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Page LM, Tangjitjaroen W, Limpichat J, Randall ZS, Boyd DA, Tongnunui S, Pfeiffer JM. A taxonomic revision of Parachela with descriptions of two new species (Cypriniformes: Xenocyprididae). JOURNAL OF FISH BIOLOGY 2024. [PMID: 39300770 DOI: 10.1111/jfb.15869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 06/12/2024] [Accepted: 06/25/2024] [Indexed: 09/22/2024]
Abstract
The taxonomy of the Parachela-Oxygaster-Macrochirichthys clade of Xenocyprididae has been confused since the original descriptions of Parachela oxygastroides and Parachela hypophthalmus in the mid-19th century. The confusion seems attributable to the substantial intraspecific variation in color and other morphological characteristics of species of Oxygaster and Parachela. Morphological data on 401 specimens from throughout the range of Parachela and molecular phylogenetic analyses indicate that six available species names for Parachela are valid: Parachela cyanea, P. hypophthalmus, Parachela ingerkongi, Parachela johorensis (removed from the synonymy of P. oxygastroides), P. oxygastroides, and Parachela williaminae. In addition, two new species of Parachela, Parachela melanosticta and Parachela microlepis, are described. Chela pointoni is a synonym of P. oxygastroides, not a valid species of Oxygaster as previously hypothesized, and Parachela maculicauda is a synonym of Parachela johorensis. Considerable morphological and genetic variation is present in all well-sampled species of Parachela.
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Affiliation(s)
- Lawrence M Page
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | | | | | - Zachary S Randall
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - David A Boyd
- Louisiana State University Museum of Natural Science, Baton Rouge, Louisiana, USA
| | - Sampan Tongnunui
- Department of Conservation Biology, Mahidol University, Kanchanaburi, Thailand
| | - John M Pfeiffer
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
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Escobar Camacho D, Barragán KS, Guayasamin JM, Gavilanes G, Encalada AC. New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding. PLoS One 2024; 19:e0298970. [PMID: 38457426 PMCID: PMC10923491 DOI: 10.1371/journal.pone.0298970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024] Open
Abstract
DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.
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Affiliation(s)
- Daniel Escobar Camacho
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Karla S. Barragán
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan M. Guayasamin
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Gabriela Gavilanes
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Andrea C. Encalada
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
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Seth JK, Roy S, Sura S, Puvala D, Mishra SS, Mohapatra A. Description of a new species of the genus Awaous Valenciennes, 1837 (Gobiiformes: Oxudercidae) from the middle stretch of the Mahanadi River, Odisha, India, with comments on the Awaous species from India. JOURNAL OF FISH BIOLOGY 2024; 104:548-563. [PMID: 37889122 DOI: 10.1111/jfb.15598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 10/06/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023]
Abstract
A new species of the genus Awaous (Oxudercidae), Awaous motla sp. nov., is described based on 18 specimens collected from the Mahanadi River near Sonepur, Subarnapur District, and 3 specimens from the same river near Boudh bridge, Boudh District of Odisha, India. This species is distinct from its congeners by having a combination of characteristics: relatively small eyes, diameter of 6.6-8.4 in head length (LH); robust and long snout, 2.0-2.6 in LH; eye diameter 2.7-4.1 in snout length; cephalic sensory pore system interrupted with eight pores; predorsal scales 13-15; longitudinal scale series 55-58; gill rakers 2 + 1 + (6-7) on the first gill arch; teeth small, conical, and in a single row on the upper jaw and multiserial (2-3) on the lower jaw. This species is also differentiated from some of its congeners in the nucleotide composition of the cytochrome c oxidase I gene by 8.3%-13.8% Kimura two-parameter (K2P) distance and belongs to a separate cluster in the maximum likelihood tree analysis. This finding is also supported by the species delimitation analysis based on Assemble Species by Automatic Partitioning. The new species holds high commercial value in its locality and needs special conservation attention for sustainable utilization.
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Affiliation(s)
- Jaya Kishor Seth
- Post Graduate Department of Zoology, Berhampur University, Berhampur, India
| | - Sanmitra Roy
- Post Graduate Department of Zoology, Berhampur University, Berhampur, India
| | - Sameer Sura
- Post Graduate Department of Zoology, Berhampur University, Berhampur, India
| | - Dilraj Puvala
- Post Graduate Department of Zoology, Berhampur University, Berhampur, India
| | | | - Anil Mohapatra
- Estuarine Biology Regional Centre, Zoological Survey of India, Ganjam, India
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Arisuryanti T, Waskito Aji K, Nur Shabrina F, Febriyanti D, Setiadi Daryono B, Sendi Priyono D. Phylogenetic and genetic variation of common mudskippers (Periophthalmus kalolo Lesson, 1831) from the southern coast of Java, Indonesia inferred from the COI mitochondrial gene. J Genet Eng Biotechnol 2024; 22:100335. [PMID: 38494250 PMCID: PMC10860878 DOI: 10.1016/j.jgeb.2023.100335] [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: 03/19/2024]
Abstract
BACKGROUND The common mudskipper (Periophthalmus kalolo Lesson, 1831) belongs to a group of fish species that exhibit amphibious lifestyles during specific daily periods. However, identifying this species poses a challenge due to its morphological similarities with other mudskipper species. These similarities have occasionally caused misidentifications of mudskippers. In Indonesia, previous studies have examined the genetic variation of common mudskippers, but these investigations have been limited to a few specific areas, particularly along the southern coast of Java. As a result, the available data remain fragmented, and no comprehensive genetic population analysis of common mudskippers on the southern coast of Java has been conducted. Therefore, our study aimed to establish DNA barcodes of COI mtDNA and explore the genetic variation and relationship among these common mudskipper populations from the southern coast of Java. We collected nine specimens from two populations, Cilacap Mangrove Forest and Kondang Bandung Beach, and supplemented our dataset with 38 previously collected COI sequences of common mudskippers from three different populations from the southern coast of Java (Pasir Mendit Beach, Bogowonto Lagoon, and Baros Beach). RESULTS The study revealed that 47 common mudskippers from five different populations are separated into three genetically distinct clades (A, B, and C). These clades display genetic divergences ranging from 0.97% to 1.91%. Each clade exhibits high levels of haplotype diversity but relatively low nucleotide diversity, suggesting a previous bottleneck in population followed by a fast expansion. However, the phylogeny, haplotype network, and principal coordinate analysis indicate overlapping populations with no geographic separation within these clades. This suggests the potential occurrence of gene flow among these populations, which might have been facilitated by past geological events. CONCLUSIONS These results enhance our understanding of common mudskipper biodiversity in Indonesia. Further studies involving common mudskipper populations from various geographical sites in Indonesia are required to further enrich our understanding of the variation and evolution of this species.
