Abstract：
:The Tibetan and Andean Plateaus and Ethiopian highlands are the largest regions to have long-term high-altitude residents. Such populations are exposed to lower barometric pressures and hence atmospheric partial pressures of oxygen. Such "hypobaric hypoxia" may limit physical functional capacity, reproductive health, and even survival. As such, selection of genetic variants advantageous to hypoxic adaptation is likely to have occurred. Identifying signatures of such selection is likely to help understanding of hypoxic adaptive processes. Here, we seek evidence of such positive selection using five Ethiopian populations, three of which are from high-altitude areas in Ethiopia. As these populations may have been recipients of Eurasian gene flow, we correct for this admixture. Using single-nucleotide polymorphism genotype data from multiple populations, we find the strongest signal of selection in BHLHE41 (also known as DEC2 or SHARP1). Remarkably, a major role of this gene is regulation of the same hypoxia response pathway on which selection has most strikingly been observed in both Tibetan and Andean populations. Because it is also an important player in the circadian rhythm pathway, BHLHE41 might also provide insights into the mechanisms underlying the recognized impacts of hypoxia on the circadian clock. These results support the view that Ethiopian, Andean, and Tibetan populations living at high altitude have adapted to hypoxia differently, with convergent evolution affecting different genes from the same pathway.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Huerta-Sánchez E,Degiorgio M,Pagani L,Tarekegn A,Ekong R,Antao T,Cardona A,Montgomery HE,Cavalleri GL,Robbins PA,Weale ME,Bradman N,Bekele E,Kivisild T,Tyler-Smith C,Nielsen Rdoi
10.1093/molbev/mst089subject
Has Abstractpub_date
2013-08-01 00:00:00pages
1877-88issue
8eissn
0737-4038issn
1537-1719pii
mst089journal_volume
30pub_type
杂志文章abstract：:Enzyme function is strongly affected by temperature, and orthologs from species adapted to different thermal environments often show temperature compensation in kinetic properties. Antarctic notothenioid fishes live in a habitat of constant, extreme cold (-1.86 +/- 2 degrees C), and orthologs of the enzyme A4-lactate ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msh237
更新日期：2004-12-01 00:00:00
abstract：:Several authors have postulated that genetic divergence between populations could result in genomic incompatibilities that would cause an increase in transposition in their hybrids, producing secondary effects such as sterility and therefore starting a speciation process. It has been demonstrated that transposition la...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a026182
更新日期：1999-07-01 00:00:00
abstract：:Next-generation sequencing opened up new possibilities in phylogenetics; however, choosing an appropriate method of sample preparation remains challenging. Here, we demonstrate that restriction-site-associated DNA sequencing (RAD-seq) generates useful data for phylogenomics. Analysis of our RAD library using current b...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msu063
更新日期：2014-05-01 00:00:00
abstract：:Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here, we describe recombination landscape estimation using recurrent neural networks (ReLERN...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msaa038
更新日期：2020-06-01 00:00:00
abstract：:The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversifi...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msz017
更新日期：2019-04-01 00:00:00
abstract：:The elongation factor 1 alpha (EF-1 alpha) has become widely employed as a phylogenetic marker for studying eukaryotic evolution. However, a disturbing problem, the artifactual polyphyly of ciliates, is always observed. It has been suggested that the addition of new sequences will help to circumvent this problem. Thus...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a026105
更新日期：1999-02-01 00:00:00
abstract：:Genetic studies of Tibetans, an ethnic group with a long-lasting presence on the Tibetan Plateau which is known as the highest plateau in the world, may offer a unique opportunity to understand the biological adaptations of human beings to high-altitude environments. We conducted a genome-wide study of 1,000,000 genet...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msq277
更新日期：2011-02-01 00:00:00
abstract：:We compared sex chromosomal and autosomal regions of similar GC contents and found that the human Y chromosome contains nine times as many full-length (FL) ancestral LINE-1 (L1) elements per megabase as do autosomes and that the X chromosome contains three times as many. In addition, both sex chromosomes contain a ca....
