1
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Kotsakiozi P, Antoniou A, Psonis N, Sagonas Κ, Karameta E, Ilgaz Ç, Kumlutaş Y, Avcı A, Jablonski D, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N. Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region. Mol Phylogenet Evol 2024; 197:108091. [PMID: 38719080 DOI: 10.1016/j.ympev.2024.108091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024]
Abstract
Cryptic diversity poses a great obstacle in our attempts to assess the current biodiversity crisis and may hamper conservation efforts. The gekkonid genus Mediodactylus, a well-known case of hidden species and genetic diversity, has been taxonomically reclassified several times during the last decade. Focusing on the Mediterranean populations, a recent study within the M. kotschyi species complex using classic mtDNA/nuDNA markers suggested the existence of five distinct species, some being endemic and some possibly threatened, yet their relationships have not been fully resolved. Here, we generated genome-wide SNPs (using ddRADseq) and applied molecular species delimitation approaches and population genomic analyses to further disentangle these relationships. Τhe most extensive nuclear dataset, so far, encompassing 2,360 loci and ∼ 699,000 bp from across the genome of Mediodactylus gecko, enabled us to resolve previously obscure phylogenetic relationships among the five, recently elevated, Mediodactylus species and to support the hypothesis that the taxon includes several new, undescribed species. Population genomic analyses within each of the proposed species showed strong genetic structure and high levels of genetic differentiation among populations.
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Affiliation(s)
- Panayiota Kotsakiozi
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece.
| | - Aglaia Antoniou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion 71003, P.O. Box 2214, Crete, Greece
| | - Nikolaos Psonis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Κostas Sagonas
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Emmanouela Karameta
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Aziz Avcı
- Department of Biology, Faculty of Science, Aydın Adnan Menderes University, Aydın 09010, Türkiye
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Diego Darriba
- Computer Architecture Group, Centro de investigación CITIC, University of A Coruña, A Coruña, Spain
| | - Alexandros Stamatakis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Greece; Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76128, Germany
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
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2
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Meghana R, Anand PP, Vardhanan YS. Molecular and morphometric analyses reveal host-specific cryptic speciation in a mite species, Tetranychus neocaledonicus (Andre, 1933) (Acari: Tetranychidae). Zootaxa 2023; 5306:61-96. [PMID: 37518535 DOI: 10.11646/zootaxa.5306.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 08/01/2023]
Abstract
Host- and habitat-induced morphological shape and size variations are common in phytophagous and parasitic taxa. Several integrated morphological and molecular techniques have been commonly used to understand host-induced morpho-cryptic species forms. Compared to other arthropods, cryptic speciation was more common in Acari. This study focused on the host-specific morphological cryptic shape and size variations of Tetranychus neocaledonicus, collected from moringa and cassava hosts. We used geometric morphometric analysis to uncover the shape and size of inter-and intra-spider mite populations, and discovered that host-specific shape and size variations existed in spider mites regardless of sex. Interestingly, there was no phylogenetic signal in spider mites, implying that the morpho-cryptic speciation of T. neocaledonicus is solely based on the host-induced selection. The molecular clock hypothesis was accepted in our CO1 and 18s rRNA phylogeny analyses, and spider mites collected from both hosts were genetically less diverse. We conclude that T. neocaledonicus exhibited morphologically detectable cryptic population diversity in each host but that these populations are evolutionarily young form. Apart from these host-induced variations, we also monitored the impact of the clearing agent (lactic acid) on the shape and size of T. neocaledonicus; from this study, we proved that the clearing agent significantly alters the taxonomically important morphological traits of spider mites irrespective of the mites' sex, as confirmed by multivariate statistical analysis. This is the first study report to investigated the host-induced morphological variations of spider mites and the impact of a clearing agent.
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Affiliation(s)
- R Meghana
- Biochemistry & Toxicology Division; Department of Zoology; University of Calicut; Kerala; India.
| | - P P Anand
- Biochemistry & Toxicology Division; Department of Zoology; University of Calicut; Kerala; India.
| | - Y Shibu Vardhanan
- Biochemistry & Toxicology Division; Department of Zoology; University of Calicut; Kerala; India.
