Molecular phylogenetics and biogeography of Neotropical tanagers in the genus Tangara.

Abstract:

:Species in the genus Tangara are distributed throughout the New World tropics and vary in their morphology, behavior, and ecology. We used data from the cytochrome b and ND 2 genes to provide the first phylogenetic perspective on the evolution of this diversity. Reconstructions based on parsimony, maximum likelihood, and Bayesian approaches were largely congruent. The genus is monophyletic and consists of two main clades. Within these clades, DNA sequence data confirm the monophyly of most previously recognized species groups within Tangara, indicating general concordance between molecular data and impressions based on geographic distribution, morphology, and behavior. Within some currently recognized species, levels of DNA sequence variation are larger than expected, suggesting multiple taxa may be involved. In contrast, some currently recognized species are only weakly differentiated from their sister species. Biogeographic analyses indicate that many early speciation events occurred in the Andes. More recently, dispersal events followed by subsequent speciation have occurred in other geographic areas of the Neotropics. Assuming a molecular clock, most speciation events occurred well before Pleistocene climatic cycles. The time frame of Tangara speciation corresponds more closely to a period of continued uplift in the Andes during the late Miocene and Pliocene.

journal_name

Mol Phylogenet Evol

authors

Burns KJ,Naoki K

doi

10.1016/j.ympev.2004.02.013

keywords:

subject

Has Abstract

pub_date

2004-09-01 00:00:00

pages

838-54

issue

3

eissn

1055-7903

issn

1095-9513

pii

S1055790304000764

journal_volume

32

pub_type

杂志文章
  • 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

  • Multi-locus fossil-calibrated phylogeny, biogeography and a subgeneric revision of the Margaritiferidae (Mollusca: Bivalvia: Unionoida).

    abstract::The taxonomy and biogeographic history of the bivalve family Margaritiferidae are controversial because previous molecular studies did not provide a well-resolved phylogenetic framework for these enigmatic freshwater mussels that have extensive but disjunct distribution in North America, Eurasia and North Africa. In t...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.07.020

    authors: Bolotov IN,Vikhrev IV,Bespalaya YV,Gofarov MY,Kondakov AV,Konopleva ES,Bolotov NN,Lyubas AA

    更新日期:2016-10-01 00:00:00

  • Phylogenetics of a recent radiation in the mallards and allies (Aves: Anas): inferences from a genomic transect and the multispecies coalescent.

    abstract::Reconstructing species trees by incorporating information from many independent gene trees reduces the confounding influence of stochastic lineage sorting. Such analyses are particularly important for taxa that share polymorphisms due to incomplete lineage sorting or introgressive hybridization. We investigated phylog...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.08.008

    authors: Lavretsky P,McCracken KG,Peters JL

    更新日期:2014-01-01 00:00:00

  • A mitochondrial control region and cytochrome b phylogeny of sika deer (Cervus nippon) and report of tandem repeats in the control region.

    abstract::Sika deer (Cervus nippon Temminck) are endemic to mainland and insular Asia. Numerous subspecies have been named, but they are not quantitatively well defined. Portions of the mitochondrial cytochrome b gene (450 bp) and control region (512 bp) were sequenced from 28 individuals belonging to five sika subspecies and t...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1998.0593

    authors: Cook CE,Wang Y,Sensabaugh G

    更新日期:1999-06-01 00:00:00

  • Phylogeny of Drosophila and related genera: conflict between molecular and anatomical analyses.

    abstract::Drosophila species are extensively used in biological research; yet, important phylogenetic relationships within the genus and with related genera remain unresolved. The combined data for three genes (Adh, Sod, and Gpdh) statistically resolves outstanding issues. We define the genus Drosophila inclusively so as to inc...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1999.0657

    authors: Kwiatowski J,Ayala FJ

    更新日期:1999-11-01 00:00:00

  • Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes.

    abstract::Two different methods of using paralogous genes for phylogenetic inference have been proposed: reconciled trees (or gene tree parsimony) and uninode coding. Gene tree parsimony suffers from 10 serious problems, including differential weighting of nucleotide and gap characters, undersampling which can be misinterpreted...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(02)00033-7

    authors: Simmons MP,Freudenstein JV

    更新日期:2002-06-01 00:00:00

  • Phylogeny and systematics of Chiroxiphia and Antilophia manakins (Aves, Pipridae).

    abstract::Chiroxiphia and Antilophia manakins are recognized as closely related genera. Nonetheless, Chiroxiphia has been recovered as paraphyletic in some studies with limited taxonomic coverage. This genus currently comprises five species, although this arrangement is still unsettled. Chiroxiphia pareola is the most widesprea...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.06.016

    authors: Silva SM,Agne CE,Aleixo A,Bonatto SL

    更新日期:2018-10-01 00:00:00

  • Systematics of snow voles (Chionomys, Arvicolinae) revisited.

