scholarly journals Phylogenetic Relationships of the Genus Homatula (Cypriniformes: Nemacheilidae), with Special Reference to the Biogeographic History around the Yunnan-Guizhou Plateau

Zootaxa ◽  
2012 ◽  
Vol 3586 (1) ◽  
pp. 78 ◽  
Author(s):  
RUI MIN ◽  
XIAO-YONG CHEN ◽  
JUN-XING YANG ◽  
RICHARD WINTERBOTTOM ◽  
RICHARD L. MAYDEN
Keyword(s):  
Early Pleistocene ◽  
Cyt B ◽  
Gene Trees ◽  
Undescribed Species ◽  
Species Relationships ◽  
Biogeographic History ◽  
Mitochondrial Cytochrome B ◽  
Complete Sequences ◽  
Rag 1 ◽  
Guizhou Plateau

Species of the nemacheilid genus Homatula are endemic to the Yunnan-Guizhou Plateau of China. Herein we provide phy-logenetic inferences of species relationships based on complete sequences of the mitochondrial cytochrome b gene (cyt b)and partial sequences of the nuclear recombination activation gene (RAG 1). Both gene trees (and the concatenated dataset) support the recognition of five clades in the genus. These analyses also support the hypothesis that two of the lineagesresolved represent undescribed species awaiting formal description, and, further, that two previously recognized speciesare junior synonyms; both are genetically indistinguishable from other previously recognized species. Divergence timesof the major clades in Homatula are inferred to be Late Pliocene and the Early Pleistocene, and are correlated with themassive geological events associated with the uplift of the Qinghai-Tibetan Plateau occurring at these times. The recon-struction of drainage histories suggests that the fish faunas of the Nu and Lancang rivers are basal relative to other riverinefaunas in the region, and that the Nanpan and the Jinsha rivers share a more recent history than with any other river systems included in our study.

A phylogeny of the enigmatic Madagascan geckos of the genus Uroplatus (Squamata: Gekkonidae)

Zootaxa ◽  
2007 ◽  
Vol 1493 (1) ◽  
pp. 41-51 ◽  
Author(s):  
ELI GREENBAUM ◽  
AARON M. BAUER ◽  
TODD R. JACKMAN ◽  
MIGUEL VENCES ◽  
FRANK GLAW
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Phylogenetic Hypothesis ◽  
Cyt B ◽  
Undescribed Species ◽  
Dna Sequence Data ◽  
Center Of Diversity ◽  
Rag 1 ◽  
High Diversity

Since its discovery in the 17th century, the morphological peculiarities of the gekkonid lizard genus Uroplatus have generated a great deal of attention. A large number of skeletal, integumentary and visceral features are autapomorphic for the genus and some of the more well-known members of the group possess such aberrant characteristics that a separate family was once recognized to accommodate them. Recent phylogenetic analyses confirm that Uroplatus is a typical gekkonid gecko, but the specific affinities of the genus, as well as its intrageneric relationships have remained unresolved. Both nuclear (RAG-1 and PDC) and mitochondrial (ND2 and cyt b) genes (~3.2 Kb) were sequenced for 10 of 13 recognized species of Uroplatus, as well as two Madagascan and mainland African outgroups. The large-bodied forms of Uroplatus (U. fimbriatus, U. giganteus, U. henkeli, and U. sikorae) form a monophyletic group, and the smallbodied, short-tailed species are also monophyletic (U. ebenaui and U. phantasticus). Uroplatus alluaudi + U. pietschmanni comprise another distinct clade, whereas U. lineatus was weakly supported as the sister taxon of the largebodied clade and U. guentheri was sister to all other members of the genus. Our phylogenetic hypothesis based on combined DNA sequence data is mostly congruent with previous hypotheses based on morphological data. Based on a larger, more inclusive dataset, the closest relatives of Uroplatus are mainland African Afrogecko and Madagascan Matoatoa, suggesting that the diverse Malagasy gecko fauna does not comprise a single evolutionary lineage. A high diversity of new taxa (either representing synonyms to resurrect or undescribed species), morphologically similar either to U. ebenaui/phantasticus or to U. henkeli/sikorae, was apparent from our data. Many of these genetically highly divergent lineages originated from localities in northern Madagascar, which indicates this region as the possible center of diversity and endemism for several subgroups of Uroplatus.

