Larger males facilitate population expansion in Ophraella communa

Abstract The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.

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Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

Parasites & Vectors ◽

10.1186/s13071-019-3740-0 ◽

2019 ◽

Vol 12 (1) ◽

Author(s):

Maysa Tiemi Motoki ◽

Dina Madera Fonseca ◽

Elliott Frederic Miot ◽

Bruna Demari-Silva ◽

Phoutmany Thammavong ◽

...

Keyword(s):

Population Structure ◽

Gene Flow ◽

Aedes Albopictus ◽

Isolation By Distance ◽

Genetic Locus ◽

Lao Pdr ◽

Phylogenetic Network ◽

Population Expansion ◽

Recent Population Expansion ◽

The Usa

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

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Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽

10.1093/genetics/163.1.147 ◽

2003 ◽

Vol 163 (1) ◽

pp. 147-157 ◽

Cited By ~ 6

Author(s):

Arjun Sivasundar ◽

Jody Hey

Keyword(s):

Genetic Variation ◽

Microsatellite Loci ◽

Population Expansion ◽

Widespread Species ◽

C Elegans ◽

Model Research ◽

The World ◽

Natural Isolates ◽

History Of ◽

Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

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Improved NSGA-II with Hierarchical Retention and Interval Population Expansion

2020 5th International Conference on Mechanical, Control and Computer Engineering (ICMCCE) ◽

10.1109/icmcce51767.2020.00491 ◽

2020 ◽

Author(s):

Liang Xiaolei ◽

Zheng Lilan ◽

Li Jun ◽

Liu Xingyu

Keyword(s):

Population Expansion ◽

Nsga Ii

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DNA Sequence Variation and the Recombinational Landscape in Drosophila pseudoobscura: A Study of the Second Chromosome

Genetics ◽

10.1093/genetics/153.2.859 ◽

1999 ◽

Vol 153 (2) ◽

pp. 859-869 ◽

Cited By ~ 7

Author(s):

Martha T Hamblin ◽

Charles F Aquadro

Keyword(s):

Population Size ◽

Effective Population Size ◽

Dna Sequence ◽

Sequence Variation ◽

Population Expansion ◽

Drosophila Pseudoobscura ◽

Effective Population ◽

Standing Variation ◽

Dna Sequence Polymorphism ◽

Slightly Deleterious Mutations

Abstract The relationship between rates of recombination and DNA sequence polymorphism was analyzed for the second chromosome of Drosophila pseudoobscura. We constructed integrated genetic and physical maps of this chromosome using molecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromosome arm (3R) in D. melanogaster. There appears to be very little centromeric suppression of recombination, and rates of recombination are quite uniform across most of the chromosome. Levels of sequence variation (θW, based on the number of segregating sites) at seven loci (tropomyosin 1, Rhodopsin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consistent with earlier studies, the average estimate of θW at total sites is 1.5-fold higher than that in D. melanogaster, while average θW at silent sites is almost 3-fold higher. These estimates of variation were analyzed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence variation in D. pseudoobscura can be explained by differences in regional rates of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymous, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima’s D statistics for 6 out of the 7 loci surveyed are negative, suggesting that D. pseudoobscura may have experienced a rapid population expansion in the recent past or, alternatively, that slightly deleterious mutations constitute an important component of standing variation in this species.

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Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

Scientific Reports ◽

10.1038/s41598-021-93050-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Wen-Wen Li ◽

Li-Qiang Liu ◽

Qiu-Ping Zhang ◽

Wei-Quan Zhou ◽

Guo-Quan Fan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Chloroplast Dna ◽

Population Expansion ◽

Prunus Armeniaca ◽

River Valley ◽

Nuclear Ribosomal Dna ◽

Glacial Refugium ◽

Ili River Valley ◽

Wild Apricot

AbstractTo clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

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Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

Animal Biology ◽

10.1163/157075610x523314 ◽

2010 ◽

Vol 60 (4) ◽

pp. 449-465

Author(s):

Wen Longying ◽

Zhang Lixun ◽

An Bei ◽

Luo Huaxing ◽

Liu Naifa ◽

...

Keyword(s):

Demographic History ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Population Expansion ◽

Population History ◽

Tibet Plateau ◽

Phylogeographic Structure ◽

Mitochondrial Cytochrome B ◽

History Of ◽

Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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