A molecular phylogeny of the Australian monitor lizards (Squamata:Varanidae) inferred from mitochondrial DNA sequences

2006 ◽  
Vol 54 (4) ◽  
pp. 253 ◽  
Author(s):  
A. J. Fitch ◽  
A. E. Goodman ◽  
S. C. Donnellan
Keyword(s):  
Dna Sequences ◽  
Mitochondrial Gene ◽  
Phylogenetic Study ◽  
Trna Genes ◽  
Preferred Habitat ◽  
Mitochondrial Data ◽  
Molecular Phylogenetic ◽  
Tree Topologies ◽  
Phylogenetic Framework ◽  
Monitor Lizards

To date no complete phylogeny of all of the currently recognised Indo-Australian varanid species and subspecies has been published. This paper presents a comprehensive mitochondrial gene phylogeny of these lizards. A portion of the mitochondrial genome comprising part of the ND4 gene and three adjacent tRNA genes (hereafter referred to as ND4) was analysed alone and, for a subset of the taxa, combined with previously published mitochondrial data. Similar tree topologies were produced by both datasets although combining the data helped resolve some of the unresolved or weakly supported nodes in the ND4 analyses. The monophyly of the Indo-Australian group was strongly supported in all analyses. This group comprised three major lineages: the gouldii group, the Odatria group and the varius group. Mitochondrial ND4 nucleotide sequences were successfully amplified from all of the Indo-Australian monitor species and subspecies currently recognised and, as such, is the first comprehensive phylogenetic study of the Australian monitor lizards published. Analysis of the tempo of diversification and evolution of preferred habitat use identified six episodes of increased net speciation rate, with two closely adjacent episodes showing the highest rates of diversification and correlating with the appearance of all preferred habitat types. The comprehensive molecular phylogenetic framework will also be useful for the identification of varanid species and traded products derived from monitors and, as such, has important applications for wildlife management and conservation.

scholarly journals Comparative Mitochondrial Genome Analysis of Two Ectomycorrhizal Fungi (Rhizopogon) Reveals Dynamic Changes of Intron and Phylogenetic Relationships of the Subphylum Agaricomycotina

2019 ◽  
Vol 20 (20) ◽  
pp. 5167 ◽  
Author(s):  
Qiang Li ◽  
Yuanhang Ren ◽  
Xiaodong Shi ◽  
Lianxin Peng ◽  
Jianglin Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Intron Loss ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Time ◽  
Dynamic Changes ◽  
Protein Coding ◽  
Tree Topologies ◽  
Nuclear Genomes

In the present study, we assembled and compared two mitogenomes from the Rhizopogon genus. The two mitogenomes of R. salebrosus and R. vinicolor comprised circular DNA molecules, with the sizes of 66,704 bp and 77,109 bp, respectively. Comparative mitogenome analysis indicated that the length and base composition of protein coding genes (PCGs), rRNA genes and tRNA genes varied between the two species. Large fragments aligned between the mitochondrial and nuclear genomes of both R. salebrosus (43.41 kb) and R. vinicolor (12.83 kb) indicated that genetic transfer between mitochondrial and nuclear genomes has occurred over evolutionary time of Rhizopogon species. Intronic regions were found to be the main factors contributing to mitogenome expansion in R. vinicolor. Variations in the number and type of introns in the two mitogenomes indicated that frequent intron loss/gain events occurred during the evolution of Rhizopogon species. Phylogenetic analyses based on Bayesian inference (BI) and Maximum likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, wherein Rhizopogon species showed close relationships with Agaricales species. This is the first study of mitogenomes within the genus Rhizopogon, and it provides a basis for understanding the evolution and differentiation of mitogenomes from the ectomycorrhizal fungal genus.

scholarly journals Determination of species boundaries of Selais fish from Arut River, Central Kalimantan based on 16S mitochondrial gene using Bayesian approach

2020 ◽  
Vol 28 ◽  
pp. 01003
Author(s):  
Tuty Arisuryanti ◽  
Bella Ulin Nikmah ◽  
Tomi Kasayev ◽  
Lukman Hakim
Keyword(s):  
Bayesian Approach ◽  
Genetic Relationships ◽  
Mitochondrial Gene ◽  
Single Species ◽  
Morphological Characters ◽  
Valid Species ◽  
Species Boundaries ◽  
Phylogenetic Study ◽  
Central Kalimantan ◽  
Molecular Phylogenetic

Selais fish is difficult to discriminate with other Silurid fish species based on morphological characters. As a result, the valid species of selais fish is uncertain. Therefore, a molecular phylogenetic study was needed to clarify species boundaries and to addresses genetic relationships of the selais fish. In this study, 16S mitochondrial gene of ten selais samples collected from Arut River (Central Kalimantan) were sequenced, from which a Bayesian trees was generated. Result revealed monophyletic of selais fish which is revealed as a single species. The Bayesian inference showed that the selais fish clade is distinguished with two other genus, Kryptopterus and Ompok, by its sequence differences. This finding can address species boundaries of selais fish using Bayesian approach, but the name of the selais species has not been clarified.