A widespread distribution for Arostrilepis tenuicirrosa (Eucestoda: Hymenolepididae) in Myodes voles (Cricetidae: Arvicolinae) from the Palearctic based on molecular and morphological evidence: historical and biogeographic implications

2013 ◽  
Vol 58 (4) ◽  
Author(s):  
Kurt Galbreath ◽  
Kristina Ragaliauskaite ◽  
Leonas Kontrimavichus ◽  
Arseny Makarikov ◽  
Eric Hoberg
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Intraspecific Diversity ◽  
Myodes Glareolus ◽  
Morphological Evidence ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Biogeographic History ◽  
Mitochondrial Cytochrome B ◽  
The Republic

AbstractHymenolepidid cestodes in Myodes glareolus from Lithuania and additional specimens originally attributed to Arostrilepis horrida from the Republic of Belarus are now referred to A. tenuicirrosa. Our study includes the first records of A. tenuicirrosa from the European (western) region of the Palearctic, and contributes to the recognition of A. horrida (sensu lato) as a complex of cryptic species distributed broadly across the Holarctic. Specimens of A. tenuicirrosa from Lithuania were compared to cestodes representing apparently disjunct populations in the eastern Palearctic based on structural characters of adult parasites and molecular sequence data from nuclear (ITS2) and mitochondrial (cytochrome b) genes. Morphological and molecular data revealed low levels of divergence between eastern and western populations. Phylogeographic relationships among populations and host biogeographic history suggests that limited intraspecific diversity within A. tenuicirrosa may reflect a Late Pleistocene transcontinental range expansion from an East Asian point of origin.

scholarly journals Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene

2020 ◽  
Vol 13 (1) ◽  
pp. 96-103
Author(s):  
Dorothea Vera Megarani ◽  
Herjuno Ari Nugroho ◽  
Zahrah Prawita Andarini ◽  
Yura Dwi Risa B. R. Surbakti ◽  
Rini Widayanti
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Cytochrome B ◽  
Genetic Characterization ◽  
Phylogenetic Study ◽  
Cyt B ◽  
Phylogenetic Structure ◽  
Mitochondrial Cytochrome B ◽  
Sperata Seenghala ◽  
Cyt B Gene

Aim: This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences. Materials and Methods: The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software. Results: Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids). Conclusion: Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with Hemibagrus nemurus and Hemibagrus wyckioides (Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with Sperata seenghala and Hemibagrus spilopterus (Bagridae family). Samples from Java (BSBJ) were clustered with Pseudolais pleurotaenia (Pangasiidae family). Samples EM (Java) were together with Mystus cavasius (Bagridae family). Samples from West Papua were clustered with Potamosilurus latirostris (Ariidae family).

scholarly journals Kajian Penanda Genetik Gen Sitokrom b DNA Mitokondria Ikan Lais dari Sungai Kampar Riau

2018 ◽  
Vol 10 (1) ◽  
pp. 6
Author(s):  
Roza Elvyra ◽  
Dedy Duryadi Solihin
Keyword(s):  
Species Diversity ◽  
Molecular Marker ◽  
Phylogenetic Relationship ◽  
Cytochrome B ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Phylogenetic Marker ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

The mitochondrial cytochrome b (cyt-b) gene as a phylogenetic marker of lais fish Kryptopterus schilbeides from Kampar River in Riau has been studied. This is a prelimininary research on the utility of cyt-b gene as a molecular marker to obtain species diversity and phylogenetic relationship among Kryptopterus fishes from Kampar River. The primers of L14841 and H15149 were used to amplify the cyt-b gene. The results showed that K. schilbeides has isoleusine at site-81 and metionine at site-114; K. schilbeides from Kampar River and K. schilbeides from GenBank form a phylogeny cluster at 45% value.

scholarly journals An overview of the mammals of the Gila region, New Mexico

Therya ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 213-236
Author(s):  
Amanda K. Jones ◽  
Schuyler W. Liphardt ◽  
Jonathan L. Dunnum
Keyword(s):  
New Mexico ◽  
Great Basin ◽  
The United States ◽  
Camera Traps ◽  
Sky Islands ◽  
Mammal Species ◽  
Landscape Complexity ◽  
Biogeographic History ◽  
Mitochondrial Cytochrome B ◽  
History Of

