scholarly journals Population Genetic Analysis of the DARC Locus (Duffy) Reveals Adaptation from Standing Variation Associated with Malaria Resistance in Humans

2016 ◽  
Author(s):  
Kimberly F. McManus ◽  
Angela Taravella ◽  
Brenna Henn ◽  
Carlos D. Bustamante ◽  
Martin Sikora ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
Evolutionary History ◽  
Sub Saharan Africa ◽  
Recent Common Ancestor ◽  
Human Populations ◽  
Selection Coefficient ◽  
Population Genetic Analysis ◽  
Most Recent Common Ancestor ◽  
Standing Variation ◽  
History Of

AbstractThe human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of its strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of a locus under positive selection in humans.Here, we use sequencing data from over 1,000 individuals in twenty-one human populations, as well as ancient human and great ape genomes, to analyze the fine scale population structure of DARC. We estimate the time to most recent common ancestor (TMRCA) of the FY*O mutation to be 42 kya (95% CI: 34–49 kya). We infer the FY*O null mutation swept to fixation in Africa from standing variation with very low initial frequency (0.1%) and a selection coefficient of 0.043 (95% CI:0.011–0.18), which is among the strongest estimated in the genome. We estimate the TMRCA of the FY*A mutation to be 57 kya (95% CI: 48–65 kya) and infer that, prior to the sweep of FY*O, all three alleles were segregating in Africa, as highly diverged populations from Asia and ≠Khomani San hunter-gatherers share the same FY*A haplotypes. We test multiple models of admixture that may account for this observation and reject recent Asian or European admixture as the cause.Author SummaryInfectious diseases have undoubtedly played an important role in ancient and modern human history. Yet, there are relatively few regions of the genome involved in resistance to pathogens that have shown a strong selection signal. We revisit the evolutionary history of a gene associated with resistance to the most common malaria-causing parasite, Plasmodium vivax, and show that it is one of regions of the human genome that has been under strongest selective pressure in our evolutionary history (selection coefficient: 5%). Our results are consistent with a complex evolutionary history of the locus involving selection on a mutation that was at a very low frequency in the ancestral African population (standing variation) and a large differentiation between European, Asian and African populations.

scholarly journals Chromosomal dynamics in space and time: evolutionary history of Mycetophylax ants across past climatic changes in the Brazilian Atlantic coast

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ricardo Micolino ◽  
Maykon Passos Cristiano ◽  
Natália Martins Travenzoli ◽  
Denilce Meneses Lopes ◽  
Danon Clemes Cardoso
Keyword(s):  
Evolutionary History ◽  
Chromosomal Rearrangements ◽  
Atlantic Coast ◽  
Ecological Impact ◽  
Divergence Time ◽  
Molecular Data ◽  
Recent Common Ancestor ◽  
Integrative Approach ◽  
Most Recent Common Ancestor ◽  
History Of

AbstractFungus-farming ants of the genus Mycetophylax exhibit intra and interspecific chromosome variability, which makes them suitable for testing hypotheses about possible chromosomal rearrangements that endure lineage diversification. We combined cytogenetic and molecular data from Mycetophylax populations from coastal environments to trace the evolutionary history of the clade in light of chromosomal changes under a historical and geographic context. Our cytogenetic analyses revealed chromosomal differences within and among species. M. morschi exhibited three distinct karyotypes and considerable variability in the localization of 45S rDNA clusters. The molecular phylogeny was congruent with our cytogenetic findings. Biogeographical and divergence time dating analyses estimated that the most recent common ancestor of Mycetophylax would have originated at about 30 Ma in an area including the Amazon and Southern Grasslands, and several dispersion and vicariance events may have occurred before the colonization of the Brazilian Atlantic coast. Diversification of the psammophilous Mycetophylax first took place in the Middle Miocene (ca. 18–10 Ma) in the South Atlantic coast, while “M. morschi” lineages diversified during the Pliocene-Pleistocene transition (ca. 3–2 Ma) through founder-event dispersal for the Northern coastal regions. Psammophilous Mycetophylax diversification fits into the major global climatic events that have had a direct impact on the changes in sea level as well as deep ecological impact throughout South America. We assume therefore that putative chromosomal rearrangements correlated with increased ecological stress during the past climatic transitions could have intensified and/or accompanied the divergence of the psammophilous Mycetophylax. We further reiterate that “M. morschi” comprises a complex of at least three well-defined lineages, and we emphasize the role of this integrative approach for the identification and delimitation of evolutionary lineages.