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Affiliation(s)
- Tuty Arisuryanti
- Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281, Indonesia.
| | - Katon Waskito Aji
- Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281, Indonesia
| | - Faizah Nur Shabrina
- Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281, Indonesia
| | - Diana Febriyanti
- Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281, Indonesia
| | - Budi Setiadi Daryono
- Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281, Indonesia
| | - Dwi Sendi Priyono
- Laboratory of Animal Systematics, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281, Indonesia
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Habib KA, Islam MJ, Sakib MN, Brishti PS, Neogi AK. DNA barcoding of reef-associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh. Ecol Evol 2023; 13:e10641. [PMID: 37877103 PMCID: PMC10590961 DOI: 10.1002/ece3.10641] [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: 05/23/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023] Open
Abstract
This study employs the DNA barcoding approach to make a molecular taxonomic catalog of reef fishes of Saint Martin's Island (SMI), an ecologically critical area (ECA), and Marine Protected Area (MPA) in Bangladesh. DNA barcoding, along with morphological analysis, confirmed 84 reef-associated fish species in SMI belonging to 16 orders, 39 families, and 67 genera. A total of 184 sequences were obtained in this study where 151 sequences (534-604 bp) of 81 species were identified from the COI barcode gene and 33 sequences (609 bp) of 19 species from the 16S rRNA gene region which were submitted to the GenBank and Barcode of Life Data System (BOLD). Among these sequences, 70 sequences of the COI gene and 16 sequences of 16S rRNA gene region from 41 species were submitted for the first time into the GenBank from Bangladesh. For molecular characterization analysis, another 37 sequences of 15 reef fish species of SMI were added from previous studies, making a total of 221 DNA sequences which comprised 179 sequences of 96 species for the COI gene and 42 sequences of 26 species for the 16S rRNA gene region. The COI sequences contain 145 haplotypes with 337 polymorphic sites, and the mean genetic distances within species, genera, and families were calculated as 0.34%, 12.26%, and 19.03%, respectively. On the contrary, 16S rRNA sequences comprised 31 haplotypes with 241 polymorphic sites, and the mean genetic divergences within species, genera, and families were 0.94%, 4.72%, and 12.43%, respectively. This study is a significant contribution to the marine biodiversity of Bangladesh which would facilitate the assessment of species diversity for strategizing management action. It is also an important input to the DNA barcode library of reef fishes of the northern Bay of Bengal.
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Affiliation(s)
- Kazi Ahsan Habib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Jayedul Islam
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Nazmus Sakib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Parsha Shanjana Brishti
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Amit Kumer Neogi
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
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Jourdan J, Bundschuh M, Copilaș-Ciocianu D, Fišer C, Grabowski M, Hupało K, Jemec Kokalj A, Kabus J, Römbke J, Soose LJ, Oehlmann J. Cryptic Species in Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1889-1914. [PMID: 37314101 DOI: 10.1002/etc.5696] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Jonas Jourdan
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Denis Copilaș-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michał Grabowski
- Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Kamil Hupało
- Department of Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Kabus
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie, Flörsheim am Main, Germany
| | - Laura J Soose
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
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7
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Wu YH, Hou SB, Yuan ZY, Jiang K, Huang RY, Wang K, Liu Q, Yu ZB, Zhao HP, Zhang BL, Chen JM, Wang LJ, Stuart BL, Chambers EA, Wang YF, Gao W, Zou DH, Yan F, Zhao GG, Fu ZX, Wang SN, Jiang M, Zhang L, Ren JL, Wu YY, Zhang LY, Yang DC, Jin JQ, Yin TT, Li JT, Zhao WG, Murphy RW, Huang S, Guo P, Zhang YP, Che J. DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs. Mol Ecol Resour 2023. [PMID: 36924341 DOI: 10.1111/1755-0998.13784] [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: 10/03/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.
