Population Genetic Analysis of Ten Geographically Isolated Tibetan Pig Populations

Several geographically isolated populations of Tibetan pigs inhabit the high-altitude environment of the Tibetan Plateau. Their genetic relationships, contribution to the pool of genetic diversity, and their origin of domestication are unclear. In this study, whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed. Population genetic analyses revealed limited genetic differentiation among the Tibetan pig populations. Evidence from deleterious variant analysis indicated that population-specific deleterious variants were the major component of all mutational loci. Contribution to the meta-population was largest in the TT (Qinghai-Tibet Plateau) population, based on gene diversity or allelic diversity. Selective sweep analysis revealed numerous genes, including RXFP1, FZD1, OR1F1, TBX19, MSTN, ESR1, MC1R, HIF3A, and EGLN2 which are involved in lung development, hard palate development, coat color, hormone metabolism, facial appearance, and perception of smell. These findings increase our understanding of the origins and domestication of the Tibetan pig, and help optimize the strategy for their conservation.

Download Full-text

Population Genetic Analysis ofLobelia rhynchopetalumHemsl. (Campanulaceae) Using DNA Sequences fromITSand Eight Chloroplast DNA Regions

The Scientific World JOURNAL ◽

10.1100/2012/276451 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Mulatu Geleta ◽

Tomas Bryngelsson

Keyword(s):

Chloroplast Dna ◽

Dna Sequences ◽

Population Genetic ◽

Sequence Data ◽

Gene Diversity ◽

Nuclear Ribosomal Dna ◽

Bootstrap Support ◽

Population Genetic Analysis ◽

Mountain Systems ◽

Chloroplast Dna Regions

DNA sequence data from the internal transcribed spacer of nuclear ribosomal DNA and eight chloroplast DNA regions were used to investigate haplotypic variation and population genetic structure of the Afroalpine giant lobelia,Lobelia rhynchopetalum.The study was based on eight populations sampled from two mountain systems in Ethiopia. A total of 20 variable sites were obtained, which resulted in 13 unique haplotypes and an overall nucleotide diversity (ND) of 0.281 ± 0.15 and gene diversity (GD) of 0.85 ± 0.04. Analysis of molecular variance (AMOVA) revealed a highly significant variation (P<0.001) among populations (FST), and phylogenetic analysis revealed that populations from the two mountain systems formed their own distinct clade with >90% bootstrap support. Each population should be regarded as a significant unit for conservation of this species. The primers designed for this study can be applied to anyLobeliaand other closely related species for population genetics and phylogenetic studies.

Download Full-text

Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure.

Journal of Bacteriology ◽

10.1128/jb.178.13.3934-3938.1996 ◽

1996 ◽

Vol 178 (13) ◽

pp. 3934-3938 ◽

Cited By ~ 157

Author(s):

M F Go ◽

V Kapur ◽

D Y Graham ◽

J M Musser

Keyword(s):

Helicobacter Pylori ◽

Population Structure ◽

Genetic Analysis ◽

Population Genetic ◽

Allelic Diversity ◽

Enzyme Electrophoresis ◽

Population Genetic Analysis ◽

Multilocus Enzyme Electrophoresis

Download Full-text

Allozyme Characterisation of the Salt Lake Spiders (Lycosa: Lycosidae: Araneae) of Southern Australia: Systematic and Population Genetic Implications.

Australian Journal of Zoology ◽

10.1071/zo9960535 ◽

1996 ◽

Vol 44 (5) ◽

pp. 535 ◽

Cited By ~ 8

Author(s):

P Hudson ◽

M Adams

Keyword(s):

