Phylogenetic relationships of xenodermid snakes (Squamata: Serpentes: Xenodermidae), with the description of a new genus

Xenodermidae is a generally poorly known lineage of caenophidian snakes found in South, East and Southeast Asia. We report molecular phylogenetic analyses for a multilocus data set comprising all five currently recognised genera and including new mitochondrial and nuclear gene sequence data for the recently described Stoliczkia vanhnuailianai. Our phylogenetic results provide very strong support for the non-monophyly of Stoliczkia, as presently constituted, with S. borneensis being more closely related to Xenodermus than to the Northeast Indian S. vanhnuailianai. Based on phylogenetic relationships and morphological distinctiveness, we transfer Stoliczkia borneensis to a new monotypic genus endemic to Borneo, Paraxenodermusgen. nov. We also present new morphological data for P. borneensis.

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Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽

10.1515/mammalia-2017-0081 ◽

2019 ◽

Vol 83 (2) ◽

pp. 180-189 ◽

Cited By ~ 2

Author(s):

Adam W. Ferguson ◽

Houssein R. Roble ◽

Molly M. McDonough

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Alternative Hypothesis ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Sister Relationship ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Molecular Phylogenetic ◽

Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

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Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽

10.1093/auk/124.1.71 ◽

2007 ◽

Vol 124 (1) ◽

pp. 71-84 ◽

Cited By ~ 5

Author(s):

W. Andrew Cox ◽

Rebecca T. Kimball ◽

Edward L. Braun

Keyword(s):

New World ◽

Sequence Data ◽

Evolutionary Relationship ◽

Strong Support ◽

Nuclear Data ◽

Morphological Data ◽

Phylogenetic Position ◽

Data Set ◽

Mitochondrial Data ◽

Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

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Phylogenetic relationships of Australian Scirtidae (Coleoptera) based on mitochondrial and nuclear sequences

Invertebrate Systematics ◽

10.1071/is13046 ◽

2014 ◽

Vol 28 (6) ◽

pp. 628 ◽

Cited By ~ 3

Author(s):

Steven J. B. Cooper ◽

Christopher H. S. Watts ◽

Kathleen M. Saint ◽

Remko Leijs

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Elongation Factor ◽

Nuclear Gene ◽

Species Complexes ◽

Close Relationship ◽

Molecular Phylogenetic ◽

Coi Sequences ◽

Elongation Factor 1 ◽

Combined Data

Scirtidae is a cosmopolitan group of beetles with aquatic or saproxylic larvae. A large diversity of species has recently been described from Australia, but their systematics is uncertain. There is evidence that current genera are polyphyletic and that Australian species were wrongly placed in northern hemisphere genera. Here we investigate the systematics of Australian Scirtidae using molecular phylogenetic analyses of combined data from the mitochondrial cytochrome c oxidase subunit 1 (COI) and nuclear gene elongation factor 1-α (EF1-α) genes. We also assess the current taxonomy of Australian Scirtidae using partial COI sequences. Bayesian phylogenetic analyses of COI and EF1-α sequence data from 81 taxa show that the Australian genera Contacyphon, Pseudomicrocara and Prionocyphon are polyphyletic. There is no close relationship between Australian and Eurasian genera, with the exception of Scirtes. Phylogenetic analyses of partial COI data from Australian Scirtidae generally support the current α taxonomy, with the exception of several species that may be associated with species complexes. Geographically a high proportion of species lineages are restricted to relict patches of wet forest suggesting that they may be relict populations. The phylogeny and sequence data presented here provide a sound basis for further systematic and biogeographical studies of the Scirtidae.

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Phylogenetic relationships and placement of the Empidoidea (Diptera: Brachycera) based on 28S rDNA and EF-1α sequences

Insect Systematics & Evolution ◽

10.1163/187631202x00226 ◽

2002 ◽

Vol 33 (4) ◽

pp. 421-444 ◽

Cited By ~ 27

Author(s):

Kenneth P. Collins ◽

Brian M. Wiegmann

Keyword(s):

Phylogenetic Relationships ◽

Elongation Factor ◽

Sister Group ◽

Morphological Data ◽

Sister Group Relationship ◽

Data Set ◽

Molecular Phylogenetic ◽

Data Partitions ◽

28S Ribosomal Dna ◽

Combined Data

AbstractThe phylogenetic relationships within the Eremoneura (Empidoidea + Cyclorrhapha) have been controversial. The monophyly of the Empidoidea, as well as the position and rank of higher-level empidoid clades remains unresolved despite numerous analyses using morphological data. In addition, the origin of the Cyclorrhapha and their relationship to the Empidoidea continues to be debated. We present the results of a molecular phylogenetic analysis using nucleotide sequences collected from 28S ribosomal DNA (rDNA) and elongation factor-1α (EF-1α) genes. All currently recognized empidoid families and subfamilies, many lower cyclorrhaphan families (including Opetiidae), and several asiloid outgroups are represented in this study. Unweighted and weighted parsimony, as well as maximum likelihood analyses were applied to individual data partitions and a combined data set. Our results support the monophyly of both Empidoidea and Cyclorrhapha (including Opetia), as well as their sister-group relationship. Within Empidoidea we find support for the following: 1) Chvála's (1983) proposal to divide Empidoidea into five families; 2) Atelestidae as the basal empidoid lineage; and 3) monophyly of Microphoridae + Dolichopodidae.