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3
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Stratakis M, Koutmanis I, Ilgaz Ç, Jablonski D, Kukushkin OV, Crnobrnja‐Isailovic J, Carretero MA, Liuzzi C, Kumlutaş Y, Lymberakis P, Poulakakis N. Evolutionary divergence of the smooth snake (Serpentes, Colubridae): The role of the Balkans and Anatolia. ZOOL SCR 2022. [DOI: 10.1111/zsc.12533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manos Stratakis
- Department of Biology School of Sciences and Engineering University of Crete Irakleio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Iraklis Koutmanis
- Department of Biology School of Sciences and Engineering University of Crete Irakleio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Çetin Ilgaz
- Department of Biology Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna and Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Daniel Jablonski
- Department of Zoology Comenius University in Bratislava Bratislava Slovakia
| | - Oleg V. Kukushkin
- Department of Biodiversity Studies and Ecological Monitoring T.I. Vyazemski Karadag Research Station – Nature Reserve of Russian Academy of Sciences Theodosia Crimea
- Department of Herpetology Institute of Zoology of Russian Academy of Sciences Saint Petersburg Russia
| | - Jelka Crnobrnja‐Isailovic
- Department of Biology and Ecology Faculty of Sciences and Mathematics University of Niš Niš Serbia
- Department of Evolutionary Biology Institute for Biological Research “Siniša Stanković” ‐ National Institute of Republic of Serbia University of Belgrade Beograd Serbia
| | - Miguel A. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Vila do Conde Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal
| | | | - Yusuf Kumlutaş
- Department of Biology Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna and Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Petros Lymberakis
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Nikos Poulakakis
- Department of Biology School of Sciences and Engineering University of Crete Irakleio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
- Institute of Molecular Biology and Biotechnology (IMBB) Foundation for Research and Technology ‐ Hellas (FORTH) Irakleio Greece
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4
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A new cryptic species of the Darevskia parvula group from NE Anatolia (Squamata, Lacertidae). ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00540-4] [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]
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5
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Wang R, Tsui CKM, You C. Cryptic Species Diversity and Phylogenetic Relationship in the Rust Genus Chrysomyxa from China. J Fungi (Basel) 2022; 8:83. [PMID: 35050023 PMCID: PMC8781690 DOI: 10.3390/jof8010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 01/26/2023] Open
Abstract
Chrysomyxa rusts are fungal pathogens widely distributed in the Northern hemisphere, causing spruce needle and cone rust diseases, and they are responsible for significant economic losses in China. Taxonomic delimitation and precise species identification are difficult within this genus because some characters often overlap in several species. Adequate species delimitation, enhanced by the use of DNA-based methodologies, will help to establish well-supported species boundaries and enable the identification of cryptic species. Here, we explore the cryptic species diversity in the rust genus Chrysomyxa from China. Species delimitation analyses are conducted using a distance-based method (ABGD) and three tree-based methods (GMYC, bPTP, and mPTP) based on combined LSU and ITS sequences of over 60 specimens. Although there is some incongruence among species delimitation methods, two new species and three putative cryptic species are identified. The key to 20 Chrysomyxa species distributed in China is presented. These results suggest that a significant level of undiscovered cryptic diversity is likely to be found in Chrysomyxa from China. Future studies should consider multiple analytical methods when dealing with multi-locus datasets.