Population Genetic ◽

Salt Lake ◽

Genetic Relationships ◽

South Australia ◽

Wolf Spider ◽

Allozyme Variation ◽

Population Genetic Analysis ◽

Additional Species ◽

Population Substructuring ◽

The Times

Allozyme electrophoresis was used to determine the genetic relationships amongst various populations of Lycosa alteripa, L. eyrei and L. salifodina, the three described species of wolf spider endemic to the normally dry salt lakes of southern Australia. A total of 185 individuals from 38 sites was analysed for allozyme variation at 31-35 loci. The results demonstrate the presence of two additional species of salt lake spider, one related to L. alteripa and the other related to L. eyrei. Limited population genetic analysis of the data indicates that population substructuring is common within most species, often to the finest level of geographic sampling. The data indicate that gene flow is limited in these species and reveal three instances of a similar macro-geographic pattern being displayed amongst subpopulations or taxa in central South Australia. Estimates of genetic divergence between the five taxa have also been used to provide a 'first-guess' estimate of the times of divergence for the major cladogenic events within this lineage.

Download Full-text

Extension of the Upper Yellow River into the Tibet Plateau: Review and New Data

Quaternary ◽

10.3390/quat4020014 ◽

2021 ◽

Vol 4 (2) ◽

pp. 14

Author(s):

Zhengchen Li ◽

Xianyan Wang ◽

Jef Vandenberghe ◽

Huayu Lu

Keyword(s):

Tibetan Plateau ◽

Yellow River ◽

Google Earth ◽

Tibet Plateau ◽

The Yellow River ◽

Published Data ◽

The Tibetan Plateau ◽

Large Lakes ◽

River Terraces ◽

The Tibet Plateau

The Wufo Basin at the margin of the northeastern Tibet Plateau connects the upstream reaches of the Yellow River with the lowland catchment downstream, and the fluvial terrace sequence in this basin provides crucial clues to understand the evolution history of the Yellow River drainage system in relation to the uplift and outgrowth of the Tibetan Plateau. Using field survey and analysis of Digital Elevation Model/Google Earth imagery, we found at least eight Yellow River terraces in this area. The overlying loess of the highest terrace was dated at 1.2 Ma based on paleomagnetic stratigraphy (two normal and two reversal polarities) and the loess-paleosol sequence (12 loess-paleosol cycles). This terrace shows the connections of drainage parts in and outside the Tibetan Plateau through its NE margin. In addition, we review the previously published data on the Yellow River terraces and ancient large lakes in the basins. Based on our new data and previous researches, we conclude that the modern Yellow River, with headwaters in the Tibet Plateau and debouching in the Bohai Sea, should date from at least 1.2 Ma. Ancient large lakes (such as the Hetao and Sanmen Lakes) developed as exorheic systems and flowed through the modern Yellow River at that time.

Download Full-text

Adaptive Evolution of Relish, a Drosophila NF-κB/IκB Protein

Genetics ◽

10.1093/genetics/154.3.1231 ◽

2000 ◽

Vol 154 (3) ◽

pp. 1231-1238 ◽

Cited By ~ 1

Author(s):

David J Begun ◽

Penn Whitley

Keyword(s):

Immune Response ◽

Innate Immunity ◽

Genetic Analysis ◽

Adaptive Evolution ◽

Strong Evidence ◽

Population Genetic ◽

Microbial Pathogens ◽

Population Genetic Analysis ◽

Evolutionary Conflict ◽

A Site

Abstract NF-κB and IκB proteins have central roles in regulation of inflammation and innate immunity in mammals. Homologues of these proteins also play an important role in regulation of the Drosophila immune response. Here we present a molecular population genetic analysis of Relish, a Drosophila NF-κB/IκB protein, in Drosophila simulans and D. melanogaster. We find strong evidence for adaptive protein evolution in D. simulans, but not in D. melanogaster. The adaptive evolution appears to be restricted to the IκB domain. A possible explanation for these results is that Relish is a site of evolutionary conflict between flies and their microbial pathogens.

