How many names for a beloved genus? - Coalescent-based species delimitation in Xanthium L. (Ambrosiinae, Asteraceae).

Abstract:

:The species category is the fundamental unit in biology. In the last decades, several studies have been carried out, using sequence information and phylogenies to resolve issues in taxonomically problematic groups. The multispecies coalescent theory, and the species-delimitation methods developed in the last years based on that, offer powerful and objective tools to determine species boundaries using sequence data. The genus Xanthium is a morphologically variable complex with several local forms, nowadays become cosmopolitan due to human-mediated dispersal. Past taxonomic treatments of the genus were based essentially on the burr morphology. They varied considerably in number of recognized species, depending on the importance that the different authors gave to burr traits such as burr size, pubescence, number and length of spines in the burrs, and the degree to which those are hooked. We used sequence information from two plastid regions (the intergenic spacer regions psbA-trnH and trnQ-rps16) and two nuclear ones (ITS1-5.8 S-ITS2 rDNA, and the single-copy nuclear marker D35). Two of the most advanced coalescent-based species delimitation methods (BP&P and STACEY) were applied, in order to objectively determine species boundaries in Xanthium. Results from the species-delimitation methods strongly support scenarios with a reduced number of species. Prior on the effective population size parameter (θ) had a strong influence on BP&P results. Analyses with large and small θ prior supported species delimitation scenarios with four and five species, respectively. STACEY recognized five cluster in the dataset, all supported by high posterior probability values. Five species are identified in Xanthium, in a great extent corresponding to the infrageneric classification given for the genus in past taxonomic revisions.

journal_name

Mol Phylogenet Evol

authors

Tomasello S

doi

10.1016/j.ympev.2018.05.024

subject

Has Abstract

pub_date

2018-10-01 00:00:00

pages

135-145

eissn

1055-7903

issn

1095-9513

pii

S1055-7903(17)30936-3

journal_volume

127

pub_type

杂志文章
  • Comparative phylogeography and genetic structure of Vanuatu birds: control region variation in a rail, a dove, and a passerine.

    abstract::We examined variation in mitochondrial control region (Domain I) sequences in three distantly related species of birds found on multiple islands in Vanuatu: the Buff-banded Rail Gallirallus philippensis (n=21, 433bp), the Emerald Dove Chalcophaps indica (n=21, 513bp), and the Streaked Fantail Rhipidura spilodera (n=17...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2006.12.013

    authors: Kirchman JJ,Franklin JD

    更新日期:2007-04-01 00:00:00

  • Cryptic patterns of diversification of a widespread Amazonian woodcreeper species complex (Aves: Dendrocolaptidae) inferred from multilocus phylogenetic analysis: implications for historical biogeography and taxonomy.

    abstract::Inferring evolutionary relationships between recently diverged taxa is still challenging, especially taking into account the likely occurrence of incomplete lineage sorting and/or introgression. The Xiphorhynchus pardalotus/ocellatus species complex includes between two to three polytypic species and eight to nine sub...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.04.018

    authors: Sousa-Neves T,Aleixo A,Sequeira F

    更新日期:2013-09-01 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

  • 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

  • Phylogeography of Helleria brevicornis (Crustacea, Oniscidea): old and recent differentiations of an ancient lineage.

    abstract::Helleria brevicornis has a disjunct, peri-Tyrrhenian distribution that mirrors that of several organisms, for which geographic vicariance is invoked, due to the geological events started with the Oligocene split of the Sardo-Corsican microplate from the Pyrenees, and successive separation between Sardinia and Corsica....

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2009.10.005

    authors: Gentile G,Campanaro A,Carosi M,Sbordoni V,Argano R

    更新日期:2010-02-01 00:00:00

  • Speciation with introgression: Phylogeography and systematics of the Ameerega petersi group (Dendrobatidae).

    abstract::The Tropical Andes contains exceptionally high diversity, much of it arising within the Quaternary period. The complex geology of the Andes and paleoclimate fluctuations within the Quaternary suggest complex speciation scenarios. This, in turn, has contributed to idiosyncratic speciation modes among shallowly diverged...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2019.05.021

    authors: French CM,Deutsch MS,Chávez G,Almora CE,Brown JL

    更新日期:2019-09-01 00:00:00

  • Total evidence, consensus, and bat phylogeny: A distance-based approach.

    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

    authors: Lapointe FJ,Kirsch JA,Hutcheon JM

    更新日期:1999-02-01 00:00:00

  • Phylogeny of the Polytrichales (Bryophyta) based on simultaneous analysis of molecular and morphological data.

