scholarly journals WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data

2014 ◽  
Author(s):  
Matthieu Foll ◽  
Hyunjin Shim ◽  
Jeffrey D. Jensen
Keyword(s):  
Genetic Parameters ◽  
Sampled Data ◽  
Effective Population ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Fisher Model ◽  
Serial Data ◽  
Population Sizes ◽  
Population Genetic Parameters ◽  
Abc Method

With novel developments in sequencing technologies, time-sampled data are becoming more available and accessible. Naturally, there have been efforts in parallel to infer population genetic parameters from these datasets. Here, we compare and analyze four recent approaches based on the Wright-Fisher model for inferring selection coefficients (s) given effective population size (Ne), with simulated temporal datasets. Furthermore, we demonstrate the advantage of a recently proposed ABC-based method that is able to correctly infer genome-wide average Ne from time-serial data, which is then set as a prior for inferring per-site selection coefficients accurately and precisely. We implement this ABC method in a new software and apply it to a classical time-serial dataset of the medionigra genotype in the moth Panaxia dominula. We show that a recessive lethal model is the best explanation for the observed variation in allele frequency by implementing an estimator of the dominance ratio (h).

scholarly journals The formation of avian montane diversity across barriers and along elevational gradients

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
José Martín Pujolar ◽  
Mozes P. K. Blom ◽  
Andrew Hart Reeve ◽  
Jonathan D. Kennedy ◽  
Petter Zahl Marki ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Differentiation ◽  
Bird Species ◽  
Geographic Area ◽  
Effective Population ◽  
Tropical Mountains ◽  
Mountainous Regions ◽  
Pleistocene Climate ◽  
Genome Wide ◽  
Population Sizes

AbstractTropical mountains harbor exceptional concentrations of Earth’s biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species’ altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.

scholarly journals Coupling Wright-Fisher and coalescent dynamics for realistic simulation of population-scale datasets

2019 ◽  
Author(s):  
Dominic Nelson ◽  
Jerome Kelleher ◽  
Aaron P. Ragsdale ◽  
Gil McVean ◽  
Simon Gravel
Keyword(s):  
State Of The Art ◽  
Demographic History ◽  
Recent Past ◽  
Computationally Efficient ◽  
Effective Population ◽  
Genome Data ◽  
Coalescent Simulations ◽  
Genome Wide ◽  
Fisher Model ◽  
Ancestry Proportions

1AbstractCoalescent simulations are widely used to examine the effects of evolution and demographic history on the genetic makeup of populations. Thanks to recent progress in algorithms and data structures, simulators such as the widely-used msprime [1] now provide genome-wide simulations for millions of individuals. However, this software relies on classic coalescent theory and the corresponding assumptions that sample sizes are small relative to effective population size and that the region being simulated is short. Here we show that coalescent simulations of long regions of the genome exhibit large biases in identity-by-descent (IBD), long-range linkage disequilibrium (LD), and ancestry patterns, particularly when sample size is large. We present a Wright-Fisher extension to msprime, and show that it produces more realistic distributions of IBD, LD, and ancestry proportions, while also addressing more subtle biases of the coalescent. Further, these extensions are more computationally efficient than state-of-the-art coalescent simulations when simulating long regions, including whole-genome data. For shorter regions, efficiency and accuracy can be maintained via a flexible hybrid model which simulates the recent past under the Wright-Fisher model and uses coalescent simulations in the distant past.

The broad-snouted caiman population recovery in Argentina. A case of genetics conservation

2017 ◽  
Vol 38 (4) ◽  
pp. 411-424 ◽  
Author(s):  
Patricia Susana Amavet ◽  
Eva Carolina Rueda ◽  
Juan César Vilardi ◽  
Pablo Siroski ◽  
Alejandro Larriera ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Population Genetic ◽  
Genetic Parameters ◽  
Population Recovery ◽  
Santa Fe ◽  
Effective Population ◽  
Population Genetic Parameters ◽  
The Impact

