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Samat K. Shibitov - One of the best experts on this subject based on the ideXlab platform.
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Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke Opisthorchis felineus Suggests Special Demographic History of This Trematode Species
2016Co-Authors: Ilja I. Brusentsov, Alexey Katokhin, Irina V. Brusentsova, Sergei V. Shekhovtsov, Sergei N. Borovikov, Grigoriy G. Goncharenko, Lyudmila A. Lider, Boris V. Romashov, Olga T. Rusinek, Samat K. ShibitovAbstract:Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and Demographic History. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations fro
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Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke Opisthorchis felineus Suggests Special Demographic History of This Trematode Species
PloS one, 2013Co-Authors: Ilja I. Brusentsov, Alexey Katokhin, Irina V. Brusentsova, Sergei V. Shekhovtsov, Sergei N. Borovikov, Grigoriy G. Goncharenko, Lyudmila A. Lider, Boris V. Romashov, Olga T. Rusinek, Samat K. ShibitovAbstract:Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and Demographic History. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species.
Ilja I. Brusentsov - One of the best experts on this subject based on the ideXlab platform.
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Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke Opisthorchis felineus Suggests Special Demographic History of This Trematode Species
2016Co-Authors: Ilja I. Brusentsov, Alexey Katokhin, Irina V. Brusentsova, Sergei V. Shekhovtsov, Sergei N. Borovikov, Grigoriy G. Goncharenko, Lyudmila A. Lider, Boris V. Romashov, Olga T. Rusinek, Samat K. ShibitovAbstract:Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and Demographic History. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations fro
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Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke Opisthorchis felineus Suggests Special Demographic History of This Trematode Species
PloS one, 2013Co-Authors: Ilja I. Brusentsov, Alexey Katokhin, Irina V. Brusentsova, Sergei V. Shekhovtsov, Sergei N. Borovikov, Grigoriy G. Goncharenko, Lyudmila A. Lider, Boris V. Romashov, Olga T. Rusinek, Samat K. ShibitovAbstract:Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and Demographic History. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species.
Quentin Rougemont - One of the best experts on this subject based on the ideXlab platform.
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Demographic History shaped geographical patterns of deleterious mutation load in a broadly distributed pacific salmon
PLOS Genetics, 2020Co-Authors: Quentin Rougemont, Jeansebastien Moore, Thibault Leroy, Eric Normandeau, Eric Rondeau, Ruth E Withler, Donald M Van Doornik, Penelope A Crane, Kerry A NaishAbstract:A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded recently, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent Demographic History of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.
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Demographic History shaped geographical patterns of deleterious mutation load in a broadly distributed pacific salmon
bioRxiv, 2020Co-Authors: Quentin Rougemont, Jeansebastien Moore, Thibault Leroy, Eric Normandeau, Eric Rondeau, Ruth E Withler, Donald M Van Doornik, Penelope A Crane, Kerry A NaishAbstract:Abstract A thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent Demographic History of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.
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Demographic History and genomics of local adaptation in blue tit populations
bioRxiv, 2020Co-Authors: Quentin Rougemont, Charles Perrier, Anne CharmantierAbstract:Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.004 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long-lasting gene flow between populations, inferred by Demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migrations, followed by isolation since the end of the last glaciation. Effective population sizes were overall large, yet smaller on the island than on the mainland. Weak and non-parallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds, and were more often found in regions of low recombination as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8Mb. These results provide insights into the Demographic History and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.
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Demographic History linked selection and recombination shape the genomic landscape of a broadly distributed pacific salmon
bioRxiv, 2019Co-Authors: Quentin Rougemont, Jeansebastien Moore, Thibault Leroy, Eric Normandeau, Eric Rondeau, Ruth E Withler, Donald M Van Doornik, Penelope A Crane, Kerry A Naish, John Carlos GarzaAbstract:Abstract Understanding the impacts of current human activities on within-species genetic variation requires a thorough description of the historical factors that have shaped the genomic and geographical distribution of nucleotide diversity. Past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential under the nearly neutral theory. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncoryhnchus kisutch) to address three issues. First, we demonstrate that a single glacial refugium is the source of the majority of present-day genetic diversity, with minor but detectable inputs from secondary micro-refugia. We propose a scenario whereby several ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Following this expansion, we identify particular populations having undergone continuous declines in population size (Ne). Second, we combine multiple evidence from Demographic modelling, analysis of recombination landscape, and genome-wide landscape of diversity to demonstrate that selection at linked sites and Hill-Robertson interference played a major role in shaping genetic diversity across the Coho salmon genome. Third, we demonstrate that this Demographic History generated subtle differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations. Taken together, we found considerable support for the joint contributions of Demographic History and linked selection in the load of deleterious mutations. We suggest that these inferences should be better integrated in conservation genetics of managed fish species which currently focuses largely on within-population adaptation. Author Summary Reconstruction of a species’ past Demographic History from genome-wide data allows understanding how historical factors interact with intrinsic genomic properties to shape the distribution of genetic diversity along its genome and its geographic range. Here, we combine genotyping-by-sequencing and whole genome sequence data with Demographic modelling to address these issues in the Coho salmon, a Pacific salmon species with rapidly declining census size in some parts of its range, notably in the south. Our Demographic reconstructions indicate a linear decrease in genetic diversity towards the north of the species range, supporting the hypothesis of a major southern refugia for the Coho salmon and a northern route of postglacial recolonization. Accordingly, the number of candidate deleterious homozygous derived mutations was higher in northern populations. Demographic modelling also suggested the existence of cryptic refugia that may have been missed with the use of simpler summary statistics. We further showed that the species’ genome was shaped by linked selection and biased gene conversion. In particular, local variation in recombination rates have modulated the efficacy of natural selection. These processes, together with a complex Demographic History, can contribute to the load of deleterious mutations – an effect we argue should be taken into account more routinely in conservation genetics studies.
