scholarly journals Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand

2017 ◽  
Author(s):  
Yeşerin Yıldırım ◽  
Marti J. Anderson ◽  
Selina Patel ◽  
Craig D. Millar ◽  
Paul B. Rainey
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Haplotype Network ◽  
Founding Population ◽  
Mtdna Sequence ◽  
Expansion Time ◽  
History Of

AbstractPleurobranchaea maculatais a rarely studied species of the Heterobranchia found throughout the south and western Pacific – and recently recorded in Argentina – whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history ofP. maculatapopulations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and theCOIandCytBregions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence from Argentinian sea slugs did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.

Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

2011 ◽  
Vol 102 (3) ◽  
pp. 333-343 ◽  
Author(s):  
K.C. Albernaz ◽  
K.L. Silva-Brandão ◽  
P. Fresia ◽  
F.L. Cônsoli ◽  
C. Omoto
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Heliothis Virescens ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Haplotype Network ◽  
Demographic Expansion ◽  
Significant Genetic Structure ◽  
History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

scholarly journals Population Genetics of New Zealand Nemadactylus macropterus (tarakihi) and Characterisation of their Mitochondrial Genome

2021 ◽  
Author(s):  
◽  
Alexander Halliwell
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Genetic Structure ◽  
East Coast ◽  
Demographic History ◽  
Variable Region ◽  
Sequencing Data ◽  
Commercial Catch ◽  
History Of ◽  
Hyper Variable Region

<p>Nemadactylus macropterus, commonly known as tarakihi in New Zealand is highly regarded by commercial and recreational fishers and considered a taonga by iwi and customary fisheries. For many years N. macropterus was New Zealand’s second most important commercial catch and is currently the third most valuable inshore commercial finfish fishery in which 90% is consumed by the domestic market. However, despite the apparent importance, relatively little is known about the population structure of the N. macropterus. In 2017 the first fully quantitative stock assessment was conducted on the east coast N. macropterus fisheries as one stock. Alarmingly, the east coast fishery was estimated to be 15.9% of the unexploited spawning biomass and predicted to have been declining for the past thirty years. In an effort to rebuild the fishery, several rebuild plans have been purposed and commercial catch limits have been reduced. In order to rebuild and successfully manage a viable future N. macropterus fishery, an understanding of demographic connectivity and genetic connectivity among N. macropterus populations is essential.  The overall goal of this thesis research was to investigate the population genetic structure, genetic diversity and demographic history of N. macropterus using fish sampled from around New Zealand. This was achieved by analysing hyper variable region one of mitochondrial DNA for 370 N. macropterus collected from 14 locations. No genetic differentiation was observed among the 14 locations, an indication that N. macropterus have a panmictic genetic structure. Furthermore, N. macropterus display a relatively high level of genetic diversity and appear to have a large stable population with a long evolutionary history. The Bayesian skyline analysis indicates the N. macropterus historic population has gone through two expansions. The mostly likely cause of this is an expansion before and after the last glacial maximum.  The genetic diversity and demographic history of N. sp was also studied using samples collected from around the Three Kings Islands of New Zealand. The complete mitochondrial genome of N. macropterus was reconstructed from bulk DNA sequencing data and a set of specific mtDNA primers were developed to amplify hyper variable region one. The DNA sequencing data provided by these primers with the addition of published control region sequences was used to reconstruct the Nemadactylus phylogeny.</p>

scholarly journals A first investigation into the evolutionary relationships, population structure and demographic history of New Zealand Trevally (Pseudocaranx georgianus) and its implications for fisheries management

2021 ◽  
Author(s):  
◽  
Leah Kemp
Keyword(s):  
Population Structure ◽  
New Zealand ◽  
Western Australia ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Whole Genome Sequence ◽  
Coi Gene ◽  
P Value

