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1. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern

   https://doi.org/10.1111/mec.16141  

   Wold, Jana ; Koepfli, Klaus‐Peter ; Galla, Stephanie J. ; Eccles, David ; Hogg, Carolyn J. ; Le Lec, Marissa F. ; Guhlin, Joseph ; Santure, Anna W. ; Steeves, Tammy E. ( December 2021 , Molecular Ecology)
2. Conservation Genomics in the Sagebrush Sea: Population Divergence, Demographic History, and Local Adaptation in Sage-Grouse (Centrocercus spp.)

   https://doi.org/10.1093/gbe/evz112  

   Oh, Kevin P ; Aldridge, Cameron L ; Forbey, Jennifer S ; Dadabay, Carolyn Y ; Oyler-McCance, Sara J ; Baer, Charles ( July 2019 , Genome Biology and Evolution)

   Abstract Sage-grouse are two closely related iconic species of the North American West, with historically broad distributions across sagebrush-steppe habitat. Both species are dietary specialists on sagebrush during winter, with presumed adaptations to tolerate the high concentrations of toxic secondary metabolites that function as plant chemical defenses. Marked range contraction and declining population sizes since European settlement have motivated efforts to identify distinct population genetic variation, particularly that which might be associated with local genetic adaptation and dietary specialization of sage-grouse. We assembled a reference genome and performed whole-genome sequencing across sage-grouse from six populations, encompassing both species and including several populations on the periphery of the species ranges. Population genomic analyses reaffirmed genome-wide differentiation between greater and Gunnison sage-grouse, revealed pronounced intraspecific population structure, and highlighted important differentiation of a small isolated population of greater sage-grouse in the northwest of the range. Patterns of genome-wide differentiation were largely consistent with a hypothesized role of genetic drift due to limited gene flow among populations. Inferred ancient population demography suggested persistent declines in effective population sizes that have likely contributed to differentiation within and among species. Several genomic regions with single-nucleotide polymorphisms exhibiting extreme population differentiation were associated with candidate genes linked to metabolism of xenobiotic compounds. In vitro activity of enzymes isolated from sage-grouse livers supported a role for these genes in detoxification of sagebrush, suggesting that the observed interpopulation variation may underlie important local dietary adaptations, warranting close consideration for conservation strategies that link sage-grouse to the chemistry of local sagebrush. 

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3. A comparative genomics multitool for scientific discovery and conservation

   https://doi.org/10.1038/s41586-020-2876-6  

   Genereux, Diane P. ; Serres, Aitor ; Armstrong, Joel ; Johnson, Jeremy ; Marinescu, Voichita D. ; Murén, Eva ; Juan, David ; Bejerano, Gill ; Casewell, Nicholas R. ; Chemnick, Leona G. ; et al ( November 2020 , Nature)

   null (Ed.)

   The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity. 

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4. The relevance of pedigrees in the conservation genomics era

   https://doi.org/10.1111/mec.16192  

   Galla, Stephanie J. ; Brown, Liz ; Couch‐Lewis ; Cubrinovska, Ilina ; Eason, Daryl ; Gooley, Rebecca M. ; Hamilton, Jill A. ; Heath, Julie A. ; Hauser, Samantha S. ; Latch, Emily K. ; et al ( January 2022 , Molecular Ecology)
5. Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop

   https://doi.org/10.1093/jhered/esaa001  

   Stahlke, Amanda ; Bell, Donavan ; Dhendup, Tashi ; Kern, Brooke ; Pannoni, Samuel ; Robinson, Zachary ; Strait, Jeffrey ; Smith, Seth ; Hand, Brian K ; Hohenlohe, Paul A ; et al ( March 2020 , Journal of Heredity)

   Abstract The increasing availability and complexity of next-generation sequencing (NGS) data sets make ongoing training an essential component of conservation and population genetics research. A workshop entitled “ConGen 2018” was recently held to train researchers in conceptual and practical aspects of NGS data production and analysis for conservation and ecological applications. Sixteen instructors provided helpful lectures, discussions, and hands-on exercises regarding how to plan, produce, and analyze data for many important research questions. Lecture topics ranged from understanding probabilistic (e.g., Bayesian) genotype calling to the detection of local adaptation signatures from genomic, transcriptomic, and epigenomic data. We report on progress in addressing central questions of conservation genomics, advances in NGS data analysis, the potential for genomic tools to assess adaptive capacity, and strategies for training the next generation of conservation genomicists. 

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