scholarly journals Temperature heterogeneity correlates with intraspecific variation in physiological flexibility in a small endotherm

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Maria Stager ◽  
Nathan R. Senner ◽  
David L. Swanson ◽  
Matthew D. Carling ◽  
Douglas K. Eddy ◽  
...  
Keyword(s):  
Population Genetic ◽  
Environmental Heterogeneity ◽  
Thermal Environment ◽  
Allelic Variation ◽  
Phenotypic Flexibility ◽  
Junco Hyemalis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Variation ◽  
Physiological Flexibility

AbstractPhenotypic flexibility allows individuals to reversibly modify trait values and theory predicts an individual’s relative degree of flexibility positively correlates with the environmental heterogeneity it experiences. We test this prediction by integrating surveys of population genetic and physiological variation with thermal acclimation experiments and indices of environmental heterogeneity in the Dark-eyed Junco (Junco hyemalis) and its congeners. We combine field measures of thermogenic capacity for 335 individuals, 22,006 single nucleotide polymorphisms genotyped in 181 individuals, and laboratory acclimations replicated on five populations. We show that Junco populations: (1) differ in their thermogenic responses to temperature variation in the field; (2) harbor allelic variation that also correlates with temperature heterogeneity; and (3) exhibit intra-specific variation in thermogenic flexibility in the laboratory that correlates with the heterogeneity of their native thermal environment. These results provide comprehensive support that phenotypic flexibility corresponds with environmental heterogeneity and highlight its importance for coping with environmental change.

scholarly journals Temperature heterogeneity correlates with intraspecific variation in physiological flexibility in a small endotherm

2020 ◽  
Author(s):  
Maria Stager ◽  
Nathan R. Senner ◽  
David L. Swanson ◽  
Matthew D. Carling ◽  
Douglas K. Eddy ◽  
...  
Keyword(s):  
Population Genetic ◽  
Environmental Heterogeneity ◽  
Thermal Environment ◽  
Phenotypic Flexibility ◽  
Junco Hyemalis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Variation ◽  
Physiological Flexibility

ABSTRACTPhenotypic flexibility allows individuals to reversibly modify trait values and theory predicts an individual’s relative degree of flexibility positively correlates with the environmental heterogeneity it experiences. We tested this prediction by integrating surveys of population genetic and physiological variation with thermal acclimation experiments and indices of environmental heterogeneity in the Dark-eyed Junco (Junco hyemalis) and its congeners. We combined measures of thermogenic capacity for ~300 individuals, >21,000 single nucleotide polymorphisms genotyped in 192 individuals, and laboratory acclimations replicated on five populations. We found that Junco populations: (1) differ in their thermal performance responses to temperature variation in situ; (2) exhibit intra-specific variation in their thermogenic flexibility in the laboratory that correlates with heterogeneity in their native thermal environment; and (3) harbor genetic variation that also correlates with temperature heterogeneity. These results provide comprehensive support that phenotypic flexibility corresponds with environmental heterogeneity and highlight its importance for coping with environmental change.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals Identification of Allelic Variation in Drought Responsive Dehydrin Gene Based on Sequence Similarity in Chickpea (Cicer arietinum L.)

2020 ◽  
Vol 11 ◽  
Author(s):  
Tapan Kumar ◽  
Neha Tiwari ◽  
Chellapilla Bharadwaj ◽  
Ashutosh Sarker ◽  
Sneha Priya Reddy Pappula ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Drought Tolerance ◽  
Cicer Arietinum ◽  
Allelic Variation ◽  
Sequence Similarity ◽  
Nucleotide Polymorphisms ◽  
Residual Moisture ◽  
Single Nucleotide ◽  
The World ◽  
Dehydrin Gene

Chickpea (Cicer arietinum L.) is an economically important food legume grown in arid and semi-arid regions of the world. Chickpea is cultivated mainly in the rainfed, residual moisture, and restricted irrigation condition. The crop is always prone to drought stress which is resulting in flower drop, unfilled pods, and is a major yield reducer in many parts of the world. The present study elucidates the association between candidate gene and morpho-physiological traits for the screening of drought tolerance in chickpea. Abiotic stress-responsive gene Dehydrin (DHN) was identified in some of the chickpea genotypes based on the sequence similarity approach to play a major role in drought tolerance. Analysis of variance revealed a significant effect of drought on relative water content, membrane stability index, plant height, and yield traits. The genotypes Pusa1103, Pusa362, and ICC4958 were found most promising genotypes for drought tolerance as they maintained the higher value of osmotic regulations and yield characters. The results were further supported by a sequence similarity approach for the dehydrin gene when analyzed for the presence of single nucleotide polymorphisms (SNPs) and indels. Homozygous indels and single nucleotide polymorphisms were found after the sequencing in some of the selected genotypes.