<p>Pseudocaranx georgianus is a commercially important fishery in New Zealand. Currently, the management of this fishery assumes that Quota Management Areas comprise single biological stocks of a single species. However, little is known regarding the population structure of New Zealand P. georgianus and morphological data suggests that a cryptic Pseudocaranx species is included within these fisheries.  Whole genome sequence data was used to assemble and describe the first P. georgianus mitogenome. Primers were developed to produce the first genetic sequence data for New Zealand P. georgianus. The cytochrome c oxidase subunit I (COI) gene was sequenced for fourteen P. georgianus from New Zealand waters. These were compared phylogenetically with existing COI sequence data for P. georgianus from Australia and other Pseudocaranx species from a world-wide distribution. The hyper-variable control region of 304 P. georgianus sampled throughout New Zealand’s North Island and 68 P. georgianus from three locations in Western Australia were also sequenced. These sequences were used to explore the population structure and demographic history of New Zealand P. georgianus using haplotype networks, AMOVA’s, genetic diversity measures, Tajima’s D, Fu’s F and Bayesian migration analyses.  The P. georgianus mitogenome is typical of Cartilaginous fish species showing no major gene rearrangements, typical gene region lengths and stop and start codons. While assembling the P. georgianus mitogenome, this thesis demonstrates the importance of key methodological choices made when assembling mitogenomes from whole genome sequence data in silco in Geneious version 11.1. The choice of reference mitogenome has the largest influence on the quality of the assembly, impacting the annotation of the final mitogenome and the resolution of uncertain DNA regions. Increasing the number of mapping iterations increased the quality of the assembly but has a limited ability to mitigate the effects of using a poor reference mitogenome. Overall, I demonstrate the need to investigate and report the quality of published mitogenomes.   All Pseudocaranx species were monophyletic on the COI gene, supporting the current taxonomy of the Pseudocaranx complex. P. georgianus from Western Australia and New Zealand’s North Island represent a monophyletic clade pending a taxonomic verification that two Pseudocaranx dentex sampled in Australia are in fact P. georgianus.   No evidence was found to suggest that either of the New Zealand or Western Australian populations of P. georgianus are isolated by distance or clearly structured as distinct stocks. However, some populations of New Zealand P. georgianus were genetically distinct, including fish sampled from Raglan and the Bay of Plenty (FST of 0.02698 (p-value: 0.00901+-0.0091) as well as the North Cape and North Taranaki Bight (FST: 0.02698, p-value: 0.00901+-0.0091).   Some evidence was found to support the claim that P. georgianus along the west coast of New Zealand’s North Island is structured and no evidence was found to refute the claim that fish from the Bay of Plenty are the same biological stock as fish from TRE2. Highly divergent control region sequences of fish sampled from Three Kings Islands and the Kermadec Islands suggest that these fish could be a species distinct from P. georgianus. Two genetically distinct populations of P. georgianus were identified in New Zealand’s North Island and Western Australia (FST: 0.03517, p-value < 0.001), but further research would be required to determine if they are distinct species or populations. One juvenile population sampled in Whangarei had a high level of genetic connectivity with adult P. georgianus throughout New Zealand’s North Island, likely reflecting the batch spawning and occasional long-distance migration behaviour of P. georgianus.  Negative Tajima’s D and Fu’s F statistics (D: -1.50612, p-value: 0.018; F: -23.54376, p-value: 0.011), unimodal mismatch distributions and skyline plots indicate that the New Zealand P. georgianus population has undergone a population expansion, possibly resulting from a geographic range expansion.The Western Australian population may also have undergone a population expansion (D: -1.27903, p-value: 0.086; F: -24.11497, p-value < 0.00001). However, a multimodal mismatch distribution (Harpending’s Raggedness index: 0.00454591, p-value: 0.02) indicated that there is some stability in the size of this population.   This thesis is a first genetic investigation into New Zealand P. georgianus and has provided important biological insights into this species. Valuable information is revealed which will inform the management of New Zealand P. georgianus fisheries as inputs for stock assessment models. Additionally, several future research directions have been revealed which will further extend our knowledge of this taonga. For example, future genetic and taxonomic analyses may reveal a cryptic Pseudocaranx species occurring in the Three Kings and Kermadec Islands.</p>

scholarly journals Population Genetics of New Zealand Nemadactylus macropterus (tarakihi) and Characterisation of their Mitochondrial Genome

2021 ◽  
Author(s):  
◽  
Alexander Halliwell
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Genetic Structure ◽  
East Coast ◽  
Demographic History ◽  
Variable Region ◽  
Sequencing Data ◽  
Commercial Catch ◽  
History Of ◽  
Hyper Variable Region

