Macrogenetic studies must not ignore limitations of genetic markers and scale

Paz‐Vinas, Ivan; Jensen, Evelyn L.; Bertola, Laura D.; Breed, Martin F.; Hand, Brian K.; Hunter, Margaret E.; Kershaw, Francine; Leigh, Deborah M.; Luikart, Gordon; Mergeay, Joachim; Miller, Joshua M.; Rees, Charles B. van; Segelbacher, Gernot; Hoban, Sean

doi:10.1111/ele.13732

Cited by 35 publications

(38 citation statements)

References 11 publications

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“…A second study found no significant trends between the current amount of human impact in a given area and the diversity in the mitochondrial cytochrome c oxidase subunit I (COI) gene of a wide variety of bird, fish, insect, and mammal species (Millette et al, 2020). The lack of signal of this study could be due to the gene studied (Paz-Vinas et al, 2021), which is under purifying selection (Pentinsaari et al 2016), and then may not capture genome-wide neutral diversity (Kardos et al, 2021). Rather than a temporal study, Millette et al's resembles a sensitivity analysis, where one may expect areas that have been more disturbed historically by humans will have lower levels of genetic diversity.…”

Section: V5 Ongoing Efforts In Characterizing Genetic Diversity Losscontrasting

confidence: 54%

Genetic diversity loss in the Anthropocene

Expósito-Alonso

Booker

Czech

et al. 2021

Preprint

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More species than ever before are at risk of extinction due to anthropogenic habitat loss and climate change. But even species that are not threatened have seen reductions in their populations and geographic ranges, likely impacting their genetic diversity. Although preserving genetic diversity is a key conservation target to maintain the adaptability of species, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. By bridging biodiversity and population genetics theories, we introduce the first mathematical framework to understand the loss of naturally occurring DNA mutations within a species--what we call genetic diversity extinction. Analyzing genome-wide variation data of 10,126 geo-tagged individuals from 19 plant and animal species, we show that genome-wide diversity follows a power law with geographic area, which can predict genetic diversity decay in simulated spatial extinctions. Given pre-21st century values of ecosystem transformations, we estimate that over 10% of genetic diversity may be extinct, already surpassing the United Nations targets for genetic preservation. These estimated losses could rapidly increase with advancing climate change and habitat destruction, highlighting the need for new forecasting tools that assist in the rapid implementation of policies to protect genetic resources.

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Section: V5 Ongoing Efforts In Characterizing Genetic Diversity Losscontrasting

confidence: 54%

Genetic diversity loss in the Anthropocene

Expósito-Alonso

Booker

Czech

et al. 2021

Preprint

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“…For example, the stalked barnacle (Watanabe et al, 2018) possesses distinct morphotypes along the CIR, but whether these morphological variations are the results of phenotypic plasticity or genetic differentiation between populations is unknown. The stalked barnacle did not appear to be genetically different across vent fields, but their phylogenetic relationship was assessed only by using the mitochondrial COI gene, which is not good enough to discriminate closely related populations (Paz-Vinas et al, 2021).…”

Section: Community Differences Across Vent Fieldsmentioning

confidence: 99%

Structure and Connectivity of Hydrothermal Vent Communities Along the Mid-Ocean Ridges in the West Indian Ocean: A Review

Perez

Sun

et al. 2021

Front. Mar. Sci.

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To date, 13 biologically active hydrothermal vent (HTV) fields have been described on the West Indian Ocean ridges. Knowledge of benthic communities of these vent ecosystems serves as scientific bases for assessing the resilience of these ecosystems under the global effort to strike an elegant balance between future deep-sea mining and biodiversity conservation. This review aims to summarize our up-to-date knowledge of the benthic community structure and connectivity of these Indian vents and to identify knowledge gaps and key research questions to be prioritized in order to assess the resilience of these communities. The HTVs in the West Indian Ocean are home to many unique invertebrate species such as the remarkable scaly-foot snail. While distinct in composition, the macrofaunal communities of the Indian HTVs share many characteristics with those of other HTVs, including high endemism, strong zonation at the local scale, and a simple food web structure. Furthermore, Indian vent benthic communities are mosaic compositions of Atlantic, Pacific, and Antarctic HTV fauna possibly owning to multiple waves of past colonization. Phylogeographic studies have shed new light into these migratory routes. Current animal connectivity across vent fields appears to be highly influenced by distance and topological barriers. However, contrasting differences in gene flow have been documented across species. Thus, a better understanding of the reproductive biology of the Indian vent animals and the structure of their population at the local scale is crucial for conservation purposes. In addition, increased effort should be given to characterizing the vents’ missing diversity (at both the meio and micro-scale) and elucidating the functional ecology of these vents.

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“…Furthermore, measures of genetic variation are often used to assess a species' or population's ability to respond to environmental (climate, habitat, biotic) changes (Frankham 2005;Hoffman and Sgró 2011), so large-scale analyses such as this, allow for targeting individual species that might be at a higher risk for extinction (Frankham et al 2014;Hoban et al 2020) and for identifying species attributes that contribute to higher levels of genetic diversity (Broadhurst et al 2017). While there is no consensus as to whether measures of genetic diversity from a single mitochondrial or chloroplast gene, the most common in our dataset, are appropriate measures of genetic diversity (Petit-Marty et al 2021;Paz-Vinas et al 2021), many species (15%; 13,960 total) have data from multiple loci in phylogatR and measures of genetic diversity across loci can be evaluated.…”

Section: Empirical Examplementioning

confidence: 99%

phylogatR: Phylogeographic data aggregation and repurposing

Pelletier

Parsons

Decker

et al. 2021

Preprint

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Patterns of genetic diversity within species contain information about the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyze sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR, large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalyzed and increase accessibility to big data for research labs and classroom instructors with limited computational expertise and resources.

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Macrogenetic studies must not ignore limitations of genetic markers and scale

Cited by 35 publications

References 11 publications

Genetic diversity loss in the Anthropocene

Genetic diversity loss in the Anthropocene

Structure and Connectivity of Hydrothermal Vent Communities Along the Mid-Ocean Ridges in the West Indian Ocean: A Review

phylogatR: Phylogeographic data aggregation and repurposing

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