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Cahill AE, Meglécz E, Chenuil A. Scientific history, biogeography, and biological traits predict presence of cryptic or overlooked species. Biol Rev Camb Philos Soc 2024; 99:546-561. [PMID: 38049930 DOI: 10.1111/brv.13034] [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: 01/03/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023]
Abstract
Genetic data show that many nominal species are composed of more than one biological species, and thus contain cryptic species in the broad sense (including overlooked species). When ignored, cryptic species generate confusion which, beyond biodiversity or vulnerability underestimation, blurs our understanding of ecological and evolutionary processes and may impact the soundness of decisions in conservation or medicine. However, very few hypotheses have been tested about factors that predispose a taxon to contain cryptic or overlooked species. To fill this gap, we surveyed the literature on free-living marine metazoans and built two data sets, one of 187,603 nominal species and another of 83 classes or phyla, to test several hypotheses, correcting for sequence data availability, taxon size and phylogenetic relatedness. We found a strong effect of scientific history: the probability of a taxon containing cryptic species was highest for the earliest described species and varied among time periods potentially consistently with an influence of prevailing scientific theories. The probability of cryptic species being present was also increased for species with large distribution ranges. They were more frequent in the north polar and south polar zones, contradicting previous predictions of more cryptic species in the tropics, and supporting the hypothesis that many cryptic species diverged recently. The number of cryptic species varied among classes, with an excess in hydrozoans and polychaetes, and a deficit in actinopterygians, for example, but precise class ranking was relatively sensitive to the statistical model used. For all models, biological traits, rather than phylum, appeared responsible for the variation among classes: there were fewer cryptic species than expected in classes with hard skeletons (perhaps because they provide good characters for taxonomy) and image-forming vision (in which selection against heterospecific mating may enhance morphological divergence), and more in classes with internal fertilisation. We estimate that among marine free-living metazoans, several thousand additional cryptic species complexes could be identified as more sequence data become available. The factors identified as important for marine animal cryptic species are likely important for other biomes and taxa and should aid many areas in biology that rely on accurate species identification.
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Affiliation(s)
- Abigail E Cahill
- Biology Department, Albion College, 611 East Porter St., Albion, MI, 49224, USA
| | - Emese Meglécz
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Station Marine d'Endoume, Chemin de la Batterie des Lions, Marseille, 13007, France
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Station Marine d'Endoume, Chemin de la Batterie des Lions, Marseille, 13007, France
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2
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Cutmore SC, Corner RD, Cribb TH. Morphological constraint obscures richness: a mitochondrial exploration of cryptic richness in Transversotrema (Trematoda: Transversotrematidae). Int J Parasitol 2023; 53:595-635. [PMID: 37488048 DOI: 10.1016/j.ijpara.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/26/2023]
Abstract
Species of Transversotrema Witenberg, 1944 (Transversotrematidae) occupy a unique ecological niche for the Trematoda, living externally under the scales of their teleost hosts. Previous studies of the genus have been impeded partly by limited variation in ribosomal DNA sequence data between closely related species and partly by a lack of morphometrically informative characters. Here, we assess richness of the tropical Indo-west Pacific species through parallel phylogenetic and morphometric analyses, generating cytochrome c oxidase subunit 1 mitochondrial sequence data and morphometric data for hologenophore specimens from Australia, French Polynesia, Japan and Palau. These analyses demonstrate that molecular data provide the only reliable basis for species identification; host distribution, and to a lesser extent morphology, are useful for identifying just a few species of Transversotrema. We infer that a combination of morphological simplicity and infection site constraint has led to the group displaying exceptionally low morphological diversification. Phylogenetic analyses of the mitochondrial data broadly support previous systematic interpretations based on ribosomal data, but also demonstrate the presence of several morphologically and ecologically cryptic species. Ten new species are described, eight from the Great Barrier Reef, Australia (Transversotrema chrysallis n. sp., Transversotrema daphnidis n. sp., Transversotrema enceladi n. sp., Transversotrema hyperionis n. sp., Transversotrema iapeti n. sp., Transversotrema rheae n. sp., Transversotrema tethyos n. sp., and Transversotrema titanis n. sp.) and two from off Japan (Transversotrema methones n. sp. and Transversotrema panos n. sp.). There are now 26 Transversotrema species known from Australian marine fishes, making it the richest trematode genus for the fauna.
