scholarly journals Inference with selection, varying population size and evolving population structure: Application of ABC to a forward-backward coalescent process with interactions

2019 ◽  
Author(s):  
Clotilde Lepers ◽  
Sylvain Billiard ◽  
Matthieu Porte ◽  
Sylvie Méléard ◽  
Viet Chi Tran
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
A Priori ◽  
Real Data ◽  
Genetic Data ◽  
Accurate Estimate ◽  
Asexual Population ◽  
Y Chromosomes ◽  
Population Structures ◽  
Approximate Bayesian

AbstractGenetic data are often used to infer history, demographic changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed a priori known, the evolution of the genetic composition of a population does not affect demography nor population structure, and there is no selection nor interaction between and within genetic strains. In this paper, we present a stochastic birth-death model with competitive interaction to describe an asexual population, and we develop an inferential procedure for ecological, demographic and genetic parameters. We first show how genetic diversity and genealogies are related to birth and death rates, and to how individuals compete within and between strains. This leads us to propose an original model of phylogenies, with trait structure and interactions, that allows multiple merging. Second, we develop an Approximate Bayesian Computation framework to use our model for analyzing genetic data. We apply our procedure to simulated and real data. We show that the procedure give accurate estimate of the parameters of the model. We finally carry an illustration on real data and analyze the genetic diversity of microsatellites on Y-chromosomes sampled from Central Asia populations in order to test whether different social organizations show significantly different fertility.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

scholarly journals Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 306
Author(s):  
Maurizio Rossetto ◽  
Peter D. Wilson ◽  
Jason Bragg ◽  
Joel Cohen ◽  
Monica Fahey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
A Priori ◽  
Genetic Data ◽  
Environmental Data ◽  
Specific Data ◽  
Acacia Species ◽  
Simple Observation ◽  
Source Plant ◽  
Species Specific

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts.

scholarly journals Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico

ZooKeys ◽  
2020 ◽  
Vol 941 ◽  
pp. 49-69
Author(s):  
Diana Ortíz-Gamino ◽  
Josefat Gregorio ◽  
Luis Cunha ◽  
Esperanza Martínez-Romero ◽  
Carlos Fragoso ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Geographic Region ◽  
Apparent Lack ◽  
Genetic Lineages ◽  
Low Genetic Diversity ◽  
Population Structures ◽  
Temperate Pastures

Pontoscolex corethrurus (Müller, 1857) is an invasive tropical earthworm, globally distributed. It reproduces through parthenogenesis, which theoretically results in low genetic diversity. The analysis of the population structure of P. corethrurus using molecular markers may significantly contribute to understanding the ecology and reproductive system of this earthworm species. This work assessed the genetic diversity and population structure of P. corethrurus with 34 polymorphic inter simple sequence repeat markers, covering four populations in tropical and temperate pastures from Veracruz State. Nuclear markers distinguished two genetic clusters, probably corresponding to two distinct genetic lineages. The number of clones detected in the AC population was lower than expected for a parthenogenetic species. Also, the apparent lack of differences in population structures related to the geographic region among the populations studied may indicate that human-mediated transference is prevalent in these areas. Still, most individuals apparently belong to lineage A, and only a few individuals seem to belong to the lineage B. Thus, the admixture signatures found among the four populations of P. corethrurus may have facilitated a successful invasion by directly increasing fitness. In summary, addressing the genetic variation of P. corethrurus with ISSR markers was a suitable approach, as it evidenced the genetic diversity and relationships in the populations evaluated.

scholarly journals Genetic diversity and population structure of sheep (Ovis aries) in Sichuan, China

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257974
Author(s):  
Mingliang Zhou ◽  
Gaofu Wang ◽  
Minghua Chen ◽  
Qian Pang ◽  
Shihai Jiang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ovis Aries ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genome Wide ◽  
High Quality Snps ◽  
Exotic Breed ◽  
Population Structures

