Yet, in insects, it has been challenging to integrate ecological, evolutionary, and geographical components when analyzing the processes leading to species richness gradients. Our study demonstrates how macrogenetics analyses of large-scale patterns of diversity provide insights into potential causes.
... Anthrome maps based on this system of classification have been used widely in teaching, research, and conservation (e.g. Chapin III et al., 2012;Martin et al., 2014;Merritts et al., 2014;National Geographic Society, 2014;Quinn et al., 2014;Miraldo et al., 2016;Gibson & Quinn, 2017;Dinerstein et al., 2017;Smith et al., 2019). ...
Anthromes, or anthropogenic biomes, characterize the globally significant ecological patterns shaped by sustained direct human interactions with ecosystems, including agriculture, urbanization, and other land uses. The emergence of anthromes has literally paved the way for the Anthropocene, and now cover more than three quarters of Earth’s ice-free land surface, including dense settlements, villages, croplands, rangelands, and cultured lands; wildlands untransformed by agriculture and settlements cover the remaining area.
... The resulting population bottleneck further reduced the adaptive potential and functional diversity of species, and poses dangers and difficulties in the recovery of populations under natural conditions. Many wild animals and plants are facing an unprecedented survival crisis [3][4][5][6][7]. ...
Understanding in the evolutionary processes, endangered mechanisms, and adaptive evolution history are key scientific issues in conservation biology. During the past decades, advances in high-throughput sequencing and multi-disciplinary crossover have triggered the development of conservation genomics, which refers to the use of new genomic technologies and genomic information in solving the existing problems in conservation biology. Conservation genomics mainly focuses on the endangered mechanism and conservation strategies aiming at protection of survivability and diversity of endangered species. Application of conservation genomics into the study of endanger plant species has provided innovated protection concept for biologists and promoted the development of population-based conservation strategies. This chapter summarizes the studies of population genomics for agronomically and commercially important plants threatened and endangered, discusses the advantages of conservation genomics for the analysis of genetic diversity, inferences about the history of population dynamics, evaluation of natural forces on wild plant populations, and the establishment of effective conservation strategies. This chapter also presents the development trends in genomics for the conservation of endangered plant species.
Initiatives to protect 30% of Earth by 2030 prompt evaluation of how to efficiently target shortcomings in the global protected area (PA) network. Focusing on amphibians, the most vulnerable vertebrate class, we illustrate the conservation value of microreserves, a term we employ here to refer to reserves of <10 km ² . We report that the network continues to under-represent threatened amphibians and that, despite this clear shortcoming in land-based conservation, the creation of PAs protecting amphibians slowed after 2010. By proving something previously assumed–that amphibians generally have smaller ranges than other terrestrial vertebrates–we demonstrate that microreserves could protect a substantial portion of many amphibian ranges, particularly threatened species. We find existing microreserves are capable of hosting an amphibian species richness similar to PAs 1000–10,00X larger, and we show that amphibians’ high beta diversity means that microreserves added to a growing PA network cover amphibian species 1.5—6x faster than larger size categories. We propose that stemming global biodiversity loss requires that we seriously consider the conservation potential of microreserves, using them to capture small-range endemics that may otherwise be omitted from the PA network entirely.
Human population growth constantly requires an increase in the production of food and products from the timber industry. To meet this demand, agriculture and planted forests are advancing over natural areas. In view of this, it is necessary to know the effects of land use for different purposes (grain production, pastures, planted forests, fruit production, among other uses) on the genetic diversity of populations of native species. This knowledge can assist in land use planning as well as in the development of conservation strategies for native species. In this study, we evaluated the effect of land use for agriculture (mainly for cereal production) and planted forests on the genetic diversity of Baccharis crispa Spreng., a herb native to South America. To achieve our goals, we compared population genetic data obtained with three molecular markers (microsatellites, ISSR [inter-simple sequence repeat] and isoenzymes) with data on land use for agriculture and planted forests from 15 different locations. Our results showed that regardless of the molecular marker used, the greater the use of land for agriculture and planted forests, the lower was the genetic diversity of B. crispa populations. Baccharis crispa is a semi-perennial species that needs at least one year to reach its reproductive period, which is prevented in agricultural areas due to the land being turned over or dissected with herbicides every six months. In the studied regions, the planted forests are of eucalypt and/or pine, which besides being species with a high production of allelopathic substances, produce strong shading and B. crispa is a species that inhabits open grassland that needs high incidence of sunlight for development. The data obtained in our study can assist in the decision-making to use land in order to reconcile the production of supplies for humanity and for the conservation of nature.
Synopsis
Intraspecific variation can be as great as variation across species, but the role of intraspecific variation in driving local and large-scale patterns is often overlooked, particularly in the field of thermal biology. In amphibians, which depend on environmental conditions and behavior to regulate body temperature, recognizing intraspecific thermal trait variation is essential to comprehensively understanding how global change impacts populations. Here, we examine the drivers of micro- and macrogeographical intraspecific thermal trait variation in amphibians. At the local scale, intraspecific variation can arise via changes in ontogeny, body size, and between the sexes, and developmental plasticity, acclimation, and maternal effects may modulate predictions of amphibian performance under future climate scenarios. At the macrogeographic scale, local adaptation in thermal traits may occur along latitudinal and elevational gradients, with seasonality and range-edge dynamics likely playing important roles in patterns that may impact future persistence. We also discuss the importance of considering disease as a factor affecting intraspecific variation in thermal traits and population resilience to climate change, given the impact of pathogens on thermal preferences and critical thermal limits of hosts. Finally, we make recommendations for future work in this area. Ultimately, our goal is to demonstrate why it is important for researchers to consider intraspecific variation to determine the resilience of amphibians to global change.