scholarly journals Four new species and further records of Dorvilleidae (Annelida, Polychaeta) from deep-sea organic substrata, NE Atlantic

2021 ◽  
Vol 736 ◽  
pp. 44-81
Author(s):  
Ascensão Ravara ◽  
Helena Wiklund ◽  
Marina R. Cunha
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Original Description ◽  
Ne Atlantic ◽  
Morphological Examination ◽  
Bathymetric Distribution ◽  
Molecular Phylogenetic

Eight species of Ophryotrocha and one of Parougia were identified from organic substrata (wood and alfalfa) sampled at the Gulf of Cadiz and Western Iberian Margin (NE Atlantic). Morphological examination and molecular phylogenetic analyses, based on the nuclear gene H3 and the mitochondrial gene 16S, indicate the presence of four species new to science: Ophryotrocha chemecoli sp. nov., O. nunezi sp. nov., O. geoffreadi sp. nov. and Parougia ougi sp. nov. The geographic and/or bathymetric distribution is extended for four previously known species: O. cantabrica, O. hartmanni, O. mammillata and O. scutellus. Another species may also have its distribution extended, pending the molecular confirmation of its identity: O. lipscombae. Full descriptions and figures are given for all the new species and, when justified, also for the previously known ones. The original description of O. scutellus is amended. New DNA sequences are given for eight of the nine species studied here. The ecology and geographic distribution of the reported species is discussed.

A molecular phylogenetic study of Hemsleya (Cucurbitaceae) based on ITS, rpl16, trnH-psbA, and trnL DNA sequences

2009 ◽  
Vol 285 (1-2) ◽  
pp. 23-32 ◽  
Author(s):  
Hong-Tao Li ◽  
Jun-Bo Yang ◽  
De-Zhu Li ◽  
Michael Möller ◽  
Amin Shah
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Study ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic

Rediscovery of the toadlet Brachycephalus bufonoides Miranda-Ribeiro, 1920 (Anura: Brachycephalidae) with osteological and acoustic descriptions

Zootaxa ◽  
2020 ◽  
Vol 4819 (2) ◽  
pp. 265-294
Author(s):  
MANUELLA FOLLY ◽  
LUCAS COUTINHO AMARAL ◽  
SERGIO POTSCH DE CARVALHO-E-SILVA ◽  
JOSÉ P. POMBAL JR.
Keyword(s):  
Atlantic Forest ◽  
Dna Sequences ◽  
Mitochondrial Gene ◽  
Transverse Process ◽  
Original Description ◽  
Species Group ◽  
Advertisement Call ◽  
Advertisement Calls ◽  
Molecular Phylogenetic

Brachycephalus bufonoides was described as a “variety” of B. ephippium based on two specimens which 90 years later was considered full species. Besides its brief original description, nothing else is known for this species. Herein we report the rediscovery of the pumpkin-toadlet Brachycephalus bufonoides from Nova Friburgo, State of Rio de Janeiro, the second most populous area within the Atlantic Forest in Brazil. A detailed osteological description of this species was also provided, including skull, hyolaryngeal skeleton and postcranium skeleton. The laryngeal skeleton of Brachycephalus genus was depicted for the first time. We conducted a molecular phylogenetic analysis of Brachycephalus using DNA sequences comprising two fragments of mitochondrial gene (16S). Both analysis with Bayesian inference and maximum parsimony supported the recognition of B. bufonoides as an exclusive lineage, allocated within the B. ephippium species group in B. vertebralis lineage. We improved the diagnosis and variation of the species, including more collected specimens, coloration in vivo and advertisement call description. Compared with its congeners, B. bufonoides has skin on head and dorsum with dermal hyperossification; skull with hyperossification of postorbital crests; a pair of hyperossified bulges about equidistant between postorbital crests; fourth presacral vertebra with transverse process hyperossified, ornamented and sacral diapophyses hyperossified, which can be seen externally (lineage of B. vertebralis sensu Condez et al. 2020); presence of dermal ossification as separated bulges of each vertebrae; general background color orange with different intensities of dark orange blotches on dorsum, including bordering of sacral region; absence of osteoderms and presence of warts on the dorsolateral surface of body; medium body size (SVL of adults: 12.0–14.5 mm for males and 14.7–16.3 mm for females; Table 1); rough dorsum; advertisement calls with 13 to 17 pulses; presence of pulse period modulation; and advertisement calls with notes longer than 0.2 s (0.22 to 0.31 s). Herein an important contribution for the taxonomy and systematics of this genus is provided, including a large amount of novel information for B. bufonoides from different sources (i.e., molecular, morphological variation, bioacoustic), allowing it to be included in future studies of species delimitation and relationships within Brachycephalus. Also, the discovery of this species reiterates the importance of Nova Friburgo for the conservation of the Atlantic Forest biodiversity.