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Affiliation(s)
- Rui Wang
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing 100083, China;
| | - Clement K. M. Tsui
- Department of Pathology, Sidra Medicine, Doha 2713, Qatar;
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha 2713, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Chongjuan You
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing 100083, China;
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6
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Candan K, Kornilios P, Ayaz D, Kumlutaş Y, GüL S, Caynak EY, Ilgaz Ç. Cryptic genetic structure within Valentin’s Lizard, Darevskia valentini (Boettger, 1892) (Squamata, Lacertidae), with implications for systematics and origins of parthenogenesis. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1909171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Kamil Candan
- Faculty of Science, Department of Biology, Dokuz Eylül University, Buca, İzmir TR-35390, Turkey
| | | | - DinÇer Ayaz
- Faculty of Science, Department of Biology, Ege University, Bornova, İzmir TR-35040, Turkey
| | - Yusuf Kumlutaş
- Faculty of Science, Department of Biology, Dokuz Eylül University, Buca, İzmir TR-35390, Turkey
- Fauna and Flora Applied and Research Center, Dokuz Eylül University, Buca, İzmir TR-35390, Turkey
| | - Serkan GüL
- Faculty of Science and Arts, Department of Biology, Recep Tayyip Erdoğan University, Rize TR-53100, Turkey
| | - Elif Yildirim Caynak
- Faculty of Science, Department of Biology, Dokuz Eylül University, Buca, İzmir TR-35390, Turkey
- Fauna and Flora Applied and Research Center, Dokuz Eylül University, Buca, İzmir TR-35390, Turkey
| | - Çetin Ilgaz
- Faculty of Science, Department of Biology, Dokuz Eylül University, Buca, İzmir TR-35390, Turkey
- Fauna and Flora Applied and Research Center, Dokuz Eylül University, Buca, İzmir TR-35390, Turkey
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7
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Wüster W, Thomson SA, O’shea M, Kaiser H. Confronting taxonomic vandalism in biology: conscientious community self-organization can preserve nomenclatural stability. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Self-published taxon descriptions, bereft of a basis of evidence, are a long-standing problem in taxonomy. The problem derives in part from the Principle of Priority in the International Code of Zoological Nomenclature, which forces the use of the oldest available nomen irrespective of scientific merit. This provides a route to ‘immortality’ for unscrupulous individuals through the mass-naming of taxa without scientific basis, a phenomenon referred to as taxonomic vandalism. Following a flood of unscientific taxon namings, in 2013 a group of concerned herpetologists organized a widely supported, community-based campaign to treat these nomina as lying outside the permanent scientific record, and to ignore and overwrite them as appropriate. Here, we review the impact of these proposals over the past 8 years. We identified 59 instances of unscientific names being set aside and overwritten with science-based names (here termed aspidonyms), and 1087 uses of these aspidonyms, compared to one instance of preference for the overwritten names. This shows that when there is widespread consultation and agreement across affected research communities, setting aside certain provisions of the Code can constitute an effective last resort defence against taxonomic vandalism and enhance the universality and stability of the scientific nomenclature.
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Affiliation(s)
- Wolfgang Wüster
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Scott A Thomson
- Museu de Zoologia da Universidade de São Paulo, Divisão de Vertebrados (Herpetologia), Avenida Nazaré, 481, Ipiranga, 04263-000, São Paulo, SP, Brazil
- Chelonian Research Institute, 401 South Central Avenue, Oviedo, FL 32765, USA
| | - Mark O’shea
- Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Hinrich Kaiser
- Department of Vertebrate Zoology, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
- Department of Biology, Victor Valley College, 18422 Bear Valley Road, Victorville, CA 92395, USA
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8
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Korábek O, Kosová T, Dolejš P, Petrusek A, Neubert E, Juřičková L. Geographic isolation and human-assisted dispersal in land snails: a Mediterranean story of Helix borealis and its relatives (Gastropoda: Stylommatophora: Helicidae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The Mediterranean basin is a major centre for land-snail diversity, with many localized endemics, but there are also species widely spread by humans. Both endemics and introductions can be found in the snail genus Helix, which comprises many large-bodied species used for human consumption in the past and present. The Mediterranean clade of Helix is currently distributed throughout this region, but the phylogenetic and biogeographic relationships among its forms from different parts of the basin remain enigmatic. The reasons include insufficient sampling, taxa with unclear taxonomy and a significant impact of human-assisted transport obscuring the natural distribution of phylogenetic lineages. We provide evidence that European and Anatolian populations of H. cincta and its relatives are not native to those regions, but originate from the northern Levant. These results have implications for taxonomy of the genus, but also for the understanding of its evolutionary history. We posit that the Mediterranean clade consists of four geographically separated groups, which diversified in Northern Africa, the Apennine Peninsula and Corsica, the Aegean and Greece, and the northern Levant. This geographic pattern has been subsequently blurred by multiple instances of human-assisted dispersal. However, revealing the founding populations with certainty requires thorough sampling in currently inaccessible countries.