Climate plays a crucial role in shaping species distribution and evolution over time. Dr Vrba's Resource‐Use hypothesis posited that zones at the extremes of temperature and precipitation conditions should host a greater number of climate specialist species than other zones because of higher historical fragmentation. Here, we tested this hypothesis by examining climate‐induced fragmentation over the past 5 million years. Our findings revealed that, as stated by Vrba, the number of climate specialist species increases with historical regional climate fragmentation, whereas climate generalist species richness decreases. This relationship is approximately 40% stronger than the correlation between current climate and species richness for climate specialist species and 77% stronger for generalist species. These evidences suggest that the effect of climate historical fragmentation is more significant than that of current climate conditions in explaining mammal biogeography. These results provide empirical support for the role of historical climate fragmentation and physiography in shaping the distribution and evolution of life on Earth.
Unified models of biological diversity across organizational levels (genes, species, communities) provide key insight into fundamental ecological processes. Theory predicts that the strength of the correlation between species abundance and genetic diversity should be related to community age in closed communities (i.e. abundant species accumulate more genetic diversity over time than rare species). Following this rationale, we hypothesize that historical climatic events are expected to impact assembly processes, hence affecting both the species abundance distribution (SAD) and the species genetic distribution (SGD) in continental communities. Therefore, we predict that, if the congruence between SADs and SGDs depends on community age, then higher congruence would be observed in localities where climate has been more stable since the Last Glacial Maximum (LGM). We tested this prediction using relative abundance and nucleotide diversity ( cox1 ‐5′) data from 20 communities of leaf beetles along a latitudinal transect in the Iberian Peninsula. We observed that the congruence between SAD and SGD curves, measured as the correlation between the species' rank orders in both distributions, was significantly related to the change in mean annual temperature since the LGM, but not to current climatic conditions. Our results suggest that, despite the high connectivity of continental communities, historical climatic stability is still a relevant predictor of the congruence between species abundance and genetic diversity. Hence, the degree of congruence between SADs and SGDs could be used as a proxy of community stability, related not only to historical climatic variation but also to any other disrupting factors, including human pressure.
Insects play important roles in the maintenance of ecosystem functioning and provide livelihoods for millions of people. However, compared to terrestrial vertebrates and angiosperms like giant panda, crested ibis and metasequoia, the conservation of insects has not attracted enough attention. We still lack a basal understanding of the geographical biodiversity patterns for major components of insects in China. Here, we investigated the geographical distribution of insect biodiversity across multiple dimensions (taxonomic, genetic and phylogenetic diversity) based on the spatial distribution and molecular DNA sequencing data of insects. Our analysis covered 18 orders, 360 families and 5,275 genera and 14,115 insect species. The results revealed that Southwestern and Southeastern China harbored higher insect distributional diversity and numerous older lineages, representing as museum, whereas regions located in Northwestern China harbored lower insect biodiversity and many younger lineages, serving as an evolutionary cradle. We also found that and mean annual temperature and precipitation had significantly positive effects, while altitude had significantly negative effects on insect biodiversity in most cases. Moreover, cultivated vegetation harbored the highest insect taxonomic and phylogenetic diversity, and needleleaf and broadleaf mixed forests harbored the highest insect genetic diversity. These results indicated that human activities may positively contribute to insect spatial diversity at a regional scale. Our study filled the knowledge gaps in relation to insect spatial diversity in China. The findings could help guide national-level conservation plans and the post-2020 biodiversity conservation framework.
Intraspecific genetic variation and phylogeographic structure can be influenced by factors such as landscape features, environmental gradients, historical biogeography, and organismal traits such as dispersal ability. Since deep genetic structure is often considered a precursor to speciation, identifying the factors that are associated with genetic structure can contribute to a greater understanding about diversification. Here, we use repurposed data to perform a global analysis of volant vertebrates (i.e., bats and birds) to estimate where intraspecific phylogeographic breaks occur and identify the factors that are important predictors of these breaks. We estimate phylogeographic breaks using Monmonier's maximum difference barrier algorithm and conduct a Random Forests analysis using the presence of a phylogeographic break as a response variable. In bats, phylogeographic breaks are concentrated in biodiversity hotspots while breaks estimated in bird species are more widespread across temperate and tropical zones. However, for both clades geographical features such as maximum latitude, measures of wing morphology, and organismal traits associated with feeding ecology were found to be important predictors of phylogeographic breaks. Our analysis identifies geographical areas as wells as suites of organismal traits that could serve as a starting point for more detailed studies of biodiversity processes.
