Phylogeny of the Falconidae (Aves): a comparison of the efficacy of morphological, mitochondrial, and nuclear data.

Abstract:

:We sequenced 2800+ bp of the RAG-1 exon for representatives of all the currently recognized genera in the avian family Falconidae. A phylogenetic analysis of these data was compared to prior analyses of mitochondrial (cytochrome-b) and morphological (syringeal) data. The nuclear RAG-1 sequences produced results that were in agreement with the morphological results, but differed from the mitochondrial results with regard to monophyly of the genus Micrastur. A reanalysis of the cytochrome-b (cyt-b) data suggested that this result was due to heterogeneity in base composition. Comparisons of data quality and quantity across the three data sets indicate that the nuclear DNA sequences and the morphological data have similar consistency and retention indices as well as noise distributions that are superior to those of cyt-b. However, the RAG-1 data identify more nodes with high bootstrap support indices than do either morphology or mitochondrial sequences. In the final assessment, RAG-1 sequences were superior in phylogenetic utility both to syringeal morphology (because of sheer number of characters) and to cyt-b sequences (because of reduced noise and homogeneity of base composition, but in spite of having many fewer characters).

journal_name

Mol Phylogenet Evol

authors

Griffiths CS,Barrowclough GF,Groth JG,Mertz L

doi

10.1016/j.ympev.2003.11.019

keywords:

subject

Has Abstract

pub_date

2004-07-01 00:00:00

pages

101-9

issue

1

eissn

1055-7903

issn

1095-9513

pii

S105579030300441X

journal_volume

32

pub_type

杂志文章
  • Molecular phylogeny of some European heteronemertean (Nemertea) species and the monophyletic status of Riseriellus, Lineus, and Micrura.

    abstract::The 16S rRNA mitochondrial gene was used to reconstruct the relationships among 10 heteronemertean species (subclass Heteronemertea, phylum Nemertea); Lineus ruber and L. viridis are represented by more than one specimen to assess intraspecific variation in these enigmatic species, and the analysis includes in total 1...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1998.0543

    authors: Sundberg P,Saur M

    更新日期:1998-12-01 00:00:00

  • Cryptic speciation and limited hybridization within Lumbricus earthworms (Clitellata: Lumbricidae).

    abstract::Cryptic mitochondrial (mt) lineages are known to exist in the earthworm morphospecies Lumbricus rubellus and L. terrestris. The latter was recently split into two species, L. terrestris and L. herculeus, based on large genetic distances and a statistical difference in body size. There is support for the separation of ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.09.011

    authors: Martinsson S,Erséus C

    更新日期:2017-01-01 00:00:00

  • Molecular phylogeny of marine mites (Acariformes: Halacaridae), the oldest radiation of extant secondarily marine animals.

    abstract::The family Halacaridae comprises more than one thousand mostly marine or rarely freshwater species. Many are predacious, but among marine mites, some genera evolved the ability to feed on macroalgae. We inferred a time-calibrated phylogeny based on 18S rDNA, 28S rDNA, and Cytochrome oxidase I (5,143 nt aligned) and al...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.08.012

    authors: Pepato AR,Vidigal THDA,Klimov PB

    更新日期:2018-12-01 00:00:00

  • Evolutionary trends in the distylous genus Pulmonaria (Boraginaceae): Evidence of ancient hybridization and current interspecific gene flow.

    abstract::The distylous genus Pulmonaria contains approximately 18 species that are widely distributed across Eurasia. Previous studies have shown that species delimitation in the genus is problematic, but have not yet explored the evolutionary history of the genus. Premating reproductive barriers between European species appea...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2015.11.022

    authors: Meeus S,Janssens S,Helsen K,Jacquemyn H

    更新日期:2016-05-01 00:00:00

  • Plio-Pleistocene diversification and biogeographic barriers in southern Australia reflected in the phylogeography of a widespread and common lizard species.

    abstract::Palaeoclimatic events and biogeographical processes since the mid-Tertiary have played an important role in shaping the evolution and distribution of Australian fauna. However, their impacts on fauna in southern and arid zone regions of Australia are not well understood. Here we investigate the phylogeography of an Au...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.12.014

    authors: Ansari MH,Cooper SJB,Schwarz MP,Ebrahimi M,Dolman G,Reinberger L,Saint KM,Donnellan SC,Bull CM,Gardner MG

    更新日期:2019-04-01 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

  • Boreotropical range expansion and long-distance dispersal explain two amphi-Pacific tropical disjunctions in Sabiaceae.