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Affiliation(s)
- Scott C Cutmore
- Queensland Museum, Biodiversity and Geosciences Program, South Brisbane, Queensland 4101, Australia.
| | - Richard D Corner
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia
| | - Thomas H Cribb
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia
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3
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Hartebrodt L, Wilson S, Costello MJ. Progress in the discovery of isopods (Crustacea: Peracarida)-is the description rate slowing down? PeerJ 2023; 11:e15984. [PMID: 37692117 PMCID: PMC10484202 DOI: 10.7717/peerj.15984] [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: 01/16/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
Taxonomic species are the best standardised metric of biodiversity. Therefore, there is broad scientific and public interest in how many species have already been named and how many more may exist. Crustaceans comprise about 6% of all named animal species and isopods about 15% of all crustaceans. Here, we review progress in the naming of isopods in relation to the number of people describing new species and estimate how many more species may yet be named by 2050 and 2100, respectively. In over two and a half centuries of discovery, 10,687 isopod species in 1,557 genera and 141 families have been described by 755 first authors. The number of authors has increased over time, especially since the 1950s, indicating increasing effort in the description of new species. Despite that the average number of species described per first author has declined since the 1910s, and the description rate has slowed down over the recent decades. Authors' publication lifetimes did not change considerably over time, and there was a distinct shift towards multi-authored publications in recent decades. Estimates from a non-homogeneous renewal process model predict that an additional 660 isopod species will be described by 2100, assuming that the rate of description continues at its current pace.
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Affiliation(s)
- Lena Hartebrodt
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Simon Wilson
- School of Computer Science and Statistics, University of Dublin, Trinity College, Dublin, Ireland
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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5
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Marrón-Becerra A, Hermoso-Salazar M. Morphological comparison and description of five new species of Hyalella (Crustacea: Amphipoda) from Veracruz and Mexico City. J NAT HIST 2022. [DOI: 10.1080/00222933.2022.2078241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Aurora Marrón-Becerra
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico
| | - Margarita Hermoso-Salazar
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Tlalpan, Ciudad de México, Mexico
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Beer A, Burns E, Randhawa HS. Natural history collections: collaborative opportunities and important sources of information about helminth biodiversity in New Zealand. NEW ZEALAND JOURNAL OF ZOOLOGY 2022. [DOI: 10.1080/03014223.2022.2067190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | | | - Haseeb S. Randhawa
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
- South Atlantic Environmental Research Institute, Stanley, Falkland Islands
- New Brunswick Museum, Saint John, Canada
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Analysis of biodiversity data suggests that mammal species are hidden in predictable places. Proc Natl Acad Sci U S A 2022; 119:e2103400119. [PMID: 35344422 PMCID: PMC9168487 DOI: 10.1073/pnas.2103400119] [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] [Indexed: 11/24/2022] Open
Abstract
Only an estimated 1 to 10% of Earth’s species have been formally described. This discrepancy between the number of species with a formal taxonomic description and actual number of species (i.e., the Linnean shortfall) hampers research across the biological sciences. To explore whether the Linnean shortfall results from poor taxonomic practice or not enough taxonomic effort, we applied machine-learning techniques to build a predictive model to identify named species that are likely to contain hidden diversity. Results indicate that small-bodied species with large, climatically variable ranges are most likely to contain hidden species. These attributes generally match those identified in the taxonomic literature, indicating that the Linnean shortfall is caused by societal underinvestment in taxonomy rather than poor taxonomic practice. Research in the biological sciences is hampered by the Linnean shortfall, which describes the number of hidden species that are suspected of existing without formal species description. Using machine learning and species delimitation methods, we built a predictive model that incorporates some 5.0 × 105 data points for 117 species traits, 3.3 × 106 occurrence records, and 9.1 × 105 gene sequences from 4,310 recognized species of mammals. Delimitation results suggest that there are hundreds of undescribed species in class Mammalia. Predictive modeling indicates that most of these hidden species will be found in small-bodied taxa with large ranges characterized by high variability in temperature and precipitation. As demonstrated by a quantitative analysis of the literature, such taxa have long been the focus of taxonomic research. This analysis supports taxonomic hypotheses regarding where undescribed diversity is likely to be found and highlights the need for investment in taxonomic research to overcome the Linnean shortfall.