Ο ευρωπαϊκός λαγόγυρος είναι ένα κινδυνεύον με εξαφάνιση εδαφόβιο σκιουροειδές τρωκτικό των χορτολιβαδικών οικοσυστημάτων της Ευρώπης. Τις τελευταίες δεκαετίες ο πληθυσμός του παρουσιάζει πτωτική τάση σε όλο το εύρος εξάπλωσης. Οι ελληνικοί πληθυσμοί αντιπροσωπεύουν το νοτιότερο όριο, ενώ η γνώση της κατάστασής τους είναι περιορισμένη. Σκοπός της παρούσας διδακτορικής διατριβής είναι η μελέτη του πληθυσμού, της οικολογίας, της γενετικής και της ηθολογίας του είδους στην Ελλάδα. Από επιτόπιες επισκέψεις μεταξύ 2019-2020 σε Δυτική και Κεντρική Μακεδονία και Θράκη συλλέχθηκαν δεδομένα παρουσίας, βιολογικού ιστού και επαγρύπνησης. Τα δεδομένα αναλύθηκαν με υπολογιστικά μέσα ανάλυσης της πληθυσμιακής πυκνότητας, ομαδοποίησης των ενδιαιτημάτων, μοντέλα μέγιστης εντροπίας κατάλληλων και διαθέσιμων ενδιαιτημάτων, δεικτών γενετικής ποικιλότητας, φυλογενετικών σχέσεων και στατιστικού ελέγχου του λόγου των πιθανοτήτων. Τα αποτελέσματα έδειξαν ότι: (α) οι υφιστάμενες αποικίες είχαν μικρή μέση πυκνότητα και αριθμό ατόμων. Η πλειονότητα των αποικιών εντοπίστηκε σε αγροτικές και τεχνητές επιφάνειες μικρής έκτασης στα πεδινά της Κεντρικής Μακεδονίας και Θράκης. Οι πληθυσμοί της Δυτικής Μακεδονίας ξεχώρισαν λόγω των διαφορετικών τοπογραφικών και κλιματικών συνθηκών· (β) τόσο ανθρωπογενείς όσο και βιοκλιματικοί παράγοντες συνέβαλαν στο πρότυπο εξάπλωσης των πληθυσμών, με τα διαθέσιμα ενδιαιτήματα να είναι ελάχιστα σε σχέση με τα κατάλληλα. Επιπλέον, προβλέφθηκε μείωση της καταλληλότητας των ενδιαιτημάτων κατά 39% – 94,3%, εξαιτίας της κλιματικής αλλαγής της επόμενης 40ετίας· (γ) η γενετική ποικιλότητα των ελληνικών πληθυσμών δε συσχετίστηκε με το γεωγραφικό πλάτος έπειτα από τη σύγκριση με σέρβικους πληθυσμούς. Λαμβάνοντας υπόψη το σύνολο των δειγμάτων από την ευρωπαϊκή εξάπλωση, φάνηκε ότι οι προγενέστεροι πληθυσμοί του είδους βρίσκονταν στη νοτιοανατολική Βουλγαρία και την Ευρωπαϊκή Τουρκία και κατά τη μεταπαγετώδη περίοδο επεκτάθηκαν ταχύτατα προς την Ελλάδα και συγκεκριμένα από τη Θράκη στην Κεντρική και Δυτική Μακεδονία· (δ) τα ενήλικα άτομα ήταν πιο επιφυλακτικά ακολουθώντας διαφορετική στρατηγική επαγρύπνησης ανάλογα με τον κύκλο ζωής και τις συνθήκες της περιοχής, ενώ τα νεαρά διακινδυνεύαν περισσότερο εξαιτίας των υψηλών ενεργειακών αναγκών και της απειρίας. Συμπερασματικά, προτείνονται δράσεις διατήρησης για την προστασία των πληθυσμών του είδους στην Ελλάδα, προσδιορίζοντας τρία in situ κλιματικά καταφύγια που θα μπορούσαν να αποτελέσουν προτεραιότητα για μελλοντικές επανεισαγωγές και βελτίωση των ενδιαιτημάτων.
Earliella scabrosa is a pantropical species of Polyporales (Basidiomycota) and well-studied concerning its morphology and taxonomy. However, its pantropical intraspecific genetic diversity and population differentiation is unknown. We initiated this study to better understand the genetic variation within E. scabrosa and to test if cryptic species are present. Sequences of three DNA regions, the nuclear ribosomal internal transcribed spacer (ITS), the large subunit ribosomal DNA (LSU), and the translation elongation factor (EF1α) were analysed for 66 samples from 15 geographical locations. We found a high level of genetic diversity (haplotype diversity, Hd = 0.88) and low nucleotide diversity (π = 0.006) across the known geographical range of E. scabrosa based on ITS sequences. The analysis of molecular variance (AMOVA) indicates that the genetic variability is mainly found among geographical populations. The results of Mantel tests confirmed that the genetic distance among populations of E. scabrosa is positively correlated with the geographical distance, which indicates that geographical isolation is an important factor for the observed genetic differentiation. Based on phylogenetic analyses of combined dataset ITS-LSU-EF1α, the low intraspecific divergences (0–0.3%), and the Automated Barcode Gap Discovery (ABGD) analysis, E. scabrosa can be considered as a single species with five different geographical populations. Each population might be in the process of allopatric divergence and in the long-term they may evolve and become distinct species.