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Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shao-Bing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ru-Yi Huang
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Zhong-Bin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hai-Peng Zhao
- School of Life Science, Henan University, Kaifeng, Henan, 475001, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Li-Jun Wang
- School of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601, USA
| | - E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720, USA
| | - Yu-Fan Wang
- Zhejiang Forest Resource Monitoring Center, Hangzhou, Zhejiang, 310020, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Da-Hu Zou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Gui-Gang Zhao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Zhong-Xiong Fu
- Yunnan Senye Biotechnology Co., Ltd, Xishuangbanna, Yunnan, 666100, China
| | - Shao-Neng Wang
- Bureau of Guangxi Mao'er Mountain Nature Reserve, Guilin, Guangxi, 541316, China
| | - Ming Jiang
- Gongshan Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan, 650224, China
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Ya-Yong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Lu-Yang Zhang
- Beijing Mountains & Seas Eco Technology Co. Ltd, Beijing, 101100, China
| | - Dian-Cheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Wen-Ge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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8
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DNA Barcoding of Fish Species Diversity in Guizhou, China. DIVERSITY 2023. [DOI: 10.3390/d15020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Guizhou is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River basins with abundant fish species. However, fish from these regions are threatened by anthropogenic activities, including overfishing and habitat destruction. Here, we assessed the fish diversity including more than half of the species from the region using DNA barcoding (partial sequence of cytochrome c oxidase subunit I (COI) gene). We obtained 800 mitochondrial COI barcode sequences from 82 genera, 18 families and 8 orders of fishes. The average Kimura two-parameter (K2P) distances within species and genera were 0.35% and 5.44%, respectively. The average interspecific distance was 15.54 times higher than the mean intraspecific distance. Moreover, DNA barcodes revealed 175 operational taxonomic units (OTUs) based on consensus demarcation schemes. Barcoding gaps were detected in 94.81% of morphospecies. Three fish species (Schistura fasciolata, Vanmanenia pingchowensis, and Misgurnus dabryanus) have considerable intraspecific variability, and each was divided into multiple molecular operational taxonomic units (MOTUs) using molecular definition methods (Automatic Barcode Gap Discovery, Refined Single Linkage, General Mixed Yule Coalescent, and Poisson Tree Processes), possibly indicating the occurrence of cryptic species. Altogether, our study reveals the complex diversity of fish species in Guizhou Province, serving as a reference for the conservation and monitoring of fish species in this region.
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Utami CY, Sholihah A, Condamine FL, Thébaud C, Hubert N. Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses. Proc Biol Sci 2022; 289:20221335. [PMID: 36382998 PMCID: PMC9667750 DOI: 10.1098/rspb.2022.1335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/26/2022] [Indexed: 12/02/2023] Open
Abstract
Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are now available. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporating DNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdowns when cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecological models received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.
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Affiliation(s)
- C. Y. Utami
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
- UMR 5174 EDB (CNRS, Université Paul Sabatier, IRD), 31062 Toulouse Cedex 9, France
| | - A. Sholihah
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung 40132, Indonesia
| | - F. L. Condamine
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - C. Thébaud
- UMR 5174 EDB (CNRS, Université Paul Sabatier, IRD), 31062 Toulouse Cedex 9, France
| | - N. Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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10
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Vargas-Rivas AG, Barba-Macias E, Sánchez AJ, Castellanos-Morales G. Lack of mtDNA genetic diversity despite phenotypic variation and environmental heterogeneity in the exotic suckermouth armored catfish (Pterygoplichthys pardalis). Biol Invasions 2022. [DOI: 10.1007/s10530-022-02961-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Abdulmalik-Labe OP, Picart NMR, Francisco MEM, Castillo RMG, Quilang JP. DNA barcoding of Glossogobius species (Teleostei: Gobiidae) from major lakes in the Philippines reveals the presence of cryptic species and species complexes. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01278-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Smith WL, Ghedotti MJ, Domínguez-Domínguez O, McMahan CD, Espinoza E, Martin RP, Girard MG, Davis MP. Investigations into the ancestry of the Grape-eye Seabass (Hemilutjanus macrophthalmos) reveal novel limits and relationships for the Acropomatiformes (Teleostei: Percomorpha). NEOTROPICAL ICHTHYOLOGY 2022. [DOI: 10.1590/1982-0224-2021-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract For 175 years, an unremarkable bass, the Grape-eye Seabass (Hemilutjanus macrophthalmos), has been known from coastal waters in the Eastern Pacific. To date, its phylogenetic placement and classification have been ignored. A preliminary osteological examination of Hemilutjanus hinted that it may have affinities with the Acropomatiformes. To test this hypothesis, we conducted a phylogenetic analysis using UCE and Sanger sequence data to study the placement of Hemilutjanus and the limits and relationships of the Acropomatiformes. We show that Hemilutjanus is a malakichthyid, and our results corroborate earlier studies that have resolved a polyphyletic Polyprionidae; accordingly, we describe Stereolepididae, new family, for Stereolepis. With these revisions, the Acropomatiformes is now composed of the: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, new family; Symphysanodontidae; Synagropidae; and Schuettea. Finally, using our new hypothesis, we demonstrate that acropomatiforms repeatedly evolved bioluminescence and transitioned between shallow waters and the deep sea.