    abstract::Sabiaceae comprises three genera and ca. 80 species with an amphi-Pacific tropical disjunct distribution. It has been unclear whether the family is monophyletic, where the family belongs within the angiosperm phylogeny, and when and how is present-day disjunct distribution originated. To address these questions, we co...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.03.005

    authors: Yang T,Lu LM,Wang W,Li JH,Manchester SR,Wen J,Chen ZD

    更新日期:2018-07-01 00:00:00

  • Out of Africa: The origins of the protozoan blood parasites of the Trypanosoma cruzi clade found in bats from Africa.

    abstract::Understanding geographic patterns of interaction between hosts and parasites can provide useful insight into the evolutionary history of the organisms involved. However, poor taxon sampling often hinders meaningful phylogenetic descriptions of groups of parasites. Trypanosome parasites that constitute the Trypanosoma ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2019.106705

    authors: Clément L,Dietrich M,Markotter W,Fasel NJ,Monadjem A,López-Baucells A,Scaravelli D,Théou P,Pigeault R,Ruedi M,Christe P

    更新日期:2020-04-01 00:00:00

  • Exploring the radiation of a diverse reef fish family: phylogenetics of the damselfishes (Pomacentridae), with new classifications based on molecular analyses of all genera.

    abstract::The damselfishes (Perciformes, Pomacentridae) are an important family of marine reef fishes that occupy a range of ecological positions in the world's oceans. In order to determine the evolutionary pattern of their radiation, we used multiple methods to examine molecular data from 104 species representing all extant g...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.12.010

    authors: James Cooper W,Smith LL,Westneat MW

    更新日期:2009-07-01 00:00:00

  • The evolutionary jigsaw puzzle of the surviving trout (Salmo trutta L. complex) diversity in the Italian region. A multilocus Bayesian approach.

    abstract::Mediterranean trout populations display a diversity of phenotypes, representing a valuable model for the study of adaptation and a puzzling dilemma for taxonomists and biogeographers, which is further entangled by the widespread introgression of allochthonous genes. In this paper we analysed DNA polymorphism at multip...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2014.06.022

    authors: Gratton P,Allegrucci G,Sbordoni V,Gandolfi A

    更新日期:2014-10-01 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

  • Molecular phylogenetics and mitochondrial genomic evolution in the chamaeleonidae (Reptilia, Squamata).

    abstract::A phylogenetic hypothesis for the lizard family Chamaeleonidae is generated from 1503 aligned base positions (883 parsimony-informative) of mitochondrial DNA for specimens representing 59 species (57 ingroup and two outgroup). Sequences are reported for a genomic segment encoding eight transfer RNAs, NADH dehydrogenas...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.2001.1076

    authors: Townsend T,Larson A

    更新日期:2002-04-01 00:00:00

  • Genome-scale transfer of mitochondrial DNA from legume hosts to the holoparasite Lophophytum mirabile (Balanophoraceae).

    abstract::Angiosperm mitochondrial horizontal gene transfer (HGT) has been widely reported during the past decades. With a few exceptions, foreign sequences are mitochondrial genes or intronic regions from other plants, indicating that HGT has played a major role in shaping mitochondrial genome evolution. Host-parasite relation...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.12.006

    authors: Sanchez-Puerta MV,Edera A,Gandini CL,Williams AV,Howell KA,Nevill PG,Small I

    更新日期:2019-03-01 00:00:00

  • Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci.

    abstract::The phylogeny of Celastraceae subfamily Hippocrateoideae (∼ 100 species and 19 genera in the Old and New World tropics) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. The subfamily is easily recognized by the synapomorphies of transversely flatten...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.02.017

    authors: Coughenour JM,Simmons MP,Lombardi JA,Yakobson K,Archer RH

    更新日期:2011-05-01 00:00:00

  • Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): a geographic and phylogenetic perspective.

    abstract::The taxonomy of the African dwarf crocodile (genus Osteolaemus) has been disputed since a novel morphotype was discovered in the early 20th Century. Because this poorly-known reptile is widely hunted throughout the forests of Central and West Africa, resolving the existence and extent of taxonomic units has important ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.11.009

    authors: Eaton MJ,Martin A,Thorbjarnarson J,Amato G

    更新日期:2009-03-01 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

  • Origin of the unisexual lizard Gymnophthalmus underwoodi (Gymnophthalmidae) inferred from mitochondrial DNA nucleotide sequences.

    abstract::Analysis of variation in nucleotide sequences in mitochondrial DNA genes among species of Gymnophthalmus supports three major conclusions. First, samples of G. underwoodi, a unisexual species of hybrid origin, have identical nucleotide sequences, supporting the hypothesis that all individuals from localities in the Gu...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1998.0591

    authors: Kizirian DA,Cole CJ

    更新日期:1999-04-01 00:00:00

  • Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: conserved features of the echinoid mitochondrial genome.

