SPIn: model selection for phylogenetic mixtures via linear invariants.

abstract：:To explore the origin of the diversity observed in natural populations, many studies have investigated the relationship between genotype and phenotype. In yeast species, especially in Saccharomyces cerevisiae, these studies are mainly conducted using recombinant offspring derived from two genetically diverse isolates,...

journal_title：Molecular biology and evolution

authors： Brion C,Caradec C,Pflieger D,Friedrich A,Schacherer J

更新日期：2020-09-01 00:00:00

abstract：:Successful fertilization in free-spawning marine organisms depends on the interactions between genes expressed on the surfaces of eggs and sperm. Positive selection frequently characterizes the molecular evolution of such genes, raising the possibility that some common deterministic process drives the evolution of gam...

journal_title：Molecular biology and evolution

authors： Riginos C,Wang D,Abrams AJ

更新日期：2006-10-01 00:00:00

abstract：:Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid spe...

journal_title：Molecular biology and evolution

authors： Wang J,Dong S,Yang L,Harris A,Schneider H,Kang M

更新日期：2020-09-01 00:00:00

abstract：:Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constan...

journal_title：Molecular biology and evolution

authors： Gingerich PD

更新日期：1986-05-01 00:00:00

abstract：:Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gene gains/losses, and genome organization. Most of our knowledge about eukaryotic genome evolution is derived from studies of multicellular model organisms. The eukaryotic phylum Apicomplexa contains obligate intracellula...

journal_title：Molecular biology and evolution

authors： DeBarry JD,Kissinger JC

更新日期：2011-10-01 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

authors： Wang MS,Li Y,Peng MS,Zhong L,Wang ZJ,Li QY,Tu XL,Dong Y,Zhu CL,Wang L,Yang MM,Wu SF,Miao YW,Liu JP,Irwin DM,Wang W,Wu DD,Zhang YP

更新日期：2015-07-01 00:00:00

abstract：:The origin and maintenance of sex remains one of the most debated topics in evolutionary biology. Investigations of the molecular genetic consequences of asexuality, such as direct estimation of mutation and recombination rates in asexual lineages, are critical for explaining the prevalence of sex in nature. In this s...

journal_title：Molecular biology and evolution

authors： Xu S,Omilian AR,Cristescu ME

更新日期：2011-01-01 00:00:00

abstract：:Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrop...

journal_title：Molecular biology and evolution

authors： Nei M,Stephens JC,Saitou N

更新日期：1985-01-01 00:00:00

abstract：:This study describes the origin and structural features of a mammalian gene, CGIN1 (Cousin of GIN1). CGIN1 proteins contain an NYN domain, retroviral RNase H and integrase domains, and a domain of unknown function (CGIN1 domain) that is also present in two other genes (N4BP1 and KIAA0323). We suggest that CGIN1 derive...

journal_title：Molecular biology and evolution

authors： Marco A,Marín I

更新日期：2009-10-01 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

authors： Adrion JR,Galloway JG,Kern AD

更新日期：2020-06-01 00:00:00

abstract：:Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. In animals, the population genetics of codon usage bias has only been studied ...

journal_title：Molecular biology and evolution

authors： Galtier N,Roux C,Rousselle M,Romiguier J,Figuet E,Glémin S,Bierne N,Duret L

更新日期：2018-05-01 00:00:00

abstract：:Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human ...

journal_title：Molecular biology and evolution

authors： Burgess R,Yang Z

更新日期：2008-09-01 00:00:00

abstract：:To investigate the potential importance of gene duplication in D. melanogaster accessory gland protein (Acp) gene evolution we carried out a computational analysis comparing annotated D. melanogaster Acp genes to the entire D. melanogaster genome. We found that two known Acp genes are actually members of small multige...

journal_title：Molecular biology and evolution

authors： Holloway AK,Begun DJ

更新日期：2004-09-01 00:00:00

abstract：:The pyrimidine exchange type of RNA editing in land plant (embryophyte) organelles has largely remained an enigma with respect to its biochemical mechanisms, the underlying specificities, and its raison d'être. Apparently arising with the earliest embryophytes, RNA editing is conspicuously absent in one clade of liver...

journal_title：Molecular biology and evolution

authors： Rüdinger M,Polsakiewicz M,Knoop V

更新日期：2008-07-01 00:00:00

abstract：:zeta-Crystallin is a novel nicotinamide adenine dinucleotide phosphate:quinone reductase, present at enzymatic levels in various tissues of different species, which is highly expressed in the lens of some hystricomorph rodents and camelids. We report here the complementary DNA (cDNA) cloning of zeta-crystallin from li...

journal_title：Molecular biology and evolution

authors： Gonzalez P,Hernández-Calzadilla C,Rao PV,Rodriguez IR,Zigler JS Jr,Borrás T

更新日期：1994-03-01 00:00:00

abstract：:Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mitochondrial DNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recen...

journal_title：Molecular biology and evolution

authors： Dalén L,Orlando L,Shapiro B,Brandström-Durling M,Quam R,Gilbert MT,Díez Fernández-Lomana JC,Willerslev E,Arsuaga JL,Götherström A

