scholarly journals Human DNA Sequence Variation in a 6.6-kb Region Containing the Melanocortin 1 Receptor Promoter

Genetics ◽  
2001 ◽  
Vol 158 (3) ◽  
pp. 1253-1268 ◽  
Author(s):  
Kateryna D Makova ◽  
Michele Ramsay ◽  
Trefor Jenkins ◽  
Wen-Hsiung Li
Keyword(s):  
Sequence Variation ◽  
Population Expansion ◽  
Purifying Selection ◽  
Phylogenetic Footprinting ◽  
Recent Common Ancestor ◽  
Coding Region ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Most Recent Common Ancestor ◽  
Dna Sequence Variation

AbstractAn ∼6.6-kb region located upstream from the melanocortin 1 receptor (MC1R) gene and containing its promoter was sequenced in 54 humans (18 Africans, 18 Asians, and 18 Europeans) and in one chimpanzee, gorilla, and orangutan. Seventy-six polymorphic sites were found among the human sequences and the average nucleotide diversity (π) was 0.141%, one of the highest among all studies of nuclear sequence variation in humans. Opposite to the pattern observed in the MC1R coding region, in the present region π is highest in Africans (0.136%) compared to Asians (0.116%) and Europeans (0.122%). The distributions of π, θ, and Fu and Li's F-statistic are nonuniform along the sequence and among continents. The pattern of genetic variation is consistent with a population expansion in Africans. We also suggest a possible phase of population size reduction in non-Africans and purifying selection acting in the middle subregion and parts of the 5′ subregion in Africans. We hypothesize diversifying selection acting on some sites in the 5′ and 3′ subregions or in the MC1R coding region in Asians and Europeans, though we cannot reject the possibility of relaxation of functional constraints in the MC1R gene in Asians and Europeans. The mutation rate in the sequenced region is 1.65 × 10—9 per site per year. The age of the most recent common ancestor for this region is similar to that for the other long noncoding regions studied to date, providing evidence for ancient gene genealogies. Our population screening and phylogenetic footprinting suggest potentially important sites for the MC1R promoter function.

scholarly journals Molecular evolution of dengue virus types 1 and 4 in Korean travelers

2021 ◽  
Vol 166 (4) ◽  
pp. 1103-1112
Author(s):  
Eun-Ha Hwang ◽  
Green Kim ◽  
Hoyin Chung ◽  
Hanseul Oh ◽  
Jong-Hwan Park ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Positive Selection ◽  
Recent Common Ancestor ◽  
Coding Region ◽  
Genotype I ◽  
Most Recent Common Ancestor ◽  
Evolutionary Features ◽  
Molecular Phylogenetic ◽  
First Time ◽  
Global Travel

AbstractDengue virus (DV) is a mosquito-borne virus that is endemic to many tropical and subtropical areas. Recently, the annual incidence of DV infection has increased worldwide, including in Korea, due to global warming and increased global travel. We therefore sought to characterize the molecular and evolutionary features of DV-1 and DV-4 isolated from Korean overseas travelers. We used phylogenetic analysis based on the full coding region to classify isolates of DV-1 in Korea into genotype I (43251, KP406802), genotype IV (KP406803), and genotype V (KP406801). In addition, we found that strains of DV-4 belonged to genotype I (KP406806) and genotype II (43257). Evidence of positive selection in DV-1 strains was identified in the C, prM, NS2A, and NS5 proteins, whereas DV-4 showed positive selection only in the non-structural proteins NS2A, NS3, and NS5. The substitution rates per site per year were 5.58 × 10-4 and 6.72 × 10-4 for DV-1 and DV-4, respectively, and the time of the most recent common ancestor was determined using the Bayesian skyline coalescent method. In this study, the molecular, phylogenetic, and evolutionary characteristics of Korean DV-1 and DV-4 isolates were evaluated for the first time.

scholarly journals Reduced Genetic Variation Occurs among Genes of the Highly Clonal Plant Pathogen Xanthomonas axonopodis pv. vesicatoria, Including the Effector Gene avrBs2

2005 ◽  
Vol 71 (5) ◽  
pp. 2418-2432 ◽  
Author(s):  
Gale Wichmann ◽  
David Ritchie ◽  
C. S. Kousik ◽  
Joy Bergelson
Keyword(s):  
Genetic Variation ◽  
Plant Pathogen ◽  
Xanthomonas Campestris ◽  
Host Plants ◽  
Population Expansion ◽  
Clonal Plant ◽  
Recent Common Ancestor ◽  
Loss Of Function ◽  
Xanthomonas Axonopodis ◽  
Most Recent Common Ancestor

