scholarly journals Appearances are deceptive: molecular phylogeny recovers the Scaly Gecko Hemidactylus scabriceps (Reptilia: Squamata: Gekkonidae) as a member of a scansorial and rupicolous clade

2018 ◽  
Vol 10 (9) ◽  
pp. 12147
Author(s):  
Achyuthan N. Srikanthan ◽  
Gandla Chethan Kumar ◽  
Aishwarya J. Urs ◽  
Sumaithangi Rajagopalan Ganesh
Keyword(s):  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Molecular Data ◽  
Habitat Associations ◽  
Phylogenetic Position ◽  
Peninsular India ◽  
Rock Formations ◽  
Clade B ◽  
Voucher Specimens ◽  
Genetic Alliance

We reassess the systematics of Hemidactylus scabriceps, a recently rediscovered and poorly known gecko, and elucidate its phylogenetic position using molecular data for the first time.  Contrary to previous speculations prompted by its morphological resemblance to other terrestrial Hemidactylus, our phylogenetic analyses recovered H. scabriceps to be a part of a clade consisting of the large-bodied, rock-dwelling Hemidactylus – the H. prashadi group.  Hemidactylus scabriceps also shows high levels of intraspecific genetic divergence, indicative of cryptic diversity.  We also confirm the synonymy of the monotypic genus Lophopholis (erected for H. scabriceps) with Hemidactylus.  We elaborate on the morphology of the type specimen and other recent voucher specimens, and compare it with sister species and other ground-dwelling Hemidactylus in peninsular India.  Species distribution of this ‘outlier’ clade member has been modeled using MaxEnt.  These exercises confirm that it is primarily a smooth-scaled, plain-dwelling, terrestrial species unlike other members in its clade.  This unexpected pattern of genetic alliance and contrasting body form plus habitat associations further underscores the unstudied complexity of peninsular India’s geological history.  Historical denudation of rock formations could have driven evolution of some of these otherwise rupicolous, scansorial gekkonids into smaller terrestrial lizards.  

A new Crocus L. (Iridaceae) species from SE Turkey, based on morphological and molecular data

Phytotaxa ◽  
2015 ◽  
Vol 239 (3) ◽  
pp. 223 ◽  
Author(s):  
Osman Erol ◽  
Doerte Harpke ◽  
Hasan Yıldırım
Keyword(s):  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Full Description ◽  
New Taxon ◽  
Internal Transcribed Spacer Region ◽  
Se Turkey

Crocus musagecitii is described as a new species. Diagnostic morphological characters, a full description and detailed illustrations are provided on the basis of the type specimen and wild specimens. Morphologically, C. musagecitii is close to Crocus biflorus subsp. pseudonubigena. Crocus musagecitii differs from C. biflorus subsp. pseudonubigena by the lack of stripes or narrow purplish tongue on outside of outer tepals, wider tepals, and homogenously yellow anthers. In order to clarify the phylogenetic position of this species within the Crocus adamii species complex, we sequenced the internal transcribed spacer region (ITS: ITS1 + 5.8SrDNA + ITS2) and 5’ external transcribed spacer (ETS) of the nuclear ribosomal DNA (rDNA). A phylogenetic tree obtained by Bayesian phylogenetic inference is given. Phylogenetic analyses revealed that the new taxon is close to C. munzurensis. Crocus musagecitii differs from its phylogenetically closest relative C. munzurensis by the corm tunics (C. musagecitii: coriaceus; C. munzurensis: membranous), the number of leaves (C. musagecitii: up to 8; C. munzurensis: up to 4) and non-hairy leaf margins.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

Clathrosporium retortum, a novel aeroaquatic fungus in the Sordariomycetidae (Ascomycota) from Brazil

Phytotaxa ◽  
2015 ◽  
Vol 239 (1) ◽  
pp. 17
Author(s):  
Larissa Bernardino Moro ◽  
Gregorio Delgado ◽  
Iracema Helena SCHOENLEIN-CRUSIUS
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Molecular Data ◽  
Sao Paulo ◽  
São Paulo ◽  
Present Fungus ◽  
Broad Concept ◽  
Morphological And Molecular Data ◽  
First Time

