1
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Scheepers M, Bragança PHN, Chakona A. Naming the other cousin: A new goldie barb (Cyprinidae: Smiliogastrininae) from the northeast escarpment in South Africa, with proposed taxonomic rearrangement of the goldie barb group in southern Africa. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39021263 DOI: 10.1111/jfb.15870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
A growing body of evidence indicates that the global diversity of freshwater fishes has not been fully documented. Studies of freshwater fishes that were previously thought to be morphologically variable have revealed the existence of deeply divergent lineages, with many distinct species. In southern Africa a number of Enteromius species exhibit either exceedingly wide or divided distribution patterns that should be rare for freshwater fishes with limited dispersal opportunities between river systems. One such species is the sidespot barb, Enteromius neefi. As currently defined, E. neefi has a disjunct distribution that is divided between rivers in the northeast escarpment in South Africa and Eswatini, and tributaries of the Upper Zambezi in Zambia and southern Congo in the Democratic Republic of Congo, with a large geographic gap between these two populations. With the use of molecular and morphological methods, the level of divergence between the two populations was examined, and a new species was described from the Steelpoort River in the Limpopo River system of South Africa. Findings from this study provide further evidence for a number of taxonomic problems within the goldie barbs of southern Africa, and some taxonomic rearrangements are proposed for this group.
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Affiliation(s)
- Martinus Scheepers
- NRF-South African Institute for Aquatic Biodiversity (NRF-SAIAB), Makhanda, South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
| | - Pedro H N Bragança
- NRF-South African Institute for Aquatic Biodiversity (NRF-SAIAB), Makhanda, South Africa
- Department of Ichthyology, American Museum of Natural History, New York, New York, USA
| | - Albert Chakona
- NRF-South African Institute for Aquatic Biodiversity (NRF-SAIAB), Makhanda, South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
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2
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Zheng LP, Geng YM. Complete mitochondrial genome of Guigarracailaoensis Wang, Chen & Zheng, 2022 (Cypriniformes, Cyprinidae) and its phylogenetic implications. Zookeys 2024; 1190:75-89. [PMID: 38298405 PMCID: PMC10825860 DOI: 10.3897/zookeys.1190.113808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/18/2023] [Indexed: 02/02/2024] Open
Abstract
Guigarracailaoensis is a member of family Cyprinidae, subfamily Labeoninae (Cypriniformes) which was recently discovered in southwestern China. Following its initial description, additional information on this species has remained notably scarce. In the current study, we assemble the complete mitochondrial genome (mitogenome) of G.cailaoensis using the Illumina sequencing platform. The mitogenome is identified as a circular, double-stranded DNA sequence of 16,593 base pairs, encompassing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Maximum-likelihood and Bayesian-inference approaches were used to construct phylogenetic trees for three datasets: (i) PCG sequences of the complete mitogenome (dataset 1); (ii) PCG sequences of the complete mitogenome combined with nuclear DNA (ncDNA) (Rag1) sequence (dataset 2); and (iii) ncDNA (Rag1) sequences (dataset 3). Phylogenetic analyses position G.cailaoensis as a sister taxon to the lineage consisting of Paraqianlabeolineatus Zhao, Sullivan, Zhang & Peng, 2014 and Pseudogyrinocheilusprochilus Fang, 1933 in dataset 1, and to Pseudogyrinocheilusprochilus in dataset 2, species lacking an oral disc on the lower lip. However, G.cailaoensis showed a close relationship to the lineage consisting of Discogobio and Discocheilus in dataset 3, species possessing an oral disc on the lower lip. Nonetheless, a variety of species with an oral disc on the lower lip are clustered into different lineages across the three datasets that may indicate that the development of the oral disc is homoplastic within the subfamily Labeoninae. The outcomes of this study have the potential to support conservation efforts for this species and to enrich our understanding of genetic resources in the area.
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Affiliation(s)
- Lan-Ping Zheng
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, Yunnan, ChinaYunnan University of Chinese MedicineKunmingChina
| | - Ying-Min Geng
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, Yunnan, ChinaYunnan University of Chinese MedicineKunmingChina
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3
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Gurganari L, Dastageer G, Mushtaq R, Khwaja S, Uddin S, Baloch MI, Hasni S. Assessment of heavy metals in cyprinid fishes: Rivers of district Khuzdar Balochistan Pakistan. BRAZ J BIOL 2024; 84:e256071. [DOI: 10.1590/1519-6984.256071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/20/2022] [Indexed: 11/21/2022] Open
Abstract
Abstract The present study was conducted to measured heavy metals in cyprinid fishes in rivers of District Khuzdar Balochistan, Pakistan. In the present study, 25 fish samples were collected that belonged to 8 order of 13 families, The Cyprinidae family had the largest number of eight fish species. Present study is focused on Heavy metals in cyprinid fishes. Heavy metals accumulation like Zinc, Manganese, Copper, and Nickel was evaluated in water and various organs of fishes. Atomic Absorption Spectroscopy was used for the identification of these heavy metals in fish species and water bodies. The average concentration (mg/L) of Zn 0.26-0.41, Mn 0.030- 0.073, Cu 0.017—0.080 and NI 0.14-0.79 were observed in water. The Concentration (mg/L), of Zn Conc 0.383-.028 Mn Conc .073- .030 Cu Conc 080-.017 NI Conc .79-.14. The concentration of heavy metals was found both similar and varied simultaneously across the whole research area. Zinc concentration was reported highest, whereas Copper was at the lowest concentration in all fish species .The concentration of heavy metals, in all the fish species under this study, was above the threshold of WHO limits.
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Affiliation(s)
| | | | | | - S. Khwaja
- Federal Urdu University of Arts Science and Technology, Pakistan
| | - S. Uddin
- University of Balochistan, Pakistan
| | | | - S. Hasni
- University of Balochistan, Pakistan
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4
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Rahmouni C, Seifertová M, Šimková A. Revealing the hidden diversity of Gyrodactylus communities (Monogenea, Gyrodactylidae) from Nearctic Catostomidae and Leuciscidae fish hosts (Teleostei, Cypriniformes), with descriptions of ten new species. Parasite 2023; 30:40. [PMID: 37768077 PMCID: PMC10537664 DOI: 10.1051/parasite/2023035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
Despite the high diversity of freshwater fishes in the Nearctic region, little is known about the composition of their parasite communities. We addressed the diversity of viviparous monogeneans of Gyrodactylus parasitizing highly diversified cypriniform fish inhabiting Nearctic watersheds. Nowadays, a thorough assessment of Gyrodactylus spp. diversity requires both morphological traits and genetic data. A combination of taxonomically important haptoral features and sequences of the ITS regions and 18S rDNA revealed 25 Gyrodactylus spp. parasitizing two catostomid and 15 leuciscid species sampled in six distinct localities in the United States and Canada. These include ten Gyrodactylus species recognized as new to science and described herein (G. ellae n. sp., G. hamdii n. sp., G. hanseni n. sp., G. huyseae n. sp., G. kuchtai n. sp., G. lummei n. sp., G. mendeli n. sp., G. prikrylovae n. sp., G. scholzi n. sp., and G. steineri n. sp.), seven already known species, and finally eight undescribed species. Overall, Nearctic Gyrodactylus spp. exhibited haptoral morphotypes known from fish hosts worldwide and those apparently restricted to Nearctic Gyrodactylus lineages like the typical ventral bar with a median knob and a plate-like membrane, or the additional filament attached to the handles of marginal hooks. The integrative approach further evidenced possible ongoing gene flow, host-switching in generalist Gyrodactylus spp., and regional translocation of monogenean fauna through fish introductions. The study highlights the hitherto underexplored morphological and genetic diversity of viviparous monogeneans throughout the Nearctic region.
