当前位置： SCI文献检索 > MOLECULAR PHYLOGENETICS AND EVOLUTION期刊下所有文献 > Species trees for spiny lizards (genus Sceloporus): identifying points of concordance and conflict between nuclear and mitochondrial data.

Species trees for spiny lizards (genus Sceloporus): identifying points of concordance and conflict between nuclear and mitochondrial data.

Abstract：

:Spiny lizards (genus Sceloporus) represent one of the most diverse and species rich clades of squamate reptiles in continental North America. Sceloporus contains 90+ species, which are partitioned into 21 species groups containing anywhere from one to 15 species. Despite substantial progress towards elucidating the phylogeographic patterns for many species of Sceloporus, efforts to resolve the phylogenetic relationships among the major species groups remain limited. In this study, the phylogenetic relationships of 53 species of Sceloporus, representing all 21 species groups, are estimated based on four nuclear genes (BDNF, PNN, R35, RAG-1; >3.3 kb) and contrasted with a new mitochondrial DNA genealogy based on six genes (12S, ND1, ND4, and the histidine, serine, and leucine tRNA genes; >2.5 kb). Species trees estimated from the nuclear loci using data concatenation or a coalescent-based inference method result in concordant topologies, but the coalescent approach provides lower resolution and support. When comparing nuclear versus mtDNA-based topologies for Sceloporus species groups, conflicting relationships outnumber concordant relationships. Incongruence is not restricted to weak or unresolved nodes as might be expected under a scenario of rapid diversification, but extends to conflicts involving strongly support clades. The points of concordance and conflict between the nuclear and mtDNA data are discussed, and arguments for preferring the species trees estimated from the multilocus nuclear data are presented.

journal_name

Mol Phylogenet Evol

journal_title

Molecular phylogenetics and evolution

authors

Leaché AD

doi

10.1016/j.ympev.2009.09.006

subject

Has Abstract

pub_date

2010-01-01 00:00:00

pages

162-71

issue

1

eissn

1055-7903

issn

1095-9513

pii

S1055-7903(09)00363-7

journal_volume

54

pub_type

杂志文章

相关文献

MOLECULAR PHYLOGENETICS AND EVOLUTION文献大全
  • Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa.

    abstract：:The deepest-level relationships amongst Euglenozoa remain poorly resolved, despite a rich history of morphological examination and numerous molecular phylogenetic studies of small subunit ribosomal RNA (SSU rRNA) data. We address this question using two nuclear-encoded proteins, the cytosolic isoforms of heat shock pr...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/s1055-7903(03)00177-5

    authors： Simpson AG,Roger AJ

    更新日期：2004-01-01 00:00:00

  • Phylogenetic relationships of the Asian palm civets (Hemigalinae & Paradoxurinae, Viverridae, Carnivora).

    abstract：:The Viverridae (Mammalia, Carnivora), one of the least studied groups of carnivorans, include two subfamilies of Asian palm civets: Hemigalinae and Paradoxurinae. The relationships between and within these two subfamilies have never been thoroughly tested using an extensive molecular sample set. In this study, we gath...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2008.03.026

    authors： Patou ML,Debruyne R,Jennings AP,Zubaid A,Rovie-Ryan JJ,Veron G

    更新日期：2008-06-01 00:00:00

  • Random local neighbor joining: a new method for reconstructing phylogenetic trees.

    abstract：:We have developed a new method for reconstructing phylogenetic trees called random local neighbor-joining (RLNJ). Our method is different from the neighbor-joining method (NJ) of Saitou and Nei and affords a more thorough sampling of solution space by randomly searching for local pair of neighbors in each step. Result...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2008.01.019

    authors： Zhang W,Sun Z

    更新日期：2008-04-01 00:00:00

  • Molecular markers reveal genetic isolation and phylogeography of the S and F intersterility groups of the wood-decay fungus Heterobasidion annosum.

    abstract：:The root-rot fungus Heterobasidion annosum (Fr.) Bref. species complex consists of three intersterility groups (S, F, and P), separated by their host affinity. The phylogenetic relationship of the species complex was studied, with the focus on the S and F groups, by comparing DNA sequences of four nuclear gene fragmen...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/s1055-7903(03)00087-3

    authors： Johannesson H,Stenlid J

    更新日期：2003-10-01 00:00:00

  • Model-based multi-locus estimation of decapod phylogeny and divergence times.

