Towards a dated molecular phylogeny of the Tanypodinae (Chironomidae, Diptera)

2017 ◽  
Vol 31 (3) ◽  
pp. 302 ◽  
Author(s):  
M. N. Krosch ◽  
P. S. Cranston ◽  
L. M. Bryant ◽  
F. Strutt ◽  
S. R. McCluen
Keyword(s):  
Molecular Phylogeny ◽  
Mixed Model ◽  
Mitochondrial Protein ◽  
Divergence Time ◽  
Molecular Data ◽  
Ribosomal Gene ◽  
Protein Coding ◽  
Weak Support ◽  
Gene Coi ◽  
Inference Methods

A dated molecular phylogeny is proposed for the Tanypodinae, a diverse subfamily of Chironomidae (Diptera). We used molecular data from fragments of one ribosomal gene (28S), one nuclear protein-coding gene (CAD), and one mitochondrial protein-coding gene (COI), analysed using mixed model Bayesian and maximum likelihood inference methods. All proposed tribes were sampled, namely, Anatopyniini, Clinotanypodini, Coelopyniini, Fittkauimyiini, Macropelopiini, Natarsiini, Pentaneurini, Procladiini and Tanypodini. A multilocus dataset of 1938 characters was compiled from 123 individuals including outgroups. Monophyly was supported for all tribes although some relationships were not robust. Relationships between tribes and some genus groups are highly congruent with a morphology-based estimate. Relationships within tribe Pentaneurini mostly find weak support, yet previously hypothesised groupings and monophyly or lack thereof in well-sampled genera are revealed. The tempo of diversification of the family was deduced by divergence time analysis (BEAST). Origination of a subfamily stem group in the late Jurassic to early Cretaceous was inferred, with all tribes and many genera of Pentaneurini originating and diversifying in the Cretaceous. Some nodes are biogeographically informative. Gene sections supported the backbone, but more extensive sampling is needed to estimate shallower phylogenies and to better understand the tempo and diversification of Tanypodinae.

Not endemic after all: Imparipecten Freeman, 1961 (Diptera: Chironomidae) described from the Neotropical Region

Zootaxa ◽  
2018 ◽  
Vol 4532 (3) ◽  
pp. 396 ◽  
Author(s):  
LÍVIA MARIA FUSARI ◽  
GALILEU P.S. DANTAS ◽  
NEUSA HAMADA ◽  
VANDERLY ANDRADE-SOUZA ◽  
KÁTIA M. LIMA ◽  
...  
Keyword(s):  
Nuclear Protein ◽  
Mitochondrial Protein ◽  
Neotropical Region ◽  
Genetic Distances ◽  
Ribosomal Gene ◽  
Monotypic Genus ◽  
Bayesian Phylogenetics ◽  
Protein Coding ◽  
Gene Coi ◽  
First Time

Imparipecten, a previously monotypic genus, was considered endemic to Australia. Here, we report Imparipecten from the Neotropical region for the first time and describe Imparipecten sychnacanthus sp. n. from Brazil. The association between larvae and adults was established by sequencing a fragment of one ribosomal gene (28S), two fragments of a nuclear protein-coding gene (CAD1 and CAD4), and one mitochondrial protein-coding gene (COI). We also show the close molecular proximity with Imparipecten pictipes through analyses of genetic distances and Bayesian phylogenetics. 

Cryptic speciation in a biodiversity hotspot: multilocus molecular data reveal new velvet worm species from Western Australia (Onychophora : Peripatopsidae : Kumbadjena)

2018 ◽  
Vol 32 (6) ◽  
pp. 1249 ◽  
Author(s):  
Shoyo Sato ◽  
Rebecca S. Buckman-Young ◽  
Mark S. Harvey ◽  
Gonzalo Giribet
Keyword(s):  
Western Australia ◽  
18S Rrna ◽  
Mitochondrial Protein ◽  
Molecular Data ◽  
12S Rrna ◽  
Protein Coding ◽  
Complex Morphology ◽  
Velvet Worm ◽  
Three New Species ◽  
Western Australian

There is a yet uncovered multitude of species to be found among Western Australian Onychophora. Kumbadjena, one of the two genera that reside in this region, has been previously suggested to house an extensive species complex. Morphology alone has not been able to elucidate the diversity in this genus and has instead muddled species delineations. Topologies and species delimitation analyses resulting from the sequences of two mitochondrial ribosomal markers (12S rRNA and 16S rRNA), one nuclear ribosomal marker (18S rRNA), and one mitochondrial protein-coding gene (cytochrome c oxidase subunit I) are indicative of several undescribed species. Fixed diagnostic nucleotide changes in the highly conserved sequences of 18S rRNA warrant distinction of three new species of Kumbadjena: K. toolbrunupensis, sp. nov., K. karricola, sp. nov., and K. extrema, sp. nov. The geographic distributions of the proposed species suggest that Kumbadjena is another example of short-range endemism, a common occurrence in the flora and fauna of the region. The extensive biodiversity and endemism in the region necessitates conservation to preserve the species and processes that promote speciation harboured by Western Australia.

