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Adalgisa Caccone - One of the best experts on this subject based on the ideXlab platform.
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the Population Genomics of multiple tsetse fly glossina fuscipes fuscipes admixture zones in uganda
Molecular Ecology, 2019Co-Authors: Norah P. Saarman, Kirstin Dion, Robert Opiro, Chaz Hyseni, Richard Echodu, Elizabeth A Opiyo, Thomas Johnson, Adalgisa CacconeAbstract:Understanding the mechanisms that enforce, maintain or reverse the process of speciation is an important challenge in evolutionary biology. This study investigates the patterns of divergence and discusses the processes that form and maintain divergent lineages of the tsetse fly Glossina fuscipes fuscipes in Uganda. We sampled 251 flies from 18 sites spanning known genetic lineages and the four admixture zones between them. We apply Population Genomics, hybrid zone and approximate Bayesian computation to the analysis of three types of genetic markers: 55,267 double-digest restriction site-associated DNA (ddRAD) SNPs to assess genome-wide admixture, 16 microsatellites to provide continuity with published data and accurate biogeographic modelling, and a 491-bp fragment of mitochondrial cytochrome oxidase I and II to infer maternal inheritance patterns. Admixture zones correspond with regions impacted by the reorganization of Uganda's river networks that occurred during the formation of the West African Rift system over the last several hundred thousand years. Because tsetse fly Population distributions are defined by rivers, admixture zones likely represent both old and new regions of secondary contact. Our results indicate that older hybrid zones contain mostly parental types, while younger zones contain variable hybrid types resulting from multiple generations of interbreeding. These findings suggest that reproductive barriers are nearly complete in the older admixture zones, while nearly absent in the younger admixture zones. Findings are consistent with predictions of hybrid zone theory: Populations in zones of secondary contact transition rapidly from early to late stages of speciation or collapse all together.
Norah P. Saarman - One of the best experts on this subject based on the ideXlab platform.
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the Population Genomics of multiple tsetse fly glossina fuscipes fuscipes admixture zones in uganda
Molecular Ecology, 2019Co-Authors: Norah P. Saarman, Kirstin Dion, Robert Opiro, Chaz Hyseni, Richard Echodu, Elizabeth A Opiyo, Thomas Johnson, Adalgisa CacconeAbstract:Understanding the mechanisms that enforce, maintain or reverse the process of speciation is an important challenge in evolutionary biology. This study investigates the patterns of divergence and discusses the processes that form and maintain divergent lineages of the tsetse fly Glossina fuscipes fuscipes in Uganda. We sampled 251 flies from 18 sites spanning known genetic lineages and the four admixture zones between them. We apply Population Genomics, hybrid zone and approximate Bayesian computation to the analysis of three types of genetic markers: 55,267 double-digest restriction site-associated DNA (ddRAD) SNPs to assess genome-wide admixture, 16 microsatellites to provide continuity with published data and accurate biogeographic modelling, and a 491-bp fragment of mitochondrial cytochrome oxidase I and II to infer maternal inheritance patterns. Admixture zones correspond with regions impacted by the reorganization of Uganda's river networks that occurred during the formation of the West African Rift system over the last several hundred thousand years. Because tsetse fly Population distributions are defined by rivers, admixture zones likely represent both old and new regions of secondary contact. Our results indicate that older hybrid zones contain mostly parental types, while younger zones contain variable hybrid types resulting from multiple generations of interbreeding. These findings suggest that reproductive barriers are nearly complete in the older admixture zones, while nearly absent in the younger admixture zones. Findings are consistent with predictions of hybrid zone theory: Populations in zones of secondary contact transition rapidly from early to late stages of speciation or collapse all together.
Saha Atal - One of the best experts on this subject based on the ideXlab platform.