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Corrigendum to: Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

Invertebrate Systematics ◽

10.1071/is02046_co ◽

2003 ◽

Vol 17 (4) ◽

pp. 605 ◽

Cited By ~ 1

Author(s):

Philip S. Ward ◽

Seán G. Brady

Keyword(s):

Sequence Data ◽

Strong Support ◽

Sister Group ◽

Molecular Data ◽

Morphological Data ◽

Recent Common Ancestor ◽

Bootstrap Support ◽

Data Set ◽

Molecular Sequence Data ◽

Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

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Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences

Antarctic Science ◽

10.1017/s0954102009990253 ◽

2009 ◽

Vol 21 (6) ◽

pp. 565-570 ◽

Cited By ~ 15

Author(s):

Kristen L. Kuhn ◽

Thomas J. Near

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Nuclear Gene ◽

Single Copy ◽

Morphological Characters ◽

Mitochondrial Genes ◽

Phylogenetic Resolution

AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

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A molecular phylogenetic approach to Longidoridae (Nematoda: Dorylaimida)

Nematology ◽

10.1163/1568541054192108 ◽

2005 ◽

Vol 7 (1) ◽

pp. 111-124 ◽

Cited By ~ 69

Author(s):

Yu He ◽

Sergei A. Subbotin ◽

Tatiana V. Rubtsova ◽

Franco Lamberti ◽

Derek J.F. Brown ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Large Subunit ◽

Strong Support ◽

Nuclear Gene ◽

Sister Group ◽

Bayesian Posterior Probability ◽

Molecular Phylogenetic ◽

Secondary Structure Models ◽

Outgroup Taxon ◽

Lsu Rrna

Abstract The Longidoridae are a group of ectoparasitic nematodes including two subfamilies and six genera with hundreds of species. Sequences of the D2 and D3 expansion region of the large subunit (LSU) rRNA nuclear gene were amplified and used to reconstruct the phylogeny of longidorids. Phylogenetic analyses with maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) were performed with one outgroup taxon and 62 longidorid sequences. Confidence of inferred clades was assessed by non-parametric bootstrapping for MP and Bayesian posterior probability for ML. All analyses placed Paralongidorus species as an inner group within the otherwise monophyletic genus Longidorus. The genus Xiphinema, except for X. americanum-group species, was placed as the sister group of Longidorus with strong support from the ML and BI analyses. The X. americanum-group was strongly supported as an exclusive clade to other genus Xiphinema species. The position of the Xiphidorus clade was not well resolved and the phylogenetic analyses did not support it as a sister group to Longidorus as previously inferred from morphology. Secondary structure models were constructed for the D2/D3 region of LSU rRNA for all studied species. It was found that sequence-based and structural morphometric rRNA phylogenies were incongruent.

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Phylogeny of the water strider genus Aquarius Schellenberg (Heteroptera: Gerridae) based on nuclear and mitochondrial DNA sequences and morphology

Insect Systematics & Evolution ◽

10.1163/187631200x00327 ◽

2000 ◽

Vol 31 (1) ◽

pp. 71-90 ◽

Cited By ~ 26

Author(s):

Nils Møller Andersen ◽

Jakob Damgaard ◽

Felix A.H. Sperling

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Mitochondrial Gene ◽

Nuclear Gene ◽

Molecular Data ◽

Morphological Data ◽

Published Data ◽

Data Sets ◽

Gene Encoding ◽

Data Set

AbstractWe examined phylogenetic relationships among gerrid water striders of the genus Aquarius Schellenberg using molecular and morphological characters. The molecular data sets included 780 bp sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI), and 515 bp sequence data from the nuclear gene encoding elongation factor I alpha (EF-1α). The morphological data set was a slightly modified version of a previously published data set. We included all 17 known species and one subspecies of Aquarius as well as five species from three related genera, Gigantometra gigas, Limnoporus esakii, L. rufoscutellatus, Gerris pingreensis, and G. lacustris. Unweighted parsimony analyses of the COI data set gave a single most parsimonious tree (MPT) with a topology quite similar to the morphological tree. Parsimony analyses of the EF-1α data set gave 3 MPT's and a strict consensus of these trees gave a tree with a slightly different topology. A combined analysis of the three data sets gave a single MPT with the same topology as for the morphological data set alone. The phylogeny of Aquarius presented here supports the monophyly of the A. najas, remigis, conformis and paludum species groups as well as previous hypotheses about their relationships. On the other hand, the inclusion of molecular data weakens the support for the monophyly of the genus Aquarius, and questions the specific status of the eastern North American A. nebularis (as separate from A. conformis) and members of the Nearctic A. remigis group. Finally, we discuss the implications of the reconstructed phylogeny in the biogeography and ecological phylogenetics of Aquarius.

