Population History | ScienceGate

Abstract We describe a unified set of methods for the inference of demographic history using genealogies reconstructed from gene sequence data. We introduce the skyline plot, a graphical, nonparametric estimate of demographic history. We discuss both maximum-likelihood parameter estimation and demographic hypothesis testing. Simulations are carried out to investigate the statistical properties of maximum-likelihood estimates of demographic parameters. The simulations reveal that (i) the performance of exponential growth model estimates is determined by a simple function of the true parameter values and (ii) under some conditions, estimates from reconstructed trees perform as well as estimates from perfect trees. We apply our methods to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B.

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Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽

10.3390/genes12020258 ◽

2021 ◽

Vol 12 (2) ◽

pp. 258

Author(s):

Karim Karimi ◽

Duy Ngoc Do ◽

Mehdi Sargolzaei ◽

Younes Miar

Keyword(s):

Population Genomics ◽

Association Studies ◽

American Mink ◽

Population History ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Effective Population ◽

Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

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Skin Barrier Damage due to Prolonged Mask Use among Healthcare Workers and the General Population during the COVID-19 Pandemic: A Prospective Cross-Sectional Survey in China

Dermatology ◽

10.1159/000517219 ◽

2021 ◽

pp. 1-8

Author(s):

Xiao Wan ◽

Quansheng Lu ◽

Dandan Sun ◽

Hong Wu ◽

Guan Jiang

Keyword(s):

General Population ◽

Healthcare Workers ◽

Response Rate ◽

Skin Barrier ◽

Population History ◽

Skin Damage ◽

Cross Sectional ◽

Effective Response ◽

Skin Injuries ◽

Popularization Of Science

Background: Coronavirus disease 2019 (COVID-19) has resurged in localized areas in China. Individuals wear masks to prevent the spread of droplets. However, skin barrier damage occurs because of the prolonged use of masks. Objective: To investigate the prevalence and associated risk factors of skin injuries among healthcare workers (HCWs) and the general population during the COVID-19 outbreak. Methods: A multicenter cross-sectional study of skin barrier damage caused by wearing masks was conducted using an online questionnaire between December 10 and December 31, 2020. Data regarding demographics, characteristics of facial skin damage, and information on masks were registered. Multivariate logistic regression was used to analyze factors associated with skin barrier damage, and odds ratios (OR) with 95% confidence intervals (CI) were used to establish correlation strength. Results: A total of 1,538 responses were retrieved from 1,700 questionnaires (response rate, 90.47%), and 1,409 questionnaires were valid (effective response rate, 91.61%). The respondents comprised 567 HCWs (40.24%) and 842 individuals from the general population (59.76%). The prevalence of skin injuries was 46.03% among HCWs and 46.20% among the general population. History of chronic skin disease (OR, 6.01; 95% CI, 4.75–7.75), type of mask used (OR, 2.77; 95% CI, 1.95–3.93), daily wearing time (OR, 1.57; 95% CI, 1.36–1.82), and mask replacement cycle (OR, 0.76; 95% CI, 0.68–0.86) were associated with skin barrier damage. Conclusion: There was a high incidence of skin barrier damage due to prolonged mask use among HCWs and the general population, and treatment and prevention were inadequate. Attention needs to be given to strengthening comprehensive health education and popularization of science.

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Mitochondrial phylogeography and population history of finless porpoises in Sino-Japanese waters

Biological Journal of the Linnean Society ◽

10.1111/j.1095-8312.2008.0932.x ◽

2008 ◽

Vol 95 (1) ◽

pp. 193-204 ◽

Cited By ~ 21

Author(s):

GUANG YANG ◽

LI GUO ◽

MICHAEL W. BRUFORD ◽

FUWEN WEI ◽

KAIYA ZHOU

Keyword(s):

Population History ◽

History Of ◽

Japanese Waters

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Genetic diversity of the extremely rare Habenaria dentata and the rare Habenaria linearifolia (Orchidaceae) in South Korea: implications for population history and conservation

Plant Ecology and Evolution ◽

10.5091/plecevo.2018.1366 ◽

2018 ◽

Vol 151 (1) ◽

pp. 48-60

Author(s):

Mi Yoon Chung ◽

Hoa Thi Quynh Le ◽

Sungwon Son ◽

Huai Zhen Tian ◽

Myong Gi Chung

Keyword(s):

Genetic Diversity ◽

Southern China ◽

Geographic Location ◽

Population History ◽

Population Variation ◽

Conservation Strategies ◽

Ancestral Population ◽

Allozyme Diversity ◽

Glacial Origin

Background and aims – Since historical events often leave an indelible mark on levels of genetic diversity of plant populations, one may indirectly infer their evolutionary history with the help of current patterns of genetic diversity. The terrestrial orchid Habenaria dentata, an element of warm-temperate/subtropical vegetation, reaches its northernmost limits in the Korean Peninsula, and thus it is extremely rare there. As H. dentata was absent from the Peninsula during the Last Glacial Maximum (LGM), it is likely to be of post-glacial origin having arrived from either a single refugium or multiple refugia. However, its rare, temperate/boreal congener H. linearifolia might have persisted in situ in either macrorefugia or microrefugia on the Peninsula during the LGM.Methods – To test which hypothesis is most appropriate for each species, we investigated levels of allozyme-based (17 loci) genetic diversity and population genetic structure in the two only known populations of H. dentata and in 12 populations of H. linearifolia.Key results – No allozyme diversity was found in H. dentata (He = 0.000), whereas H. linearifolia exhibited low within-population variation (He = 0.060) and high among-population differentiation (FST = 0.237). We found little association between populations in relation to their geographic location; several populations presented individuals belonging to different clusters.Conclusions – Our results suggest that H. dentata likely originated from a single ancestral population (perhaps from southern Japan or southern China) through post-glacial dispersal, whereas H. linearifolia probably survived the LGM in situ in microrefugia situated at low to mid-elevated regions. We further suggest that separate conservation strategies for each species should be employed, given that the two taxa have different ecological and demographic traits and harbour different levels of genetic diversity.

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Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris)

BMC Evolutionary Biology ◽

10.1186/1471-2148-10-278 ◽

2010 ◽

Vol 10 (1) ◽

pp. 278 ◽

Cited By ~ 32

Author(s):

Benoit de Thoisy ◽

Anders da Silva ◽

Manuel Ruiz-García ◽

Andrés Tapia ◽

Oswaldo Ramirez ◽

...

Keyword(s):

Conservation Genetics ◽

Population History ◽

Tapirus Terrestris

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Human mitochondrial DNA lineages in Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry

Scientific Reports ◽

10.1038/s41598-019-51045-8 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Sanni Översti ◽

Kerttu Majander ◽

Elina Salmela ◽

Kati Salo ◽

Laura Arppe ◽

...

Keyword(s):

Iron Age ◽

High Mobility ◽

Human Remains ◽

Population History ◽

Hunter Gatherers ◽

East Europe ◽

North East ◽

Mtdna Diversity ◽

The Baltic ◽

Genetic Shift

AbstractHuman ancient DNA studies have revealed high mobility in Europe’s past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300–1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns.

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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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