Abstract:
:Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared with the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh). After ranking SNPs by these statistics, we identified the top 10 highly differentiated SNPs in five genome regions in the LSBL tests of Brazilian Amerindian ancestry compared to European and African; and the top 10 SNPs in eight regions comparing their Amerindian component to the closest Asian 1000 Genomes population. We found SNPs within or proximal to the genes CIITA (rs6498115), SMC6 (rs1834619), and KLHL29 (rs2288697) were most differentiated in the Amerindian-specific branch, while SNPs in the genes ADAMTS9 (rs7631391), DOCK2 (rs77594147), SLC28A1 (rs28649017), ARHGAP5 (rs7151991), and CIITA (rs45601437) were most highly differentiated in the Asian comparison. These genes are known to influence immune function, metabolic and anthropometry traits, and embryonic development. These analyses have identified candidate genes for selection within Amerindian ancestry, and by comparison of the two analyses, those for which the differentiation may have arisen during the migration from Asia to the Americas.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Mychaleckyj JC,Havt A,Nayak U,Pinkerton R,Farber E,Concannon P,Lima AA,Guerrant RLdoi
10.1093/molbev/msw249subject
Has Abstractpub_date
2017-03-01 00:00:00pages
559-574issue
3eissn
0737-4038issn
1537-1719pii
msw249journal_volume
34pub_type
杂志文章abstract::Operons coding for the enzyme arsenite oxidase have been detected in the genomes from Archaea and Bacteria by Blast searches using the amino acid sequences of the respective enzyme characterized in two different beta-proteobacteria as templates. Sequence analyses show that in all these species, arsenite oxidase is tra...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg071
更新日期:2003-05-01 00:00:00
abstract::Septate junctions (SJs) insure barrier properties and control paracellular diffusion of solutes across epithelia in invertebrates. However, the origin and evolution of their molecular constituents in Metazoa have not been firmly established. Here, we investigated the genomes of early branching metazoan representatives...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu265
更新日期:2015-01-01 00:00:00
abstract::Horizontal gene transfer (HGT) can equip organisms with novel genes, expanding the repertoire of genetic material available for evolutionary innovation and allowing recipient lineages to colonize new environments. However, few studies have characterized the functions of HGT genes experimentally or examined postacquisi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy082
更新日期:2018-08-01 00:00:00
abstract::In numerous species, individual dispersal is restricted in space so that "continuous" populations evolve under isolation by distance. A method based on individual genotypes assuming a lattice population model was recently developed to estimate the product Dsigma2, where D is the population density and sigma2 is the av...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg034
更新日期:2003-04-01 00:00:00
abstract::Modifications to transcriptional regulators play a major role in adaptation. Here, we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase β subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adapti...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx216
更新日期:2017-11-01 00:00:00
abstract::Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolate...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx178
更新日期:2017-10-01 00:00:00
abstract::Convergent and parallel amino acid substitutions in protein evolution, collectively referred to as molecular convergence here, have small probabilities under neutral evolution. For this reason, molecular convergence is commonly viewed as evidence for similar adaptations of different species. The surge in the number of...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv091
更新日期:2015-08-01 00:00:00
abstract::Finding correct species relationships using phylogeny reconstruction based on molecular data is dependent on several empirical and technical factors. These include the choice of DNA sequence from which phylogeny is to be inferred, the establishment of character homology within a sequence alignment, and the phylogeny a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026285
更新日期:2000-12-01 00:00:00
abstract::Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to crea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz185
更新日期:2019-12-01 00:00:00
abstract::Knotted-like (KNOX) proteins constitute a group of homeodomain proteins involved in pattern formation in developing tissues of angiosperms and other green plants. We conducted phylogenetic analyses of nucleotide and amino acid sequences of all known KNOX proteins in order to examine their evolution. Our analyses revea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026136
更新日期:1999-04-01 00:00:00
abstract::Microarray platforms are used increasingly to make comparative inferences through genome-wide surveys of gene expression. Although recent studies focus on describing the evidence for natural selection using estimates of the within- and between-taxa mutational variances, these methods do not explicitly or flexibly acco...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp149
更新日期:2009-10-01 00:00:00
abstract::Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa154
更新日期:2020-11-01 00:00:00
