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Sun CH, Lu CH, Wang ZJ. Comparison and phylogenetic analysis of the mitochondrial genomes of Synodontis eupterus and Synodontis polli. Sci Rep 2024; 14:15393. [PMID: 38965284 PMCID: PMC11224264 DOI: 10.1038/s41598-024-65809-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
We aimed to distinguish Synodontis eupterus and Synodontis polli. We performed sequencing and bioinformatic analysis of their mitochondrial genomes and constructed a phylogenetic tree of Mochokidae fish using maximum likelihood and Bayesian methods based on protein-coding gene (PCG) sequences of 14 Mochokidae species. The total length of the S. eupterus mitochondrial genome was 16,579 bp, including 13 (PCGs), 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (56.0%). The total length of the S. polli mitochondrial genome was 16,544 bp, including 13 PCGs, 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (55.0%). In both species, except for COI, PCGs use ATG as the starting codon, the vast majority use TAG or TAA as the ending codon, and a few use incomplete codons (T - or TA -) as the ending codon. Phylogenetic analysis showed that S. eupterus and Synodontis clarias converged into one branch, S. polli and Synodontis petricola converged into one branch, Mochokiella paynei, Mochokus brevis, and nine species of the genus Synodontis converged into one branch, and M. paynei clustered with the genus Synodontis. This study lays a foundation for rebuilding a clearer Mochokidae fish classification system.
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Affiliation(s)
- Cheng-He Sun
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Chang-Hu Lu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Zi-Jian Wang
- Agriculture and Rural Bureau of Gaochun District, Nanjing, 211300, China
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2
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Muhala V, Guimarães-Costa A, Macate IE, Rabelo LP, Bessa-Silva AR, Watanabe L, dos Santos GD, Sambora L, Vallinoto M, Sampaio I. DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique. PLoS One 2024; 19:e0293345. [PMID: 38319915 PMCID: PMC10846724 DOI: 10.1371/journal.pone.0293345] [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: 05/01/2023] [Accepted: 10/10/2023] [Indexed: 02/08/2024] Open
Abstract
The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.
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Affiliation(s)
- Valdemiro Muhala
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
- Divisão de Agricultura, Instituto Superior Politécnico de Gaza, Chókwè, Mozambique
| | - Aurycéia Guimarães-Costa
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Isadola Eusébio Macate
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilheus, BA, Brazil
| | - Luan Pinto Rabelo
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Adam Rick Bessa-Silva
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Luciana Watanabe
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Gisele Damasceno dos Santos
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Luísa Sambora
- Departamento de Produção Agrária, Escola Superior de Desenvolvimento Rural, Universidade Eduardo Mondlane, Vilankulos, Moçambique
| | - Marcelo Vallinoto
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
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3
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Hubert N, Phillips JD, Hanner RH. Delimiting Species with Single-Locus DNA Sequences. Methods Mol Biol 2024; 2744:53-76. [PMID: 38683311 DOI: 10.1007/978-1-0716-3581-0_3] [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] [Indexed: 05/01/2024]
Abstract
DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.
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Affiliation(s)
- Nicolas Hubert
- UMR ISEM (IRD, UM, CNRS), Université de Montpellier, Montpellier, France.
| | - Jarrett D Phillips
- School of Computer Science, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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4
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Dziedzic E, Sidlauskas B, Cronn R, Anthony J, Cornwell T, Friesen TA, Konstantinidis P, Penaluna BE, Stein S, Levi T. Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA. Mol Ecol Resour 2023; 23:1880-1904. [PMID: 37602732 DOI: 10.1111/1755-0998.13855] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
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Affiliation(s)
- Emily Dziedzic
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brian Sidlauskas
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Richard Cronn
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - James Anthony
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Trevan Cornwell
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Thomas A Friesen
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Peter Konstantinidis
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brooke E Penaluna
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - Staci Stein
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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5
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Bagley JC, Johnson CC, McGregor SW, Breitman MF, Armbruster JW, Harris PM, Oneil PE. Marine and freshwater fishes of Alabama: a revised checklist and discussion of taxonomic issues. Zootaxa 2023; 5357:301-341. [PMID: 38220642 DOI: 10.11646/zootaxa.5357.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Indexed: 01/16/2024]
Abstract
Checklists are fundamental and important tools for organizing information about biodiversity that provide a basis for conservation and additional scientific research. While Alabama is recognized as an aquatic biodiversity hotspot with the highest native freshwater fish diversity in the contiguous United States, we currently lack an up-to-date list of the states fishes. In particular, much has changed over the past ~20 years regarding our knowledge of fishes from Alabama and the Mobile River Basin, rendering past comprehensive treatments by Mettee et al. (1996) and Boschung and Mayden (2004) out of date. Here, we provide a revised checklist of marine and freshwater fishes known from the coastal and inland waters of Alabama that includes 463 species (335 primarily freshwater fishes, and 128 marine or diadromous fishes) in 35 orders, 78 families, and 176 genera. Extant, extirpated, and extinct species are included, as are putative candidate species. The checklist is based on prior work, searches of the literature and online sources, as well as parsing a large compilation of >140,000 fish records for Alabama and the Mobile River Basin from 37 data providers in the global Fishnet2 database (www.fishnet2.net) and >4000 marine survey records from the SEAMAP database (https://www.gsmfc.org/seamap.php). After editing and quality control checks, the final combined database contained 144,215 collection records, ~95% of which were georeferenced. We discuss the species descriptions, nomenclatural changes, and updates to marine species that account for changes to the state list, and we close with a discussion of ~13 candidate species forms that remain undescribed, which represent outstanding taxonomic issues in need of further research attention.
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Affiliation(s)
- Justin C Bagley
- Department of Biology and Environmental Science; Auburn University at Montgomery; 301 Goodwyn Hall; Montgomery; AL 36124; USA; Department of Biology; Virginia Commonwealth University; 1000 W Cary St.; Suite 126; Richmond; VA 23284; USA; Field Operations Division; Alabama Department of Environmental Management; P.O. Box 301463; Montgomery; AL 36130; USA.
| | - Cal C Johnson
- Decatur Field Office; Alabama Department of Environmental Management; 2715 Sandlin Rd SW; Decatur; AL 35603; USA.
| | - Stuart W McGregor
- Geological Survey of Alabama; Walter B. Jones Hall; 420 Hackberry Lane; Tuscaloosa; AL 35487; USA.
| | - Maria F Breitman
- Department of Biology and Environmental Science; Auburn University at Montgomery; 301 Goodwyn Hall; Montgomery; AL 36124; USA.
| | - Jonathan W Armbruster
- Department of Biological Sciences; Auburn University; 120 W Samford Ave; Auburn; AL 36849; USA.
| | - Phillip M Harris
- Department of Biological Sciences, The University of Alabama, 1325 Hackberry Ln, Tuscaloosa, AL 35401, USA.
| | - Patrick E Oneil
- Geological Survey of Alabama, Walter B. Jones Hall, 420 Hackberry Lane, Tuscaloosa, AL 35487, USA.
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6
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Shelley JJ, Delaval A, Feuvre MCLE. A revision of the gudgeon genus Hypseleotris (Gobiiformes: Gobioidei: Eleotridae) of northwest Australia, describing three new species and synonymizing the genus Kimberleyeleotris. Zootaxa 2023; 5311:340-374. [PMID: 37518639 DOI: 10.11646/zootaxa.5311.3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 08/01/2023]
Abstract
Species within the northwest Australian clade of Hypseleotris (six species) and the genus Kimberleyeleotris (two species) are reviewed following the recording of new populations in the region and a molecular study of the group that identified three undescribed candidate species. Based on the analysis of extensive morphological and nuclear and mitochondrial molecular datasets, Kimberleyeleotris is here formally synonymised with Hypseleotris. Furthermore, three species from the Kimberley region, Western Australia, are described to science: Hypseleotris maranda sp. nov., Hypseleotris wunduwala sp. nov., and Hypseleotris garawudjirri sp. nov. The presence of, or number of scales across the head and body, the pattern of sensory papillae on the head, fin ray counts, dorsal and anal fin colouration (particularly in breeding males), and body depth, can be used to distinguish the members of the northwest Australia lineage. Furthermore, the newly described species were genetically separated from all northwest Australian congeners by K2P distances ranging from 7.8-11.3% based on the CO1 gene, and 7.7-16.3 % based on the entire mitochondrial genome. Two of the new species, H. maranda sp. nov. and H. wunduwala sp. nov., have extremely narrow ranges being found in single sub-catchments of the Roe and King Edward Rivers respectively. On the other hand, H. garawudjirri sp. nov. is moderately widespread, being found across the Charnley, Calder, and Sale rivers. While the conservation risk to H. maranda sp. nov. and H. wunduwala sp. nov. is inherently high due to their small range, there are currently no obvious local threatening processes to either of these species given their remote locations that are little impacted by human activities.
