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Escobar Camacho D, Barragán KS, Guayasamin JM, Gavilanes G, Encalada AC. New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding. PLoS One 2024; 19:e0298970. [PMID: 38457426 PMCID: PMC10923491 DOI: 10.1371/journal.pone.0298970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024] Open
Abstract
DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.
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Affiliation(s)
- Daniel Escobar Camacho
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Karla S. Barragán
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan M. Guayasamin
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Gabriela Gavilanes
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Andrea C. Encalada
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
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2
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Gonçalves AS, Netto-Ferreira AL, Saldanha SC, Rocha ACG, Gales SM, Silva DJF, Carvalho DC, Sales JBL, Burlamaqui TCT, Ready JS. Convergent and environmentally associated chromatic polymorphism in Bryconops Kner, 1858 (Ostariophysi: Characiformes: Iguanodectidae). PLoS One 2024; 19:e0298170. [PMID: 38358968 PMCID: PMC10868817 DOI: 10.1371/journal.pone.0298170] [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: 06/26/2023] [Accepted: 01/20/2024] [Indexed: 02/17/2024] Open
Abstract
Bryconops Kner, 1858, includes two well defined subgenera based on morphological evidence, with each containing at least one species (B. (Bryconops) caudomaculatus and B. (Creatochanes) melanurus) with a very wide distribution, within which regional populations present color variations. To test if phenotypic variation is related to cladogenetic events, we performed tests for phylogenetic independence and determined the strength of convergence for color characters in relation to water type, as the variation between clear, black and white waters is considered to be one of the major driving forces in the evolution of Amazonian fishes. Color characters for fins above the median line of the body were generally found to be independent from phylogeny and the Wheatsheaf test strongly supports convergence of the dorsal fin color between populations of species in the same type of water, with a similar trend suggested for the color of the dorsal lobe of the caudal fin. This means that simple color characters cannot necessarily be relied upon for taxonomic revisions of the genus as local phenotypic variants may represent environmentally determined plasticity or convergent evolution. Further studies are required to determine the validity of these characters.
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Affiliation(s)
- Andressa S. Gonçalves
- Group for Integrated Biological Investigation (GIBI), Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), Belém, Pará, Brazil
| | - André L. Netto-Ferreira
- Laboratory of Ichthyology, Zoology Department, Biological Sciences Institute, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Samantha C. Saldanha
- Group for Integrated Biological Investigation (GIBI), Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), Belém, Pará, Brazil
| | - Ana C. G. Rocha
- Group for Integrated Biological Investigation (GIBI), Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), Belém, Pará, Brazil
| | - Suellen M. Gales
- Group for Integrated Biological Investigation (GIBI), Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), Belém, Pará, Brazil
| | - Derlan J. F. Silva
- Group for Integrated Biological Investigation (GIBI), Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), Belém, Pará, Brazil
| | - Daniel C. Carvalho
- Laboratório de Genética da Conservação, Programa de Pós Graduação em Biologia dos Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - João B. L. Sales
- Group for Integrated Biological Investigation (GIBI), Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), Belém, Pará, Brazil
| | - Tibério C. T. Burlamaqui
- Group for Integrated Biological Investigation (GIBI), Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), Belém, Pará, Brazil
- Instituto Tecnologico Vale, Belém, Pará, Brazil
| | - Jonathan S. Ready
- Group for Integrated Biological Investigation (GIBI), Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), Belém, Pará, Brazil
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Robillard AJ, Trizna MG, Ruiz‐Tafur M, Dávila Panduro EL, de Santana CD, White AE, Dikow RB, Deichmann JL. Application of a deep learning image classifier for identification of Amazonian fishes. Ecol Evol 2023; 13:e9987. [PMID: 37143991 PMCID: PMC10151603 DOI: 10.1002/ece3.9987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/10/2023] [Accepted: 03/24/2023] [Indexed: 05/06/2023] Open
Abstract
Given the sharp increase in agricultural and infrastructure development and the paucity of widespread data available to support conservation management decisions, a more rapid and accurate tool for identifying fish fauna in the world's largest freshwater ecosystem, the Amazon, is needed. Current strategies for identification of freshwater fishes require high levels of training and taxonomic expertise for morphological identification or genetic testing for species recognition at a molecular level. To overcome these challenges, we built an image masking model (U-Net) and a convolutional neural net (CNN) to classify Amazonian fish in photographs. Fish used to generate training data were collected and photographed in tributaries in seasonally flooded forests of the upper Morona River valley in Loreto, Peru in 2018 and 2019. Species identifications in the training images (n = 3068) were verified by expert ichthyologists. These images were supplemented with photographs taken of additional Amazonian fish specimens housed in the ichthyological collection of the Smithsonian's National Museum of Natural History. We generated a CNN model that identified 33 genera of fishes with a mean accuracy of 97.9%. Wider availability of accurate freshwater fish image recognition tools, such as the one described here, will enable fishermen, local communities, and citizen scientists to more effectively participate in collecting and sharing data from their territories to inform policy and management decisions that impact them directly.
