Multilocus species-delimitation in the Xerotyphlops vermicularis (Reptilia: Typhlopidae) species complex.

Abstract:

:Scolecophidia (worm snakes) are a vertebrate group with high ecomorphological conservatism due to their burrowing lifestyle. The Eurasian or Greek blindsnake Xerotyphlops vermicularis is their only European representative, a species-complex with an old diversification history. However, its systematics and taxonomy has remained untouched. Here, we extend previous work that relied heavily on mitochondrial markers, following a multi-locus approach and applying several species-delimitation methods, including a Bayesian coalescence-based approach (STACEY). Four "species" delimitation analyses based on the mtDNA (ABGD, bGMYC, mPTP, parsimony networks) returned 14, 11, 9 and 10 clusters, respectively. By mitotyping twice as many specimens as before, we have a complete picture of each cluster's distribution. With the exception of the highly-divergent Levantine lineage, the three independent nuclear markers did not help with phylogenetic resolution, as demonstrated in haplotype networks, concatenated and species-trees, a result of incomplete lineage sorting. The prevailing model from the coalescence-based species-delimitation identified two species: the lineage from the Levant and all others. We formally recognize them as distinct species and resurrect Xerotyphlops syriacus (Jan, 1864) to include the Levantine blindsnakes. Finally, X. vermicularis and X. syriacus may represent species-complexes themselves, since they include high levels of cryptic diversity.

journal_name

Mol Phylogenet Evol

authors

Kornilios P,Jablonski D,Sadek RA,Kumlutaş Y,Olgun K,Avci A,Ilgaz C

doi

10.1016/j.ympev.2020.106922

subject

Has Abstract

pub_date

2020-11-01 00:00:00

pages

106922

eissn

1055-7903

issn

1095-9513

pii

S1055-7903(20)30194-9

journal_volume

152

pub_type

杂志文章
  • Phylogeny and evolution of Orchis and allied genera based on ITS DNA variation: morphological gaps and molecular continuity.

    abstract::Phylogenetic relationships among members of genus Orchis and allied genera Aceras, Anacamptis, Barlia, Dactylorhiza, Gymnadenia, Himantoglossum, Neotinea, Ophrys, Platanthera, and Serapias were inferred from nucleotide sequence variation in the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Sequen...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1999.0628

    authors: Aceto S,Caputo P,Cozzolino S,Gaudio L,Moretti A

    更新日期:1999-10-01 00:00:00

  • Radiation of southern African daisies: biogeographic inferences for subtribe Arctotidinae (Asteraceae, Arctotideae).

    abstract::The majority of the approximately 80-90 species in subtribe Arctotidinae occur in southern Africa with the centre of diversity in the winter-rainfall region. Three species are restricted to afromontane eastern Africa and three species are endemic to Australia. To investigate biogeographic and phylogenetic relationship...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.07.007

    authors: McKenzie RJ,Barker NP

    更新日期:2008-10-01 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

  • Capsid protein evolution and comparative phylogeny of novel porcine parvoviruses.

    abstract::In addition to the well known "classical" porcine parvovirus (PPV1; responsible for reproductive failure of susceptible sows) several new porcine parvoviruses have been recognized (PPV2, PPV3 and PPV4) in recent years. The genetic variation, characteristics and evolutionary factors shaping these novel PPVs were studie...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2012.09.030

    authors: Cadar D,Cságola A,Kiss T,Tuboly T

    更新日期:2013-01-01 00:00:00

  • Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca).

    abstract::Caenogastropoda is the dominant group of marine gastropods in terms of species numbers, diversity of habit and habitat and ecological importance. This paper reports the first comprehensive multi-gene phylogenetic study of the group. Data were collected from up to six genes comprising parts of 18S rRNA, 28S rRNA (five ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2006.10.009

    authors: Colgan DJ,Ponder WF,Beacham E,Macaranas J

    更新日期:2007-03-01 00:00:00

  • Phylogenetic relationships in the spoon tarsus subgroup of Hawaiian Drosophila: conflict and concordance between gene trees.