    abstract::To elucidate the evolutionary history of snow voles, genus Chionomys, we studied the phylogeography of Chionomysnivalis across its range and investigated its relationships with two congeneric species, Chionomysgud and Chionomysroberti, using independent molecular markers. Analyses were based on mitochondrial (~940 bp ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.12.004

    authors: Yannic G,Burri R,Malikov VG,Vogel P

    更新日期:2012-03-01 00:00:00

  • Phylogeography of the bark beetle Dendroctonus mexicanus Hopkins (Coleoptera: Curculionidae: Scolytinae).

    abstract::Dendroctonus mexicanus is polyphagous within the Pinus genus and has a wide geographical distribution in Mexico and Guatemala. We examined the pattern of genetic variation across the range of this species to explore its demographic history and its phylogeographic pattern. Analysis of the mtDNA sequences of 173 individ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.09.005

    authors: Anducho-Reyes MA,Cognato AI,Hayes JL,Zúñiga G

    更新日期:2008-12-01 00:00:00

  • Phylogeny and host-plant association in the leaf beetle genus Trirhabda LeConte (Coleoptera: Chrysomelidae).

    abstract::The leaf beetle genus Trirhabda contains 26 described species from the United States and Canada, feeding on host plants from the families Asteraceae and Hydrophyllaceae. In this study, we present a phylogeny for the genus that was reconstructed from mitochondrial COI and 12S rRNA fragments, nuclear ITS2 rRNA, and morp...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2004.02.010

    authors: Swigonová Z,Kjer KM

    更新日期:2004-07-01 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

  • Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization.

    abstract::Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life hi...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2020.107023

    authors: Sharanowski BJ,Ridenbaugh RD,Piekarski PK,Broad GR,Burke GR,Deans AR,Lemmon AR,Moriarty Lemmon EC,Diehl GJ,Whitfield JB,Hines HM

    更新日期:2021-03-01 00:00:00

  • Acrobat ants go global--origin, evolution and systematics of the genus Crematogaster (Hymenoptera: Formicidae).

    abstract::This study unravels the evolution and biogeographic history of the globally distributed ant genus Crematogaster on the basis of a molecular phylogeny, reconstructed from five nuclear protein-coding genes and a total of 3384 bp of sequence data. A particular emphasis is placed on the evolutionary history of these ants ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2012.06.028

    authors: Blaimer BB

    更新日期:2012-11-01 00:00:00

  • AFLP and breeding system studies indicate vicariance origin for scattered populations and enigmatic low fecundity in the Moroccan endemic Hypochaeris angustifolia (Asteraceae), sister taxon to all of the South American Hypochaeris species.

    abstract::We used Amplified Fragment Length Polymorphism markers (AFLP) and breeding system studies to investigate the population structure and reproductive biology of Hypochaeris angustifolia (Asteraceae: Cichorieae). This species is endemic to altiplanos of the Atlas Mountains (Morocco) where it occurs in scattered population...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2009.06.008

    authors: Terrab A,Ortiz MA,Talavera M,Ariza MJ,Moriana Mdel C,García-Castaño JL,Tremetsberger K,Stuessy TF,Baeza CM,Urtubey E,Ruas Cde F,Casimiro-Soriguer R,Balao F,Gibbs PE,Talavera S

    更新日期:2009-10-01 00:00:00

  • A large-scale systematic framework of Chinese snakes based on a unified multilocus marker system.

    abstract::Snakes are one of the most diverse groups of terrestrial vertebrates, with approximately 3500 extant species. A robust phylogeny and taxonomy of snakes is crucial for us to know, study and protect them. For a large group such as snakes, broad-scale phylogenetic reconstructions largely rely on data integration. Increas...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2020.106807

    authors: Li JN,Liang D,Wang YY,Guo P,Huang S,Zhang P

    更新日期:2020-07-01 00:00:00

  • Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions.

    abstract::Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.10.008

    authors: Zhu T,Xu PZ,Liu JP,Peng S,Mo XC,Gao LZ

    更新日期:2014-01-01 00:00:00

  • Does dispersal across an aquatic geographic barrier obscure phylogeographic structure in the diamond-backed watersnake (Nerodia rhombifer)?

    abstract::The impact of barriers to dispersal and gene flow is often inferred to be the primary cause of lineage divergence and phylogeographic structure in terrestrial organisms. In particular, the Mississippi River has been implicated as a barrier to gene flow in many species, including aquatic taxa. However, if barriers are ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2010.07.015

    authors: Brandley MC,Guiher TJ,Pyron RA,Winne CT,Burbrink FT

    更新日期:2010-11-01 00:00:00

  • Starting to unravel the toxoglossan knot: molecular phylogeny of the "turrids" (Neogastropoda: Conoidea).

    abstract::The superfamily Conoidea is one of the most speciose groups of marine mollusks, with estimates of about 340 recent valid genera and subgenera, and 4000 named living species. Previous classifications were based on shell and anatomical characters, and clades and phylogenetic relationships are far from well assessed. Bas...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2007.11.007

    authors: Puillandre N,Samadi S,Boisselier MC,Sysoev AV,Kantor YI,Cruaud C,Couloux A,Bouchet P