In this chapter, we discuss other patterns that can be obtained from assemblages from a macroecological perspective, expanding the reasoning of the previous chapter on species richness. We discuss the phylogenetic and functional estimates of diversity, rebuilding the concept of diversity beyond richness and improving our understanding of processes underlying broad-scale patterns. We can compare patterns in PD and FD by considering phylogenies as backbones for comparative analyses of trait diversification or as surrogates for diversity. We then show macroecological patterns comparing distinct assemblages (β-diversity), using different approaches, and discuss the relationship between metrics and scale issues. Several methodological advances have been made in partitioning β-diversity into nestedness (richness-derived) and turnover components and expanding the concept to incorporate phylogenetic and functional dimensions. Nevertheless, there are also interesting applications of the distinct approaches used to evaluate β-diversity to evaluate continuous geographic patterns of dissimilarity among assemblages (distance-decay similarity) and establish regionalization schemes.
In ecology and evolution, genetic and genomic data are commonly collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, such data are typically used only once by the data-generating authors. The repurposing of genetic and genomic datasets remains uncommon because it is often difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new research field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible, they could be reused for many additional purposes, far beyond their initial intended impact. In this review, we outline the main challenges with existing genetic and genomic data archives, factors underlying the challenges, and current best practices for archiving genetic and genomic data. Recognising that this is a longstanding issue due to an absence of formal data management training within the research field of ecology and evolution, we highlight key steps that universities, funding bodies, and scientific publishers could take to ensure timely change towards good data archiving.
This planetary boundaries framework update finds that six of the nine boundaries are transgressed, suggesting that Earth is now well outside of the safe operating space for humanity. Ocean acidification is close to being breached, while aerosol loading regionally exceeds the boundary. Stratospheric ozone levels have slightly recovered. The transgression level has increased for all boundaries earlier identified as overstepped. As primary production drives Earth system biosphere functions, human appropriation of net primary production is proposed as a control variable for functional biosphere integrity. This boundary is also transgressed. Earth system modeling of different levels of the transgression of the climate and land system change boundaries illustrates that these anthropogenic impacts on Earth system must be considered in a systemic context.
This package provides tools to assess the association between two spatial processes. Currently, three methodologies are implemented: An adapted t-test to perform hypothesis testing about the independence between the processes, a suitable nonparametric correlation coefficient, and the codispersion coefficient. SpatialPack gives methods to complement methodologies that are available in geoR for one spatial process. With contributions of Francisco Cuevas and Diego Mancilla.
Human activity is leaving a pervasive and persistent signature on Earth. Vigorous debate continues about whether this warrants recognition as a new geologic time unit known as the Anthropocene. We review anthropogenic markers of functional changes in the Earth system through the stratigraphic record. The appearance of manufactured materials in sediments, including aluminum, plastics, and concrete, coincides with global spikes in fallout radionuclides and particulates from fossil fuel combustion. Carbon, nitrogen, and phosphorus cycles have been substantially modified over the past century. Rates of sea-level rise and the extent of human perturbation of the climate system exceed Late Holocene changes. Biotic changes include species invasions worldwide and accelerating rates of extinction. These combined signals render the Anthropocene stratigraphically distinct from the Holocene and earlier epochs. Copyright
The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes
that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus
on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific
advances over the past 5 years. Several of the boundaries now have a two-tier approach, reflecting the importance of cross-scale
interactions and the regional-level heterogeneity of the processes that underpin the boundaries. Two core boundaries—climate
change and biosphere integrity—have been identified, each of which has the potential on its own to drive the Earth system
into a new state should they be substantially and persistently transgressed.
The integration of species distributions and evolutionary relationships is one of the most rapidly moving research fields today and has led to considerable advances in our understanding of the processes underlying biogeographical patterns. Here, we develop a set of metrics, the specific overrepresentation score ( SOS ) and the geographic node divergence ( GND ) score, which together combine ecological and evolutionary patterns into a single framework and avoids many of the problems that characterize community phylogenetic methods in current use.
This approach goes through each node in the phylogeny and compares the distributions of descendant clades to a null model. The method employs a balanced null model, is independent of phylogeny size, and allows an intuitive visualization of the results.
We demonstrate how this novel implementation can be used to generate hypotheses for biogeographical patterns with case studies on two groups with well‐described biogeographical histories: a local‐scale community data set of hummingbirds in the North Andes, and a large‐scale data set of the distribution of all species of New World flycatchers. The node‐based analysis of these two groups generates a set of intuitively interpretable patterns that are consistent with current biogeographical knowledge.
Importantly, the results are statistically tractable, opening many possibilities for their use in analyses of evolutionary, historical and spatial patterns of species diversity. The method is implemented as an upcoming R package nodiv , which makes it accessible and easy to use.
We live amid a global wave of anthropogenically driven biodiversity loss: species and population extirpations and, critically,
declines in local species abundance. Particularly, human impacts on animal biodiversity are an under-recognized form of global
environmental change. Among terrestrial vertebrates, 322 species have become extinct since 1500, and populations of the remaining
species show 25% average decline in abundance. Invertebrate patterns are equally dire: 67% of monitored populations show 45%
mean abundance decline. Such animal declines will cascade onto ecosystem functioning and human well-being. Much remains unknown
about this “Anthropocene defaunation”; these knowledge gaps hinder our capacity to predict and limit defaunation impacts.
Clearly, however, defaunation is both a pervasive component of the planet’s sixth mass extinction and also a major driver
of global ecological change.
