scholarly journals Why panmictic bacteria are rare

2018 ◽  
Author(s):  
Chao Yang ◽  
Yujun Cui ◽  
Xavier Didelot ◽  
Ruifu Yang ◽  
Daniel Falush
Keyword(s):  
Nucleotide Diversity ◽  
Bacterial Species ◽  
Structured Populations ◽  
Effective Population ◽  
Recombination Rates ◽  
Continuous Increase ◽  
Population Structures ◽  
Population Sizes ◽  
Current Value ◽  
Neutral Models

AbstractBackgroundBacteria typically have more structured populations than higher eukaryotes, but this difference is surprising given high recombination rates, enormous population sizes and effective geographical dispersal in many bacterial species.ResultsWe estimated the recombination scaled effective population size Ner in 21 bacterial species and find that it does not correlate with synonymous nucleotide diversity as would be expected under neutral models of evolution. Only two species have estimates substantially over 100, consistent with approximate panmixia, namely Helicobacter pylori and Vibrio parahaemolyticus. Both species are far from demographic equilibrium, with diversity predicted to increase more than 30 fold in V. parahaemolyticus if the current value of Ner were maintained, to values much higher than found in any species. We propose that panmixia is unstable in bacteria, and that persistent environmental species are likely to evolve barriers to genetic exchange, which act to prevent a continuous increase in diversity by enhancing genetic drift.ConclusionsOur results highlight the dynamic nature of bacterial population structures and imply that overall diversity levels found within a species are poor indicators of its size.

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.

scholarly journals More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

2010 ◽  
Vol 365 (1556) ◽  
pp. 3277-3288 ◽  
Author(s):  
Anne C. Stone ◽  
Fabia U. Battistuzzi ◽  
Laura S. Kubatko ◽  
George H. Perry ◽  
Evan Trudeau ◽  
...  
Keyword(s):  
Demographic History ◽  
Time Estimation ◽  
Divergence Times ◽  
Effective Population ◽  
Founding Population ◽  
Time Estimates ◽  
Population Structures ◽  
Population Sizes ◽  
History Of ◽  
Mtdna Diversity

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees ( Pan troglodytes ) from each of the three established subspecies ( P. t. troglodytes , P. t. schweinfurthii and P. t. verus ) and the proposed fourth subspecies ( P. t. ellioti ). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human–chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1–1.5, 1.1–0.76 and 0.25–0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.

scholarly journals Patterns of Nucleotide Diversity of theldpACircadian Gene in Closely Related Species of Cyanobacteria from Extreme Cold Deserts

2012 ◽  
Vol 79 (5) ◽  
pp. 1516-1522 ◽  
Author(s):  
Ka Wai Ng ◽  
Stephen B. Pointing ◽  
Volodymyr Dvornyk
Keyword(s):  
Related Species ◽  
Nucleotide Diversity ◽  
Population Expansion ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Closely Related Species ◽  
Content Type ◽  
Population Sizes ◽  
Extreme Cold ◽  
Small Effective Population Size

ABSTRACTIn the circadian system of cyanobacteria, theldpAgene is a component of the input to the clock. We comparatively analyzed nucleotide polymorphism of this gene in populations of two closely related species of cyanobacteria (denoted asSynechococcusspecies S1 and S2, respectively) from extreme cold deserts in Antarctica, the Canadian Arctic, and Tibet. Although both species manifested similarly high haplotype diversities (0.990 and 0.809, respectively), the nucleotide diversity differed significantly (0.0091 in S1 and 0.0037 in S2). The populations of species S2 were more differentiated (FST= 0.2242) compared to those of species S1 (FSTbetween 0.0296 and 0.1188). An analysis of positive selection with several tests yielded highly significant values (P< 0.01) for both species. On the other hand, these results may be somewhat compromised by fluctuating population sizes of the species. The apparent selection pressure coupled with the pronounced demographic factors, such as population expansion, small effective population size, and genetic drift, may thus result in the observed significant interpopulation differentiation and subsequent speciation of cyanobacteria.

scholarly journals Retriever and Pointer: Software to Evaluate Inbreeding and Genetic Management in Captive Populations

