scholarly journals Does selection occur at the intermediate zone of two insufficiently isolated populations? A whole-genome analysis along an altitudinal gradient

2021 ◽  
Author(s):  
Naofumi Yoshida ◽  
Shin-Ichi Morinaga ◽  
Takeshi Wakamiya ◽  
Yuu Ishii ◽  
Shosei Kubota ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Altitudinal Gradient ◽  
Intermediate Zone ◽  
Adaptive Divergence ◽  
Population Divergence ◽  
Whole Genome ◽  
Isolated Populations ◽  
Whole Genome Analysis ◽  
Single Nucleotide

Abstract Adaptive divergence would occur even between the insufficiently isolated populations when there is a great difference in the environments of their habitats. The individuals present in the intermediate zone of the two divergent populations are expected to have an admixed genetic structure due to gene flow. A selective pressure that acts on the genetically admixed individuals may limit the gene flow and promote the adaptive divergence. Here, we addressed a question whether the selection occurs in the genetically admixed individuals between the divergent populations and assessed its effects on the population divergence. We obtained the whole-genome sequences of a perennial montane plant, Arabidopsis halleri, which has clear phenotypic dimorphisms between altitudes, along an altitudinal gradient of 359–1,317 m with a high spatial resolution (mean altitudinal interval of 20 m). We found the zone where the highland and lowland genes were mixing. Using the FST approach, we found that 35 and 13 genes in the admixed zone had a high frequency of alleles that are accumulated in highland and lowland subpopulations, respectively, suggesting that these genes have been selected in the admixed zone. This selection might limit the gene flow and contribute to the adaptive divergence along the altitudes. In the single-nucleotide polymorphism (SNP)-based analysis, 3,000 out of 27,792 Altitude-Dependent SNPs had extremely high homozygosity in the admixed zone. In 84.7% of these SNPs, the frequency of homozygotes of highland alleles was comparable to that of lowland alleles, suggesting that these alleles are neutral but the heterozygotes were selectively eliminated. The distribution of highland and lowland alleles of these SNPs was not clearly separated between altitudes, implying that such selection did not impede the gene flow. We conclude that the selection occurring at the intermediate altitude affects the genetic structure in the admixed zone and adaptive divergence along the altitudes.

Genetic structure of the arboreal squirrels (Glaucomys sabrinus and Tamiasciurus hudsonicus) in the North American Black Hills

2012 ◽  
Vol 90 (9) ◽  
pp. 1191-1200 ◽  
Author(s):  
A.M. Kiesow ◽  
E.M. Monroe ◽  
H.B. Britten
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Management Practices ◽  
Allelic Diversity ◽  
Black Hills ◽  
Tamiasciurus Hudsonicus ◽  
Glaucomys Sabrinus ◽  
Red Squirrel ◽  
Isolated Populations ◽  
Red Squirrels

We selected two isolated mammalian populations, the Black Hills northern flying squirrel ( Glaucomys sabrinus (Shaw, 1801)) and red squirrel ( Tamiasciurus hudsonicus (Erxleben, 1777)), to elucidate their genetic structure. We trapped both squirrels from 2005 to 2007, in three regions of the Black Hills, differing in geology and vegetation, to collect ear samples for genetic analyses. Microsatellite loci (northern flying (9) and red squirrel (13)) were used to examine genetic structure. Data analyses estimated genetic variability, substructure, and gene flow. Northern flying and red squirrel populations have allelic diversity and observed heterozygosity similar to other isolated populations. Each species shows weak substructure from STRUCTURE and GENELAND analyses, suggesting squirrel movements may be inhibited by topography or unsuitable habitat. Recent gene flow estimates from BAYESASS indicate that both species experience some within population gene flow and red squirrels may be more structured than northern flying squirrels because of lower migration rates. Concordant patterns of genetic structure in northern flying and red squirrels indicate that other species’ movements in the Black Hills may be affected by topography and habitat. Because their habitat is isolated in the Black Hills, management practices and conservation measures are recommended to promote viability and survival of each species.