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New collections of blood flukes (Aporocotylidae) from fishes of the tropical Indo-west Pacific, including a new genus, two new species and molecular evidence that Elaphrobates chaetodontis (Yamaguti, 1970) is widespread in the region. Parasitol Int 2022; 88:102565. [PMID: 35218938 DOI: 10.1016/j.parint.2022.102565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/20/2022] [Indexed: 11/24/2022]
Abstract
We report new collections of the Aporocotylidae from Australia, French Polynesia, and Japan. A new species of Cardicola Short, 1953 is described from Scomberomorus commerson (Lacépède) (Scombridae), off Lizard Island. Cardicola nolani n. sp. can be distinguished from its congeners based on the position of the oötype, the position of the male genital pore, and the absence of an oral sucker. A new species is described from Abalistes stellatus (Anonymous) (Balistidae), also from off Lizard Island. Phylogenetically the new species forms a strongly-supported clade with Cardicola yuelao Yong, Cutmore & Cribb, 2018, which also infects balistids. These two species are distinct from all other aporocotylids in the combination of exceptionally short anterior and long posterior caeca, a lanceolate body, a single testis, an entirely post-ovarian uterus and the position of the oötype; a new genus, Balistidicola, is proposed for them. Balistidicola corneri n. sp. and B. yuelao (Yong, Cutmore & Cribb, 2018) n. comb. are essentially morphologically cryptic, only distinguishable by the form of the spination (B. corneri has five spines per row and B. yuelao has six). Elaphrobates chaetodontis (Yamaguti, 1970) is reported from 21 species of butterflyfishes (Chaetodontidae) from nine locations in tropical Indo-west Pacific; cox1 sequence data demonstrate extensive geographical structuring in this species. Braya jexi Nolan & Cribb, 2006, Elaphrobates milleri (Nolan & Cribb, 2006), and P. corventum Overstreet & Køie, 1989 are each re-reported from their type-hosts, and Pearsonellum pygmaeus Nolan & Cribb, 2004 and Balistidicola yuelao are each reported from a new host.
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Sousa-Paula LCD, Pessoa FAC, Otranto D, Dantas-Torres F. Beyond taxonomy: species complexes in New World phlebotomine sand flies. MEDICAL AND VETERINARY ENTOMOLOGY 2021; 35:267-283. [PMID: 33480064 DOI: 10.1111/mve.12510] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
A species complex (= species group, species series) is an assemblage of species, which are related morphologically and phylogenetically. Recent research has revealed several arthropod vector species that were believed to be a single nominal species actually representing a group of closely related species, which are sometimes morphologically indistinguishable at one or more developmental stages. In some instances, differences in terms of vector competence, capacity, or both have been recorded. It highlights the importance of detecting and studying species complexes to improve our understanding of pathogen transmission patterns, which may be vectored more or less efficiently by different species within the complex. Considering more than 540 species, about one-third of the phlebotomine sand flies in the New World present males and/or females morphologically indistinguishable to one or more species. Remarkably, several of these species may act in transmission of pathogenic agents. In this article, we review recent research on species complexes in phlebotomine sand flies from the Americas. Possible practical implications of recently acquired knowledge and future research needs are also discussed.