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1332
Author(s):  
Jack J. Windig ◽  
Ina Hulsegge
Keyword(s):  
Population Structure ◽  
Allelic Diversity ◽  
Captive Population ◽  
Pedigree Data ◽  
Effective Population ◽  
Genetic Management ◽  
Captive Populations ◽  
Population Structures ◽  
Population Sizes ◽  
Well Data

The Retriever and Pointer software has been developed for genetic management of (small) captive populations The Retriever program uses as input pedigree data and extracts data on population structure that determine inbreeding rates such as skewness of sire contributions. Levels and rates of inbreeding and kinship and effective population sizes are determined as well. Data on population structure can be used as input for the Pointer program. This program uses stochastic simulation to evaluate a population and provides expected levels and rates of inbreeding and kinship, and optionally allelic diversity. The user can simulate different options for genetic management such as sire restrictions, restrictions on inbreeding levels, mean kinships and breeding circles. Both Retriever and Pointer can analyze populations with subpopulations and different rates of exchange between them. Although originally devised for dogs, the software can be, and has been, used for any captive population including livestock and zoo populations, and a number of examples are provided. The pointer software is also suitable in education where students may generate their own populations and evaluate effects of different population structures and genetic management on genetic diversity. Input is provided via a graphical user interface. The software can be downloaded for free.

Estimating Ancestral Population Sizes and Divergence Times

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 395-404 ◽  
Author(s):  
Jeffrey D Wall
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Sequence Data ◽  
Ancestral Population ◽  
Divergence Times ◽  
Intragenic Recombination ◽  
Intergenic Sequence ◽  
Effective Population ◽  
Recombination Rates ◽  
Population Sizes

Abstract This article presents a new method for jointly estimating species divergence times and ancestral population sizes. The method improves on previous ones by explicitly incorporating intragenic recombination, by utilizing orthologous sequence data from closely related species, and by using a maximum-likelihood framework. The latter allows for efficient use of the available information and provides a way of assessing how much confidence we should place in the estimates. I apply the method to recently collected intergenic sequence data from humans and the great apes. The results suggest that the human-chimpanzee ancestral population size was four to seven times larger than the current human effective population size and that the current human effective population size is slightly &gt;10,000. These estimates are similar to previous ones, and they appear relatively insensitive to assumptions about the recombination rates or mutation rates across loci.

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.

scholarly journals Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three relatedPopulusspecies

2015 ◽  
Author(s):  
Jing Wang ◽  
Nathaniel R Street ◽  
Douglas G Scofield ◽  
Pär K Ingvarsson
Keyword(s):  
Natural Selection ◽  
Rate Variation ◽  
Sequencing Data ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Recombination Rates ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Population Sizes ◽  
Wide Scale

AbstractA central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome re-sequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum and population-scaled recombination rates in three species ofPopulus:P. tremula, P. tremuloidesandP. trichocarpa. We find thatP. tremuloideshas the highest level of genome-wide variation, skewed allele frequencies and population-scaled recombination rates, whereasP. trichocarpaharbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, both due to purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination are largely explaining the disparate magnitudes and signatures of linked selection we observe among species. The present work provides the first phylogenetic comparative study at genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

scholarly journals Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Nicola F Müller ◽  
Gytis Dudas ◽  
Tanja Stadler
Keyword(s):  
Population Dynamics ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Structured Populations ◽  
Model Parameters ◽  
Effective Population ◽  
Genetic Sequence ◽  
Migration Rates ◽  
Population Sizes ◽  
Structured Coalescent

