scholarly journals Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini)

2021 ◽  
Vol 12 ◽  
Author(s):  
Lourdes Valdez ◽  
Guillermo D’Elía
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
Population Expansion ◽  
Principal Component ◽  
Tierra Del Fuego ◽  
Local Fauna ◽  
Recent Population Expansion ◽  
Genetic Groups ◽  
History Of ◽  
Species Specific

Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

scholarly journals Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 338 ◽  
Author(s):  
Xue Zhang ◽  
Yuan-Huan Liu ◽  
Yue-Hua Wang ◽  
Shi-Kang Shen
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Population Decline ◽  
Population Expansion ◽  
Distribution Models ◽  
Recent Population Expansion

Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000–100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.

scholarly journals Assessing the origin, genetic structure and demographic history of the common pheasant (Phasianus colchicus) in the introduced European range

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohammad Reza Ashrafzadeh ◽  
Rasoul Khosravi ◽  
Carlos Fernandes ◽  
Cecilia Aguayo ◽  
Zoltán Bagi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Demographic History ◽  
Population Expansion ◽  
Game Species ◽  
Recent Population Expansion ◽  
Biogeographic Patterns ◽  
Clustering Model ◽  
History Of ◽  
Common Pheasant ◽  
The Common

AbstractThe common pheasant, a game species widely introduced throughout the world, can be considered as an ideal model to study the effects of introduction events on local adaptations, biogeographic patterns, and genetic divergence processes. We aimed to assess the origin, spatial patterns of genetic variation, and demographic history of the introduced populations in the contact zone of Central and Southeast Europe, using mitochondrial DNA control region sequences and microsatellite loci. Both types of molecular markers indicated relatively low to moderate levels of genetic variation. The mtDNA analyses revealed that common pheasants across the study area are divided into two distinct clades: B (mongolicus group) and F (colchicus group). Analyses of the microsatellite data consistently suggested a differentiation between Hungary and Serbia, with the pheasant population in Hungary being much more genetically homogeneous, while that of Serbia has much more genetic mixture and admixture. This cryptic differentiation was not detected using a non-spatial Bayesian clustering model. The analyses also provided strong evidence for a recent population expansion. This fundamental information is essential for adequate and effective conservation management of populations of a game species of great economic and ecological importance in the studied geographical region.

scholarly journals Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean

ZooKeys ◽  
2019 ◽  
Vol 830 ◽  
pp. 127-144 ◽  
Author(s):  
Lu Liu ◽  
Xiumei Zhang ◽  
Chunhou Li ◽  
Hui Zhang ◽  
Takashi Yanagimoto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Fishery Management ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Northwestern Pacific ◽  
Distribution Analysis ◽  
Recent Population Expansion

Sebastiscusmarmoratus is an ovoviviparous fish widely distributed in the northwestern Pacific. To examine the gene flow and test larval dispersal strategy of S.marmoratus in Chinese and Japanese coastal waters, 421 specimens were collected from 22 localities across its natural distribution. A 458 base-pair fragment of the mitochondrial DNA (mtDNA) control region was sequenced to examine genetic diversity and population structure. One-hundred-six variable sites defined 166 haplotypes. The populations of S.marmoratus showed high haplotype diversity with a range from 0.8587 to 0.9996, indicating a high level of intrapopulation genetic diversity. Low non-significant genetic differentiation was estimated among populations except those of Hyogo, Behai, and Niiigata, which showed significant genetic differences from the other populations. The demographic history examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden population expansion dating to the late Pleistocene. Recent population expansion in the last glacial period, wide dispersal of larvae by coastal currents, and the homogeneity of the environment may have important influences on the population genetic pattern. Knowledge of genetic diversity and genetic structure will be crucial to establish appropriate fishery management of S.marmoratus.