A study of the mammals of the Gila region of New Mexico was conducted from 2012 through 2020, with 2,919 voucher specimens collected through fieldwork and collaborations with commercial trappers, in addition to data from camera traps, review of major holdings at 46 museums (n = 12,505 georeferenced specimens), and literature review.  Specimens cover a 170-year span, dating back to 1850 and were unevenly distributed spatially and temporally across the Gila region.  Most areas were very poorly represented and when summed across all mammal species, ranged from 0.02 to 3.7 specimens per km2.  The survey documented 108 species (104 now extant) for the region.  High species richness, greater than that reported for 38 states in the United States, is likely due to the juxtaposition of multiple biomes in the Gila, including the Sonoran, Chihuahuan, and Great Basin deserts, the Rocky Mountains and Sierra Madre Occidental, and nearby “sky islands’’ of the Southwest.  Two species, Leptonycteris yerbabuenae and Zapus luteus, are documented for the first time from the study area.  Expansions of the known range of these species, and Sciurus arizonensis are described from specimen and camera data.  Preliminary phylogeographic studies of four species (Notiosorex crawfordi, Neotoma albigula, Perognathus flavus, and Thomomys bottae) using the mitochondrial cytochrome-b gene reveal the dynamic biogeographic history of the region and reinforce how landscape complexity and climate change have jointly contributed to diversification and thus high mammalian diversity in the region.

Reciprocal monophyly of Craspedia and Pycnosorus (Asteraceae, Gnaphalieae) and the problems of using ribosomal DNA at the lowest taxonomic levels

2013 ◽  
Vol 26 (3) ◽  
pp. 233 ◽  
Author(s):  
Alexander N. Schmidt-Lebuhn
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Species Tree ◽  
Gene Trees ◽  
Species Relationships ◽  
Reciprocal Monophyly ◽  
Molecular Phylogenies

The reciprocal monophyly of Craspedia and Pycnosorus (Asteraceae, Gnaphalieae) is tested, with a phylogenetic analysis of ribosomal and chloroplast DNA. Although one species of the latter genus was not sampled, the results of the present study indicated that it is most likely monophyletic as opposed to paraphyletic with respect to Craspedia. Within Craspedia, deeper sampling results in the appearance of several species (C. aurantia, C. coolaminica, C. glabrata and C. variabilis) in both major Australian rDNA clades, indicating that the available molecular phylogenies have to be considered gene trees instead of species phylogenies. Additional studies using more independent loci and species-tree approaches are needed to resolve species relationships in the genus.

scholarly journals Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh

2019 ◽  
Vol 5 (1) ◽  
pp. 25-30
Author(s):  
RA Begum ◽  
MT Alam ◽  
H Jahan ◽  
MS Alam
Keyword(s):  
Genetic Diversity ◽  
Cytochrome B ◽  
Tissue Sample ◽  
Sequence Similarity ◽  
Cytochrome B Gene ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Multiple Sequence ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30

scholarly journals Isotopic reconstruction of Proboscidean habitats and diets on enigmatic island of Sulawesi

2021 ◽  
Vol 47 (3) ◽  
pp. 79-80
Author(s):  
Mika Rizki Puspaningrum ◽  
Allan R. Chivas ◽  
Iwan Kurniawan ◽  
Unggul P. Wibowo ◽  
Yahdi Zaim ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Southeast Asia ◽  
Stable Isotope Analysis ◽  
Isotope Analysis ◽  
Early Pleistocene ◽  
Stable Carbon ◽  
Faunal Assemblage ◽  
Biogeographic History ◽  
Closed Canopy ◽  
Pleistocene Sediment

Sulawesi is known for its complex geological and biogeographic history, which is reflected in their extinct and extant faunal assemblage. Evidence of oldest terrestrial fauna in Sulawesi was found in the Early Pleistocene sediment and evolved since then. Despite being mostly isolated from the mainland Southeast Asia; four successive Proboscidean taxa have been found from the southern part of the island. The four taxa are: Stegoloxodon celebensis, Stegodon sompoensis, Stegodon sp. B, and cf. Palaeoloxodon namadicus, in which respective taxa are included in successive faunal stages. The aim of this research is to reconstruct the diet and palaeoenvironment of these Proboscidean taxa by incorporating stable isotope analysis with the fossil faunal record, geology, and stratigraphy. Stable carbon (δ13C) and oxygen (δ18O) isotope analysis were especially used in this study. Our result suggests that Stegoloxodon celebensis and Stegodon sompoensis were flexible feeders and were able to adapt to different niches, from closed canopy forest to open vegetation, while the diets of Stegodon sp. B, Celebochoerus heekereni and cf. Palaeoloxodon namadicus suggest that they were more specialized.

