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 phylogenetic relationships among 14 closely related taxa from the mallard (Anas spp.) complex using the multispecies coalescent and 20 nuclear loci sampled from a genomic transect. We also examined how treating recombining loci and hybridizing species influences results by partitioning the data using various protocols. In general, topologies were similar among the various species trees, with major clades consistently composed of the same taxa. However, relationships among these clades and among taxa within clades changed among partitioned data sets. Posterior support generally decreased when filtering for recombination, whereas excluding mallards (Anas platyrhynchos) increased posterior support for taxa known to hybridize with them. Furthermore, branch lengths decreased substantially for recombination-filtered data. Finally, concordance between nuclear and morphometric topologies conflicted with those in the mitochondrial tree, particularly with regard to the placement of the Hawaiian duck (A. wyvilliana), Philippine duck (A. luzonica), and two spot-billed ducks (A. zonorhyncha and A. poecilorhyncha). These results demonstrate the importance of maximizing sequence length and taxon sampling when inferring taxonomic relationships that are confounded by extensive allele sharing.
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
Lavretsky P,McCracken KG,Peters JLdoi
10.1016/j.ympev.2013.08.008subject
Has Abstractpub_date
2014-01-01 00:00:00pages
402-11eissn
1055-7903issn
1095-9513pii
S1055-7903(13)00316-3journal_volume
70pub_type
杂志文章abstract：:Phylogenetic relationships and timings of major cladogenesis events are investigated in the Balearic Island lizards Podarcislilfordi and P.pityusensis using 2675bp of mitochondrial and nuclear DNA sequences. Partitioned Bayesian and Maximum Parsimony analyses provided a well-resolved phylogeny with high node-support v...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2008.04.013
更新日期：2008-07-01 00:00:00
abstract：:Nucleotide sequences of the small subunit ribosomal RNA (18S) gene were used to investigate evolutionary relationships within the Fungi. The inferred tree topologies are in general agreement with traditional classifications in the following ways: (1) the Chytridiomycota and Zygomycota appear to be basal groups within ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/1055-7903(92)90020-h
更新日期：1992-09-01 00:00:00
abstract：:Nucleotide sequences of the nuclear c-mos gene and the mitochondrial cytochrome b and ND2 genes were used to assess the monophyly of Sibley and Monroe's [Distribution and Taxonomy of Birds of the World, Yale University Press, New Haven, 1990] Muscicapoidea superfamily. The relationships and monophyly of major lineages...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/s1055-7903(03)00191-x
更新日期：2004-02-01 00:00:00
abstract：:Polygonatum is a widespread temperate genus with approximately 75 species centered in the Eastern Himalaya and Indo-Burma biodiversity hotspots. A complete assessment of the remarkable diversity of Polygonatum in these areas requires an accurate circumscription of the genus, as well as a clear understanding of generic...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2018.08.017
更新日期：2018-12-01 00:00:00
abstract：:Adelanthaceae (including Jamesoniellaceae) represent a major lineage of jungermannialean liverworts that is characterized by ventral-intercalary, often flagelliform branches, succubous leaves, ovoid to cylindrical, plicate perianths with a contracted mouth, often connate bracts and bracteoles, and 4-7 stratose capsule...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.11.009
更新日期：2010-04-01 00:00:00
abstract：:Comparative phylogeography of widespread species that span the same geographic areas can elucidate the influence of historical events on current patterns of biodiversity, identify patterns of co-vicariance, and therefore aid the understanding of general evolutionary processes. Soil-dwelling animals present characteris...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2015.07.017
更新日期：2016-01-01 00:00:00
abstract：:Conflicting phylogenies have been proposed for the Chelidae (Testudines: Pleurodira), a family of side-necked turtles found only in Australasia and South America. Sequence data from the mitochondrial 12S rRNA gene were used to test these phylogenies. In total, 411 nucleotides were sequenced for each of 16 chelid speci...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1996.0372
更新日期：1997-02-01 00:00:00
abstract：:Resolution of the total evidence (i.e., character congruence) versus consensus (i.e., taxonomic congruence) debate has been impeded by (1) a failure to employ validation methods consistently across both tree-building and consensus analyses, (2) the incomparability of methods for constructing as opposed to those for co...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1998.0561
更新日期：1999-02-01 00:00:00
abstract：:Several recent studies have suggested that a substantial portion of today's plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than vicariance, but more data are needed to substantiate this claim. Guatteria (Annonaceae) is, with 265 species, the third largest genus of Neo...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2007.02.017
更新日期：2007-07-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2008.10.012
更新日期：2009-01-01 00:00:00