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Affiliation(s)
- Chahrazed Rahmouni
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Mária Seifertová
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
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5
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Řehulková E, Seifertová M, Francová K, Šimková A. Nearctic Dactylogyrus species (Platyhelminthes, Monogenea) parasitizing cypriniform fishes in the context of morphology and phylogeny, with descriptions of seven new species. Parasite 2023; 30:30. [PMID: 37589452 PMCID: PMC10433842 DOI: 10.1051/parasite/2023032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/16/2023] [Indexed: 08/18/2023] Open
Abstract
Ribosomal DNA sequences are currently available for 32 morphologically recognized species of Dactylogyrus parasitizing Nearctic cypriniforms, but only 16 of them are assigned to nominal species. Herein, morphological data on 28 of the 32 species are provided, together with comments on their phylogenetic relationships in the context of the morphology of taxonomically important structures. Seven new species of Dactylogyrus are described from five species of leuciscids and one species of catostomids, as follows: D. aduncus n. sp. from Campostoma spadiceum, D. cloutmani n. sp. from Luxilus chrysocephalus isolepis, D. cornifrons n. sp. from Cyprinella venusta, D. fimbratus n. sp. from Rhinichthys cataractae, D. mcallisteri n. sp. from Semotilus atromaculatus, and D. chieni n. sp. and D. haneki n. sp. from Hypentelium nigricans. Four previously described species of Dactylogyrus, D. atromaculatus from S. atromaculatus, D. eos from C. neogaeus, D. parvicirrus from Notemigonus crysoleucas and D. perlus from L. c. isolepis, are redescribed and/or figured. As for the remaining 17 species, only the male copulatory organs (MCOs) taken from the respective hologenophores are illustrated. On the basis of phylogenetic analyses, two main clades of Nearctic Dactylogyrus were recognized and supported by the different morphology of the MCO. The first one included 22 strictly Nearctic species sharing the same MCO type with Dactylogyrus spp. parasitizing cyprinids likely of Asian origin. The second clade encompassed Dactylogyrus spp. with diverse MCO morphology and was placed in the sister position to Dactylogyrus spp. parasitizing European leuciscids and North-West African cyprinids.
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Affiliation(s)
- Eva Řehulková
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Mária Seifertová
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Kateřina Francová
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
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6
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Mu X, Yang Y, Sun J, Yi liu, Xu M, Shao C, Chu KH, Li W, Liu C, Gu D, Fang M, Zhang C, Liu F, Song H, Wang X, Chen J, Ma KY. FishPIE: a universal phylogenetically informative exon markers set for ray-finned fishes. iScience 2022; 25:105025. [PMID: 36105587 PMCID: PMC9464953 DOI: 10.1016/j.isci.2022.105025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/11/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
Understanding the evolutionary history of the highly diverse ray-finned fishes has been challenging, and the development of more universal primers for phylogenetic analyses may help overcoming these challenges. We developed FishPIE, a nested PCR primer set of 82 phylogenetically informative exon markers, and tested it on 203 species from 31 orders of Actinopterygii. We combined orthologous sequences of the FishPIE markers obtained from published genomes and transcriptomes and constructed the phylogeny of 710 species belonging to 190 families and 60 orders. The resulting phylogenies had topologies comparable to previous phylogenomic studies. We demonstrated that the FishPIE markers could address phylogenetic questions across broad taxonomic levels. By incorporating the newly sequenced taxa, we were able to shed new light on the phylogeny of the highly diverse Cypriniformes. Thus, FishPIE holds great promise for generating genetic data for broad taxonomic groups and accelerating our understanding of the fish tree of life. FishPIE is a nested PCR primer set of 82 markers for fish phylogenetic analysis The markers can be broadly applied to all orders of ray-finned fishes Their phylogenetic performance is comparable to that of genomic analyses
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7
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Yi W, Mueller T, Rücklin M, Richardson MK. Developmental neuroanatomy of the rosy bitterling Rhodeus ocellatus (Teleostei: Cypriniformes)-A microCT study. J Comp Neurol 2022; 530:2132-2153. [PMID: 35470436 PMCID: PMC9245027 DOI: 10.1002/cne.25324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 02/09/2022] [Accepted: 03/17/2022] [Indexed: 11/11/2022]
Abstract
Bitterlings are carp-like teleost fish (Cypriniformes: Acheilanathidae) known for their specialized brood parasitic lifestyle. Bitterling embryos, in fact, develop inside the gill chamber of their freshwater mussel hosts. However, little is known about how their parasitic lifestyle affects brain development in comparison to nonparasitic species. Here, we document the development of the brain of the rosy bitterling, Rhodeus ocellatus, at four embryonic stages of 165, 185, 210, 235 hours postfertilization (hpf) using micro-computed tomography (microCT). Focusing on developmental regionalization and brain ventricular organization, we relate the development of the brain divisions to those described for zebrafish using the prosomeric model as a reference paradigm. Segmentation and three-dimensional visualization of the ventricular system allowed us to identify changes in the longitudinal brain axis as a result of cephalic flexure during development. The results show that during early embryonic and larval development, histological differentiation, tissue boundaries, periventricular proliferation zones, and ventricular spaces are all detectable by microCT. The results of this study visualized with differential CT profiles are broadly consistent with comparable histological studies, and with the genoarchitecture of teleosts like the zebrafish. Compared to the zebrafish, our study identifies distinct developmental heterochronies in the rosy bitterling, such as a precocious development of the inferior lobe.
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Affiliation(s)
- Wenjing Yi
- Institute of Biology, University of Leiden, Sylvius Laboratory, Leiden, the Netherlands.,Vertebrate Evolution, Development and Ecology, Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Thomas Mueller
- Vertebrate Evolution, Development and Ecology, Naturalis Biodiversity Center, Leiden, the Netherlands.,Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Martin Rücklin
- Institute of Biology, University of Leiden, Sylvius Laboratory, Leiden, the Netherlands.,Vertebrate Evolution, Development and Ecology, Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Michael K Richardson
- Institute of Biology, University of Leiden, Sylvius Laboratory, Leiden, the Netherlands.,Vertebrate Evolution, Development and Ecology, Naturalis Biodiversity Center, Leiden, the Netherlands
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8
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Xu X, Guan W, Niu B, Guo D, Xie QP, Zhan W, Yi S, Lou B. Chromosome-Level Assembly of the Chinese Hooksnout Carp (Opsariichthys bidens) Genome Using PacBio Sequencing and Hi-C Technology. Front Genet 2022; 12:788547. [PMID: 35126459 PMCID: PMC8807397 DOI: 10.3389/fgene.2021.788547] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Xiaojun Xu
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wenzhi Guan
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baolong Niu
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dandan Guo
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qing-Ping Xie
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wei Zhan
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shaokui Yi
- School of Life Sciences, Huzhou University, Huzhou, China
- *Correspondence: Shaokui Yi, ; Bao Lou,
| | - Bao Lou
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Shaokui Yi, ; Bao Lou,
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9
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Zhang Z, Li S, Zhang J, Song W, Yang J, Mu J. The complete mitochondrial genome of an endangered minnow Aphyocypris lini (Cypriniformes: Xenocyprididae): genome characterization and phylogenetic consideration. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00811-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Kartavtsev YP. Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society. Animals (Basel) 2021; 11:1473. [PMID: 34065552 PMCID: PMC8160991 DOI: 10.3390/ani11051473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 01/27/2023] Open
Abstract
Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
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11
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Characterization of two complete mitochondrial genomes of Pterocryptis anomala (Siluridae) and its phylogeny and cryptic diversity. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00582-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Complete mitochondrial genome of the freshwater fish Acrossocheilus longipinnis (Teleostei: Cyprinidae): genome characterization and phylogenetic analysis. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00440-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Rehman A, Khan MF, Bibi S, Riaz M, Nouroz F. Comparative phylogenetic analysis of Schizothorax plagiostomus and Schizothorax esocinus with other members of subfamilies of cyprinidae on the basis of complete mitochondrial genome and 12S, 16S ribosomal RNA from Northren areas of Pakistan. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:250-256. [PMID: 32634032 DOI: 10.1080/24701394.2020.1787397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We assessed the relationship of Schizothoracinae species with other subfamilies Alburninae, Xenocyprinae, Cultrinae and Squaliobarbinae of family Cyprinidae by creating the phylogenetic trees using complete mitogenome and 12S and 16S RNA. Our representative species show the great affiliation with other but separated from a group composed of Metzia mesembrinum, Metzia longinasus, Metzia lineata and Metzia formosae of subfamily Alburninae while other subfamilies formed distinct group. The members of subfamily Schizothoracinae shows separate line of evolution from subfamily Barbinae.