ABSTRACT The bacterial plant pathogen Xanthomonas axonopodis pv. vesicatoria, also known as Xanthomonas campestris pv. vesicatoria group A, is the causal agent of bacterial spot in pepper and tomato. In order to test different models that may explain the coevolution of avrBs2 with its host plants, we sequenced avrBs2 and six chromosomal loci (total of 5.5 kb per strain) from a global sample of 55 X. axonopodis pv. vesicatoria strains collected from diseased peppers. We found an extreme lack of genetic variation among all X. axonopodis pv. vesicatoria genomic loci (average nucleotide diversity, π = 9.1 × 10−5), including avrBs2. This lack of diversity is consistent with X. axonopodis pv. vesicatoria having undergone a recent population bottleneck and/or selective sweep followed by population expansion. Coalescent analysis determined that approximately 1.4 × 104 to 7.16 × 104 bacterial generations have passed since the most recent common ancestor (MRCA) of the current X. axonopodis pv. vesicatoria population. Assuming a range of 50 to 500 bacterial generations per year, only 28 to 1,432 years have passed since the MRCA. This time frame coincides with human intervention with the pathogen's host plants, from domestication to modern agricultural practices. Examination of 19 mutated (loss-of-function) avrBs2 alleles detected nine classes of mutations. All mutations affected protein coding, while no synonymous changes were found. The nature of at least one of the avrBs2 mutations suggests that it may be possible to observe one stage of an evolutionary arms race as X. axonopodis pv. vesicatoria responds to selection pressure to alter avrBs2 to escape host plant resistance.

DNA sequence variation in a non-coding region of low recombination on the human X chromosome

10.1038/8785 ◽  
1999 ◽  
Vol 22 (1) ◽  
pp. 78-81 ◽  
Author(s):  
Henrik Kaessmann ◽  
Florian Heißig ◽  
Arndt von Haeseler ◽  
Svante Pääbo
Keyword(s):  
Dna Sequence ◽  
X Chromosome ◽  
Sequence Variation ◽  
Coding Region ◽  
Dna Sequence Variation

scholarly journals Population genomics of Mycobacterium tuberculosis in the Inuit

2015 ◽  
Vol 112 (44) ◽  
pp. 13609-13614 ◽  
Author(s):  
Robyn S. Lee ◽  
Nicolas Radomski ◽  
Jean-Francois Proulx ◽  
Ines Levade ◽  
B. Jesse Shapiro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mycobacterium Tuberculosis ◽  
Population Genomics ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Nonsynonymous Snps ◽  
Recent Common Ancestor ◽  
Nucleotide Polymorphisms ◽  
Most Recent Common Ancestor ◽  
Bacterial Genetic

Nunavik, Québec suffers from epidemic tuberculosis (TB), with an incidence 50-fold higher than the Canadian average. Molecular studies in this region have documented limited bacterial genetic diversity among Mycobacterium tuberculosis isolates, consistent with a founder strain and/or ongoing spread. We have used whole-genome sequencing on 163 M. tuberculosis isolates from 11 geographically isolated villages to provide a high-resolution portrait of bacterial genetic diversity in this setting. All isolates were lineage 4 (Euro-American), with two sublineages present (major, n = 153; minor, n = 10). Among major sublineage isolates, there was a median of 46 pairwise single-nucleotide polymorphisms (SNPs), and the most recent common ancestor (MRCA) was in the early 20th century. Pairs of isolates within a village had significantly fewer SNPs than pairs from different villages (median: 6 vs. 47, P < 0.00005), indicating that most transmission occurs within villages. There was an excess of nonsynonymous SNPs after the diversification of M. tuberculosis within Nunavik: The ratio of nonsynonymous to synonymous substitution rates (dN/dS) was 0.534 before the MRCA but 0.777 subsequently (P = 0.010). Nonsynonymous SNPs were detected across all gene categories, arguing against positive selection and toward genetic drift with relaxation of purifying selection. Supporting the latter possibility, 28 genes were partially or completely deleted since the MRCA, including genes previously reported to be essential for M. tuberculosis growth. Our findings indicate that the epidemiologic success of M. tuberculosis in this region is more likely due to an environment conducive to TB transmission than a particularly well-adapted strain.

scholarly journals Sequence Variation of Melanocortin 1 Receptor (MC1R) Gene and Association with Plumage Color in Domestic Geese

2014 ◽  
Vol 51 (3) ◽  
pp. 270-274 ◽  
Author(s):  
Jing Huang ◽  
Bing Zhou ◽  
Da-Qian He ◽  
Shi-Yi Chen ◽  
Qing Zhu ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Plumage Color ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene

scholarly journals Recent and rapid colonization of the Lesser Sundas Archipelago from adjacent Sundaland by seven amphibian and reptile species