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Affiliation(s)
- L C de Sousa-Paula
- Laboratory of Immunoparasitology, Department of Immunology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (FIOCRUZ), Recife, Pernambuco, Brazil
| | - F A C Pessoa
- Laboratório de Ecologia e Doenças Transmissíveis na Amazônia, Leônidas e Maria Deane Institute, Oswaldo Cruz Foundation (FIOCRUZ), Manaus, Amazonas, Brazil
| | - D Otranto
- Parasitology Unit, Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - F Dantas-Torres
- Laboratory of Immunoparasitology, Department of Immunology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (FIOCRUZ), Recife, Pernambuco, Brazil
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10
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Walters AD, Cannizzaro AG, Trujillo DA, Berg DJ. Addressing the Linnean shortfall in a cryptic species complex. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Biodiversity is being lost at an alarming rate, but the rate of this loss is likely to be underestimated as a result of a deficit in taxonomic knowledge (i.e. the Linnean shortfall). This knowledge gap is more extensive for morphologically indistinct taxa. The advancement of molecular techniques and delimitation methods has facilitated the identification of such cryptic species, but a majority of these taxa remain undescribed. To investigate the effects of taxonomic uncertainty on understanding of biodiversity, we applied the general lineage concept of species to an amphipod species complex, the Gammaruslacustris lineage that occupies springs of the northern Chihuahuan Desert, which is emerging in contemporary times. We investigated species boundaries using a validation-based approach and examined genetic structure of the lineage using a suite of microsatellite markers to identify independently evolving metapopulations. Our results show that each spring contains a genetically distinct population that is geographically isolated from other springs, suggesting evolutionary independence and status as separate species. Additionally, we observed subtle interspecific morphological variation among the putative species. We used multiple lines of evidence to formally describe four new species (Gammarus langi sp. nov., G. percalacustris sp. nov., G. colei sp. nov. and G. malpaisensis sp. nov.) endemic to the northern Chihuahuan Desert. Cryptic speciation is likely to be high in other aquatic taxa within these ecosystems, and across arid landscapes throughout North America and elsewhere, suggesting that the magnitude of the Linnean shortfall is currently underestimated in desert springs worldwide.
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Affiliation(s)
| | | | | | - David J Berg
- Department of Biology, Miami University, Hamilton, OH USA
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11
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Neves JMM, Almeida JPFA, Sturaro MJ, FabrÉ NN, Pereira RJ, Mott T. Deep genetic divergence and paraphyly in cryptic species of Mugil fishes (Actinopterygii: Mugilidae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1729892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Jessika M. M. Neves
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - JoÃo P. F. A. Almeida
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Marcelo J. Sturaro
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Nidia N. FabrÉ
- Laboratório de Ecologia, Peixes e Pesca, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Ricardo J. Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - TamÍ Mott
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
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12
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Kerkhove TRH, Boyen J, De Backer A, Mol JH, Volckaert FAM, Leliaert F, De Troch M. Multilocus data reveal cryptic species in the Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Decapoda). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe recognition of cryptic biodiversity provides valuable insights for the management of exploited species. The Atlantic seabob shrimp (Xiphopenaeus kroyeri) is a commercially important fishery resource in the Guianan ecoregion, South America. Previous research in Brazil suggested the presence of cryptic species within the genus. Here, we confirm this presence and delimit the species by applying a multilocus approach based on two mitochondrial (COI and cytb) and two nuclear (PEPCK and NaK) genes. Species boundaries were tested using BPP, GMYC and bPTP delimitation algorithms. These analyses provided strong support for three clades within the genus Xiphopenaeus, including one undescribed clade, which occurs sympatrically with X. kroyeri in the Western Atlantic. Unexpectedly, this undescribed clade is more closely related to the Pacific Xiphopenaeus riveti than to their Atlantic congener. Our DNA-based species delimitation was further supported by new ecological information on habitat and morphology (colour). We also expand the known distribution range of the cryptic species, currently restricted to Brazil, to include French Guiana, Suriname and Colombia. Our findings have important consequences for the management of the species, in terms of both biodiversity management and fisheries management.