<p>Nemadactylus macropterus, commonly known as tarakihi in New Zealand is highly regarded by commercial and recreational fishers and considered a taonga by iwi and customary fisheries. For many years N. macropterus was New Zealand’s second most important commercial catch and is currently the third most valuable inshore commercial finfish fishery in which 90% is consumed by the domestic market. However, despite the apparent importance, relatively little is known about the population structure of the N. macropterus. In 2017 the first fully quantitative stock assessment was conducted on the east coast N. macropterus fisheries as one stock. Alarmingly, the east coast fishery was estimated to be 15.9% of the unexploited spawning biomass and predicted to have been declining for the past thirty years. In an effort to rebuild the fishery, several rebuild plans have been purposed and commercial catch limits have been reduced. In order to rebuild and successfully manage a viable future N. macropterus fishery, an understanding of demographic connectivity and genetic connectivity among N. macropterus populations is essential.  The overall goal of this thesis research was to investigate the population genetic structure, genetic diversity and demographic history of N. macropterus using fish sampled from around New Zealand. This was achieved by analysing hyper variable region one of mitochondrial DNA for 370 N. macropterus collected from 14 locations. No genetic differentiation was observed among the 14 locations, an indication that N. macropterus have a panmictic genetic structure. Furthermore, N. macropterus display a relatively high level of genetic diversity and appear to have a large stable population with a long evolutionary history. The Bayesian skyline analysis indicates the N. macropterus historic population has gone through two expansions. The mostly likely cause of this is an expansion before and after the last glacial maximum.  The genetic diversity and demographic history of N. sp was also studied using samples collected from around the Three Kings Islands of New Zealand. The complete mitochondrial genome of N. macropterus was reconstructed from bulk DNA sequencing data and a set of specific mtDNA primers were developed to amplify hyper variable region one. The DNA sequencing data provided by these primers with the addition of published control region sequences was used to reconstruct the Nemadactylus phylogeny.</p>

scholarly journals Demographic History of Indigenous Populations in Mesoamerica Based on mtDNA Sequence Data

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0131791 ◽  
Author(s):  
Antonio González-Martín ◽  
Amaya Gorostiza ◽  
Lucía Regalado-Liu ◽  
Sergio Arroyo-Peña ◽  
Sergio Tirado ◽  
...  
Keyword(s):  
Sequence Data ◽  
Demographic History ◽  
Indigenous Populations ◽  
Mtdna Sequence ◽  
History Of

scholarly journals A first investigation into the evolutionary relationships, population structure and demographic history of New Zealand Trevally (Pseudocaranx georgianus) and its implications for fisheries management

2021 ◽  
Author(s):  
◽  
Leah Kemp
Keyword(s):  
Population Structure ◽  
New Zealand ◽  
Western Australia ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Whole Genome Sequence ◽  
Coi Gene ◽  
P Value

