Quantifying Temporal Genomic Erosion in Endangered Species

Díez-del-Molino, David; Sánchez-Barreiro, Fátima; Barnes, Ian; Gilbert, M. Thomas P.; Dalén, Love

doi:10.1016/j.tree.2017.12.002

Cited by 161 publications

(191 citation statements)

References 88 publications

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“…Understanding historical genetic variation can help managers prioritize species and populations for active conservation initiatives. For example, populations that have naturally and historically low genetic variation may not be the highest priority for management efforts compared to populations that may have similarly low genetic variation but which historically were genetically diverse (Díez‐del‐Molino, Sánchez‐Barreiro, Barnes, Gilbert, & Dalén, ). In addition, identifying historic genetic variation may highlight important connections to now‐extinct populations that could inform reintroduction efforts for species of conservation concern (Godoy et al, ).…”

Section: Case Studies and Empirical Datamentioning

confidence: 99%

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

Billerman

Walsh

2019

Molecular Ecology Resources

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Museum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high‐throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections.

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Section: Case Studies and Empirical Datamentioning

confidence: 99%

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

Billerman

Walsh

2019

Molecular Ecology Resources

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“…Nonetheless, single time-point analysis cannot disentangle contemporary declines in variation from historically low values caused, for example, by ancient population crashes, colonization population dynamics, or species-specific traits and histories (Díez-del-Molino, Sánchez-Barreiro, Barnes, Gilbert, & Dalén, 2018;Habel, Husemann, Finger, Danley, & Zachos, 2014). Assessment of global changes in within-population genetic variation requires cross-generational genetic comparisons of the same population, ideally over long periods of time.…”

Section: Introductionmentioning

confidence: 99%

Estimated six per cent loss of genetic variation in wild populations since the industrial revolution

Leigh

Hendry

Vázquez‐Domínguez

et al. 2019

Evolutionary Applications

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Genetic variation is fundamental to population fitness and adaptation to environmental change. Human activities are driving declines in many wild populations and could have similar effects on genetic variation. Despite the importance of estimating such declines, no global estimate of the magnitude of ongoing genetic variation loss has been conducted across species. By combining studies that quantified recent changes in genetic variation across a mean of 27 generations for 91 species, we conservatively estimate a 5.4%–6.5% decline in within‐population genetic diversity of wild organisms since the industrial revolution. This loss has been most severe for island species, which show a 27.6% average decline. We identified taxonomic and geographical gaps in temporal studies that must be urgently addressed. Our results are consistent with single time‐point meta‐analyses, which indicated that genetic variation is likely declining. However, our results represent the first confirmation of a global decline and provide an estimate of the magnitude of the genetic variation lost from wild populations.

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“…In particular, human-mediated translocations can obscure biogeographic patterns, confound reconstructions of evolutionary history (Gippoliti & Amori, 2006;Helgen & Wilson, 2003), and remove spatial barriers to gene flow, promoting hybridization between taxa that were once geographically isolated (Fitzpatrick et al, 2010;Ladle & Whittaker, 2011). Conservation researchers and managers therefore increasingly make use of environmental archives (Bonebrake, Christensen, Boggs, & Ehrlich, 2010;Davies, Colombo, & Hanley, 2014), such as historical museum collections (Díez-Del-Molino, Sánchez-Barreiro, Barnes, Gilbert, & Dalén, 2018;Hekkala et al, 2011;Turvey, Barnes, Marr, & Brace, 2017), to reconstruct past environmental baselines in systems that have experienced human modification of biodiversity, and to obtain novel insights into the evolution, ecology, and biogeography of species that have undergone historical range modifications. Understanding historical baselines and the extent to which human activities have disrupted biodiversity is of particular importance for regions with long histories of human modification that are now experiencing extreme anthropogenic pressure, notably ecosystems in eastern and southeast Asia (Marks, 2017;Turvey, Crees, Li, Bielby, & Yuan, 2017).…”

Section: Introductionmentioning

confidence: 99%

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians

Turvey

Marr

Barnes

et al. 2019

Ecology and Evolution

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Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human‐mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human‐mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next‐Generation Sequencing methods, using historical museum specimens and late 20th‐century samples, and retrieved partial or near‐complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene–Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai‐Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.

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Quantifying Temporal Genomic Erosion in Endangered Species

Cited by 161 publications

References 88 publications

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

Estimated six per cent loss of genetic variation in wild populations since the industrial revolution

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians

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