The class of beta regression models is commonly used by practitioners to model variables that assume values in the standard unit interval (0,1). It is based on the assumption that the dependent variable is beta-distributed and that its mean is related to a set of regressors through a linear predictor with unknown coefficients and a link function. The model also includes a precision parameter which may be constant or depend on a (potentially different) set of regressors through a link function as well. This approach naturally incorporates features such as heteroskedasticity or skewness which are commonly observed in data taking values in the standard unit interval, such as rates or proportions. This paper describes the betareg package which provides the class of beta regressions in the R system for statistical computing. The underlying theory is briefly outlined, the implementation discussed and illustrated in various replication exercises.
Reducing the rate of biodiversity loss and averting dangerous biodiversity change are international goals, reasserted by the Aichi Targets for 2020 by Parties to the United Nations (UN) Convention on Biological Diversity (CBD) after failure to meet the 2010 target ( 1, 2). However, there is no global, harmonized observation system for delivering regular, timely data on biodiversity change ( 3). With the first plenary meeting of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) soon under way, partners from the Group on Earth Observations Biodiversity Observation Network (GEO BON) ( 4) are developing—and seeking consensus around—Essential Biodiversity Variables (EBVs) that could form the basis of monitoring programs worldwide.
It has been proposed that inbreeding contributes to the decline and
eventual extinction of small and isolated populations,. There is ample
evidence of fitness reduction due to inbreeding (inbreeding depression)
in captivity and from a few experimental, and observational field
studies,, but no field studies on natural populations have been
conducted to test the proposed effect on extinction. It has been argued
that in natural populations the impact of inbreeding depression on
population survival will be insignificant in comparison to that of
demographic and environmental stochasticity,. We have now studied the
effect of inbreeding on local extinction in a large metapopulation of
the Glanville fritillary butterfly (Melitaea cinxia). We found that
extinction risk increased significantly with decreasing heterozygosity,
an indication of inbreeding, even after accounting for the effects of
the relevant ecological factors. Larval survival, adult longevity and
egg-hatching rate were found to be adversely affected by inbreeding and
appear to be the fitness components underlying the relationship between
inbreeding and extinction. To our knowledge, this is the first
demonstration of an effect of inbreeding on the extinction of natural
populations. Our results are particularly relevant to the increasing
number of species with small local populations due to habitat loss and
fragmentation.
Aim To map and characterize anthropogenic transformation of the terrestrial biosphere before and during the Industrial Revolution, from 1700 to 2000.
Location Global.
Methods Anthropogenic biomes (anthromes) were mapped for 1700, 1800, 1900 and 2000 using a rule‐based anthrome classification model applied to gridded global data for human population density and land use. Anthropogenic transformation of terrestrial biomes was then characterized by map comparisons at century intervals.
Results In 1700, nearly half of the terrestrial biosphere was wild, without human settlements or substantial land use. Most of the remainder was in a seminatural state (45%) having only minor use for agriculture and settlements. By 2000, the opposite was true, with the majority of the biosphere in agricultural and settled anthromes, less than 20% seminatural and only a quarter left wild. Anthropogenic transformation of the biosphere during the Industrial Revolution resulted about equally from land‐use expansion into wildlands and intensification of land use within seminatural anthromes. Transformation pathways differed strongly between biomes and regions, with some remaining mostly wild but with the majority almost completely transformed into rangelands, croplands and villages. In the process of transforming almost 39% of earth's total ice‐free surface into agricultural land and settlements, an additional 37% of global land without such use has become embedded within agricultural and settled anthromes.
Main conclusions Between 1700 and 2000, the terrestrial biosphere made the critical transition from mostly wild to mostly anthropogenic, passing the 50% mark early in the 20th century. At present, and ever more in the future, the form and process of terrestrial ecosystems in most biomes will be predominantly anthropogenic, the product of land use and other direct human interactions with ecosystems. Ecological research and conservation efforts in all but a few biomes would benefit from a primary focus on the novel remnant, recovering and managed ecosystems embedded within used lands.
Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.Contact:
peter@biomatters.com
We introduce glmulti, an R package for automated model selection and multi-model inference with glm and related functions. From a list of explanatory variables, the pro- vided function glmulti builds all possible unique models involving these variables and, optionally, their pairwise interactions. Restrictions can be specied for candidate models, by excluding specic terms, enforcing marginality, or controlling model complexity. Mod- els are tted with standard R functions like glm. The n best models and their support (e.g., (Q)AIC, (Q)AICc, or BIC) are returned, allowing model selection and multi-model inference through standard R functions. The package is optimized for large candidate sets by avoiding memory limitation, facilitating parallelization and providing, in addition to exhaustive screening, a compiled genetic algorithm method. This article brie y presents the statistical framework and introduces the package, with applications to simulated and real data.
Marine ecosystems are centrally important to the biology of the planet, yet a comprehensive understanding of how anthropogenic
climate change is affecting them has been poorly developed. Recent studies indicate that rapidly rising greenhouse gas concentrations
are driving ocean systems toward conditions not seen for millions of years, with an associated risk of fundamental and irreversible
ecological transformation. The impacts of anthropogenic climate change so far include decreased ocean productivity, altered
food web dynamics, reduced abundance of habitat-forming species, shifting species distributions, and a greater incidence of
disease. Although there is considerable uncertainty about the spatial and temporal details, climate change is clearly and
fundamentally altering ocean ecosystems. Further change will continue to create enormous challenges and costs for societies
worldwide, particularly those in developing countries.