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Affiliation(s)
- Aqsa Rehman
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | | | - Saira Bibi
- Department of Zoology, Hazara University, Mansehra, Pakistan.,Department of Zoology, Women University Swabi, Pakistan
| | - Mehreen Riaz
- Department of Zoology, Women University Swabi, Pakistan
| | - Faisal Nouroz
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
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14
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Benovics M, Desdevises Y, Šanda R, Vukić J, Šimková A. Cophylogenetic relationships betweenDactylogyrus(Monogenea) ectoparasites and endemic cyprinoids of the north‐eastern European peri‐Mediterranean region. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12341] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michal Benovics
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Yves Desdevises
- CNRS Biologie Intégrative des Organismes Marins (BIOM) Observatoire Océanologique Sorbonne Université Banyuls/Mer France
| | | | - Jasna Vukić
- Department of Ecology Faculty of Science Charles University Prague Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
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15
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Yang L, Wang Y, Wang T, Duan S, Dong Y, Zhang Y, He S. A Chromosome-Scale Reference Assembly of a Tibetan Loach, Triplophysa siluroides. Front Genet 2019; 10:991. [PMID: 31681425 PMCID: PMC6807559 DOI: 10.3389/fgene.2019.00991] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/18/2019] [Indexed: 01/03/2023] Open
Abstract
Cobitoidea is one of the two superfamilies in Cypriniformes; however, few genomes have been sequenced for Cobitoidea fishes. Here, we obtained a total of 252.90 Gb of short Illumina reads and 31.60 Gb of long PacBio Sequel reads, representing approximate genome coverage of 256× and 50×, respectively. The final assembled genome is about 583.47 Mb with contig N50 sizes of 2.87 Mb, which accounts for 91.44% of the estimated genome size of 638.07 Mb. Using Hi-C-based chromatin contact maps, 99.31% of the genome assembly was placed into 25 chromosomes, and the N50 is 22.3 Mb. The gene annotation completeness was evaluated by BUSCO, and 2,470 of the 2,586 conserved genes (95.5%) could be found in our assembly. Repetitive elements were calculated to reach 33.08% of the whole genome. Moreover, we identified 25,406 protein-coding genes, of which 92.59% have been functionally annotated. This genome assembly will be a valuable genomic resource to understand the biology of the Tibetan loaches and will also set a stage for comparative analysis of the classification, diversification, and adaptation of fishes in Cobitoidea.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ying Wang
- School of Life Sciences, Jianghan University, Wuhan, China
| | - Tai Wang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics Breeding, Gansu Fishers Research Institute, Lanzhou, China
| | | | - Yang Dong
- Nowbio Biotechnology Company, Kunming, China
| | - Yanping Zhang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics Breeding, Gansu Fishers Research Institute, Lanzhou, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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16
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Yang K, Jiang W, Wang X, Zhang Y, Pan X, Yang J. Evolution of the intermuscular bones in the Cyprinidae (Pisces) from a phylogenetic perspective. Ecol Evol 2019; 9:8555-8566. [PMID: 31410261 PMCID: PMC6686301 DOI: 10.1002/ece3.5374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 01/15/2023] Open
Abstract
Intermuscular bones (IBs) are widely present in morphologically generalized teleost fishes and are commonly found in the Cyprinidae. Intermuscular bones are small, hard spicules of bone that are formed by ossification in the myosepta between neighboring myomeres. Why fish have IBs, and whether there is any evolutionary pattern to their occurrence, has been poorly understood. However, the presence of IBs does substantially affect the meat quality and commercial values of many cyprinid fishes in aquaculture. In this study, we sampled 592 individuals of cyprinid fishes to systematically investigate the evolution of IBs from a phylogenetic point of view. We found that the total number of IBs in the Cyprinidae ranged from 73 to 169, and we clarified that only two categories of IBs (epineural and epipleural) were present in all examined cyprinids. Most of the IBs were distributed in the posterior region of the fish, which might be an optimal target for selecting fewer IB strains in aquaculture. There was a positive correlation between IBs and the number of vertebrae, thus making it possible to predict the approximate number of IBs by counting the number of vertebrae. Although the IBs displayed some correlation with phylogenetic relationships in some lineages and to ecological factors such as diet (especially carnivore), in an overall view the variations of IBs in cyprinids were extremely diverse. The number and patterns of IBs in these fishes may reflect their phylogenetic history, but have been shaped by multiple environment factors. In this study, we also confirmed that X-ray photography remains an optimal and reliable method for the study of IBs.
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Affiliation(s)
- Kunfeng Yang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Wansheng Jiang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Xiaoai Wang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Yuanwei Zhang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Xiaofu Pan
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Junxing Yang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
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17
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Phylogenetic relationships of Cypriniformes and plasticity of pharyngeal teeth in the adaptive radiation of cyprinids. SCIENCE CHINA-LIFE SCIENCES 2019; 62:553-565. [DOI: 10.1007/s11427-019-9480-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/01/2018] [Indexed: 12/23/2022]
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18
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Touil A, Casal-Lopez M, Bouhadad R, Doadrio I. Phylogeny and phylogeography of the genus Luciobarbus (Haeckel, 1843) in Algeria inferred from mitochondrial DNA sequence variation. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:332-344. [DOI: 10.1080/24701394.2018.1526928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Amira Touil
- LBEIG, Population Genetics and Conservation Unit, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Bab Ezzouar, Algeria
| | - Miriam Casal-Lopez
- Biodiversity and Evolutionary Group, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Rachid Bouhadad
- LBEIG, Population Genetics and Conservation Unit, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Bab Ezzouar, Algeria
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Group, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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19
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Jiang W, Qiu Y, Pan X, Zhang Y, Wang X, Lv Y, Bian C, Li J, You X, Chen J, Yang K, Yang J, Sun C, Liu Q, Cheng L, Yang J, Shi Q. Genome Assembly for a Yunnan-Guizhou Plateau "3E" Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications. Front Genet 2018; 9:614. [PMID: 30564274 PMCID: PMC6288284 DOI: 10.3389/fgene.2018.00614] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/21/2018] [Indexed: 11/26/2022] Open
Abstract
A Yunnan-Guizhou Plateau fish, the Kanglang white minnow (Anabarilius grahami), is a typical “3E” (Endangered, Endemic, and Economic) species in China. Its distribution is limited to Fuxian Lake, the nation’s second deepest lake, with a significant local economic value but a drastically declining wild population. This species has been evaluated as VU (Vulnerable) in the China Species Red List. As one of the “Four Famous Fish” in Yunnan province, the artificial breeding has been achieved since 2003. It has not only re-established its wild natural populations by reintroduction of the artificial breeding stocks, but also brought a wide and popular utilization of this species to the local fish farms. A. grahami has become one of the main native aquaculture species in Yunnan province, and the artificial production has been emerging in steady growth each year. To promote the conservation and sustainable utilization of this fish, we initiated its whole genome sequencing project using an Illumina Hiseq2500 platform. The assembled genome size of A. grahami is 1.006 Gb, accounting for 98.63% of the estimated genome size (1.020 Gb), with contig N50 and scaffold N50 values of 26.4 kb and 4.41 Mb, respectively. Approximately about 50.38% of the genome was repetitive. A total of 25,520 protein-coding genes were subsequently predicted. A phylogenetic tree based on 4,580 single-copy genes from A. grahami and 18 other cyprinids revealed three well-supported subclades within the Cyprinidae. This is the first inter-subfamily relationship of cyprinids at genome level, providing a simple yet useful framework for understanding the traditional but popular subfamily classification systems. Interestingly, a further population demography of A. grahami uncovered a historical relationship between this fish and Fuxian Lake, suggesting that range expansion or shrinkage of the habitat has had a remarkable impact on the population size of endemic plateau fishes. Additionally, a total of 33,836 simple sequence repeats (SSR) markers were identified, and 11 loci were evaluated for a preliminary genetic diversity analysis in this study, thus providing another useful genetic resource for studying this “3E” species.
