scholarly journals Understanding population structure in an evolutionary context: population-specific FST and pairwise FST

2021 ◽  
Author(s):  
Shuichi Kitada ◽  
Reiichiro Nakamichi ◽  
Hirohisa Kishino
Keyword(s):  
Population Structure ◽  
Evolutionary History ◽  
Population Genomics ◽  
Atlantic Cod ◽  
Ancestral Population ◽  
Source Population ◽  
Moment Estimators ◽  
Current Population ◽  
Evolutionary Context ◽  
History Of

Abstract Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares estimate of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to coastal areas with abundant rainfall, and to the south where summers are dry. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable processing times and are useful in population genomics studies.

scholarly journals Understanding population structure in an evolutionary context: population-specific FST and pairwise FST

2020 ◽  
Author(s):  
Shuichi Kitada ◽  
Reiichiro Nakamichi ◽  
Hirohisa Kishino
Keyword(s):  
Population Structure ◽  
Evolutionary History ◽  
Population Genomics ◽  
Ancestral Population ◽  
Source Population ◽  
Moment Estimators ◽  
Current Population ◽  
Evolutionary Context ◽  
History Of ◽  
Representation Method

AbstractPopulations are shaped by their history. Therefore, it is crucial to interpret population structure in an evolutionary context. Wright’s FST measures current population structure, whereas population-specific FST measures deviation from the ancestral population. To understand current population structure and a population’s history of range expansion, we propose a novel representation method that overlays population-specific FST estimates on an unrooted neighbor-joining tree inferred from a pairwise FST distance matrix and on a map of sampling locations. We examined the usefulness of our procedure by conducting simulations that mimicked population colonization from an ancestral population and analyzing published human, Atlantic cod, and wild poplar genotype data sets. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations based on genetic diversity. In contrast, pairwise FST values represent the current population structure. By integrating results of both estimators, we obtained a new picture of current population structure that incorporates evolutionary history. The generalized least squares of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north where it adapted to longer day lengths, to seashores where it adapted to abundant rainfall, and to the south where it adapted to dry summers. Genomic data highlight the power of the bias-corrected moment estimators of FST. All FST moment estimators described in this paper have reasonable CPU times and are useful in population genomics studies. The R codes for our representation method and simulations are available in the Supporting Information.

scholarly journals The Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history

2018 ◽  
Author(s):  
Danièle Filiault ◽  
Evangeline S. Ballerini ◽  
Terezie Mandáková ◽  
Gökçe Aköz ◽  
Nathan Derieg ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Evolutionary History ◽  
Wide Distribution ◽  
Allele Sharing ◽  
Sequencing Data ◽  
High Coverage ◽  
The World ◽  
Entire Chromosome ◽  
Evolutionary Context ◽  
History Of

AbstractThe columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea ‘Goldsmith’, complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome – a phenomenon which we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

scholarly journals Genome-wide population structure and evolutionary history of the Frizarta dairy sheep

animal ◽  
2017 ◽  
Vol 11 (10) ◽  
pp. 1680-1688 ◽  
Author(s):  
A. Kominakis ◽  
A.L. Hager-Theodorides ◽  
A. Saridaki ◽  
G. Antonakos ◽  
G. Tsiamis
Keyword(s):  
Population Structure ◽  
Evolutionary History ◽  
Dairy Sheep ◽  
Genome Wide ◽  
History Of ◽  
Wide Population

scholarly journals Inferring number of populations and changes in connectivity under the n-island model

Heredity ◽  
2021 ◽  
Author(s):  
Armando Arredondo ◽  
Beatriz Mourato ◽  
Khoa Nguyen ◽  
Simon Boitard ◽  
Willy Rodríguez ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Demographic History ◽  
Simulated Data ◽  
Fixed Number ◽  
Ancestral Population ◽  
Demographic Model ◽  
History Of ◽  
Time Periods

AbstractInferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate). The IICR can be estimated for a single diploid individual using the PSMC method of Li and Durbin (2011). For an isolated panmictic population, the IICR matches the population size history, and this is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme with limited connection to population size changes. Our method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise stationary symmetrical island models. In our models we assume a fixed number of time periods during which gene flow is constant, but gene flow is allowed to change between time periods. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.

scholarly journals An African origin for Mycobacterium bovis

2020 ◽  
Vol 2020 (1) ◽  
pp. 49-59 ◽  
Author(s):  
Chloé Loiseau ◽  
Fabrizio Menardo ◽  
Abraham Aseffa ◽  
Elena Hailu ◽  
Balako Gumi ◽  
...  
Keyword(s):  
Population Structure ◽  
West Africa ◽  
Mycobacterium Bovis ◽  
Evolutionary History ◽  
Whole Genome ◽  
Genome Sequences ◽  
The World ◽  
History Of ◽  
Global Population ◽  
Different Parts