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Affiliation(s)
- Alexander J. Robillard
- Data Science LabOffice of the Chief Information Officer, Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
- Center for Conservation and SustainabilitySmithsonian National Zoo and Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
- Chesapeake Biological LaboratoryUniversity of Maryland Center for Environmental ScienceSolomonsMarylandUSA
| | - Michael G. Trizna
- Data Science LabOffice of the Chief Information Officer, Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Morgan Ruiz‐Tafur
- Center for Conservation and SustainabilitySmithsonian National Zoo and Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
- Laboratorio de Taxonomía de PecesInstituto de Investigaciones de la Amazonía Peruana (IIAP)San Juan BautistaPeru
| | - Edgard Leonardo Dávila Panduro
- Center for Conservation and SustainabilitySmithsonian National Zoo and Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
| | - C. David de Santana
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Alexander E. White
- Data Science LabOffice of the Chief Information Officer, Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Rebecca B. Dikow
- Data Science LabOffice of the Chief Information Officer, Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Jessica L. Deichmann
- Center for Conservation and SustainabilitySmithsonian National Zoo and Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
- Working Land and Seascapes, Conservation CommonsSmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
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Aguirre WE, Alvarez‐Mieles G, Anaguano‐Yancha F, Burgos Morán R, Cucalón RV, Escobar‐Camacho D, Jácome‐Negrete I, Jiménez Prado P, Laaz E, Miranda‐Troya K, Navarrete‐Amaya R, Nugra Salazar F, Revelo W, Rivadeneira JF, Valdiviezo Rivera J, Zárate Hugo E. Conservation threats and future prospects for the freshwater fishes of Ecuador: A hotspot of Neotropical fish diversity. JOURNAL OF FISH BIOLOGY 2021; 99:1158-1189. [PMID: 34235726 PMCID: PMC8518725 DOI: 10.1111/jfb.14844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/04/2021] [Accepted: 07/04/2021] [Indexed: 06/01/2023]
Abstract
Freshwater fish communities in Ecuador exhibit some of the highest levels of diversity and endemism in the Neotropics. Unfortunately, aquatic ecosystems in the country are under serious threat and conditions are deteriorating. In 2018-19, the government of Ecuador sponsored a series of workshops to examine the conservation status of Ecuador's freshwater fishes. Concerns were identified for 35 species, most of which are native to the Amazon region, and overfishing of Amazonian pimelodid catfishes emerged as a major issue. However, much of the information needed to make decisions across fish groups and regions was not available, hindering the process and highlighting the need for a review of the conservation threats to Ecuador's freshwater fishes. Here, we review how the physical alteration of rivers, deforestation, wetland and floodplain degradation, agricultural and urban water pollution, mining, oil extraction, dams, overfishing, introduced species and climate change are affecting freshwater fishes in Ecuador. Although many of these factors affect fishes throughout the Neotropics, the lack of data on Ecuadorian fish communities is staggering and highlights the urgent need for more research. We also make recommendations, including the need for proper enforcement of existing environmental laws, restoration of degraded aquatic ecosystems, establishment of a national monitoring system for freshwater ecosystems, investment in research to fill gaps in knowledge, and encouragement of public engagement in citizen science and conservation efforts. Freshwater fishes are an important component of the cultural and biological legacy of the Ecuadorian people. Conserving them for future generations is critical.