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Affiliation(s)
- Wansheng Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ying Qiu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yuanwei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yunyun Lv
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Chao Bian
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Jieming Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Kunfeng Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Chao Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qian Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Le Cheng
- BGI-Yunnan, BGI-Shenzhen, Kunming, China
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
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20
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Ndeda VM, Mateos M, Hurtado LA. Evolution of African barbs from the Lake Victoria drainage system, Kenya. PeerJ 2018; 6:e5762. [PMID: 30386696 PMCID: PMC6204829 DOI: 10.7717/peerj.5762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/16/2018] [Indexed: 12/02/2022] Open
Abstract
The Lake Victoria drainage basin (LVD) in Kenya is home to ten nominal species of small barbs (Enteromius) and one of large barbs (Labeobarbus altianalis). A recent molecular study genetically characterized small barbs in this region and found evidence of introgression between certain species, complicating the taxonomy and species identification of these fishes. This study aimed to extend our understanding on the evolution of these fishes by: (1) determining whether putatively pure individuals of Enteromius cercops are found in the Kenyan LVD, as the previous study only found hybrid individuals of this species in this region; (2) testing the sister relationship between Enteromius profundus, endemic to Lake Victoria, and Enteromius radiatus, also found in Lake Victoria, which had been previously synonymized; (3) examining the phylogenetic relationships of small barbs of the Kenyan LVD with those reported from other ichthyological provinces of Africa; and (4) examining the phylogenetic relationships of Labeobarbus altianalis with other Labeobarbus species. To this end, we obtained mitochondrial Cytochrome b and nuclear Growth Hormone (GH) intron 2 gene sequences of nine Enteromius species from the LVD in Kenya, as well as cytochrome b sequences for L. altianalis. We conducted Maximum likelihood and Bayesian phylogenetic analyses to establish their evolutionary relationships in relation to many other barbs specimens from Africa. Phylogenetic analyses did not reveal instances of hybridization/introgression among the individuals sequenced by us. A sister relationship between E. profundus and E. radiatus was not found. This latter species shows instead a sister relationship with a lineage comprised of two species from West Africa. Other sister relationships between taxa from the East coast and other ecoregions from Africa are observed, suggesting that past drainage connections and vicariant events contributed to the diversification of Enteromius. Finally, only a single haplotype was recovered among the L. altianalis individuals examined, which is most similar to a specimen from Lake Edward in Uganda.
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Affiliation(s)
- Violet M Ndeda
- Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America.,Department of Zoology, Maseno University, Maseno, Kenya
| | - Mariana Mateos
- Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
| | - Luis A Hurtado
- Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
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21
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Keskar A, Raghavan R, Paingankar MS, Kumkar P, Katwate U, Jadhav S, Padhye A, Dahanukar N. Molecular phylogeny unveils hidden diversity of hillstream loaches (Cypriniformes: Cobitoidea) in the northern Western Ghats of India. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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22
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Bagley JC, Mayden RL, Harris PM. Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils. PeerJ 2018; 6:e5168. [PMID: 30013838 PMCID: PMC6035723 DOI: 10.7717/peerj.5168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/15/2018] [Indexed: 11/25/2022] Open
Abstract
Catostomidae ("suckers") is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian "total-evidence" methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous-Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian-North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning.
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Affiliation(s)
- Justin C. Bagley
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal, Brazil
- Departamento de Zoologia e Botânica, IBiLCE, Universidade Estadual Paulista, São José do Rio Preto, São Paulo, Brazil
| | | | - Phillip M. Harris
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
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23
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Schönhuth S, Vukić J, Šanda R, Yang L, Mayden RL. Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei). Mol Phylogenet Evol 2018; 127:781-799. [PMID: 29913311 DOI: 10.1016/j.ympev.2018.06.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022]
Abstract
The phylogenetic relationships and classification of the freshwater fish order Cypriniformes, like many other species-rich groups of vertebrates, has evolved over time with some consistency and inconsistencies of relationships across various studies. Within Cypriniformes, the Holarctic family Leuciscidae is one of the most widely distributed and highly diverse monophyletic groups of cyprinoids. Despite several studies conducted on this group, alternative hypotheses exist as to the composition and relationships within Leuciscidae. Here we assess the extent, composition, phylogenetic relationships, and taxonomy of this highly diverse group of fishes, using multiple mitochondrial and nuclear loci and a comprehensive and dense taxonomic sampling. Analyses of 418 specimens (410 species) resolve a well-supported Leuciscidae including 362 specimens (358 taxa) in six well-supported subfamilies/major clades: Pseudaspininae/Far East Asian clade (FEA); Laviniinae/North American Western clade (WC); Plagopterinae/North American Creek Chub-Plagopterin clade (CC-P); Leuciscinae/Eurasian Old World clade (OW) (minus Phoxinus) plus North American Notemigonus; Phoxininae/Eurasian Phoxinus clade (PHX); and Pogonichthyinae/North American clade (NA) including all remaining leuciscids. Within Leuciscidae, neither the traditional phoxinins (Phoxinus, FEA, Nearctic genera) nor all Nearctic genera (minus Notemigonus) are resolved as monophyletic; whereas the WC and CC-P form two independent lineages from remaining North American cyprinoids. A close relationship exists between Eurasian Phoxinus, NA, and OW clades, while FEA is the sister group to all remaining Leuciscidae. Major lineages resolved within these six subfamilies are mostly congruent with some previous studies. Our results suggests a complex evolutionary history of this diverse and widespread group of fishes.
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Affiliation(s)
- Susana Schönhuth
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA.
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Vaclavske namesti 68, 115 79 Prague, Czech Republic
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, 1659 Museum Rd., Gainesville, FL 32611, USA
| | - Richard L Mayden
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA
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24
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Shi LX, Zhang C, Wang YP, Tang QY, Danley PD, Liu HZ. Evolutionary relationships of two balitorids (Cypriniformes, Balitoridae) revealed by comparative mitogenomics. ZOOL SCR 2018. [DOI: 10.1111/zsc.12282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Li-Xia Shi
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Chen Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Yin-Ping Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Qiong-Ying Tang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- College of Life Sciences; Huzhou University; Huzhou, Zhejiang China
| | | | - Huan-Zhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
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25
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Tang QY, Li XB, Yu D, Zhu YR, Ding BQ, Liu HZ, Danley PD. Saurogobio punctatus sp. nov., a new cyprinid gudgeon (Teleostei: Cypriniformes) from the Yangtze River, based on both morphological and molecular data. JOURNAL OF FISH BIOLOGY 2018; 92:347-364. [PMID: 29431222 DOI: 10.1111/jfb.13498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 09/30/2017] [Indexed: 06/08/2023]
Abstract
A new cyprinid gudgeon, Saurogobio punctatus sp. nov., is described based on specimens collected from the Yangtze River, China. The new species can be distinguished from its congeners by differences in both morphology and the cytochrome b (cytb) gene sequence. Numerous minute blackish spots are scattered on dorsal and caudal fins in S. punctatus sp. nov. v. absent in the other seven valid Saurogobio species. The new species can be further distinguished from its congeners by the following unique combination of characters: a dorsal fin with eight branched rays; absence of scales in chest area before pectoral origin; upper and lower lips thick, covered with papillae; and a papillose mental pad approximately triangular. Morphologically, the new species most resembles the Chinese lizard gudgeon Saurogobio dabryi, but the new species lays yellowish adhesive eggs v. white pelagic eggs in S. dabryi. A phylogenetic analysis of all Saurogobio species based on cytb gene sequences indicated that S. punctatus sp. nov was distinctly separated from its congeners, with mean sequence divergence ranging from 12·6 to 21·0%. Therefore, molecular data further supported the distinctiveness of the new species.