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Affiliation(s)
- Thomas R H Kerkhove
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
| | - Jens Boyen
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
| | - Annelies De Backer
- Institute for Agricultural and Fisheries Research (ILVO), Animal Sciences, Bio-Environmental Research Group, Ankerstraat, Ostend, Belgium
| | - Jan H Mol
- Anton de Kom University of Suriname, Faculty of Mathematics and Natural Sciences, Department of Biology, Leysweg, Postbus, Paramaribo, Suriname
| | - Filip A M Volckaert
- University of Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Ch. Deberiotstraat, Leuven, Belgium
| | - Frederik Leliaert
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
- Meise Botanic Garden, Nieuwelaan, Meise, Belgium
| | - Marleen De Troch
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
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Poulin R, Hay E, Jorge F. Taxonomic and geographic bias in the genetic study of helminth parasites. Int J Parasitol 2019; 49:429-435. [PMID: 30797772 DOI: 10.1016/j.ijpara.2018.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 11/25/2022]
Abstract
The use of genetic information is now fundamental in parasite taxonomy and systematics, for resolving parasite phylogenies, discovering cryptic species, and elucidating patterns of gene flow among parasite populations. The accumulation of available gene sequences per geographical area or per parasite taxonomic group is likely proportional to species richness, but not without some biases. Certain areas and certain taxonomic groups receive more research effort than others, possibly causing a deficit in the relative number of parasite species being characterized genetically in some areas or taxonomic groups. Here, we use data on the number of parasite records per country or helminth family from the London Natural History Museum host-parasite database, and matching data on the number of gene sequences available from the National Center for Biotechnology Information (NCBI) GenBank database, to determine how available gene sequences scale with species richness across countries or parasitic helminth families. Our quantitative analysis identified countries/regions of the world and helminth families that have received the most effort in genetic research. More importantly, it allowed us to generate lists (based on residuals from the statistical model) of the 20 countries/regions and the 20 helminth families with the largest deficit in available gene sequences relative to their helminth species richness. We propose these lists as useful guides toward future allocation of effort to maximise advances in parasite biodiscovery, systematics and population structure.
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Affiliation(s)
- Robert Poulin
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
| | - Eleanor Hay
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Fátima Jorge
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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Pinacho-Pinacho CD, García-Varela M, Sereno-Uribe AL, Pérez-Ponce de León G. A hyper-diverse genus of acanthocephalans revealed by tree-based and non-tree-based species delimitation methods: Ten cryptic species of Neoechinorhynchus in Middle American freshwater fishes. Mol Phylogenet Evol 2018; 127:30-45. [PMID: 29783021 DOI: 10.1016/j.ympev.2018.05.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/12/2018] [Accepted: 05/17/2018] [Indexed: 12/20/2022]
Abstract
The genus Neoechinorhynchus represents a hyper-diverse group of acanthocephalans, parasites of fresh and brackish water fish and freshwater turtles, with approximately 116 species described worldwide. Forty-nine species have been recorded in the Americas, nine of them in Middle America. Even though species delimitation methods using DNA sequences have been rarely used for parasitic helminths, the genetic library for species of Neoechinorhynchus has grown in the past few years, enhancing the possibility of using these methods for inferring evolutionary relationships and for establishing more robust species boundaries. In this study, we used non-tree-based and tree-based methods through a coalescent approach to explore the species limits of specimens of Neoechinorhynchus collected in 57 localities across Middle America. We sequenced a large number of individuals to build a comprehensive dataset for three genes: the mitochondrial cytochrome c oxidase subunit I (352 individuals), the internal transcribed spacers (330 individuals), and the D2 + D3 domains of the large subunit (278 individuals). Several species delimitation methods were implemented, i.e., Automatic Barcode Gap Discovery (ABGD), General Mixed Yule-Coalescent Model (GMYC), Bayesian species delimitation (BPP) and species tree (∗BEAST). Additionally, we conducted a detailed morphological study of the diagnostic traits associated with the proboscis of 184 males and 169 females. Overall, our analyses allowed us to validate nine nominal species of Neoechinorhynchus and to identify 10 additional genetic lineages herein regarded as candidate species. This unexpected genetic diversity and the lack of reliable morphological traits show that the genus Neoechinorhynchus includes a group of cryptic species, at least in Middle America.
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Affiliation(s)
- Carlos Daniel Pinacho-Pinacho
- Investigador Cátedra CONACyT, Instituto de Ecología, A.C., Red de Estudios Moleculares Avanzados, Km 2.5 Ant. Carretera a Coatepec, Xalapa, Veracruz 91070, Mexico.
| | - Martín García-Varela
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, C.P. 04510, Ap. Postal 70-153, Ciudad Universitaria, Ciudad de México, Mexico.
| | - Ana L Sereno-Uribe
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, C.P. 04510, Ap. Postal 70-153, Ciudad Universitaria, Ciudad de México, Mexico.
| | - Gerardo Pérez-Ponce de León
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, C.P. 04510, Ap. Postal 70-153, Ciudad Universitaria, Ciudad de México, Mexico.