    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

    authors: Hyvönen J,Koskinen S,Merrill GL,Hedderson TA,Stenroos S

    更新日期:2004-06-01 00:00:00

  • Incomplete sterols and hopanoids pathways in ciliates: gene loss and acquisition during evolution as a source of biosynthetic genes.

    abstract::Polycyclic triterpenoids, such as sterols and hopanoids, are essential components of plasmatic membrane in eukaryotic organisms. Although it is generally assumed that ciliates do not synthesize sterols, and many of them are indeed auxotrophic, a large set of annotated genomic sequences and experimental data from recen...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章,评审

    doi:10.1016/j.ympev.2014.01.026

    authors: Tomazic ML,Poklepovich TJ,Nudel CB,Nusblat AD

    更新日期:2014-05-01 00:00:00

  • Parthenogenesis through the ice ages: A biogeographic analysis of Caucasian rock lizards (genus Darevskia).

    abstract::Darevskia rock lizards include both sexual and parthenogenetic species, mostly distributed in the heterogeneous and ecologically diverse Caucasus. The parthenogenetic species originated via directional hybridogenesis, with only some of the sexual species known to serve as parentals. However, it remains unclear when an...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 历史文章,杂志文章

    doi:10.1016/j.ympev.2016.05.035

    authors: Freitas S,Rocha S,Campos J,Ahmadzadeh F,Corti C,Sillero N,Ilgaz Ç,Kumlutaş Y,Arakelyan M,Harris DJ,Carretero MA

    更新日期:2016-09-01 00:00:00

  • Using phylogenomics to reconstruct phylogenetic relationships within tribe Polygonateae (Asparagaceae), with a special focus on Polygonatum.

    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

    authors: Floden A,Schilling EE

    更新日期:2018-12-01 00:00:00

  • The Hyalella (Crustacea: Amphipoda) species cloud of the ancient Lake Titicaca originated from multiple colonizations.

    abstract::Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalell...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.03.004

    authors: Adamowicz SJ,Marinone MC,Menu-Marque S,Martin JW,Allen DC,Pyle MN,De Los Ríos P,Sobel CN,Ibañez C,Pinto J,Witt JDS

    更新日期:2018-08-01 00:00:00

  • Phylogenetic relationships inferred from ribosomal its sequences and biogeographic patterns in representatives of the genus Calopteryx (Insecta: Odonata) of the West Mediterranean and adjacent West European zone.

    abstract::Western Europe is a reinvasion zone for the riverine dragonfly genus Calopteryx (Insecta: Odonata). Reinvasion may have been from central West Asia or from the West Mediterranean refugium. Phylogenetic relationships of West Mediterranean and West European taxa of the genus Calopteryx from different localities were inf...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.2001.0947

    authors: Weekers PH,De Jonckheere JF,Dumont HJ

    更新日期:2001-07-01 00:00:00

  • Phylogeography and systematics of the Peromyscus eremicus species group and the historical biogeography of North American warm regional deserts.

    abstract::Phylogeographic relationships among 26 populations from throughout the geographic range of the Peromyscus eremicus species group are described based on sequence data for a 699-bp fragment of the mitochondrial DNA COIII gene. Distance, maximum-likelihood, and maximum-parsimony analyses of phylogenetic trees generated u...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.2000.0841

    authors: Riddle BR,Hafner DJ,Alexander LF

    更新日期:2000-11-01 00:00:00

  • Biogeography and diversification dynamics of the African woodpeckers.

    abstract::The dynamics of species accumulation of African terrestrial vertebrates over time remains underexplored in comparison with those in the New World, despite Africa hosting about 25% of the world's avian diversity. This lack of knowledge hampers our understanding of the fundamental processes that drive biodiversity and t...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2017.01.007

    authors: Fuchs J,Pons JM,Bowie RC

    更新日期:2017-03-01 00:00:00

  • Evolution and phylogeny of old world deer.

    abstract::The phylogenetic pattern and timing of the radiation of Old World deer was determined based on the complete mitochondrial cytochrome b gene from 33 Cervinae taxa. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with mun...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2004.07.013

    authors: Pitra C,Fickel J,Meijaard E,Groves PC

    更新日期:2004-12-01 00:00:00

  • Molecular phylogeny and historical biogeography of Nacella (Patellogastropoda: Nacellidae) in the Southern Ocean.

    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

    authors: González-Wevar CA,Nakano T,Cañete JI,Poulin E

    更新日期:2010-07-01 00:00:00

  • The gene tree delusion.

    abstract::Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are requi...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2015.07.018

    authors: Springer MS,Gatesy J

    更新日期:2016-01-01 00:00:00

  • Phylogeographic patterns in the Australasian genus Chionohebe (Veronica s.l., Plantaginaceae) based on AFLP and chloroplast DNA sequences.

    abstract::The alpine genus Chionohebe is one of seven genera in the southern hemisphere Hebe complex. The main aims of this study were to infer the evolutionary relationships and assess phylogeographic patterns among the six species of Chionohebe, determine the origin of the two species with trans-Tasman distributions, and test...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2007.12.019

    authors: Meudt HM,Bayly MJ

    更新日期:2008-04-01 00:00:00

  • Phylogeny and age of diversification of the planitibia species group of the Hawaiian Drosophila.

