Abstract:
:The level of DNA polymorphism in the ancestral species at the time of speciation can be estimated using DNA sequences from many loci sampled from 2 or more extant species. The comparison between ancestral and extant polymorphism can be informative about the population genetics of speciation. In this study, we collected and analyzed DNA sequences of approximately 60 genes from 4 species of Sonneratia, a common genus of mangroves on the Indo-Pacific coasts. We found that the 3 ancestral species were comparable to each other in terms of level of polymorphism. However, the ancestral species at the time of speciation were substantially more polymorphic than the extant geographical populations. This ancestral polymorphism is in fact larger than, or at least equal to, the level of polymorphism of the entire species across extant geographical populations. The observations are not fully compatible with speciation by strict allopatry. We suggest that, at the time of speciation, the ancestral species consisted of interconnected but strongly divided geographical populations. This population structure would give rise to high level of polymorphism across species range. This approach of studying the speciation history by genomic means should be applicable to nonmodel organisms.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Zhou R,Zeng K,Wu W,Chen X,Yang Z,Shi S,Wu CIdoi
10.1093/molbev/msm209subject
Has Abstractpub_date
2007-12-01 00:00:00pages
2746-54issue
12eissn
0737-4038issn
1537-1719pii
msm209journal_volume
24pub_type
杂志文章abstract::Male sexual behavior in the fruit fly Drosophila melanogaster is regulated by fruitless (fru), a sex-determination gene specifying the synthesis of BTB-Zn finger proteins that likely function as male-specific transcriptional regulators. Expression of fru in the nervous system specifies male sexual behavior and the mus...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj070
更新日期:2006-03-01 00:00:00
abstract::A phylogenetic analysis of sex-chromosomal zinc-finger genes (Zfx and Zfy) indicates that the genes have not evolved completely independently since their initial separation. The sequence similarities suggest gene conversion in the last exon between the duplicated Y-chromosomal genes Zfy-1 and Zfy-2 in the mouse. There...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040003
更新日期:1993-03-01 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::The cadherin-catenin complex (CCC) mediates cell-cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-bind...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw084
更新日期:2016-08-01 00:00:00
abstract::The cost of reproduction is a pivotal trade-off with various biological processes during the evolution of organisms. However, the genes and molecular mechanisms underlying the evolution of balancing reproductive capacity and its cost are still largely unknown. Here, we present a comprehensive study on the evolution, e...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr299
更新日期:2012-05-01 00:00:00
abstract::In this study, we used an empirical example based on 100 mitochondrial genomes from higher teleost fishes to compare the accuracy of parsimony-based jackknife values with Bayesian support values. Phylogenetic analyses of 366 partitions, using differential taxon and character sampling from the entire data matrix of 100...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh014
更新日期:2004-01-01 00:00:00
abstract::We determine the phylogenetic backbone of the East Asian mtDNA tree by using published complete mtDNA sequences and assessing both coding and control region variation in 69 Han individuals from southern China. This approach assists in the interpretation of published mtDNA data on East Asians based on either control re...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003996
更新日期:2002-10-01 00:00:00
abstract::The quantitative immunological technique of micro-complement fixation (MC'F) has been routinely used during the past decade to assess evolutionary relationships among living vertebrate species. The large data base that has been generated, along with the excellent correlations between immunologically measured genetic d...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040405
更新日期:1986-09-01 00:00:00
abstract::TATA box, the core promoter element, exists in a broad range of eukaryotes, and the expression of TATA-containing genes usually responds to various environmental stresses. Hence, the evolution of TATA-box in duplicate genes may provide some clues for the interrelationship among environmental stress, expression differe...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr116
更新日期:2011-10-01 00:00:00
abstract::How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since g...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa288
更新日期:2020-11-10 00:00:00
abstract::Gene unscrambling in spirotrichous ciliates involves massive genome-wide DNA deletion and rearrangement events during development. During each sexual cycle, the somatic nucleus (macronucleus) regenerates from the germ line nucleus (micronucleus). Development of the polyploid somatic genome requires programmed DNA dele...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj089
更新日期:2006-04-01 00:00:00
abstract::The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp278
更新日期:2010-03-01 00:00:00
abstract::The occurrence of a fish-specific genome duplication (FSGD) in the lineage leading to teleost fishes is widely accepted, but the consequences of this event remain elusive. Teleosts, and the cichlid fishes from the species flocks in the East African Great Lakes in particular, evolved a unique complexity and diversity o...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msk003