Using two genetic approaches and seven different plant systems, we present findings from a meta-analysis examining the strength of the effects of plant genetic introgression and genotypic diversity across individual, community and ecosystem levels with the goal of synthesizing the patterns to date. We found that (i) the strength of plant genetic effects can be quite high; however, the overall strength of genetic effects on most response variables declined as the levels of organization increased. (ii) Plant genetic effects varied such that introgression had a greater impact on individual phenotypes than extended effects on arthropods or microbes/fungi. By contrast, the greatest effects of genotypic diversity were on arthropods. (iii) Plant genetic effects were greater on above-ground versus below-ground processes, but there was no difference between terrestrial and aquatic environments. (iv) The strength of the effects of intraspecific genotypic diversity tended to be weaker than interspecific genetic introgression. (v) Although genetic effects generally decline across levels of organization, in some cases they do not, suggesting that specific organisms and/or processes may respond more than others to underlying genetic variation. Because patterns in the overall impacts of introgression and genotypic diversity were generally consistent across diverse study systems and consistent with theoretical expectations, these results provide generality for understanding the extended consequences of plant genetic variation across levels of organization, with evolutionary implications.
The mitochondrial DNA of plant and animal cells is a transcriptionally active genome that traces its origins to a symbiotic infection of eucaryotic cells by bacterial progenitors. As prescribed by the Serial Endosymbiosis Theory, symbiotic organelles have gradually transferred their genes to the eucaryotic genome, producing a functional interaction of nuclear and mitochondrial genes in organelle function. We report here a recent remarkable transposition of 7.9 kb of a typically 17.0-kb mitochondrial genome to a specific nuclear chromosomal position in the domestic cat. The intergrated segment has subsequently become amplified 38-76 times and now occurs as a tandem repeat macrosatellite with multiple-length alleles resolved by pulse-field gel electrophoresis (PFGE) segregating in cat populations. Sequence determination of the nuclear mitochondrial DNA segment, Numt, revealed a d(CA)-rich 8-bp motif [ACACACGT] repeated imperfectly five times at the deletion junction that is a likely target for recombination. The extent and pattern of sequence divergence of Numt genes from the cytoplasmic mtDNA homologues plus the occurrence of Numt in other species of the family Felidae allowed an estimate for the origins of Numt at 1.8-2.0 million years ago in an ancestor of four modern species in the genus Felis. Numt genes do not function in cats; rather, the locus combines properties of nuclear minisatellites and pseudogenes. These observations provide an empirical glimpse of historic genomic events that may parallel the accommodation of organelles in eucaryotes.
There is controversy concerning the role of genetic factors in species extinctions. Many authors have asserted that species are usually driven to extinction before genetic factors have time to impact them, but few studies have seriously addressed this issue. If this assertion is true, there will be little difference in genetic diversity between threatened and taxonomically related nonthreatened species. We compared average heterozygosities in 170 threatened taxa with those in taxonomically related nonthreatened taxa in a comprehensive metaanalysis. Heterozygosity was lower in threatened taxa in 77% of comparisons, a highly significant departure from the predictions of the no genetic impact hypothesis. Heterozygosity was on average 35% lower (median 40%) in threatened taxa than in related nonthreatened ones. These differences in heterozygosity indicate lowered evolutionary potential, compromised reproductive fitness, and elevated extinction risk in the wild. Independent evidence from stochastic computer projections has demonstrated that inbreeding depression elevates extinction risk for threatened species in natural habitats when all other threatening processes are included in the models. Thus, most taxa are not driven to extinction before genetic factors affect them adversely.
DNA techniques, analytical methods and palaeoclimatic studies are greatly advancing our knowledge of the global distribution of genetic diversity, and how it evolved. Such phylogeographic studies are reviewed from Arctic, Temperate and Tropical regions, seeking commonalities of cause in the resulting genetic patterns. The genetic diversity is differently patterned within and among regions and biomes, and is related to their histories of climatic changes. This has major implications for conservation science.
Uncorrectable skew and heteroscedasticity are among the “lemons” of psychological data, yet many important variables naturally exhibit these properties. For scales with a lower and upper bound, a suitable candidate for models is the beta distribution, which is very flexible and models skew quite well. The authors present maximum-likelihood regression models assuming that the dependent variable is conditionally beta distributed rather than Gaussian. The approach models both means (location) and variances (dispersion) with their own distinct sets of predictors (continuous and/or categorical), thereby modeling heteroscedasticity. The location submodel link function is the logit and thereby analogous to logistic regression, whereas the dispersion submodel is log linear. Real examples show that these models handle the independent observations case readily. The article discusses comparisons between beta regression and alternative techniques, model selection and interpretation, practical estimation, and software.
Species-energy theory indicates that recent climate warming should have driven increases in species richness in cool and species-poor parts of the Northern Hemisphere. We confirm that the average species richness of British butterflies has increased since 1970-82, but much more slowly than predicted from changes of climate: on average, only one-third of the predicted increase has taken place. The resultant species assemblages are increasingly dominated by generalist species that were able to respond quickly. The time lag is confirmed by the successful introduction of many species to climatically suitable areas beyond their ranges. Our results imply that it may be decades or centuries before the species richness and composition of biological communities adjusts to the current climate.
