Conservation macrogenetics: harnessing genetic data to meet conservation commitments

Schmidt, Chloé; Hoban, Sean; Jetz, Walter

doi:10.1016/j.tig.2023.08.002

Cited by 7 publications

(4 citation statements)

References 87 publications

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“…Although hybridization could pose a threat to the genetic integrity of cold-adapted species, it could also become the solution to increase the adaptive potential of alpine species and preserve at least partially their genetic legacy in the future ( Charles and Stehlik, 2021 ). Technological advances in genomics could nowadays provide important evidence to monitor biological processes and inform decision-making in biodiversity management ( Schmidt et al., 2023 ; Theissinger et al., 2023 ). Therefore, the potential eco-evolutionary outcomes of interspecific hybridization should receive special attention in developing conservation strategies for cold-adapted species in view of progressing global warming.…”

Section: Discussionmentioning

confidence: 99%

Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia

Wróbel,

Klichowska,

Nobis

2024

Front. Plant Sci.

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Hybridization is one of the key processes shaping lineage diversification, particularly in regions that experienced strong climate oscillations. The alpine biome with its rich history of glacial-interglacial cycles and complex patterns of species distribution shifts offers an excellent system to investigate the impact of gene flow on population dynamics and speciation, important issues for evolutionary biology and biodiversity conservation. In this study, we combined genomic data (DArTseq), chloroplast markers, and morphology to examine phylogenetic relationships and the permeability of species boundaries and their evolutionary outcomes among the alpine extremophilic species of Puccinellia (Poaceae) in the Pamir Mountains, a part of the Mountains of Central Asia biodiversity hotspot. We determined the occurrence of interspecific hybrids between P. himalaica and P. pamirica, which demonstrated almost symmetric ancestry from their parental species and did not show signals of introgression. According to our integrative revision, the natural hybrids between P. himalaica and P. pamirica should be classified as Puccinellia ×vachanica (pro species). Using approximate Bayesian computation for population history inference, we uncovered that P. himalaica hybridized with P. pamirica independently in multiple localities over the Holocene. Hybrids inherited the fine-scale genetic structure from their parental species, which developed these patterns earlier, during the Late Pleistocene. Hybridization had different consequences for the involved parental lineages, likely playing an important role in a continuing decline of P. himalaica in the Pamir Mountains over the Holocene. Our results show that P. himalaica should be considered a critically endangered species in the Pamir Mountains and could also be retreating across its entire range of distribution in High Mountain Asia. Using a comparative phylogeographic framework, we revealed the risk of extinction of a cold-adapted alpine species in a global biodiversity hotspot. This study highlights that genomics could unravel diversity trends under climate change and provides valuable evidence for conservation management.

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Section: Discussionmentioning

confidence: 99%

Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia

Wróbel,

Klichowska,

Nobis

2024

Front. Plant Sci.

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“…Simultaneously, we must develop protocols for managing genomic data processed with diverse bioinformatic pipelines 66 .…”

Section: Discussionmentioning

confidence: 99%

Southern marsh deer (Blastocerus dichotomus) populations assessed using Amplicon Sequencing on fecal samples

Wolfenson,

Pereira,

Ruzzante

et al. 2024

Sci Rep

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Populations in isolated and small fragments lose genetic variability very fast and are usually of conservation concern because they are at greater risk of local extinction. The largest native deer in South America, Blastocerus dichotomus (Illiger, 1815), is a Vulnerable species according to the IUCN categorization, which inhabits tropical and subtropical swampy areas. In Argentina, its presence has been restricted to four isolated fragments. Here we examine the genetic diversity and differentiation among three of them, including the three different patches that form the southernmost population, using 18 microsatellite markers genotyped by Amplicon Sequencing of DNA extracted from fecal samples. Genetic diversity was low (HE < 0.45) in all three populations studied. We found three genetic clusters compatible with the geographic location of the samples. We also found a metapopulation dynamics that involves the patches that make up the southernmost population, with evidence of a barrier to gene flow between two of them. Our results point to the creation of a corridor as a necessary and urgent management action. This is the first study, at the population level, employing microsatellite genotyping by Amplicon Sequencing with non-invasive samples in an endangered species.

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“…A global assessment of how well wild populations fulfill 50/500 criteria is timely due to its benefits for forecasting adaptive responses of at-risk populations to environmental change. Furthermore, assessing the spatial positioning of N e estimates across taxa in relation to human activities could provide significant benefits for conservation planning by contributing to emerging literature on the processes affecting population genetic diversity at broad, macrogenetic scales (e.g., Lawrence & Fraser, 2020; Leigh et al, 2019; Schmidt et al, 2023). Estimates of N e in wild populations have accumulated rapidly in more than a decade since previous reviews of N̂ e were conducted.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, assessing the spatial positioning of Ne estimates across taxa in relation to human activities could provide significant benefits for conservation planning by contributing to emerging literature on the processes affecting population genetic diversity at broad, macrogenetic scales (e.g., Lawrence & Fraser, 2020;Leigh et al, 2019;Schmidt et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Global assessment of effective population sizes: consistent taxonomic differences in meeting the 50/500 rule

Clarke,

Lawrence,

Matte

et al. 2023

Preprint

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Effective population size (Ne) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum Neof 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential, respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between Neand human activities. Through a quantitative review, we generated a dataset with 4145 georeferenced Ne estimates from 3576 unique populations, extracted from 712 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal, and amphibian populations had a ≤52% probability of reaching Ne= 50 and a <5% probability of reaching Ne= 500. Populations listed as being of conservation concern according to the IUCN Red List had a lower Nethan unlisted populations, and this relationship held true across all taxonomic groups. Newas reduced in areas with a greater Global Human Footprint, especially for amphibians and mammals, however relationships varied between taxa. We also highlight several considerations for future works estimating Ne, including the role that gene flow and subpopulation structure plays in the estimation of Nein wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on Neand help prioritize assessment of populations from taxa most at risk of failing to meet conservation thresholds.

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Conservation macrogenetics: harnessing genetic data to meet conservation commitments

Cited by 7 publications

References 87 publications

Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia

Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia

Southern marsh deer (Blastocerus dichotomus) populations assessed using Amplicon Sequencing on fecal samples

Global assessment of effective population sizes: consistent taxonomic differences in meeting the 50/500 rule

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