Abstract Background and objectives Mycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis in livestock and the most important causes of zoonotic tuberculosis in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens. Methodology We compiled a global collection of 3364 whole-genome sequences from M.bovis and M.caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age. Results Our results resolved the phylogenetic relationship among the four previously defined clonal complexes of M.bovis, and another eight newly described here. Our phylogeographic analysis showed that M.bovis likely originated in East Africa. While some groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world. Conclusions and implications Our results allow a better understanding of the global population structure of M.bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M.bovis in settings where whole-genome sequencing cannot easily be implemented. Lay summary During the last few years, analyses of large globally representative collections of whole-genome sequences (WGS) from the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages have enhanced our understanding of the global population structure, phylogeography and evolutionary history of these pathogens. In contrast, little corresponding data exists for M. bovis, the most important agent of tuberculosis in livestock. Using whole-genome sequences of globally distributed M. bovis isolates, we inferred the genetic relationships among different M. bovis genotypes distributed around the world. The most likely origin of M. bovis is East Africa according to our inferences. While some M. bovis groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world driven by cattle movements.

scholarly journals Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9980
Author(s):  
José J. Nuñez ◽  
Elkin Y. Suárez-Villota ◽  
Camila A. Quercia ◽  
Angel P. Olivares ◽  
Jack W. Sites Jr
Keyword(s):  
Population Structure ◽  
Species Distribution ◽  
Evolutionary History ◽  
Environmental Changes ◽  
Glacial Refugia ◽  
Species Distribution Modelling ◽  
Wood Frog ◽  
Type I ◽  
Distribution Modelling ◽  
History Of

Background The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population structure and diversification of the biota, because they are sensitive to environmental changes and have restricted dispersal capabilities. We test hypotheses regarding putative forest refugia and expansion events associated with past climatic changes in the wood frog Batrachyla leptopus distributed along ∼1,000 km of length including glaciated and non-glaciated areas in southwestern Patagonia. Methods Using three mitochondrial regions (D-loop, cyt b, and coI) and two nuclear loci (pomc and crybA1), we conducted multilocus phylogeographic analyses and species distribution modelling to gain insights of the evolutionary history of this species. Intraspecific genealogy was explored with maximum likelihood, Bayesian, and phylogenetic network approaches. Diversification time was assessed using molecular clock models in a Bayesian framework, and demographic scenarios were evaluated using approximate Bayesian computation (ABC) and extended Bayesian skyline plot (EBSP). Species distribution models (SDM) were reconstructed using climatic and geographic data. Results Population structure and genealogical analyses support the existence of four lineages distributed north to south, with moderate to high phylogenetic support (Bootstrap > 70%; BPP > 0.92). The diversification time of B. leptopus’ populations began at ∼0.107 mya. The divergence between A and B lineages would have occurred by the late Pleistocene, approximately 0.068 mya, and divergence between C and D lineages was approximately 0.065 mya. The ABC simulations indicate that lineages coalesced at two different time periods, suggesting the presence of at least two glacial refugia and a postglacial colonization route that may have generated two southern lineages (p = 0.93, type I error: <0.094, type II error: 0.134). EBSP, mismatch distribution and neutrality indexes suggest sudden population expansion at ∼0.02 mya for all lineages. SDM infers fragmented distributions of B. leptopus associated with Pleistocene glaciations. Although the present populations of B. leptopus are found in zones affected by the last glacial maximum (∼0.023 mya), our analyses recover an older history of interglacial diversification (0.107–0.019 mya). In addition, we hypothesize two glacial refugia and three interglacial colonization routes, one of which gave rise to two expanding lineages in the south.

scholarly journals Inferring number of populations and changes in connectivity under the n-island model

2020 ◽  
Author(s):  
Armando Arredondo ◽  
Beatriz Mourato ◽  
Khoa Nguyen ◽  
Simon Boitard ◽  
Willy Rodríguez ◽  
...  
Keyword(s):  
Population Structure ◽  
Demographic History ◽  
A Priori ◽  
Simulated Data ◽  
Fixed Number ◽  
Ancestral Population ◽  
Demographic Model ◽  
Automated Method ◽  
History Of ◽  
Diploid Individual

AbstractInferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, thus ignoring population structure. Alternatively, structure is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate), which can be estimated using the PSMC method of Li and Durbin (2011) for a single diploid individual. For an isolated population, the IICR matches the population size history, which is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme. Our automated method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise-stationary symmetrical island models, in which we assume a fixed number of time periods during which gene flow is constant. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the widely accepted view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.

scholarly journals Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

2019 ◽  
Author(s):  
Maria Luisa Martin Cerezo ◽  
Marek Kucka ◽  
Karol Zub ◽  
Yingguang Frank Chan ◽  
Jarosław Bryk
Keyword(s):  
Population Structure ◽  
Restriction Site ◽  
Population Genomics ◽  
Large Degree ◽  
Apodemus Flavicollis ◽  
Ecological Genomics ◽  
Genome Data ◽  
Northern Poland ◽  
Show Evidence ◽  
History Of

AbstractBackgroundMice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context.ResultsHere we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST < 0.086.ConclusionOur study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.

scholarly journals Donkey genomes provide new insights into domestication and selection for coat color

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Changfa Wang ◽  
Haijing Li ◽  
Yu Guo ◽  
Jinming Huang ◽  
Yan Sun ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genetic Basis ◽  
Population Genomics ◽  
De Novo ◽  
Coat Color ◽  
Current Knowledge ◽  
Inhibitory Effect ◽  
Reproductive Management ◽  
History Of ◽  
Selection For

AbstractCurrent knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.

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