scholarly journals Homologous Recombination within Large Chromosomal Regions Facilitates Acquisition of β-Lactam and Vancomycin Resistance in Enterococcus faecium

2016 ◽  
Vol 60 (10) ◽  
pp. 5777-5786 ◽  
Author(s):  
Mónica García-Solache ◽  
Francois Lebreton ◽  
Robert E. McLaughlin ◽  
James D. Whiteaker ◽  
Michael S. Gilmore ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Genomic Dna ◽  
Large Scale ◽  
Vancomycin Resistance ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Single Nucleotide ◽  
Content Type ◽  
Donor Chromosome ◽  
Vancomycin Resistant

ABSTRACTThe transfer of DNA betweenEnterococcus faeciumstrains has been characterized both by the movement of well-defined genetic elements and by the large-scale transfer of genomic DNA fragments. In this work, we report on the whole-genome analysis of transconjugants resulting from mating events between the vancomycin-resistantE. faeciumC68 strain and the vancomycin-susceptible D344RRF strain to discern the mechanism by which the transferred regions enter the recipient chromosome. Vancomycin-resistant transconjugants from five independent matings were analyzed by whole-genome sequencing. In all cases but one, the penicillin binding protein 5 (pbp5) gene and the Tn5382vancomycin resistance transposon were transferred together and replaced the correspondingpbp5region of D344RRF. In one instance, Tn5382inserted independently downstream of the D344RRFpbp5gene. Single nucleotide variant (SNV) analysis suggested that entry of donor DNA into the recipient chromosome occurred by recombination across regions of homology between donor and recipient chromosomes, rather than through insertion sequence-mediated transposition. The transfer of genomic DNA was also associated with the transfer of C68 plasmid pLRM23 and another putative plasmid. Our data are consistent with the initiation of transfer by cointegration of a transferable plasmid with the donor chromosome, with subsequent circularization of the plasmid-chromosome cointegrant in the donor prior to transfer. Entry into the recipient chromosome most commonly occurred across regions of homology between donor and recipient chromosomes.

Association of SLC15A2 genomic variation with the response to sorafenib treatment: Whole-genome analysis in patients with hepatocellular carcinoma.

2015 ◽  
Vol 33 (3_suppl) ◽  
pp. 308-308
Author(s):  
Bo Hyun Kim ◽  
Yeon-Su Lee ◽  
Byung Chul Kim ◽  
Aesun Shin ◽  
Jin Sook Kim ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Functional Analysis ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Single Nucleotide ◽  
Sorafenib Treatment ◽  
Genomic Variations ◽  
Validation Tests

308 Background: Reliable biomarkers are required to predict patient response to sorafenib. We attempted to investigate genomic variations associated with responsiveness to sorafenib treatment in patients with unresectable hepatocellular carcinoma (HCC) and their functional relevance. Methods: We obtained blood samples from 4 strong and 3 poor responders to sorafenib treatment and subjected these samples to whole-genome analysis. Next, we performed validation tests for candidate single-nucleotide polymorphisms (SNPs) in the samples of 174 HCC patients who were treated with sorafenib, followed by in vitro functional analysis and in silico analyses of candidate SNPs. Results: On average, 90 gigabases/sample was generated at ~34X sequencing depth. In total, 1813 genomic variations were perfectly matched to sorafenib responses in the clinical data; 708 were located within regions for sorafenib-target genes or drug absorption, distribution, metabolism, and excretion (ADME)-related genes—36 within the coding regions and 6 identified as non-synonymous single-nucleotide variants from 4 ADME-related genes (ABCB1, FMO3, MUSK, and SLC15A2), which potentially cause functional alterations. Validation tests of 174 patients confirmed sequencing results and revealed that patients with the C/C genotype for rs2257212 in SCL15A2 displayed higher risk for cancer progression than did patients with C/T or T/T genotypes (HR: 2.18; 95% CI, 1.15–4.15; P = 0.018). In vitro functional analysis revealed that cells harboring C/C genotype for this SNP displayed lower response to sorafenib treatment than did cells harboring the T/T genotype. Structural prediction analysis revealed change in protein phosphorylation levels, potentially affecting sorafenib-associated enzymatic activity. Conclusions: SLC15A2 could be a robust biomarker of response to sorafenib treatment in HCC patients.

