scholarly journals Phylogenetic relationships of the European newts (genus Triturus) tested with mitochondrial DNA sequence data

1999 ◽  
Vol 68 (2) ◽  
pp. 73-81 ◽  
Author(s):  
I. Zajc ◽  
J.W. Arntzen
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Data ◽  
A Priori ◽  
Strong Support ◽  
Species Group ◽  
Rrna Genes ◽  
Sister Taxon ◽  
Phylogenetic Position ◽  
12S Rrna ◽  
16S Rrna Sequence

European newts (genus Triturus) are widely studied, but their phylogeny is not yet unambiguously resolved. Fragments of mitochondrial DNA experiencing different rates of evolution (the ATPase and 12S rRNA genes) were sequenced in order to test a phylogenetic hypothesis derived from biochemical and behavioral data. Well-supported branches of the existing phylogeny gained support in our study. The monophyletic origin of the hypothesized T. boscai – T. italicus clade remained ambiguous, whereas strong support was gained for the sister-taxon relationship of T. vulgaris and T. montandoni. The position of T. vittatus as a sister taxon to the T. marmoratus species group was also supported. The phylogenetic position of T. alpestris could not be clarified. With an in-group taxon sampling denser than in previous molecular phylogenetic studies and under the a priori selection of species from the genera Cynops, Neurergus and Paramesotriton as out-groups, the monophyly of Triturus was strongly supported. It cannot be excluded, however, that the presumed out-group actually belongs to the in-group, rendering Triturus paraphyletic as was concluded from recently published 12S and 16S rRNA sequence data.

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

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
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

scholarly journals New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Kevin M. Kocot ◽  
Albert J. Poustka ◽  
Isabella Stöger ◽  
Kenneth M. Halanych ◽  
Michael Schrödl
Keyword(s):  
Mixture Models ◽  
Strong Support ◽  
Housekeeping Genes ◽  
Data Matrix ◽  
Quality Data ◽  
Sister Taxon ◽  
Phylogenetic Position ◽  
Morphological Studies ◽  
Homogeneous Models ◽  
Molluscan Evolution

AbstractRelationships among the major lineages of Mollusca have long been debated. Morphological studies have considered the rarely collected Monoplacophora (Tryblidia) to have several plesiomorphic molluscan traits. The phylogenetic position of this group is contentious as morphologists have generally placed this clade as the sister taxon of the rest of Conchifera whereas earlier molecular studies supported a clade of Monoplacophora + Polyplacophora (Serialia) and phylogenomic studies have generally recovered a clade of Monoplacophora + Cephalopoda. Phylogenomic studies have also strongly supported a clade including Gastropoda, Bivalvia, and Scaphopoda, but relationships among these taxa have been inconsistent. In order to resolve conchiferan relationships and improve understanding of early molluscan evolution, we carefully curated a high-quality data matrix and conducted phylogenomic analyses with broad taxon sampling including newly sequenced genomic data from the monoplacophoran Laevipilina antarctica. Whereas a partitioned maximum likelihood (ML) analysis using site-homogeneous models recovered Monoplacophora sister to Cephalopoda with moderate support, both ML and Bayesian inference (BI) analyses using mixture models recovered Monoplacophora sister to all other conchiferans with strong support. A supertree approach also recovered Monoplacophora as the sister taxon of a clade composed of the rest of Conchifera. Gastropoda was recovered as the sister taxon of Scaphopoda in most analyses, which was strongly supported when mixture models were used. A molecular clock based on our BI topology dates diversification of Mollusca to ~546 MYA (+/− 6 MYA) and Conchifera to ~540 MYA (+/− 9 MYA), generally consistent with previous work employing nuclear housekeeping genes. These results provide important resolution of conchiferan mollusc phylogeny and offer new insights into ancestral character states of major mollusc clades.

scholarly journals Kaindipsocinae is a sister taxon to the rest of Psocidae (Insecta:Psocodea:'Psocoptera'

2011 ◽  
Vol 25 (2) ◽  
pp. 81 ◽  
Author(s):  
Kazunori Yoshizawa ◽  
Emilie Bess ◽  
Kevin P. Johnson
Keyword(s):  
Strong Support ◽  
Molecular Data ◽  
Species Group ◽  
Sister Taxon ◽  
Sister Relationship ◽  
Systematic Status ◽  
Data Support ◽  
Morphological And Molecular Data

The systematic status of Kaindipsocinae (formerly Kaindipsocini) is revised based on morphology of the male terminalia and on molecular data. The genera Clematostigma, Lasiopsocus and Tanystigma are newly assigned to this subfamily. The ‘Blaste’ lunulata species-group is also placed within Kaindipsocinae and is probably closest to Kaindipsocus. Both morphological and molecular data provide strong support for monophyly of Kaindipsocinae and molecular data support a sister relationship between this subfamily and the rest of Psocidae.

Hidden in the highlands: the description and phylogenetic position of a novel endemic freshwater crab species (Potamonautidae : Potamonautes) from Zimbabwe

2013 ◽  
Vol 27 (5) ◽  
pp. 530 ◽  
Author(s):  
Ethel E. Phiri ◽  
Savel R. Daniels
Keyword(s):  
Southern Africa ◽  
Sequence Data ◽  
Phylogenetic Position ◽  
12S Rrna ◽  
Mountain Range ◽  
Freshwater Crab ◽  
Crab Species ◽  
Mountainous Regions ◽  
Freshwater Crabs ◽  
Mtdna Sequence

A recent sampling endeavour of freshwater crabs along the high-lying streams of the Nyanga mountain range in Mutare (Eastern Highlands, Zimbabwe) yielded a morphologically distinct, as yet undescribed species. The novel Zimbabwean species is compared to the 16 described species from southern Africa based on mtDNA sequence data derived from three partial gene sequences (12S rRNA, 16S rRNA and COI). The new Zimbabwean species was found to be a sister taxon to Potamonautes mulanjeensis. These two species are morphologically and genetically easily differentiated. The new species is described as Potamonautes mutareensis, sp. nov. and is compared morphologically to the known freshwater crab species of southern Africa. A dichotomous key to the four described freshwater crab species that occur in Zimbabwe is also provided. Our results suggest that species diversity and endemism of freshwater decapods and other habitat specialists is likely to be high in unsampled mountainous regions.

