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Patil GS, Pinto N, Nath R, Goswami M. Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach. Mol Biol Rep 2024; 51:528. [PMID: 38637345 DOI: 10.1007/s11033-024-09487-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes. METHODS AND RESULTS In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae. CONCLUSIONS In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.
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Affiliation(s)
- Grishma S Patil
- ICAR-Central Institute of Fisheries Education, Mumbai, India
- Mangalore University, Mangaluru, Karnataka, India
| | - Nevil Pinto
- ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Rupak Nath
- St. Anthony's College, Shillong, Meghalaya, India
| | - Mukunda Goswami
- ICAR-Central Institute of Fisheries Education, Mumbai, India.
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Kok PJR. Bones and all: a new critically endangered Pantepui species of Stefania (Anura: Hemiphractidae) and a new osteological synapomorphy for the genus. Zoological Lett 2023; 9:11. [PMID: 37231482 DOI: 10.1186/s40851-023-00209-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
The hemiphractid frog genus Stefania is one of the many ancient (near-) endemic lineages of vertebrates inhabiting the biodiverse Pantepui biogeographical region in the Guiana Shield Highlands of northern South America-the famous "Lost World" of Arthur Conan Doyle. Previous molecular analyses of the genus Stefania have indicated that species boundaries and phylogenetic relationships are often incongruent with morphological traits in that clade. A substantial number of "taxonomically cryptic" species, often microendemic, remain to be described. This is notably the case for an isolated population from the summit of Wei-Assipu-tepui, a small table-top mountain at the border between Guyana and Brazil. That population was previously known as Stefania sp. 6 and belongs to the S. riveroi clade. The new species is phylogenetically distinct, but phenotypically extremely similar to S. riveroi, a taxon found only on the summit of Yuruaní-tepui in Venezuela and recovered as sister to all the other known species in the S. riveroi clade. The new taxon is described based on morphology and osteology. Data about genetic divergences within the S. riveroi clade are provided. A new synapomorphy for the genus Stefania is proposed: the presence of a distal process on the third metacarpal. Amended definitions are offered for the three other species in the S. riveroi clade (S. ayangannae, S. coxi, S. riveroi). The new species should be listed as Critically Endangered according to IUCN criteria.
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Affiliation(s)
- Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str, 90-237, Łódź, Poland.
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
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Meirmans PG. Analyzing Autopolyploid Genetic Data Using GenoDive. Methods Mol Biol 2023; 2545:261-277. [PMID: 36720818 DOI: 10.1007/978-1-0716-2561-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Analyzing autopolyploid genetic data still presents numerous challenges due to, e.g., missing dosage information of genotypes and the presence of multiple ploidy levels within species or populations, but also because the choice of software is limited when compared to what is available for diploid data. However, over the last years, the number of software programs that can deal with polyploid data is slowly increasing. The software GENODIVE is one of the most widely used programs for the analysis of polyploid genetic data, presenting a wide array of different methods. In this chapter, I outline several frequently used types of population genetic analyses and explain how these apply to polyploid data, including possible pitfalls and biases. I then explain how GENODIVE approaches these analyses and whether and how it can overcome possible biases. Specifically, I focus on analyses of genetic diversity, Hardy-Weinberg equilibrium, quantifying population differentiation, clustering, and calculation of genetic distances. GENODIVE can be downloaded freely from http://www.patrickmeirmans.com/software .
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Affiliation(s)
- Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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Ramírez-Cañas SA, López-Caballero JD, Mata-López R. Morphological and Molecular Data Reveal Two New Species of Viannaia (Nematoda: Viannaiidae), Parasitizing Opossums (Mammalia: Didelphidae) in Mexico. J Parasitol 2021; 107:388-403. [PMID: 33971012 DOI: 10.1645/18-199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Two new species of Viannaia from the intestine of the North American opossums, Didelphis virginiana (Virginia opossum), and Philander opossum (gray four-eyed opossum), are described based on morphological and molecular data, through an integrative taxonomic approach. Maximum likelihood and Bayesian inference analyses for each dataset and the concatenated dataset were performed using a mitochondrial cytochrome c oxidase subunit 1 (COI) gene, and the nuclear ribosomal internal transcribed spacer region (ITS1-5.8S-ITS2). The phylogenetic analyses revealed 2 new species that occur in Mexico, one from the western state of Colima and another from the southern state of Chiapas. Our phylogenetic trees for both molecular markers and concatenated datasets yielded similar topologies with high bootstrap values and posterior probabilities. Viannaia is recovered as a monophyletic group, but the family Viannaiidae appears as non-monophyletic, due to the position of Travassostrongylus scheibelorum, similar to previous studies. Finally, the morphology of Viannaia and Hoineffia is discussed.