    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

    authors: Lapoint RT,Gidaya A,O'Grady PM

    更新日期:2011-03-01 00:00:00

  • The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae.

    abstract::The phylogenetic utility of chloroplast (atpB-rbcL, petD, rps16, trnL-F) and nuclear (ETS, ITS) DNA regions was investigated for the tribe Spermacoceae of the coffee family (Rubiaceae). ITS was, despite often raised cautions of its utility at higher taxonomic levels, shown to provide the highest number of parsimony in...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.09.025

    authors: Kårehed J,Groeninckx I,Dessein S,Motley TJ,Bremer B

    更新日期:2008-12-01 00:00:00

  • Phylogeny, species limits, and biogeography of the Brazilian lizards of the genus Eurolophosaurus (Squamata: Tropiduridae) as inferred from mitochondrial DNA sequences.

    abstract::Phylogenetic relationships and divergence times for 10 populations of the three recognized "species" of Brazilian lizards of genus Eurolophosaurus were estimated from 1229bp of cyt b, COI, 12S, and 16S rRNA mitochondrial gene segments. Eurolophosaurus is monophyletic and the basal split within the genus separates E. d...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2007.10.022

    authors: Passoni JC,Benozzati ML,Rodrigues MT

    更新日期:2008-02-01 00:00:00

  • Root probabilities for intraspecific gene trees under neutral coalescent theory.

    abstract::The rooting of intraspecific gene or haplotype trees has proven to be difficult using the traditional techniques of rooting species trees such as outgroups. As an alternative, we apply neutral coalescent theory to the problems of determining the root of an intraspecific gene tree and the relative ages of the haplotype...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1994.1013

    authors: Castelloe J,Templeton AR

    更新日期:1994-06-01 00:00:00

  • Integrative inference of population history in the Ibero-Maghrebian endemic Pleurodeles waltl (Salamandridae).

    abstract::Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2017.04.022

    authors: Gutiérrez-Rodríguez J,Barbosa AM,Martínez-Solano Í

    更新日期:2017-07-01 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 systematics, species delimitation and diversification patterns of the Phyllodactylus lanei complex (Gekkota: Phyllodactylidae) in Mexico.

    abstract::The description of cryptic gecko species worldwide has revealed both that many putative species are, in fact, conformed by a complex of morphologically conserved species that are genetically distinct and highly divergent, and that gecko species diversity could be underestimated. The taxonomy and species delimitation o...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2017.07.008

    authors: Ramírez-Reyes T,Piñero D,Flores-Villela O,Vázquez-Domínguez E

    更新日期:2017-10-01 00:00:00

  • Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).

    abstract::Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2010.11.018

    authors: Vélez-Zuazo X,Agnarsson I

    更新日期:2011-02-01 00:00:00

  • Model-based multi-locus estimation of decapod phylogeny and divergence times.

    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

    authors: Porter ML,Pérez-Losada M,Crandall KA

    更新日期:2005-11-01 00:00:00

  • Molecular phylogeny and biogeography of Oriental voles: genus Eothenomys (Muridae, Mammalia).

    abstract::Oriental voles of the genus Eothenomys are predominantly distributed along the Southeastern shoulder of the Qinghai-Tibetan Plateau. Based on phylogenetic analyses of the mitochondrial cytochrome b gene (1143 bp) obtained from 23 specimens (eight species) of Oriental voles collected from this area, together with nucle...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2004.06.005

    authors: Luo J,Yang D,Suzuki H,Wang Y,Chen WJ,Campbell KL,Zhang YP

    更新日期:2004-11-01 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

  • 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

  • Phylogenetic reconstruction of the wolf spiders (Araneae: Lycosidae) using sequences from the 12S rRNA, 28S rRNA, and NADH1 genes: implications for classification, biogeography, and the evolution of web building behavior.

    abstract::Current knowledge of the evolutionary relationships amongst the wolf spiders (Araneae: Lycosidae) is based on assessment of morphological similarity or phylogenetic analysis of a small number of taxa. In order to enhance the current understanding of lycosid relationships, phylogenies of 70 lycosid species were reconst...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.09.004

    authors: Murphy NP,Framenau VW,Donnellan SC,Harvey MS,Park YC,Austin AD

    更新日期:2006-03-01 00:00:00

  • Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences.

