当前位置： SCI文献检索 > MOLECULAR PHYLOGENETICS AND EVOLUTION期刊下所有文献 > The PNarec method for detection of ancient recombinations through phylogenetic network analysis.

The PNarec method for detection of ancient recombinations through phylogenetic network analysis.

Abstract：

:Recombinations are known to disrupt bifurcating tree structure of gene genealogies. Although recently occurred recombinations are easily detectable by using conventional methods, recombinations may have occurred at any time. We devised a new method for detecting ancient recombinations through phylogenetic network analysis, and detected five ancient recombinations in gibbon ABO blood group genes [Kitano et al., 2009. Mol. Phylogenet. Evol., 51, 465-471]. We present applications of this method, now named as "PNarec", to various virus sequences as well as HLA genes.

journal_name

Mol Phylogenet Evol

journal_title

Molecular phylogenetics and evolution

authors

Saitou N,Kitano T

doi

10.1016/j.ympev.2012.09.015

subject

Has Abstract

pub_date

2013-02-01 00:00:00

pages

507-14

issue

2

eissn

1055-7903

issn

1095-9513

pii

S1055-7903(12)00372-7

journal_volume

66

pub_type

杂志文章

相关文献

MOLECULAR PHYLOGENETICS AND EVOLUTION文献大全
  • Genetic diversity, phylogeny and evolution of alkaloid sequestering in Cuban miniaturized frogs of the Eleutherodactylus limbatus group.

    abstract：:The miniaturized frogs of the Eleutherodactylus limbatus group, endemic to Cuba, have recently been shown to contain alkaloids in their skin, representing the fifth independent evolutionary origin of alkaloid sequestering in anurans. Based on a comprehensive sampling of all known species of the group we here assess th...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2013.04.031

    authors： Rodríguez A,Poth D,Schulz S,Gehara M,Vences M

    更新日期：2013-09-01 00:00:00

  • A phylogenetic hypothesis for the recently diversified Ruschieae (Aizoaceae) in southern Africa.

    abstract：:The Ruschieae is a large tribe of about 1600 species of succulent perennials. They form a major component of the arid parts of the Greater Cape Floristic Region, both in numbers of species and in their density of coverage. So far phylogenetic relationships within the tribe have been unresolved, largely through the pau...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2013.05.030

    authors： Klak C,Bruyns PV,Hanáček P

    更新日期：2013-12-01 00:00:00

  • What's missing from avian global diversification analyses?

    abstract：:The accumulation of vast numbers of molecular phylogenetic studies has contributed to huge knowledge gains in the evolutionary history of birds. This permits subsequent analyses of avian diversity, such as how and why diversification varies across the globe and among taxonomic groups. However, available genetic data f...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章,评审

    doi：10.1016/j.ympev.2014.04.023

    authors： Reddy S

    更新日期：2014-08-01 00:00:00

  • Analyzing the functional divergence of Slo1 and Slo3 channel subfamilies.

    abstract：:Slo1 and Slo3 encode close paralogues of the Slo potassium (K+) channels family. Despite their evolutionary relatedness, Slo1 and Slo3 channels show marked functional differences and evolutionary dynamics. Whereas Slo1 is a highly conserved and widely expressed channel, Slo3 is a rapidly evolving channel restricted to...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2018.12.026

    authors： Vicens A,Vinuesa P,Arenas M,Treviño CL

    更新日期：2019-04-01 00:00:00

  • Multigenic phylogeographic divergence in the paleoendemic southern Appalachian opilionid Fumontana deprehendor Shear (Opiliones, Laniatores, Triaenonychidae).

    abstract：:The paleoendemic opilionid Fumontana deprehendor is restricted to a small area of mid-elevation forested habitats in the southern Blue Ridge province of the Appalachian Mountains. In a recent study we reported on the discovery of 22 new montane populations of this monotypic genus, specimens from which exhibit remarkab...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2007.10.013

    authors： Thomas SM,Hedin M

    更新日期：2008-02-01 00:00:00

  • Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences.

    abstract：:In spite of several classification attempts among taxa of the genus Lepus, phylogenetic relationships still remain poorly understood. Here, we present molecular genetic evidence that may resolve some of the current incongruities in the phylogeny of the leporids. The complete mitochondrial cytb, 12S genes, and parts of...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2005.05.006

    authors： Wu C,Wu J,Bunch TD,Li Q,Wang Y,Zhang YP

    更新日期：2005-10-01 00:00:00

  • Phylogeography and systematics of the Peromyscus eremicus species group and the historical biogeography of North American warm regional deserts.