scholarly journals Molecular phylogeny of Culex subgenus Melanoconion (Diptera: Culicidae) based on nuclear and mitochondrial protein-coding genes

2018 ◽  
Vol 5 (5) ◽  
pp. 171900 ◽  
Author(s):  
Carolina Torres-Gutierrez ◽  
Tatiane M. P. de Oliveira ◽  
Kevin J. Emerson ◽  
Eduardo Sterlino Bergo ◽  
Maria Anice Mureb Sallum
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Phylogenetic Signal ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Single Copy ◽  
Neotropical Region ◽  
Nuclear Genes ◽  
Morphological Identification ◽  
Protein Coding

The subgenus Melanoconion of the mosquito genus Culex is taxonomically diverse and is widely distributed in the Neotropical Region, with 10 species occurring in the Nearctic Region. Species of this subgenus pose a taxonomical challenge because morphological identification is based largely on anatomical characters of the male genitalia. We addressed the monophyly of the Spissipes and Melanoconion Sections of the subgenus Melanoconion and some of the informal groups in each section. Our sample taxa included 97 specimens representing 43 species, from which we analysed fragments of two single-copy nuclear genes ( CAD , HB ) and one mitochondrial gene ( COI ). Phylogenetic relationships within the subgenus are presented based on results of maximum-likelihood and Bayesian analyses using a multi-locus matrix of DNA sequences. We show a molecular phylogeny of Melanoconion in which both sections were recovered as monophyletic groups. The monophyly of the Atratus and Pilosus groups was confirmed. Within each section, other monophyletic groups were recovered highlighting the potential need for future nomenclature rearrangement. The phylogenetic signal contained in nuclear genes, when analysed together, was more informative than each gene analysed separately, corroborating monophyly of Melanoconion relative to Culex ( Culex ) species included in the analyses, the Melanoconion and Spissipes Sections and some species groups. Our results provide new information for the classification of the subgenus and additional data that can be used to improve species identification when a more representative taxon sampling is available.

Molecular phylogeny and systematics of Prostanthera (Lamiaceae)

2012 ◽  
Vol 25 (5) ◽  
pp. 341 ◽  
Author(s):  
Trevor C. Wilson ◽  
Barry J. Conn ◽  
Murray J. Henwood
Keyword(s):  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Morphological Variation ◽  
Maximum Parsimony ◽  
Sequence Data ◽  
Morphological Characters ◽  
Molecular Data ◽  
Sister Relationship ◽  
Definition Of ◽  
Inference Methods

Prostanthera is the largest genus of Lamiaceae in Australia and was last comprehensively revised in 1870. To test the classification, and the homology of the morphological characters on which it is based, we analysed nuclear (ETS) and chloroplast (trnT–F and ndhF–rpl32) sequence data for 71 species of Westringieae (Lamiaceae) in separate and combined datasets by using maximum-parsimony and Bayesian-inference methods. Results supported the monophyly of the Westringieae, but indicated that Prostanthera is paraphyletic with respect to Wrixonia, requiring the latter to be synonymised with the former. Although combinations of datasets provided some degree of infrageneric resolution within Prostanthera sensu lato, none of its sections or series could be recovered unambiguously. Prostanthera section Prostanthera and P. section Klanderia (regarded as entomophilous and ornithophilous, respectively) did not form a sister relationship, and neither could be unequivocally resolved as monophyletic. However, all species of P. section Klanderia nested within P. section Prostanthera raising the possibility that P. section Prostanthera is paraphyletic. Similarly, the phylogeny of Prostanthera based on molecular data could not be reconciled with the morphological definition of the traditionally recognised series. We recommend abandoning Bentham’s series as a means of organising morphological variation within the genus, but acknowledge that it is premature to discard Bentham’s sections. The evolutionary and systematic implications of the lack of congruence between our molecular phylogeny and morphologically defined subgeneric taxa are discussed.

scholarly journals A molecular phylogeny of Schizothoracinae (Teleostei: Cypriniformes: Cyprinidae) based on 12 protein-coding mitochondrial genes and RAG1 gene analysis

2019 ◽  
Author(s):  
Yurong Du ◽  
Ting Wang ◽  
Delin Qi ◽  
Desheng Qi ◽  
Weilin Li ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Sister Group ◽  
Mitochondrial Genes ◽  
Tibet Plateau ◽  
Divergence Times ◽  
Protein Coding ◽  
Rag1 Gene ◽  
The Times