    abstract::In spite of several classification attempts among taxa of the genus Lepus, phylogenetic relationships still remain poorly understood. Here, we present molecular genetic evidence that may resolve some of the current incongruities in the phylogeny of the leporids. The complete mitochondrial cytb, 12S genes, and parts of...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.05.006

    authors: Wu C,Wu J,Bunch TD,Li Q,Wang Y,Zhang YP

    更新日期:2005-10-01 00:00:00

  • Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails.

    abstract::Using DNA sequence data from multiple genes (often from more than one genome compartment) to reconstruct phylogenetic relationships has become routine. Augmenting this approach with genomic structural characters (e.g., intron gain and loss, changes in gene order) as these data become available from comparative studies...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.04.008

    authors: Wikström N,Pryer KM

    更新日期:2005-09-01 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

  • The hemagglutinin mutation E391K of pandemic 2009 influenza revisited.

    abstract::Phylogenetic analyses based on small to moderately sized sets of sequential data lead to overestimating mutation rates in influenza hemagglutinin (HA) by at least an order of magnitude. Two major underlying reasons are: the incomplete lineage sorting, and a possible absence in the analyzed sequences set some of key mi...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.08.020

    authors: Radomski JP,Płoński P,Zagórski-Ostoja W

    更新日期:2014-01-01 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

  • Poxvirus genome evolution by gene gain and loss.

    abstract::The poxviruses (Poxviridae) are a family of viruses with double-stranded DNA genomes and substantial numbers (often >200) of genes per genome. We studied the patterns of gene gain and loss over the evolutionary history of 17 poxvirus complete genomes. A phylogeny based on gene family presence/absence showed good agree...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2004.12.008

    authors: Hughes AL,Friedman R

    更新日期:2005-04-01 00:00:00

  • Nuclear and mitochondrial DNA evidence of polyphyly in the avian superfamily Muscicapoidea.

    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

    authors: Voelker G,Spellman GM

    更新日期:2004-02-01 00:00:00

  • Raising names from the dead: A time-calibrated phylogeny of frog shells (Bursidae, Tonnoidea, Gastropoda) using mitogenomic data.

    abstract::With 59 Recent species, Bursidae, known as «frog shells», are a small but widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo-West Pacific. The present study is aimed at reconstructing phylogenetic relationships of bursid gastropods based on extensive and representative ta...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2020.107040

    authors: Sanders MT,Merle D,Laurin M,Bonillo C,Puillandre N

    更新日期:2021-03-01 00:00:00

  • Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

    abstract::Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylog...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.12.002

    authors: Kay RF

    更新日期:2015-01-01 00:00:00

  • A rapid diversification of rainforest trees (Guatteria; Annonaceae) following dispersal from Central into South America.

    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

    authors: Erkens RH,Chatrou LW,Maas JW,van der Niet T,Savolainen V

    更新日期:2007-07-01 00:00:00

  • Further consideration on the phylogeny of the Ciliophora: Analyses using both mitochondrial and nuclear data with focus on the extremely confused class Phyllopharyngea.

    abstract::Most ciliate phylogenetic analyses have largely relied on the nuclear small subunit ribosome DNA (nSSU-rDNA) locus. However, single locus or multi-loci from the same genome or chromosome may not be sufficient enough to elucidate phylogenetic relationships among ciliate taxa. Therefore, in addition to nSSU-rDNA, the mi...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2017.04.018

    authors: Wang P,Wang Y,Wang C,Zhang T,Al-Farraj SA,Gao F

    更新日期:2017-07-01 00:00:00

  • From America to Eurasia: a multigenomes history of the genus Abies.

    abstract::The origin of conifer genera, the main components of mountain temperate and boreal forests, was deemed to arise in the Mesozoic, although paleontological records and molecular data point to a recent diversification, presumably related to Neogene cooling. The geographical area(s) where the modern lines of conifers emer...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.03.009

    authors: Semerikova SA,Khrunyk YY,Lascoux M,Semerikov VL

    更新日期:2018-08-01 00:00:00