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Affiliation(s)
- James J Shelley
- School of BioSciences; University of Melbourne; Victoria 3010; Australia.
| | - Aurélien Delaval
- School of BioSciences; University of Melbourne; Victoria 3010; Australia; Ichthyology; Sciences Department; Museums Victoria; Victoria 3001; Australia; Institute of Marine Research; Bergen 5817; Norway.
| | - Matthew C LE Feuvre
- School of BioSciences; University of Melbourne; Victoria 3010; Australia; Ichthyology; Sciences Department; Museums Victoria; Victoria 3001; Australia.
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7
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Stokes MF, Kim D, Gallen SF, Benavides E, Keck BP, Wood J, Goldberg SL, Larsen IJ, Mollish JM, Simmons JW, Near TJ, Perron JT. Erosion of heterogeneous rock drives diversification of Appalachian fishes. Science 2023; 380:855-859. [PMID: 37228195 DOI: 10.1126/science.add9791] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
The high levels of biodiversity supported by mountains suggest a possible link between geologic processes and biological evolution. Freshwater biodiversity is high not only in tectonically active settings but also in tectonically quiescent montane regions such as the Appalachian Mountains. We show that erosion through different rock types drove allopatric divergence between lineages of the Greenfin Darter (Nothonotus chlorobranchius), a fish species endemic to rivers draining metamorphic rocks in the Tennessee River basin in the United States. In the past, metamorphic rock preferred by N. chlorobranchius was more widespread, but as erosion exposed other rock types, lineages of this species were progressively isolated in tributaries farther upstream, where metamorphic rock remained. Our results suggest a geologic mechanism for initiating allopatric diversification in mountains long after tectonic activity ceases.
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Affiliation(s)
- Maya F Stokes
- Yale Institute for Biospheric Studies, New Haven, CT 06511, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL 32304, USA
| | - Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Sean F Gallen
- Department of Geosciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Benjamin P Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Julia Wood
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Samuel L Goldberg
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isaac J Larsen
- Department of Earth, Geographic, and Climate Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Jon Michael Mollish
- Fisheries and Aquatic Monitoring, Tennessee Valley Authority, Chattanooga, TN 37415, USA
| | - Jeffrey W Simmons
- Fisheries and Aquatic Monitoring, Tennessee Valley Authority, Chattanooga, TN 37415, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - J Taylor Perron
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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8
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Tellier JM, Winsmann B, Humphreys M, Minoudi S, Triantafyllidis A, Schultz ET. What Are You Doing Here? A Sculpin Endemic to Arkansas and Missouri (Cottus immaculatus) Appears in Connecticut. ICHTHYOLOGY & HERPETOLOGY 2023. [DOI: 10.1643/i2020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Joshua M. Tellier
- Department of Ecology and Evolutionary Biology, University of Connecticut, U-3043, Storrs, Connecticut 06269-3043; (BW) brooke.
; and (ETS)
| | - Brooke Winsmann
- Department of Ecology and Evolutionary Biology, University of Connecticut, U-3043, Storrs, Connecticut 06269-3043; (BW) brooke.
; and (ETS)
| | - Michael Humphreys
- Fisheries Division, Connecticut Department of Energy and Environmental Protection, 54 Harris Rd., Litchfield, Connecticut 06759;
| | - Stella Minoudi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University, 54124 Thessaloniki, Greece; (SM) ; and (AT)
| | - Alexandros Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University, 54124 Thessaloniki, Greece; (SM) ; and (AT)
| | - Eric T. Schultz
- Department of Ecology and Evolutionary Biology, University of Connecticut, U-3043, Storrs, Connecticut 06269-3043; (BW) brooke.
; and (ETS)
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9
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MacGuigan DJ, Orr OD, Near TJ. Phylogeography, hybridization, and species discovery in the Etheostoma nigrum complex (Percidae: Etheostoma: Boleosoma). Mol Phylogenet Evol 2023; 178:107645. [PMID: 36252933 DOI: 10.1016/j.ympev.2022.107645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/29/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Abstract
The history of riverine fish diversification is largely a product of geographic isolation. Physical barriers that reduce or eliminate gene flow between populations facilitate divergence via genetic drift and natural selection, eventually leading to speciation. For freshwater organisms, diversification is often the product of drainage basin rearrangements. In young clades where the history of isolation is the most recent, evolutionary relationships can resemble a tangled web. One especially recalcitrant group of freshwater fishes is the Johnny Darter (Etheostoma nigrum) species complex, where traditional taxonomy and molecular phylogenetics indicate a history of gene flow and conflicting inferences of species diversity. Here we assemble a genomic dataset using double digest restriction site associated DNA (ddRAD) sequencing and use phylogenomic and population genetic approaches to investigate the evolutionary history of the complex of species that includes E. nigrum, E. olmstedi, E. perlongum, and E. susanae. We reveal and validate several evolutionary lineages that we delimit as species, highlighting the need for additional work to formally describe the diversity of the Etheostoma nigrum complex. Our analyses also identify gene flow among recently diverged lineages, including one instance involving E. susanae, a localized and endangered species. Phylogeographic structure within the Etheostoma nigrum species complex coincides with major geologic events, such as parallel divergence in river basins during Pliocene inundation of the Atlantic coastal plain and multiple northward post-glacial colonization routes tracking river basin rearrangements. Our study serves as a nuanced example of how low dispersal rates coupled with geographic isolation among disconnected river systems in eastern North America has produced one of the world's freshwater biodiversity hotspots.
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Affiliation(s)
- Daniel J MacGuigan
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo, Buffalo, NY 14260, USA.
| | - Oliver D Orr
- Department of Ecology and Evolutionary Biology, 165 Prospect Street, Yale University, New Haven, CT 06520, USA; Yale Peabody Museum of Natural History, 170 Whitney Ave, New Haven, CT 06520, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, 165 Prospect Street, Yale University, New Haven, CT 06520, USA; Yale Peabody Museum of Natural History, 170 Whitney Ave, New Haven, CT 06520, USA
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10
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Nascimento BM, de Paula TS, Brito PMM. DNA barcode of tilapia fish fillet from the Brazilian market and a standardized COI haplotyping for molecular identification of Oreochromis spp. (Actinopterygii, Cichlidae). FORENSIC SCIENCE INTERNATIONAL: ANIMALS AND ENVIRONMENTS 2022. [DOI: 10.1016/j.fsiae.2022.100059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Brownstein CD, Kim D, Orr OD, Hogue GM, Tracy BH, Pugh MW, Singer R, Myles-McBurney C, Mollish JM, Simmons JW, David SR, Watkins-Colwell G, Hoffman EA, Near TJ. Hidden species diversity in an iconic living fossil vertebrate. Biol Lett 2022; 18:20220395. [PMID: 36448369 PMCID: PMC9709656 DOI: 10.1098/rsbl.2022.0395] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Ancient, species-poor lineages persistently occur across the Tree of life. These lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils. Halecomorphi is a lineage of ray-finned fishes that diverged from its closest relatives before 200 Ma and is represented by only one living species in eastern North America, the bowfin, Amia calva Linnaeus. Here, we use double digest restriction-site-associated DNA sequencing and morphology to illuminate recent speciation in bowfins. Our results support the delimitation of a second living species of Amia, with the timing of diversification dating to the Plio-Pleistocene. This delimitation expands the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development, yet is facing growing conservation threats driven by the caviar fishery.