Clathrosporium retortum sp. nov., collected on submerged mixed leaf litter samples at Ilha do Cardoso State Park, São Paulo state, Brazil, is described based on morphological and molecular data. The fungus is characterized by forming whitish, dense, subglobose to irregular propagules, hyaline to subhyaline when young, subhyaline to dark brown at maturity, that are formed by densely interwoven conidial filaments with each conidial cell repeatedly branching bilaterally or occasionally unilaterally. Phylogenetic analyses using partial LSU nrDNA sequence data suggest that C. retortum belongs in the Sordariomycetes (Ascomycota) where it forms a well-supported clade with Clohesia corticola in the Sordariomycetidae, but its ordinal or familial placement remains unresolved. Its phylogenetic placement confirms the polyphyletic nature of aeroaquatic fungi like Clathrosporium, as it was distantly related to one available sequence in GenBank named as C. intricatum, the type species, which is phylogenetically related to the Helotiales (Leotiomycetes). However, due to lack of authenticity of the identity of this sequence with the type specimen of C. intricatum, a broad concept of Clathrosporium is tentatively adopted here to accommodate the present fungus instead of introducing a new genus. Beverwykella clathrata, Helicoön septatissimum and Peyronelina glomerulata are recorded for the first time from Brazil. Cancellidium applanatum and Candelabrum brocchiatum are new records for the state of São Paulo.

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

scholarly journals Fungia fungites (Linnaeus, 1758) (Scleractinia, Fungiidae) is a species complex that conceals large phenotypic variation and a previously unrecognized genus

2020 ◽  
Vol 89 (2) ◽  
pp. 188-209
Author(s):  
Yutaro Oku ◽  
Kenji Iwao ◽  
Bert W. Hoeksema ◽  
Naoko Dewa ◽  
Hiroyuki Tachikawa ◽  
...  
Keyword(s):  
Species Complex ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Scleractinian Corals ◽  
Type Specimens ◽  
Mitochondrial Coi ◽  
Clade B ◽  
Unknown Species ◽  
Molecular Phylogenetic ◽  
Morphological Differences

Recent molecular phylogenetic analyses of scleractinian corals have resulted in the discovery of cryptic lineages. To understand species diversity in corals, these lineages need to be taxonomically defined. In the present study, we report the discovery of a distinct lineage obscured by the traditional morphological variation of Fungia fungites. This taxon exists as two distinct morphs: attached and unattached. Molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers as well as morphological comparisons were performed to clarify their phylogenetic relationships and taxonomic positions. Molecular data revealed that F. fungites consists of two genetically distinct clades (A and B). Clade A is sister to a lineage including Danafungia scruposa and Halomitra pileus, while clade B formed an independent lineage genetically distant from these three species. The two morphs were also found to be included in both clades, although the attached morph was predominantly found in clade A. Morphologically, both clades were statistically different in density of septal dentation, septal number, and septal teeth shape. These results indicate that F. fungites as presently recognized is actually a species complex including at least two species. After checking type specimens, we conclude that specimens in clade A represent true F. fungites with two morphs (unattached and attached) and that all of those in clade B represent an unknown species and genus comprising an unattached morph with only one exception. These findings suggest that more unrecognized taxa with hitherto unnoticed morphological differences can be present among scleractinian corals.

scholarly journals Nine Mitochondrial Genomes of the Pyraloidea and Their Phylogenetic Implications (Lepidoptera: Pyraloidea)

Insects ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1039
Author(s):  
Xiaomeng Liu ◽  
Mujie Qi ◽  
Haizhen Xu ◽  
Zhipeng Wu ◽  
Lizong Hu ◽  
...  
Keyword(s):  
Crop Production ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Morphological Evidence ◽  
Pest Species ◽  
Great Loss ◽  
Phylogenetic Implications ◽  
Important Pest ◽  
High Level