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Genetic complexity in the marine environment: Population Genomics of saithe (Pollachius virens), Greenland halibut (Reinhardtius hippoglossoides), beaked and golden redfish (Sebastes mentella and S. norvegicus) in the North Atlantic
UiT Norges arktiske universitet, 2016Co-Authors: Saha AtalAbstract:The papers of this thesis are not available in Munin. Paper I. Saha A et al.: Seascape genetics of saithe (Pollachius virens) across the North Atlantic using single nucleotide polymorphisms. Available in ICES Journal of Marine Science (2015), 72(9), 2732–2741 Paper II. Westgaard J-I, Saha A et al.: SNP markers from RAD sequences reveal management relevant genetic patterns in Greenland halibut (Reinhardtius hippoglossoides). (Manuscript). Paper III. Saha A et al.: Geographic extent of introgression in Sebastes mentella and its effect on genetic Population structure. (Manuscript). Paper IV. Saha A et al.: Cryptic Sebastes norvegicus species in Greenland waters revealed by microsatellites. (Manuscript).In this work, I investigated genetic complexity in four commercially exploited species from the North Atlantic: saithe (Pollachius virens L.), Greenland halibut (Reinhardtius hippoglossoides), and beaked and golden redfish (Sebastes mentella and S. norvegicus). The results were used 1) to assess the consistency between current management units and units identified by results based on genetic data for each species, and 2) to assess the efficiency of SNP data compared to conventional markers in studying Population Genomics. Panels of nuclear genomic markers, including single nucleotide polymorphisms (SNPs) and microsatellites, derived from modern genomic approaches, and data on species life history traits, were analyzed to explore genetic complexity within these highly migratory and continuously distributed species. The investigation reveals biologically distinct Populations within each of these species. Four genetic clusters of saithe and two clusters of Greenland halibut were found in the North Atlantic. For beaked redfish, results using both the genome-wide SNP and microsatellite data supported one group (‘shallow’) throughout the North Atlantic and a second group (‘deep’) in the central North Atlantic and Canadian waters. A localized group (‘slope’) of beaked redfish was identified in Greenland and Icelandic waters. Microsatellite DNA supported three unrecognized cryptic species of golden redfish in Greenland and nearby waters. Genetic isolation in golden and beaked redfish was greater than in saithe and Greenland halibut, which is possibly associated with unique life history features of redfishes. The results indicate a correlation between genetic differentiation and life history differences in the studied species. These findings imply that distinct genetic heterogeneity can exist in different marine species and may be influenced by different biotic and abiotic factors. The results highlight that in most cases the current management units of these species are comprised of multiple biological Populations. The new definition of gene pools may serve to define biologically meaningful management units to ensure their sustainable exploitation and preserve evolutionary legacies. This study provides the first SNP-based Population genomic investigation in saithe, Greenland halibut and beaked redfish. Comparative analyses of SNP and conventional marker systems demonstrate a higher resolution for SNP markers. Results from genome-wide SNP data identified the three genetic groups of beaked redfish from a much smaller sample set, and the estimated genetic differentiation was much greater than that found by other marker. Both in beaked redfish and Greenland halibut a sub-set of outlier SNPs were identified, implying possible signals of selection in these loci or nearby genomic sites. These outliers may provide increased power in Population assignment of the species. The present work illustrates outstanding opportunities of SNP marker system for investigating Population Genomics of non-model organisms
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Genetic complexity in the marine environment: Population Genomics of saithe (Pollachius virens), Greenland halibut (Reinhardtius hippoglossoides), beaked and golden redfish (Sebastes mentella and S. norvegicus) in the North Atlantic
'UiT The Arctic University of Norway', 2016Co-Authors: Saha AtalAbstract:In this work, I investigated genetic complexity in four commercially exploited species from the North Atlantic: saithe (Pollachius virens L.), Greenland halibut (Reinhardtius hippoglossoides), and beaked and golden redfish (Sebastes mentella and S. norvegicus). The results were used 1) to assess the consistency between current management units and units identified by results based on genetic data for each species, and 2) to assess the efficiency of SNP data compared to conventional markers in studying Population Genomics. Panels of nuclear genomic markers, including single nucleotide polymorphisms (SNPs) and microsatellites, derived from modern genomic approaches, and data on species life history traits, were analyzed to explore genetic complexity within these highly migratory and continuously distributed species. The investigation reveals biologically distinct Populations within each of these species. Four genetic clusters of saithe and two clusters of Greenland halibut were found in the North Atlantic. For beaked redfish, results using both the genome-wide SNP and microsatellite data supported one group (‘shallow’) throughout the North Atlantic and a second group (‘deep’) in