2019 ◽  
Author(s):  
Sean B. Reilly ◽  
Alexander L. Stubbs ◽  
Benjamin R. Karin ◽  
Evy Arida ◽  
Djoko T. Iskandar ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Continental Shelf ◽  
Population Expansion ◽  
Phylogeographic Structure ◽  
Recent Common Ancestor ◽  
Stepping Stones ◽  
Terrestrial Vertebrate ◽  
Most Recent Common Ancestor ◽  
Short Time Span ◽  
Genetic Signatures

AbstractThe Lesser Sundas Archipelago is comprised of two parallel chains of islands that extend between the Asian continental shelf (Sundaland) and Australo-Papuan continental shelf (Sahul). These islands have served as stepping-stones for taxa dispersing between the Asian and Australo-Papuan biogeographic realms. While the oceanic barriers have prevented many species from colonizing the archipelago, a number of terrestrial vertebrate species have colonized the islands either by rafting/swimming or human introduction. Here we examine phylogeographic structure within the Lesser Sundas for three snake, two lizard, and two frog species that each have a Sunda Shelf origin. These species are suspected to have recently colonized the archipelago, though all have inhabited the Lesser Sundas for over 100 years. We sequenced mtDNA from 230 samples to test whether there is sufficiently deep genetic structure within any of these taxa to reject human-mediated introduction. Additionally, we tested for genetic signatures of population expansion consistent with recent introduction, and estimated the ages of Lesser Sundas clades, if any exist. Our results show little to no genetic structure between populations on different islands in five species, and moderate structure in two species. Nucleotide diversity is low for all species, and the ages of the most recent common ancestor for species with monophyletic Lesser Sundas lineages date to the Holocene or late Pleistocene. These results support the hypothesis that these species entered the archipelago relatively recently and either naturally colonized or were introduced by humans to most of the islands within the archipelago within a short time span.

scholarly journals Molecular Phylogenesis and Spatiotemporal Spread of SARS-CoV-2 in Southeast Asia

2021 ◽  
Vol 9 ◽  
Author(s):  
Mingjian Zhu ◽  
Jian Shen ◽  
Qianli Zeng ◽  
Joanna Weihui Tan ◽  
Jirapat Kleepbua ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
Population Expansion ◽  
Principal Component ◽  
Viral Population ◽  
Recent Common Ancestor ◽  
Tropical Region ◽  
Effective Population ◽  
Most Recent Common Ancestor

Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region.Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model.Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10−3 (1.292 × 10−3 to 1.613 × 10−3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia.Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.

scholarly journals Intercity Spread of Echovirus 6 in Shandong Province, China: Application of Environmental Surveillance in Tracing Circulating Enteroviruses

2012 ◽  
Vol 78 (19) ◽  
pp. 6946-6953 ◽  
Author(s):  
Zexin Tao ◽  
Yanyan Song ◽  
Haiyan Wang ◽  
Yong Zhang ◽  
Hiromu Yoshida ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Gene Diversity ◽  
Likelihood Method ◽  
Recent Common Ancestor ◽  
Environmental Surveillance ◽  
Coding Region ◽  
Most Recent Common Ancestor ◽  
Two Cities ◽  
Echovirus 6 ◽  
Transmission Pathways

ABSTRACTEnvironmental surveillance is an effective approach in investigating circulating enteroviruses and had been conducted in the cities of Jinan and Linyi since February 2008 and April 2010, respectively. This study analyzed 46 sewage samples collected in the two cities in 2011 and found that echovirus 6 (E6) was the predominant serotype, with 134 isolates (65 in Jinan and 69 in Linyi) from 23 (50%) samples. This differs from the 2010 data that found 29 E6 isolates in Jinan and only 3 in Linyi. Phylogenetic analysis of the VP1 coding region showed that all environmental E6 samples from 2008 to 2011 (n= 167) segregated into two lineages and revealed an increase in VP1 gene diversity in 2011, suggesting that the increased number of E6 detections reflects a real epidemic in the two cities. Most Linyi isolates (n= 61, or 88%) in 2011 segregated into sublineage 1a, together with 18 Jinan isolates in 2011. Interestingly, the ancestral VP1 sequence of sublineage 1a inferred using the maximum-likelihood method had 100% identity with the sequence of one environmental isolate from Jinan in August 2010, suggesting an intercity spread from Jinan to Linyi. By Bayesian phylodynamic methods, the most recent common ancestor of Linyi isolates in sublineage 1a dated back to 24 December 2010, revealing that this sublineage was likely imported into Linyi from August to December in 2010. This study demonstrates that environmental surveillance is a sensitive method in tracing transmission pathways of circulating enteroviruses among different regions and reveals that E6-associated aseptic meningitis is an emerging concern in China.

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