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Affiliation(s)
- Chase D. Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Oliver D. Orr
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | | | - Bryn H. Tracy
- North Carolina Museum of Natural Science, Raleigh, NC 27601, USA
| | - M. Worth Pugh
- Department of Biological Science, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Randal Singer
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jon Michael Mollish
- River and Reservoir Compliance Monitoring, Tennessee Valley Authority, Chattanooga, TN 37402, USA
| | - Jeffrey W. Simmons
- River and Reservoir Compliance Monitoring, Tennessee Valley Authority, Chattanooga, TN 37402, USA
| | - Solomon R. David
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70310, USA
| | | | - Eva A. Hoffman
- Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA,Peabody Museum, Yale University, New Haven, CT 06520, USA
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12
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Bektas Y, Aksu İ, Kaya C, Bayçelebi E, Turan D. DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia. JOURNAL OF FISH BIOLOGY 2022; 101:505-514. [PMID: 35607971 DOI: 10.1111/jfb.15114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.
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Affiliation(s)
- Yusuf Bektas
- Deparment of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - İsmail Aksu
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Cüneyt Kaya
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Esra Bayçelebi
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Davut Turan
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
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Laskar BA, Adimalla H, Kundu S, Jaiswal D, Chandra K. DNA barcoding of a lesser-known catfish, Clupisoma bastari (Actinopterygii: Ailiidae) from Deccan Peninsula, India. JOURNAL OF THREATENED TAXA 2022. [DOI: 10.11609/jott.6900.14.8.21605-21611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
DNA barcoding substantiates species identification, and simultaneously indicates the misnomer taxa. Based on the morphological descriptions, we identified a lesser-known catfish, Clupisoma bastari, from Godavari River basin, and contributed novel DNA barcode data to the GenBank. The Kimura 2 parameter genetic divergence between species, and the neighbour-joining phylogeny clearly depicted a distinct clade of C. bastari in the studied dataset. Clupisoma bastari maintained sufficient K2P genetic divergence (8.3% to 11.2%) with other congeners, and branched as a sister-species of C. garua. The present study highlights possible existence of a few misnomer taxa in the GenBank. We encourage further extensive sampling of different congeners of Clupisoma from a wide range of habitats to explore the species diversity and phylogenetic relationship.
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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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15
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Young MK, Smith R, Pilgrim KL, Isaak DJ, McKelvey KS, Parkes S, Egge J, Schwartz MK. A Molecular Taxonomy of Cottus in western North America. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0208] [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]
Affiliation(s)
- Michael K. Young
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Rebecca Smith
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Kristine L. Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Daniel J. Isaak
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Kevin S. McKelvey
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Sharon Parkes
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Jacob Egge
- Department of Biology, Pacific Lutheran University, Tacoma, WA 98447
| | - Michael K. Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
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16
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Chen W, Hubert N, Li Y, Xiang D, Cai X, Zhu S, Yang J, Zhou C, Li X, Li J. Large scale DNA barcoding of the subfamily Culterinae (Cypriniformes: Xenocyprididae) in East Asia unveils geographic scale effect, taxonomic warnings and cryptic diversity. Mol Ecol 2022; 31:3871-3887. [PMID: 35593525 PMCID: PMC9542215 DOI: 10.1111/mec.16540] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/28/2022]
Abstract
Geographical scale might be expected to impact significantly the efficiency of DNA barcoding as spatially comprehensive sampling provides opportunities to uncover intricate relationships among closely related species and to detect cryptic diversity for widespread taxa. Here, we present a DNA barcoding study on a Xencyprididae subfamily (Culterinae) involving the production of 998 newly generated DNA barcodes from East Asian drainages (80 localities). Together with 513 barcodes mined from BOLD and GenBank, a reference library consisting of 1511 DNA barcodes (116 localities) for 42 species was assembled, accounting for 66% of known Culterinae species. Intraspecific genetic distances are positively correlated to geographical scale, while a negative correlation is detected between interspecific genetic distances and geographical scale. The present study demonstrates that geographical scale influences the efficiency of DNA barcoding by narrowing the width of the barcoding gap. DNA‐based species delimitation analyses delimited 44 molecular operational taxonomic units (MOTUs). Rampant cryptic diversity is detected within eight species with multiple MOTUs, whereas 25 species present mismatch between morphological and molecular delimitations. A total of 18 species are lumped into nine MOTUs due to low interspecific divergence and/or mixed lineages. Several MOTU divergences are hypothesized to relate to known biogeographical barriers and geological events during the Pliocene and Pleistocene. This study provides new insights into the taxonomy and phylogeography of the subfamily Culterinae.
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Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 226 ISEM (UM-CNRS-IRD), Montpellier cedex 05, France
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Denggao Xiang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China
| | - Xingwei Cai
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Jiping Yang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Chuanjiang Zhou
- College of Fisheries, Henan Normal University, Xinxiang, Henan, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
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17
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FREYHOF JÖRG, KAYA CÜNEYT, GEIGER MATTHIASF. A practical approach to revise the Oxynoemacheilus bergianus species group (Teleostei: Nemacheilidae). Zootaxa 2022; 5128:151-194. [DOI: 10.11646/zootaxa.5128.2.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 11/04/2022]
Abstract
The Oxynoemacheilus bergianus species group is revised based on tree topology (ML, NJ, MP), distance (K2P and ASAP) and Poisson tree process analyses of DNA barcode data tested against morphometric and morphological characters including colour patterns. The O. bergianus species group is distinguished from other Oxynoemacheilus groups based on morphological characters: its constituent species have a slender caudal peduncle, a suborbital flap in the male, a mottled or blotched colour pattern, and lack bold, black spots on the caudal-fin base. It is also supported as a monophyletic unit in our molecular analysis.
The O. bergianus group includes 10 molecular clades following congruently well-supported NJ, MP and ML based entities. Species described as O. bergianus, O. banarescui, O. erdali, O. fatsaensis, O. samanticus, and O. simavicus from Turkey, O. lenkoranensis from Azerbaijan, and O. longipinnis and O. parvinae from Iran belong to this species group. The group includes also four unnamed molecular clades. We were unable to detect external differences between any of the molecular clades in colour pattern or any morphometric or morphological characters examined. In the 10 molecular clades in the O. bergianus species group, the intraclade K2P distance ranges from 0.0–1.8% while the distances between molecular clades ranges from 0.6–5.9%. To resolve the species diversity of this group, we also analysed the intraspecific and interspecific variability in the K2P distance of DNA barcode data from 53 other Oxynoemacheilus species. Here, the intraspecific variability ranges from 0.0–2.4% while the interspecific K2P distance ranges from 1.2–20.8%. In the O. bergianus species group, only four groups are detected by the mPTP species delimitation approach distinguished by a K2P distance of 2.9% or more. We treat these four groups as valid species, corresponding to O. banarescui, O. bergianus, O. fatsaensis, and O. simavicus. Oxynoemacheilus samanticus from the Kızılırmak and Seyhan drainages, O. lenkoranensis from the Caspian basin, O. erdali from the Euphrates, and O. longipinnis and O. parvinae from the Tigris drainage are treated as synonyms of O. bergianus. Fishes from an unnamed molecular clade from the upper Tigris, and from a second unnamed clade from the upper Euphrates, are both identified as O. bergianus. Oxynoemacheilus bergianus might be a junior synonym of O. bergi from the Kura. The distribution range of O. simavicus, described from the Simav drainage in the Marmara basin, is expanded to the east and two molecularly differentiated population groups occur in the Sakarya drainage, the Büyük Melen River and potentially in other adjacent coastal streams. Oxynoemacheilus fatsaensis, described from the coastal stream Elekçi in northern Anatolia, is also widespread in the Yeşilırmak drainage. Morphological characters proposed to distinguish O. fatsaensis from the other species of the O. bergianus group could not be confirmed by our data on fishes from the Yeşilırmak. This study also discusses the theoretical background, our reasons for conducting this revision in the way we did, and what the alternatives would be.