    abstract：:Phylogeographic relationships among 26 populations from throughout the geographic range of the Peromyscus eremicus species group are described based on sequence data for a 699-bp fragment of the mitochondrial DNA COIII gene. Distance, maximum-likelihood, and maximum-parsimony analyses of phylogenetic trees generated u...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.2000.0841

    authors： Riddle BR,Hafner DJ,Alexander LF

    更新日期：2000-11-01 00:00:00

  • A multilocus molecular phylogeny of Fasciolariidae (Neogastropoda: Buccinoidea).

    abstract：:The neogastropod family Fasciolariidae Gray, 1853 - tulips, horse-conchs, spindles, etc., comprises important representatives of tropical and subtropical molluscan assemblages, with over 500 species in the subfamilies Fasciolariinae Gray, 1853, Fusininae Wrigley, 1927 and Peristerniinae Tryon, 1880. Fasciolariids have...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2016.03.025

    authors： Couto DR,Bouchet P,Kantor YI,Simone LRL,Giribet G

    更新日期：2016-06-01 00:00:00

  • Comparative analysis of phylogenetic relationships of grain amaranths and their wild relatives (Amaranthus; Amaranthaceae) using internal transcribed spacer, amplified fragment length polymorphism, and double-primer fluorescent intersimple sequence repeat

    abstract：:The most economically important group of species in the genus Amaranthus is the A. hybridus species complex, including three cultivated grain amaranths, A. cruentus, A. caudatus, and A. hypochondriacus, and their putative wild progenitors, A. hybridus, A. quitensis, and A. powellii. Taxonomic confusion exists among th...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.2001.1016

    authors： Xu F,Sun M

    更新日期：2001-12-01 00:00:00

  • Molecular phylogenetics of the Brazilian giant bromeliads (Alcantarea, Bromeliaceae): implications for morphological evolution and biogeography.

    abstract：:The genus Alcantarea comprises near 30 species endemic to rocky outcrops from eastern Brazil. Most species are ornamental and several are threatened due to habitat loss and over collection. In this paper we examine the phylogenetics of Alcantarea and its relationship with the Brazilian members of Vriesea, a genus of w...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2012.03.015

    authors： Versieux LM,Barbará T,Wanderley Md,Calvente A,Fay MF,Lexer C

    更新日期：2012-07-01 00:00:00

  • Phylogeography of the Galápagos hawk (Buteo galapagoensis): a recent arrival to the Galápagos Islands.

    abstract：:Galápagos hawks (Buteo galapagoensis) are one of the most inbred bird species in the world, living in small, isolated island populations. We used mitochondrial sequence and nuclear minisatellite data to describe relationships among Galápagos hawk populations and their colonization history. We sampled 10 populations (e...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2005.11.014

    authors： Bollmer JL,Kimball RT,Whiteman NK,Sarasola JH,Parker PG

    更新日期：2006-04-01 00:00:00

  • Bricklebush (Brickellia) phylogeny reveals dimensions of the great Asteraceae radiation in Mexico.

    abstract：:Data from molecular phylogenetics were used to assess aspects of diversity and relationships in Brickellia, a large and widespread genus of Eupatorieae. The dataset included sequence data from nuclear ribosomal ITS, ETS, and plastid psbA-trnH regions. An initial question was to assess the monophyly of the genus and wh...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2015.02.007

    authors： Schilling EE,Panero JL,Crozier BS,Scott RW,Dávila P

    更新日期：2015-04-01 00:00:00

  • A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach.

    abstract：:Multi-gene phylogenetic analyses were conducted to address the evolution of Clavicipitaceae (Ascomycota). Data are presented here for approximately 5900 base pairs from portions of seven loci: the nuclear ribosomal small and large subunit DNA (nrSSU and nrLSU), beta-tubulin, elongation factor 1alpha (EF-1alpha), the l...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2007.03.011

    authors： Sung GH,Sung JM,Hywel-Jones NL,Spatafora JW

    更新日期：2007-09-01 00:00:00

  • A very short, functionally constrained sequence diagnoses cone snails in several Conasprella clades.

    abstract：:The traditional taxonomy of ca. 700 cone snails assigns all species to a single genus, Conus Linnaeus 1758. However, an increasing body of evidence suggests that some belong to a phylogenetically distinct clade that is sometimes referred to as Conasprella. Previous work (Kraus et al., 2011) showed that a short (259 bp...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2012.06.014

    authors： Kraus NJ,Watkins M,Bandyopadhyay PK,Seger J,Olivera BM,Corneli PS

    更新日期：2012-10-01 00:00:00

  • RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids.