更新日期:2006-06-01 00:00:00
abstract::We describe a method to establish chronologies of ancient ribosomal evolution. The method uses structure-based and sequence-based comparison of the large subunits (LSUs) of Haloarcula marismortui and Thermus thermophilus. These are the highest resolution ribosome structures available and represent disparate regions of...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp163
更新日期:2009-11-01 00:00:00
abstract::We present the first molecular phylogenetic examination of the evolutionary position of retortamonads, a group of mitochondrion-lacking flagellates usually found as commensals of the intestinal tracts of vertebrates. Our phylogenies include small subunit ribosomal gene sequences from six retortamonad isolates-four fro...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004135
更新日期:2002-05-01 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::Phylogeny estimation is extremely crucial in the study of molecular evolution. The increase in the amount of available genomic data facilitates phylogeny estimation from multilocus sequence data. Although maximum likelihood and Bayesian methods are available for phylogeny reconstruction using multilocus sequence data,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn043
更新日期:2008-05-01 00:00:00
abstract::Chromosomal DNA from 23 closely related, pathogenic strains of Escherichia coli was digested and probed for the insertion sequences IS1, IS2, IS4, IS5, and IS30. Under the assumption that elements residing in DNA restriction fragments of the same apparent length are identical by descent, parsimony analysis of these ch...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040531
更新日期:1989-01-01 00:00:00
abstract::A large majority of bacterial genomes show strand asymmetry, such that G and T preferentially accumulate on the leading strand. The mechanisms are unknown, but cytosine deaminations are thought to play an important role. Here, we have examined DNA strand asymmetry in three strains of the aphid endosymbiont Buchnera ap...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj107
更新日期:2006-05-01 00:00:00
abstract::The mutational process varies at many levels, from within genomes to among taxa. Many mechanisms have been linked to variation in mutation, but understanding of the evolution of the mutational process is rudimentary. Physiological condition is often implicated as a source of variation in microbial mutation rate and ma...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy213
更新日期:2019-02-01 00:00:00
abstract::Positive selection sites (PSSs), a class of amino acid sites with an excess of nonsynonymous to synonymous substitutions, are indicators of adaptive molecular evolution and have been detected in many protein families involved in a diversity of biological processes by statistical approaches. However, few studies are co...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw065
更新日期:2016-08-01 00:00:00
abstract::The mammalian family Talpidae (moles, shrew moles, desmans) is characterized by diverse ecomorphologies associated with terrestrial, semi-aquatic, semi-fossorial, fossorial, and aquatic-fossorial lifestyles. Prominent specializations involved with these different lifestyles, and the transitions between them, pose outs...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw221
更新日期:2017-01-01 00:00:00
abstract::The ability to counter periods of low humidity is an important determinant of distribution range in Drosophila. Climate specialists with low physiological tolerance to desiccation stress are restricted to the tropics and may lack the ability to further increase resistance through evolution. Although the physiological ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr294
更新日期:2012-05-01 00:00:00
abstract::The relative evolutionary rates at individual sites in proteins are informative measures of conservation or adaptation. Often used as evolutionarily aware conservation scores, relative rates reveal key functional or strongly selected residues. Estimating rates in a phylogenetic context requires specifying a protein su...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy127
更新日期:2018-09-01 00:00:00
abstract::We investigate the effect of purifying selection at multiple sites on both the shape of the genealogy and the distribution of mutations on the tree. We find that the primary effect of purifying selection on a genealogy is to shift the distribution of mutations on the tree, whereas the shape of the tree remains largely...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004199
更新日期:2002-08-01 00:00:00
abstract::We have used analysis of variance to partition the variation in synonymous and amino acid substitution rates between three effects (gene, lineage, and a gene-by-lineage interaction) in mammalian nuclear and mitochondrial genes. We find that gene effects are stronger for amino acid substitution rates than for synonymou...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004231
更新日期:2003-01-01 00:00:00
abstract::Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa194
更新日期:2020-12-16 00:00:00
abstract::4.5SH RNA is a 94-nt small RNA with unknown function. This RNA is known to be present in the mouse, rat, and hamster cells; however, it is not found in human, rabbit, and chicken. In the mouse genome, the 4.5SH RNA gene is a part of a long (4.2 kb) tandem repeat ( approximately 800 copies) unit. Here, we found that 4....
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi140
更新日期:2005-07-01 00:00:00
abstract::Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw048
更新日期:2016-07-01 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