更新日期：2012-08-01 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

authors： Xu S,Li S,Yang Y,Tan J,Lou H,Jin W,Yang L,Pan X,Wang J,Shen Y,Wu B,Wang H,Jin L

更新日期：2011-02-01 00:00:00

abstract：:Clines in chromosomal inversion polymorphisms-presumably driven by climatic gradients-are common but there is surprisingly little evidence for selection acting on them. Here we address this long-standing issue in Drosophila melanogaster by using diagnostic single nucleotide polymorphism (SNP) markers to estimate inver...

journal_title：Molecular biology and evolution

authors： Kapun M,Fabian DK,Goudet J,Flatt T

更新日期：2016-05-01 00:00:00

abstract：:Full-length mariner-like elements (MLEs) were identified from both a parasitoid wasp, Ascogaster reticulatus, and its moth host, Adoxophyes honmai. MLEs were detected in two related Tortricid moths, but not in another Ascogaster species. The MLEs of A. reticulatus and A. honmai were 97.6% identical in DNA sequence. Th...

journal_title：Molecular biology and evolution

authors： Yoshiyama M,Tu Z,Kainoh Y,Honda H,Shono T,Kimura K

更新日期：2001-10-01 00:00:00

abstract：:Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one s...

journal_title：Molecular biology and evolution

authors： Sun S,Evans BJ,Golding GB

更新日期：2011-09-01 00:00:00

abstract：:Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-ga...

journal_title：Molecular biology and evolution

authors： Nakagome S,Sato T,Ishida H,Hanihara T,Yamaguchi T,Kimura R,Mano S,Oota H,Asian DNA Repository Consortium.

更新日期：2015-06-01 00:00:00

abstract：:Past analyses of the genome of the yeast Saccharomyces cerevisiae have revealed substantial regional variation in G+C content. Important questions remain, though, as to the origin, nature, significance, and generality of this variation. We conducted an extensive analysis of the yeast genome to try to answer these ques...

journal_title：Molecular biology and evolution

authors： Bradnam KR,Seoighe C,Sharp PM,Wolfe KH

更新日期：1999-05-01 00:00:00

abstract：:It is known that the effective population size (Ne) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variatio...

journal_title：Molecular biology and evolution

authors： Zeng K,Jackson BC,Barton HJ

更新日期：2019-02-01 00:00:00

abstract：:Male reproductive fitness is strongly affected by seminal fluid. In addition to interacting with the female environment, seminal fluid mediates important physiological characteristics of sperm, including capacitation and motility. In mammals, the male reproductive tract shows a striking degree of compartmentalization,...

journal_title：Molecular biology and evolution

authors： Dean MD,Clark NL,Findlay GD,Karn RC,Yi X,Swanson WJ,MacCoss MJ,Nachman MW

更新日期：2009-08-01 00:00:00

abstract：:Endogenous retroviruses provide molecular fossils for studying the ancient evolutionary history of retroviruses. Here, we report our independent discovery and analysis of endogenous lentiviral insertions (Mustelidae endogenous lentivirus [MELV]) within the genomes of weasel family (Mustelidae). Genome-scale screening ...

journal_title：Molecular biology and evolution

authors： Han GZ,Worobey M

更新日期：2012-10-01 00:00:00

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

authors： Roy SW

更新日期：2016-10-01 00:00:00

abstract：:Adaptive evolution at the molecular level can be studied by detecting convergent and parallel evolution at the amino acid sequence level. For a set of homologous protein sequences, the ancestral amino acids at all interior nodes of the phylogenetic tree of the proteins can be statistically inferred. The amino acid sit...

journal_title：Molecular biology and evolution

authors： Zhang J,Kumar S

更新日期：1997-05-01 00:00:00

abstract：:Genetic incompatibilities are commonly observed between hybridizing species. Although this type of isolating mechanism has received considerable attention, we have few examples describing how genetic incompatibilities evolve. We investigated the evolution of two loci involved in a classic example of a Bateson-Dobzhans...

journal_title：Molecular biology and evolution

authors： Scarpino SV,Hunt PJ,Garcia-De-Leon FJ,Juenger TE,Schartl M,Kirkpatrick M

更新日期：2013-10-01 00:00:00

abstract：:Methods such as maximum parsimony (MP) are frequently criticized as being statistically unsound and not being based on any "model." On the other hand, advocates of MP claim that maximum likelihood (ML) has some fundamental problems. Here, we explore the connection between the different versions of MP and ML methods, p...

journal_title：Molecular biology and evolution

authors： Steel M,Penny D

更新日期：2000-06-01 00:00:00

abstract：:Hox genes encode a family of transcriptional regulators that operate differential developmental programs along the anteroposterior axis of bilateral animals. Regulatory changes affecting Hox gene expression are believed to have been crucial for the evolution of animal body plans. In Drosophila melanogaster, Hox expres...

journal_title：Molecular biology and evolution

authors： Patraquim P,Warnefors M,Alonso CR

更新日期：2011-09-01 00:00:00