Composition and interrelationships of a large Neotropical freshwater fish group, the subfamily Cheirodontinae (Characiformes: Characidae): A case study based on mitochondrial and nuclear DNA sequences

The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species,Curtos costipennisandC. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups,C. costipennisin the Amami region,C. okinawanusin the Okinawa region, andC. costipennisin the Sakishima region. Their mtDNA sequences suggested that ancestralC. costipennispopulation was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided betweenC. costipennisin the Amami andC. okinawanusin the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0–1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene.

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Callophrys rubi (Linnaeus, 1758) and C. chalybeitincta Sovynski, 1905 (Lepidoptera: Lycaenidae): a comparative analysis of mitochondrial and nuclear DNA sequences

Caucasian Entomological Bulletin ◽

10.23885/1814-3326-2011-7-1-79-80 ◽

2011 ◽

Vol 7 (1) ◽

pp. 79-80 ◽

Cited By ~ 1

Author(s):

B.V. Stradomsky ◽

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D.I. Vodolazhsky ◽

Keyword(s):

Comparative Analysis ◽

Dna Sequences ◽

Nuclear Dna

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Molecular phylogeny of Kazimierzus Plisko, 2006 (Clitellata, Kazimierzidae) from the Western and Northern Cape Province inferred from mitochondrial DNA sequences

African Invertebrates ◽

10.3897/afrinvertebr.61.53380 ◽

2020 ◽

Vol 61 (2) ◽

pp. 83-92

Author(s):

Thembeka Clara Nxele ◽

Jadwiga Danuta Plisko ◽

Tarombera Mwabvu ◽

Oliver Tendayi Zishiri

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Integrative Taxonomy ◽

Cryptic Diversity ◽

Undescribed Species ◽

Mitochondrial Marker ◽

Phylogenetic Reconstructions ◽

Northern Cape ◽

Tree Building ◽

Close Relatedness

Species identification of earthworms using morphology can be challenging and inconclusive as homoplasy in many characters is high. The use of molecular DNA technology, such as the use of conserved regions in mtDNA and nuclear DNA has unravelled the phylogenetic background of several earthworm species. The current study utilised the cytochrome c oxidase subunit I (COI) mitochondrial marker to reconstruct the phylogeny of Kazimierzus Plisko, 2006 species from the Western and Northern Cape provinces of South Africa. Phylogenetic reconstructions were implemented using Bayesian Inference, as well as Maximum Likelihood. Both tree building methods adhered to the monophyly of the majority of the taxa. Results showed that species fell into two clades and validated eleven currently known Kazimierzus species (K. circulatus (Plisko, 1998), K. franciscus (Pickford, 1975), K. guntheri (Pickford, 1975), K. hamerae (Plisko, 1998), K. kleinoodi Nxele & Plisko, 2017, K. nietvoorbiji Nxele & Plisko, 2017, K. nieuwoudtvillensis Nxele & Plisko, 2017, K. occidualis (Plisko, 1998), K. pearsonianus (Pickford, 1975), K. phumlani Nxele & Plisko, 2017, K. sophieae (Plisko, 2002)). Cryptic diversity is evident in K. occidualis with genetic divergence greater than 12% amongst populations. Kazimierzus franciscus and K. ljungstroemi (Pickford, 1975) have a low genetic variability suggesting close relatedness or probably conspecificity. A group of specimens from Clanwilliam are morphologically identical to K. sophieae, but are genetically distinct and may belong to undescribed species. This study demonstrates the importance of integrative taxonomy in earthworms in order to present reliable taxonomic and biogeographic data.

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Testing hypotheses of diversification in Panamanian frogs and freshwater fishes using hierarchical approximate Bayesian computation with model averaging

10.7287/peerj.preprints.26623 ◽

2018 ◽

Author(s):

Justin C Bagley ◽

Michael J Hickerson ◽

Jerald B Johnson

Keyword(s):

Freshwater Fish ◽

Dna Sequences ◽

Approximate Bayesian Computation ◽

Bayes Factor ◽

Fish Assemblages ◽

Model Averaging ◽

External Information ◽

Bayesian Computation ◽

Genetic Structuring ◽

Approximate Bayesian

Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Mol. Ecol. 1998, 7: 499-517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels.

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Discovery of a new family of amphibians from northeast India with ancient links to Africa

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.0150 ◽

2012 ◽

Vol 279 (1737) ◽

pp. 2396-2401 ◽

Cited By ~ 59

Author(s):

Rachunliu G. Kamei ◽

Diego San Mauro ◽

David J. Gower ◽

Ines Van Bocxlaer ◽

Emma Sherratt ◽

...

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Phylogenetic Analyses ◽

Sister Group ◽

Northeast India ◽

Sister Group Relationship ◽

New Family ◽

Ancient Lineage ◽

Molecular Phylogenetic ◽

Threatened Habitats

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

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