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

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.

scholarly journals Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia

2010 ◽  
Vol 76 (6) ◽  
pp. 1946-1954 ◽  
Author(s):  
C. C. Linde ◽  
J. A. Liles ◽  
P. H. Thrall
Keyword(s):  
Genetic Diversity ◽  
Plant Pathogens ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Alternaria Brassicicola ◽  
Evolutionary Potential ◽  
Recent Population Expansion ◽  
Fungal Plant Pathogens ◽  
Cakile Maritima ◽  
Founder Populations

ABSTRACT Founder populations of fungal plant pathogens are expected to have low levels of genetic diversity coupled with further genetic drift due to, e.g., limited host availability, which should result in additional population bottlenecks. This study used microsatellite markers in the interaction between Cakile maritima and the fungal pathogen Alternaria brassicicola to explore genetic expectations associated with such situations. The host, C. maritima, was introduced into Australia approximately 100 years ago, but it is unknown whether the pathogen was already present in Australia, as it has a wide occurrence, or whether it was introduced to Australia on brassicaceous hosts. Eleven A. brassicicola populations were studied, and all showed moderate levels of gene and genotypic diversity. Chi-square tests of the frequencies of mating type alleles, a large number of genotypes, and linkage equilibrium among microsatellite loci all suggest A. brassicicola reproduces sexually. Significant genetic differentiation was found among populations, but there was no evidence for isolation by distance effects. Bayesian analyses identified eight clusters where the inferred clusters did not represent geographical populations but instead consisted of individuals admixed from all populations. Further analysis indicated that fungal populations were more likely to have experienced a recent population expansion than a population bottleneck. It is suggested that A. brassicicola has been introduced into Australia multiple times, potentially increasing the diversity and size of any A. brassicola populations already present there. Combined with its ability to reproduce sexually, such processes appear to have increased the evolutionary potential of the pathogen through recent population expansions.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

Signatures of mito-nuclear discordance in Schistosoma turkestanicum indicate a complex evolutionary history of emergence in Europe

Parasitology ◽  
2017 ◽  
Vol 144 (13) ◽  
pp. 1752-1762 ◽  
Author(s):  
SCOTT P. LAWTON ◽  
LAUREN I. BOWEN ◽  
AIDAN M. EMERY ◽  
GÁBOR MAJOROS
Keyword(s):  
Evolutionary History ◽  
Molecular Diversity ◽  
Population Expansion ◽  
Its Sequences ◽  
Cox1 Gene ◽  
Internal Transcribed Spacer Region ◽  
Recent Population Expansion ◽  
Haplotype Frequencies ◽  
History Of ◽  
Low Levels

SUMMARYHigh levels of molecular diversity were identified in mitochondrial cytochrome c oxidase (cox1) gene sequences of Schistosoma turkestanicum from Hungary. These cox1 sequences were all specific to Hungary which contrasted with the low levels of diversity seen in the nuclear internal transcribed spacer region (ITS) sequences, the majority of which were shared between China and Iran isolates. Measures of within and between host molecular variation within S. turkestanicum showed there to be substantial differences in molecular diversity, with cox1 being significantly more diverse than the ITS. Measures of haplotype frequencies revealed that each host contained its own subpopulation of genetically unique parasites with significant levels of differentiation. Pairwise mismatch analysis of cox1 sequences indicated S. turkestanicum populations to have a bimodal pairwise difference distribution and to be stable unlike the ITS sequences, which appeared to have undergone a recent population expansion event. Positive selection was also detected in the cox1 sequences, and biochemical modelling of the resulting protein illustrated significant mutational events causing an alteration to the isoelectric point of the cox1 protein, potentially altering metabolism. The evolutionary signature from the cox1 indicates local adaptation and long establishment of S. turkestanicum in Hungary with continual introgression of nuclear genes from Asian isolates. These processes have led to the occurrence of mito-nuclear discordance in a schistosome population

scholarly journals High genetic diversity and demographic history of captive Siamese and Saltwater crocodiles suggest the first step toward the establishment of a breeding and reintroduction program in Thailand

PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184526 ◽  
Author(s):  
Sorravis Lapbenjakul ◽  
Watcharaporn Thapana ◽  
Panupon Twilprawat ◽  
Narongrit Muangmai ◽  
Thiti Kanchanaketu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
High Genetic Diversity ◽  
History Of
Sign in / Sign up

Export Citation Format

Share Document