Single nucleotide polymorphism analysis of exons 3 and 4 of IGF-1 gene in pigs

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Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

INTRODUCTION: The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale. METHODS: In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context. RESULTS AND DISCUSSION: We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian F ST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism ( BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation ( SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity

A comparison of climate change impacts on park values on four Queensland World Heritage National Parks in Australia

Protected areas will vary in how they respond to climate-related threats and impacts. An important step in adapting protected area management to respond to climate change is identifying how protected areas and their values may be impacted. This requires an understanding of the ecological and social system impacting on the particular values so that consideration of management options and issues can be informed by this understanding. A set of Bayesian belief networks were developed to assess impacts and management issues for three key values (stream-dwelling frogs, cool temperate forest and recreational walking access) across four National Parks (Springbrook, Lamington, Mount Barney and Main Range) in Queensland, Australia. The aim was to assess how those values may be impacted by climate change, how the parks differ in relation to likely impact and options for management adaptation. We observed, depending on a protected area's physical and socio-ecological characteristics, that the values were likely to be differently affected across the parks and management responses will need to take account of these differences

Leveraging large scale beef cattle genomic data to identify the architecture of polygenic selection and local adaptation

Includes vita.Since the invention of the first array-based genotyping assay for cattle in 2008, millions of animals have been genotyped worldwide. Leveraging these genotypes offers exciting opportunities to explore both basic and applied research questions. Commercial genotyping assays are of adequate variant density to perform well in prediction contexts but are not sufficient for mapping studies. Using reference panels made up of individuals genotyped at higher densities, we can statistically infer the missing variation of low-density assays through the process of imputation. Here, we explore the best practices for performing routine imputation in large commercially generated genomic datasets of U.S. beef cattle. We find that using a large multi-breed imputation reference maximizes accuracy, particularly for rare variants. Using three of these large, imputed datasets, we explore two major population genetics questions. First, we map polygenic selection in the bovine genome, using Generation Proxy Selection Mapping (GPSM). This identifies hundreds of regions of the genome actively under selection in cattle populations. Using a similar approach, we identify dozens of genomic variants associated with environments across the U.S., likely involved local adaptation. Understanding the genomic basis of local adaptation in cattle will enable select and breed cattle better suited to a changing climate.Includes bibliographical references (pages 203-228

Aerospace Medicine and Biology: A cumulative index to a continuing bibliography

This publication is a cumulative index to the abstracts contained in Supplements 138 through 149 of AEROSPACE MEDICINE AND BIOLOGY: A CONTINUING BIBLIOGRAPHY. It includes three indexes -- subject, personal author, and corporate source

The Genetic Basis of Divergence and Speciation in Alpine and Arctic Finches

Identifying the genetic basis of adaptive traits is an integral part of understanding the mechanisms that cause speciation. Speciation relies on the formation of barriers to reproduction, and traits that differ among closely related species (e.g., coloration) may play an important role in the formation and maintenance of these barriers. However, the genetic architecture of trait variation may influence lineage divergence and speciation. By examining trait variation with corresponding genome sequence in recently diverged and hybridizing lineages, the genetic controls of traits can be characterized. My dissertation research examines the genomic basis of population differentiation in two recently diverged avian species complexes and identifies regions of the genome that underlie potentially adaptive traits that differ between species or ecotypes. This work combines whole genome sequence data with morphological and environmental data for alpine and arctic distributed rosy-finches (Leucosticte spp.), and holarctic distributed redpoll finches (Acanthis spp.). I start by highlighting patterns from recent studies of genetic associations with plumage coloration in birds to frame a primary hypothesis regarding the influence of genetic architecture on speciation. I then examine genetic divergence and assess phylogenetic relationships in rosy-finches. Despite little genetic divergence and widespread introgression, many strongly supported clades correspond to described taxa and plumage morphs. I then examine the genetic basis of the traits that distinguish rosy-finch clades, including plumage patches and breeding elevation. I identify 11 candidate genes involved in either melanogenesis or adaptation to hypoxia. The modularity of these traits has likely allowed for theshuffling of the associated genomic regions, resulting in phenotypic diversity and lineage divergence. Finally, I contrast the modular genetic architecture found in rosy-finches to a large inversion supergene found in redpolls that contains many candidate genes related to plumage coloration and bill morphology. Unlike in rosy-finches, the supergene trait genetic architecture in redpolls appears to maintain variation within a single evolving redpoll lineage through a combination of natural selection and assortative mating. My work identifies the genetic basis of both ecological and morphological variation in two bird systems that exhibit considerable morphological variation and highlights the role of genetic architecture in divergence and speciation.</p