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Tsoupas A, Papavasileiou S, Minoudi S, Gkagkavouzis K, Petriki O, Bobori D, Sapounidis A, Koutrakis E, Leonardos I, Karaiskou N, Triantafyllidis A. DNA barcoding identification of Greek freshwater fishes. PLoS One 2022; 17:e0263118. [PMID: 35081163 PMCID: PMC8791500 DOI: 10.1371/journal.pone.0263118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.
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Affiliation(s)
- Alexandros Tsoupas
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Papavasileiou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Styliani Minoudi
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Olga Petriki
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Bobori
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail: (DB); (AT)
| | - Argyrios Sapounidis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Emmanouil Koutrakis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Ioannis Leonardos
- Department of Biological Applications and Technologies, Laboratory of Zoology, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Nikoleta Karaiskou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
- * E-mail: (DB); (AT)
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Yin Y, Yao LF, Hu Y, Shao ZK, Hong XY, Hebert PDN, Xue XF. DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea). Mol Ecol Resour 2022; 22:1986-1998. [PMID: 35178894 DOI: 10.1111/1755-0998.13599] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022]
Abstract
Eriophyoid mites (Acari: Eriophyoidea) are among the smallest of terrestrial arthropods and the most species-rich group of herbivorous mites with a high host specificity. However, knowledge of their species diversity has been impeded by the difficulty of their morphological differentiation. This study assembles a DNA barcode reference library that includes 1,850 mitochondrial COI sequences which provides coverage for 45% of the 930 species of eriophyoid mites known from China, and for 37 North American species. Sequence analysis showed a clear barcode gap in nearly all species, reflecting the fact that intraspecific divergences averaged 0.97% versus a mean of 18.51% for interspecific divergences (minimum nearest-neighbor distances) in taxa belonging to three families. Based on these results, we used DNA barcoding to explore the species diversity of eriophyoid mites as well as their host interactions. The 1,850 sequences were assigned to 531 Barcode Index Numbers (BINs). Analyses examining the correspondence between these BINs and species identifications based on morphology revealed that members of 45 species were assigned to two or more BINs, resulting in 1.16 times more BINs than morphospecies. Richness projections suggest that over 2,345 BINs occurred at the sampled locations. Host plant analysis showed that 89% of these mites (BINs) attack only one or two congeneric host species, but the others have several hosts. Furthermore, host-mite network analyses demonstrate that eriophyoid mites are high host-specific, and modularity is high in plant-mite networks. By creating a highly effective identification system for eriophyoid mites in BOLD, DNA barcoding will advance our understanding of the diversity of eriophyoid mites and their host interactions.
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Affiliation(s)
- Yue Yin
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada
| | - Liang-Fei Yao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yue Hu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zi-Kai Shao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Tarkan AS, Emiroğlu Ö, Aksu S, Başkurt S, Aksu İ, Vilizzi L, Yoğurtçuoğlu B. Coupling molecular and risk analysis to investigate the origin, distribution and potential impact of non-native species: an application to ruffe Gymnocephalus cernua in Turkey. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2021.2022222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- A. S. Tarkan
- Faculty of Fisheries, Muğla Sıtkı Koçman University, Muğla, Turkey
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Ö. Emiroğlu
- Department of Biology, Faculty of Science, Eskişehir Osmangazi University, Eskişehir, Turkey
| | - S. Aksu
- Vocational School of Health Services, Eskişehir Osmangazi University, Eskişehir, Turkey
| | - S. Başkurt
- Department of Biology, Faculty of Science, Eskişehir Osmangazi University, Eskişehir, Turkey
| | - İ. Aksu
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - L. Vilizzi
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - B. Yoğurtçuoğlu
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
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Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
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22
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Hashemzadeh Segherloo I, Freyhof J, Berrebi P, Ferchaud AL, Geiger M, Laroche J, Levin BA, Normandeau E, Bernatchez L. A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)? Mol Phylogenet Evol 2021; 162:107204. [PMID: 34015446 DOI: 10.1016/j.ympev.2021.107204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.
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Affiliation(s)
- Iraj Hashemzadeh Segherloo
- Department of Fisheries and Environmental Sciences, Faculty of Natural Resources and Earth Sciences, Shahr-e-Kord University, Shahr-e-Kord, Iran; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada.
| | - Jörg Freyhof
- Museum für Naturkunde Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, 10115 Berlin, Germany
| | - Patrick Berrebi
- Genome - Research & Diagnostic, 697 avenue de Lunel, 34400 Saint-Just, France
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Matthias Geiger
- Zoologisches Forschungsmuseum Museum Alexander Koenig, Leibniz Institute for Animal Biodiversity, 53133 Bonn, Germany
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Boris A Levin
- Papanin Institute of Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia & Cherepovets State University, Cherepovets, Vologda Region, Russia
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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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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Pereira LHG, Castro JRC, Vargas PMH, Gomez JAM, Oliveira C. The use of an integrative approach to improve accuracy of species identification and detection of new species in studies of stream fish diversity. Genetica 2021; 149:103-116. [PMID: 33877495 DOI: 10.1007/s10709-021-00118-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/05/2021] [Indexed: 11/26/2022]
Abstract
In this study, we made an inventory of the stream and headwater ichthyofauna of the left bank of the Itaipu Dam Reservoir, located in the lower part of the Upper Paraná River basin, using an integrative approach of molecular and morphological data. The area is located in the western portion of the Paraná state in Brazil, in an area of about 8,000 km2 highly impacted by deforestation and intensive agriculture. For taxonomic identification of species, we used an identification key combined with the DNA barcoding approach. We found 48 species belonging to six orders, 13 families, and 37 genera. The Siluriformes and Characiformes were the most representative orders (75%) and the Characidae was the most representative family (20.8%). Nine species prevailed in this region, making up to 86% of all specimens collected. The integrative approach proved to be useful by allowing the unambiguous identification of all species, including those cases in which morphological characters were not conclusive for species identification, cases of cryptic species, and species with high morphological plasticity. In addition, the integrative approach highlighted six to 13 new putative species depending on the approach considered. Our study provides a relevant contribution to the knowledge of fish diversity in a poorly studied area of the Paraná River basin. We showed that the use of an integrative approach in inventory studies improves species identification and the discovery of new, cryptic, and overlooked species, being a powerful and necessary tool to quantify biodiversity.
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Affiliation(s)
- Luiz Henrique Garcia Pereira
- Laboratório de Biodiversidade e Ecologia Molecular, Instituto Latino-Americano de Ciências da Vida e da Natureza - ILACVN, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brasil.
| | - Jerson Rogelio Chanchay Castro
- Laboratório de Biodiversidade e Ecologia Molecular, Instituto Latino-Americano de Ciências da Vida e da Natureza - ILACVN, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brasil
| | - Pilar Mireya Huatatoca Vargas
- Laboratório de Biodiversidade e Ecologia Molecular, Instituto Latino-Americano de Ciências da Vida e da Natureza - ILACVN, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brasil
| | - Jose Alejandro Morales Gomez
- Laboratório de Biodiversidade e Ecologia Molecular, Instituto Latino-Americano de Ciências da Vida e da Natureza - ILACVN, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brasil
| | - Claudio Oliveira
- Departamento de Biologia estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho - UNESP, Botucatu, SP, Brasil
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Almeida MS, Moraes PSS, Nascimento MHS, Birindelli JLO, Assega FM, Barros MC, Fraga EC. New records of the occurrence of Megaleporinus macrocephalus () (Characiformes, Anostomidae) from the basins of the Itapecuru and Mearim rivers in Maranhão, Northeastern Brazil. BRAZ J BIOL 2021; 82:e232868. [PMID: 33681896 DOI: 10.1590/1519-6984.232868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/15/2020] [Indexed: 11/22/2022] Open
Abstract
The "piaussu", Megaleporinus macrocephalus is an anostomatid fish species native to the basin of the Paraguay River, in the Pantanal biome of western Brazil. However, this species has now been recorded in a number of other drainages, including those of the upper Paraná, Uruguay, Jacuí, Doce, Mucuri, and Paraíba do Sulrivers. This study presents two new records of the occurrence of M. macrocephalus, in the basins of the Itapecuru and Mearim rivers in the state of Maranhão, in the Brazilian Northeast. The piaussu is a large-bodied fish of commercial interest that is widely raised on fish farms, and its occurrence in the Itapecuru and Mearim rivers is likely the result of individuals escaping from fish tanks when they overflow during the rainy season. Morphological analyses and sequences of the Cytochrome Oxidase Subunit I (COI) gene confirmed the taxonomic identification of the specimens as M. macrocephalus. The COI sequences were 99.66% similar to those of M. macrocephalus deposited in the BOLDSystems database. These records extend the known distribution of M. macrocephalus to the basins of the Itapecuru and Mearim rivers in the Brazilian Northeast, highlighting a new case of introduction of exotic fish species into Brazilian river basins.
