Taxonomic re-examination of the hermit crab species Pagurus forceps and Pagurus comptus (Decapoda: Paguridae) by molecular analysis

Zootaxa ◽  
2009 ◽  
Vol 2133 (1) ◽  
pp. 20-32 ◽  
Author(s):  
FERNANDO LUIS MANTELATTO ◽  
LUIS MIGUEL PARDO ◽  
LEONARDO GOMES PILEGGI ◽  
DARRYL L. FELDER
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Hermit Crab ◽  
Sequence Similarity ◽  
Ribosomal Gene ◽  
Similar Species ◽  
Crab Species ◽  
Putative Species ◽  
Complex Relationships

The current taxonomy of two poorly known hermit crab species Pagurus forceps H. Milne Edwards, 1836 and Pagurus comptus White, 1847 from temperate Pacific and Atlantic coastlines of South America is based only on adult morphology. Past studies have questioned the separation of these two very similar species, which occur sympatrically. We included specimens morphologically assignable to P. forceps and P. comptus in a phylogenetic analysis, along with other selected anomuran decapods, based on 16S ribosomal gene sequences. Differences between samples putatively assigned to either P. forceps and P. comptus were moderate, with sequence similarity ranging from 98.2 to 99.4% for the fragments analyzed. Our comparison of mitochondrial DNA sequences (16S rRNA) revealed diagnostic differences between the two putative species, suggesting that P. forceps and P. comptus are indeed phylogenetically close but different species, with no genetic justification to support their synonymization. The polyphyly of Pagurus is not corroborated here among the represented Atlantic species, despite obviously complex relationships among the members of the genus.

scholarly journals Phylogenetic analysis based on mitochondrial DNA sequences of wild rats, and the relationship with Seoul virus infection in Hubei, China

2017 ◽  
Vol 32 (3) ◽  
pp. 235-244 ◽  
Author(s):  
Dong-Ying Liu ◽  
Jing Liu ◽  
Bing-Yu Liu ◽  
Yuan-Yuan Liu ◽  
Hai-Rong Xiong ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Virus Infection ◽  
Dna Sequences ◽  
Seoul Virus ◽  
Wild Rats ◽  
The Relationship

scholarly journals Phylogenetic Analysis of Mitochondrial Genes of Malaysian Tupaia Reveals Composite Species in Tupaia Glis

2021 ◽  
Vol 3 (1) ◽  
pp. 197-203
Author(s):  
Jayaraj Vijaya Kumaran ◽  
Ahmad Sofiman Othman ◽  
Shahrul-Anuar Mohd Sah ◽  
Seri Intan Mokhtar
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Mitochondrial Genes ◽  
Peninsular Malaysia ◽  
Universal Primers ◽  
Cyt B ◽  
Southern Thailand ◽  
Tupaia Glis

Recent morphometric analysis on T. glis in Peninsular Malaysia indicates that there were more than one morphotypes in this species. Thus this study attempts to examine this phenomenon using mitochondrial DNA sequences of Cyt b and CO1 genes. A total of 74 DNA sequences for both genes were generated using available universal primers. Samples from Southern Thailand were found to be misidentified as T. glis when in fact these samples clustered with T. belangeri while one T. tana from Borneo was miss-identified as T. minor. The phylogenetic trees showed that there are at least one confirmed morphotype of Tupaia (new Tupaia sp.) that have yet to be described. The results also showed that the separation of T. glis morphotype 1 and 11 were visible in the combined genes tree, congruent with the morphometric phylogeny but had poor phylogenetic support.

Molecular Phylogenetic Analysis of Archaeal Intron-Containing Genes Coding for rRNA Obtained from a Deep-Subsurface Geothermal Water Pool

1999 ◽  
Vol 65 (12) ◽  
pp. 5586-5589 ◽  
Author(s):  
Ken Takai ◽  
Koki Horikoshi
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Similarity ◽  
Homing Endonuclease ◽  
Open Reading Frames ◽  
Molecular Phylogenetic Analysis ◽  
Homing Endonucleases ◽  
Deep Subsurface ◽  
Molecular Phylogenetic ◽  
Sequence Similarity Analysis

ABSTRACT Molecular phylogenetic analysis of a naturally occurring microbial community in a deep-subsurface geothermal environment indicated that the phylogenetic diversity of the microbial population in the environment was extremely limited and that only hyperthermophilic archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA sequences contained intron-like sequences, some of which had open reading frames with repeated homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of these homing endonucleases suggested the possible phylogenetic relationship among archaeal rRNA-encoded homing endonucleases.