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Affiliation(s)
- Q Y Tang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, P. R. China
| | - X B Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, P. R. China
| | - D Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, P. R. China
| | - Y R Zhu
- College of Fisheries, Huazhong Agricultural University, Hubei, Wuhan, 430070, P. R. China
| | - B Q Ding
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, CT, 06269-3043, U.S.A
| | - H Z Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, P. R. China
| | - P D Danley
- Department of Biology, Baylor University, One Bear Place #97388, Waco, TX, 76798, U.S.A
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26
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Huang SP, Wang FY, Wang TY. Molecular Phylogeny of the Opsariichthys Group (Teleostei: Cypriniformes) Based On Complete Mitochondrial Genomes. Zool Stud 2017; 56:e40. [PMID: 31966239 PMCID: PMC6517700 DOI: 10.6620/zs.2017.56-40] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 12/06/2017] [Indexed: 11/18/2022]
Abstract
Shih-Pin Huang, Feng-Yu Wang, and Tzi-Yuan Wang (2017) The complete mitochondrial genomes of 76 species from 43 genera under Cyprinidae sensu lato were collected to reassess the molecular phylogeny of Opsariichthyinae sensu Liao et al. 2011. The mitogenomes of three species, Candidia barbata, Opsariichthys evolans, and Opsariichthys pachycephalus, were newly sequenced. Phylogenetic trees were reconstructed based on 13 concatenated multiple protein-coding genes with two ribosomal RNA genes. The concatenated dataset provided a new perspective on systematics and relationships. Tree topologies show that a monophyletic group containing Parazacco, Candidia, Nipponocypris, Zacco, and Opsariichthys should belong to the Opsariichthys group. In addition, the present results also strongly support that Candidia and Nipponocypris should be regarded as distinct genera within the Opsariichthys group. Aphyocypris, Yaoshanicus, Nicholsicypris, and Pararasbora form a monophyletic group within Xenocyprididae, distinct from the Opsariichthys group. Furthermore, Hemigrammocypris is nested with four species of Metzia, a genus of ex-Cultrinae in Xenocyprididae. In addition, two major types of distinct stripes - longitudinal and vertical - were observed among species of the Opsariichthys group and were highly correlated with molecular phylogenetic relationships. Such types of vertical and longitudinal stripes presented in the Opsariichthys group might have originated in an ancestor species, after which distinct vertical stripes might have been lost among these cyprinids but retained in the Opsariichthys group.
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Affiliation(s)
- Shih-Pin Huang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan. E-mail:
| | - Feng-Yu Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, Taiwan. E-mail:
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan. E-mail:
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27
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Biswal JR, Singh RK, Dutta N, Pathak A, Lal KK, Mohindra V, Sah RS, Jena JK. The complete mitochondrial genome of olive barb, Systomus sarana sarana (Hamilton, 1822) and its phylogenetic status. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:940-942. [PMID: 33474046 PMCID: PMC7800531 DOI: 10.1080/23802359.2017.1413319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Systomus sarana sarana, commonly known as olive barb, is an important food and ornamental fish species with wide distribution in South Asia. Here, the complete mitogenome was sequenced on HiSeq 2500. With 16,590 nucleotides, the base composition was 32.9% (A), 26% (C), 15.4% (G) and 25.7% (T), comparable with other carps. The clustering pattern depicted the monophyly of S. sarana sarana with sister cyprinids.
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Affiliation(s)
- J R Biswal
- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajeev K Singh
- National Bureau of Fish Genetic Resources, Lucknow, India
| | - Nimisha Dutta
- National Bureau of Fish Genetic Resources, Lucknow, India
| | - Abhinav Pathak
- National Bureau of Fish Genetic Resources, Lucknow, India
| | - Kuldeep K Lal
- National Bureau of Fish Genetic Resources, Lucknow, India
| | | | - R S Sah
- National Bureau of Fish Genetic Resources, Lucknow, India
| | - J K Jena
- Indian Council of Agricultural Research, New Delhi
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28
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Casal-López M, Perea S, Sousa-Santos C, Robalo JI, Torralva M, Oliva-Paterna FJ, Doadrio I. Paleobiogeography of an Iberian endemic species,Luciobarbus sclateri(Günther, 1868) (Actinopterygii, Cyprinidae), inferred from mitochondrial and nuclear markers. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miriam Casal-López
- Biodiversity and Evolutionary Group; Museo Nacional de Ciencias Naturales, CSIC; Madrid Spain
| | - Silvia Perea
- Biodiversity and Evolutionary Group; Museo Nacional de Ciencias Naturales, CSIC; Madrid Spain
| | - Carla Sousa-Santos
- Insituto Superior de Psicologia Aplicada; Unidade de Investigaçao em Eco-Etologia; Lisboa Portugal
| | - Joana I. Robalo
- Insituto Superior de Psicologia Aplicada; Unidade de Investigaçao em Eco-Etologia; Lisboa Portugal
| | - Mar Torralva
- Department of Zoology; University of Murcia; Murcia Spain
| | | | - Ignacio Doadrio
- Biodiversity and Evolutionary Group; Museo Nacional de Ciencias Naturales, CSIC; Madrid Spain
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The yolk syncytial layer of loach, Misgurnus fossilis (Teleostei) during early development. ZYGOTE 2017; 25:489-497. [DOI: 10.1017/s0967199417000314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
SummaryThe yolk syncytial layer (YSL) of Teleostei is a dynamic multifunctional temporary system. This paper describes the YSL structure of Misgurnus fossilis (Cobitidae) during its early developmental stages, studied using histological methods. YSL formation is prolonged. From the late blastula stage, the basal surface of the YSL is uneven and has protuberances, but becomes smoother during development. There are syncytial ‘islands’ with 1–2 yolk syncytial nuclei in the yolk mass. During epiboly, gastrulation and early segmentation, loach YSL is of different thickness in different regions along the dorso-ventral and antero-posterior axes of an embryo. The YSL is thickened in the dorsal region of gastrulae compared with the ventral region. Although the development of M. fossilis is similar to the development of zebrafish, there are important differences in YSL formation and organization that await further study and analysis. The study of YSL organization contributes to our knowledge of teleost developmental diversity and to the biology of temporary structures.
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Malato G, Shervette VR, Navarrete Amaya R, Valdiviezo Rivera J, Nugra Salazar F, Calle Delgado P, Karpan KC, Aguirre WE. Parallel body shape divergence in the Neotropical fish genus Rhoadsia (Teleostei: Characidae) along elevational gradients of the western slopes of the Ecuadorian Andes. PLoS One 2017; 12:e0179432. [PMID: 28658255 PMCID: PMC5489170 DOI: 10.1371/journal.pone.0179432] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/29/2017] [Indexed: 12/26/2022] Open
Abstract
Neotropical mountain streams are important contributors of biological diversity. Two species of the characid genus Rhoadsia differing for an ecologically important morphological trait, body depth, have been described from mountain streams of the western slopes of the Andes in Ecuador. Rhoadsia altipinna is a deeper-bodied species reported from low elevations in southwestern Ecuador and northern Peru, and Rhoadsia minor is a more streamlined species that was described from high elevations (>1200 m) in the Esmeraldas drainage in northwestern Ecuador. Little is known about these species and their validity as distinct species has been questioned. In this study, we examine how their body shape varies along replicated elevational gradients in different drainages of western Ecuador using geometric morphometrics and the fineness ratio. We also use sequences of the mitochondrial cytochrome oxidase c I gene and the second intron of the S7 nuclear gene to examine whether genetic data are consistent with the existence of two species. We found that body depth varies continuously among populations within drainages as a function of elevation, and that body shape overlaps among drainages, such that low elevation populations of R. minor in the Esmeraldas drainage have similar body depths to higher elevation R. altipinna in southern drainages. Although a common general trend of declining body depth with elevation is clear, the pattern and magnitude of body shape divergence differed among drainages. Sequencing of mitochondrial and nuclear genes failed to meet strict criteria for the recognition of two species (e.g., reciprocal monophyly and deep genetic structure). However, there was a large component of genetic variation for the COI gene that segregated among drainages, indicating significant genetic divergence associated with geographic isolation. Continued research on Rhoadsia in western Ecuador may yield significant insight into adaptation and speciation in Neotropical mountain streams.
