Abstract:
:Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation of living organisms. Although the genome of a species as a whole is important, chromosomes are the basic units subjected to genetic events that coin evolution to a large extent. Now many complete genome sequences are available, we can address evolution and variation of individual chromosomes across species. For example, "How are the repeat and nonrepeat proportions of genetic codes distributed among different chromosomes in a multichromosome species?" "Is there a general rule behind the intuitive observation that chromosome lengths tend to be similar in a species, and if so, can we generalize any findings in chromosome content and size across different taxonomic groups?" Here, we show that chromosomes within a species do not show dramatic fluctuation in their content of mobile genetic elements as the proliferation of these elements increases from unicellular eukaryotes to vertebrates. Furthermore, we demonstrate that, notwithstanding the remarkable plasticity, there is an upper limit to chromosome-size variation in diploid eukaryotes with linear chromosomes. Strikingly, variation in chromosome size for 886 chromosomes in 68 eukaryotic genomes (including 22 human autosomes) can be viably captured by a single model, which predicts that the vast majority of the chromosomes in a species are expected to have a base pair length between 0.4035 and 1.8626 times the average chromosome length. This conserved boundary of chromosome-size variation, which prevails across a wide taxonomic range with few exceptions, indicates that cellular, molecular, and evolutionary mechanisms, possibly together, confine the chromosome lengths around a species-specific average chromosome length.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Li X,Zhu C,Lin Z,Wu Y,Zhang D,Bai G,Song W,Ma J,Muehlbauer GJ,Scanlon MJ,Zhang M,Yu Jdoi
10.1093/molbev/msr011subject
Has Abstractpub_date
2011-06-01 00:00:00pages
1901-11issue
6eissn
0737-4038issn
1537-1719pii
msr011journal_volume
28pub_type
杂志文章abstract::Ever since Luria and Delbruck, the notion that mutation is random with respect to fitness has been foundational to modern biology. However, various studies have claimed striking exceptions to this rule. One influential case involves toxin-encoding genes in snails of the genus Conus, termed conotoxins, a large gene fam...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msw140
更新日期:2016-10-01 00:00:00
abstract::Inference of intraspecific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh212
更新日期:2004-10-01 00:00:00
abstract::Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptati...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz194
更新日期:2019-12-01 00:00:00
abstract::Noncoding DNA sequences, which play various roles in gene expression and regulation, are under evolutionary pressure. Gene regulation requires specific protein-DNA binding events, and our previous studies showed that both DNA sequence and shape readout are employed by transcription factors (TFs) to achieve DNA binding...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy099
更新日期:2018-08-01 00:00:00
abstract::An attempt to use phylogenetic invariants for tree reconstruction was made at the end of the 80s and the beginning of the 90s by several researchers (the initial idea due to Lake [1987] and Cavender and Felsenstein [1987]). However, the efficiency of methods based on invariants is still in doubt (Huelsenbeck 1995; Jin...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl153
更新日期:2007-01-01 00:00:00
abstract::The human scavenger receptor class B type I (SR-BI and splice variant SR-BII) plays a central role in HDL cholesterol metabolism and represents a candidate gene for a number of related diseases. We examined the genetic diversity of its coding and flanking regions in a sample of 178 chromosomes from individuals of Euro...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh074
更新日期:2004-04-01 00:00:00
abstract::Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes clinical isolate that killed a patient and was resistant to almost all current antibiotics (except gentamicin) commonly used to treat Enterobacterial infections, including colistin. Genomic and phylogenetic analyses explain the discrepanc...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss236
更新日期:2013-02-01 00:00:00
abstract::Epidemiological processes leave a fingerprint in the pattern of genetic structure of virus populations. Here, we provide a new method to infer epidemiological parameters directly from viral sequence data. The method is based on phylogenetic analysis using a birth-death model (BDM) rather than the commonly used coalesc...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr217
更新日期:2012-01-01 00:00:00
abstract::Inactivation of the X chromosome in the male germ line has been suggested to contribute to the excess of gene movement off the X chromosome and the paucity of X-linked male-biased genes that have been observed in Drosophila species. Recent experimental work has demonstrated the transcriptional inactivation of the X ch...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq355
更新日期:2011-05-01 00:00:00
abstract::Cysteine-rich secretory proteins (CRISPs) are glycoproteins found exclusively in vertebrates and have broad diversified functions. They are hypothesized to play important roles in mammalian reproduction and in reptilian venom, where they disrupt homeostasis of the prey through several mechanisms, including among other...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss058
更新日期:2012-07-01 00:00:00
abstract::Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv206
更新日期:2016-01-01 00:00:00
abstract::The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wol...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz311
更新日期:2020-05-01 00:00:00