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Affiliation(s)
- Sara Angélica Ramírez-Cañas
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, C. P. 04510, Mexico City, Mexico.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Apartado 70-153, C. P. 04510, Mexico City, Mexico
| | - Jorge D López-Caballero
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, C. P. 04510, Mexico City, Mexico
| | - Rosario Mata-López
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, C. P. 04510, Mexico City, Mexico
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Abstract
Background Bayesian MCMC has become a common approach for phylogenetic inference. But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phylogenetic inference algorithms. Results This paper develops a new algorithm to improve the efficiency of Bayesian phylogenetic inference for models that include a per-branch rate parameter. In a Markov chain Monte Carlo algorithm, the presented proposal kernel changes evolutionary rates and divergence times at the same time, under the constraint that the implied genetic distances remain constant. Specifically, the proposal operates on the divergence time of an internal node and the three adjacent branch rates. For the root of a phylogenetic tree, there are three strategies discussed, named Simple Distance, Small Pulley and Big Pulley. Note that Big Pulley is able to change the tree topology, which enables the operator to sample all the possible rooted trees consistent with the implied unrooted tree. To validate its effectiveness, a series of experiments have been performed by implementing the proposed operator in the BEAST2 software. Conclusions The results demonstrate that the proposed operator is able to improve the performance by giving better estimates for a given chain length and by using less running time for a given level of accuracy. Measured by effective samples per hour, use of the proposed operator results in overall mixing more efficient than the current operators in BEAST2. Especially for large data sets, the improvement is up to half an order of magnitude.
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Affiliation(s)
- Rong Zhang
- School of Computer Science, University of Auckland, Auckland, New Zealand.
| | - Alexei Drummond
- School of Computer Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Murillo P, Klimov P, Hubert J, OConnor B. Investigating species boundaries using DNA and morphology in the mite Tyrophagus curvipenis (Acari: Acaridae), an emerging invasive pest, with a molecular phylogeny of the genus Tyrophagus. Exp Appl Acarol 2018; 75:167-189. [PMID: 29700678 DOI: 10.1007/s10493-018-0256-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 04/14/2018] [Indexed: 05/09/2023]
Abstract
Mites of the genus Tyrophagus (Acari: Acaridae) are among the most widespread and common mites, inhabiting diverse natural and anthropogenic habitats. Some species are pests of agricultural products and stored food and/or live in house dust, causing allergies to humans. We sequenced 1.2 kb of the mitochondrial COI gene for 38 individuals belonging to seven species of Tyrophagus, including T. curvipenis, T. putrescentiae, T. fanetzhangorum, T. longior, T. perniciosus, and T. cf. similis. Molecular phylogenetic analyses (1) recovered two major clades corresponding to the presence or absence of eyespots, and (2) separated all included morphological species. Tyrophagus curvipenis and T. putrescentiae had the lowest between-species genetic distances (range, mean ± SD): 14.20-16.30, 15.17 ± 0.40 (K2P). The highest within-species variation was found in T. putrescentiae 0.00-4.33, 1.78 ± 1.44 (K2P). In this species, we recovered two distinct groups; however, no geographical or ecological dissimilarities were observed between them. Based on our analyses, we document important morphological differences between T. curvipenis and T. putrescentiae. For the first time, we record the occurrence of T. curvipenis in the New World and suggest that it may be an emerging pest as it is currently spreading in agricultural produce.
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Affiliation(s)
- Pamela Murillo
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Laboratorio de Acarologia- CIPROC, Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San Pedro, 2060, Costa Rica.
| | - Pavel Klimov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Faculty of Biology, Tyumen State University, Tyumen, Russia
| | - Jan Hubert
- Biologically Active Substances in Crop Protection, Crop Research Institute, Prague, Czech Republic
| | - Barry OConnor
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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Pandey SK, Dasgupta T, Rathore A, Vemula A. Relationship of Parental Genetic Distance with Heterosis and Specific Combining Ability in Sesame (Sesamum indicum L.) Based on Phenotypic and Molecular Marker Analysis. Biochem Genet 2018; 56:188-209. [PMID: 29322371 DOI: 10.1007/s10528-017-9837-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/29/2017] [Indexed: 11/30/2022]
Abstract
The genetic distance analysis for selection of suitable parents has been established and effectively used in many crops; however, there is dearth of conclusive report of relationship of genetic distance analysis with heterosis in sesame. In the present study, an attempt was made to estimate the associations of genetic distances using SSR (GDSSR), seed-storage protein profiling (GDSDS) and agro-morphological traits (GDMOR) with hybrid performance. Seven parents were selected from 60 exotic and Indian genotypes based on genetic distance from clustering pattern based on SSR, seed-storage protein, morphological traits and per se performance. For combining ability analysis, 7 parents and 21 crosses generated from 7 × 7 half diallel evaluated at two environments in a replicated field trial during pre-kharif season of 2013. Compared with the average parents yield (12.57 g plant-1), eight hybrids had a significant (P < 0.01) yield advantage across environments, with averages of 26.94 and 29.99% for better-parent heterosis (BPH) and mid-parent heterosis (MPH), respectively, across environments. Highly significant positive correlation was observed between specific combining ability (SCA) and per se performance (0.97), while positive non-significant correlation of BPH with GDSSR (0.048), and non-significant negative correlations with GDMOR (- 0.01) and GDSDS (- 0.256) were observed. The linear regressions of SCA on MPH, BPH and per se performance of F1s were significant with R2 value of 0.88, 0.84 and 0.95 respectively. The present findings revealed a weak association of GDSSR with F1's performance; however, SCA has appeared as an important factor in the determination of heterosis and per se performance of the hybrids. The present findings also indicated that parental divergence in the intermediate group would likely produce high heterotic crosses in sesame.
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Affiliation(s)
- Sarita K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India. .,Department of Genetics and Plant Breeding, Institute of Agricultural Science, Calcutta University, Kolkata, India.
| | - Tapash Dasgupta
- Department of Genetics and Plant Breeding, Institute of Agricultural Science, Calcutta University, Kolkata, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Anilkumar Vemula
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
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