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1. SNP discovery in candidate adaptive genes using exon capture in a free‐ranging alpine ungulate

   https://doi.org/10.1111/1755-0998.12560  

   Roffler, Gretchen H. ; Amish, Stephen J. ; Smith, Seth ; Cosart, Ted ; Kardos, Marty ; Schwartz, Michael K. ; Luikart, Gordon ( July 2016 , Molecular Ecology Resources)

   Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identifySNPmarkers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein‐coding and nearby 5′ and 3′ untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (Ovis canadensis) exon capture data and directly from the domestic sheep genome (Ovis ariesv. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR‐basedSNPchip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (lositanandbayescan), we detected 28SNPloci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease‐regulating functions (e.g. Ovar‐DRA,APC,BATF2,MAGEB18), cell regulation signalling pathways (e.g.KRIT1,PI3K,ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene‐targetedSNPdiscovery and subsequentSNPchip genotyping using low‐quality samples in a nonmodel species.

    

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2. Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in Cornus florida L.—Insights from GWAS and GBS data

   https://doi.org/10.1111/jse.12592  

   Pais, Andrew L. ; Whetten, Ross W. ; Xiang, Qiu‐Yun ( May 2020 , Journal of Systematics and Evolution)

   Understanding the consequences of exotic diseases on native forests is important to evolutionary ecology and conservation biology because exotic pathogens have drastically altered US eastern deciduous forests.Cornus floridaL. (flowering dogwood tree) is one such species facing heavy mortality. Characterizing the genetic structure ofC. floridapopulations and identifying the genetic signature of adaptation to dogwood anthracnose (an exotic pathogen responsible for high mortality) remain vital for conservation efforts. By integrating genetic data from genotype by sequencing (GBS) of 289 trees across the host species range and distribution of disease, we evaluated the spatial patterns of genetic variation and population genetic structure ofC. floridaand compared the pattern to the distribution of dogwood anthracnose. Using genome‐wide association study and gradient forest analysis, we identified genetic loci under selection and associated with ecological and diseased regions. The results revealed signals of weak genetic differentiation of three or more subgroups nested within two clusters—explaining up to 2%–6% of genetic variation. The groups largely corresponded to the regions within and outside the eastern Hot‐Continental ecoregion, which also overlapped with areas within and outside the main distribution of dogwood anthracnose. The fungal sequences contained in the GBS data of sampled trees bolstered visual records of disease at sampled locations and were congruent with the reported range ofDiscula destructiva, suggesting that fungal sequences within‐host genomic data were informative for detecting or predicting disease. The genetic diversity between populations at diseased vs. disease‐free sites across the range ofC. floridashowed no significant difference. We identified 72 single‐nucleotide polymorphisms (SNPs) from 68 loci putatively under selection, some of which exhibited abrupt turnover in allele frequencies along the borders of the Hot‐Continental ecoregion and the range of dogwood anthracnose. One such candidate SNP was independently identified in two prior studies as a possible L‐type lectin‐domain containing receptor kinase. Although diseased and disease‐free areas do not significantly differ in genetic diversity, overall there are slight trends to indicate marginally smaller amounts of genetic diversity in disease‐affected areas. Our results were congruent with previous studies that were based on a limited number of genetic markers in revealing high genetic variation and weak population structure inC. florida.

    

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3. Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation

   https://doi.org/10.1186/s12870-022-04026-5  

   Hanlon, Meredith T. ; Vejchasarn, Phanchita ; Fonta, Jenna E. ; Schneider, Hannah M. ; McCouch, Susan R. ; Brown, Kathleen M. ( January 2023 , BMC Plant Biology)

   Genome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (Oryza sativa) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth. Using lines from the Rice Diversity Panel-1, we explored the diversity of root hair length and density across four subpopulations of rice (aus,indica,temperate japonica, andtropical japonica). GWA analysis was completed using the high-density rice array (HDRA) and the rice reference panel (RICE-RP) SNP sets.