    abstract：:Phylogenetic relationships among all of the major decapod infraorders have never been estimated using molecular data, while morphological studies produce conflicting results. In the present study, the phylogenetic relationships among the decapod basal suborder Dendrobranchiata and all of the currently recognized decap...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2005.06.021

    authors： Porter ML,Pérez-Losada M,Crandall KA

    更新日期：2005-11-01 00:00:00

  • Phylogenomics, life history and morphological evolution of ophiocomid brittlestars.

    abstract：:Brittlestars in the family Ophiocomidae are large and colourful inhabitants of tropical shallow water habitats across the globe. Here we use targeted capture and next-generation sequencing to generate robust phylogenomic trees for 39 of the 43 species in order to test the monophyly of existing genera. The large genus ...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2018.10.003

    authors： O'Hara TD,Hugall AF,Cisternas PA,Boissin E,Bribiesca-Contreras G,Sellanes J,Paulay G,Byrne M

    更新日期：2019-01-01 00:00:00

  • Molecular phylogeny of the nettle family (Urticaceae) inferred from multiple loci of three genomes and extensive generic sampling.

    abstract：:Urticaceae is one of the larger Angiosperm families, but relationships within it remain poorly known. This study presents the first densely sampled molecular phylogeny of Urticaceae, using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) to analyze the DNA sequence data from two nuclear (ITS...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2013.06.022

    authors： Wu ZY,Monro AK,Milne RI,Wang H,Yi TS,Liu J,Li DZ

    更新日期：2013-12-01 00:00:00

  • Mitochondrial and nuclear multilocus phylogeny of Rhipicephalus ticks from Kenya.

    abstract：:The morphological diversity of African ticks of the genus Rhipicephalus and subgenus Boophilus have been studied in detail. However, their taxonomy remains poorly resolved with limited molecular studies performed to improve inter-species discrimination. Herein, ribosomal cytochrome c oxidase I (COI), 12S ribosomal DNA...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2019.106579

    authors： Kanduma EG,Bishop RP,Githaka NW,Skilton RA,Heyne H,Mwacharo JM

    更新日期：2019-11-01 00:00:00

  • A molecular perspective on the phylogenetic relationships of the barbeled minnows, historically assigned to the genus Hybopsis (Cyprinidae: Cypriniformes).

    abstract：:Allozyme products of 32 gene loci were compared for the North American cyprinid fishes Campostoma oligolepis, Cyprinella galactura, Cyprinella monacha, Erimystax cahni, E. dissimilis, E. insignis, E. x-punctatus, Hybopsis amblops, H. labrosa, H. rubriforns, H. zanema, Macrhybopsis aestivalis, M. gelida, M. meeki, Noco...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.1993.1018

    authors： Dimmick WW

    更新日期：1993-09-01 00:00:00

  • Plastome organization, genome-based phylogeny and evolution of plastid genes in Podophylloideae (Berberidaceae).

    abstract：:Species of Podophylloideae (Berberidaceae, Ranunculales) are of great pharmacogenetic importance and represent the classic biogeographic disjunction between eastern Asia (EA; 10 ssp.) and eastern North America (ENA; 2 ssp.). However, previous molecular studies of this group suffered from low phylogenetic resolution an...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2018.07.001

    authors： Ye WQ,Yap ZY,Li P,Comes HP,Qiu YX

    更新日期：2018-10-01 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

  • Sympatric lineages in the Mantidactylus ambreensis complex of Malagasy frogs originated allopatrically rather than by in-situ speciation.

    abstract：:Madagascar's biota is characterized by a high degree of microendemism at different taxonomic levels, but how colonization and in-situ speciation contribute to the assembly of local species communities has rarely been studied on this island. Here we analyze the phylogenetic relationships of riparian frogs of the Mantid...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2019.106700

    authors： Rasolonjatovo SM,Scherz MD,Hutter CR,Glaw F,Rakotoarison A,Razafindraibe JH,Goodman SM,Raselimanana AP,Vences M

    更新日期：2020-03-01 00:00:00

  • High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae.

    abstract：:A new paradigm has slowly emerged regarding the diversification of bryophytes, with inferences from molecular data highlighting a dynamic evolution of their genome. However, comparative studies of expressed genes among closely related taxa is so far missing. Here we contrast the dimensions of the vegetative transcript...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2020.106965

    authors： Rahmatpour N,Perera NV,Singh V,Wegrzyn JL,Goffinet B

    更新日期：2021-01-01 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

  • Conflicting signal within a single gene confounds syllid phylogeny (Syllidae, Annelida).