Sichuan, China, has abundant genetic resources of sheep (Ovis aries). However, their genetic diversity and population structure have been less studied, especially at the genome-wide level. In the present study, we employed the specific-locus amplified fragment sequencing for identifying genome-wide single nucleotide polymorphisms (SNPs) among five breeds of sheep distributed in Sichuan, including three local pure breeds, one composite breed, and one exotic breed of White Suffolk. From 494 million clean paired-end reads, we obtained a total of 327,845 high-quality SNPs that were evenly distributed among all 27 chromosomes, with a transition/transversion ratio of 2.56. Based on this SNP panel, we found that the overall nucleotide diversity was 0.2284 for all five breeds, with the highest and lowest diversity observed in Mage sheep (0.2125) and Butuo Black (0.1963) sheep, respectively. Both Wright’s fixation index and Identity-by-State distance revealed that all individuals of Liangshan Semifine-wool, White Suffolk, and Butuo Black sheep were respectively clustered together, and the breeds could be separated from each other, whereas Jialuo and Mage sheep had the closest genetic relationship and could not be distinguished from each other. In conclusion, we provide a reference panel of genome-wide and high-quality SNPs in five sheep breeds in Sichuan, by which their genetic diversity and population structures were investigated.

scholarly journals Conservation aspects of natural populations and captive-bred stocks of turbot (Scophthalmus maximus) and Dover sole (Solea solea) using estimates of genetic diversity

2007 ◽  
Vol 64 (6) ◽  
pp. 1173-1181 ◽  
Author(s):  
Athanasios Exadactylos ◽  
Mark J. Rigby ◽  
Audrey J. Geffen ◽  
John P. Thorpe
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Natural Populations ◽  
Genetic Data ◽  
Scophthalmus Maximus ◽  
Effective Population ◽  
Solea Solea ◽  
Population Sizes ◽  
Turbot Scophthalmus Maximus ◽  
Dover Sole

Exadactylos, A., Rigby, M. J., Geffen, A. J., and Thorpe, J. P. 2007. Conservation aspects of natural populations and captive-bred stocks of turbot (Scophthalmus maximus) and Dover sole (Solea solea) using estimates of genetic diversity. – ICES Journal of marine Science, 64: 1173–1181. Population genetic analyses have been highly successful in predicting inter- and intraspecific evolutionary relationships, levels of gene flow, genetic divergence, and effective population sizes. Parameters estimated are evolutionary averages and are therefore relevant for addressing contemporary ecological or conservation issues. Changes in genetic variation within the range of a species may indicate patterns of population structure resulting from past ecological and demographic events that are otherwise difficult to infer, so may provide an insight into evolutionary development. Genetic data, drawn from 14 enzyme loci amplified from two populations of turbot (Scophthalmus maximus) and five populations of Dover sole (Solea solea) from the Irish Sea were used to examine population structure estimated from measures of genetic diversity. The aim was to provide an empirical assessment of whether artificial propagation poses a genetic threat to conservation of naturally spawning populations, and whether the fitness for natural spawning and rearing can be rapidly and substantially reduced or increased by artificial propagation. Because of prolonged overfishing, turbot and sole populations in the region are below natural levels, and survive in small local populations in fragmented habitats. Genetic data derived from allozymes have shown that populations are characterized by relatively low levels of genetic diversity. A hypothetical model supporting genetic population substructure, such as range expansion with founder-flush effects, and subsequent population decline with small effective population sizes was considered. Observations support our belief that conservation measures based on genetic diversity have to be developed to ensure the survival of this diverse gene pool.

scholarly journals Molecular Genetic Diversity and Population Structure in Ethiopian Chickpea Germplasm Accessions

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 247
Author(s):  
Tsegaye Getahun ◽  
Kassahun Tesfaye ◽  
Asnake Fikre ◽  
Teklehaimanot Haileslassie ◽  
Annapurna Chitikineni ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Molecular Genetic ◽  
Conservation Strategies ◽  
Molecular Genetic Diversity ◽  
Population Structure Analysis ◽  
Trait Improvement ◽  
Population Structures ◽  
Germplasm Accessions

Chickpea (Cicer arietinum L.) is a cheap source of protein and rich in minerals for people living in developing countries. In order to assess the existing molecular genetic diversity and determine population structures in selected Ethiopian chickpea germplasm accessions (118), a set of 46 simple sequence repeat (SSR) markers equally distributed on the chickpea genome were genotyped. A total of 572 alleles were detected from 46 SSR markers, and the number of alleles per locus varied from 2 (ICCM0289) to 28 (TA22). The average number of alleles per locus, polymorphism information content, and expected heterozygosity were 12, 0.684, and 0.699, respectively. Phylogenetic analysis grouped the 118 chickpea genotypes from diverse sources into three evolutionary and/or biological groups (improved desi, improved kabuli, and landraces). The population structure analysis revealed six sub-populations from 118 chickpea genotypes studied. AMOVA revealed that 57%, 29%, and 14% of the total genetic variations were observed among individuals, within populations, and among populations. The insights into the genetic diversity at molecular levels in the Ethiopian germplasm lines can be used for designing conservation strategies as well as the diverse germplasm lines identified in this study can be used for trait dissection and trait improvement.