   We identified 18 genomic regions related to root hair traits, 14 of which related to RHD and four to RHL. No genomic regions were significantly associated with both traits. Two regions overlapped with previously identified quantitative trait loci (QTL) associated with root hair density in rice. We identified candidate genes in these regions and present those with previously published expression data relevant to root hair development. We re-phenotyped a subset of lines with extreme RHD phenotypes and found that the variation in RHD was due to differences in cell differentiation, not cell size, indicating genes in an associated genomic region may influence root hair cell fate. The candidate genes that we identified showed little overlap with previously characterized genes in rice andArabidopsis.

   Root hair length and density are quantitative traits with complex and independent genetic control in rice. The genomic regions described here could be used as the basis for QTL development and further analysis of the genetic control of root hair length and density. We present a list of candidate genes involved in root hair formation and growth in rice, many of which have not been previously identified as having a relation to root hair growth. Since little is known about root hair growth in grasses, these provide a guide for further research and crop improvement.

    

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4. SNP s across time and space: population genomic signatures of founder events and epizootics in the House Finch ( Haemorhous mexicanus )

   https://doi.org/10.1002/ece3.2444  

   Shultz, Allison J. ; Baker, Allan J. ; Hill, Geoffrey E. ; Nolan, Paul M. ; Edwards, Scott V. ( September 2016 , Ecology and Evolution)

   Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen‐induced selection event. Using ddRADseq, we genotyped over 18,000SNPs across the genome in native pre‐epizootic westernUSbirds, introduced birds from Hawaii and the eastern United States, post‐epizootic eastern birds, and western birds sampled across a similar time span. We found 14% and 7% reductions in nucleotide diversity, respectively, in Hawaiian and pre‐epizootic eastern birds relative to pre‐epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre‐epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.

    

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5. Modelling management strategies for chronic disease in wildlife: Predictions for the control of respiratory disease in bighorn sheep

   https://doi.org/10.1111/1365-2664.14084  

   Almberg, Emily S. ; Manlove, Kezia R. ; Cassirer, E. Frances ; Ramsey, Jennifer ; Carson, Keri ; Gude, Justin ; Plowright, Raina K. ( December 2021 , Journal of Applied Ecology)

   Controlling persistent infectious disease in wildlife populations is an ongoing challenge for wildlife managers and conservationists worldwide, and chronic diseases in particular remain a pernicious problem.

   Here, we develop a dynamic pathogen transmission model capturing key features ofMycoplasma ovipneumoniaeinfection, a major cause of population declines in North American bighorn sheepOvis canadensis. We explore the effects of model assumptions and parameter values on disease dynamics, including density‐ versus frequency‐dependent transmission, the inclusion of a carrier class versus a longer infectious period, host survival rates, disease‐induced mortality and recovery rates and the epidemic growth rate. Along the way, we estimate the basic reproductive ratio,R₀, forM. ovipneumoniaein bighorn sheep to fall between approximately 1.36 and 1.74.

   We apply the model to compare efficacies across a suite of management actions following an epidemic, including test‐and‐remove, depopulation‐and‐reintroduction, range expansion, herd augmentation and density reduction.

   Our results suggest that test‐and‐remove, depopulation‐and‐reintroduction and range expansion could help persistently infected bighorn sheep herds recovery following an epidemic. By contrast, augmentation could lead to worse outcomes than those expected in the absence of management. Other management actions that improve host survival or reduce disease‐induced mortality are also likely to improve population size and persistence of chronically infected herds.

   Synthesis and applications. Dynamic transmission models like the one employed here offer a structured, logical approach for exploring hypotheses, planning field experiments and designing adaptive management. We find that management strategies that removed infected animals or isolated them within a structured metapopulation were most successful at facilitating herd recovery from a low‐prevalence, chronic pathogen. Ideally, models like ours should operate iteratively with field experiments to triangulate on better approaches for managing wildlife diseases.

    

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