    abstract：:The phylogenetic relationships within the family Syllidae have been analyzed previous to this study and a new subfamily (Anoplosyllinae) defined. However, the monophyly of the family Syllidae was not well-supported. A conflict between the different molecular data sets combined in previous preceding molecular analyses ...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2010.01.012

    authors： Aguado MT,Bleidorn C

    更新日期：2010-06-01 00:00:00

  • The distribution of group I introns in lichen algae suggests that lichenization facilitates intron lateral transfer.

    abstract：:The nuclear-encoded small subunit ribosomal DNA gene of many lichen-forming green algae in the genus Trebouxia contains a group I intron at Escherichia coli genic position 1512. We studied the evolutionary history of the 1512 intron in Trebouxia spp. (Trebouxiophyceae) by analyzing intron and "host" cell phylogenies. ...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.1999.0711

    authors： Friedl T,Besendahl A,Pfeiffer P,Bhattacharya D

    更新日期：2000-03-01 00:00:00

  • Cleaners among wrasses: Phylogenetics and evolutionary patterns of cleaning behavior within Labridae.

    abstract：:Cleaner fishes remove and consume ectoparasites and are often categorized by whether they perform this behavior: (1) predominately as juveniles, (2) facultatively throughout ontogeny, or (3) obligately. Through a literature search, we confirmed that with at least 58 species exhibiting cleaning behavior, the Labridae (...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2015.09.006

    authors： Baliga VB,Law CJ

    更新日期：2016-01-01 00:00:00

  • Multiple patterns of rDNA evolution following polyploidy in Oryza.

    abstract：:Ribosomal ITS sequences are commonly used for phylogenetic reconstruction because they are included in rDNA repeats, and hence are ubiquitous and present in high copy number. Ribosomal rDNA repeats often undergo rapid concerted evolution within and between arrays. Interspecific hybridization merges divergent repeat ty...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2009.10.023

    authors： Bao Y,Wendel JF,Ge S

    更新日期：2010-04-01 00:00:00

  • Late Miocene diversification and phylogenetic relationships of the huge toads in the Rhinella marina (Linnaeus, 1758) species group (Anura: Bufonidae).

    abstract：:We investigated the phylogeny and biogeography of the Rhinella marina group, using molecular, morphological, and skin-secretion data, contributing to an understanding of Neotropical faunal diversification. The maximum-parsimony and Bayesian analyzes of the combined data recovered a monophyletic R. marina group. Molecu...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2010.08.025

    authors： Maciel NM,Collevatti RG,Colli GR,Schwartz EF

    更新日期：2010-11-01 00:00:00

  • Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema species complex (Serpentes: Elapidae).

    abstract：:New world coralsnakes of the genus Micrurus are a diverse radiation of highly venomous and brightly colored snakes that range from North Carolina to Argentina. Species in this group have played central roles in developing and testing hypotheses about the evolution of mimicry and aposematism. Despite their diversity an...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2020.106770

    authors： Reyes-Velasco J,Adams RH,Boissinot S,Parkinson CL,Campbell JA,Castoe TA,Smith EN

    更新日期：2020-06-01 00:00:00

  • The Cryptocercus punctulatus species complex (Dictyoptera: Cryptocercidae) in the eastern United States: comparison of cuticular hydrocarbons, chromosome number, and DNA sequences.

    abstract：:The goal of the current study was to determine if cuticular hydrocarbons could be used to empirically delimit taxa within the Cryptocercus punctulatus species complex in the eastern United States. Cockroaches were collected from rotting logs in 22 locations across four states. Hydrocarbon phenotypes and two mitochondr...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2008.03.011

    authors： Everaerts C,Maekawa K,Farine JP,Shimada K,Luykx P,Brossut R,Nalepa CA

    更新日期：2008-06-01 00:00:00

  • Detection of homologous recombination among bacteriophage P2 relatives.

    abstract：:Sequencing of five late genes from 18 isolates of P2-like bacteriophages showed that these are at least 96% identical to the genes of phage P2. A maximum-parsimony phylogenetic analysis of these genes showed excess homoplasy of a magnitude three to six times higher than that expected. Examination of the distribution o...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.2001.1020

    authors： Nilsson AS,Haggård-Ljungquist E

    更新日期：2001-11-01 00:00:00

  • Spiny trapdoor spiders (Euoplos) of eastern Australia: Broadly sympatric clades are differentiated by burrow architecture and male morphology.