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Maeda K, Kobayashi H, Palla HP, Shinzato C, Koyanagi R, Montenegro J, Nagano AJ, Saeki T, Kunishima T, Mukai T, Tachihara K, Laudet V, Satoh N, Yamahira K. Do colour-morphs of an amphidromous goby represent different species? Taxonomy of Lentipes (Gobiiformes) from Japan and Palawan, Philippines, with phylogenomic approaches. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1971792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ken Maeda
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Hirozumi Kobayashi
- University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Herminie P. Palla
- College of Fisheries and Aquatic Sciences, Western Philippines University, Puerto Princesa Campus, Puerto Princesa City, 5300, Palawan, Philippines
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Ryo Koyanagi
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Javier Montenegro
- University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | | | | | - Taiga Kunishima
- Wakayama Prefectural Museum of Natural History, 370-1 Funoo, Kainan, Wakayama, 642-0001, Japan
| | - Takahiko Mukai
- Faculty of Regional Studies, Gifu University, Gifu, 501-1193, Japan
| | | | - Vincent Laudet
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Kazunori Yamahira
- University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
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14
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Ng CKC, Tan J. Cryptic species and grey zone speciation of the Barbodes binotatus complex (Teleostei, Cyprinidae) in Sundaland. JOURNAL OF FISH BIOLOGY 2021; 99:1256-1273. [PMID: 34159593 DOI: 10.1111/jfb.14829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/03/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Morphology-based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination-activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus-like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions.
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Affiliation(s)
- Casey Keat-Chuan Ng
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Ji Tan
- Department of Agricultural and Food Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar, Malaysia
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15
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Ahmad Sobri NZ, Lavoué S, Aziz F, Mohd Nor SA, Mohammed Akib NA, Khaironizam MZ. To lump, to split or to maintain? Molecular taxonomy of the spotted barb Barbodes binotatus (Cyprinidae) and closely related species in Peninsular Malaysia. JOURNAL OF FISH BIOLOGY 2021; 99:656-668. [PMID: 33855740 DOI: 10.1111/jfb.14754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
The taxonomic status of the Southeast Asian spotted barb, Barbodes binotatus (Teleostei: Cyprinidae), has puzzled researchers because of large but inconsistent geographic variation of its body melanin marking pattern. In this study, the authors appraise the differentiation of B. binotatus and two closely related species, Barbodes rhombeus and saddle barb, Barbodes banksi, in Peninsular Malaysia using mitochondrial and nuclear markers. The results of this study reveal that the Peninsular Malaysia populations of each of the three species form largely reciprocal monophyletic lineages that differ from each other by a minimum of 2.3% p-genetic distance using COI gene. Nonetheless, specimens of B. binotatus in Peninsular Malaysia are only distantly related to specimens of B. binotatus in Java (type locality). The monophyly of B. banksi is not refuted although specimens of Peninsular Malaysia are genetically distinct from those of Sarawak (type locality). The authors discuss alternative hypotheses whether each of these three valid species is a single species or each of the main five genetic lineages revealed in this study represents a distinct species. Preliminary investigations reveal a mito-nuclear discordance at one locality in Peninsular Malaysia where B. binotatus and B. banksi co-occur. Further studies should inform on the extent of reproductive porousness between these two lineages and others.
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Affiliation(s)
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Fazimah Aziz
- Department of Aquatic Science, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Noor Adelyna Mohammed Akib
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
- Centre for Global and Sustainability Studies, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Md Zain Khaironizam
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
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16
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Abstract
Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.
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17
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Hammer MP, Taillebois L, King AJ, Crook DA, Wedd D, Adams M, Unmack PJ, Hoese DF, Bertozzi T. Unravelling the taxonomy and identification of a problematic group of benthic fishes from tropical rivers (Gobiidae: Glossogobius). JOURNAL OF FISH BIOLOGY 2021; 99:87-100. [PMID: 33583039 DOI: 10.1111/jfb.14701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/01/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
Flathead gobies (genus Glossogobius) include c. 40 small- to medium-sized benthic fishes found primarily in freshwater habitats across the Indo-Pacific, having biodiversity value as well as cultural and economic value as food fishes, especially in developing countries. To help resolve considerable confusion regarding the identification of some of the larger-growing Glossogobius species, a systematic framework was established using nuclear genetic markers, mitochondrial DNA barcoding and phenotypic evidence for a geographically widespread collection of individuals from the waterways of tropical northern Australia. Species boundaries and distribution patterns were discordant with those previously reported, most notably for the tank goby Glossogobius giuris, which included a cryptic species. Genetic divergence was matched with accompanying unique visual characters that aid field identification. Additional taxonomic complexity was also evident, by comparison with DNA barcodes from international locations, suggesting that the specific names applicable for two of the candidate species in Australia remain unresolved due to confusion surrounding type specimens. Although flathead gobies are assumed to be widespread and common, this study demonstrates that unrealised taxonomic and ecological complexity is evident, and this will influence assessments of tropical biodiversity and species conservation. This study supports the need for taxonomic studies of freshwater fishes to underpin management in areas subject to significant environmental change.
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Affiliation(s)
- Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
| | - Laura Taillebois
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Alison J King
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - David A Crook
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Dion Wedd
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mark Adams
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - Peter J Unmack
- Centre of Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Doug F Hoese
- Australian Museum, Sydney, New South Wales, Australia
| | - Terry Bertozzi
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
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18
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Arida E, Ashari H, Dahruddin H, Fitriana YS, Hamidy A, Irham M, Kadarusman, Riyanto A, Wiantoro S, Zein MSA, Hadiaty RK, Apandi, Krey F, Kurnianingsih, Melmambessy EHP, Mulyadi, Ohee HL, Saidin, Salamuk A, Sauri S, Suparno, Supriatna N, Suruwaky AM, Laksono WT, Warikar EL, Wikanta H, Yohanita AM, Slembrouck J, Legendre M, Gaucher P, Cochet C, Delrieu-Trottin E, Thébaud C, Mila B, Fouquet A, Borisenko A, Steinke D, Hocdé R, Semiadi G, Pouyaud L, Hubert N. Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes. Mol Ecol Resour 2021; 21:2369-2387. [PMID: 33942522 DOI: 10.1111/1755-0998.13411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.
