Abstract:
:It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRNA, 16S rRNA, ND1, ND2, ND4, Cyt b, and associated tRNA genes), and >2.2kb from three nuclear genes (RAG-1, BDNF, and GAPD) for most taxa. We conduct separate and combined phylogenetic analyses of these data using maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic relationships inferred from the mtDNA data are congruent with previous mtDNA analyses based on fewer characters and provide strong support for most branches. However, we detected strong incongruence between the mtDNA and nuclear data using comparisons of branch support and Shimodaira-Hasegawa tests, with the (P. platyrhinos+P. goodei) clade identified as the primary source of this conflict. Our analysis of a P. mcalliixP. goodei hybrid suggests that this incongruence is caused by reticulation via introgressive hybridization. Our preferred phylogeny based on an analysis of the combined data (excluding the introgressed mtDNA data) provides a new framework for interpreting character evolution and biogeography within Phrynosoma. In the context of this improved phylogeny we propose a phylogenetic taxonomy highlighting four clades: (1) Tapaja, containing the viviparous short-horned lizards P. ditmarsi, P. hernandesi, P. douglasii, and P. orbiculare; (2) Anota, containing species with prominent cranial horns (P. solare, P. mcallii, and the P. coronatum group); (3) Doliosaurus, containing three species lacking antipredator blood-squirting (P. modestum, P. platyrhinos, and P. goodei); and (4) Brevicauda, containing two viviparous species with extremely short tails that lack blood-squirting (P. braconnieri and P. taurus).
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
Leaché AD,McGuire JAdoi
10.1016/j.ympev.2005.12.016keywords:
subject
Has Abstractpub_date
2006-06-01 00:00:00pages
628-44issue
3eissn
1055-7903issn
1095-9513pii
S1055-7903(06)00007-8journal_volume
39pub_type
杂志文章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
更新日期:2008-05-01 00:00:00
abstract::Allopolyploid speciation is widespread in plants, yet the molecular requirements for successful orchestration of coordinated gene expression for two divergent and reunited genomes are poorly understood. Recent studies in several plant systems have revealed that allopolyploid genesis under both synthetic and natural co...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章,评审
doi:10.1016/s1055-7903(03)00213-6
更新日期:2003-12-01 00:00:00
abstract::The purpose of this study was to determine the higher-level phylogenetic relationships among Carnivora, using a conditional data combination (CDC) approach to analyzing multiple data sets. New nucleotide sequences (851 base pairs from intron I of the transthyretin gene) among 22 representatives of the 11 families of C...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.1998.0504
更新日期:1998-06-01 00:00:00
abstract::A lot is known about the evolution and architecture of plastid, mitochondrial, and nuclear genomes, but surprisingly little is known about their relative rates of mutation. Most available relative-rate data come from seed plants, which, with few exceptions, have a mitochondrial mutation rate that is lower than those o...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2014.07.001
更新日期:2014-10-01 00:00:00
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
更新日期:2001-08-01 00:00:00
abstract::The genus Brachycybe Wood is a little known group of millipedes comprising eight nominal species distributed throughout North America, Japan, South Korea, Taiwan, and China. The group's species are relatively morphologically homogenous and have been described primarily on the basis of differences in somatic morphology...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2012.04.003
更新日期:2012-07-01 00:00:00
abstract::A continuous 10.1kb fragment of the Cephalothrix rufifrons (Nemertea, Palaeonemertea) mitochondrial genome was sequenced and characterized to further assess organization of protostome mitochondrial genomes and evaluate the phylogenetic potential of gene arrangement and amino acid characters. The genome is A-T rich (72...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2006.10.025
更新日期:2007-06-01 00:00:00
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
更新日期:2014-01-01 00:00:00
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
更新日期:2009-07-01 00:00:00
abstract::We assess the phylogeographic structure and test several species delimitation methods in the forest-living Pondo flat-gecko, Afroedura pondolia, by sampling specimens from across the entire distribution in the Eastern Cape and KwaZulu-Natal provinces of South Africa. Phylogenetic results, using Bayesian inferences and...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2019.106549
更新日期:2019-10-01 00:00:00
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
更新日期:2015-04-01 00:00:00
abstract::Plate tectonics constitute one of the main mechanisms of biological diversification on Earth, often being associated with cladogenetic events at different phylogenetic levels, as well as with exchange of faunas and floras across previously isolated biogeographic regions. North Africa and Arabia share a complex geologi...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2020.106969
更新日期:2021-02-01 00:00:00
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
更新日期:1997-10-01 00:00:00