    abstract：:Two, apparently functional, paralogues of the RPB2 gene, which encodes the second largest subunit of RNA polymerase II, are shown to be present in two major groups of asterid plants. Although all other land plants surveyed so far have been found to have only one of these two copies, the RPB2 gene phylogeny inferred fr...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2004.01.014

    authors： Oxelman B,Yoshikawa N,McConaughy BL,Luo J,Denton AL,Hall BD

    更新日期：2004-08-01 00:00:00

  • Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants.

    abstract：:We explore the phylogeny of the polygrammoid ferns using nucleotide sequences derived from three plastid loci for each of 98 selected species. Our analyses recovered four major monophyletic lineages: the loxogrammoids, two clades consisting of taxa restricted to the Old World, and a largely neotropical clade that also...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2003.09.018

    authors： Schneider H,Smith AR,Cranfill R,Hildebrand TJ,Haufler CH,Ranker TA

    更新日期：2004-06-01 00:00:00

  • A recent evolutionary origin of a bacterial small RNA that controls multicellular fruiting body development.

    abstract：:In animals and plants, non-coding small RNAs regulate the expression of many genes at the post-transcriptional level. Recently, many non-coding small RNAs (sRNAs) have also been found to regulate a variety of important biological processes in bacteria, including social traits, but little is known about the phylogeneti...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2014.01.001

    authors： Chen IC,Griesenauer B,Yu YT,Velicer GJ

    更新日期：2014-04-01 00:00:00

  • Raising names from the dead: A time-calibrated phylogeny of frog shells (Bursidae, Tonnoidea, Gastropoda) using mitogenomic data.

    abstract：:With 59 Recent species, Bursidae, known as «frog shells», are a small but widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo-West Pacific. The present study is aimed at reconstructing phylogenetic relationships of bursid gastropods based on extensive and representative ta...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2020.107040

    authors： Sanders MT,Merle D,Laurin M,Bonillo C,Puillandre N

    更新日期：2021-03-01 00:00:00

  • Peripatric speciation of an endemic species driven by Pleistocene climate change: The case of the Mexican prairie dog (Cynomys mexicanus).

    abstract：:The hypothesis that endemic species could have originated by the isolation and divergence of peripheral populations of widespread species can be tested through the use of ecological niche models (ENMs) and statistical phylogeography. The joint use of these tools provides complementary perspectives on historical dynami...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 历史文章,杂志文章

    doi：10.1016/j.ympev.2015.08.027

    authors： Castellanos-Morales G,Gámez N,Castillo-Gámez RA,Eguiarte LE

    更新日期：2016-01-01 00:00:00

  • Monophyly and relationships of wrens (Aves: Troglodytidae): a congruence analysis of heterogeneous mitochondrial and nuclear DNA sequence data.

    abstract：:The wrens (Aves: Troglodytidae) are a group of primarily New World insectivorous birds, the monophyly of which has long been recognized, but whose intergeneric relationships are essentially unknown. In order to test the monophyly of the group, and to attempt to resolve relationships among genera within it, sequences f...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2003.08.005

    authors： Barker FK

    更新日期：2004-05-01 00:00:00

  • Crescendo, diminuendo and subito of the trumpets: winds of change in the concerted evolution between flowers and pollinators in Salpichroa (Solanaceae).

    abstract：:'Gradual' vs 'punctuated' and 'unidirectional' (only lengthening) vs. 'bidirectional'(lengthenings and shortenings) modes of evolution are explanations that compete to explain adaptive changes of flower tube length in angiosperm. The nightshade genus Salpichroa Miers, with 21 species mostly growing in the tropical And...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2018.11.020

    authors： Ibañez AC,Moré M,Salazar G,Leiva S,Barboza GE,Cocucci AA

    更新日期：2019-03-01 00:00:00

  • Rediscovery of Protohynobius puxiongensis (Caudata: Hynobiidae) and its phylogenetic position based on complete mitochondrial genomes.

    abstract：:The mysterious Asian hynobiid salamander, Protohynobius puxiongensis, was described based on a single specimen collected in 1965 and never found again since then. Because the specimen had an internasal bone, Pr. puxiongensis was thought to retain a primitive character lost by a common ancestor of all other hynobiid sa...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2009.12.011

    authors： Peng R,Zhang P,Xiong JL,Gu HJ,Zeng XM,Zou FD

    更新日期：2010-07-01 00:00:00

  • Phylogeny of the leafy liverwort Ptilidium: cryptic speciation and shared haplotypes between the Northern and Southern Hemispheres.