Theory predicts, and recent empirical studies have shown, that the diversity of plant species determines the diversity of
associated herbivores and mediates ecosystem processes, such as aboveground net primary productivity (ANPP). However, an often-overlooked
component of plant diversity, namely population genotypic diversity, may also have wide-ranging effects on community structure
and ecosystem processes. We showed experimentally that increasing population genotypic diversity in a dominant old-field plant
species, Solidago altissima, determined arthropod diversity and community structure and increased ANPP. The effects of genotypic diversity on arthropod
diversity and ANPP were comparable to the effects of plant species diversity measured in other studies.
Global conservation strategies commonly assume that different taxonomic groups show congruent geographical patterns of diversity, and that the distribution of extinction-prone species in one group can therefore act as a surrogate for vulnerable species in other groups when conservation decisions are being made. The validity of these assumptions remains unclear, however, because previous tests have been limited in both geographical and taxonomic extent. Here we use a database on the global distribution of 19,349 living bird, mammal and amphibian species to show that, although the distribution of overall species richness is very similar among these groups, congruence in the distribution of rare and threatened species is markedly lower. Congruence is especially low among the very rarest species. Cross-taxon congruence is also highly scale dependent, being particularly low at the finer spatial resolutions relevant to real protected areas. 'Hotspots' of rarity and threat are therefore largely non-overlapping across groups, as are areas chosen to maximize species complementarity. Overall, our results indicate that 'silver-bullet' conservation strategies alone will not deliver efficient conservation solutions. Instead, priority areas for biodiversity conservation must be based on high-resolution data from multiple taxa.
A phylogeny and timescale derived from analyses of multilocus nuclear DNA sequences for Holarctic genera of plethodontid salamanders reveal them to be an old radiation whose common ancestor diverged from sister taxa in the late Jurassic and underwent rapid diversification during the late Cretaceous. A North American origin of plethodontids was followed by a continental-wide diversification, not necessarily centered only in the Appalachian region. The colonization of Eurasia by plethodontids most likely occurred once, by dispersal during the late Cretaceous. Subsequent diversification in Asia led to the origin of Hydromantes and Karsenia, with the former then dispersing both to Europe and back to North America. Salamanders underwent rapid episodes of diversification and dispersal that coincided with major global warming events during the late Cretaceous and again during the Paleocene–Eocene thermal optimum. The major clades of plethodontids were established during these episodes, contemporaneously with similar phenomena in angiosperms, arthropods, birds, and mammals. Periods of global warming may have promoted diversification and both inter- and transcontinental dispersal in northern hemisphere salamanders by making available terrain that shortened dispersal routes and offered new opportunities for adaptive and vicariant evolution.
• historical biogeography
• paleogeography
• Plethodontidae dispersal
• salamander phylogeny
• phylogeny
Recent studies have generated an explosion of phylogenetic and biogeographic data and have provided new tools to investigate the processes driving large-scale gradients in species diversity. Fossils and phylogenetic studies of plants and animals demonstrate that tropical regions are the source for almost all groups of organisms, and these groups are composed of a mixture of ancient and recently derived lineages. These findings are consistent with the hypothesis that the large extent of tropical environments during the past 10-50 million years, together with greater climatic stability, has promoted speciation and reduced extinction rates. Energy availability appears to only indirectly contribute to global patterns of species diversity, especially considering how some marine diversity gradients can be completely decoupled from temperature and productivity gradients. Instead, climate stability and time-integrated area together determine the baselines of both terrestrial and marine global diversity patterns. Biotic interactions likely augment diversification and coexistence in the tropics.
Current predictions of extinction risks from climate change vary widely depending on the specific assumptions and geographic and taxonomic focus of each study. I synthesized published studies in order to estimate a global mean extinction rate and determine which factors contribute the greatest uncertainty to climate change-induced extinction risks. Results suggest that extinction risks will accelerate with future global temperatures, threatening up to one in six species under current policies. Extinction risks were highest in South America, Australia, and New Zealand, and risks did not vary by taxonomic group. Realistic assumptions about extinction debt and dispersal capacity substantially increased extinction risks. We urgently need to adopt strategies that limit further climate change if we are to avoid an acceleration of global extinctions.
Copyright © 2015, American Association for the Advancement of Science.
Clifford, Richardson, and Hemon (1989, Biometrics 45, 123-134) presented modified tests of association between two spatially autocorrelated processes, for lattice and non-lattice data. These tests are built on the sample covariance and on the sample correlation coefficient; they require the estimation of an effective sample size that takes into account the spatial structure of both processes. Clifford et al. developed their method on the basis of an approximation of the variance of the sample correlation coefficient and assessed it by Monte Carlo simulations for lattice and non-lattice networks of moderate to large size. In the present paper, the variance of the sample covariance is computed for a finite number of locations, under the multinormality assumption, and the mathematical derivation of the definition of effective sample size is given. The theoretically expected number of degrees of freedom for the modified t test with renewed modifications is compared with that computed on the basis of equation (2.9) of Clifford et al. (1989). The largest differences are observed for small numbers of locations and high autocorrelation, in particular when the latter is present with opposite sign in the two processes. Basic references that were missing in Clifford et al. (1989) are given and inherent ambiguities are discussed.