Caiman latirostriswild populations have suffered a drastic reduction in the past, and for that reason, a management and monitoring plan was applied since 1990 in Santa Fe, Argentina in order to achieve population recovery. Although ranching system has a noteworthy success in terms of population size recovering, there is no information about the estimation of population genetic parameters. In particular, the consequence of the bottleneck underwent by these populations has not been assessed. We evaluated variability and genetic structure ofC. latirostrispopulations from Santa Fe through time, using microsatellites and mitochondrial DNA. Population genetic parameters were compared among four sites and three different periods to assess the impact of management activities, and effective population size was estimated in order to detect bottleneck events. We observed an increase in microsatellite variability and low genetic variability in mitochondrial lineages through time. Variability estimates are similar among sites in each sampling period; and there is scarce differentiation among them. The genetic background of each sampling site has changed through time; we assume this fact may be due to entry of individuals of different origin, through management and repopulation activities. Moreover, taking into account the expected heterozygosity and effective population size values, it can be assumed that bottleneck events indeed have occurred in the recent past. Our results suggest that, in addition to increasing population size, genetic variability of the species has been maintained. However, the information is still incomplete, and regular monitoring should continue in order to arrive to solid conclusions.

scholarly journals The Limits to Estimating Population-Genetic Parameters with Temporal Data

2020 ◽  
Vol 12 (4) ◽  
pp. 443-455
Author(s):  
Michael Lynch ◽  
Wei-Chin Ho
Keyword(s):  
Population Genetic ◽  
Genetic Parameters ◽  
Natural Populations ◽  
Estimation Methods ◽  
Frequency Change ◽  
Sampling Variance ◽  
Effective Population ◽  
Closed Population ◽  
Temporal Variance ◽  
Population Genetic Parameters

Abstract The ability to obtain genome-wide sequences of very large numbers of individuals from natural populations raises questions about optimal sampling designs and the limits to extracting information on key population-genetic parameters from temporal-survey data. Methods are introduced for evaluating whether observed temporal fluctuations in allele frequencies are consistent with the hypothesis of random genetic drift, and expressions for the expected sampling variances for the relevant statistics are given in terms of sample sizes and numbers. Estimation methods and aspects of statistical reliability are also presented for the mean and temporal variance of selection coefficients. For nucleotide sites that pass the test of neutrality, the current effective population size can be estimated by a method of moments, and expressions for its sampling variance provide insight into the degree to which such methodology can yield meaningful results under alternative sampling schemes. Finally, some caveats are raised regarding the use of the temporal covariance of allele-frequency change to infer selection. Taken together, these results provide a statistical view of the limits to population-genetic inference in even the simplest case of a closed population.

scholarly journals Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle

Animals ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 83 ◽  
Author(s):  
Lei Xu ◽  
Bo Zhu ◽  
Zezhao Wang ◽  
Ling Xu ◽  
Ying Liu ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genomic Selection ◽  
Haplotype Block ◽  
Block Structure ◽  
Effective Population ◽  
Chinese Cattle ◽  
Genome Wide ◽  
Population Sizes ◽  
Haplotype Block Structure ◽  
Selection For

Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.

scholarly journals Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 350 ◽  
Author(s):  
Haile Berihulay ◽  
Rabiul Islam ◽  
Lin Jiang ◽  
Yuehui Ma
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Parameter ◽  
Genetic Selection ◽  
Chromosome 1 ◽  
Effective Population ◽  
Genome Wide ◽  
Population Sizes ◽  
Trait Locus ◽  
D Values ◽  
Genome Wide Linkage Disequilibrium

Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the accumulation of mutations, and the effectiveness of selection. In this study, a total of 193 individuals were genotyped to assess the extent of LD and Ne in six Chinese goat populations using the SNP 50K BeadChip. Across the determined autosomal chromosomes, we found an average of 0.02 and 0.23 for r2 and D’ values, respectively. The average r2 between all the populations varied little and ranged from 0.055 r2 for the Jining Grey to 0.128 r2 for the Guangfeng, with an overall mean of 0.083. Across the 29 autosomal chromosomes, minor allele frequency (MAF) was highest on chromosome 1 (0.321) and lowest on chromosome 25 (0.309), with an average MAF of 0.317, and showing the lowest (25.5% for Louping) and highest (28.8% for Qingeda) SNP proportions at MAF values > 0.3. The inbreeding coefficient ranged from 0.064 to 0.085, with a mean of 0.075 for all the autosomes. The Jining Grey and Qingeda populations showed higher Ne estimates, highlighting that these animals could have been influenced by artificial selection. Furthermore, a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng populations, and their estimated values were closer to 64 and 95, respectively, 13 generations ago, which indicates that these breeds were exposed to strong selection. This study provides an insight into valuable genetic information and will open up the opportunity for further genomic selection analysis of Chinese goat populations.