Phylogeography and evolutionary history of hepatitis E virus genotype 3 in Argentina

2021 ◽  
Author(s):  
María B Pisano ◽  
Andrés C A Culasso ◽  
Nancy Altabert ◽  
Maribel G Martínez Wassaf ◽  
Silvia V Nates ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Recent Common Ancestor ◽  
Genotype 3 ◽  
Posterior Density ◽  
Virus Genotype ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
Highest Posterior Density

Abstract Background Few studies about the evolutionary history of the hepatitis E virus (HEV) have been conducted. The aim of our work was to investigate and make inferences about the origin and routes of dispersion of HEV-3 in Argentina. Methods Phylogenetic, coalescent and phylogeographic analyses were performed using a 322-bp ORF2 genomic fragment of all HEV-3 sequences with known date and place of isolation published at GenBank until May 2018 (n=926), including 16 Argentinian sequences (isolated from pigs, water and humans). Results Phylogenetic analysis revealed two clades within HEV-3: abchij and efg. All Argentinian samples were grouped intermingled within clade 3abchij. The coalescent analysis showed that the most recent common ancestor for the clade 3abchij would have existed around the year 1967 (95% highest posterior density (HPD): 1963–1970). The estimated substitution rate was 1.01×10−2 (95%HPD: 9.3×10ˉ3–1.09×10ˉ2) substitutions/site/y, comparable with the rate previously described. The phylogeographic approach revealed a correspondence between phylogeny and place of origin for Argentinian samples, suggesting many HEV introductions in the country, probably from Europe and Japan. Conclusions This is the first evolutionary inference of HEV-3 that includes Argentinian strains, showing the circulation of many HEV-3 subtypes, obtained from different sources and places, with recent diversification processes. Accession numbers [KX812460], [KX812461], [KX812462], [KX812465], [KX812466], [KX812467], [KX812468], [KX812469].

scholarly journals New kinship and FST estimates reveal higher levels of differentiation in the global human population

2019 ◽  
Author(s):  
Alejandro Ochoa ◽  
John D. Storey
Keyword(s):  
Population Structure ◽  
Genetic Relatedness ◽  
Genetic Distances ◽  
Recent Common Ancestor ◽  
Human Populations ◽  
Population Genetic Analysis ◽  
Most Recent Common Ancestor ◽  
Complex Population ◽  
Population Structures ◽  
Modern Population

Kinship coefficients and FST, which measure genetic relatedness and the overall population structure, respectively, have important biomedical applications. However, existing estimators are only accurate under restrictive conditions that most natural population structures do not satisfy. We recently derived new kinship and FST estimators for arbitrary population structures [1, 2]. Our estimates on human datasets reveal a complex population structure driven by founder effects due to dispersal from Africa and admixture. Notably, our new approach estimates larger FST values of 26% for native worldwide human populations and 23% for admixed Hispanic individuals, whereas the existing approach estimates 9.8% and 2.6%, respectively. While previous work correctly measured FST between subpopulation pairs, our generalized FST measures genetic distances among all individuals and their most recent common ancestor (MRCA) population, revealing that genetic differentiation is greater than previously appreciated. This analysis demonstrates that estimating kinship and FST under more realistic assumptions is important for modern population genetic analysis.

Reconstructing ancestral chromosome numbers and inflorescence features in Eleusininae (Poaceae: Chloridoideae: Cynodonteae)

2020 ◽  
Vol 193 (3) ◽  
pp. 402-418
Author(s):  
Raquel B Chiavegatto ◽  
Angelino Carta ◽  
Diego G S Pereira ◽  
Flavio R G Benites ◽  
Vânia H Techio ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Numbers ◽  
Evolutionary History ◽  
Basic Chromosome Number ◽  
High Rate ◽  
Recent Common Ancestor ◽  
Basic Chromosome ◽  
Most Recent Common Ancestor ◽  
Chromosome Number Evolution ◽  
History Of

Abstract The chromosome number in Poaceae has changed widely over 77 Myr of evolution and polyploidization. Chromosome number changes can suggest a high rate of diversification and evolutionary novelties, and such changes can contribute to speciation. Despite this, chromosome numbers alone do not allow the evolutionary history of a group to be traced. Combined phylogenetic and karyological analyses can clarify the evolutionary history of taxa and allow taxonomic relationships and hierarchical levels to be inferred. The subtribe Eleusininae is the largest of the subfamily Chloridoideae. This study aims to reconstruct their chromosome number evolution, for which ChromEvol 2.0 software was used. Haploid chromosome numbers of Eleusininae were retrieved from the literature, and a consensus phylogenetic tree of Eleusininae was reconstructed. It was possible to infer 41 events of chromosome rearrangements along the evolutionary history of Eleusininae, according to the probabilistic model used. Chromosome number evolution in Eleusininae was mainly influenced by polyploidy events. The ancestral basic chromosome number for Eleusininae was p = 6, but the most recent common ancestor showed p2 = 10. In addition, some derived basic chromosome numbers, such as x = 9, arose through dysploidy, whereas x = 20 was generated via polyploidy.