    abstract::The Hawaiian Drosophila offer a unique opportunity to examine evolutionary questions because of the known ages of the Hawaiian Islands and the large number of species endemic to this archipelago. One of the more well studied groups of Hawaiian Drosophila is the planitibia species group, a long-standing population gene...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.03.008

    authors: Bonacum J,O'Grady PM,Kambysellis M,Desalle R

    更新日期:2005-10-01 00:00:00

  • The mitochondrial genome of the firefly, Pyrocoelia rufa: complete DNA sequence, genome organization, and phylogenetic analysis with other insects.

    abstract::The complete nucleotide sequences of the mt genome from the firefly, Pyrococelia rufa (Coeleoptera: Lampyridae) was determined. The circular genome is 17,739-bp long, and contains a typical gene complement, order, and arrangement identical to Drosophila yacuba. The presence of 1,724-bp long intergenic spacer in the P....

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2004.03.009

    authors: Bae JS,Kim I,Sohn HD,Jin BR

    更新日期:2004-09-01 00:00:00

  • Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae).

    abstract::All taxa endemic to the Qinghai-Tibet Plateau are hypothesized to have originated in situ or from immediately adjacent areas because of the relatively recent formation of the plateau since the Pliocene, followed by the large-scaled biota extinction and recession caused by the Quaternary ice sheet. However, identificat...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(02)00039-8

    authors: Liu JQ,Gao TG,Chen ZD,Lu AM

    更新日期:2002-06-01 00:00:00

  • Molecular phylogenetics and floral evolution of the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae): Evolutionary transitions and phylogenetic signal variation.

    abstract::The Cirrhopetalum alliance is a loosely circumscribed species-rich group within the mega-diverse genus Bulbophyllum (Orchidaceae). The monophyletic status of the alliance has been challenged by previous studies, although established sectional classifications have yet to be tested in a phylogenetic context. We used max...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2019.106689

    authors: Hu AQ,Gale SW,Liu ZJ,Suddee S,Hsu TC,Fischer GA,Saunders RMK

    更新日期:2020-02-01 00:00:00

  • 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, ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2004.02.013

    authors: Burns KJ,Naoki K

    更新日期:2004-09-01 00:00:00

  • Phylogeny of the grassland leafhopper genus Flexamia (Homoptera: Cicadellidae) based on mitochondrial DNA sequences.

    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

    authors: Dietrich CH,Whitcomb RF,Black WC

    更新日期:1997-10-01 00:00:00

  • Resolving the phylogenetic relationships and evolutionary history of the Drosophila virilis group using multilocus data.

    abstract::The Drosophila virilis group is one of the major lineages of Drosophila previously recognised and it has been used as a model for different types of studies. It comprises 13 species whose phylogenetic relationships are not well resolved. In the present study, six nuclear genes (Adh, fused, Gpdh, NonA, CG9631 and CG721...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.04.022

    authors: Morales-Hojas R,Reis M,Vieira CP,Vieira J

    更新日期:2011-08-01 00:00:00

  • Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds.

    abstract::Phylogenetic relationships of the lyrebirds are investigated using DNA sequence data. The aligned data matrix consists of 4027 bp obtained from three nuclear genes (c-myc, RAG-1 and myoglobin intron II) and two mitochondrial genes (cytochrome b and ND2). Both maximum-likelihood and parsimony analyses show that the lyr...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(02)00215-4

    authors: Ericson PG,Christidis L,Irestedt M,Norman JA

    更新日期:2002-10-01 00:00:00

  • Discovery of an old, archipelago-wide, endemic radiation of Philippine snakes.

    abstract::The extraordinarily rich land vertebrate biodiversity of the Philippines includes at least 112 species of terrestrial snakes (74% of which are endemic to the archipelago) in 41 genera (12% endemic). Endemic Philippine snake genera include Cyclocorus (two species), Hemibungarus (three species), Hologerrhum (two species...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2017.11.004

    authors: Weinell JL,Brown RM

    更新日期:2018-02-01 00:00:00

  • Phylogeography of surface and cave Astyanax (Teleostei) from Central and North America based on cytochrome b sequence data.

    abstract::Astyanax fasciatus has become a model organism for the study of regressive and adaptive evolution in cave animals. To fully understand these processes, it is important to have background information on the systematics and phylogeography of surface and cave populations of this species. Here we investigate the phylogeog...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2004.07.001

    authors: Strecker U,Faúndez VH,Wilkens H

    更新日期:2004-11-01 00:00:00

  • Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples.

    abstract::As an endangered animal group, musk deer (genus Moschus) are not only a great concern of wildlife conservation, but also of special interest to evolutionary studies due to long-standing arguments on the taxonomic and phylogenetic associations in this group. Using museum samples, we sequenced complete mitochondrial cyt...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1999.0616

    authors: Su B,Wang YX,Lan H,Wang W,Zhang Y

    更新日期:1999-08-01 00:00:00