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Affiliation(s)
- M S Almeida
- Universidade Estadual do Maranhão - UEMA, Departamento de Química e Biologia, Programa de Pós-Graduação em Recursos Aquáticos e Pesca, São Luís, MA, Brasil
| | - P S S Moraes
- Universidade Estadual do Maranhão - UEMA, Laboratório de Genética e Biologia Molecular - GENBIMOL, Caxias, MA, Brasil
| | - M H S Nascimento
- Universidade Estadual do Maranhão - UEMA, Centro de Ciências Agrárias - CCA, Programa de Mestrado em Ciência Animal - CCMA, São Luís, MA, Brasil
| | - J L O Birindelli
- Universidade Estadual de Londrina, Departamento de Biologia Animal e Vegetal, Londrina, PR, Brasil
| | - F M Assega
- Universidade Estadual de Londrina, Departamento de Biologia Animal e Vegetal, Londrina, PR, Brasil
| | - M C Barros
- Universidade Estadual do Maranhão - UEMA, Laboratório de Genética e Biologia Molecular - GENBIMOL, Caxias, MA, Brasil
| | - E C Fraga
- Universidade Estadual do Maranhão - UEMA, Departamento de Química e Biologia, Programa de Pós-Graduação em Recursos Aquáticos e Pesca, São Luís, MA, Brasil
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28
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Consumers of mislabeled tropical fish exhibit increased risks of ciguatera intoxication: A report on substitution patterns in fish imported at Frankfurt Airport, Germany. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107647] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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29
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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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30
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Molecular identification and temporal genetic differentiation of Cyprinus carpio (Cypriniformes: Cyprinidae) eggs attached on artificial fish nests. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01189-5] [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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31
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Hoffman JC, Meredith C, Pilgrim E, Trebitz A, Hatzenbuhler C, Kelly JR, Peterson G, Lietz J, Okum S, Martinson J. Comparison of Larval Fish Detections Using Morphology-Based Taxonomy versus High-Throughput Sequencing for Invasive Species Early Detection. CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES. JOURNAL CANADIEN DES SCIENCES HALIEUTIQUES ET AQUATIQUES 2021; 78:752-764. [PMID: 35619733 PMCID: PMC9132201 DOI: 10.1139/cjfas-2020-0224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
When first introduced, invasive species typically evade detection; DNA barcoding coupled with high-throughput sequencing (HTS) may be more sensitive and accurate than morphology-based taxonomy, and thereby improve invasive (or rare) species detection. We quantified the relative error of species detection between morphology-based and HTS-based taxonomic identification of ichthyoplankton collections from the Port of Duluth, Minnesota, an aquatic non-native species introduction 'hot-spot' in the Laurentian Great Lakes. We found HTS-based taxonomy identified 28 species and morphology-based taxonomy 30 species, of which 27 were common to both. Among samples, 76% of family-level taxonomic assignments agreed; however, only 42% of species assignments agreed. Most errors were attributed to morphology-based taxonomy, whereas HTS-based taxonomy error was low. For this study system, for most non-native fishes, the detection probability by randomized survey for larvae was similar to that by a survey that is optimized for non-native species early detection of juveniles and adults. We conclude that classifying taxonomic errors by comparing HTS results against morphology-based taxonomy is an important step toward incorporating HTS-based taxonomy into biodiversity surveys.
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Affiliation(s)
- Joel Christopher Hoffman
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Christy Meredith
- Montana Department of Environmental Quality, 1520 E. 6th Avenue, Helena, Montana, 59601, USA
| | - Erik Pilgrim
- US Environmental Protection Agency Office of Research and Development, Watershed and Ecosystem Characterization Division, 26 West Martin Luther King Dr, Cincinnati, Ohio, 45268, USA
| | - Anett Trebitz
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Chelsea Hatzenbuhler
- Badger Technical Services c/o US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - John Russell Kelly
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Gregory Peterson
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Julie Lietz
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Sara Okum
- US Environmental Protection Agency Office of Research and Development, Watershed and Ecosystem Characterization Division, 26 West Martin Luther King Dr, Cincinnati, Ohio, 45268, USA
| | - John Martinson
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 26 West Martin Luther King Dr, Cincinnati, Ohio, 45268, USA
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On the Challenge to Correctly Identify Rasboras (Teleostei: Cyprinidae: Danioninae) Inhabiting the Mesangat Wetlands, East Kalimantan, Indonesia. DIVERSITY 2020. [DOI: 10.3390/d13010008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Within the subfamily Danioninae, rasborine cyprinids are known as a ‘catch-all’ group, diagnosed by only a few characteristics. Most species closely resemble each other in morphology. Species identification is therefore often challenging. In this study, we attempted to determine the number of rasborine species occurring in samples from the Mesangat wetlands in East Kalimantan, Indonesia, by using different approaches. Morphological identification resulted in the distinction of five species (Trigonopoma sp., Rasbora cf. hubbsi Brittan, 1954, R. rutteni Weber and de Beaufort, 1916, R. trilineata Steindachner, 1870, and R. vaillantii, Popta 1905). However, genetic species delimitation methods (Poisson tree processes (PTP) and multi-rate PTP (mPTP)) based on DNA barcodes and principal component analysis (PCA) based on homologous geometric morphometric landmarks, revealed a single cluster for Trigonopoma sp. and R. trilineata, respectively, whereas the remaining traditionally identified species were distinguished neither by DNA barcodes nor by the morphometry approach. A k-mean clustering based on the homologous landmarks divided the sample into 13 clusters and was thus found to be inappropriate for landmark data from species extremely resembling each other in morphology. Due to inconsistent results between the applied methods we refer to the traditional identifications and distinguish five rasborine species for the Mesangat wetlands.
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33
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Naseka AM, Renaud CB. Morphology-based taxonomic re-assessment of the Arctic lamprey, Lethenteron camtschaticum (Tilesius, 1811) and taxonomic position of other members of the genus. Zookeys 2020; 991:1-67. [PMID: 33223898 PMCID: PMC7674401 DOI: 10.3897/zookeys.991.54938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/03/2020] [Indexed: 11/29/2022] Open
Abstract
The lamprey genus Lethenteron Creaser & Hubbs, 1922 is widespread across Eurasia and North America, but the number and distribution of its constituent species is not firmly established. After a morphological examination of extant type material of the currently recognized species and their synonyms, Lethenteronmitsukurii (Hatta, 1901) is resurrected with Le.matsubarai Vladykov & Kott, 1978 as its junior synonym. Amongst nonparasitic species Le.reissneri (Dybowski, 1869) and Le.mitsukurii are confirmed as present in Japan and the former is also present on Sakhalin. An in-depth study of large samples of nonparasitic lamprey adults from Japan and Sakhalin Island is needed to determine whether the lower trunk myomere (< 66) individuals from these areas represent one or more undescribed species, or Le.mitsukurii, or Le.reissneri, or a mixture of these three alternatives. The material from the Anadyr Estuary identified by Berg (1931, 1948) as Lampetrajaponicakessleri has been re-identified as Le.camtschaticum and there is no evidence that Le.kessleri occurs there. Lethenteronreissneri is reported from the Angara River system, Yenisei River drainage, Russia. Lethenteronalaskense Vladykov & Kott, 1978 is provisionally considered to be a junior synonym of Le.kessleri (Anikin, 1905). Petromyzonernstii Dybowski, 1872, Ammocoetesaureus Bean, 1881, Petromyzondentex Anikin, 1905, Lampetramitsukuriimajor Hatta, 1911, and Lampetrajaponicaseptentrionalis Berg, 1931 are junior synonyms of Petromyzonmarinuscamtschaticus Tilesius, 1811. A key is provided to adults of the six species recognized as belonging in the genus Lethenteron.
