scholarly journals Estimation of Speciation Times Under the Multispecies Coalescent

2019 ◽  
Author(s):  
Jing Peng ◽  
David Swofford ◽  
Laura Kubatko
Keyword(s):  
Asymptotic Variance ◽  
Sequence Evolution ◽  
Computationally Efficient ◽  
Effective Population ◽  
Nonparametric Bootstrap ◽  
Multispecies Coalescent ◽  
Population Sizes ◽  
Genome Scale ◽  
Dna Sequence Evolution ◽  
Model Based Analysis

AbtractMotivationThe coalescent model is now widely accepted as a necessary component for phylogenetic inference from genome-scale data. However, because model-based analysis under the coalescent is computationally prohibitive, a variety of inferential frameworks and corresponding algorithms have been proposed for estimation of species-level phylogenies and the associated parameters, including the speciation times and effective population sizes.ResultsWe consider the problem of estimating the timing of speciation events along a phylogeny in a coalescent framework. We propose a pseudolikelihood method for estimation of these speciation times under a model of DNA sequence evolution for which exact site pattern probabilities can be computed. We demonstrate that the pseudolikelihood estimates are statistically consistent and asymptotically normally distributed, and we show how this result can be used to estimate their asymptotic variance. We also provide a more computationally efficient estimator of the asymptotic variance based on the nonparametric bootstrap. We evaluate the performance of our method using simulation and by application to an empirical dataset on gibbons.

scholarly journals Multispecies coalescent analysis unravels the non-monophyly and controversial relationships of Hexapoda

2017 ◽  
Author(s):  
Lucas A. Freitas ◽  
Beatriz Mello ◽  
Carlos G. Schrago
Keyword(s):  
Phylogenetic Relationships ◽  
Gene Tree ◽  
Genomic Data ◽  
Population Level ◽  
Phylogenetic Inference ◽  
Evolutionary Relationships ◽  
Effective Population ◽  
Multispecies Coalescent ◽  
Population Sizes ◽  
Phylogenomic Analyses

AbstractWith the increase in the availability of genomic data, sequences from different loci are usually concatenated in a supermatrix for phylogenetic inference. However, as an alternative to the supermatrix approach, several implementations of the multispecies coalescent (MSC) have been increasingly used in phylogenomic analyses due to their advantages in accommodating gene tree topological heterogeneity by taking account population-level processes. Moreover, the development of faster algorithms under the MSC is enabling the analysis of thousands of loci/taxa. Here, we explored the MSC approach for a phylogenomic dataset of Insecta. Even with the challenges posed by insects, due to large effective population sizes coupled with short deep internal branches, our MSC analysis could recover several orders and evolutionary relationships in agreement with current insect systematics. However, some phylogenetic relationships were not recovered by MSC methods. Most noticeable, a remiped crustacean was positioned within the Insecta. Additionally, the interordinal relationships within Polyneoptera and Neuropteroidea contradicted recent works, by suggesting the non-monophyly of Neuroptera. We notice, however, that these phylogenetic arrangements were also poorly supported by previous analyses and that they were sensitive to gene sampling.

scholarly journals Contrasting Patterns of Nonneutral Evolution in Proteins Encoded in Nuclear and Mitochondrial Genomes

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 385-399 ◽  
Author(s):  
Daniel M Weinreich ◽  
David M Rand
Keyword(s):  
Amino Acid ◽  
Population Size ◽  
Germ Line ◽  
Nuclear Data ◽  
Data Sets ◽  
Sequence Evolution ◽  
Effective Population ◽  
Amino Acid Polymorphism ◽  
Protein Coding ◽  
Dna Sequence Evolution

Abstract We report that patterns of nonneutral DNA sequence evolution among published nuclear and mitochondrially encoded protein-coding loci differ significantly in animals. Whereas an apparent excess of amino acid polymorphism is seen in most (25/31) mitochondrial genes, this pattern is seen in fewer than half (15/36) of the nuclear data sets. This differentiation is even greater among data sets with significant departures from neutrality (14/15 vs. 1/6). Using forward simulations, we examined patterns of nonneutral evolution using parameters chosen to mimic the differences between mitochondrial and nuclear genetics (we varied recombination rate, population size, mutation rate, selective dominance, and intensity of germ line bottleneck). Patterns of evolution were correlated only with effective population size and strength of selection, and no single genetic factor explains the empirical contrast in patterns. We further report that in Arabidopsis thaliana, a highly self-fertilizing plant with effectively low recombination, five of six published nuclear data sets also exhibit an excess of amino acid polymorphism. We suggest that the contrast between nuclear and mitochondrial nonneutrality in animals stems from differences in rates of recombination in conjunction with a distribution of selective effects. If the majority of mutations segregating in populations are deleterious, high linkage may hinder the spread of the occasional beneficial mutation.