<p>Pseudocaranx georgianus is a commercially important fishery in New Zealand. Currently, the management of this fishery assumes that Quota Management Areas comprise single biological stocks of a single species. However, little is known regarding the population structure of New Zealand P. georgianus and morphological data suggests that a cryptic Pseudocaranx species is included within these fisheries.  Whole genome sequence data was used to assemble and describe the first P. georgianus mitogenome. Primers were developed to produce the first genetic sequence data for New Zealand P. georgianus. The cytochrome c oxidase subunit I (COI) gene was sequenced for fourteen P. georgianus from New Zealand waters. These were compared phylogenetically with existing COI sequence data for P. georgianus from Australia and other Pseudocaranx species from a world-wide distribution. The hyper-variable control region of 304 P. georgianus sampled throughout New Zealand’s North Island and 68 P. georgianus from three locations in Western Australia were also sequenced. These sequences were used to explore the population structure and demographic history of New Zealand P. georgianus using haplotype networks, AMOVA’s, genetic diversity measures, Tajima’s D, Fu’s F and Bayesian migration analyses.  The P. georgianus mitogenome is typical of Cartilaginous fish species showing no major gene rearrangements, typical gene region lengths and stop and start codons. While assembling the P. georgianus mitogenome, this thesis demonstrates the importance of key methodological choices made when assembling mitogenomes from whole genome sequence data in silco in Geneious version 11.1. The choice of reference mitogenome has the largest influence on the quality of the assembly, impacting the annotation of the final mitogenome and the resolution of uncertain DNA regions. Increasing the number of mapping iterations increased the quality of the assembly but has a limited ability to mitigate the effects of using a poor reference mitogenome. Overall, I demonstrate the need to investigate and report the quality of published mitogenomes.   All Pseudocaranx species were monophyletic on the COI gene, supporting the current taxonomy of the Pseudocaranx complex. P. georgianus from Western Australia and New Zealand’s North Island represent a monophyletic clade pending a taxonomic verification that two Pseudocaranx dentex sampled in Australia are in fact P. georgianus.   No evidence was found to suggest that either of the New Zealand or Western Australian populations of P. georgianus are isolated by distance or clearly structured as distinct stocks. However, some populations of New Zealand P. georgianus were genetically distinct, including fish sampled from Raglan and the Bay of Plenty (FST of 0.02698 (p-value: 0.00901+-0.0091) as well as the North Cape and North Taranaki Bight (FST: 0.02698, p-value: 0.00901+-0.0091).   Some evidence was found to support the claim that P. georgianus along the west coast of New Zealand’s North Island is structured and no evidence was found to refute the claim that fish from the Bay of Plenty are the same biological stock as fish from TRE2. Highly divergent control region sequences of fish sampled from Three Kings Islands and the Kermadec Islands suggest that these fish could be a species distinct from P. georgianus. Two genetically distinct populations of P. georgianus were identified in New Zealand’s North Island and Western Australia (FST: 0.03517, p-value < 0.001), but further research would be required to determine if they are distinct species or populations. One juvenile population sampled in Whangarei had a high level of genetic connectivity with adult P. georgianus throughout New Zealand’s North Island, likely reflecting the batch spawning and occasional long-distance migration behaviour of P. georgianus.  Negative Tajima’s D and Fu’s F statistics (D: -1.50612, p-value: 0.018; F: -23.54376, p-value: 0.011), unimodal mismatch distributions and skyline plots indicate that the New Zealand P. georgianus population has undergone a population expansion, possibly resulting from a geographic range expansion.The Western Australian population may also have undergone a population expansion (D: -1.27903, p-value: 0.086; F: -24.11497, p-value < 0.00001). However, a multimodal mismatch distribution (Harpending’s Raggedness index: 0.00454591, p-value: 0.02) indicated that there is some stability in the size of this population.   This thesis is a first genetic investigation into New Zealand P. georgianus and has provided important biological insights into this species. Valuable information is revealed which will inform the management of New Zealand P. georgianus fisheries as inputs for stock assessment models. Additionally, several future research directions have been revealed which will further extend our knowledge of this taonga. For example, future genetic and taxonomic analyses may reveal a cryptic Pseudocaranx species occurring in the Three Kings and Kermadec Islands.</p>

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

scholarly journals Reef development and Sea level changes drive Acanthaster Population Expansion in the Indo-Pacific region

2020 ◽  
Author(s):  
P.C. Pretorius ◽  
T.B. Hoareau
Keyword(s):  
Population Size ◽  
Sea Level ◽  
Environmental Changes ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Population Level ◽  
Sea Level Changes ◽  
Reef Development ◽  
Curve Fitting Method

AbstractMolecular clock calibration is central in population genetics as it provides an accurate inference of demographic history, whereby helping with the identification of driving factors of population changes in an ecosystem. This is particularly important for coral reef species that are seriously threatened globally and in need of conservation. Biogeographic events and fossils are the main source of calibration, but these are known to overestimate timing and parameters at population level, which leads to a disconnection between environmental changes and inferred reconstructions. Here, we propose the Last Glacial Maximum (LGM) calibration that is based on the assumptions that reef species went through a bottleneck during the LGM, which was followed by an early yet marginal increase in population size. We validated the LGM calibration using simulations and genetic inferences based on Extended Bayesian Skyline Plots. Applying it to mitochondrial sequence data of crown-of-thorns starfish Acanthaster spp., we obtained mutation rates that were higher than phylogenetically based calibrations and varied among populations. The timing of the greatest increase in population size differed slightly among populations, but all started between 10 and 20 kya. Using a curve-fitting method, we showed that Acanthaster populations were more influenced by sea-level changes in the Indian Ocean and by reef development in the Pacific Ocean. Our results illustrate that the LGM calibration is robust and can probably provide accurate demographic inferences in many reef species. Application of this calibration has the potential to help identify population drivers that are central for the conservation and management of these threatened ecosystems.

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

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