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Affiliation(s)
- Windsor E. Aguirre
- Department of Biological SciencesDePaul UniversityChicagoIllinoisUSA
- Instituto Nacional de BiodiversidadQuitoEcuador
- Field Museum of Natural HistoryChicagoIllinoisUSA
| | | | | | | | - Roberto V. Cucalón
- Department of Biological SciencesDePaul UniversityChicagoIllinoisUSA
- Present address:
Program in Ecology, Evolution, and Conservation BiologyUniversity of Illinois at Urbana‐ChampaignChampaignIllinoisUSA
| | | | - Iván Jácome‐Negrete
- Facultad de Ciencias Biológicas, Instituto de Estudios Amazónicos e InsularesUniversidad Central del EcuadorQuitoEcuador
| | - Pedro Jiménez Prado
- Pontificia Universidad Católica del Ecuador Sede EsmeraldasEsmeraldasEcuador
- Área de Ecología, Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de HuescaUniversidad de ZaragozaHuescaSpain
| | - Enrique Laaz
- Instituto Público de Investigación de Acuicultura y PescaGuayaquilEcuador
| | | | | | - Fredy Nugra Salazar
- ONG Bosque Medicinal, ONG Forest.inkGualaquizaEcuador
- Laboratorio de Limnología de la Universidad del AzuayCuencaEcuador
| | - Willan Revelo
- Unidad de Recursos Demersales Bentónicos de Agua Dulce y EmbalsesInstituto Público de Investigación de Acuicultura y PescaGuayaquilEcuador
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de Santana CD, Parenti LR, Dillman CB, Coddington JA, Bastos DA, Baldwin CC, Zuanon J, Torrente-Vilara G, Covain R, Menezes NA, Datovo A, Sado T, Miya M. The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes. Sci Rep 2021; 11:18159. [PMID: 34518574 PMCID: PMC8438044 DOI: 10.1038/s41598-021-97128-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.
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Affiliation(s)
- C David de Santana
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA.
| | - Lynne R Parenti
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Casey B Dillman
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Douglas A Bastos
- Programa de Pós-Graduação em Ciências Biológicas (BADPI), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Carole C Baldwin
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Gislene Torrente-Vilara
- Instituto do Mar, Universidade Federal de São Paulo, Campus Baixada Santista, Santos, São Paulo, Brazil
| | - Raphaël Covain
- Museum of Natural History, Department of Herpetology and Ichthyology, route de Malagnou 1, PO Box 6434, 1211, Geneva 6, Switzerland
| | - Naércio A Menezes
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - Aléssio Datovo
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - T Sado
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
| | - M Miya
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
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García-Melo JE, Oliveira C, Da Costa Silva GJ, Ochoa-Orrego LE, Garcia Pereira LH, Maldonado-Ocampo JA. Species delimitation of neotropical Characins (Stevardiinae): Implications for taxonomy of complex groups. PLoS One 2019; 14:e0216786. [PMID: 31166941 PMCID: PMC6550444 DOI: 10.1371/journal.pone.0216786] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 04/29/2019] [Indexed: 12/21/2022] Open
Abstract
Accurate species delimitation is crucial for studies of phylogeny, phylogeography, ecology, conservation and biogeography. The limits of species and genera in the Characidae family are controversial due to its uncertain phylogenetic relationships, high level of morphological homoplasy and the use of ambiguous morphological characters for descriptions. Here we establish species boundaries for Bryconamericus, Hemibrycon, Knodus and Eretmobrycon (Stevardiinae: Characidae), previously diagnosed with morphology, using three different barcoding approaches (GMYC, PTP, ABGD). Results revealed that species delimitation was successful by the use of a single-gene approach and by following a workflow in the context of integrative taxonomy, making evident problems and mistakes in the cataloging of Characidae species. Hence, it was possible to infer boundaries at genus level for clusters in the trees (GMYC and PTP) and automatic partitions (ABGD) which were consistent with some of recent taxonomic changes proposed in Characidae. We found that discordance cases between methods were linked to limitations of the methods and associated to putative species cluster closely related, some historically problematic in their diagnosis and identification. Furthermore, we suggested taxonomic changes and possibly new species, revealing a high degree of hidden diversity. Finally, we propose a workflow as a fast, accurate and objective way to delimit species from mitochondrial DNA sequences and to help clarify the classification of this group.