    更新日期:2008-06-01 00:00:00

  • Analysis of the complete mitochondrial DNA from Anopheles funestus: an improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution.

    abstract::Virtually no information regarding timing of deep lineage divergences within mosquito family (Culicidae) exists, which poses an important problem in the postgenomic era. To address this issue, the complete 15,354 bp mitochondrial genome of Anopheles funestus was assembled from both mtDNA and cDNA sequences generated f...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2006.01.006

    authors: Krzywinski J,Grushko OG,Besansky NJ

    更新日期:2006-05-01 00:00:00

  • Systematics of holometabolous insect orders based on 18S ribosomal RNA.

    abstract::Phylogenetic relationships of 19 species representing nine holometabolous insect orders and three outgroup orders were examined using sequence data from two-thirds of the 18S nuclear ribosomal RNA molecule. Of 1330 aligned nucleotide sites in 19 taxa, 460 were variable and used for phylogenetic analysis. Parsimony ana...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1993.1013

    authors: Pashley DP,McPheron BA,Zimmer EA

    更新日期:1993-06-01 00:00:00

  • Phylogenetic analysis revealed reticulate evolution of allotetraploid Elymus ciliaris.

    abstract::Increasing evidence has shown the complex and dynamic nature of polyploids. Two single copy nuclear genes were used to explore genome evolutionary dynamics and the origin of tetraploid E. ciliaris: the phosphoglycerate kinase (PGK1) and the second largest subunit of RNA polymerase II (RPB2) together with a chloroplast...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.06.023

    authors: Hu Q,Yan C,Sun G

    更新日期:2013-12-01 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 phylogenetics of Australo-Papuan possums and gliders (family Petauridae).

    abstract::Phylogenetic relationships within the possums of the family Petauridae, including their affinities with the family Pseudocheiridae, were inferred from DNA sequences obtained for the mitochondrial ND2 gene (1040 bp) combined with previously published partial 12S rDNA sequences. Short, deep internodes characterize some ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.2001.0960

    authors: Osborne MJ,Christidis L

    更新日期:2001-08-01 00:00:00

  • The human progesterone receptor shows evidence of adaptive evolution associated with its ability to act as a transcription factor.

    abstract::The gene encoding the progesterone receptor (PGR) acts as a transcription factor, and participates in the regulation of reproductive processes including menstruation, implantation, pregnancy maintenance, parturition, mammary development, and lactation. Unlike other mammals, primates do not exhibit progesterone withdra...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2007.12.026

    authors: Chen C,Opazo JC,Erez O,Uddin M,Santolaya-Forgas J,Goodman M,Grossman LI,Romero R,Wildman DE

    更新日期:2008-05-01 00:00:00

  • A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics.

    abstract::Austropurcellia, a genus of dispersal-limited arachnids endemic to isolated patches of coastal rainforest in Queensland, Australia, has a remarkable biogeographic history. The genus is a member of the family Pettalidae, which has a classical temperate Gondwanan distribution; previous work has suggested that Austropurc...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.06.029

    authors: Oberski JT,Sharma PP,Jay KR,Coblens MJ,Lemon KA,Johnson JE,Boyer SL

    更新日期:2018-10-01 00:00:00

  • A cladistic analysis of mitochondrial ribosomal DNA from the Bovidae.

    abstract::There is a huge data base of genetic information for the domestic artiodactyl species Bos taurus (cow), Ovis aries (sheep), and Capra hircus (goat). However, the phylogenetic relationships of these economically critical taxa and their close relatives, family Bovidae, remain for the most part unresolved. In this report...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1997.0402

    authors: Gatesy J,Amato G,Vrba E,Schaller G,DeSalle R

    更新日期:1997-06-01 00:00:00

  • Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade.

    abstract::The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined anal...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2020.106960

    authors: Natusch DJD,Esquerré D,Lyons JA,Hamidy A,Lemmon AR,Lemmon EM,Riyanto A,Keogh JS,Donnellan S

    更新日期:2020-09-18 00:00:00

  • Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae).

    abstract::Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonie...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.01.023

    authors: Fonseca LHM,Lohmann LG

    更新日期:2018-06-01 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

  • Detection of the new cosmopolitan genus Thermoleptolyngbya (Cyanobacteria, Leptolyngbyaceae) using the 16S rRNA gene and 16S-23S ITS region.

    abstract::Cyanobacteria are widespread prokaryotes that are able to live in extreme conditions such as thermal springs. Strains attributable to the genus Leptolyngbya are among the most common cyanobacteria sampled from thermal environments. Leptolyngbya is a character-poor taxon that was demonstrated to be polyphyletic based o...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.08.010

    authors: Sciuto K,Moro I

    更新日期:2016-12-01 00:00:00