The Pyraloidea is one of the species-rich superfamilies of Lepidoptera and contains numerous economically important pest species that cause great loss in crop production. Here, we sequenced and annotated nine complete mitogenomes for Pyraloidea, and further performed various phylogenetic analyses, to improve our understanding of mitogenomic evolution and phylogeny of this superfamily. The nine mitogenomes were circular, double-stranded molecules, with the lengths ranging from 15,214 bp to 15,422 bp, which are comparable to other reported pyraloid mitogenomes in size. Gene content and arrangement were highly conserved and are typical of Lepidoptera. Based on the hitherto most extensive mitogenomic sampling, our various resulting trees showed generally congruent topologies among pyraloid subfamilies, which are almost in accordance with previous multilocus studies, indicating the suitability of mitogenomes in inferring high-level relationships of Pyraloidea. However, nodes linking subfamilies in the “non-PS clade” were not completely resolved in terms of unstable topologies or low supports, and future investigations are needed with increased taxon sampling and molecular data. Unexpectedly, Orybina Snellen, represented in a molecular phylogenetic investigation for the first time, was robustly placed as basal to the remaining Pyralidae taxa across our analyses, rather than nested in Pyralinae of Pyralidae as morphologically defined. This novel finding highlights the need to reevaluate Orybina monophyly and its phylogenetic position by incorporating additional molecular and morphological evidence.

A new predatory leech from Vietnam (Hirudinida : Arhynchobdellida : Salifidae): its phylogenetic position with comments on the classification of the family

2015 ◽  
Vol 29 (5) ◽  
pp. 473 ◽  
Author(s):  
Takafumi Nakano ◽  
Son Truong Nguyen
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
12S Rrna ◽  
The Family ◽  
Morphological And Molecular Data ◽  
First Time

The family Salifidae is a predaceous leech taxon in the suborder Erpobdelliformes. Although Salifidae is widely distributed in the African, Oriental, Indo-Malayan, Sino-Japanese and Australasian regions, the phylogenetic relationships of the family Salifidae have never been tested using molecular data obtained from leeches collected from the family distributional range. A salifid species was collected for the first time in Vietnam, and relevant morphological and molecular data are presented here. Because the Vietnamese salifid species possesses unique morphological characteristics among the known salifid species, this species is herein described as a new species, Salifa motokawai, sp. nov. Phylogenetic analyses based on nuclear 18S rRNA and histone H3, as well as mitochondrial cytochrome c oxidase subunit I, tRNACys, tRNAMet, 12S rRNA, tRNAVal, 16S rRNA, tRNALeu and NADH dehydrogenase subunit 1 markers demonstrate that the Vietnamese salifid species is a close congener with the African Salifa perspicax and the Malagasy Linta be. Furthermore, molecular data revealed non-monophyly of the Asian salifid leeches. According to the observed phylogenetic relationships and morphological characteristics of the Vietnamese Salifa motokawai, sp. nov., the current classification of salifid taxa should be revised.

Phylogenetic Relationships in the Salicornioideae / Suaedoideae / Salsoloideae s.l. (Chenopodiaceae) Clade and a Clarification of the Phylogenetic Position of Bienertia and Alexandra Using Multiple DNA Sequence Datasets

2006 ◽  
Vol 31 (3) ◽  
pp. 571-585 ◽  
Author(s):  
Maxim V. Kapralov ◽  
Hossein Akhani ◽  
Elena V. Voznesenskaya ◽  
Gerald Edwards ◽  
Vincent Franceschi ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Kranz Anatomy ◽  
Statistical Support ◽  
Chloroplast Dna Regions

The Chenopodiaceae includes taxa with both C3 and C4 photosynthesis with diverse kinds of Kranz anatomy and single-celled C4 species without Kranz anatomy; thus, it is of key importance for understanding evolution of C4 photosynthesis. All of the C4 genera except Atriplex, which belongs to Chenopodioideae, are in the Salicornioideae / Suaedoideae / Salsoloideae s.l. (including Camphorosmeae and Sclerolaeneae) clade. Our study focused on the relationships of the main lineages within this clade with an emphasis on the placement of the single cell functioning C4 genus Bienertia using maximum parsimony, maximum likelihood, and Bayesian inference phylogenetic analyses of the nuclear ribosomal ITS and five chloroplast DNA regions (atpB-rbcL, matK, psbB-psbH, rbcL, and trnL-trnF). Further we provide a detailed phylogeny of Alexandra and Suaeda based on ITS, atpB-rbcL, and psbB-psbH. Our molecular data provide strong statistical support for the monophyly of: (1) a Salicornioideae / Suaedoideae / Salsoloideae s.l. clade; (2) a Salicornioideae / Suaedoideae clade; (3) the subfamilies Salicornioideae, Suaedoideae (including Bienertia) and Salsoloideae s.l.; (4) the tribes Suaedeae, Salsoleae, and Camphorosmeae; (5) the Salicornieae if Halopeplideae is included; and (6) Suaeda if Alexandra is included. Alexandra lehmannii is therefore reclassified as Suaeda lehmannii and a new section of Suaeda is created, section Alexandra. There are four independent origins of C4 photosynthesis within the Suaedoideae including two parallel origins of Kranz C4 anatomy (in Suaeda sections Salsina s.l. and Schoberia) and two independent origins of C4 systems without Kranz anatomy (in Bienertia and in Suaeda section Borszczowia).