Download Full-text

Unexpectedly High Allelic Diversity at the KIT Locus Causing Dominant White Color in the Domestic Pig

Genetics ◽

10.1093/genetics/160.1.305 ◽

2002 ◽

Vol 160 (1) ◽

pp. 305-311

Author(s):

G Pielberg ◽

C Olsson ◽

A-C Syvänen ◽

L Andersson

Keyword(s):

Coat Color ◽

Allelic Diversity ◽

Growth Factor Receptor ◽

Small Sample ◽

Color Variation ◽

Large White ◽

High Genetic Diversity ◽

High Allelic Diversity ◽

Stem Cell Growth Factor ◽

New Alleles

Abstract Mutations in KIT encoding the mast/stem cell growth factor receptor (MGF) are responsible for coat color variation in domestic pigs. The dominant white phenotype is caused by two mutations, a gene duplication and a splice mutation in one of the copies leading to skipping of exon 17. Here we applied minisequencing and pyrosequencing for quantitative analysis of the number of copies with the splice form. An unexpectedly high genetic diversity was revealed in white pigs. We found four different KIT alleles in a small sample of eight Large White females used as founder animals in a wild boar intercross. A similar number of KIT alleles was found in commercial populations of white Landrace and Large White pigs. We provide evidence for at least two new KIT alleles in pigs, both with a triplication of the gene. The results imply that KIT alleles with the duplication are genetically unstable and new alleles are most likely generated by unequal crossing over. This study provides an improved method for genotyping the complicated Dominant white/KIT locus in pigs. The results also suggest that some alleles may be associated with negative pleiotropic effects on other traits.

Download Full-text

Population genetic analysis of Enterocytozoon bieneusi in humans

International Journal for Parasitology ◽

10.1016/j.ijpara.2012.01.003 ◽

2012 ◽

Vol 42 (3) ◽

pp. 287-293 ◽

Cited By ~ 44

Author(s):

Wei Li ◽

Vitaliano Cama ◽

Yaoyu Feng ◽

Robert H. Gilman ◽

Caryn Bern ◽

...

Keyword(s):

Genetic Analysis ◽

Population Genetic ◽

Enterocytozoon Bieneusi ◽

Population Genetic Analysis

Download Full-text

Population Genetic Analysis Corroborates Dispersal of Fusarium oxysporum f. sp. radicis-lycopersici from Florida to Europe

Phytopathology ◽

10.1094/phyto.1999.89.8.623 ◽

1999 ◽

Vol 89 (8) ◽

pp. 623-630 ◽

Cited By ~ 35

Author(s):

U. Liane Rosewich ◽

R. E. Pettway ◽

Talma Katan ◽

H. C. Kistler

Keyword(s):

Fusarium Oxysporum ◽

Gene Diversity ◽

Population Subdivision ◽

Founder Population ◽

Palm Beach County ◽

Population Genetic Analysis ◽

Low Frequencies ◽

The United Kingdom ◽

Crown And Root Rot ◽

Southern Florida

Fusarium oxysporum isolates from tomato plants displaying crown and root rot symptoms were collected in central and southern Florida and analyzed using vegetative compatibility grouping (VCG) and nuclear restriction fragment length polymorphism (RFLP) data. VCG 0094 of F. oxysporum f. sp. radicis-lycopersici, previously known only from northwestern Europe, was predominant among 387 isolates assessed. In addition, two newly described VCGs (0098 and 0099) were detected at low frequencies. Floridian VCG 0094 isolates displayed a continuum of compatibilities, which is in contrast to the three distinct subgroups previously identified among European VCG 0094 isolates. RFLP haplotypes were constructed using one repetitive and three low-copy probes. Population subdivision of VCG 0094 from various Floridian counties and from northwestern Europe (Belgium, the Netherlands, and the United Kingdom) was evaluated by analysis of molecular variance. A “natural” population structure was revealed, differentiating populations from the east and west coasts of Florida. In addition, isolates from Europe were statistically indistinguishable from the Palm Beach County, FL, population. Furthermore, gene diversity among Palm Beach County VCG 0094 isolates was more than five times greater than among European isolates. Results from both VCG and RFLP analyses strongly support the inference that the European VCG 0094 constitutes a founder population that resulted from intercontinental migration of a few isolates from Palm Beach County, FL.

Download Full-text