the central North Atlantic and Canadian waters. A localized group (‘slope’) of beaked redfish was identified in Greenland and Icelandic waters. Microsatellite DNA supported three unrecognized cryptic species of golden redfish in Greenland and nearby waters. Genetic isolation in golden and beaked redfish was greater than in saithe and Greenland halibut, which is possibly associated with unique life history features of redfishes. The results indicate a correlation between genetic differentiation and life history differences in the studied species. These findings imply that distinct genetic heterogeneity can exist in different marine species and may be influenced by different biotic and abiotic factors. The results highlight that in most cases the current management units of these species are comprised of multiple biological Populations. The new definition of gene pools may serve to define biologically meaningful management units to ensure their sustainable exploitation and preserve evolutionary legacies. This study provides the first SNP-based Population genomic investigation in saithe, Greenland halibut and beaked redfish. Comparative analyses of SNP and conventional marker systems demonstrate a higher resolution for SNP markers. Results from genome-wide SNP data identified the three genetic groups of beaked redfish from a much smaller sample set, and the estimated genetic differentiation was much greater than that found by other marker. Both in beaked redfish and Greenland halibut a sub-set of outlier SNPs were identified, implying possible signals of selection in these loci or nearby genomic sites. These outliers may provide increased power in Population assignment of the species. The present work illustrates outstanding opportunities of SNP marker system for investigating Population Genomics of non-model organisms
Michael J Dover - One of the best experts on this subject based on the ideXlab platform.
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a Population Genomics analysis of the native irish galway sheep breed
Frontiers in Genetics, 2019Co-Authors: Gillian P Mchugo, Samuel S Browett, I A S Randhawa, Dawn J Howard, Michael P Mullen, Ian W Richardson, Stephen David Edward Park, David A Magee, Erik Scraggs, Michael J DoverAbstract:The Galway sheep Population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as ‘at-risk’. In the present study, comparative Population Genomics analyses of Galway sheep and other sheep Populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective Population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in production and health traits.
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a Population Genomics analysis of the native irish galway sheep breed
bioRxiv, 2019Co-Authors: Gillian P Mchugo, Samuel S Browett, I A S Randhawa, Dawn J Howard, Michael P Mullen, Ian W Richardson, Stephen David Edward Park, David A Magee, Erik Scraggs, Michael J DoverAbstract:The Galway sheep Population is the only native Irish sheep breed and represents an important livestock genetic resource, which is currently categorised as "at-risk". In the present study, comparative Population Genomics analyses of Galway sheep and other sheep Populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway breed and suggest more recent gene flow from the Suffolk sheep breed. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective Population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in meat and wool production.
Robert Opiro - One of the best experts on this subject based on the ideXlab platform.
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the Population Genomics of multiple tsetse fly glossina fuscipes fuscipes admixture zones in uganda
Molecular Ecology, 2019Co-Authors: Norah P. Saarman, Kirstin Dion, Robert Opiro, Chaz Hyseni, Richard Echodu, Elizabeth A Opiyo, Thomas Johnson, Adalgisa CacconeAbstract:Understanding the mechanisms that enforce, maintain or reverse the process of speciation is an important challenge in evolutionary biology. This study investigates the patterns of divergence and discusses the processes that form and maintain divergent lineages of the tsetse fly Glossina fuscipes fuscipes in Uganda. We sampled 251 flies from 18 sites spanning known genetic lineages and the four admixture zones between them. We apply Population Genomics, hybrid zone and approximate Bayesian computation to the analysis of three types of genetic markers: 55,267 double-digest restriction site-associated DNA (ddRAD) SNPs to assess genome-wide admixture, 16 microsatellites to provide continuity with published data and accurate biogeographic modelling, and a 491-bp fragment of mitochondrial cytochrome oxidase I and II to infer maternal inheritance patterns. Admixture zones correspond with regions impacted by the reorganization of Uganda's river networks that occurred during the formation of the West African Rift system over the last several hundred thousand years. Because tsetse fly Population distributions are defined by rivers, admixture zones likely represent both old and new regions of secondary contact. Our results indicate that older hybrid zones contain mostly parental types, while younger zones contain variable hybrid types resulting from multiple generations of interbreeding. These findings suggest that reproductive barriers are nearly complete in the older admixture zones, while nearly absent in the younger admixture zones. Findings are consistent with predictions of hybrid zone theory: Populations in zones of secondary contact transition rapidly from early to late stages of speciation or collapse all together.