scholarly journals GENE FLOW AND THE GEOGRAPHICAL DISTRIBUTION OF A MOLECULAR POLYMORPHISM IN DROSOPHILA PSEUDOOBSCURA

Genetics ◽  
1981 ◽  
Vol 98 (1) ◽  
pp. 157-178
Author(s):  
J S Jones ◽  
S H Bryant ◽  
R C Lewontin ◽  
J A Moore ◽  
T Prout
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Geographical Distribution ◽  
Enzyme Polymorphism ◽  
Seasonal Abundance ◽  
Drosophila Pseudoobscura ◽  
Isolated Population ◽  
Molecular Polymorphism ◽  
Isolated Populations ◽  
High Level

ABSTRACT This paper discusses the relation between the geographical distribution of an enzyme polymorphism and population structure in Drosophila pseudoobscura. California populations of this species living in very different montane and lowland habitats separated by several kilometers are similar to each other in the frequency of an esterase allele. Previous estimates suggest that gene flow is too limited to account for this homogeneity of genetic structure, so that it must reflect some balancing force of natural selection. We show, however, that dispersal over unfavorable habitats is much greater than earlier supposed. Isolated populations of D. pseudoobscura separated by 15 km from other populations are subject to large amounts of immigration. This is shown by changes in the seasonal abundance of this species and in the annual pattern of lethal alleles in such populations. The genetic structure of an experimentally perturbed isolated population in an oasis returned to normal within a single year, suggesting that such populations are ephemeral and that the oasis is subject to annual recolonization by distant migrants. Direct assessment of marked flies shows that they can move at least 10 km in 24 hours over a desert. Such extensive gene flow may help explain the distribution of the esterase allele, and is relevant to the high level of molecular polymorphism and its general lack of geographic differentiation throughout the range of D. pseudoobscura.

scholarly journals Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.)

2010 ◽  
Vol 60 (4) ◽  
pp. 390-397 ◽  
Author(s):  
Kaworu Ebana ◽  
Jun-ichi Yonemaru ◽  
Shuichi Fukuoka ◽  
Hiroyoshi Iwata ◽  
Hiroyuki Kanamori ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Oryza Sativa ◽  
Genetic Structure ◽  
Oryza Sativa L ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Asian Rice

Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient

2015 ◽  
Vol 29 (2) ◽  
pp. 241-252 ◽  
Author(s):  
W. C. Funk ◽  
M. A. Murphy ◽  
K. L. Hoke ◽  
E. Muths ◽  
S. M. Amburgey ◽  
...  
Keyword(s):  
Gene Flow ◽  
Altitudinal Gradient ◽  
Adaptive Divergence ◽  
Restricted Gene Flow

Structure et variabilité génétique de populations d'épinette noire (Piceamariana (Mill.) B.S.P.) dans la zone hémiarctique du Nouveau-Québec

1987 ◽  
Vol 17 (9) ◽  
pp. 1006-1012 ◽  
Author(s):  
Mireille Desponts ◽  
Jean-Pierre Simon
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Variability ◽  
Gel Electrophoresis ◽  
Black Spruce ◽  
Geographic Isolation ◽  
Marginal Populations ◽  
Isolated Populations ◽  
Subarctic Region ◽  
Enzyme Systems

The genetic structure of five populations of black spruce located at l'Eau Claire Lake, in the subarctic region of Nouveau-Québec, were analysed by acrylamide gel electrophoresis of seven enzyme systems. The analysis of 25 loci disclosed an average polymorphism of 0.80 and a level of heterozygosity of 0.351. Results indicate that there is no loss of genetic variability in these marginal populations that could be attributed to genetic drift. Data based on Wright's statistics indicate an excess of heterozygotes for most loci. Populations share the same alleles at most loci and are only slightly differentiated from each other (Fst = 0.06). Results suggest that gene flow between these isolated populations remains sufficiently high to override the effect of geographic isolation.

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