abstract::The evolution of DNA base composition evolution is simplified to a six-parameter model when there are no strand biases for mutation and selection. We analyzed the dynamics of this model with special attention to the influence of a change in substitution rates. The G + C content of the DNA sequence tends to an equilibr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026156
更新日期:1999-06-01 00:00:00
abstract::Nei and Gojobori (1986) developed a simple method to estimate the numbers of synonymous (ds) and nonsynonymous (dN) substitutions per site. In the present paper, we have developed a method for computing variances and covariances of ds's and dN's and of the proportions of synonymous (ps) and nonsynonymous (pN) differen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040140
更新日期:1994-07-01 00:00:00
abstract::The DnaK-DnaJ-GrpE (KJE) chaperone system functions at the fulcrum of protein homeostasis in bacteria. It interacts both with nascent polypeptides and with proteins that have become unfolded, either funneling its clients toward the native state or ushering misfolded proteins into degradation. In line with its key role...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss152
更新日期:2012-11-01 00:00:00
abstract::The transposable element hobo has been introduced into the previously empty Drosophila melanogaster strain Hikone so that its dynamics can be followed and it can be compared with the P element. Five transformed lines were followed over 58 generations. The results were highly dependent on the culture temperature, the s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040251
更新日期:1995-09-01 00:00:00
abstract::Interspecific hybridization is one of the major factors leading to phylogenetic incongruence among loci, but the knowledge is still limited about the potential of each locus to introgress between species. By directly sequencing three DNA regions: chloroplast DNAs (matK gene and trnL-F noncoding region), the nuclear ri...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi016
更新日期:2005-02-01 00:00:00
abstract::Although any genotype-phenotype relationships are a result of evolution, little is known about how natural selection and neutral drift, two distinct driving forces of evolution, operate to shape the relationships. By analyzing ∼500 yeast quantitative traits, we reveal a basic "supervisor-worker" gene architecture unde...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx288
更新日期:2018-03-01 00:00:00
abstract::One challenge of analyzing samples of DNA sequences is to account for the nonnegligible polymorphisms produced by error when the sequencing error rate is high or the sample size is large. Specifically, those artificial sequence variations will bias the observed single nucleotide polymorphism (SNP) frequency spectrum, ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp059
更新日期:2009-07-01 00:00:00
abstract::We compared the single-nucleotide polymorphisms (SNPs) in humans in 182 housekeeping and 148 tissue-specific genes. SNPs were divided into rare and common polymorphisms based on their frequencies. We found that housekeeping genes tend to be less polymorphic than tissue-specific genes for both rare and common SNPs. Usi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi240
更新日期:2005-12-01 00:00:00
abstract::Lethality in hybrids between Drosophila melanogaster and its sibling species Drosophila simulans is caused in part by the interaction of the genes Hybrid male rescue (Hmr) and Lethal hybrid rescue (Lhr). Hmr and Lhr have diverged under positive selection in the hybridizing species. Here we test whether positive select...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn190
更新日期:2008-11-01 00:00:00
abstract::The diversity of color vision systems found in extant vertebrates suggests that different evolutionary selection pressures have driven specializations in photoreceptor complement and visual pigment spectral tuning appropriate for an animal's behavior, habitat, and life history. Aquatic vertebrates in particular show h...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz269
更新日期:2020-03-01 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::A central goal in biology is to determine the ways in which evolution repeats itself. One of the most remarkable examples in nature of convergent evolutionary novelty is animal venom. Across diverse animal phyla, various specialized organs and anatomical structures have evolved from disparate developmental tissues to ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa133
更新日期:2020-10-01 00:00:00
abstract::Parentally biased expression of transcripts (genomic imprinting) in adult tissues, including the brain, can influence and possibly drive the evolution of behavioral traits. We have previously found that paternally determined cues are involved in population-specific mate choice decisions between two populations of the ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu257
更新日期:2014-12-01 00:00:00
abstract::The ParaHox and Hox gene clusters control aspects of animal anterior-posterior development and are related as paralogous evolutionary sisters. Despite this relationship, it is not clear if the clusters operate in similar ways, with similar constraints. To compare clusters, we examined the transposable-element (TE) con...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msp235
更新日期:2010-02-01 00:00:00
abstract::MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)(3)), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)(3) Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-wor...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst043
更新日期:2013-06-01 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::Molecular systematists need increased access to nuclear genes. Highly conserved, low copy number protein-encoding nuclear genes have attractive features for phylogenetic inference but have heretofore been applied mostly to very ancient divergences. By virtue of their synonymous substitutions, such genes should contain...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040244
更新日期:1995-07-01 00:00:00
abstract::Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv148
更新日期:2015-10-01 00:00:00