The Transformative Impact of Genomics on Sage-Grouse Conservation and Management

Oyler‐McCance, Sara J.; Oh, Kevin P.; Zimmerman, Shawna J.; Aldridge, Cameron L.

doi:10.1007/13836_2019_65

Cited by 5 publications

(3 citation statements)

References 94 publications

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“…Primarily, generation of SNP datasets requires relatively large quantities of high quality DNA, which is often difficult to obtain from species of conservation concern. However, investing in the development of a SNP panel or using a target capture approach can facilitate use of low quality samples [88]. On the other hand, microsatellites are extremely useful with low quality samples, are becoming less costly and time consuming to develop (e.g., Castoe et al [89]), and have already been widely used in conservation and management programs for long-term monitoring of many species.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, microsatellites are extremely useful with low quality samples, are becoming less costly and time consuming to develop (e.g., Castoe et al [89]), and have already been widely used in conservation and management programs for long-term monitoring of many species. Although general usefulness of microsatellites in the future is uncertain, microsatellite loci will likely remain useful for relatedness, parentage analysis, and genetic mark-recapture due to their highly polymorphic nature and mixed performance with SNP data [46,47,49,53,54,88].…”

Section: Discussionmentioning

confidence: 99%

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An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern

2020

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Background Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted. Results Here we used microsatellite and SNP data generated from Gunnison sage-grouse (Centrocercus minimus) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity (HO, HE, FIS, AR) and differentiation (FST, GST, DJost). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for HE, FIS, AR, and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data. Conclusion We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern

2020

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“…Improvements in molecular technology and laboratory methods over the last decade have facilitated the collection and analysis of large-scale genetic data sets [9,[11][12][13] enabling comprehensive research efforts for wide-ranging species. An array of analytical tools exists to examine population genetic structure in wild populations including both population and individualbased methods [14] as well as those that include spatial information and those that do not [15].…”

Section: Introductionmentioning

confidence: 99%

New strategies for characterizing genetic structure in wide-ranging, continuously distributed species: A Greater Sage-grouse case study

et al. 2022

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Characterizing genetic structure across a species’ range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity. Wide-ranging species residing in continuously distributed habitat pose substantial challenges for the characterization of genetic structure as many analytical methods used are less effective when isolation by distance is an underlying biological pattern. Here, we illustrate strategies for overcoming these challenges using a species of significant conservation concern, the Greater Sage-grouse (Centrocercus urophasianus), providing a new method to identify centers of genetic differentiation and combining multiple methods to help inform management and conservation strategies for this and other such species. Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation and, following our novel method, 12 subpopulation centers of differentiation. Gene flow was greater, and differentiation reduced in areas of contiguous habitat (eastern Montana, most of Wyoming, much of Oregon, Nevada, and parts of Idaho). As expected, areas of fragmented habitat such as in Utah (with 6 subpopulation centers) exhibited the greatest genetic differentiation and lowest effective migration. The subpopulation centers defined here could be monitored to maintain genetic diversity and connectivity with other subpopulation centers. Many areas outside subpopulation centers are contact zones where different genetic groups converge and could be priorities for maintaining overall connectivity. Our novel method and process of leveraging multiple different analyses to find common genetic patterns provides a path forward to characterizing genetic structure in wide-ranging, continuously distributed species.

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Population Genomics Advances and Opportunities in Conservation of Kiwi (Apteryx spp.)

Ramstad

Dunning

2020

Population Genomics

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The Transformative Impact of Genomics on Sage-Grouse Conservation and Management

Cited by 5 publications

References 94 publications

An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern

An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern

New strategies for characterizing genetic structure in wide-ranging, continuously distributed species: A Greater Sage-grouse case study

Population Genomics Advances and Opportunities in Conservation of Kiwi (Apteryx spp.)

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