The evolutionary history and conservation value of disjunct Bartonia paniculata subsp. paniculata (Branched Bartonia) populations in Canada

Botany ◽  
2013 ◽  
Vol 91 (9) ◽  
pp. 605-613 ◽  
Author(s):  
Claudia Ciotir ◽  
Chris Yesson ◽  
Joanna Freeland
Keyword(s):  
Great Lakes ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Great Lakes Region ◽  
Conservation Value ◽  
Most Recent Common Ancestor ◽  
Disjunct Populations ◽  
Management Plans ◽  
Global Status

Understanding the spatial distribution of genetic diversity and its evolutionary history is an essential part of developing effective biodiversity management plans. This may be particularly true when considering the value of peripheral or disjunct populations. Although conservation decisions are often made with reference to geopolitical boundaries, many policy-makers also consider global distributions, and therefore a species’ global status may temper its regional status. Many disjunct populations can be found in the Great Lakes region of North America, including those of Bartonia paniculata subsp. paniculata, a species that has been designated as threatened in Canada but globally secure. We compared chloroplast sequences between disjunct (Canada) and core (USA) populations of B. paniculata subsp. paniculata separated by 600 km, which is the minimum distance between disjunct and core populations in this subspecies. We found that although lineages within the disjunct populations shared a relatively recent common ancestor, the genetic divergence between plants from Ontario and New Jersey was substantially greater than expected for a consubspecific comparison. A coalescence-based analysis dated the most recent common ancestor of the Canadian and US populations at approximately 534 000 years ago with the lower confidence estimate at 226 000 years ago. This substantially predates the Last Glacial Maximum and suggests that disjunct and core populations have followed independent evolutionary trajectories throughout multiple glacial–interglacial cycles. Our findings provide important insight into the diverse processes that have resulted in numerous disjunct species in the Great Lakes region and highlight a need for additional work on Canadian B. paniculata subsp. paniculata taxonomy prior to a reevaluation of its conservation value.

scholarly journals Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

2019 ◽  
Author(s):  
Laura Hernández ◽  
Alberto Vicens ◽  
Luis Enrique Eguiarte ◽  
Valeria Souza ◽  
Valerie De Anda ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Functional Divergence ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Common Ancestry ◽  
Demethylation Pathway ◽  
History Of ◽  
New Gene

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

scholarly journals Evolutionary history of regulatory variation in human populations

2010 ◽  
Vol 19 (R2) ◽  
pp. R197-R203 ◽  
Author(s):  
T. Lappalainen ◽  
E. T. Dermitzakis
Keyword(s):  
Evolutionary History ◽  
Human Populations ◽  
Regulatory Variation ◽  
History Of

scholarly journals Age and rate of diversification of the Hawaiian silversword alliance (Compositae)

1998 ◽  
Vol 95 (16) ◽  
pp. 9402-9406 ◽  
Author(s):  
Bruce G. Baldwin ◽  
Michael J. Sanderson
Keyword(s):  
Common Ancestor ◽  
Error Variance ◽  
Diversification Rate ◽  
Recent Common Ancestor ◽  
Divergence Times ◽  
Sequence Evolution ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
Fossil Records ◽  
Fossil Data

Comparisons between insular and continental radiations have been hindered by a lack of reliable estimates of absolute diversification rates in island lineages. We took advantage of rate-constant rDNA sequence evolution and an “external” calibration using paleoclimatic and fossil data to determine the maximum age and minimum diversification rate of the Hawaiian silversword alliance (Compositae), a textbook example of insular adaptive radiation in plants. Our maximum-age estimate of 5.2 ± 0.8 million years ago for the most recent common ancestor of the silversword alliance is much younger than ages calculated by other means for the Hawaiian drosophilids, lobelioids, and honeycreepers and falls approximately within the history of the modern high islands (≤5.1 ± 0.2 million years ago). By using a statistically efficient estimator that reduces error variance by incorporating clock-based estimates of divergence times, a minimum diversification rate for the silversword alliance was estimated to be 0.56 ± 0.17 species per million years. This exceeds average rates of more ancient continental radiations and is comparable to peak rates in taxa with sufficiently rich fossil records that changes in diversification rate can be reconstructed.

Mitochondrial DNA Diversity and Evolutionary History of Native Human Populations of Argentinean Northwest Patagonia

Human Biology ◽  
2019 ◽  
Vol 91 (2) ◽  
pp. 57
Author(s):  
Postillone ◽  
Cobos ◽  
Urrutia ◽  
Dejean ◽  
Gonzalez ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Evolutionary History ◽  
Human Populations ◽  
Dna Diversity ◽  
History Of
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