    abstract：:The small, phylogenetically isolated liverwort genus Ptilidium has been regarded as of cool-Gondwanic origin with the bipolar, terrestrial Ptilidium ciliare giving rise to the Northern Hemisphere epiphytes Ptilidium pulcherrimum and Ptilidium californicum. This hypothesis is examined using a dataset including three ch...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2010.10.002

    authors： Kreier HP,Feldberg K,Mahr F,Bombosch A,Schmidt AR,Zhu RL,von Konrat M,Shaw B,Shaw AJ,Heinrichs J

    更新日期：2010-12-01 00:00:00

  • Phylogeny of Drosophilinae (Diptera: Drosophilidae), with comments on combined analysis and character support.

    abstract：:Drosophilidae (Diptera) is a diverse, cosmopolitan family of flies. Here, we present a combined analysis phylogeny of Drosophilinae, one of the two subfamilies of Drosophilidae, based on data from six different data partitions, including both molecular and morphological characters. Although our data show support for t...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/s1055-7903(02)00226-9

    authors： Remsen J,O'Grady P

    更新日期：2002-08-01 00:00:00

  • Molecular phylogenetics and historical biogeography of Hawaiian Dryopteris (Dryopteridaceae).

    abstract：:The fern genus Dryopteris (Dryopteridaceae) is represented in the Hawaiian Islands by 18 endemic taxa and one non-endemic, native species. The goals of this study were to determine whether Dryopteris in Hawai'i is monophyletic and to infer the biogeographical origins of Hawaiian Dryopteris by determining the geographi...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2004.11.001

    authors： Geiger JM,Ranker TA

    更新日期：2005-02-01 00:00:00

  • Phylogeny and character behavior in the family Lemuridae.

    abstract：:A phylogenetic analysis of the family Lemuridae was accomplished using multiple gene partitions and morphological characters. The results of the study suggest that several nodes in the lemurid phylogeny can be robustly resolved; however, the relationships of the species within the genus Eulemur are problematically non...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.1999.0723

    authors： Wyner Y,DeSalle R,Absher R

    更新日期：2000-04-01 00:00:00

  • Multigene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes.

    abstract：:Despite its great diversity and biomedical importance, the rodent subfamily Murinae is poorly resolved phylogenetically. We present the first cladistic analysis sampling multiple representatives of most major groups based on DNA sequence for three nuclear (GHR, RAG1, and AP5) and one mitochondrial (COII and parts of C...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2005.04.016

    authors： Steppan SJ,Adkins RM,Spinks PQ,Hale C

    更新日期：2005-11-01 00:00:00

  • Integrative description of bisexual Paramacrobiotus experimentalis sp. nov. (Macrobiotidae) from republic of Madagascar (Africa) with microbiome analysis.

    abstract：:In a moss samples collected on Madagascar two populations of Paramacrobiotus experimentalis sp. nov. were found. Paramacrobiotus experimentalis sp. nov. with the presence of a microplacoid and areolatus type of eggs is similar to Pam. danielae, Pam. garynahi, Pam. hapukuensis, Pam. peteri, Pam. rioplatensis and Pam. s...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2019.106730

    authors： Kaczmarek Ł,Roszkowska M,Poprawa I,Janelt K,Kmita H,Gawlak M,Fiałkowska E,Mioduchowska M

    更新日期：2020-04-01 00:00:00

  • Global phylogeny and new classification of the Rapaninae (Gastropoda: Muricidae), dominant molluscan predators on tropical rocky seashores.

    abstract：:The monophyly of the muricid subfamily Rapaninae has recently been confirmed with molecular techniques, but its composition and the relationships among its constituent genera remain unclear. We use four genes (28S rRNA, 12S rRNA, 16S rRNA and cytochrome c oxidase subunit I, COI) to construct a Bayesian phylogeny of 80...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2012.09.014

    authors： Claremont M,Vermeij GJ,Williams ST,Reid DG

    更新日期：2013-01-01 00:00:00

  • From America to Eurasia: a multigenomes history of the genus Abies.

    abstract：:The origin of conifer genera, the main components of mountain temperate and boreal forests, was deemed to arise in the Mesozoic, although paleontological records and molecular data point to a recent diversification, presumably related to Neogene cooling. The geographical area(s) where the modern lines of conifers emer...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2018.03.009

    authors： Semerikova SA,Khrunyk YY,Lascoux M,Semerikov VL

    更新日期：2018-08-01 00:00:00