scholarly journals A complete time-calibrated multi-gene phylogeny of the European butterflies

ZooKeys ◽  
2020 ◽  
Vol 938 ◽  
pp. 97-124 ◽  
Author(s):  
Martin Wiemers ◽  
Nicolas Chazot ◽  
Christopher Wheat ◽  
Oliver Schweiger ◽  
Niklas Wahlberg
Keyword(s):  
Dna Sequences ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Butterfly Species ◽  
Consensus Tree ◽  
Bayesian Inferences ◽  
The Third ◽  
Gene Coi ◽  
Phylogenetic Framework ◽  
First Time

With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localised endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to eleven nuclear gene fragments, using Bayesian inferences of phylogeny. To avoid analytical biases that could result from our region-focussed sampling, our European tree was grafted upon a global genus-level backbone butterfly phylogeny for analyses. In addition to a consensus tree, the posterior distribution of trees and the fully concatenated alignment are provided for future analyses. Altogether a complete phylogenetic framework of European butterflies for use by the ecological and evolutionary communities is presented.

Phylogenetic study of the genus Pohlia (Mielichhoferiaceae, Bryophyta) based on chloroplast DNA sequences

2021 ◽  
Vol 44 (1) ◽  
Author(s):  
TAKAYUKI OHGUE ◽  
HIROYUKI AKIYAMA ◽  
HIROSHI SUZUKI-AZUMA ◽  
HIDETOSHI NAGAMASU
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Taxonomic Revision ◽  
Phylogenetic Study ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Traditional Sense ◽  
Chloroplast Dna Sequences

The phylogenetic circumscription and taxonomic status of the genus Pohlia in the Mniaceae sensu lato was investigated based on chloroplast DNA sequences (rbcL, rps4, and trnL-F), with a focus on species occurring in Japan. The maximum likelihood and Bayesian inference analyses of sequences obtained from 34 species of Mniaceae s.l., including 13 Pohlia species, suggested that the genus Pohlia and the family Mielichhoferiaceae are not monophyletic in their present circumscription, but confirmed that the family Mniaceae is monophyletic in its traditional sense. These results are congruent with previous molecular phylogenetic studies. Three distinct clades were recognized in the Mielichhoferiaceae, almost corresponding to three sections of Pohlia (Pohlia, Cacodon and Apalodictyon). One of them branched off first within the Mniaceae s.l., and the other two were sister to the remainder of the Mniaceae s.l. The single included Schizymenium formed a monophyletic group with Pohlia sect. Pohlia and Epipterygium with Pohlia sect. Apalodictyon, confirming the results of previous studies. The results indicate that the taxonomic status of the genus Pohlia and family Mielichhoferiaceae are in need of revision. Phylogenetic analyses nested the accessions of P. camptotrachela within P. annotina and P. flexuosa clades, highlighting the need for taxonomic revision of Japanese propaguliferous Pohlia species.

A pilot study on the molecular phylogeny of Drepanoidea (Insecta: Lepidoptera) inferred from the nuclear gene EF-1α and the mitochondrial gene COI

2009 ◽  
Vol 100 (2) ◽  
pp. 207-216 ◽  
Author(s):  
C.G. Wu ◽  
H.X. Han ◽  
D.Y. Xue
Keyword(s):  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Phylogenetic Study ◽  
Sister Relationship ◽  
Molecular Phylogenetic Study ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Gene Coi ◽  
Coi Sequences ◽  
Definition Of

AbstractA molecular phylogenetic study of the Drepanoidea based on the EF-1α sequences and combined EF-1α and COI sequences was carried out in order to infer higher classification at and above the subfamily level. The sample contained 14 taxa representing 13 genera recognized in the Drepanoidea. The results revealed that the Drepaninae, Thyatirinae and Cyclidiinae respectively form monophyletic groups. The sister relationship between the Drepaninae and the Thyatirinae was validated. The monophyly of the Cyclidiinae with the Drepaninae+Thyatirinae was supported robustly.Hypsomadius insignisandOreta vatamawithin the traditional definition of the Drepaninae formed an individual clade with robust support (100%) and constitutes a sister relationship to a clade containing the rest of the Drepaninae in all the topologies, which means that the subfamily Oretinae of the Drepanidae should be restored. The family Drepanidae is divided into four subfamilies: Drepaninae, Oretinae, Thyatirinae and Cyclidiinae in this work. The family Epicopeiidae formed a monophyly with high bootstrap values. The result of combined analysis of EF-1α and COI showed that the Epicopeiidae have a closer phylogenetic relationship with the Geometridae than with the Drepanidae and belong to neither the Drepanoidea nor the Geometroidea.

Sign in / Sign up

Export Citation Format

Share Document