scholarly journals Genetic diversity and natural selection footprints of the glycine amidinotransferase gene in various human populations

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Asifullah Khan ◽  
Lei Tian ◽  
Chao Zhang ◽  
Kai Yuan ◽  
Shuhua Xu
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Human Populations

scholarly journals Genetic diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium falciparum on Bioko Island, Equatorial Guinea and global comparative analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Li-Yun Lin ◽  
Hui-Ying Huang ◽  
Xue-Yan Liang ◽  
Dong-De Xie ◽  
Jiang-Tao Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Natural Selection ◽  
Protein Structure ◽  
Transmembrane Protein ◽  
Fixation Index ◽  
Bioko Island ◽  
Adhesive Protein ◽  
Trap Gene ◽  
Selection Of

Abstract Background Thrombospondin-related adhesive protein (TRAP) is a transmembrane protein that plays a crucial role during the invasion of Plasmodium falciparum into liver cells. As a potential malaria vaccine candidate, the genetic diversity and natural selection of PfTRAP was assessed and the global PfTRAP polymorphism pattern was described. Methods 153 blood spot samples from Bioko malaria patients were collected during 2016–2018 and the target TRAP gene was amplified. Together with the sequences from database, nucleotide diversity and natural selection analysis, and the structural prediction were preformed using bioinformatical tools. Results A total of 119 Bioko PfTRAP sequences were amplified successfully. On Bioko Island, PfTRAP shows its high degree of genetic diversity and heterogeneity, with π value for 0.01046 and Hd for 0.99. The value of dN–dS (6.2231, p < 0.05) hinted at natural selection of PfTRAP on Bioko Island. Globally, the African PfTRAPs showed more diverse than the Asian ones, and significant genetic differentiation was discovered by the fixation index between African and Asian countries (Fst > 0.15, p < 0.05). 667 Asian isolates clustered in 136 haplotypes and 739 African isolates clustered in 528 haplotypes by network analysis. The mutations I116T, L221I, Y128F, G228V and P299S were predicted as probably damaging by PolyPhen online service, while mutations L49V, R285G, R285S, P299S and K421N would lead to a significant increase of free energy difference (ΔΔG > 1) indicated a destabilization of protein structure. Conclusions Evidences in the present investigation supported that PfTRAP gene from Bioko Island and other malaria endemic countries is highly polymorphic (especially at T cell epitopes), which provided the genetic information background for developing an PfTRAP-based universal effective vaccine. Moreover, some mutations have been shown to be detrimental to the protein structure or function and deserve further study and continuous monitoring.

scholarly journals Dynamics of natural selection in two generations (on the example of the population of the Kirovograd region)

2021 ◽  
Vol 29 ◽  
pp. 152-156
Author(s):  
K. K. Kovleva ◽  
N.A. Kozak
Keyword(s):  
Natural Selection ◽  
First Generation ◽  
Second Generation ◽  
Selection Index ◽  
Genetic Load ◽  
Modern Medicine ◽  
Reproductive Age ◽  
Human Populations ◽  
Medical Histories ◽  
Total Selection

Aim. In connection with the success of modern medicine, the pressure of natural selection in various civilized human populations is weakening, which leads to the accumulation of a genetic load. The purpose of this work was to trace the change in the intensity of natural selection among population of the Kirovograd region in two successive generations. Methods. The collection of material was carried out in 2020 and 2021. Anonymous questionnaires were conducted and medical histories of women of post-reproductive age of the Kirovograd region were studied. The first generation included 40 women born in 1937–1959; the second generation consists of 273 women born in 1960–1981. Results. The total selection index was 0.27 in the first generation, and 0.37 in the second generation. The percentage of women who have not had pregnancies increased from the first generation to the second from 2.5 to 3.7, respectively. Conclusions. The index of total selection in the Kirovograd region population for one generation increased by almost one and a half times (from 0.27 to 0.37), as well as the index of differential fertility (from 0.25 to 0.35). Keywords: reproductive characteristics, Kirovograd population, Crow's index, selection, generations.

scholarly journals Genomic and demographic processes differentially influence genetic variation across the X chromosome

2021 ◽  
Author(s):  
Daniel J. Cotter ◽  
Timothy H. Webster ◽  
Melissa A. Wilson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
X Chromosome ◽  
Global Scale ◽  
Careful Consideration ◽  
Human Populations ◽  
Evolutionary Forces ◽  
Ideal System ◽  
Demographic Patterns

AbstractMutation, recombination, selection, and demography affect genetic variation across the genome. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. The X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these processes, notably the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. Here we investigate diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. We find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1 and highest on the non-recombining X chromosome, with the XTR falling in between, suggesting that the XTR (usually included in the non-recombining X) may need to be considered separately in future studies. We also observed strong population-specific effects on genetic diversity; not only does genetic variation differ on the X and autosomes among populations, but the effects of linked selection on the X relative to autosomes have been shaped by population-specific history. The substantial variation in patterns of variation across these regions provides insight into the unique evolutionary history contained within the X chromosome.Significance StatementDemography and selection affect the X chromosome differently from non-sex chromosomes. However, the X chromosome can be subdivided into multiple distinct regions that facilitate even more fine-scaled assessment of these processes. Here we study regions of the human X chromosome in 26 populations to find evidence that recombination may be mutagenic in humans and that the X-transposed region may undergo recombination. Further we observe that the effects of selection and demography act differently on the X chromosome relative to the autosomes across human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.