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the Demographic History of atlantic salmon salmo salar across its distribution range reconstructed from approximate bayesian computations
Evolution, 2018Co-Authors: Quentin Rougemont, Louis BernatchezAbstract:Understanding the dual roles of Demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the Demographic History of Atlantic salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo-genetic maps, and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern American populations, but also identified secondary contacts in European populations from different glacial refugia. We further identified the major sources of admixture from the southern range of North America into more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflect the spatial redistribution of ancestral variation across the entire North American range. Results also support a role for linked selection and differential introgression that likely played an underappreciated role in shaping the genomic landscape of species in the Northern hemisphere. We conclude that studies between partially isolated populations should systematically include heterogeneity in selective and introgressive effects among loci to perform more rigorous Demographic inferences of the divergence process.
Antonio Molina - One of the best experts on this subject based on the ideXlab platform.
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A genome-wide perspective about the diversity and Demographic History of seven Spanish goat breeds
Genetics Selection Evolution, 2016Co-Authors: A Manunza, Eva Munoz, Jordi Jordana, Juan Manuel Serradilla, Juan Vicente Delgado, Félix Goyache, Juan Capote, Antonia Noce, Amparo Martínez, Antonio MolinaAbstract:BackgroundThe main goal of the current work was to infer the Demographic History of seven Spanish goat breeds (Malagueña, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genome-wide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonké and Sahel) were also included in this analysis (N = 80) for comparative purposes.ResultsOur results show that the genetic background of Spanish goats traces back mainly to European breeds although signs of North African admixture were detected in two Andalusian breeds (Malagueña and Murciano-Granadina). In general, observed and expected heterozygosities were quite similar across the seven Spanish goat breeds under analysis irrespective of their population size and conservation status. For the Mallorquina and Blanca de Rasquera breeds, which have suffered strong population declines during the past decades, we observed increased frequencies of large-sized (ROH), a finding that is consistent with recent inbreeding. In contrast, a substantial part of the genome of the Palmera goat breed comprised short ROH, which suggests a strong and ancient founder effect.ConclusionsAdmixture with African goats, genetic drift and inbreeding have had different effects across the seven Spanish goat breeds analysed in the current work. This has generated distinct patterns of genome-wide diversity that provide new clues about the Demographic History of these populations.
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a genome wide perspective about the diversity and Demographic History of seven spanish goat breeds
Genetics Selection Evolution, 2016Co-Authors: A Manunza, Amparo Martinez Martinez, Eva Munoz, Jordi Jordana, Juan Manuel Serradilla, Annalisa Noce, Juan Vicente Delgado, Félix Goyache, Juan Capote, Antonio MolinaAbstract:Background The main goal of the current work was to infer the Demographic History of seven Spanish goat breeds (Malaguena, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genome-wide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonke and Sahel) were also included in this analysis (N = 80) for comparative purposes.
K. Gharbi - One of the best experts on this subject based on the ideXlab platform.
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Deciphering the Demographic History of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa
Molecular Ecology, 2018Co-Authors: Raphaël Leblois, Mathieu Gautier, Audrey Rohfritsch, Julien Foucaud, Christian Burban, Maxime Galan, Anne Loiseau, Laure Saune, M. Branco, K. GharbiAbstract:Understanding the processes of adaptive divergence, which may ultimately lead to speciation, is a major question in evolutionary biology. Allochronic differentiation refers to a particular situation where gene flow is primarily impeded by temporal isolation between early and late reproducers. This process has been suggested to occur in a large array of organisms, even though it is still overlooked in the literature. We here focused on a well-documented case of incipient allochronic speciation in the winter pine processionary moth Thaumetopoea pityocampa. This species typically reproduces in summer and larval development occurs throughout autumn and winter. A unique, phenologically shifted population (SP) was discovered in 1997 in Portugal. It was proved to be strongly differentiated from the sympatric "winter population" (WP), but its evolutionary History could only now be explored. We took advantage of the recent assembly of a draft genome and of the development of pan-genomic RAD-seq markers to decipher the Demographic History of the differentiating populations and develop genome scans of adaptive differentiation. We showed that the SP diverged relatively recently, that is, few hundred years ago, and went through two successive bottlenecks followed by population size expansions, while the sympatric WP is currently experiencing a population decline. We identified outlier SNPs that were mapped onto the genome, but none were associated with the phenological shift or with subsequent adaptations. The strong genetic drift that occurred along the SP lineage certainly challenged our capacity to reveal functionally important loci.