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Affiliation(s)
- Grace Malato
- Department of Biological Sciences, DePaul University, Chicago, Illinois, United States of America
| | - Virginia R. Shervette
- Department of Biology/Geology, University of South Carolina, Aiken, South Carolina, United States of America
| | | | | | - Fredy Nugra Salazar
- Laboratorio de Zoología de Vertebrados de la Universidad del Azuay, Cuenca, Ecuador
| | - Paola Calle Delgado
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Kirby C. Karpan
- Department of Biological Sciences, DePaul University, Chicago, Illinois, United States of America
| | - Windsor E. Aguirre
- Department of Biological Sciences, DePaul University, Chicago, Illinois, United States of America
- * E-mail:
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31
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Chakraborty M, Dhar B, Ghosh SK. Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes. Mol Ecol Resour 2017; 17:1359-1370. [PMID: 28332322 DOI: 10.1111/1755-0998.12671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/26/2017] [Accepted: 03/07/2017] [Indexed: 11/29/2022]
Abstract
The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification.
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Affiliation(s)
- Mohua Chakraborty
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Bishal Dhar
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar, Assam, India.,University of Kalyani, Kalyani, West Bengal, India
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Kartavtsev YP. Barcode index number, taxonomic rank and modes of speciation: examples from fish. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:535-542. [PMID: 28481646 DOI: 10.1080/24701394.2017.1315570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of Co-1-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (R2 ≈ 0.84-0.98). Knowledge of deviations from these data can help to find out new taxa and improve biodiversity description. It is concluded that delimiting is successful for bulk of cases because the geographic mode of speciation prevails in nature. It takes a long time for new taxa to form in isolation, which allows accumulation of random mutations and many different nucleotide substitutions between them that can be detected by molecular markers and give unique DNA barcodes. The use of BIN approach, described here, can aid greatly in making this important question clearer especially under wider examination of other organisms.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- a Laboratory of Molecular Systematics, A.V. Zhirmunsky Institute of Marine Biology , National Scientific Center of Marine Biology, Russian Academy of Sciences , Vladivostok , Russia.,b Chair of Biodiversity and Marine Bioresources, Far Eastern Federal University , Vladivostok , Russia
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Tang QY, Shi LX, Liu F, Yu D, Liu HZ. Evolution and phylogenetic application of the MC1R gene in the Cobitoidea (Teleostei: Cypriniformes). Zool Res 2017; 37:281-9. [PMID: 27686787 DOI: 10.13918/j.issn.2095-8137.2016.5.281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Fish of the superfamily Cobitoidea sensu stricto (namely loaches) exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene (MC1R) plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MC1R gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae+ (Cobitidae+(Balitoridae+Nemacheilidae)). Gene evolutionary analyses indicated that MC1R in loaches was under purifying selection pressure, with various sites having different dN/dS values. Both Botiidae and Cobitidae had lower dN/dS values than those of background lineages, suggesting their evolution might be strongly affected by purifying selection pressure. For Balitoridae and Nemacheilidae, both had larger dN/dS values than those of background lineages, suggesting they had a faster evolutionary rate under more relaxed selection pressure. Consequently, we inferred that the relatively stable color patterns in Botiidae and Cobitidae might result from the strong purifying selection pressure on the MC1R gene, whereas the complicated and diverse color patterns in Balitoridae and Nemacheilidae might be associated with the relaxed selection pressure. Given the easy experimental procedure for the partial MC1R gene and its excellent performance in reconstructing phylogeny, we suggest this gene could be used as a good molecular marker for the phylogenetic study of fish species.
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Affiliation(s)
- Qiong-Ying Tang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Li-Xia Shi
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dan Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Huan-Zhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Schmidt RC, Bart HL, Nyingi WD. Multi-locus phylogeny reveals instances of mitochondrial introgression and unrecognized diversity in Kenyan barbs (Cyprininae: Smiliogastrini). Mol Phylogenet Evol 2017; 111:35-43. [PMID: 28323052 DOI: 10.1016/j.ympev.2017.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 03/05/2017] [Accepted: 03/16/2017] [Indexed: 10/19/2022]
Abstract
The phylogenetics and taxonomic status of small African barbs (Cyprininae: Smiliogastrini) remains unresolved despite the recent decision to elevate the genus name Enteromius for the group. The main barrier to understanding the origin of African small barbs and evolutionary relationships within the group is the poor resolution of phylogenies published to date. These phylogenies usually rely on mitochondrial markers and have limited taxon sampling. Here we investigate the phylogenetic relationships of small barbs of Kenya utilizing cytochrome b, Growth Hormone (GH) intron 2, and RAG1 markers from multiple populations of many species in the region. This multi-locus study produced well-supported phylogenies and revealed additional issues that complicate understanding the relationships among East African barbs. We observed widespread mtDNA introgression within the Kenyan barbs, highlighting the need to include nuclear markers in phylogenetic studies of the group. The GH intron 2 resolved heterospecific individuals and aided in inferring the species level phylogeny. The study reveals unrecognized diversity within the group, including within species reported to occur throughout East Africa, and it provides the groundwork for future taxonomic work in the region and across Africa.
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Affiliation(s)
- Ray C Schmidt
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Boggs Hall, New Orleans, LA 70118, United States; Smithsonian Institution, Smithsonian Mpala Postdoctoral Fellow, Mpala Research Centre, PO Box 555-10400, Nanyuki, Kenya.
| | - Henry L Bart
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Boggs Hall, New Orleans, LA 70118, United States
| | - Wanja Dorothy Nyingi
- Ichthyology Section, National Museums of Kenya, PO Box 40658-00100, Nairobi, Kenya
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35
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Sungani H, Ngatunga BP, Koblmüller S, Mäkinen T, Skelton PH, Genner MJ. Multiple colonisations of the Lake Malawi catchment by the genus Opsaridium (Teleostei: Cyprinidae). Mol Phylogenet Evol 2017; 107:256-265. [DOI: 10.1016/j.ympev.2016.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 09/13/2016] [Accepted: 09/29/2016] [Indexed: 01/19/2023]
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36
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Stout CC, Tan M, Lemmon AR, Lemmon EM, Armbruster JW. Resolving Cypriniformes relationships using an anchored enrichment approach. BMC Evol Biol 2016; 16:244. [PMID: 27829363 PMCID: PMC5103605 DOI: 10.1186/s12862-016-0819-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). RESULTS Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. CONCLUSIONS Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.
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Affiliation(s)
- Carla C. Stout
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Milton Tan
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306 USA
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306 USA
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
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37
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The Gastric Phenotype in the Cypriniform Loaches: A Case of Reinvention? PLoS One 2016; 11:e0163696. [PMID: 27783698 PMCID: PMC5082673 DOI: 10.1371/journal.pone.0163696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/13/2016] [Indexed: 12/15/2022] Open
Abstract
The stomach, which is characterized by acid peptic digestion in vertebrates, has been lost secondarily multiple times in the evolution of the teleost fishes. The Cypriniformes are largely seen as an agastric order; however, within the superfamily Cobitoidea, the closely related sister groups Nemacheilidae and Balitoridae have been identified as gastric families. The presence of these most recently diverged gastric families in an otherwise agastric clade indicates that either multiple (>2–3) loss events occurred with the Cyprinidae, Catostomidae and Cobitidae, or that gastric reinvention arose in a recent ancestor of the Nemacheilidae/Balitoridae sister clade. In the present study, the foregut regions of Cobitidae, Nemacheilidae/Balitoridae and the ancestral Botiidae family members were examined for the presence of gastric glands and gastric proton pump (Atp4a) α subunit expression by histology and immunohistochemistry respectively. Atp4a gene expression was assessed by reverse transcriptase-polymerase chain reaction (RT-PCR). Gastric glands expressing apical H+/K+-ATPase α subunit and isolated partial sequences of atp4a, identified using degenerate primers showing clear orthology to other vertebrate atp4a sequences, were detected in representative species from Nemacheilidae/ Balitoridae and Botiidae, but not Cobitidae (Misgurnus anguillicaudatus). In summary, we provide evidence for an uninterrupted gastric evolutionary lineage in the Cobitoidea, making it highly improbable that the stomach was reinvented in the Nemacheilidae/Balitoridae clade consistent with Dollo’s principle. These results also indicate that the gastric trait may be present elsewhere in the Cobitoidea.