scholarly journals Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

2019 ◽  
Author(s):  
Quentin Rougemont ◽  
Jean-Sébastien Moore ◽  
Thibault Leroy ◽  
Eric Normandeau ◽  
Eric B. Rondeau ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Demographic History ◽  
Glacial Refugium ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Geographical Patterns ◽  
Genome Wide Data

AbstractA thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

scholarly journals Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Tian-Qi Shi ◽  
Hai-Mo Shen ◽  
Shen-Bo Chen ◽  
Kokouvi Kassegne ◽  
Yan-Bing Cui ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Positive Selection ◽  
Plasmodium Vivax ◽  
Yunnan Province ◽  
Duffy Binding Protein ◽  
Synonymous Mutations ◽  
Selection Of

Malaria incidence has declined dramatically over the past decade and China was certified malaria-free in 2021. However, the presence of malaria in border areas and the importation of cases of malaria parasites are major challenges for the consolidation of the achievements made by China. Plasmodium vivax Duffy binding protein (PvDBP) performs a significant role in erythrocyte invasion, and is considered a promising P. vivax vaccine. However, the highly polymorphic region of PvDBP (PvDBP-II) impedes the development of blood-stage vaccine against P. vivax. In this study, we investigated the genetic diversity and natural selection of PvDBP-II among 124 P. vivax isolates collected from the China-Myanmar border (CMB) in Yunnan Province, China, during 2009–2011. To compare genetic diversity, natural selection, and population structure with CMB isolates, 85 pvdbp-II sequences of eastern Myanmar isolates were obtained from GenBank. In addition, global sequences of pvdbp-II were retrieved from GenBank to establish genetic differentiation relationships and networks with the CMB isolates. In total, 22 single nucleotide polymorphisms reflected in 20 non-synonymous and two synonymous mutations were identified. The overall nucleotide diversity of PvDBP-II from the 124 CMB isolates was 0.0059 with 21 haplotypes identified (Hd = 0.91). The high ratio of non-synonymous to synonymous mutations suggests that PvDBP-II had evolved under positive selection. Population structure analysis of the CMB and eastern Myanmar isolates were optimally grouped into five sub-populations (K = 5). Polymorphisms of PvDBP-II display that CMB isolates were genetically diverse. Mutation, recombination, and positive selection promote polymorphism of PvDBP-II of P. vivax population. Although low-level genetic differentiation in eastern Myanmar was identified along with the more effective malaria control measures, the complexity of population structure in malaria parasites has maintained. In conclusion, findings from this study advance knowledge of the understanding of the dynamic of P. vivax population, which will contribute to guiding the rational design of a PvDBP-II based vaccine.

Genetic diversity of the HLA system in human populations from the Sierra (Andean), Oriente (Amazonian) and Costa (Coastal) regions of Ecuador

2018 ◽  
Vol 79 (9) ◽  
pp. 639-650 ◽  
Author(s):  
Juan M. Galarza ◽  
Rodrigo Barquera ◽  
Ana M. Tito Álvarez ◽  
Diana I. Hernández Zaragoza ◽  
Gabriela Peralta Sevilla ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Human Populations ◽  
Coastal Regions ◽  
Hla System

scholarly journals Latitudinal gradients in genetic diversity and natural selection at a highly adaptive gene in terrestrial mammals

Ecography ◽  
2020 ◽  
Author(s):  
Li Yiming ◽  
Wang Siqi ◽  
Cheng Chaoyuan ◽  
Zhang Jiaqi ◽  
Wang Supen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Latitudinal Gradients ◽  
Terrestrial Mammals

scholarly journals The emergence of latent infection in the early evolution of Mycobacterium tuberculosis

2016 ◽  
Vol 283 (1831) ◽  
pp. 20160499 ◽  
Author(s):  
Rebecca H. Chisholm ◽  
Mark M. Tanaka
Keyword(s):  
Mathematical Model ◽  
Immune Response ◽  
Mycobacterium Tuberculosis ◽  
Genetic Variation ◽  
Natural Selection ◽  
Natural History ◽  
Latent Infection ◽  
Human Populations ◽  
Safe Harbour ◽  
Active Disease

Mycobacterium tuberculosis has an unusual natural history in that the vast majority of its human hosts enter a latent state that is both non-infectious and devoid of any symptoms of disease. From the pathogen perspective, it seems counterproductive to relinquish reproductive opportunities to achieve a détente with the host immune response. However, a small fraction of latent infections reactivate to the disease state. Thus, latency has been argued to provide a safe harbour for future infections which optimizes the persistence of M. tuberculosis in human populations. Yet, if a pathogen begins interactions with humans as an active disease without latency, how could it begin to evolve latency properties without incurring an immediate reproductive disadvantage? We address this question with a mathematical model. Results suggest that the emergence of tuberculosis latency may have been enabled by a mechanism akin to cryptic genetic variation in that detrimental latency properties were hidden from natural selection until their expression became evolutionarily favoured.

Sign in / Sign up

Export Citation Format

Share Document