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Affiliation(s)
- Ondřej Korábek
- Department of Ecology, Faculty of Science, Charles University, Viničná, Praha, CZ, Czechia
| | - Tereza Kosová
- Department of Zoology, Faculty of Science, Charles University, Viničná, Praha, CZ, Czechia
| | - Petr Dolejš
- Department of Zoology, Natural History Museum, National Museum, Cirkusová, Praha 9-Horní Počernice, CZ, Czechia
| | - Adam Petrusek
- Department of Ecology, Faculty of Science, Charles University, Viničná, Praha, CZ, Czechia
| | - Eike Neubert
- Natural History Museum of the Burgergemeinde Bern, Bernastrasse, Bern, CH, Switzerland
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse, Bern, CH, Switzerland
| | - Lucie Juřičková
- Department of Zoology, Faculty of Science, Charles University, Viničná, Praha, CZ, Czechia
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9
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Annousis I, Kapsalas G, Pafilis P. Review of the herpetofauna of Attica, mainland Greece. HERPETOZOA 2021. [DOI: 10.3897/herpetozoa.34.e60668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the insular distribution of the rich herpetofauna of Greece has been studied more extensively, the mainland one is still underexplored. The region of Attica in central Greece represents one of these “black spots” in the mainland. Thus, in 2019 we surveyed for the first time the herpetofauna of Attica in a systematic way. We collected 794 field records of 31 species (4 amphibians, 27 reptiles); Testudo graeca and Trachemys elegans were documented for the first time for Attica.
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10
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Kornilios P, Jablonski D, Sadek RA, Kumlutaş Y, Olgun K, Avci A, Ilgaz C. Multilocus species-delimitation in the Xerotyphlops vermicularis (Reptilia: Typhlopidae) species complex. Mol Phylogenet Evol 2020; 152:106922. [PMID: 32771550 DOI: 10.1016/j.ympev.2020.106922] [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: 04/28/2020] [Revised: 07/21/2020] [Accepted: 08/03/2020] [Indexed: 02/09/2023]
Abstract
Scolecophidia (worm snakes) are a vertebrate group with high ecomorphological conservatism due to their burrowing lifestyle. The Eurasian or Greek blindsnake Xerotyphlops vermicularis is their only European representative, a species-complex with an old diversification history. However, its systematics and taxonomy has remained untouched. Here, we extend previous work that relied heavily on mitochondrial markers, following a multi-locus approach and applying several species-delimitation methods, including a Bayesian coalescence-based approach (STACEY). Four "species" delimitation analyses based on the mtDNA (ABGD, bGMYC, mPTP, parsimony networks) returned 14, 11, 9 and 10 clusters, respectively. By mitotyping twice as many specimens as before, we have a complete picture of each cluster's distribution. With the exception of the highly-divergent Levantine lineage, the three independent nuclear markers did not help with phylogenetic resolution, as demonstrated in haplotype networks, concatenated and species-trees, a result of incomplete lineage sorting. The prevailing model from the coalescence-based species-delimitation identified two species: the lineage from the Levant and all others. We formally recognize them as distinct species and resurrect Xerotyphlops syriacus (Jan, 1864) to include the Levantine blindsnakes. Finally, X. vermicularis and X. syriacus may represent species-complexes themselves, since they include high levels of cryptic diversity.