Abstract Population dynamics can be inferred from genetic sequence data by using phylodynamic methods. These methods typically quantify the dynamics in unstructured populations or assume migration rates and effective population sizes to be constant through time in structured populations. When considering rates to vary through time in structured populations, the number of parameters to infer increases rapidly and the available data might not be sufficient to inform these. Additionally, it is often of interest to know what predicts these parameters rather than knowing the parameters themselves. Here, we introduce a method to  infer the predictors for time-varying migration rates and effective population sizes by using a generalized linear model (GLM) approach under the marginal approximation of the structured coalescent. Using simulations, we show that our approach is able to reliably infer the model parameters and its predictors from phylogenetic trees. Furthermore, when simulating trees under the structured coalescent, we show that our new approach outperforms the discrete trait GLM model. We then apply our framework to a previously described Ebola virus dataset, where we infer the parameters and its predictors from genome sequences while accounting for phylogenetic uncertainty. We infer weekly cases to be the strongest predictor for effective population size and geographic distance the strongest predictor for migration. This approach is implemented as part of the BEAST2 package MASCOT, which allows us to jointly infer population dynamics, i.e. the parameters and predictors, within structured populations, the phylogenetic tree, and evolutionary parameters.

scholarly journals Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

2018 ◽  
Author(s):  
Nicola F. Müller ◽  
Gytis Dudas ◽  
Tanja Stadler
Keyword(s):  
Population Dynamics ◽  
Phylogenetic Trees ◽  
Ebola Virus ◽  
Sequence Data ◽  
Geographic Distance ◽  
Structured Populations ◽  
Effective Population ◽  
Genetic Sequence ◽  
Migration Rates ◽  
Population Sizes

AbstractPopulation dynamics can be inferred from genetic sequence data using phylodynamic methods. These methods typically quantify the dynamics in unstructured populations or assume the parameters describing the dynamics to be constant through time in structured populations. Inference methods allowing for structured populations and parameters to vary through time involve many parameters which have to be inferred. Each of these parameters might be however only weakly informed by data. Here we introduce an approach that uses so-called predictors, such as geographic distance between locations, within a generalized linear model to inform the population dynamic parameters, namely the time-varying migration rates and effective population sizes under the marginal approximation of the structured coalescent. By using simulations, we show that we are able to reliably infer the parameters from phylogenetic trees. We then apply this framework to a previously described Ebola virus dataset. We infer incidence to be the strongest predictor for effective population size and geographic distance the strongest predictor for migration. This allows us to show not only on simulated data, but also on real data, that we are able to identify reasonable predictors. Overall, we provide a novel method that allows to identify predictors for migration rates and effective population sizes and to use these predictors to quantify migration rates and effective population sizes. Its implementation as part of the BEAST2 software package MASCOT allows to jointly infer population dynamics within structured populations, the phylogenetic tree, and evolutionary parameters.

scholarly journals PERIODIC SELECTION, INFECTIOUS GENE EXCHANGE AND THE GENETIC STRUCTURE OF E. COLI POPULATIONS

Genetics ◽  
1981 ◽  
Vol 99 (1) ◽  
pp. 1-23 ◽  
Author(s):  
Bruce R Levin
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Bacterial Species ◽  
A Priori ◽  
Natural Populations ◽  
Gene Exchange ◽  
Effective Population ◽  
Bacterial Populations ◽  
E Coli ◽  
Population Sizes

ABSTRACT As a consequence of sequential replacements by clones of higher fitness (periodic selection), bacterial populations would be continually purged of genetic variability, and the fate of selectively neutral alleles in very large populations of bacteria would be similar to that in demes of sexually reproducing organisms with small genetically effective population sizes. The significance of periodic selection in reducing genetic variability in these clonally reproducing species is dependent on the amount of genetic exchange between clones (recombination). In an effort to determine the relationship between the rates of periodic selection, recombination and the genetically effective sizes of bacterial populations, a model for periodic selection and infectious gene exchange has been developed and its properties analyzed. It shows that, for a given periodic selection regime, genetically effective population size increases exponentially with the rate of recombination.—With the parameters of this model in the range anticipated for natural populations of E. coli, the purging effects of periodic selection on genetic variability are significant; individual populations or lineages of this bacterial species would have very small genetically effective population sizes.—Based on this result, some other a priori considerations and a review of the results of epidemiological and genetic variability studies, it is postulated that E. coli is composed of a relatively limited number of geographically widespread and genetically nearly isolated and monomorphic lineages. The implications of these considerations of the genetic structure of E. coli populations of the interpretation of protein variation and the neutral gene hypothesis are discussed.

Sign in / Sign up

Export Citation Format

Share Document