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Affiliation(s)
- Evy Arida
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hadi Dahruddin
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Yuli Sulistya Fitriana
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir Hamidy
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Kadarusman
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Awal Riyanto
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Sigit Wiantoro
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Moch Syamsul Arifin Zein
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Renny K Hadiaty
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Apandi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Frengky Krey
- Jurusan Perikanan, Fakultas Perikanan dan Ilmu Kelautan, Universitas Papua, Jl. Gunung Salju Amban, Manokwari, Indonesia
| | - Kurnianingsih
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Edy H P Melmambessy
- Program Studi Manajemen Sumberdaya Perairan, Fakultas Pertanian, Universitas Musamus, Jl. Kamizaun Mopah Lama, Rimba Jaya, Merauke, Indonesia
| | - Mulyadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Henderite L Ohee
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Saidin
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Ayub Salamuk
- Dinas Kelautan dan Perikanan Kabupaten Kaimana, Jl.Utarum Kampung Coa, Kaimana, Indonesia
| | - Sopian Sauri
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Nanang Supriatna
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir M Suruwaky
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Wahyudi Tri Laksono
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Evie L Warikar
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Hadi Wikanta
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Aksamina M Yohanita
- Jurusan Biologi, Fakultas MIPA, Universitas Papua Jl. Gunung Salju - Amban, Manokwari, Indonesia
| | - Jacques Slembrouck
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Marc Legendre
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Philippe Gaucher
- USR LEEISA- Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens, Centre de Recherche de Montabo, cayenne, French Guiana
| | - Christophe Cochet
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | | | | | - Borja Mila
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Antoine Fouquet
- UMR 5174 EDB CNRS, Université Paul Sabatier, IRD, Toulouse, France
| | - Alex Borisenko
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Régis Hocdé
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER), Université de Montpellier, Montpellier, France
| | - Gono Semiadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
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19
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Jaafar F, Na-Nakorn U, Srisapoome P, Amornsakun T, Duong TY, Gonzales-Plasus MM, Hoang DH, Parhar IS. A Current Update on the Distribution, Morphological Features, and Genetic Identity of the Southeast Asian Mahseers, Tor Species. BIOLOGY 2021; 10:biology10040286. [PMID: 33915909 PMCID: PMC8065745 DOI: 10.3390/biology10040286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The mahseer, particularly the Tor species, is of significant cultural and economic importance as a high-value freshwater food fish in the Southeast (SE) Asian region. However, overexploitation of natural stocks because of high demand and their deteriorating habitat has resulted in a marked decline of Tor species in the wild. There are 13 Tor species that inhabit SE Asian rivers. All these species share distinct morphology, which is the presence of the median lobe. The unique characteristics, including body color, mouth position, and number of lateral scales, distinguish one species from another. Nonetheless, the taxonomy of the Tor species remains unstable and confusing, with contradictory data presented by different authors from different countries for a single Tor species. Therefore, in this review, we have gathered data for the SE Asian Tor species, outlining their distribution, morphology, and genetic identification. In addition, the present review also proposes a list of valid Tor species in the SE Asian region. The proposed list will serve as a standard and template for improving SE Asia’s Tor taxonomy, enhancing the study’s continuity, and a better understanding of specific Tor species. Abstract The king of rivers or mahseer comprises three genera: Tor, Neolissochilus, and Naziritor, under the Cyprinidae family. The Tor genus has been classified as the true mahseer due to the presence of a median lobe among the three genera. The Tor species are widely distributed across Southeast (SE) Asia, and 13 Tor species have been reported previously: Tor ater, Tor dongnaiensis, Tor douronensis, Tor laterivittatus, Tor mosal, Tor mekongensis, Tor putitora, Tor sinensis, Tor soro, Tor tambra, Tor tambroides, Tor tor and Tor yingjiangensis. However, the exact number of valid Tor species remains debatable. Different and unstandardized approaches of applying genetic markers in taxonomic identification and morphology variation within the same species have further widened the gap and ameliorated the instability of Tor species taxonomy. Therefore, synchronized and strategized research among Tor species researchers is urgently required to improve and fill the knowledge gap. This review is a current update of SE Asia’s Tor species, outlining their distribution, morphology, and genetic identification. In addition, the present review proposes that there are ten valid Tor species in the SE Asian region. This list will serve as a template and standard to improve the taxonomy of the SE Asian Tor species, which could serve as a basis to open new directions in Tor research.