abstract：:The freshwater sculpins, genus Cottus (Teleostei; Cottidae), comprise bottom-dwelling fishes that exhibit various life-history styles, having radiated throughout Northern Hemisphere freshwater habitats. The phylogenetic relationships among Cottus and related taxa were estimated from mitochondrial DNA 12S rRNA and cont...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2005.06.004
更新日期：2005-09-01 00:00:00
abstract：:Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2018.05.009
更新日期：2018-10-01 00:00:00
abstract：:Calocidae constitute a hypothesised monophyletic group of caddisflies (Trichoptera) being geographically restricted to New Zealand (one genus) and Australia (five genera). This analysis tests the monophyly of the family based on sequences from five different molecular genes. The complete data set includes 29 species a...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.09.025
更新日期：2010-02-01 00:00:00
abstract：:The complex orogenic history and structure of Southern South America, coupled with Pleistocene glacial cycles, have generated paleoclimatic and environmental changes that influenced the spatial distribution and genetic composition of natural populations. Despite the increased number of phylogeographic studies in this ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2017.08.016
更新日期：2017-11-01 00:00:00
abstract：:The subspecies concept has received considerable debate throughout the past century. Subspecies were originally used to delineate potential incipient species, but were later employed to simply capture geographical variation. There is a recent trend to eliminate the trinomial in light of new evidence. Discrete, diagnos...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2007.12.012
更新日期：2008-03-01 00:00:00
abstract：:Squirrel adenovirus (SqAdV) was reported previously. However, only partial sequences of its hexon and polymerase genes have been revealed. For the first time, we report the full-length genome of SqAdV including the complete hexon and penton base genes. From internal body organs of 59 red squirrels archived in Korea Ba...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2017.08.008
更新日期：2017-11-01 00:00:00
abstract：:Because of their importance for proper development of the bilaterian embryo, Hox genes have taken center stage for investigations into the evolution of bilaterian metazoans. Taxonomic surveys of major protostome taxa have shown that Hox genes are also excellent phylogenetic markers, as specific Hox genes are restricte...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2003.10.007
更新日期：2004-06-01 00:00:00
abstract：:Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and ha...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2017.10.018
更新日期：2018-02-01 00:00:00
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
更新日期：1996-04-01 00:00:00
abstract：:Tribe Rhipsalideae is composed of unusual epiphytic or lithophytic cacti that inhabit humid tropical and subtropical forests. Members of this tribe present a reduced vegetative body, a specialized adventitious root system, usually spineless areoles and flowers and fruits reduced in size. Despite the debate surrounding...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2011.01.001
更新日期：2011-03-01 00:00:00
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
更新日期：2018-07-01 00:00:00
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
更新日期：1999-04-01 00:00:00
abstract：:The ambush bugs (Heteroptera: Reduviidae: Phymatinae) are a diverse clade of predators known for their cryptic hunting behavior and morphologically diverse raptorial forelegs. Despite their striking appearance, role as pollinator predators, and intriguing biogeographic distribution, phylogenetic relationships within P...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2017.06.010
更新日期：2017-09-01 00:00:00
abstract：:The Hawaiian Drosophilidae contains approximately 1000 species, placed in species groups and subgroups based largely on secondary sexual modifications to wings, forelegs and mouthparts. Members of the spoon tarsus subgroup possess a cup-shaped structure on the foretarsi of males. Eight of the twelve species in this su...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2010.12.015
更新日期：2011-03-01 00:00:00
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
更新日期：1993-09-01 00:00:00
abstract：:Sexually deceptive Chiloglottis orchids lure their male thynnine wasp pollinators to the flower by emitting semiochemicals that mimic the specific sex pheromone of the wasp. Sexual deception is possible because chemical rather than visual cues play the key role in wasp mate search, suggesting that cryptic wasp species...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2011.02.004
更新日期：2011-04-01 00:00:00
abstract：:The oceanic squid family Gonatidae (Mollusca: Cephalopoda) is widely distributed in subpolar and temperate waters, exhibiting behavioral and physiological specializations associated with reproduction. Females of several species undergo muscular degeneration upon maturation; origins of this complex morphogenic change a...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2004.12.009
更新日期：2005-07-01 00:00:00
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
更新日期：2012-03-01 00:00:00
abstract：:Leafhoppers (Cicadellidae) are a highly diverse group of sap-sucking insects, many species of which specialize on grasses. Past attempts to examine the roles of host transfer or host plant coevolution in the diversification of leafhopper species using cladistic methods have been hindered by a paucity of discrete, phyl...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1997.0415
更新日期：1997-10-01 00:00:00
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
更新日期：2002-04-01 00:00:00