    abstract：:Spiders of the infraorder Mygalomorphae are fast becoming model organisms for the study of biogeography and speciation. However, these spiders can be difficult to study in the absence of fundamental life history information. In particular, their cryptic nature hinders comprehensive sampling, and linking males with con...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2018.01.022

    authors： Wilson JD,Hughes JM,Raven RJ,Rix MG,Schmidt DJ

    更新日期：2018-05-01 00:00:00

  • Molecular phylogeny of the Southeast Asian freshwater fish family Botiidae (Teleostei: Cobitoidea) and the origin of polyploidy in their evolution.

    abstract：:The freshwater fish family Botiidae is represented by seven genera on the Indian subcontinent and in East and Southeast Asia and includes diploid as well as evolutionary tetraploid species. We present a phylogeny of Botiidae including 33 species representing all described genera using the mitochondrial cytochrome b an...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2005.09.018

    authors： Slechtová V,Bohlen J,Freyhof J,Ráb P

    更新日期：2006-05-01 00:00:00

  • Evidence of a cenozoic Betic-Kabilian connection based on freshwater fish phylogeography (Luciobarbus, Cyprinidae).

    abstract：:The phylogenetic relationships among 26 species of the subgenus Luciobarbus were examined through comparison of the complete sequence of the mitochondrial genes ATPase 6 and 8 and cytochrome b. The monophyletic condition of the Luciobarbus subgenus was confirmed by several data treatment methods. Findings indicate a c...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.2000.0876

    authors： Machordom A,Doadrio I

    更新日期：2001-02-01 00:00:00

  • Rhodinocichla rosea is an emberizid (Aves; Passeriformes) based on mitochondrial DNA analyses.

    abstract：:The systematic position of the avian species Rhodinocichla rosea is unclear. Recent opinions are that it is either a mockingbird (family Mimidae) or a tanager (Thraupinae; Emberizidae). In either case, it would be an atypical member of the family. We sequenced approximately 600 bases of the mitochondrial cytochrome ox...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.1997.0426

    authors： Seutin G,Bermingham E

    更新日期：1997-10-01 00:00:00

  • Amino acid vs. nucleotide characters: challenging preconceived notions.

    abstract：:The 567-terminal analysis of atpB, rbcL, and 18S rDNA was used as an empirical example to test the use of amino acid vs. nucleotide characters for protein-coding genes at deeper taxonomic levels. Nucleotides for atpB and rbcL had 6.5 times the amount of possible synapomorphy as amino acids. Based on parsimony analyses...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/s1055-7903(02)00202-6

    authors： Simmons MP,Ochoterena H,Freudenstein JV

    更新日期：2002-07-01 00:00:00

  • Biogeography and speciation of a direct developing frog from the coastal arid zone of Western Australia.

    abstract：:Within the southwestern Australian biodiversity hotspot, the Shark Bay region displays high levels of plant and animal endemism, particularly in the herpetofauna. The region has been subjected to dramatic climatic fluctuations and has been geologically active from the Late Miocene to the present. The myobatrachid frog...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2007.05.023

    authors： Edwards DL

    更新日期：2007-11-01 00:00:00

  • Quaternary range dynamics and polyploid evolution in an arid brushland plant species (Melampodium cinereum, Asteraceae).

    abstract：:Pleistocene climatic fluctuations played a principal role for range formation and population history of many biota, including regions not directly affected by glaciations, such as the arid habitats of the southwestern United States and adjacent Mexico. Specifically, drought-adapted species are expected to have persist...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2009.10.010

    authors： Rebernig CA,Weiss-Schneeweiss H,Schneeweiss GM,Schönswetter P,Obermayer R,Villaseñor JL,Stuessy TF

    更新日期：2010-02-01 00:00:00

  • Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae).

    abstract：:Open-habitat chats (genera Myrmecocichla, Cercomela, Oenanthe and relative) are a morphologically and ecologically cohesive group of genera with unclear phylogenetic relationships. They are distributed mostly in open, arid and/or rocky habitats of Africa and Eurasia. Here, we present the most comprehensive molecular p...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2012.05.011

    authors： Aliabadian M,Kaboli M,Förschler MI,Nijman V,Chamani A,Tillier A,Prodon R,Pasquet E,Ericson PG,Zuccon D

    更新日期：2012-10-01 00:00:00