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Affiliation(s)
- Faizul Jaafar
- Brain Research Institute Monash Sunway (BRIMS), Jeffrey Cheah School of Medicine and Health Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; (U.N.-N.); (P.S.)
| | - Prapansak Srisapoome
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; (U.N.-N.); (P.S.)
| | - Thumronk Amornsakun
- Department of Technology and Industries, Prince of Songkla University Pattani Campus, Pattani 94000, Thailand;
| | - Thuy-Yen Duong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City 94000, Vietnam;
| | - Maria Mojena Gonzales-Plasus
- College of Fisheries and Aquatic Science, Puerto Princesa Campus, Western Philippines University, Puerto Princesa City 5300, Philippines;
| | - Duc-Huy Hoang
- Department of Ecology and Evolutionary, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City 700000, Vietnam;
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Ishwar S. Parhar
- Brain Research Institute Monash Sunway (BRIMS), Jeffrey Cheah School of Medicine and Health Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
- Correspondence: ; Tel.: +60-3-5514-6304
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Hammer MP, Adams M, Unmack PJ, Hassell KL, Bertozzi T. Surprising Pseudogobius: Molecular systematics of benthic gobies reveals new insights into estuarine biodiversity (Teleostei: Gobiiformes). Mol Phylogenet Evol 2021; 160:107140. [PMID: 33711446 DOI: 10.1016/j.ympev.2021.107140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 02/22/2021] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
Snubnose gobies (genus Pseudogobius: Gobionellinae) are ubiquitous to, and important components of, estuarine ecosystems of the Indo-west Pacific. These small benthic fishes occur in freshwater, brackish and marine habitats such as mangroves, sheltered tide pools and lowland streams, and represent a model group for understanding the biodiversity and biogeography of estuarine fauna. To develop the species-level framework required for a concurrent morphological taxonomic appraisal, we undertook thorough sampling around the extensive Australian coastline, referenced to international locations, as part of a molecular systematic review using both nuclear and mitochondrial markers. The results indicate that while there are currently eight recognised species, the true diversity is close to double this, with a hotspot of endemism located in Australia. Complicated patterns were observed in southern Australia owing to two differing zones of introgression/admixture. Key drivers of diversity in the group appear to include plate tectonics, latitude, and historic barriers under glacial maxima, where an interplay between ready dispersal and habitat specialisation has led to regional panmixia but frequent geographic compartmentalisation within past and present landscapes. The findings have significant implications for biodiversity conservation, coastal and estuarine development, the basic foundations of field ecology, and for applied use such as in biomonitoring.
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Affiliation(s)
- Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory 0801, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia.
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia; School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, ACT 2601, Australia
| | - Kathryn L Hassell
- Centre for Aquatic Pollution Identification and Management, School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia; Aquatic Environmental Stress Research Group, School of Science, Royal Melbourne Institute of Technology University, Melbourne, Victoria 3083, Australia
| | - Terry Bertozzi
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia; School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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21
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Sholihah A, Delrieu-Trottin E, Condamine FL, Wowor D, Rüber L, Pouyaud L, Agnèse JF, Hubert N. Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots. Syst Biol 2021; 70:940-960. [PMID: 33560439 DOI: 10.1093/sysbio/syab006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 01/23/2023] Open
Abstract
Pleistocene Climatic Fluctuations (PCF) are frequently highlighted as important evolutionary engines that triggered cycles of biome expansion and contraction. While there is ample evidence of the impact of PCF on biodiversity of continental biomes, the consequences in insular systems depend on the geology of the islands and the ecology of the taxa inhabiting them. The idiosyncratic aspects of insular systems are exemplified by the islands of the Sunda Shelf in Southeast Asia (Sundaland), where PCF-induced eustatic fluctuations had complex interactions with the geology of the region, resulting in high species diversity and endemism. Emergent land in Southeast Asia varied drastically with sea level fluctuations during the Pleistocene. Climate-induced fluctuations in sea level caused temporary connections between insular and continental biodiversity hotspots in Southeast Asia. These exposed lands likely had freshwater drainage systems that extended between modern islands: the Paleoriver Hypothesis. Built upon the assumption that aquatic organisms are among the most suitable models to trace ancient river boundaries and fluctuations of landmass coverage, the present study aims to examine the evolutionary consequences of PCF on the dispersal of freshwater biodiversity in Southeast Asia. Time-calibrated phylogenies of DNA-delimited species were inferred for six species-rich freshwater fish genera in Southeast Asia (Clarias, Channa, Glyptothorax, Hemirhamphodon, Dermogenys, Nomorhamphus). The results highlight rampant cryptic diversity and the temporal localization of most speciation events during the Pleistocene, with 88% of speciation events occurring during this period. Diversification analyses indicate that sea level-dependent diversification models poorly account for species proliferation patterns for all clades excepting Channa. Ancestral area estimations point to Borneo as the most likely origin for most lineages, with two waves of dispersal to Sumatra and Java during the last 5 Myr. Speciation events are more frequently associated with boundaries of the paleoriver watersheds, with 60%, than islands boundaries, with 40%. In total, one-third of speciation events are inferred to have occured within paleorivers on a single island, suggesting that habitat heterogeneity and factors other than allopatry between islands substantially affected diversification of Sundaland fishes. Our results suggest that species proliferation in Sundaland is not wholly reliant on Pleistocene sea-level fluctuations isolating populations on different islands.