abstract::That natural selection affects molecular evolution at synonymous sites in protein-coding sequences is well established and is thought to predominantly reflect selection for translational efficiency/accuracy mediated through codon bias. However, a recently developed maximum likelihood framework, when applied to 18 codi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm196
更新日期:2007-12-01 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::Seminal fluid proteins (SFPs) mediate an array of postmating reproductive processes that influence fertilization and fertility. As such, it is widely held that SFPs may contribute to postmating, prezygotic reproductive barriers between closely related taxa. We investigated seminal fluid (SF) diversification in a recen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz235
更新日期:2020-02-01 00:00:00
abstract::How is adaptability generated in a system composed of interacting cellular machineries, each with a separate and functionally critical job to perform? The machinery for organelle inheritance is precisely one such system, requiring coordination between robust and ancient cellular modules, including the cell cycle, cyto...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr264
更新日期:2012-03-01 00:00:00
abstract::DNA supercoiling is the master function that interconnects chromosome structure and global gene transcription. This function has recently been shown to be under strong selection in Escherichia coli. During the evolution of 12 initially identical populations propagated in a defined environment for 20,000 generations, p...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq099
更新日期:2010-09-01 00:00:00
abstract::Simple sequence repeats (SSRs) or microsatellites are a common component of genomes but vary greatly across species in their abundance. We tested the hypothesis that this variation is due in part to AT/GC content of genomes, with genomes biased toward either high AT or high CG generating more short random repeats that...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq266
更新日期:2011-02-01 00:00:00
abstract::Previous studies have shown that splicing efficiency, and thus maturation of pre-mRNA, depends on the correct folding of the RNA molecule into a secondary or higher order structure. When disrupted by a mutation, aberrant folding may result in a lower splicing efficiency. However, the structure can be restored by a sec...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn195
更新日期:2008-11-01 00:00:00
abstract::Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening pro...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst206
更新日期:2014-02-01 00:00:00
abstract::A combination of three independent biological features, genomic organization, diagnostic amino acid sites, and rare indels, was used to elucidate the phylogeny of the vertebrate serpin (serine protease inhibitor) superfamily. A strong correlation between serpin gene families displaying (1) a conserved exon-intron patt...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003838
更新日期:2001-04-01 00:00:00
abstract::Analysis of mitochondrial DNA restriction fragment length polymorphism in European anchovy (Engraulis encrasicolus) revealed a large number of mitotypes that form two distinct clusters (phylads). Phylad A consists of one common mitotype and many rare secondary mitotypes that are one mutational step removed from the ma...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025554
更新日期:1996-01-01 00:00:00
abstract::Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis-acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, w...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw096
更新日期:2016-08-01 00:00:00
abstract::Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200-4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome o...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv071
更新日期:2015-07-01 00:00:00
abstract::The proportion of functional sequence in the human genome is currently a subject of debate. The most widely accepted figure is that approximately 5% is under purifying selection. In Drosophila, estimates are an order of magnitude higher, though this corresponds to a similar quantity of sequence. These estimates depend...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp299
更新日期:2010-04-01 00:00:00
abstract::Detecting positive selection in species with heterogeneous habitats and complex demography is notoriously difficult and prone to statistical biases. The model plant Arabidopsis thaliana exemplifies this problem: In spite of the large amounts of data, little evidence for classic selective sweeps has been found. Moreove...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu247
更新日期:2014-11-01 00:00:00
abstract::Many methods exist for detecting introgression between nonsister species, but the most commonly used require either a single sequence from four or more taxa or multiple sequences from each of three taxa. Here, we present a test for introgression that uses only a single sequence from three taxa. This test, denoted D3, ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz178
更新日期:2019-12-01 00:00:00
abstract::A common problem in molecular phylogenetics is choosing a model of DNA substitution that does a good job of explaining the DNA sequence alignment without introducing superfluous parameters. A number of methods have been used to choose among a small set of candidate substitution models, such as the likelihood ratio tes...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh123
更新日期:2004-06-01 00:00:00
abstract::Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inf...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx294
更新日期:2018-04-01 00:00:00
abstract::A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg139
更新日期:2003-08-01 00:00:00