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Affiliation(s)
- Alexander M Naseka
- Naturhistorisches Museum Wien, Burgring 7, 1010 Vienna, Austria Naturhistorisches Museum Wien Vienna Austria
| | - Claude B Renaud
- Centre for Arctic Knowledge and Exploration, Research & Collections, Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, ON K1P 6P4 Canada Canadian Museum of Nature Ottawa Canada
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May JA, Feng Z, Orton MG, Adamowicz SJ. The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach. J Mol Evol 2020; 88:689-702. [PMID: 33009923 DOI: 10.1007/s00239-020-09967-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 09/22/2020] [Indexed: 11/25/2022]
Abstract
Myriad environmental and biological traits have been investigated for their roles in influencing the rate of molecular evolution across various taxonomic groups. However, most studies have focused on a single trait, while controlling for additional factors in an informal way, generally by excluding taxa. This study utilized a dataset of cytochrome c oxidase subunit I (COI) barcode sequences from over 7000 ray-finned fish species to test the effects of 27 traits on molecular evolutionary rates. Environmental traits such as temperature were considered, as were traits associated with effective population size including body size and age at maturity. It was hypothesized that these traits would demonstrate significant correlations with substitution rate in a multivariable analysis due to their associations with mutation and fixation rates, respectively. A bioinformatics pipeline was developed to assemble and analyze sequence data retrieved from the Barcode of Life Data System (BOLD) and trait data obtained from FishBase. For use in phylogenetic regression analyses, a maximum likelihood tree was constructed from the COI sequence data using a multi-gene backbone constraint tree covering 71% of the species. A variable selection method that included both single- and multivariable analyses was used to identify traits that contribute to rate heterogeneity estimated from different codon positions. Our analyses revealed that molecular rates associated most significantly with latitude, body size, and habitat type. Overall, this study presents a novel and systematic approach for integrative data assembly and variable selection methodology in a phylogenetic framework.
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Affiliation(s)
- Jacqueline A May
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Matthew G Orton
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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35
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Sterling KA, Warren ML. Description of a new species of cryptic snubnose darter (Percidae: Etheostomatinae) endemic to north-central Mississippi. PeerJ 2020; 8:e9807. [PMID: 32944422 PMCID: PMC7469936 DOI: 10.7717/peerj.9807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/03/2020] [Indexed: 11/29/2022] Open
Abstract
Many subclades within the large North American freshwater fish genus Etheostoma (Percidae) show brilliant male nuptial coloration during the spring spawning season. Traditionally, perceived differences in color were often used to diagnose closely related species. More recently, perceived differences in male nuptial color have prompted further investigation of potential biodiversity using genetic tools. However, cryptic diversity among Etheostoma darters renders male nuptial color as unreliable for detecting and describing diversity, which is foundational for research and conservation efforts of this group of stream fishes. Etheostoma raneyi (Yazoo Darter) is an imperiled, range-limited fish endemic to north-central Mississippi. Existing genetic evidence indicates cryptic diversity between disjunctly distributed E. raneyi from the Little Tallahatchie and Yocona river watersheds despite no obvious differences in male color between the two drainages. Analysis of morphological truss and geometric measurements and meristic and male color characters yielded quantitative differences in E. raneyi from the two drainages consistent with genetic evidence. Morphological divergence is best explained by differences in stream gradients between the two drainages. Etheostoma faulkneri, the Yoknapatawpha Darter, is described as a species under the unified species concept. The discovery of cryptic diversity within E. raneyi would likely not have occurred without genetic tools. Cryptic diversity among Etheostoma darters and other stream fishes is common, but an overreliance on traditional methods of species delimitation (e.g., identification of a readily observable physical character to diagnose a species) impedes a full accounting of the diversity in freshwater fishes in the southeastern United States.
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Affiliation(s)
- Ken A Sterling
- USDA Forest Service, Southern Research Station, Stream Ecology Laboratory, Oxford, MS, United States of America
| | - Melvin L Warren
- USDA Forest Service, Southern Research Station, Stream Ecology Laboratory, Oxford, MS, United States of America
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DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01155-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractWithin Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.
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Riva-Rossi C, Barrasso DA, Baker C, Quiroga AP, Baigún C, Basso NG. Revalidation of the Argentinian pouched lamprey Geotria macrostoma (Burmeister, 1868) with molecular and morphological evidence. PLoS One 2020; 15:e0233792. [PMID: 32470001 PMCID: PMC7259705 DOI: 10.1371/journal.pone.0233792] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 05/12/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The Argentinian pouched lamprey, classified as Petromyzon macrostomus Burmeister, 1868 was first described in 1867 in De La Plata River, in Buenos Aires, Argentina, and subsequently recorded in several rivers from Patagonia. Since its original description, the validity of P. macrostomus was questioned by several ichthyologists and 36 years after its original discovery it was considered a junior synonym of Geotria australis Gray, 1851. For a long time, the taxonomic status of G. australis has been uncertain, largely due to the misinterpretations of the morphological alterations that occur during sexual maturation, including the arrangement of teeth, size and position of fins and cloaca, and the development of an exceptionally large gular pouch in males. In this study, the taxonomic status of Geotria from across the "species" range was evaluated using both molecular analysis and examination of morphological characteristics. METHODOLOGY/PRINCIPAL FINDINGS Phylogenetic and species delimitation analyses based on mitochondrial DNA sequences of Cytochrome b (Cyt b) and Cytochrome C Oxidase Subunit 1 (COI) genes, along with morphological analysis of diagnostic characters reported in the original descriptions of the species were used to assess genetic and morphological variation within Geotria and to determine the specific status of the Argentinian lamprey. These analyses revealed that Geotria from Argentina constitutes a well differentiated lineage from Chilean and Australasian populations. The position of the cloaca and the distance between the second dorsal and caudal fins in sub-adult individuals, and at previous life stages, can be used to distinguish between the two species. In addition, the genetic distance between G. macrostoma and G. australis for the COI and Cyt b mitochondrial genes is higher than both intra- and inter-specific distances reported for other Petromyzontiformes. CONCLUSIONS/SIGNIFICANCE Our results indicate that the Argentinian pouched lamprey, found along a broad latitudinal gradient on the south-west Atlantic coast of South America, should be named as Geotria macrostoma (Burmeister, 1868) and not as G. australis Gray 1851, returning to its earliest valid designation in Argentina. Geotria macrostoma can now be considered as the single lamprey species inhabiting Argentinian Patagonia, with distinct local adaptations and evolutionary potential. It is essential that this distinctiveness is recognized in order to guide future conservation and management actions against imminent threats posed by human actions in the major basins of Patagonia.
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Affiliation(s)
- Carla Riva-Rossi
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
| | - Diego Andrés Barrasso
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
- Sección Herpetología, División Zoología Vertebrados, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (UNLP), La Plata, Buenos Aires, Argentina
| | - Cindy Baker
- National Institute of Water & Atmospheric Research Ltd (NIWA), Hamilton, New Zealand
| | - Analía Pamela Quiroga
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
| | - Claudio Baigún
- Instituto de Investigación e Ingeniería Ambiental (CONICET-UNSAM), San Martín, Buenos Aires, Argentina
| | - Néstor Guillermo Basso
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
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Bourret V, Albert V, April J, Côté G, Morissette O. Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation. Evol Appl 2020; 13:1420-1434. [PMID: 32684967 PMCID: PMC7359848 DOI: 10.1111/eva.12977] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.