scholarly journals Single-Nucleotide Polymorphisms in LPA Explain Most of the Ancestry-Specific Variation in Lp(a) Levels in African Americans

PLoS ONE ◽  
2011 ◽  
Vol 6 (1) ◽  
pp. e14581 ◽  
Author(s):  
Rahul C. Deo ◽  
James G. Wilson ◽  
Chao Xing ◽  
Kim Lawson ◽  
W. H. Linda Kao ◽  
...  
Keyword(s):  
African Americans ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Variation

scholarly journals A Study of Relationships Between Single Nucleotide Polymorphisms from the Growth Hormone-Insulin-like Growth Factor Axis and Bone Mass: the Hertfordshire Cohort Study

2009 ◽  
Vol 36 (7) ◽  
pp. 1520-1526 ◽  
Author(s):  
ELAINE M. DENNISON ◽  
HOLLY E. SYDDALL ◽  
KAREN A. JAMESON ◽  
AVAN AIHIE SAYER ◽  
TOM R. GAUNT ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Lumbar Spine ◽  
Growth Factor ◽  
Allelic Variation ◽  
Receptor Gene ◽  
Growth Hormone Releasing Hormone ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Single Nucleotide ◽  
Hormone Receptor Gene

Objective.We sought evidence of association of candidate single nucleotide polymorphisms (SNP) within the growth hormone-insulin-like growth factor 1 (IGF1) axis, largely selected on the basis of functional data available at the time of our study, with adult bone mass.Methods.Four hundred ninety-eight men and 468 women aged 59–71 years were recruited. A lifestyle questionnaire was administered, and bone mineral content (BMC) and bone mineral density (BMD) were measured at the lumbar spine and femoral neck. Two hundred fifty-four men and 271 women had repeat bone densitometry 4 years later. DNA was obtained from whole blood samples using standard extraction techniques. Single nucleotide variants in the growth hormone releasing hormone gene (GHRH, G/A 223 Phe75Leu, rs4988492), growth hormone releasing hormone receptor gene (GHRHR, G/A 217, Ala57Thr, rs4988496), the growth hormone secretagogue receptor gene (GHSR, T/C, Gly57Gly, rs495225), and the growth hormone receptor gene (GHR, T/G, noncoding, rs2940944) were analyzed.Results.In both sexes, allelic variation in the gene encoding GHRH was associated with BMC and BMD at the proximal femur and lumbar spine, with results generally stronger in women. In women, the mean BMC lumbar spine within the GHRH 11 genotype was 56.9 g, while that of the GHRH 12 genotype was 68.4 g [p < 0.001, fully adjusted for age, body mass index, cigarette and alcohol consumption, dietary calcium intake, physical activity, years since menopause, and hormone replacement therapy (HRT) use]; corresponding figures for BMD lumbar spine (GHRH 11 genotype) were 0.96 g/cm2 versus 1.10 g/cm2 (p < 0.001 fully adjusted).Conclusion.We have demonstrated a relationship between allelic variation in the gene encoding GHRH and bone density; we welcome attempts at replication in other populations.

scholarly journals Single nucleotide polypmorphisms of fimH associated with adherence and biofilm formation by serovars of Salmonella enterica

Microbiology ◽  
2011 ◽  
Vol 157 (11) ◽  
pp. 3162-3171 ◽  
Author(s):  
Brett E. Dwyer ◽  
Karly L. Newton ◽  
Dagmara Kisiela ◽  
Evgeni V. Sokurenko ◽  
Steven Clegg
Keyword(s):  
Amino Acid ◽  
Guinea Pig ◽  
Biofilm Formation ◽  
Allelic Variation ◽  
Single Amino Acid ◽  
Predicted Amino Acid Sequence ◽  
Nucleotide Polymorphisms ◽  
Cell Type ◽  
Single Nucleotide