Comparison of mitochondrial cytochrome b lineages and morphospecies of two avian malaria parasites of the subgenera Haemamoeba and Giovannolaia (Haemosporida: Plasmodiidae)

Zootaxa ◽  
2007 ◽  
Vol 1626 (1) ◽  
pp. 39-50 ◽  
Author(s):  
VAIDAS PALINAUSKAS ◽  
VLAD KOSAREV ◽  
ANATOLY SHAPOVAL ◽  
STAFFAN BENSCH ◽  
GEDIMINAS VALKINAS
Keyword(s):  
Cytochrome B ◽  
Avian Malaria ◽  
Passer Domesticus ◽  
Morphological Identification ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Malaria Parasites ◽  
Mitochondrial Cytochrome B ◽  
The Baltic ◽  
Avian Malaria Parasites

PCR-based methods have been increasingly used in diagnosis of parasitic diseases. Over 40 morphospecies of avian malaria parasites of the genus Plasmodium have been described. However, only nine of them have been identified on the level of their mitochondrial cytochrome b (cyt b) gene lineages, which are frequently used in molecular biology studies of avian blood haemosporidian parasites. In this study, we linked two common mitochondrial cyt b lineages P-SGS1 and P-TURDUS1 with their morphospecies. Light infections with two species of malaria parasites of the subgenera Haemamoeba and Giovannolaia were isolated from naturally infected adult Hawfinches, Coccothraustes coccothraustes Linnaeus, on the Curonian Spit in the Baltic Sea. These parasites were inoculated to naive juveniles of the Common Crossbill, Loxia curvirostra Linnaeus, and House Sparrow, Passer domesticus Linnaeus. Heavy parasitemia of Plasmodium (Haemamoeba) relictum Grassi & Feletti, 1891 (lineage P-SGS1) and Plasmodium (Giovannolaia) circumflexum Kikuth, 1931 (P-TURDUS1) developed in the subinoculated Common Crossbills and House Sparrows, respectively, which enabled the detailed illustration of all main blood stages of these parasites and the deposition of their voucher specimens. The parasites of both lineages are actively transmitted in Europe and inhabit a broad range of avian hosts. Lineages closely related to P. relictum and P. circumflexum were identified. This study contributes to establishing of combined PCR-based and morphological identification of avian malaria parasites.

scholarly journals Molecular detection of cattle and buffalo species meat origin using mitochondrial cytochrome b (Cyt b) gene

2016 ◽  
Vol 2 (2) ◽  
pp. 177-182
Author(s):  
Sirazum Munira ◽  
Fatema Tuz Jahura ◽  
Md Munir Hossain ◽  
Mohammad Shamsul Alam Bhuiyan
Keyword(s):  
Cytochrome B ◽  
Genomic Dna ◽  
Molecular Technique ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Dna Yield ◽  
Mitochondrial Cytochrome B ◽  
Meat Samples ◽  
Species Specific ◽  
Cyt B Gene

The study was conducted to adopt PCR based technique for identification of species origin from meat samples of cattle and buffalo using mitochondrial cytochrome b (Cyt b) gene fragment. A total of 42 ear tissue and meat samples were collected from different slaughterhouses and farms of Mymensingh, Bogra and Rangpur districts and stored in 96% ethanol at room temperature. Genomic DNA was extracted from all samples using GeNet Bio genomic DNA isolation kit. The average DNA yield of considered samples was found 204.57 ng/?l where the purity ranged from 1.82–1.99. Two (2) pair species-specific primers were used to amplify Cyt b gene fragments of 472 bp and 124 bp for cattle and buffalo, respectively. The PCR results revealed different species specific amplified fragments which could discriminate between cattle (472 bp) and buffalo (124 bp) species precisely from pure and mixed samples of those species. This study suggests an accurate molecular technique for identification of cattle and buffalo species meat origin and differentiates species present in adulterated meat samples. In conclusion, this DNA based technique could be utilized for prevention of malpractice in slaughterhouse and chain shops and thereby to protect consumer’s right.Asian J. Med. Biol. Res. June 2016, 2(2): 177-182

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