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Affiliation(s)
- Vincent Bourret
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Vicky Albert
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Julien April
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Guillaume Côté
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Olivier Morissette
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
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Sterling KA, Nielsen SV, Brown AJ, Warren ML, Noonan BP. Cryptic diversity among Yazoo Darters (Percidae: Etheostoma raneyi) in disjunct watersheds of northern Mississippi. PeerJ 2020; 8:e9014. [PMID: 32411520 PMCID: PMC7204820 DOI: 10.7717/peerj.9014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/27/2020] [Indexed: 11/20/2022] Open
Abstract
The Yazoo Darter, Etheostoma raneyi (Percidae), is an imperiled freshwater fish species endemic to tributaries of the Yocona and Little Tallahatchie rivers of the upper Yazoo River basin, in northern Mississippi, USA. The two populations are allopatric, isolated by unsuitable lowland habitat between the two river drainages. Relevant literature suggests that populations in the Yocona River represent an undescribed species, but a lack of data prevents a thorough evaluation of possible diversity throughout the range of the species. Our goals were to estimate phylogenetic relationships of the Yazoo Darter across its distribution and identify cryptic diversity for conservation management purposes. Maximum likelihood (ML) phylogenetic analyses of the mitochondrial cytochrome b (cytb) gene returned two reciprocally monophyletic clades representing the two river drainages with high support. Bayesian analysis of cytb was consistent with the ML analysis but with low support for the Yocona River clade. Analyses of the nuclear S7 gene yielded unresolved relationships among individuals in the Little Tallahatchie River drainage with mostly low support, but returned a monophyletic clade for individuals from the Yocona River drainage with high support. No haplotypes were shared between the drainages for either gene. Additional cryptic diversity within the two drainages was not indicated. Estimated divergence between Yazoo Darters in the two drainages occurred during the Pleistocene (<1 million years ago) and was likely linked to repeated spatial shifts in suitable habitat and changes in watershed configurations during glacial cycles. Individuals from the Yocona River drainage had lower genetic diversity consistent with the literature. Our results indicate that Yazoo Darters in the Yocona River drainage are genetically distinct and that there is support for recognizing Yazoo Darter populations in the Yocona River drainage as a new species under the unified species concept.
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Affiliation(s)
- Ken A Sterling
- USDA Forest Service, Southern Research Station, Stream Ecology Laboratory, Oxford, MS, United States of America
| | - Stuart V Nielsen
- Division of Herpetology, Florida Museum of Natural History, Gainesville, FL, United States of America
| | - Andrew J Brown
- Louisiana Purchase Gardens and Zoo, Monroe, LA, United States of America
| | - Melvin L Warren
- USDA Forest Service, Southern Research Station, Stream Ecology Laboratory, Oxford, MS, United States of America
| | - Brice P Noonan
- Department of Biology, University of Mississippi, University, MS, United States of America
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40
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Gagnaire PA. Comparative genomics approach to evolutionary process connectivity. Evol Appl 2020; 13:1320-1334. [PMID: 32684961 PMCID: PMC7359831 DOI: 10.1111/eva.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/01/2023] Open
Abstract
The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses of species to anthropogenic landscape alterations. Genetic connectivity and its evolutionary outcomes depend on a variety of spatially dependent evolutionary processes, such as population structure, local adaptation, genetic admixture, and speciation. Over the last years, population genomic studies have been interrogating these processes with increasing resolution, revealing a large diversity of species responses to spatially structured landscapes. In parallel, multispecies meta-analyses usually based on low-genome coverage data have provided fundamental insights into the ecological determinants of genetic connectivity, such as the influence of key life history traits on population structure. However, comparative studies still lack a thorough integration of macro- and micro-evolutionary scales to fully realize their potential. Here, I present how a comparative genomics framework may provide a deeper understanding of evolutionary process connectivity. This framework relies on coupling the inference of long-term demographic and selective history with an assessment of the contemporary consequences of genetic connectivity. Standardizing this approach across several species occupying the same landscape should help understand how spatial environmental heterogeneity has shaped the diversity of historical and contemporary connectivity patterns in different taxa with contrasted life history traits. I will argue that a reasonable amount of genome sequence data can be sufficient to resolve and connect complex macro- and micro-evolutionary histories. Ultimately, implementing this framework in varied taxonomic groups is expected to improve scientific guidelines for conservation and management policies.
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Cushman EL, Métris KLK, Kanno Y, Pregler KC, Peoples BK, Darden TL. Optimization of a Suite of Microsatellite Markers for Nocomis leptocephalus (Bluehead Chub) and Genetic Characterization of Two Populations in South Carolina. SOUTHEAST NAT 2020. [DOI: 10.1656/058.019.0202] [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]
Affiliation(s)
- Elizabeth L. Cushman
- South Carolina Department of Natural Resources, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412
| | - Kimberly L. Kanapeckas Métris
- South Carolina Department of Natural Resources, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412
| | - Yoichiro Kanno
- Department of Forestry and Environmental Conservation, Clemson University, 261 Lehotsky Hall, Clemson, SC 29634
| | - Kasey C. Pregler
- Department of Forestry and Environmental Conservation, Clemson University, 261 Lehotsky Hall, Clemson, SC 29634
| | - Brandon K. Peoples
- Department of Forestry and Environmental Conservation, Clemson University, 261 Lehotsky Hall, Clemson, SC 29634
| | - Tanya L. Darden
- South Carolina Department of Natural Resources, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412
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Limmon G, Delrieu-Trottin E, Patikawa J, Rijoly F, Dahruddin H, Busson F, Steinke D, Hubert N. Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia). Ecol Evol 2020; 10:3356-3366. [PMID: 32273993 PMCID: PMC7141007 DOI: 10.1002/ece3.6128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
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Affiliation(s)
- Gino Limmon
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Erwan Delrieu-Trottin
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- Museum für Naturkunde Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der Humboldt-Universität zu Berlin Berlin Germany
| | - Jesaya Patikawa
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Frederik Rijoly
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Hadi Dahruddin
- Division of Zoology Research Center for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia
| | - Frédéric Busson
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN) Muséum National d'Histoire Naturelle Paris France
| | - Dirk Steinke
- Department of Integrative Biology Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
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O'Sullivan AM, Samways KM, Perreault A, Hernandez C, Gautreau MD, Curry RA, Bernatchez L. Space invaders: Searching for invasive Smallmouth Bass ( Micropterus dolomieu) in a renowned Atlantic Salmon ( Salmo salar) river. Ecol Evol 2020; 10:2588-2596. [PMID: 32185004 PMCID: PMC7069312 DOI: 10.1002/ece3.6088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 11/11/2022] Open
Abstract
Humans have the ability to permanently alter aquatic ecosystems and the introduction of species is often the most serious alteration. Non-native Smallmouth Bass (Micropterus dolomieu) were identified in Miramichi Lake c. 2008, which is a headwater tributary to the Southwest Miramichi River, a renowned Atlantic Salmon (Salmo salar) river whose salmon population is dwindling. A containment programme managed by the Department of Fisheries and Oceans, Canada (DFO) was implemented in 2009 to confine Smallmouth Bass (SMB) to the lake. We utilized environmental DNA (eDNA) as a detection tool to establish the potential escape of SMB into the Southwest Miramichi River. We sampled at 26 unique sites within Miramichi Lake, the outlet of Miramichi Lake (Lake Brook), which flows into the main stem Southwest Miramichi River, and the main stem Southwest Miramichi River between August and October 2017. We observed n = 6 positive detections located in the lake, Lake Brook, and the main stem Southwest Miramichi downstream of the lake. No detections were observed upstream of the confluence of Lake Brook and the main stem Southwest Miramichi. The spatial pattern of positive eDNA detections downstream of the lake suggests the presence of individual fish versus lake-sourced DNA in the outlet stream discharging to the main river. Smallmouth Bass were later confirmed by visual observation during a snorkeling campaign, and angling. Our results, both eDNA and visual confirmation, definitively show Smallmouth Bass now occupy the main stem of the Southwest Miramichi.