Copro-PCR based detection of bovine schistosome infection in India

2015 ◽  
Vol 90 (1) ◽  
pp. 102-107 ◽  
Author(s):  
B. Lakshmanan ◽  
K. Devada ◽  
S. Joseph ◽  
T.V. Aravindakshan ◽  
L. Sabu
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Rna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
12S Rrna ◽  
Gene Sequences ◽  
Schistosome Infection ◽  
Faecal Samples ◽  
Polymerase Chain ◽  
Trematode Infections

AbstractSchistosomosis and amphistomosis are the two economically important and widely prevalent snail-borne trematode infections in grazing cattle of southern India. Acute infections are symptomatically similar and difficult to detect by routine microscopy for eggs. The present study was directed towards the development of a copro-polymerase chain reaction (copro-PCR) for detection of bovine schistosome species, using custom-designed primers targeting 18S and 28S ribosomal RNA as well as mitochondrial DNA. The study demonstrated the enhanced diagnostic specificity of mitochondrial DNA markers over ribosomal RNA genes as genus-specific probes to detect schistosomes. We developed a sensitive PCR assay using primers designed from mitochondrial DNA sequences targeting the partialrrnl(16S rRNA), tCys (transfer RNA for cysteine) and partialrrnS(12S rRNA) genes ofSchistosoma spindaleto specifically detect schistosome infection from faecal samples of naturally infected bovines. The salient findings of the work also throw light on to the high similarity of the ribosomal RNA gene sequences of schistosomes with those ofGastrothylax crumeniferandFischoederius elongatus,the most prevalent pouched amphistomes of the region. Further investigation has to be directed towards unravelling the complete gene sequences of 18S and 28S ribosomal RNA as well as mitochondrial DNA sequences of amphistome isolates from India.

scholarly journals PHYLOGENETIC RELATIONSHIPS OF LEPTOBRACHIUM HASSELTII TSCHUDI, 1838 (AMPHIBIA, ANURA, MEGOPHRYIDAE) - DETECTION OF A POSSIBLE CRYPTIC SPECIES

TREUBIA ◽  
2018 ◽  
Vol 44 ◽  
pp. 15 ◽  
Author(s):  
Amir Hamidy ◽  
Masafumi Matsui
Keyword(s):  
Sequence Data ◽  
Taxonomic Status ◽  
Species Level ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
12S Rrna ◽  
The West ◽  
Major Clade ◽  
Dna Phylogeny ◽  
Acoustic Data

By examining mitochondrial DNA phylogeny using 2424bp of sequence data 12S rRNA, tRNAval, and 16S rRNA genes, we evaluated the taxonomic relationships among Javan litter frogs Leptobrachium hasseltii from southern Sumatra, Java, and Bali. Leptobrachium hasseltii formed a well-supported monophyletic group, which comprised two major clades. One major clade represented the southern Sumatran and Javan populations and the other consisted of the population from Bali. The Javan and southern Sumatran clade included two subclades: the West Javan-southern Sumatran group and the Central Javan group. The genetic divergence between the two major clades (Bali vs. Java-Sumatra) suggested their separation happen at species level. Further studies using morphological and acoustic data are needed to determine the taxonomic status of Bali population.

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

A new species of Hyloscirtus (Anura, Hylidae) from the Colombian and Venezuelan slopes of Sierra de Perijá, and the phylogenetic position of Hyloscirtus jahni (Rivero, 1961)

Zootaxa ◽  
2018 ◽  
Vol 4382 (1) ◽  
pp. 121 ◽  
Author(s):  
FERNANDO J. M. ROJAS-RUNJAIC ◽  
EDWIN E. INFANTE-RIVERO ◽  
PATRICIA E. SALERNO ◽  
FABIO LEONARDO MEZA-JOYA
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Internal Surface ◽  
Molecular Data ◽  
Species Group ◽  
Sister Species ◽  
Phylogenetic Position ◽  
Advertisement Call ◽  
12S Rrna ◽  
A New Species

A new species of Hyloscirtus, belonging to the H. bogotensis species Group, is described from the Venezuelan and Colombian slopes of the Sierra de Perijá. The new species can be readily distinguished from its congeners by the combination of the following characters: mental gland present, disc-shaped and small; ulnar, outer, and inner tarsal folds present; calcar tubercle absent; whitish stripes on external border of upper eyelids and supratympanic folds, longitudinally on the mid-dorsum, on supracloacal fold, outer ulnar folds, inner and outer tarsal folds, and also on dorsal internal surface of shanks. We estimate phylogenetic relationships based on mtDNA (spanning fragments of 12S rRNA, tRNA-Val and 16S rRNA), of all Hyloscirtus species available in Genbank, as well as the new species described herein, H. callipeza, H. jahni, and H. platydactylus, all of which have not been previously sequenced. Our molecular data support the hypothesis of the new species as sister species of H. callipeza and indicates that H. jahni does not belong to the H. bogotensis species Group, but rather is sister species of all other Hyloscirtus (sensu Faivovich et al. 2005). Based on this last result we propose a new species group for H. jahni and the synonymy of Colomascirtus in Hyloscirtus. We also provide the first description of the advertisement call of H. callipeza. With the new species described herein, the number of Hyloscirtus species increases to 37. 

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