    abstract::The complete nucleotide sequence (15,719 nucleotides) of the mitochondrial DNA (mtDNA) from the sea urchin Arbacia lixula is presented. The comparison of gene arrangement between different echinoderm orders of the same class provides evidence that the gene organization is conserved within the same echinoderm class. Th...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1996.0027

    authors: De Giorgi C,Martiradonna A,Lanave C,Saccone C

    更新日期:1996-04-01 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

  • Divergent paralogues of ribosomal DNA in eucalypts (Myrtaceae).

    abstract::The presence of divergent paralogues of nuclear ribosomal DNA, from the 18S-5.8S-26S cistron, is reported in members of Eucalyptus subg. Eucalyptus. These paralogues, which include non-functional pseudogenes, probably diverged prior to the differentiation of species groups in subg. Eucalyptus. When compared with presu...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2006.10.027

    authors: Bayly MJ,Ladiges PY

    更新日期:2007-07-01 00:00:00

  • Taxonomic status and evolutionary history of the Saxicola torquata complex.

    abstract::We explored variation in mitochondrial ND2 gene sequences from 171 stonechats (Saxicola torquata complex) collected from 27 Eurasian and 3 African localities. We found that two widespread neighboring Eurasian subspecies of Siberian stonechat, Saxicola maura maura and S. m. stejnegeri, although very similar in appearan...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2009.05.016

    authors: Zink RM,Pavlova A,Drovetski S,Wink M,Rohwer S

    更新日期:2009-09-01 00:00:00

  • Isolation, phylogeny and evolution of the SymRK gene in the legume genus Lupinus L.

    abstract::SymRK is one of the key genes involved in initial steps of legume symbiotic association with fungi (mycorrhization) and nitrogen-fixing bacteria (nodulation). A large portion of the sequence encoding the extracellular domain of SYMRK was obtained for 38 lupine accessions and 2 outgroups in order to characterize this r...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.04.017

    authors: Mahé F,Markova D,Pasquet R,Misset MT,Aïnouche A

    更新日期:2011-07-01 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

  • Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes.

    abstract::Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problem...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.08.021

    authors: Lopes-Lima M,Froufe E,Do VT,Ghamizi M,Mock KE,Kebapçı Ü,Klishko O,Kovitvadhi S,Kovitvadhi U,Paulo OS,Pfeiffer JM 3rd,Raley M,Riccardi N,Şereflişan H,Sousa R,Teixeira A,Varandas S,Wu X,Zanatta DT,Zieritz A,Bogan AE

    更新日期:2017-01-01 00:00:00

  • Phylogenetic analysis of chloroplast DNA variation in Coffea L.

    abstract::The trnL-trnF intergenic spacer of cpDNA has been sequenced from 38 tree samples representing 23 Coffea taxa and the related genus Psilanthus. These sequences were used for phylogenetic reconstruction using parsimony analyses. The results suggest a radial mode of speciation and a recent origin in Africa for the genus ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1997.0453

    authors: Cros J,Combes MC,Trouslot P,Anthony F,Hamon S,Charrier A,Lashermes P

    更新日期:1998-02-01 00:00:00

  • The effects of sampling on delimiting species from multi-locus sequence data.

    abstract::As a fundamental unit in biology, species are used in a wide variety of studies, and their delimitation impacts every subfield of the life sciences. Thus, it is of utmost importance that species are delimited in an accurate and biologically meaningful way. However, due to morphologically similar, cryptic species, and ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2012.06.031

    authors: Rittmeyer EN,Austin CC

    更新日期:2012-11-01 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

  • Nuclear ribosomal DNA sequence variation and evolution of spotted marsh-orchids (Dactylorhiza maculata group).

    abstract::Sequences of both internal and external transcribed spacers of nuclear ribosomal DNA were sequenced for four species belonging to the Dactylorhiza maculata group or "spotted marsh-Orchids". These four species are D. fuchsii, D. saccifera, D. foliosa, and D. maculata. Extensive nuclear ribosomal DNA polymorphism was un...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.04.014

    authors: Devos N,Oh SH,Raspé O,Jacquemart AL,Manos PS

    更新日期:2005-09-01 00:00:00

  • Diversification and repeated morphological transitions in endoparasitic cnidarians (Myxozoa: Malacosporea).

    abstract::Malacosporeans are a poorly known myxozoan clade that uniquely demonstrates a tissue level of organisation. Thus, when exploiting their invertebrate hosts (freshwater bryozoans) they occur as non-motile sacs or vermiform stages capable of active swimming. We combine phylogenetic analyses of SSU and LSU rDNA with morph...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2014.03.010

    authors: Hartikainen H,Gruhl A,Okamura B

    更新日期:2014-07-01 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