COMPARATIVE POPULATION GENOMICS INCOLLINSIASISTER SPECIES REVEALS EVIDENCE FOR REDUCED EFFECTIVE POPULATION SIZE, RELAXED SELECTION, AND EVOLUTION OF BIASED GENE CONVERSION WITH AN ONGOING MATING SYSTEM SHIFT

AbstractSelection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. Codon usage bias in animals has only been studied in a handful of model organisms so far, and can be affected by confounding, non-adaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data we analysed the relationship between codon usage, gene expression, allele frequency distribution and recombination rate in 31 non-model species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analysing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons are generally preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT↔GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.

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The effective population size modulates the strength of GC biased gene conversion in two passerines

10.1101/2021.04.20.440602 ◽

2021 ◽

Author(s):

Henry J Barton ◽

Kai Zeng

Keyword(s):

Population Size ◽

Gene Conversion ◽

Effective Population Size ◽

Zebra Finch ◽

Nucleotide Diversity ◽

Gc Content ◽

Effective Population ◽

Coding Regions ◽

Crossover Rate ◽

Biased Gene Conversion

Understanding the determinants of genomic base composition is fundamental to understanding genome evolution. GC biased gene conversion (gBGC) is a key driving force behind genomic GC content, through the preferential incorporation of GC alleles over AT alleles during recombination, driving them towards fixation. The majority of work on gBGC has focussed on its role in coding regions, largely to address how it confounds estimates of selection. Non-coding regions have received less attention, particularly in regard to the interaction of gBGC and the effective population size (Ne) within and between species. To address this, we investigate how the strength of gBGC (B = 4Neb, where b is the conversion bias) varies within the non-coding genome of two wild passerines. We use a dataset of published high coverage genomes (10 great tits and 10 zebra finches) to estimate B, nucleotide diversity, changes in Ne, and crossover rates from linkage maps, in 1Mb homologous windows in each species. We demonstrate remarkable conservation of both B and crossover rate between species. We show that the mean strength of gBGC in the zebra finch is more than double that in the great tit, consistent with its twofold greater effective population size. B also correlates with both crossover rate and nucleotide diversity in each species. Finally, we estimate equilibrium GC content from both divergence and polymorphism data, which indicates that B has been increasing in both species, and provide support for population expansion explaining a large proportion of this increase in the zebra finch.

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Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.

10.21203/rs.2.15863/v1 ◽

2019 ◽

Author(s):

Valeria Souza ◽

Mirna Vazquez-Rosas-Landa ◽

Gabriel Yaxal Ponce-Soto ◽

Jonás A. Aguirre-Liguori ◽

Shalabh Thakur ◽

...

Keyword(s):

Population Size ◽

Effective Population Size ◽

Local Adaptation ◽

Population Genomics ◽

Gene Families ◽

Effective Population ◽

Pan Genome ◽

Rare Biosphere ◽

Recent Origin ◽

Cuatro Ciénegas Basin

Abstract Background In bacteria, pan-genomes are the result of the evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size, resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.Results We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high effective population size ( N e ) estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N e , suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae estimations; however, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes under this SNPs were related to sodium transport.Conclusions Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their microhabitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.

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The Influence of Mating System and Overlapping Generations on Effective Population Size

Evolution ◽

10.2307/2410151 ◽

1993 ◽

Vol 47 (5) ◽

pp. 1329 ◽

Cited By ~ 147

Author(s):

Leonard Nunney

Keyword(s):

Mating System ◽

Population Size ◽

Effective Population Size ◽

Overlapping Generations ◽

Effective Population

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Mating system, multiple paternity and effective population size in the endemic flatback turtle (Natator depressus) in Australia

Conservation Genetics ◽

10.1007/s10592-008-9583-4 ◽

2008 ◽

Vol 10 (2) ◽

pp. 329-346 ◽

Cited By ~ 28

Author(s):

Kathrin Theissinger ◽

N. N. FitzSimmons ◽

C. J. Limpus ◽

C. J. Parmenter ◽

A. D. Phillott

Keyword(s):

Mating System ◽

Population Size ◽

Effective Population Size ◽

Multiple Paternity ◽

Effective Population ◽

Natator Depressus

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Mating System and Effective Population Size of the Overexploited Neotropical Tree (Myroxylon peruiferum L.f.) and Their Impact on Seedling Production

Journal of Heredity ◽

10.1093/jhered/esx096 ◽

2017 ◽

Vol 109 (3) ◽

pp. 264-271 ◽

Cited By ~ 4

Author(s):

Ellida de Aguiar Silvestre ◽

Kaiser Dias Schwarcz ◽

Carolina Grando ◽

Jaqueline Bueno de Campos ◽

Patricia Sanae Sujii ◽

...

Keyword(s):

Mating System ◽

Population Size ◽

Effective Population Size ◽

Seedling Production ◽

Effective Population ◽

Neotropical Tree

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Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.88.10.4494 ◽

1991 ◽

Vol 88 (10) ◽

pp. 4494-4497 ◽

Cited By ~ 256

Author(s):

D. J. Schoen ◽

A. H. Brown

Keyword(s):

Mating System ◽

Population Size ◽

Effective Population Size ◽

Intraspecific Variation ◽

Gene Diversity ◽

Effective Population

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THE INFLUENCE OF MATING SYSTEM AND OVERLAPPING GENERATIONS ON EFFECTIVE POPULATION SIZE

Evolution ◽

10.1111/j.1558-5646.1993.tb02158.x ◽

1993 ◽

Vol 47 (5) ◽

pp. 1329-1341 ◽

Cited By ~ 183

Author(s):

Leonard Nunney

Keyword(s):

Mating System ◽

Population Size ◽

Effective Population Size ◽

Overlapping Generations ◽

Effective Population

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Temporal analysis of effective population size and mating system in a social wasp

Journal of Heredity ◽

10.1093/jhered/esab057 ◽

2021 ◽

Author(s):

Carl J Dyson ◽

Olivia L Piscano ◽

Rebecca M Durham ◽

Veronica J Thompson ◽

Catherine H Johnson ◽

...

Keyword(s):

Mating System ◽

Population Size ◽

Effective Population Size ◽

Temporal Analysis ◽

Social Wasp ◽

Stabilizing Selection ◽

Effective Population ◽

Genetic Changes ◽

Reproductive Division Of Labor ◽

Eusocial Species

Abstract Highly social species are successful because they cooperate in obligately integrated societies. We examined temporal genetic variation in the eusocial wasp Vespula maculifrons in order to gain a greater understanding of evolution in highly social taxa. First, we wished to test if effective population sizes of eusocial species were relatively low due to the reproductive division of labor that characterizes eusocial taxa. We thus estimated the effective population size of V. maculifrons by examining temporal changes in population allele frequencies. We sampled the genetic composition of a V. maculifrons population at three separate time points spanning a 13-year period. We found that effective population size ranged in the hundreds of individuals, which is similar to estimates in other, non-eusocial taxa. Second, we estimated levels of polyandry in V. maculifrons in different years in order to determine if queen mating system varied over time. We found no significant change in the number or skew of males mated to queens. In addition, mating skew was not significant within V. maculifrons colonies. Therefore, our data suggest that queen mate number may be subject to stabilizing selection in this taxon. Overall, our study provides novel insight into the selective processes operating in eusocial species by analyzing temporal genetic changes within populations.

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