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Affiliation(s)
- Jorge E. García-Melo
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Campus de Botucatu, Botucatu, SP, Brazil
| | - Guilherme José Da Costa Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Campus de Botucatu, Botucatu, SP, Brazil
- Universidade Santo Amaro, Rua Prof. Enéas de Siqueira Neto, Jardim das Imbuias, São Paulo—SP, Brazil
| | - Luz E. Ochoa-Orrego
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Campus de Botucatu, Botucatu, SP, Brazil
| | - Luiz Henrique Garcia Pereira
- Centro de Ciências da Vida e da Natureza, Universidade Federal da Integração Latino-Americana–UNILA, Foz do Iguaçu, Paraná, Brazil
| | - Javier A. Maldonado-Ocampo
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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Keskar A, Raghavan R, Paingankar MS, Kumkar P, Katwate U, Jadhav S, Padhye A, Dahanukar N. Molecular phylogeny unveils hidden diversity of hillstream loaches (Cypriniformes: Cobitoidea) in the northern Western Ghats of India. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Hidden species diversity in Sylvirana nigrovittata (Amphibia: Ranidae) highlights the importance of taxonomic revisions in biodiversity conservation. PLoS One 2018. [PMID: 29538432 PMCID: PMC5851555 DOI: 10.1371/journal.pone.0192766] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Accurately delimiting species and their geographic ranges is imperative for conservation, especially in areas experiencing rapid habitat loss. Southeast Asia currently has one of the highest rates of deforestation in the world, is home to multiple biodiversity hotspots, and the majority of its countries have developing economies with limited resources for biodiversity conservation. Thus, accurately delimiting species and their ranges is particularly important in this region. We examined genetic and morphological variation in the widespread frog species Sylvirana nigrovittata (and its long-treated junior synonym S. mortenseni) with the goal of clarifying its taxonomic content and geographic range boundaries for conservation. We present evidence that the current concept of S. nigrovittata contains at least eight species, two of which are each known from only two localities, but that S. mortenseni is more geographically widespread than currently realized. Five of these species are described as new to science.
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Campbell DC, Piller KR. Let's jump in: A phylogenetic study of the great basin springfishes and poolfishes, Crenichthys and Empetrichthys (Cyprinodontiformes: Goodeidae). PLoS One 2017; 12:e0185425. [PMID: 29077708 PMCID: PMC5659628 DOI: 10.1371/journal.pone.0185425] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/12/2017] [Indexed: 12/04/2022] Open
Abstract
North America's Great Basin has long been of interest to biologists due to its high level of organismal endemicity throughout its endorheic watersheds. One example of such a group is the subfamily Empetricthyinae. In this paper, we analyzed the relationships of the Empetrichtyinae and assessed the validity of the subspecies designations given by Williams and Wilde within the group using concatenated phylogenetic tree estimation and species tree estimation. Samples from 19 populations were included covering the entire distribution of the three extant species of Empetricthyinae-Crenichthys nevadae, Crenichthys baileyi and Empetricthys latos. Three nuclear introns (S8 intron 4, S7 intron 1, and P0 intron 1) and one mitochondrial gene (Cytb) were sequenced for phylogenetic analysis. Using these sequences, we generated two separate hypotheses of the evolutionary relationships of Empetrichtyinae- one based on the mitochondrial data and one based on the nuclear data using Bayesian phylogenetics. Haplotype networks were also generated to look at the relationships of the populations within Empetrichthyinae. After comparing the two phylogenetic hypotheses, species trees were generated using *BEAST with the nuclear data to further test the validity of the subspecies within Empetrichthyinae. The mitochondrial analyses supported four lineages within C. baileyi and 2 within C. nevadae. The concatenated nuclear tree was more conserved, supporting one clade and an unresolved polytomy in both species. The species tree analysis supported the presence of two species within both C. baileyi and C. nevadae. Based on the results of these analyses, the subspecies designations of Williams and Wilde are not valid, rather a conservative approach suggests there are two species within C. nevadae and two species within C. baileyi. No structure was found for E. latos or the populations of Empetricthyinae. This study represents one of many demonstrating the invalidity of subspecies and their detriment to species identification, conservation, and understanding.
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Affiliation(s)
- D. Cooper Campbell
- Southeastern Louisiana University, Dept. of Biological Sciences, Hammond,United States of America
| | - Kyle R. Piller
- Southeastern Louisiana University, Dept. of Biological Sciences, Hammond,United States of America
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Melo BF, Ochoa LE, Vari RP, Oliveira C. Cryptic species in the Neotropical fish genusCurimatopsis(Teleostei, Characiformes). ZOOL SCR 2016. [DOI: 10.1111/zsc.12178] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Bruno F. Melo
- Departamento de Morfologia, Instituto de Biociências; Universidade Estadual Paulista; Distr. Rubião Jr. s/n 18618-970 Botucatu São Paulo Brazil
- Department of Vertebrate Zoology; National Museum of Natural History, Smithsonian Institution; 20013-7012 Washington DC USA
| | - Luz E. Ochoa
- Departamento de Morfologia, Instituto de Biociências; Universidade Estadual Paulista; Distr. Rubião Jr. s/n 18618-970 Botucatu São Paulo Brazil
| | - Richard P. Vari
- Department of Vertebrate Zoology, MCR-159; National Museum of Natural History, Smithsonian Institution; PO Box 37012 20013-7012 Washington DC USA
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências; Universidade Estadual Paulista; Distr. Rubião Jr. s/n 18618-970 Botucatu São Paulo Brazil
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