Genomics‐informed delineation of conservation units in a desert amphibian

Abstract

Delineating conservation units (CUs, e.g., evolutionarily significant units, ESUs, and management units, MUs) is critical to the recovery of declining species because CUs inform both listing status and management actions. Genomic data have strengths and limitations in informing CU delineation and related management questions in natural systems. We illustrate the value of using genomic data in combination with landscape, dispersal and occupancy data to inform CU delineation in Nevada populations of the Great Basin Distinct Population Segment of the Columbia spotted frog (Rana luteiventris). R. luteiventris occupies naturally fragmented aquatic habitats in this xeric region, but beaver removal, climate change and other factors have put many of these populations at high risk of extirpation without management intervention. We addressed three objectives: (i) assessing support for ESUs within Nevada; (ii) evaluating and revising, if warranted, the current delineation of MUs; and (iii) evaluating genetic diversity, effective population size, adaptive differentiation and functional connectivity to inform ongoing management actions. We found little support for ESUs within Nevada but did identify potential revisions to MUs based on unique landscape drivers of connectivity that distinguish these desert populations from those in the northern portion of the species range. Effective sizes were uniformly small, with low genetic diversity and weak signatures of adaptive differentiation. Our findings suggest that management actions, including translocations and genetic rescue, might be warranted. Our study illustrates how a carefully planned genetic study, designed to address priority management goals that include CU delineation, can provide multiple insights to inform conservation action.

Re‐evaluating Coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data

“…The increasing feasibility of generating genomic data sets provides an opportunity to incorporate more precise estimates of population genetic statistics, inferences of population genetic structure across multiple spatial scales, and information about local adaptation into conservation and management planning across a range of species. The general approach used in this study is not limited to aquatic species and has been applied to delineate different types of CUs, including ESUs, MUs and/or AUs for other taxa including terrestrial mammals (Barbosa et al, 2018 ), plants (Silva et al, 2020 ) and amphibians (Forester et al, 2022 ) of conservation concern. In cases where CUs have already been established, the power of large SNP data sets can be harnessed to validate and potentially adjust existing boundaries to improve management approaches (Forester et al, 2022 ; Waples et al, 2020 ).…”

“…The general approach used in this study is not limited to aquatic species and has been applied to delineate different types of CUs, including ESUs, MUs and/or AUs for other taxa including terrestrial mammals (Barbosa et al, 2018 ), plants (Silva et al, 2020 ) and amphibians (Forester et al, 2022 ) of conservation concern. In cases where CUs have already been established, the power of large SNP data sets can be harnessed to validate and potentially adjust existing boundaries to improve management approaches (Forester et al, 2022 ; Waples et al, 2020 ). Although we found a strong match between genomically derived units based on either neutral or outlier loci and currently defined CUs for Coho salmon in Canada, other studies have raised important questions concerning the possible revision of CUs for Chinook salmon ( O. tshawytscha ) and steelhead ( O. mykiss ) after strong genomic associations with adult migration timing that may not be reflected in the current configuration of CUs were identified (Waples et al, 2022 ; Waples & Lindley, 2018 ).…”

Low genetic diversity and high gene flow in the Aquatic Warbler (Acrocephalus paludicola), a threatened marshland songbird with a fragmented breeding range

“…2019, Forester et al . 2022, Alves et al . 2023), guides the creation of stepping‐stones between highly isolated populations (Holderegger et al .…”

“…Studying population genetics is therefore vital and informative for effective species conservation and management (Haig et al 2011, Holderegger et al 2019. For instance, knowledge on genetic differentiation aids the delineation of conservation management units (Palsbøll et al 2007, Lindsay et al 2008, Dom ınguez et al 2017, Tournayre et al 2019, Forester et al 2022, Alves et al 2023, guides the creation of stepping-stones between highly isolated populations (Holderegger et al 2019) and enables assignment of individuals to a population (Webster et al 2002, Ruegg et al 2014, Bounas et al 2018, DeSaix et al 2019, Dominguez et al 2019. Determining genetic diversity, effective population size and past genetic bottlenecks allows more accurate assessment of extinction risks (Schwartz et al 2007, Lawton et al 2011, Potvin et al 2017, Stojanovic et al 2018, Wilder et al 2023 and informs decisions on translocation to rescue genetically an isolated and declining population (Bouzat et al 2009, Coleman et al 2013, van Rossum & Rasp e 2018, Scott et al 2020.…”

Genomics and conservation: Guidance from training to analyses and applications

“…Assessment of contemporary migration (gene flow) aids in delineation of conservation units (Lowe & Allendorf, 2010) and is a common application that conservation geneticists encounter (Burgess et al., 2022; Forester et al., 2022). Despite this conservation importance, methods of migration assessment often focus on coalescent‐based approaches to determine historical migration rates and population dynamics (Al‐Asadi et al., 2019; Beerli & Felsenstein, 2001; Hey & Nielsen, 2007; Nielsen & Wakeley, 2001).…”