Management implications of highly resolved hierarchical population genetic structure in thinhorn sheep

Sim, Zijian; Davis, Corey S.; Jex, Bill; Hegel, Troy; Coltman, David W.

doi:10.1007/s10592-018-1123-2

Cited by 7 publications

(4 citation statements)

References 44 publications

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“…Demographic breaks coinciding with the Brooks Range have been identified in other Arctic and alpine vertebrates (e.g. Galbreath et al, 2011;Krejsa et al, 2021;Sim et al, 2019;Sonsthagen et al, 2011). Furthermore, population genomic variation is arrayed in an IBD pattern (Figure 2c), which suggests that willow ptarmigan expanded from a single northern Beringia refugium once habitat became available during glacial retreat (e.g.…”

Section: Landscape Features Influencing Genomic Structurementioning

confidence: 80%

Species‐specific responses to landscape features shaped genomic structure within Alaska galliformes

Sonsthagen

Wilson

Talbot

2022

Journal of Biogeography

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Aim: Connectivity is vital to the resiliency of populations to environmental change and stochastic events, especially for cold-adapted species as Arctic and alpine tundra habitats retract as the climate warms. We examined the influence of past and current landscapes on genomic connectivity in cold-adapted galliformes as a critical first step to assess the vulnerability of Alaska ptarmigan and grouse to environmental change.We hypothesize that the mosaic of physical features and habitat within Alaska promoted the formation of genetic structure across species.Location: Alaska, United States of America.Taxa: Ptarmigan and Grouse (Galliformes: Tetraoninae). Methods:We collected double digest restriction-site-associated DNA sequence data from six ptarmigan and grouse species (N = 13-145/species) sampled across multiple ecosystems up to ~10 degrees of latitude. Spatial genomic structure was analysed using methods that reflect different temporal scales: (1) principal components analysis to identify major trends in the distribution of genomic variation; (2) maximum likelihood clustering analyses to test for the presence of multiple genomic groupings; (3) shared co-ancestry analyses to assess contemporary relationships and (4) effective migration surfaces to identify regions that deviate from a null model of isolation by distance.Results: Levels of genomic structure varied across species (Φ ST =0.009-0.042). Three general patterns of structure emerged: (1) east-west partition located near the Yukon-Tanana uplands; (2) north-south split coinciding with the Alaska Range and (3) northern group near the Brooks Range. Species-specific patterns were observed; not all landscape features were barriers to gene flow for all ptarmigan and grouse and temporal contrasts were detected at the Brooks Range.Main conclusions: Within Alaska galliformes, patterns of genomic structure coincide with physiographic features and highlight the importance of physical and ecological barriers in shaping how genomic diversity is arrayed across the landscape. Lack of concordance in spatial patterns indicates that species behaviour and habitat affinities play key roles in driving the contrasting patterns of genomic structure.

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Section: Landscape Features Influencing Genomic Structurementioning

confidence: 80%

Species‐specific responses to landscape features shaped genomic structure within Alaska galliformes

Sonsthagen

Wilson

Talbot

2022

Journal of Biogeography

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“…Inference of population structure based on Δ K only provides the most probable value of K , and there are often further levels of sub-structuring within regions that are important to detect in conservation of threatened species (e.g. [ 76 ]). Wild populations rarely fall into distinct units and the power required to detect structure is dependent on the scale of analysis and complexity of evolutionary history.…”

Section: Resultsmentioning

confidence: 99%

How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India

Aylward

Sagar

Natesh

et al. 2022

Phil. Trans. R. Soc. B

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Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60–70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.

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“…Former research on livestock in the Pantanal biome suggests that local preferences among farmers may explain morphological variation among indigenous horses [32], as well as the fact that the presence of research institutions may explain greater distinctiveness among private farms that keep indigenous cattle [33]. Of main concern is that this may alter gene flow and inbreeding (homozygosity) and could relate to isolation by distance [34][35][36].…”

Section: Variability Of the Morphological Charactersmentioning

confidence: 99%

Qualitative Characters of Indigenous Sheep in Central Brazil: Putting Phenotype into Perspective

et al. 2021

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For centuries, indigenous sheep have been bred in extensive low-input systems in Midwestern Brazil. The hypothesis of this study was the assumption that phenotypic evaluation of indigenous livestock may drive the establishment of breed standards and official breed recognition, and, therefore, promote more local business opportunities. On the basis of more integrative and participatory theoretical background to applying any decision based on phenotype, we designed this research to determine the most typical and unusual phenotypes of Pantaneiro sheep. Pantaneiro ewes (281 ewes from five conservation units in five counties) were evaluated, bearing in mind both conservation and development. Descriptive statistics were used to classify ewes into typical, intermediate, and unusual phenotypes. Chi-squared tests for association were performed to test if morphological variation in the different sampling sites occurred randomly (p > 0.05) or not (p < 0.05). Some results suggest some sort of diversifying selection pressure, i.e., distinct preferences among keepers. We observed considerable morphologic variation among ewes, but it was straightforward to determine the predominant phenotypes. The study evokes integrative agrobiodiversity by putting phenotypical characterization of indigenous livestock into perspective. Discussions coming from this study may support innovative governance and participative decision-making, allied with strategies that value the socioeconomic, biocultural, and adaptive aspects of indigenous livestock in tropical regions and developing countries. This is a challenge for government, rare-breed keepers, value-chain actors, and civil society.

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Management implications of highly resolved hierarchical population genetic structure in thinhorn sheep

Cited by 7 publications

References 44 publications

Species‐specific responses to landscape features shaped genomic structure within Alaska galliformes

Species‐specific responses to landscape features shaped genomic structure within Alaska galliformes

How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India

Qualitative Characters of Indigenous Sheep in Central Brazil: Putting Phenotype into Perspective

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