scholarly journals Adaptation in outbred sexual yeast is repeatable, polygenic, and favors rare haplotypes

2021 ◽  
Author(s):  
Robert A. Linder ◽  
Behzad Zabanavar ◽  
Arundhati Majumder ◽  
Hannah Chiao-Shyan Hoang ◽  
Vanessa Genesaret Delgado ◽  
...  
Keyword(s):  
Rare Variants ◽  
Intermediate Frequency ◽  
Effective Population ◽  
Entire Genome ◽  
Frequency Shifts ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Population Sizes ◽  
Drug Treatments ◽  
Per Gene

AbstractWe describe the results of a 200 generation Evolve and Resequence (E&R) study initiated from an outbred dipliod recombined synthetic base population derived from 18 genetically diverse founders. Replicate populations were maintained at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing implies a per gene per cell-division recombination rate higher than that achieved in Drosophila E&R studies. In 55 sexual populations we observe large fitness gains and highly repeatable patterns of genome-wide haplotype change within each chemical challenge. There was little evidence for pervasive pleiotropy, as evidenced by patterns of haplotype change between drug treatments. Within treatment adaptation appears highly polygenic with almost the entire genome showing significant consistent haplotype change. Finally, adaptation was almost always associated with only one of the 18 founder alleles, suggesting selection primarily acts on rare variants private to a founder or haplotype blocks harboring multiple mutations. This observation contradicts the notion that adaptation is often due to subtle frequency shifts at intermediate frequency variants.

scholarly journals Structure and genetic variability of the Mexican Sardo Negro breed

2022 ◽  
Vol 52 (5) ◽  
Author(s):  
Joel Domínguez-Viveros ◽  
Antonio Reyes-Cerón ◽  
Juan Fernando Saiz-Pineda ◽  
Cesar Villegas-Gutiérrez ◽  
Guadalupe Nelson Aguilar-Palma ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Genetic Parameters ◽  
Inbreeding Coefficient ◽  
Structure Evolution ◽  
Effective Number ◽  
Effective Population ◽  
Population Genetic Parameters ◽  
Additive Genetic Relationship ◽  
Over Time

ABSTRACT: This study analyzed the Sardo Negro breed pedigree (41,521 animals registered from 1958 to 2019) to determine its structure, evolution, and genetic variability (GV). The population genetic parameters evaluated were effective number of founders (fe) and ancestors (fa), pedigree integrity, additive genetic relationship (AGR); number of complete generations (NCG), maximum generations traced (NMGT), and equivalent complete generations (NECG); effective population size (Ne), inbreeding coefficient (F), and generation interval (GI). The average GI was 7.45 years. A total of 7,804 founders and 4,856 ancestors were identified for a fe of 185 and a fa of 97. The average and maximum values of NCG, NECG, and NMGT were 1.6 and 5.0, 2.5 and 6.5, 4.3 and 12, with Ne estimates of 15.9, 25.9, and 69.0, respectively. The increase in F, linked to Ne, ranged from 0.72% to 3.1% per generation. The average values for F and AGR were 3.6% and 1.0%, respectively. The proportion of inbred individuals was 32.0%, with F values ranging from 0.01 to 62.2% and an average of 11.3%. The rate of inbred population was 1.3% per year. The annual rate of AGR was 0.04%. For the continuity and projection of the breed, the evolution of F as a function of Ne and the possible implications of the selection schemes must be considered. The genetic variability sustained over time results from the Ne.

scholarly journals Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species

2019 ◽  
Vol 11 (10) ◽  
pp. 2875-2886 ◽  
Author(s):  
Venkat Talla ◽  
Lucile Soler ◽  
Takeshi Kawakami ◽  
Vlad Dincă ◽  
Roger Vila ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Nucleotide Diversity ◽  
Gene Annotation ◽  
Rate Variation ◽  
Butterfly Species ◽  
Relative Role ◽  
Effective Population ◽  
Genome Wide ◽  
Population Sizes

Abstract The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.

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