REGIONAL POPULATION STRUCTURE IN POSTCLASSIC MEXICO

2017 ◽  
Vol 28 (2) ◽  
pp. 357-369 ◽  
Author(s):  
Corey S. Ragsdale
Keyword(s):  
Population Structure ◽  
Morphological Variation ◽  
Genetic Data ◽  
Postclassic Period ◽  
Trade Networks ◽  
Archaeological Data ◽  
West Mexico ◽  
Population Structures ◽  
Regional Population ◽  
Geographic Regions

AbstractThe majority of our knowledge about population structure in Mexico during the Postclassic period (a.d. 900–1520) is based on archaeological data. During this time, populations were in contact with each other through extensive trade networks and via the expansion of powerful empires in central and west Mexico. Though archaeological data provides a wealth of information about these relationships, little is known about the effects of these processes on population structure and biological, morphological variation or whether these effects vary across geographic regions. In this study, dental morphological observations are used as a proxy for genetic data in order to assess the differences in regional population structures throughout Mexico. Our analyses show differences in population structure between the various cultural and geographic areas around Mexico. We further conclude that population structures are affected by economic, political, or religious processes. This study provides bioarchaeological support for archaeological interpretations of population structure in Postclassic Mexico.

scholarly journals Distinguishing coalescent models - which statistics matter most?

2019 ◽  
Author(s):  
Fabian Freund ◽  
Arno Siri-Jégousse
Keyword(s):  
Genetic Diversity ◽  
Random Forest ◽  
Model Selection ◽  
Exponential Growth ◽  
Approximate Bayesian Computation ◽  
Genetic Data ◽  
Specific Question ◽  
Approximate Bayesian ◽  
Fitting Model ◽  
Kingman’S Coalescent

AbstractModelling genetic diversity needs an underlying genealogy model. To choose a fitting model based on genetic data, one can perform model selection between classes of genealogical trees, e.g. Kingman’s coalescent with exponential growth or multiple merger coalescents. Such selection can be based on many different statistics measuring genetic diversity. A random forest based Approximate Bayesian Computation is used to disentangle the effects of different statistics on distinguishing between various classes of genealogy models. For the specific question of inferring whether genealogies feature multiple mergers, a new statistic, the minimal observable clade size, is introduced. When combined with classical site frequency based statistics, it reduces classification errors considerably.

Genetic diversity, population structure, and immigration, in a partially hunted puma population of south-central Argentina

2020 ◽  
Vol 101 (3) ◽  
pp. 766-778
Author(s):  
Orlando Gallo ◽  
Diego F Castillo ◽  
Raquel Godinho ◽  
Emma B Casanave
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Puma Concolor ◽  
Population Control ◽  
A Priori ◽  
Wildlife Habitat ◽  
Predator Species ◽  
Hunting Pressure ◽  
South Central

Abstract Carnivores are decreasing globally due in part to anthropogenic ecological disturbances. In Argentina, human activities have fragmented wildlife habitat, thereby intensifying puma–livestock conflict and leading to population control of the predator species by hunting. We investigated genetic variability and population structure of pumas (Puma concolor) from three south-central Argentine provinces with two different management policies for the species: full protection versus legal hunting. All genetic estimates were based on 83 individuals genotyped at 25 species-specific microsatellite loci. The overall genetic diversity was high (observed heterozygosity = 0.63), but lower than in other South American populations. Spatial analyses revealed the presence of two bottlenecked genetic clusters with very similar diversity and low gene flow (3% per generation) between them. However, analyses based on a priori separated groups showed that gene flow follows increasing values of hunting pressure, converging to the area with the greatest number of individuals harvested. Our results suggest that hunting pressure likely is contributing to the gene flow pattern, limiting pumas’ movements and creating a metapopulation dynamic among geographic subpopulations. Integrated demographic and genetic approaches are needed to better understand pumas’ movements across the landscape and adopt successful management plans to achieve long-term population viability.

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