Type 1 fimbriae produced by serovars of Salmonella are characterized by their ability to agglutinate guinea pig erythrocytes in the absence of d-mannose but not in its presence. The FimH protein is the adhesin that mediates this reaction; it is distinct from the major fimbrial protei.n (FimA) that composes the fimbrial shaft. Avian-adapted serovars of Salmonella produce non-haemagglutinating fimbriae that have been reported to mediate adherence to avian cells. A single amino acid substitution is present in the FimH adhesin of these strains compared to that of a Typhimurium isolate. Also, previous studies have shown that single nucleotide polymorphisms in two strains of the Typhimurium fimH alter the binding specificity. We therefore investigated the allelic variation of fimH from a range of serotypes (both host-adapted and non-host-adapted) and isolates of Salmonella. Most FimH adhesins mediated the mannose-sensitive haemagglutination of guinea pig erythrocytes, but many did not facilitate adherence to HEp-2 cells. A small number of isolates also produced fimbriae but did not mediate adherence to either cell type. Transformants possessing cloned fimH genes exhibited a number of different substitutions within the predicted amino acid sequence of the FimH polypeptide. No identical FimH amino sequence was found between strains that adhere to erythrocytes and/or HEp-2 cells and those produced by non-adherent strains. FimH-mediated adherence to HEp-2 cells was invariably associated with the ability to form biofilms on mannosylated bovine serum albumin.

Single nucleotide polymorphisms, putatively neutral DNA markers and population genetic parameters in Indian Plasmodium vivax isolates

Parasitology ◽  
2010 ◽  
Vol 137 (12) ◽  
pp. 1721-1730 ◽  
Author(s):  
BHAVNA GUPTA ◽  
ADITYA P. DASH ◽  
NALINI SHRIVASTAVA ◽  
APARUP DAS
Keyword(s):  
Population Genetics ◽  
Single Nucleotide Polymorphisms ◽  
Plasmodium Vivax ◽  
Population Genetic ◽  
Syntenic Region ◽  
Sequence Information ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Intergenic Regions ◽  
Neutral Markers

SUMMARYWith a view to developing putatively neutral markers based on Single Nucleotide Polymorphisms (SNPs) in the human malaria parasite, Plasmodium vivax, we utilized the published whole genome sequence information of P. falciparum and P. vivax to find a ~200 kb conserved syntenic region between these two species. We have selected 27 non-coding DNA fragments (in introns and intergenic regions) of variable length (300–750 bp) in P. vivax in this syntenic region. PCR of P. vivax isolates of a population sample from India could successfully amplify 17 fragments. Subsequently, DNA sequencing and sequence analysis confirmed the polymorphic status of only 11 fragments. Altogether, 18 SNPs were detected and 2 different measures of nucleotide diversity showed variable patterns across different fragments; in general, introns were less variable than the intergenic regions. All 11 polymorphic fragments were found to be evolving according to a neutral equilibrium model and thus could be utilized as putatively neutral markers for population genetic studies in P. vivax. Different molecular population genetics parameters were also estimated, providing initial insight into the population genetics of Indian P. vivax.

scholarly journals Genome-Wide Analysis of Synonymous Single Nucleotide Polymorphisms in Mycobacterium tuberculosis Complex Organisms: Resolution of Genetic Relationships Among Closely Related Microbial Strains

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1533-1543
Author(s):  
Michaela M Gutacker ◽  
James C Smoot ◽  
Cristi A Lux Migliaccio ◽  
Stacy M Ricklefs ◽  
Su Hua ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Allelic Variation ◽  
Genetic Relationships ◽  
The United States ◽  
Sensu Stricto ◽  
Phylogenetic Position ◽  
Nucleotide Polymorphisms ◽  
Tuberculosis Complex ◽  
Single Nucleotide

Abstract Several human pathogens (e.g., Bacillus anthracis, Yersinia pestis, Bordetella pertussis, Plasmodium falciparum, and Mycobacterium tuberculosis) have very restricted unselected allelic variation in structural genes, which hinders study of the genetic relationships among strains and strain-trait correlations. To address this problem in a representative pathogen, 432 M. tuberculosis complex strains from global sources were genotyped on the basis of 230 synonymous (silent) single nucleotide polymorphisms (sSNPs) identified by comparison of four genome sequences. Eight major clusters of related genotypes were identified in M. tuberculosis sensu stricto, including a single cluster representing organisms responsible for several large outbreaks in the United States and Asia. All M. tuberculosis sensu stricto isolates of previously unknown phylogenetic position could be rapidly and unambiguously assigned to one of the eight major clusters, thus providing a facile strategy for identifying organisms that are clonally related by descent. Common clones of M. tuberculosis sensu stricto and M. bovis are distinct, deeply branching genotypic complexes whose extant members did not emerge directly from one another in the recent past. sSNP genotyping rapidly delineates relationships among closely related strains of pathogenic microbes and allows construction of genetic frameworks for examining the distribution of biomedically relevant traits such as virulence, transmissibility, and host range.

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