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Affiliation(s)
- Arni Sholihah
- Institut Teknologi Bandung, School of Life Sciences and Technology, Jalan Ganesha 10, Bandung 40132, Indonesia.,UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Erwan Delrieu-Trottin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung an der Humboldt-Universität zu Berlin
| | - Fabien L Condamine
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Daisy Wowor
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong 16911, Indonesia
| | - Lukas Rüber
- Naturhistorisches Museum Bern, Bernastrasse 15, 3005 Bern, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Jean-François Agnèse
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
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22
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EDITORIAL NOTES AND NEWS. COPEIA 2020. [DOI: 10.1643/ct2020113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Lavoué S, Zafirah Ghazali S, Amirul Firdaus Jamaluddin J, Azizah Mohd Nor S, Zain KM. Genetic evidence for the recognition of two allopatric species of Asian bronze featherback Notopterus (Teleostei, Osteoglossomorpha, Notopteridae). ZOOSYST EVOL 2020. [DOI: 10.3897/zse.96.51350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The fish genus Notopterus Lacepède, 1800 (Notopteridae) currently includes only one species, the Asian bronze featherback Notopterus notopterus (Pallas, 1769). This common freshwater species is widely distributed in the Oriental region, from the Indus basin in the west, the Mekong basin in the east and Java Island in the south. To examine the phylogeographic structure of N. notopterus across its range, we analysed 74 publicly available cytochrome oxidase I (COI) sequences, 72 of them determined from known-origin specimens, along with four newly-determined sequences from Peninsular Malaysian specimens. We found that N. notopterus is a complex of two allopatric species that diverge from each other by 7.5% mean p-distance. The first species is endemic to South Asia (from Indus basin to Ganga-Brahmaputra system), whereas the distribution of the second species is restricted to Southeast Asia. The exact limit between the distributions of these two species is not known, but it should fall somewhere between the Ganga-Brahmaputra and Salween basins, a region already identified as a major faunal boundary in the Oriental region. The name N. notopterus is retained for the Southeast Asian species, while the name Notopterus synurus (Bloch & Schneider, 1801) should be applied to the South Asian species. A comparative morphological study is needed to reveal the degree of morphological differentiation between the two species.
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24
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Sholihah A, Delrieu-Trottin E, Sukmono T, Dahruddin H, Risdawati R, Elvyra R, Wibowo A, Kustiati K, Busson F, Sauri S, Nurhaman U, Dounias E, Zein MSA, Fitriana Y, Utama IV, Muchlisin ZA, Agnèse JF, Hanner R, Wowor D, Steinke D, Keith P, Rüber L, Hubert N. Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes. Sci Rep 2020; 10:2818. [PMID: 32071342 PMCID: PMC7028728 DOI: 10.1038/s41598-020-59544-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/20/2020] [Indexed: 11/25/2022] Open
Abstract
Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.
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Affiliation(s)
- Arni Sholihah
- Instut Teknologi Bandung, School of Life Sciences and Technology, Bandung, Indonesia.,UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France
| | - Erwan Delrieu-Trottin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstrasse 43, Berlin, 10115, Germany
| | - Tedjo Sukmono
- Universitas Jambi, Department of Biology, Jalan Lintas Jambi - Muara Bulian Km15, 36122, Jambi, Sumatra, Indonesia
| | - Hadi Dahruddin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.,Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Renny Risdawati
- Department of Biology Education, STKIP PGRI Sumatera Barat, Jl Gunung Pangilun, Padang, 25137, Indonesia
| | - Roza Elvyra
- Universitas Riau, Department of Biology, Simpang Baru, Tampan, Pekanbaru, 28293, Indonesia
| | - Arif Wibowo
- Southeast Asian Fisheries Development Center, Inland Fisheries Resources Development and Management Department, 8 Ulu, Seberang Ulu I, Palembang, 30267, Indonesia.,Research Institute for Inland Fisheries and Fisheries extensions, Agency for Marine and Fisheries Research, Ministry of Marine Affairs and Fisheries., Jl. H.A. Bastari No. 08, Jakabaring, Palembang, 30267, Indonesia
| | - Kustiati Kustiati
- Universitas Tanjungpura, Department of Biology, Jalan Prof. Dr. H. Hadari Nawawi, Pontianak, 78124, Indonesia
| | - Frédéric Busson
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.,UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231, Paris, cedex, 05, France
| | - Sopian Sauri
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Ujang Nurhaman
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Edmond Dounias
- UMR 5175 CEFE (IRD, UM, CNRS, EPHE), 1919 route de Mende, 34293, Montpellier, cedex, 05, France
| | - Muhamad Syamsul Arifin Zein
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Yuli Fitriana
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Ilham Vemendra Utama
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | | | - Jean-François Agnèse
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France
| | - Robert Hanner
- Department of Integrative Biology, Centre for Biodiversity Genomics, 50 Stone Rd E, Guelph, ON, N1G2W1, Canada
| | - Daisy Wowor
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, 50 Stone Rd E, Guelph, ON, N1G2W1, Canada
| | - Philippe Keith
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231, Paris, cedex, 05, France
| | - Lukas Rüber
- Naturhistorisches Museum Bern, Bernastrasse 15, Bern, 3005, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.