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Affiliation(s)
- Antóin M. O'Sullivan
- Canadian Rivers InstituteUniversity of New BrunswickFrederictonNBCanada
- Faculty of Forestry and Environmental ManagementUniversity of New BrunswickFrederictonNBCanada
| | - Kurt M. Samways
- Canadian Rivers InstituteUniversity of New BrunswickFrederictonNBCanada
- Department of Biological SciencesUniversity of New BrunswickSaint JohnNBCanada
| | - Alysse Perreault
- Institut de Biologie Intégrative et des Systèmes (IBIS)Pavillon Charles‐Eugène Marchand, Université LavalQuébecQCCanada
| | - Cécilia Hernandez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Pavillon Charles‐Eugène Marchand, Université LavalQuébecQCCanada
| | - Mark D. Gautreau
- Canadian Rivers InstituteUniversity of New BrunswickFrederictonNBCanada
- Department of BiologyUniversity of New BrunswickFrederictonNBCanada
| | - R. Allen Curry
- Canadian Rivers InstituteUniversity of New BrunswickFrederictonNBCanada
- Faculty of Forestry and Environmental ManagementUniversity of New BrunswickFrederictonNBCanada
- Department of BiologyUniversity of New BrunswickFrederictonNBCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Pavillon Charles‐Eugène Marchand, Université LavalQuébecQCCanada
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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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Phillips JD, French SH, Hanner RH, Gillis DJ. HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves. PeerJ Comput Sci 2020; 6:e243. [PMID: 33816897 PMCID: PMC7924493 DOI: 10.7717/peerj-cs.243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/07/2019] [Indexed: 05/25/2023]
Abstract
Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are currently represented by only one or a few sequences in existing databases, which can safely be assumed to be undersampled. Unfortunately, sample sizes of 5-10 specimens per species typically seen in DNA barcoding studies are often insufficient to adequately capture within-species genetic diversity. Here, we introduce a novel iterative extrapolation simulation algorithm of haplotype accumulation curves, called HACSim (Haplotype Accumulation Curve Simulator) that can be employed to calculate likely sample sizes needed to observe the full range of DNA barcode haplotype variation that exists for a species. Using uniform haplotype and non-uniform haplotype frequency distributions, the notion of sampling sufficiency (the sample size at which sampling accuracy is maximized and above which no new sampling information is likely to be gained) can be gleaned. HACSim can be employed in two primary ways to estimate specimen sample sizes: (1) to simulate haplotype sampling in hypothetical species, and (2) to simulate haplotype sampling in real species mined from public reference sequence databases like the Barcode of Life Data Systems (BOLD) or GenBank for any genomic marker of interest. While our algorithm is globally convergent, runtime is heavily dependent on initial sample sizes and skewness of the corresponding haplotype frequency distribution.
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Affiliation(s)
| | - Steven H. French
- School of Computer Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert H. Hanner
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Daniel J. Gillis
- School of Computer Science, University of Guelph, Guelph, Ontario, Canada
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Wang D, Gao L, Tian H, Dong W, Duan X, Liu S, Chen D. Population genetics and sympatric divergence of the freshwater gudgeon, Gobiobotia filifer, in the Yangtze River inferred from mitochondrial DNA. Ecol Evol 2020; 10:50-58. [PMID: 31993113 PMCID: PMC6972953 DOI: 10.1002/ece3.5746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/02/2022] Open
Abstract
The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.
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Affiliation(s)
- Dengqiang Wang
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Lei Gao
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Huiwu Tian
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Weiwei Dong
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
- School of Life ScienceSouthwest UniversityChongqingChina
| | - Xinbin Duan
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Shaoping Liu
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Daqing Chen
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
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Hashimoto S, Py-Daniel LHR, Batista JS. A molecular assessment of species diversity in Tympanopleura and Ageneiosus catfishes (Auchenipteridae: Siluriformes). JOURNAL OF FISH BIOLOGY 2020; 96:14-22. [PMID: 31631341 DOI: 10.1111/jfb.14173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
In order to test the congruence of genetic data to the morphologically defined Neotropical catfish genera Tympanopleura and Ageneiosus and explore species diversity, we generated 17 DNA barcodes from five of six species of Tympanopleura and 12 of 13 species of Ageneiosus. To discriminate limits between species, an automatic barcode gap discovery (ABGD), a generalised mixed yule-coalescent model (GYMC) and fixed distance thresholds Kimura two-parameter (K2P; 3%) were used to discriminate putative species limits from the DNA barcodes. The ABGD, GMYC and K2P methods agreed by each generating 13 clusters: six in Tympanopleura (five nominal plus one undescribed species) and seven in Ageneiosus. These clusters corresponded broadly to the described species, except in the case of the Ageneiosus ucayalensis group (A. akamai, A. dentatus, A. intrusus, A. ucayalensis, A. uranophthalmus and A. vittatus). Haplotype sharing and low divergences may have prevented molecular methods from distinguishing these species. We hypothesise that this is the result of a recent radiation of a sympatric species group distributed throughout the Amazon Basin. One putative new species of Tympanopleura was also supported by the molecular data. These results taken together highlight the utility of molecular methods such as DNA barcoding in understanding patterns of diversification across large geographic areas and in recognising overlooked diversity.
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Affiliation(s)
- Shizuka Hashimoto
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Manaus, Amazonas, Brazil
- Instituto Nacional de Pesquisas da Amazônia, Coleção de Peixes, Programa de Coleções Científicas, Manaus, Amazonas, Brazil
| | - Lúcia H Rapp Py-Daniel
- Instituto Nacional de Pesquisas da Amazônia, Coleção de Peixes, Programa de Coleções Científicas, Manaus, Amazonas, Brazil
| | - Jacqueline S Batista
- Instituto Nacional de Pesquisas da Amazônia, Laboratório Temático de Biologia Molecular, Manaus, Amazonas, Brazil
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Phylogeographic evidence that the distribution of cryptic euryhaline species in the Gambusia punctata species group in Cuba was shaped by the archipelago geological history. Mol Phylogenet Evol 2019; 144:106712. [PMID: 31862460 DOI: 10.1016/j.ympev.2019.106712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/22/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022]
Abstract
The main drivers of diversification of freshwater fishes in Cuba are not yet well understood. For example, salt tolerance was thought as the main factor involved in the diversification of Gambusia punctata species group in this archipelago. However, evidence from a recent DNA barcoding survey suggested the presence of cryptic species and no correlation between species delimitation and level of salinity. In this study, we analyzed the cryptic diversification of G. punctata species group in Cuba, based on a comprehensive sampling of its distribution and including habitats with different salinity levels. We evaluated the patterns of molecular divergence of the samples by sequencing a set of mitochondrial DNA (mtDNA) regions and genotyping nine nuclear microsatellite loci. We also used cytochrome b gene (cytb) partial sequences and these microsatellite loci to analyze population structure inside putative species. Five mtDNA well-differentiated haplogroups were found, four of them also identified by the analysis of the microsatellite polymorphism which corresponds to two already recognized species, G. punctata, and G. rhizophorae, and three putative new species. The extent of hybrid zones between these groups is also described. In each group, populations inhabiting environments with contrasting salinity levels were identified, indicating a generalized trait not specific to G. rhizophorae. The geographic distribution of the groups suggested a strong association with major relict territories of the Cuban Archipelago that was periodically joined or split-up by changes in seawater levels and land uplifts. Salinity tolerance might have facilitated sporadic and long-distance oversea dispersal but did not prevent speciation in the Cuban archipelago.
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Hoy MS, Ostberg CO. Development of two quantitative PCR assays for detection of several Cottus species from environmental DNA in Pacific coast watersheds of North America. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01118-7] [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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50
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Fluker BL, Jones KD, Kuhajda BR. Genetic structure and diversity of the blueface darter Etheostoma cyanoprosopum, a microendemic freshwater fish in the southeastern USA. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00986] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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