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New genera, species and combinations in the Pseudomicrocara Armstrong group (Coleoptera: Scirtidae) based on morphology supported by mitochondrial and nuclear gene sequence data

Zootaxa ◽

10.11646/zootaxa.4831.1.1 ◽

2020 ◽

Vol 4831 (1) ◽

pp. 1-66

Author(s):

C.H.S. WATTS ◽

S.J.B. COOPER ◽

M.L. LIBONATTI

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Elongation Factor ◽

Nuclear Gene ◽

New Genera ◽

Elongation Factor 1 Alpha ◽

Distinct Lineage ◽

Elongation Factor 1 ◽

Nuclear Gene Sequence

The Australian Scirtidae genus Pseudomicrocara Armstrong, previously shown to be polyphyletic, is revised using both morphology and sequence data from the mitochondrial gene cytochrome oxidase subunit 1 and two nuclear genes, elongation factor 1-alpha and topoisomerase. Twenty-three genera, 16 of which are new, are recognised based on morphology, primarily of the mandibles and maxillary palpi, and male and female genitalia. Maximum likelihood and Bayesian phylogenetic analyses were used to examine relationships among species from 21 of the 23 recognised genera. Fifteen of the genera were recovered as distinct lineages. A further six, Accolabass Watts, Anocyphon gen. nov., Copiacyphon gen. nov., Nasutuscyphon gen. nov., Pseudomicrocara and Saprocyphon gen. nov. were considered to be genera based on both morphology and phylogenetic analysis but their species composition is uncertain and will require more work to confirm. The 17 new genera are fully described, keys are provided to all the genera in the Pseudomicrocara group, and to all the species in the genera Copiacyphon gen. nov., Spilotocyphon gen. nov., Accolabass Watts, Saltuscyphon gen. nov. and Vadumcyphon gen. nov. The male aedeagi of all new genera and species are illustrated, as are the female prehensors of some species. The following genera are described as new: Alpestriscyphon gen. nov., Anthocara gen. nov., Anocyphon gen. nov., Copiacyphon gen. nov., Furcacyphon gen. nov., Latuscara gen. nov., Pictacara gen. nov., Nasutuscyphon gen. nov., Nektriscyphon gen. nov., Pumiliocara gen. nov., Ruborcara gen. nov., Saltuscyphon gen. nov., Saprocyphon gen. nov., Sisyracyphon gen. nov., Spilotocyphon gen. nov., Tenebriocyphon gen. nov. and Vadumcyphon gen. nov. A total of 45 new combinations are proposed. The following species are described as new: Accolabass monteithi sp. nov.; Alpestriscyphon bartlefrere sp. nov., Al. spurgeon sp. nov.; Anocyphon lepus sp. nov.; Copiacyphon brindaleensis sp. nov., C. cardinalis sp. nov., C. dytikos sp. nov.; Pumiliocara peneparva sp. nov.; Ruborcara saintae sp. nov.; Saltuscyphon montanus sp. nov., Sal. teraniaensis sp. nov.; Saprocyphon bithongensis sp. nov.; Sisyracyphon brisbanensis sp. nov., S. bulburinensis sp. nov.; Spilotocyphon occidentalis sp. nov., Sp. orientalis sp. nov., Sp. zwicki sp. nov.; Vadumcyphon centralis sp. nov., V. rugosus sp. nov. A checklist of all Australian taxa in the redefined Pseudomicrocara group is included. Sequence data of the Argentinian species Pseudomicrocara antarctica (Fairmaire) is included. Phylogenetic analyses place this species as a distinct lineage within the Pseudomicrocara group.

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Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

10.1101/824623 ◽

2019 ◽

Author(s):

Sigrid Liede-Schumann ◽

Guido W. Grimm ◽

Nicolai M. Nürk ◽

Alastair J. Potts ◽

Ulrich Meve ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Cape Floristic Region ◽

Rapid Radiation ◽

Data Set ◽

Widespread Species ◽

Dna Sequence Data ◽

Phylogenetic Affinities

AbstractBackgroundDrosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum together with the highly succulent and species-rich tribe Ruschieae constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.MethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species represented by multiple accessions of Drosanthemum. A well-curated, geo-referenced occurrence data set comprising the phylogenetically studied and 867 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.ResultsPhylogenetic inference supports nine clades within Drosanthemum, seven of them group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region revealed phylogenetic affinities not obvious in the phylogenetic tree. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are molecular and morphologically diverse. In contrast, less species-rich, molecularly less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest initial rapid radiation generating the main lineages, with some clades showing subsequent diversification.

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