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a003893
更新日期：2001-06-01 00:00:00
abstract：:Evolution of sequences mostly involves independent changes at different sites. However, substitutions at neighboring sites may co-occur as multinucleotide replacement events (MNRs). Here, we compare noncoding sequences of several species of primates, and of three species of Drosophila fruit flies, in a phylogenetic an...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/mst036
更新日期：2013-06-01 00:00:00
abstract：:Transcriptional control of gene expression is regulated by biochemical interactions between cis-regulatory DNA sequences and trans-acting factors that form complex regulatory networks. Genetic changes affecting both cis- and trans-acting sequences in these networks have been shown to alter patterns of gene expression ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msx068
更新日期：2017-06-01 00:00:00
abstract：:Siberia is one of the coldest environments on Earth and has great seasonal temperature variation. Long-term settlement in northern Siberia undoubtedly required biological adaptation to severe cold stress, dramatic variation in photoperiod, and limited food resources. In addition, recent archeological studies show that...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msx226
更新日期：2017-11-01 00:00:00
abstract：:Naked lobose amoebae (gymnamoebae) are among the most abundant group of protists present in all aquatic and terrestrial biotopes. Yet, because of lack of informative morphological characters, the origin and evolutionary history of gymnamoebae are poorly known. The first molecular studies revealed multiple origins for ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a003777
更新日期：2001-12-01 00:00:00
abstract：:During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a004125
更新日期：2002-05-01 00:00:00
abstract：:Signatures of balancing selection can highlight polymorphisms and functions that are important to the long-term fitness of a species. We performed a first genome-wide scan for balancing selection in a bacterial species, Staphylococcus aureus, which is a common cause of serious antimicrobial-resistant infections of hum...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msr286
更新日期：2012-04-01 00:00:00
abstract：:Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a025995
更新日期：1998-07-01 00:00:00
abstract：:The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonpar...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a004094
更新日期：2002-04-01 00:00:00
abstract：:The complete nucleotide sequence of the mt (mitochondrial) and cp (chloroplast) genomes of the unicellular green alga Ostreococcus tauri has been determined. The mt genome assembles as a circle of 44,237 bp and contains 65 genes. With an overall average length of only 42 bp for the intergenic regions, this is the most...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msm012
更新日期：2007-04-01 00:00:00
abstract：:Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between des...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msr228
更新日期：2012-02-01 00:00:00
abstract：:Current sequencing methods produce large amounts of data, but genome assemblies constructed from these data are often fragmented and incomplete. Incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. This means that methods attempting to estimate...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/mst100
更新日期：2013-08-01 00:00:00
abstract：:The Orthonectida is a small, poorly known phylum of parasites of marine invertebrates. Their phylogenetic placement is obscure; they have been considered to be multicellular protozoans, primitive animals at a "mesozoan" grade of organization, or secondarily simplified flatworm-like organisms. The best known species in...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a025683
更新日期：1996-11-01 00:00:00
abstract：:We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light o...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msg198
更新日期：2003-10-01 00:00:00
abstract：:We implement an isolation with migration model for three species, with migration occurring between two closely related species while an out-group species is used to provide further information concerning gene trees and model parameters. The model is implemented in the likelihood framework for analyzing multilocus geno...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/mss118
更新日期：2012-10-01 00:00:00
abstract：:Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msz159
更新日期：2019-07-12 00:00:00
abstract：:Some of the assumptions underlying estimates of DNA and protein sequence divergence are examined. A solution for the variance of these estimates that allows for different mutation rates and different population sizes in each species and for an arbitrary structure in the initial population is obtained. It is shown that...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a040303
更新日期：1983-12-01 00:00:00
abstract：:An improved understanding of the biological and numerical properties of measures of population differentiation across loci is becoming increasingly more important because of their growing use in analyzing genome-wide polymorphism data for detecting population structures, inferring the rates of migration, and identifyi...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/mss187
更新日期：2012-12-01 00:00:00
abstract：:As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cha...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msq131
更新日期：2010-10-01 00:00:00
abstract：:Recent results from large-scale genomic projects suggest that allele frequencies, which are highly relevant for medical purposes, differ considerably across different populations. The need for a detailed catalog of local variability motivated the whole-exome sequencing of 267 unrelated individuals, representative of t...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msw005
更新日期：2016-05-01 00:00:00
abstract：:We report the genomic organization and deduced protein sequence of a cephalochordate member of the Otx homeobox gene family (AmphiOtx) and show its probable single-copy state in the genome. We also present molecular phylogenetic analysis indicating that there was single ancestral Otx gene in the first chordates which ...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a025961
更新日期：1998-05-01 00:00:00
abstract：:Two recent studies have presented conflicting views on variation present within the 294 base third domain of the 12S rRNA gene in the genus Drosophila, and in D. pseudoobscura in particular. One study suggested that this gene is highly invariant across the genus, while another recovered 22 distinct haplotypes from 22 ...
journal_title：Molecular biology and evolution
pub_type： 评论,杂志文章
doi：10.1093/oxfordjournals.molbev.a026374
更新日期：2000-06-01 00:00:00
abstract：:This report describes a lysozyme expressed at high levels in the stomach of the hoatzin, the only known foregut-fermenting bird. Evolutionary comparison places it among the calcium-binding lysozymes rather than among the conventional types. Conventional lysozymes were recruited as digestive enzymes twice in the evolut...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a040173
更新日期：1994-11-01 00:00:00