abstract::Phylogenetic relationships among members of the New World searobin genera Bellator and Prionotus (Family Triglidae, Subfamily Prionotinae) and among other searobins in the families Triglidae and Peristediidae were investigated using both mitochondrial and nuclear DNA sequences. Phylogenetic hypotheses derived from max...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2016.11.017
更新日期:2017-02-01 00:00:00
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
更新日期:2011-05-01 00:00:00
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
更新日期:2005-11-01 00:00:00
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
更新日期:2010-11-01 00:00:00
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
更新日期:2018-10-01 00:00:00
abstract::Acestrorhynchus is the sole genus of the family Acestrorhynchidae which includes 14 species currently recognized as valid. Species of Acestrorhynchus comprise small-to-medium sized piscivorous fishes and have been traditionally grouped on the basis of well-defined color patterns. A recent phylogeny, based on morpholog...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2008.12.025
更新日期:2009-08-01 00:00:00
abstract::The Ciminalis section of Gentiana comprises seven species, two of them growing on siliceous substrates (G. alpina and G. acaulis), the other ones being calcareous taxa (G. clusii, G. angustifolia, G. ligustica, G. occidentalis and G. dinarica). A total of 515 individuals from 183 populations over the entire Ciminalis ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2013.09.022
更新日期:2014-01-01 00:00:00
abstract::Phylogenetic analyses of Polytrichales were conducted using morphology and sequence data from the chloroplast genes rbcL and rps4 plus the trnL-F gene region, part of the mitochondrial nad5 and the nuclear-encoded 18S rDNA. Our analyses included 46 species representing all genera of Polytrichales. Phylogenetic trees w...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2003.11.003
更新日期:2004-06-01 00:00:00
abstract::The pattern of genetic variation of the lizard Mabuya maculilabris from São Tomé Island (Gulf of Guinea) was investigated using a combination of three mitochondrial DNA gene fragments. Forty-eight haplotypes were recovered among 66 individuals covering the whole island. The genealogy inferred from the most parsimoniou...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2005.04.032
更新日期:2005-11-01 00:00:00
abstract::Phylogenetic analyses based on mitochondrial DNA have yielded widely differing relationships among members of the arthropod lineage Arachnida, depending on the nucleotide coding schemes and models of evolution used. We enhanced taxonomic coverage within the Arachnida greatly by sequencing seven new arachnid mitochondr...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2008.10.010
更新日期:2009-01-01 00:00:00
abstract::Banana is one of the most important subtropical crops. The genetic system, however, is relatively unknown and is complicated by specific interhybridization, heterozygosity, and polyploidy, which are common in most clones. These factors make identification of closely related banana cultivars difficult, particularly whe...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.2000.0848
更新日期:2000-12-01 00:00:00
abstract::The diversification of gall-inducing Australian Kladothrips (Insecta: Thysanoptera) on Acacia has produced a pair of sister-clades, each of which includes a suite of lineages that utilize virtually the same set of 15 closely related host plant species. This pattern of parallel insect-host plant radiation may be driven...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.03.007
更新日期:2007-06-01 00:00:00
abstract::In this study, we present a molecular phylogeny for the west Palaearctic Helicidae sensu lato based on sequence data from two mitochondrial (COI, 16S rDNA) and two nuclear (ITS-1, 18S rDNA) genes. Maximum likelihood analysis and Bayesian inference revealed well supported monophyletic clades partly conflicting traditio...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2004.03.004
更新日期:2004-09-01 00:00:00
abstract::The evolution and the historical biogeography of the Southern Ocean marine benthic fauna are closely related to major tectonic and climatic changes that occurred in this region during the last 55 million years (Ma). Several families, genera and even species of marine organisms are shared between distant biogeographic ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2010.02.001
更新日期:2010-07-01 00:00:00
abstract::The status of subspecies in systematic zoology is the focus of controversy. Recent studies use DNA sequences to evaluate the status of subspecies within species complexes and to recognize and delimit species. Here, we assessed the phylogenetic relationships, the taxonomic status of the proposed subspecies, and the spe...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2015.04.024
更新日期:2015-09-01 00:00:00
abstract::The region coding for the second largest subunit of RNA polymerase II (RPB2) was explored for resolving interspecific relationships in Arnica and lower level taxa in general. The region between exons 17 and 23 was cloned and sequenced for 33 accessions of Arnica and four outgroup taxa. Three paralogues of the RPB2-d c...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2012.02.032
更新日期:2012-08-01 00:00:00
abstract::Onuphid polychaetes are tubicolous marine worms commonly reported worldwide from intertidal areas to hadal depths. They often dominate in benthic communities and have economic importance in aquaculture and recreational fishing. Here we report the phylogeny of the family Onuphidae based on the combined analyses of nucl...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2015.10.011
更新日期:2016-01-01 00:00:00