Geothelphusa makatao sp. nov. (Crustacea: Brachyura: Potamidae), a new freshwater crab from an uplifted Pleistocene reef in Taiwan

Zootaxa ◽  
2009 ◽  
Vol 2106 (1) ◽  
pp. 51-60 ◽  
Author(s):  
HSI-TE SHIH ◽  
JHY-YUN SHY
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
New Species ◽  
Morphological Characters ◽  
Similar Species ◽  
Freshwater Crab ◽  
Closely Related Species ◽  
Dna Evidence ◽  
Southwestern Taiwan ◽  
A New Species

A new species of potamid freshwater crab, Geothelphusa makatao, is described from southwestern Taiwan, based on morphological characters and mitochondrial DNA evidence. The new species differs from close congeners, G. pingtung Tan & Liu, 1998, G. shernshan Chen, Cheng & Shy, 2005, and G. ancylophallus Shy, Ng & Yu, 1994 and a superficially similar species, G. albogilva Shy, Ng & Yu, 1994, in the structure of its ambulatory legs, thoracic sternum, male abdomen, and male first pleopods. The unique gene sequences of 16S rRNA and cytochrome oxidase I also support the recognition of this coastal population, which is isolated from other closely related species inhabiting montane areas. Except for G. makatao, the phylogenetic analysis showed that there are three additional hill subclades within the G. pingtung clade, G. shernshan, G. pingtung and the Liangshan subclade, situated in different watersheds of rivers or streams near the Central Range in the southwestern Taiwan.

Phylogenetic analysis of mitochondrial DNA sequences reveals polyphyly in the goitred gazelle (Gazella subgutturosa)

2010 ◽  
Vol 12 (3) ◽  
pp. 827-831 ◽  
Author(s):  
Timothy Wacher ◽  
Torsten Wronski ◽  
Robert L. Hammond ◽  
Bruce Winney ◽  
Mark J. Blacket ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Gazella Subgutturosa ◽  
Goitred Gazelle

Species delimitation in trematodes using DNA sequences: Middle-American Clinostomum as a case study

Parasitology ◽  
2016 ◽  
Vol 143 (13) ◽  
pp. 1773-1789 ◽  
Author(s):  
GERARDO PÉREZ-PONCE DE LEÓN ◽  
MARTÍN GARCÍA-VARELA ◽  
CARLOS D. PINACHO-PINACHO ◽  
ANA L. SERENO-URIBE ◽  
ROBERT POULIN
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Species Delimitation ◽  
Nuclear Gene ◽  
Species Tree ◽  
Coi Gene ◽  
Complex Life Cycle ◽  
Species Boundaries ◽  
Intermediate Hosts ◽  
Putative Species

SUMMARYThe recent development of genetic methods allows the delineation of species boundaries, especially in organisms where morphological characters are not reliable to differentiate species. However, few empirical studies have used these tools to delineate species among parasitic metazoans. Here we investigate the species boundaries of Clinostomum, a cosmopolitan trematode genus with complex life cycle. We sequenced a mitochondrial [cytochrome c oxidase subunit I (COI)] gene for multiple individuals (adults and metacercariae) from Middle-America. Bayesian phylogenetic analysis of the COI uncovered five reciprocally monophyletic clades. COI sequences were then explored using the Automatic Barcode Gap Discovery to identify putative species; this species delimitation method recognized six species. A subsample was sequenced for a nuclear gene (ITS1, 5·8S, ITS2), and a concatenated phylogenetic analysis was performed through Bayesian inference. The species delimitation of Middle-American Clinostomum was finally validated using a multispecies coalescent analysis (species tree). In total, five putative species are recognized among our samples. Mapping the second intermediate hosts (fish) onto the species tree suggests that metacercariae of these five species exhibit some level of host specificity towards their fish intermediate host (at the family level), irrespective of geographical distribution.

scholarly journals Evidence from nature: interspecies spread of heron hepatitis B viruses

2005 ◽  
Vol 86 (5) ◽  
pp. 1335-1342 ◽  
Author(s):  
Li Lin ◽  
Alexej Prassolov ◽  
Anneke Funk ◽  
Laura Quinn ◽  
Heinz Hohenberg ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B ◽  
Dna Sequences ◽  
Sequence Similarity ◽  
Isolated Populations ◽  
Ardea Herodias ◽  
Virus Adaptation ◽  
Free Ranging ◽  
First Time ◽  
Lateral Transmission

Heron hepatitis B viruses (HHBVs) in three subspecies of free-living great blue herons (Ardea herodias) from Florida, USA, were identified and characterized. Eight of 13 samples were positive in all assays used, whereas sera from egrets, which are also members of the family Ardeidae, were negative in the same assays. Comparative phylogenetic analysis of viral DNA sequences from the preS/S region of previously reported and novel HHBV strains isolated from captive grey herons (Germany) and free-ranging great blue herons (USA), respectively, revealed a strong conservation (95 % sequence similarity) with two separate clusters, implying a common ancestor of all strains. Our data demonstrate for the first time that different subspecies of herons are infected by HHBV and that these infections exist in non-captive birds. Phylogenetic analysis and the fact that the different heron species are geographically isolated populations suggest that lateral transmission, virus adaptation and environmental factors all play a role in HHBV spreading and evolution.

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