We established replicated experimental populations of the annual plant Clarkia pulchella to evaluate the existence of a causal relationship between loss of genetic variation and population survival probability. Two treatments differing in the relatedness of the founders, and thus in the genetic effective population size (Ne), were maintained as isolated populations in a natural environment. After three generations, the low Ne treatment had significantly lower germination and survival rates than did the high Ne treatment. These lower germination and survival rates led to decreased mean fitness in the low Ne populations: estimated mean fitness in the low Ne populations was only 21% of the estimated mean fitness in the high Ne populations. This inbreeding depression led to a reduction in population survival: at the conclusion of the experiment, 75% of the high Ne populations were still extant, whereas only 31% of the low Ne populations had survived. Decreased genetic effective population size, which leads to both inbreeding and the loss of alleles by genetic drift, increased the probability of population extinction over that expected from demographic and environmental stochasticity alone. This demonstrates that the genetic effective population size can strongly affect the probability of population persistence.
As climates change across already stressed ecosystems, there is no doubt that species will be affected, but to what extent
and which will be most vulnerable remain uncertain. The fossil record suggests that most species persisted through past climate
change, whereas forecasts of future impacts predict large-scale range reduction and extinction. Many species have altered
range limits and phenotypes through 20th-century climate change, but responses are highly variable. The proximate causes of
species decline relative to resilience remain largely obscure; however, recent examples of climate-associated species decline
can help guide current management in parallel with ongoing research.
This paper begins with a brief survey of the numbers of species that have been named and recorded on land and in the sea. It then assesses how many species there may be in total, giving particular attention to recent suggestions for dramatic upward revision of species totals for tropical invertebrates, fungi, benthic macrofauna, and microorganisms in general. Against this background, I comment on patterns of diversity on land and in the sea at higher taxonomic levels - orders through phyla - and on the possible causes and consequences of these patterns. I conclude with some estimates of impending extinction rates.
Hypotheses that attempt to explain latitudinal gradients in species diversity are reviewed. Some hypotheses are circular, i.e. they are based on the assumption that some taxa have greater diversity in the tropics. These include explanations assuming different degrees of competition, mutualism, predation, epiphyte load, epidemics, biotic spatial heterogeneity, host diversity, population size, niche width, population growth rate, environmental harshness, and patchiness at different latitudes. Other explanations are not supported by sufficient evidence, i.e. there is no consistent correlation between species diversity and environmental stability, environmental predictability, productivity, abiotic rarefaction, physical heterogeneity, latitudinal decrease in the angle of the sun above the horizon, area, aridity, seasonality, number of habitats, and latitudinal ranges. The ecological and evolutionary time hypotheses, as usually understood, also cannot explain the gradients, nor does the temperature dependence of chemical reactions permit predictions on species richness. Only differences in solar energy are consistently correlated with diversity gradients along latitude, altitude and perhaps depth. It is concluded that greater species diversity is due to greater "effective" evolutionary time (evolutionary speed) in the tropics, probably as the result of shorter generation times, faster mutation rates, and faster selection at greater temperatures. There is an urgent need for experimental studies of temperature effects on speed of selection.
Global biodiversity change is one of the most pressing environmental is-sues of our time. Here, we review current scientific knowledge on global biodiversity change and identify the main knowledge gaps. We discuss two components of biodiversity change—biodiversity alterations and biodiversity loss—across four dimensions of biodiversity: species extinc-tions, species abundances, species distributions, and genetic diversity. We briefly review the impacts that modern humans and their ancestors have had on biodiversity and discuss the recent declines and alterations in biodiversity. We analyze the direct pressures on biodiversity change: habitat change, overexploitation, exotic species, pollution, and climate change. We discuss the underlying causes, such as demographic growth and resource use, and review existing scenario projections. We identify successes and impending opportunities in biodiversity policy and man-agement, and highlight gaps in biodiversity monitoring and models. Finally, we discuss how the ecosystem services framework can be used to identify undesirable biodiversity change and allocate conservation efforts.
A fundamental assumption underlying the application of genetics within conservation biology is that inbreeding increases the risk of extinction. However, there is no information on the shape of the relationship, the available evidence has not distinguished genetic and nongenetic effects, and the issue is controversial. Methods were devised to separate genetic and nongenetic causes of extinction in inbred populations, and they were used to analyze data from Drosophila melanogaster, D. virilis and Mus musculus. Inbreeding markedly increased rates of extinction in all cases. All showed a threshold relationship between incremental extinction and inbreeding with low initial extinction, but they showed notably increased extinction beginning at intermediate levels of inbreeding. There was no difference in extinction levels at similar inbreeding coefficients in populations inbred at different rates (full sibling versus double first cousin). Endangered species may give little warning of impending extinction crises due to inbreeding.
In many large-scale conservation or ecological problems where experiments are intractable or unethical, regression methods are used to attempt to gauge the impact of a set of nominally independent variables (X) upon a dependent variable (Y). Workers often want to assert that a given X has a major influence on Y, and so, by using this indirection to infer a probable causal relationship. There are two difficulties apart from the demonstrability issue itself: (1) multiple regression is plagued by collinear relationships in X; and (2) any regression is designed to produce a function that in some way minimizes the overall difference between the observed and predicted Ys, which does not necessarily equate to determining probable influence in a multivariate setting. Problem (1) may be explored by comparing two avenues, one in which a single best regression model is sought and the other where all possible regression models are considered contemporaneously. It is suggested that if the two approaches do not agree upon which of the independent variables are likely to be significant, then the deductions must be subject to doubt.