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Zimmermann BL, Crivellaro MS, Hauschild CB, Bartholomei-Santos ML, Crandall KA, Pérez-Losada M, Giri F, Collins P, Santos S. Phylogeography reveals unexpectedly low genetic diversity in a widely distributed species: the case of the freshwater crab Aegla platensis (Decapoda: Anomura). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bianca L Zimmermann
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Marcelo S Crivellaro
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Caroline B Hauschild
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Marlise L Bartholomei-Santos
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, George Washington University, Ashburn, VA, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
| | - Federico Giri
- Laboratorio de Macrocrustáceos, Instituto Nacional de Limnología, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Pablo Collins
- Laboratorio de Macrocrustáceos, Instituto Nacional de Limnología, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Sandro Santos
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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16
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Finding Evolutionary Processes Hidden in Cryptic Species. Trends Ecol Evol 2018; 33:153-163. [DOI: 10.1016/j.tree.2017.11.007] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/18/2022]
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17
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Gordy MA, Locke SA, Rawlings TA, Lapierre AR, Hanington PC. Molecular and morphological evidence for nine species in North American Australapatemon (Sudarikov, 1959): a phylogeny expansion with description of the zygocercous Australapatemon mclaughlini n. sp. Parasitol Res 2017. [PMID: 28623502 DOI: 10.1007/s00436-017-5523-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Zygocercous (aggregating) cercarial larvae were recently discovered emerging from a physid snail during a molecular survey of cercariae from molluscs in lakes in central Alberta, Canada. This manuscript delves into the characterization of these cercariae through morphological and molecular techniques and provides the first genetic information for a zygocercous larval trematode. Analyses of cytochrome c oxidase I of mitochondrial DNA and two partial regions of nuclear ribosomal DNA sequences revealed the zygocercous cercariae to belong to the genus Australapatemon Sudarikov, 1959. Further analyses of sequences of Australapatemon burti (Miller, 1923), from cercariae and adults collected from across North America, indicate a complex of nine genetically-distinct lineages within this species, a surprising level of diversity. The zygocercous cercariae, along with adult worms collected from ducks in Manitoba, Canada, and from Mexico, represent one of these lineages, and are herein described as Australapatemon mclaughlini n. sp. Seven lineages cannot yet be identified, but one is tentatively identified as Australapatemon burti.
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Affiliation(s)
- Michelle A Gordy
- University of Alberta School of Public Health, 357F South Academic Building, Edmonton, AB, T6G 2G7, Canada
| | - Sean A Locke
- Department of Biology, University of Puerto Rico at Mayagüez, Box 9000, Mayagüez, 00681-9000, Puerto Rico
| | - Timothy A Rawlings
- Department of Biology, Cape Breton University, 1250 Grand Lake Road, PO Box 5300, Sydney, NS, B1P 6L2, Canada
| | - Angela R Lapierre
- Department of Biology, Concordia University, 7141 Sherbrooke West, Montreal, QC, H4B 1R6, Canada
| | - Patrick C Hanington
- University of Alberta School of Public Health, 357F South Academic Building, Edmonton, AB, T6G 2G7, Canada.
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18
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An updated look at the uneven distribution of cryptic diversity among parasitic helminths. J Helminthol 2017; 92:197-202. [PMID: 28260533 DOI: 10.1017/s0022149x17000189] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cryptic parasite diversity is a major issue for taxonomy and systematics, and for attempts to control diseases of humans, domestic animals and wildlife. Here, we re-examine an earlier report that, after correcting for sampling effort, more cryptic species of trematodes are found per published study than for other helminth taxa. We performed a meta-analysis of 110 studies that used DNA sequences to search for cryptic species in parasitic helminth taxa. After correcting for study effort and accounting for the biogeographical region of origins, we found that more cryptic species tend to be uncovered among trematodes, and fewer among cestodes and animal-parasitic nematodes, than in other helminth groups. However, this pattern was only apparent when we included only studies using nuclear markers in the analysis; it was not seen in a separate analysis based only on mitochondrial markers. We propose that the greater occurrence of cryptic diversity among trematodes may be due to some of their unique features, such as their mode of reproduction or frequent lack of hard morphological structures, or to the way in which trematode species are described. Whatever the reason, the high frequency of cryptic species among trematodes has huge implications for estimates of parasite diversity and for future taxonomic research.
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