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38
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Zheng LP, Yang JX, Chen XY. Molecular phylogeny and systematics of the Barbinae (Teleostei: Cyprinidae) in China inferred from mitochondrial DNA sequences. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Zheng LP, Chen XY, Yang JX. Molecular systematics of the Labeonini inhabiting the karst regions in southwest China (Teleostei, Cypriniformes). Zookeys 2016:133-48. [PMID: 27667927 PMCID: PMC5027668 DOI: 10.3897/zookeys.612.9085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/18/2016] [Indexed: 11/17/2022] Open
Abstract
The major phylogenetic pattern of the cyprinid tribe Labeonini has been revealed by previous molecular studies; however, the relationships within a clade that mainly inhabits the karst regions, which we refer to as the “karst group”, in southwest China remain unresolved due to the low taxon sampling. This group includes more than 50% of the genera and species of Labeonini in China. Moreover, more than 90% of the genera of this group are endemic to China. In addition, some new genera and species of Labeonini have been discovered from these karst regions, but their taxonomic validity and phylogenetic position have not been examined. In this contribution, partial sequences of four nuclear (exon 3 of recombination activating protein 1, rhodopsin, early growth response protein 2B gene and interphotoreceptor retinoid binding protein gene) and three mitochondrial genes (cytochrome b, cytochrome oxidase subunit I and 16S ribosomal RNA) from 36 ingroup taxa and 25 outgroup taxa were analyzed to provide a hypothesis of the phylogenetic relationships within the labeonins of the karst regions in China. We propose that the monophyly of Parasinilabeo, Ptychidio, Rectoris and Semilabeo are supported. A new genus, Prolixicheilus, is erected for Pseudogyrinocheiluslongisulcus. Cophecheilusbamen is the sister to Prolixicheiluslongisulcus. Ptychidio, Pseudocrossocheilus, Semilabeo, Rectoris and Stenorynchoacrum are closely related with high support values. Sinocrossocheilus, Pseudogyrinocheilus, Paraqianlabeo, Hongshuia, Discogobio and Discocheilus form a clade together with high support. Considering molecular results and morphological differences, Parasinilabeolongicorpus and Ptychidiomacrops might be the synonyms of Parasinilabeoassimilis and Ptychidiojordani respectively. Comprehensive taxonomic revisions of the two genera Parasinilabeo and Ptychidio may be necessary.
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Affiliation(s)
- Lan-Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, Yunnan, China
| | - Xiao-Yong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, Yunnan, China; Southeast Asia Biodiversity Research Institute, the Chinese Academy of Sciences, (CAS-SEABRI), Nay Pyi Taw 05282, Yezin, Myanmar
| | - Jun-Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, Yunnan, China
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Wang Y, Shen Y, Feng C, Zhao K, Song Z, Zhang Y, Yang L, He S. Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude. Sci Rep 2016; 6:29690. [PMID: 27417983 PMCID: PMC4945904 DOI: 10.1038/srep29690] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/23/2016] [Indexed: 01/11/2023] Open
Abstract
Tibetan loaches are the largest group of Tibetan fishes and are well adapted to the Tibetan Plateau. To investigate the origin of Tibetan loaches and their adaptations to the Tibetan Plateau, we determined 32 complete mitochondrial genomes that included 29 Tibetan loach species, two Barbatula species and Schistura longus. By combining these newly determined sequences with other previously published mitochondrial genomes, we assembled a large mitogenomic data set (11,433 bp) of 96 species in the superfamily Cobitoidea, to investigate the phylogenetic status of the genus Triplophysa. The resulting phylogeny strongly supported that the genus Triplophysa forms a monophyletic group within Nemacheilidae. Our molecular dating time suggests that the lineage leading to the Tibetan loaches and other loaches diverged approximately 23.5 Ma, which falls within the period of recent major uplifts of the Tibetan Plateau in the Early Miocene. Selection analyses revealed that the mitochondrial protein-coding genes of Tibetan loaches have larger ratios of nonsynonymous to synonymous substitutions than do those of non-Tibetan loaches, indicating that Tibetan loaches accumulated more nonsynonymous mutations than non-Tibetan loaches and exhibited rapid evolution. Two positively selected sites were identified in the ATP8 and ND1 genes.
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Affiliation(s)
- Ying Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenguang Feng
- University of the Chinese Academy of Sciences, Beijing 100049, PR China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yanping Zhang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics Breeding, Gansu Fishers Research Institute, Lanzhou 730030, PR China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
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Kartavtsev YP, Batischeva NM, Bogutskaya NG, Katugina AO, Hanzawa N. Molecular systematics and DNA barcoding of Altai osmans, oreoleuciscus (pisces, cyprinidae, and leuciscinae), and their nearest relatives, inferred from sequences of cytochrome b (Cyt-b), cytochrome oxidase c (Co-1), and complete mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:502-517. [PMID: 27159700 DOI: 10.3109/24701394.2016.1149822] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondrial DNA (mtDNA) at the protein-coding Cyt-b gene along with data retrieved from GenBank for Co-1 gene fragments and complete mitochondrial genome (mitogenome) of Altai osmans and the nearest relatives of Leuciscinae fish species were compared for the estimation of variability and phylogenetic tree building. Phylogenetic trees were built by four techniques: Bayesian (BA), maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ). Resolution of Cyt-b trees for species of two genera (Oreoleuciscus and Phoxinus) was quite distinct at all the approaches. For Tribolodon, the single gene trees were not well resolved; however, the mitogenome tree was resolved. Species identification on per individual basis (DNA barcoding) was high for both Cyt-b and Co-1 genes. The trees built using the data for 13 protein mitochondrial genes revealed a complicated phylogenetic pattern within the subfamily Leuciscinae. Scores of the average p-distances at three taxonomic levels were considerably different: (1) 1.16 ± 0.96, (2) 8.21 ± 1.01, and (3) 16.41 ± 0.85 for Cyt-b and (1) 1.04 ± 0.78, (2) 8.30 ± 0.92, and (3) 10.74 ± 0.79 for 13 protein genes of mitogenome, where (1) is intraspecies, (2) is intragenus, and (3) is intrasubfamily levels. Data on mitogenome distances were summarized for the taxonomic hierarchy for the first time. A concordant increase in distance score with growth of the rank of taxa (having the minimum score at the intraspecies level), both for a single gene and the whole mitogenome, substantiates the concept that speciation in the subfamily Leuciscinae in most cases follows the geographic mode. The distinct clustering of Altai osmans, Oreoleuciscus potanini and O. humilis, in the Cyt-b and Co-1 gene trees with small overall genetic distances, obtained for both genes, allows us to consider these taxa as separate but genetically sister species.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- a A.V. Zhirmunsky Institute of Marine Biology FEB RAS , Vladivostok , Russian Federation.,b Far Eastern Federal University, School of Natural Sciences , Vladivostok , Russian Federation
| | - Natalia M Batischeva
- a A.V. Zhirmunsky Institute of Marine Biology FEB RAS , Vladivostok , Russian Federation
| | | | - Anna O Katugina
- a A.V. Zhirmunsky Institute of Marine Biology FEB RAS , Vladivostok , Russian Federation.,b Far Eastern Federal University, School of Natural Sciences , Vladivostok , Russian Federation
| | - Naoto Hanzawa
- d Yamagata University, Graduate school of Science and Engineering , Yamagata , Japan
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42
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Armbruster JW, Stout CC, Hayes MM. An empirical test for convergence using African barbs (Cypriniformes: Cyprinidae). Evol Ecol 2015. [DOI: 10.1007/s10682-015-9811-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Polyakova NE, Semina AV, Brykov VA. Analysis of mtDNA and nuclear markers points to homoploid hybrid origin of the new species of Far Eastern redfins of the genus Tribolodon (Pisces, Cyprinidae). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415110137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bock SL, Malley MM, Lema SC. Complete mitochondrial genome of the speckled dace Rhinichthys osculus, a widely distributed cyprinid minnow of western North America. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4416-4418. [PMID: 26488409 DOI: 10.3109/19401736.2015.1089551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The speckled dace Rhinichthys osculus (order Cypriniformes), also known as the carpita pinta, is a small cyprinid minnow native to western North America. Here, we report the sequencing of the full mitochondrial genome (mitogenome) of R. osculus from a male fish collected from the Amargosa River Canyon in eastern California, USA. The assembled mitogenome is 16 658 base pair (bp) nucleotides, and encodes 13 protein-coding genes, and includes both a 12S and a 16S rRNA, 22 tRNAs, and a 985 bp D-loop control region. Mitogenome synteny reflects that of other Ostariophysian fishes with the majority of genes and RNAs encoded on the heavy strand (H-strand) except nd6, tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Glu, and tRNA-Pro. The availability of this R. osculus mitochondrial genome - the first complete mitogenome within the lineage of Rhinichthys riffle daces - provides a foundation for resolving evolutionary relationships among morphologically differentiated populations of R. osculus.