scholarly journals Island songbirds as windows into evolution in small populations

2020 ◽  
Author(s):  
Thibault Leroy ◽  
Marjolaine Rousselle ◽  
Marie-Ka Tilak ◽  
Aude Caizergues ◽  
Celine Scornavacca ◽  
...  
Keyword(s):  
Natural Selection ◽  
Bird Species ◽  
Empirical Support ◽  
Sequence Evolution ◽  
Large Set ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Evolutionary Forces ◽  
Island Species ◽  
Population Sizes

Due to their limited ranges and inherent isolation, island species have long been recognized as crucial systems for tackling a range of evolutionary questions, including in the early study of speciation. Such species have been less studied in the understanding of the evolutionary forces driving DNA sequence evolution. Island species usually have lower census population sizes (N) than continental species and, supposedly, lower effective population sizes (Ne). Given that both the rates of change caused by genetic drift and by selection are dependent upon Ne, island species are theoretically expected to exhibit (i) lower genetic diversity, (ii) less effective natural selection against slightly deleterious mutations, and (iii) a lower rate of adaptive evolution. Here, we have used a large set of newly sequenced and published whole genome sequences of Passerida bird species or subspecies (14 insular and 11 continental) to test these predictions. We empirically confirm that island species exhibit lower census size and Ne, supporting the hypothesis that the smaller area available on islands constrains the upper bound of Ne. In the insular species, we find significantly lower nucleotide diversity in coding regions, higher ratios of non-synonymous to synonymous polymorphisms, and lower adaptive substitution rates. Our results provide robust evidence that the lower Ne experienced by island species has affected both the ability of natural selection to efficiently remove weakly deleterious mutations and also the adaptive potential of island species, therefore providing considerable empirical support for the nearly neutral theory. We discuss the implications for both evolutionary and conservation biology.

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 73 (3) ◽  
pp. 513-530
Author(s):  
J P Hanrahan ◽  
E J Eisen ◽  
J E Legates
Keyword(s):  
Population Size ◽  
Selection Response ◽  
Selection Intensity ◽  
Realized Heritability ◽  
Family Selection ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For ◽  
Selection Intensities ◽  
Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

Paternity analysis with microsatellites in a Danish Abies nordmanniana clonal seed orchard reveals dysfunctions

2006 ◽  
Vol 36 (4) ◽  
pp. 1054-1058 ◽  
Author(s):  
O K Hansen ◽  
E D Kjær
Keyword(s):  
Asymptotic Variance ◽  
Seed Orchard ◽  
Paternity Analysis ◽  
Effective Population ◽  
Population Number ◽  
Clonal Seed Orchard ◽  
Relative Contribution ◽  
Male Gametes ◽  
Abies Nordmanniana ◽  
The Status

A paternity analysis using five microsatellite markers was conducted in a Danish clonal seed orchard with 13 Abies nordmanniana (Stev.) Spach clones. The purpose was to investigate potential seed-orchard dysfunctions, with special emphasis on nonequal pollen contributions and selfing. Male paternity was found for 232 seedlings germinated from seeds collected on three ramets, each of eight clones, and the relative contribution of each clone to the gene pool of male gametes was calculated. Furthermore, 49 ramets were genotyped to check for erroneous grafting. The effect of an unbalanced male contribution was quantified by means of two measures: (1) the status number (NS), which reflects buildup of coancestry in the seed-orchard crop as a result of a low number of clones and an unequal male contribution, and (2) the asymptotic variance effective population number (Ne(v)). The contributions by pollen donors from the 13 clones were highly skewed. Three clones were fathers to more than 75% of the progenies, while making up only 24% of the ramets in the seed orchard. Four clones sired no progenies at all. The unequal contribution on the male side corresponded to NS = 4.2 and Ne(v) = 5.8. Some selfing was observed, which may give rise to concern if clonal seed orchards with few clones are established. The estimated maximum pollen contamination from outside the seed orchard was 4.3%. No grafting–labelling errors were identified.

Rates of DNA sequence evolution differ between taxonomic groups

Science ◽  
1986 ◽  
Vol 231 (4744) ◽  
pp. 1393-1398 ◽  
Author(s):  
R. Britten
Keyword(s):  
Dna Sequence ◽  
Sequence Evolution ◽  
Taxonomic Groups ◽  
Dna Sequence Evolution

scholarly journals The effect of life-history and mode of inheritance on neutral genetic variability

2001 ◽  
Vol 77 (2) ◽  
pp. 153-166 ◽  
Author(s):  
BRIAN CHARLESWORTH
Keyword(s):  
Sequence Variation ◽  
Adult Mortality ◽  
Structured Populations ◽  
Human Populations ◽  
Effective Population ◽  
Transmission Modes ◽  
Population Sizes ◽  
Age Structured ◽  
Infinite Sites Model ◽  
Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

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