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25
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Chu C, Loh KH, Ng CC, Ooi AL, Konishi Y, Huang SP, Chong VC. Using DNA Barcodes to Aid the Identification of Larval Fishes in Tropical Estuarine Waters (Malacca Straits, Malaysia). Zool Stud 2019; 58:e30. [PMID: 31966331 PMCID: PMC6917562 DOI: 10.6620/zs.2019.58-30] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/18/2019] [Indexed: 11/18/2022]
Abstract
Larval descriptions of tropical marine and coastal fishes are very few, and this taxonomic problem is further exacerbated by the high diversity of fish species in these waters. Nonetheless, accurate larval identification in ecological and early life history studies of larval fishes is crucial for fishery management and habitat protection. The present study aimed to evaluate the usefulness of DNA barcodes to support larval fish identification since conventional dichotomous keys based on morphological traits are not efficient due to the lack of larval traits and the rapid morphological changes during ontogeny. Our molecular analysis uncovered a total of 48 taxa (21 families) from the larval samples collected from the Klang Strait waters encompassing both spawning and nursery grounds of marine and estuarine fishes. Thirty-two (67%) of the larval taxa were identified at the species level, two taxa (4%) at the genus level, and 14 taxa (29%) at family level. The relatively low rate of species-level identification is not necessarily due to the DNA barcoding method per se, but a general lack of reference sequences for speciose and non- commercial fish families such as Gobiidae, Blenniidae, and Callionymidae. Larval morphology remains important in species diagnoses when molecular matches are ambiguous. A lower ethanol percentage (50%) for larva preservation is also useful to keep the body of larvae intact for morphological identification, and to preserve DNA for subsequent molecular analyses. The 10% Chelex resin used to extract DNA is also cost- effective for long term monitoring of larval fishes. Hence, the DNA barcoding method is an effective and easy way to aid the identification of estuarine larval fishes at the species level.
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Affiliation(s)
- Cecilia Chu
- Institute of Ocean and Earth Sciences, University of
Malaya, Kuala Lumpur, Malaysia. E-mail: (Chu);
(Loh)
| | - Kar Hoe Loh
- Institute of Ocean and Earth Sciences, University of
Malaya, Kuala Lumpur, Malaysia. E-mail: (Chu);
(Loh)
| | - Ching Ching Ng
- Institute of Biological Sciences, Faculty of Science,
University of Malaya, Kuala Lumpur, Malaysia. E-mail: (Chong); (Ng)
| | - Ai Lin Ooi
- Department of Agricultural and Food Science, Faculty of
Science, Universiti Tunku Abdul Rahman, Kampar, Perak. E-mail:
| | - Yoshinobu Konishi
- Seikai National Fisheries Research Institute, Nagasaki,
Japan. E-mail:
| | - Shih-Pin Huang
- Biodiversity Research Center, Academia Sinica, Taipei
115, Taiwan. E-mail:
| | - Ving Ching Chong
- Institute of Biological Sciences, Faculty of Science,
University of Malaya, Kuala Lumpur, Malaysia. E-mail: (Chong); (Ng)
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26
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Shen Y, Hubert N, Huang Y, Wang X, Gan X, Peng Z, He S. DNA barcoding the ichthyofauna of the Yangtze River: Insights from the molecular inventory of a mega‐diverse temperate fauna. Mol Ecol Resour 2019; 19:1278-1291. [DOI: 10.1111/1755-0998.12961] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/07/2018] [Accepted: 09/24/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Yanjun Shen
- 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
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM2‐CNRS‐IRD) Montpellier cedex 05 France
| | - Yan Huang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Xuzheng Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing 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
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27
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Revisiting species boundaries and distribution ranges of Nemacheilus spp. (Cypriniformes: Nemacheilidae) and Rasbora spp. (Cypriniformes: Cyprinidae) in Java, Bali and Lombok through DNA barcodes: implications for conservation in a biodiversity hotspot. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01152-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Cancian de Araujo B, Schmidt S, Schmidt O, von Rintelen T, Ubaidillah R, Balke M. The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia. Biodivers Data J 2018:e29927. [PMID: 30598619 PMCID: PMC6306476 DOI: 10.3897/bdj.6.e29927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/28/2018] [Indexed: 11/12/2022] Open
Abstract
The Indonesian archipelago features an extraordinarily rich biota. However, the actual taxonomic inventory of the archipelago remains highly incomplete and there is hardly any significant taxonomic activity that utilises recent technological advances. The IndoBioSys project was established as a biodiversity information system aiming at, amongst other goals, creating inventories of the Indonesian entomofauna using DNA barcoding. Here, we release the first large scale assessment of the megadiverse insect groups that occur in the Mount Halimun-Salak National Park, one of the largest tropical rain-forest ecosystem in West Java, with a focus on Hymenoptera, Coleoptera, Diptera and Lepidoptera collected with Malaise traps. From September 2015 until April 2016, 34 Malaise traps were placed in different localities in the south-eastern part of the Halimun-Salak National Park. A total of 4,531 specimens were processed for DNA barcoding and in total, 2,382 individuals produced barcode compliant records, representing 1,195 exclusive BINs or putative species in 98 insect families. A total of 1,149 BINs were new to BOLD. Of 1,195 BINs detected, 804 BINs were singletons and more than 90% of the BINs incorporated less than five specimens. The astonishing heterogeneity of BINs, as high as 1.1 exclusive BIN per specimen of Diptera successfully processed, shows that the cost/benefit relationship of the discovery of new species in those areas is very low. In four genera of Chalcidoidea, a superfamily of the Hymenoptera, the number of discovered species was higher than the number of species known from Indonesia, suggesting that our samples contain many species that are new to science. Those numbers shows how fast molecular pipelines contribute substantially to the objective inventorying of the fauna giving us a good picture of how potentially diverse tropical areas might be.
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Affiliation(s)
- Bruno Cancian de Araujo
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
| | - Olga Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung Berlin Germany
| | - Rosichon Ubaidillah
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences Cibinong Indonesia
| | - Michael Balke
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
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29
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Hutama A, Dahruddin H, Busson F, Sauri S, Keith P, Hadiaty RK, Hanner R, Suryobroto B, Hubert N. Identifying spatially concordant evolutionary significant units across multiple species through DNA barcodes: Application to the conservation genetics of the freshwater fishes of Java and Bali. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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