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Affiliation(s)
- Samantha L Bock
- a Department of Biological Sciences , Center for Coastal Marine Sciences, California Polytechnic State University , San Luis Obispo , CA , USA
| | - Morgan M Malley
- a Department of Biological Sciences , Center for Coastal Marine Sciences, California Polytechnic State University , San Luis Obispo , CA , USA
| | - Sean C Lema
- a Department of Biological Sciences , Center for Coastal Marine Sciences, California Polytechnic State University , San Luis Obispo , CA , USA
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Buonerba L, Zaccara S, Delmastro GB, Lorenzoni M, Salzburger W, Gante HF. Intrinsic and extrinsic factors act at different spatial and temporal scales to shape population structure, distribution and speciation in Italian Barbus (Osteichthyes: Cyprinidae). Mol Phylogenet Evol 2015; 89:115-29. [DOI: 10.1016/j.ympev.2015.03.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 03/26/2015] [Accepted: 03/28/2015] [Indexed: 10/23/2022]
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Guinot G, Cavin L. 'Fish' (Actinopterygii and Elasmobranchii) diversification patterns through deep time. Biol Rev Camb Philos Soc 2015; 91:950-981. [PMID: 26105527 DOI: 10.1111/brv.12203] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/20/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Abstract
Actinopterygii (ray-finned fishes) and Elasmobranchii (sharks, skates and rays) represent more than half of today's vertebrate taxic diversity (approximately 33000 species) and form the largest component of vertebrate diversity in extant aquatic ecosystems. Yet, patterns of 'fish' evolutionary history remain insufficiently understood and previous studies generally treated each group independently mainly because of their contrasting fossil record composition and corresponding sampling strategies. Because direct reading of palaeodiversity curves is affected by several biases affecting the fossil record, analytical approaches are needed to correct for these biases. In this review, we propose a comprehensive analysis based on comparison of large data sets related to competing phylogenies (including all Recent and fossil taxa) and the fossil record for both groups during the Mesozoic-Cainozoic interval. This approach provides information on the 'fish' fossil record quality and on the corrected 'fish' deep-time phylogenetic palaeodiversity signals, with special emphasis on diversification events. Because taxonomic information is preserved after analytical treatment, identified palaeodiversity events are considered both quantitatively and qualitatively and put within corresponding palaeoenvironmental and biological settings. Results indicate a better fossil record quality for elasmobranchs due to their microfossil-like fossil distribution and their very low diversity in freshwater systems, whereas freshwater actinopterygians are diverse in this realm with lower preservation potential. Several important diversification events are identified at familial and generic levels for elasmobranchs, and marine and freshwater actinopterygians, namely in the Early-Middle Jurassic (elasmobranchs), Late Jurassic (actinopterygians), Early Cretaceous (elasmobranchs, freshwater actinopterygians), Cenomanian (all groups) and the Paleocene-Eocene interval (all groups), the latter two representing the two most exceptional radiations among vertebrates. For each of these events along with the Cretaceous-Paleogene extinction, we provide an in-depth review of the taxa involved and factors that may have influenced the diversity patterns observed. Among these, palaeotemperatures, sea-levels, ocean circulation and productivity as well as continent fragmentation and environment heterogeneity (reef environments) are parameters that largely impacted on 'fish' evolutionary history, along with other biotic constraints.
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Affiliation(s)
- Guillaume Guinot
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland.
| | - Lionel Cavin
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland
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Sevigny JL, Kirouac LE, Thomas WK, Ramsdell JS, Lawlor KE, Sharifi O, Grewal S, Baysdorfer C, Curr K, Naimie AA, Okamoto K, Murray JA, Newcomb JM. The Mitochondrial Genomes of the Nudibranch Mollusks, Melibe leonina and Tritonia diomedea, and Their Impact on Gastropod Phylogeny. PLoS One 2015; 10:e0127519. [PMID: 25996944 PMCID: PMC4440745 DOI: 10.1371/journal.pone.0127519] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/15/2015] [Indexed: 01/28/2023] Open
Abstract
The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra), two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa). In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group.
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Affiliation(s)
- Joseph L. Sevigny
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - Lauren E. Kirouac
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - William Kelley Thomas
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Jordan S. Ramsdell
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Kayla E. Lawlor
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - Osman Sharifi
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Simarvir Grewal
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Christopher Baysdorfer
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Kenneth Curr
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Amanda A. Naimie
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - Kazufusa Okamoto
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - James A. Murray
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - James M. Newcomb
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
- * E-mail:
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Hubert N, Kadarusman, Wibowo A, Busson F, Caruso D, Sulandari S, Nafiqoh N, Pouyaud L, Rüber L, Avarre JC, Herder F, Hanner R, Keith P, Hadiaty RK. DNA Barcoding Indonesian freshwater fishes: challenges and prospects. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractWith 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.
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Keith Barker F. Mitogenomic data resolve basal relationships among passeriform and passeridan birds. Mol Phylogenet Evol 2014; 79:313-24. [DOI: 10.1016/j.ympev.2014.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 05/31/2014] [Accepted: 06/11/2014] [Indexed: 11/29/2022]
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Chang CH, Li F, Shao KT, Lin YS, Morosawa T, Kim S, Koo H, Kim W, Lee JS, He S, Smith C, Reichard M, Miya M, Sado T, Uehara K, Lavoué S, Chen WJ, Mayden RL. Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species. Mol Phylogenet Evol 2014; 81:182-94. [PMID: 25238947 DOI: 10.1016/j.ympev.2014.08.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 10/24/2022]
Abstract
Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships. In this study, we provide the most comprehensive phylogenetic reconstruction of species relationships of the group based on partitioned maximum likelihood and Bayesian methods using DNA sequence variation of nuclear and mitochondrial genes on 41 species, several subspecies and three undescribed species. Our findings support the monophyly of the Acheilognathidae. Two of the three currently recognized genera are not monophyletic and the family can be subdivided into six clades. These clades are further regarded as genera based on both their phylogenetic relationships and a reappraisal of morphological characters. We present a revised classification for the Acheilognathidae with five genera/lineages: Rhodeus, Acheilognathus (new constitution), Tanakia (new constitution), Paratanakia gen. nov., and Pseudorhodeus gen. nov. and an unnamed clade containing five species currently referred to as "Acheilognathus". Gene trees of several bitterling species indicate that the taxa are not monophyletic. This result highlights a potentially dramatic underestimation of species diversity in this family. Using our new phylogenetic framework, we discuss the evolution of the Acheilognathidae relative to classification, taxonomy and biogeography.
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Affiliation(s)
- Chia-Hao Chang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan; Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Fan Li
- Department of Oceanography, National Sun Yet-sen University, Kaohsiung 80424, Taiwan; Institute of Biodiversity Science, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai 200433, China
| | - Kwang-Tsao Shao
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yeong-Shin Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan; Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan
| | | | - Sungmin Kim
- School of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Hyeyoung Koo
- Department of Biological Science, Sangji University, Wonju 220-702, Republic of Korea
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Carl Smith
- School of Biology, University of St Andrews, St Andrews, Fife KY16 8LB, UK; Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - Martin Reichard
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - Masaki Miya
- Natural History Museum & Institute, Chiba 260-8682, Japan
| | - Tetsuya Sado
- Natural History Museum & Institute, Chiba 260-8682, Japan
| | - Kazuhiko Uehara
- Aquatic Life Conservation Research Center, Research Institute of Environment, Agriculture and Fisheries, Osaka 572-0088, Japan
| | - Sébastien Lavoué
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan.
| | - Richard L Mayden
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
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