Signatures of Selection and Genomic Diversity of Muskellunge (Esox masquinongy) from Two Populations in North America.
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ABSTRACT:
SUBMITTER: Chinchilla-Vargas J
PROVIDER: S-EPMC8303616 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:We report a study of genome-wide, dense SNP (? 900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region.
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Project description:Background:The introduction of northern snakehead (Channa argus; Anabantiformes: Channidae) and their subsequent expansion is one of many problematic biological invasions in the United States. This harmful aquatic invasive species has become established in various parts of the eastern United States, including the Potomac River basin, and has recently become established in the Mississippi River basin in Arkansas. Effective management of C. argus and prevention of its further spread depends upon knowledge of current population structure in the United States. Methods:Novel methods for invasive species using whole genomic scans provide unprecedented levels of data, which are able to investigate fine scale differences between and within populations of organisms. In this study, we utilize 2b-RAD genomic sequencing to recover 1,007 single-nucleotide polymorphism (SNP) loci from genomic DNA extracted from 165 C. argus individuals: 147 individuals sampled along the East Coast of the United States and 18 individuals sampled throughout Arkansas. Results:Analysis of those SNP loci help to resolve existing population structure and recover five genetically distinct populations of C. argus in the United States. Additionally, information from the SNP loci enable us to begin to calculate the long-term effective population size ranges of this harmful aquatic invasive species. We estimate long-term Ne to be 1,840,000-18,400,000 for the Upper Hudson River basin, 4,537,500-45,375,000 for the Lower Hudson River basin, 3,422,500-34,225,000 for the Potomac River basin, 2,715,000-7,150,000 for Philadelphia, and 2,580,000-25,800,000 for Arkansas populations. Discussion and Conclusions:This work provides evidence for the presence of more genetic populations than previously estimated and estimates population size, showing the invasive potential of C. argus in the United States. The valuable information gained from this study will allow effective management of the existing populations to avoid expansion and possibly enable future eradication efforts.
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Project description:A novel sublineage of the piscine novirhabdovirus (synonym: viral hemorrhagic septicemia virus), genotype IVb, emerged in the Laurentian Great Lakes, causing serious losses in resident fish species as early as 2003. Experimentally infected juvenile muskellunge (Esox masquinongy) were challenged with VHSV-IVb at high (1 × 105 PFU mL-1), medium (4 × 103 PFU mL-1), and low (100 PFU mL-1) doses. Samples from spleen, kidneys, heart, liver, gills, pectoral fin, large intestine, and skin/muscle were collected simultaneously from four fish at each predetermined time point and processed for VHSV-IVb reisolaton on Epitheliosum papulosum cyprini cell lines and quantification by plaque assay. The earliest reisolation of VHSV-IVb occurred in one fish from pectoral fin samples at 24 h post-infection. By 6 days post-infection (dpi), all tissue types were positive for VHSV-IVb. Statistical analysis suggested that virus levels were highest in liver, heart, and skin/muscle samples. In contrast, the kidneys and spleen exhibited reduced probability of virus recovery. Virus distribution was further confirmed by an in situ hybridization assay using a VHSV-IVb specific riboprobe. Heart muscle fibers, hepatocytes, endothelia, smooth muscle cells, and fibroblast-like cells of the pectoral fin demonstrated riboprobe labeling, thus highlighting the broad cellular tropism of VHSV-IVb. Histopathologic lesions were observed in areas where the virus was visualized.
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Project description:Admixture has been a pervasive phenomenon in human history, extensively shaping the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as "adaptive admixture." However, the role of adaptive admixture in human evolution and the power to detect it remain poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, assuming multiple admixture scenarios. We show that statistics based on admixture proportions, Fadm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas other statistics, including iHS and FST, falsely detect neutral mutations that have been selected in the source populations only. By combining Fadm and LAD into a single, powerful statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africans and in Malagasy, North Africans, and South Asians, respectively. Our approach also uncovers other cases of adaptive admixture, including APOL1 in Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides evidence that adaptive admixture has occurred in human populations whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.
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Project description:As the Cordilleran and Laurentide Ice Sheets retreated, North America was colonized by human populations; however, the spatial patterns of subsequent population growth are unclear. Temporal frequency distributions of aggregated radiocarbon ((14)C) dates are used as a proxy of population size and can be used to track this expansion. The Canadian Archaeological Radiocarbon Database contains more than 35,000 (14)C dates and is used in this study to map the spatiotemporal demographic changes of Holocene populations in North America at a continental scale for the past 13,000 y. We use the kernel method, which converts the spatial distribution of (14)C dates into estimates of population density at 500-y intervals. The resulting maps reveal temporally distinct, dynamic patterns associated with paleodemographic trends that correspond well to genetic, archaeological, and ethnohistoric evidence of human occupation. These results have implications for hypothesizing and testing migration routes into and across North America as well as the relative influence of North American populations on the evolution of the North American ecosystem.
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