AbstractThe ever-increasing interest in the investigation of origin and speciation of schizothoracine fishes can be dated to 20th century. However, molecular phylogeny of Schizothoracinae and their phylogenetic relationships, as well as the divergence times still remain controversial. In this study, two DNA sets consisting of 12 protein-coding mitochondrial genes from 254 individuals and RAG1 gene from 106 individuals were used to reconstruct the phylogenetic relationships and calculate the divergence times among the subfamily schizothoracinae. Our results indicated that both of the data sets supported a non-monophyletic relationship due to involving of species of Barbinae. However, the phylogenetic relationships based on mtDNA genes were more reliable than that inferred from RAG1 gene. The highly specialized grade formed a monophyletic group, together with Ptychobarbus as a sister group of Diptychus and Gymnodiptychus, which was belonging to specialized grade, indicating that Ptychobarbus may be transition species to involve to highly specialized schizothoracianae. In addition, the primitive grade clustered with Percocypris pingi, a species of Barbinae. Based on mtDNA gene, the speciation time of Schizothoracinae was 66 Ma, and the divergence time of the primitive grade and Percocypris pingi was 64 Ma. The speciation times of the three grades Schizothoracinae were 57 Ma, 51 Ma and 43 Ma, respectively; and the divergence time of specialized and highly specialized grade was 46 Ma. The divergence times of three grades were not consistent with the three stages of uplift of Qinghai-Tibet Plateau, which is older than the times.

scholarly journals Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8033
Author(s):  
Siuli Mitra ◽  
Vaishnavi Kunteepuram ◽  
Klaus-Peter Koepfli ◽  
Neha Mehra ◽  
Wajeeda Tabasum ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Divergence Time ◽  
Protein Coding ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Phylogenetic Implications ◽  
The Family

The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.

Dissecting the major African snake radiation: a molecular phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia)

Zootaxa ◽  
2008 ◽  
Vol 1945 (1) ◽  
pp. 51-66 ◽  
Author(s):  
NICOLAS VIDAL ◽  
WILLIAM R. BRANCH ◽  
OLIVIER S. G. PAUWELS ◽  
S. BLAIR HEDGES ◽  
DONALD G. BROADLEY ◽  
...  
Keyword(s):  
Mitochondrial Protein ◽  
Sister Group ◽  
Molecular Data ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Mitochondrial Rrna ◽  
Protein Coding Genes ◽  
History Of

The Elapoidea includes the Elapidae and a large (~60 genera, 280 sp.) and mostly African (including Madagascar) radiation termed Lamprophiidae by Vidal et al. (2007), that includes at least four major groups: the psammophiines, atractaspidines, lamprophiines and pseudoxyrhophiines. In this work, we reviewed the recent taxonomic history of the lamprophiids, and built a data set including two nuclear protein-coding genes (c-mos and RAG2), two mitochondrial rRNA genes (12S and 16S rRNA) and two mitochondrial protein-coding genes (cytochrome b and ND4) for 85 species belonging to 45 genera (thus representing about 75% of the generic diversity and 30% of the specific diversity of the radiation), in order to clarify the phylogenetic relationships of this large and neglected group at the subfamilial and generic levels. To this aim, 480 new sequences were produced. The vast majority of the investigated genera fall into four main monophyletic clusters, that correspond to the four subfamilies mentioned above, although the content of atractaspidines, lamprophiines and pseudoxyrhophiines is revised. We confirm the polyphyly of the genus Stenophis, and the relegation of the genus name Dromophis to the synonymy of the genus name Psammophis. Gonionotophis brussauxi is nested within Mehelya. The genus Lamprophis Fitzinger, 1843 is paraphyletic with respect to Lycodonomorphus Fitzinger, 1843. Lamprophis swazicus is the sister-group to Hormonotus modestus, and may warrant generic recognition. Molecular data do not support the traditional placement of Micrelaps within the Atractaspidinae, but its phylogenetic position, along with that of Oxyrhabdium (previously considered to belong to the Xenodermatidae), requires additional molecular data and they are both treated as Elapoidea incertae sedis. The interrelationships of Psammophiinae, Atractaspidinae, Lamprophiinae, Pseudoxyrhophiinae, Prosymna (13 sp.), Pseudaspis (1 sp.) and Pythonodipsas (1 sp.), Buhoma (2 species), and Psammodynastes (1 sp.) remain unresolved. Finally, the genus Lycognathophis, endemic to the Seychelles, does not belong to the African radiation, but to the Natricidae.

Polyphyletic Origins of Schizothoracinae Fishes (Cyprinidae) in Respect to Their Mitochondrial Protein-Coding Genes

2019 ◽  
Vol 07 (02) ◽  
Author(s):  
Saira Bibi ◽  
Muhammad Fiaz Khan ◽  
Aqsa Rehman ◽  
Faisal Nouroz
Keyword(s):  
Mitochondrial Protein ◽  
Protein Coding ◽  
Protein Coding Genes
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