scholarly journals Orange is the new white: taxonomic revision of Tritonia species (Gastropoda: Nudibranchia) from the Weddell Sea and Bouvet Island

Polar Biology ◽  
2021 ◽  
Author(s):  
Maria Eleonora Rossi ◽  
Conxita Avila ◽  
Juan Moles
Keyword(s):  
Southern Ocean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Molecular Data ◽  
Molecular Techniques ◽  
Weddell Sea ◽  
Valid Species ◽  
Phylogenetic Position ◽  
Antarctic Waters

AbstractAmong nudibranch molluscs, the family Tritoniidae gathers taxa with an uncertain phylogenetic position, such as some species of the genus Tritonia Cuvier, 1798. Currently, 37 valid species belong to this genus and only three of them are found in the Southern Ocean, namely T. challengeriana Bergh, 1884, T. dantarti Ballesteros & Avila, 2006, and T. vorax (Odhner, 1926). In this study, we shed light on the long-term discussed systematics and taxonomy of Antarctic Tritonia species using morpho-anatomical and molecular techniques. Samples from the Weddell Sea and Bouvet Island were dissected and prepared for scanning electron microscopy. The three molecular markers COI, 16S, and H3 were sequenced and analysed through maximum-likelihood and Bayesian methods. The phylogenetic analyses and species delimitation tests clearly distinguished two species, T. challengeriana widely spread in the Southern Ocean and T. dantarti endemic to Bouvet Island. Colouration seems to be an unreliable character to differentiate among species since molecular data revealed both species can either have orange or white colour morphotypes. This variability could be explained by pigment sequestration from the soft coral species they feed on. Morphological analyses reveal differences between Antarctic and Magellanic specimens of T. challengeriana. However, the relationship between T. challengeriana specimens from these two regions remains still unclear due to the lack of molecular data. Therefore, the validity of the T. antarctica Martens & Pfeffer, 1886, exclusively found in Antarctic waters requires further systematic work.

scholarly journals Gastronautidae Deroux, 1994 and Trithigmostoma Jankowski, 1967: Evolutionary Links Among Cyrtophorian Ciliates (Protista, Ciliophora, and Phyllopharyngea)

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhishuai Qu ◽  
Hongbo Pan ◽  
Congcong Wang ◽  
Honggang Ma ◽  
Thorsten Stoeck ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Ssu Rdna ◽  
Phylogenetic Position ◽  
Special Position ◽  
Morphological Taxonomy ◽  
Rdna Sequences ◽  
Closed Circle ◽  
The Family ◽  
Morphological Research

Studies on cyrtophorian ciliates (Cyrtophoria) have accumulated much knowledge on morphological taxonomy and molecular phylogeny, and the general classification and phylogenetic relationships of most families have thereby been revealed. However, the phylogenetic position of the family Gastronautidae Deroux, 1994 remains uncertain. This is due to the presence of specialized characteristics (in particular a circumoral kinety in a closed circle), and most importantly, the lack of molecular data of this family. In addition, TrithigmostomaJankowski, 1967 holds a special position among genera in Chilodonellidae Deroux, 1976 due to its divergent characteristics. In the present work, we studied a new gastronautid, Gastronauta paraloisi sp. n., and three populations of Trithigmostoma cucullulus (Müller, 1786) Jankowski, 1967, using integrative methods. Species identifications were confirmed by morphological research. We also obtained SSU rDNA sequences, which included the first available sequence of Gastronautidae. The following SSU rDNA-inferred phylogenetic analyses showed that the establishment of the family Gastronautidae is necessary, and Gastronautidae and Trithigmostoma may represent intermediate evolutionary links in the order Chlamydodontida.

Sign in / Sign up

Export Citation Format

Share Document