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Affiliation(s)
- P Kornilios
- Department of Biology, University of Patras, GR-26500 Patras, Greece.
| | - D Jablonski
- Department of Zoology, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - R A Sadek
- Biology Department, American University of Beirut, Bliss Street, 1107 2020 Beirut, Lebanon
| | - Y Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, 35160 Buca, İzmir, Turkey
| | - K Olgun
- Department of Biology, Faculty of Science and Arts, Aydın Adnan Menderes University, Aydın, Turkey
| | - A Avci
- Department of Biology, Faculty of Science and Arts, Aydın Adnan Menderes University, Aydın, Turkey
| | - C Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, 35160 Buca, İzmir, Turkey
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11
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Wang YL, Cao HL, Chen HW. Molecular phylogeny and species delimitation of Amiota alboguttata and Amiota basdeni species groups (Diptera: Drosophilidae) from East Asia. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Phylogenetic relationships of the two largest species groups in the genus Amiota [the Amiota alboguttata group (29 known and six new species) and the Amiota basdeni group (17 known and three new species)] were reconstructed using two mitochondrial gene sequences (COI and ND2). The paraphyly of the A. alboguttata group was identified based on molecular evidence. The monophyletic A. basdeni group is found to be nested in the A. alboguttata group, rendering the latter paraphyletic. Automatic barcode gap discovery and Bayesian phylogenetics and phylogeography methods were used to assess species limits of the A. alboguttata and A. basdeni groups. The results indicate that most analysed species could be delimited clearly, including nine new species (Amiota beama sp. nov., Amiota cyclophylla sp. nov., Amiota flormontana sp. nov., Amiota obtusa sp. nov., Amiota planiceps sp. nov., Amiota scrobicula sp. nov., Amiota jianjuni sp. nov., Amiota tentacula sp. nov. and Amiota xinglaii sp. nov.), except for some closely related morphospecies. Furthermore, based on the highly biased distributions of these two groups, southwestern China is hypothesized to be a possible centre of origin and diversification for Amiota in East Asia.
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Affiliation(s)
- Ya-Lian Wang
- Department of Entomology, South China Agricultural University, Tianhe, Guangzhou, China
| | - Hui-Luo Cao
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Hong-Wei Chen
- Department of Entomology, South China Agricultural University, Tianhe, Guangzhou, China
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12
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Myers TC, de Mello PLH, Glor RE. A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractCryptic species – genetically distinct species that are morphologically difficult to distinguish – present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole use of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean bark anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternative species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best-supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.
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Affiliation(s)
- Tanner C Myers
- Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - Pietro L H de Mello
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Herpetology Division, Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Richard E Glor
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Herpetology Division, Biodiversity Institute, University of Kansas, Lawrence, KS, USA
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13
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Evidence for cryptic diversification in a rupicolous forest-dwelling gecko (Gekkonidae: Afroedura pondolia) from a biodiversity hotspot. Mol Phylogenet Evol 2019; 139:106549. [DOI: 10.1016/j.ympev.2019.106549] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 11/22/2022]
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14
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Kornilios P, Thanou E, Lymberakis P, Ilgaz Ç, Kumlutaş Y, Leaché A. A phylogenomic resolution for the taxonomy of Aegean green lizards. ZOOL SCR 2019. [DOI: 10.1111/zsc.12385] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Panagiotis Kornilios
- Department of Biology University of Washington Seattle WA USA
- Institute of Evolutionary Biology (CSIC – Universitat Pompeu Fabra) Barcelona Spain
- The Molecular Ecology Backshop Loutraki Greece
| | - Evanthia Thanou
- Department of Biology University of Washington Seattle WA USA
- The Molecular Ecology Backshop Loutraki Greece
| | - Petros Lymberakis
- Natural History Museum of Crete University of Crete Irakleio, Crete Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Adam Leaché
- Department of Biology University of Washington Seattle WA USA
- Burke Museum of Natural History and Culture University of Washington Seattle WA USA
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15
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Duarte ME, de Mendonça RS, Skoracka A, Silva ES, Navia D. Integrative taxonomy of Abacarus mites (Eriophyidae) associated with hybrid sugarcane plants, including description of a new species. EXPERIMENTAL & APPLIED ACAROLOGY 2019; 78:373-401. [PMID: 31278610 DOI: 10.1007/s10493-019-00388-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/30/2019] [Indexed: 06/09/2023]
Abstract
Phytophagous mites belonging to the Eriophyoidea are extremely diverse and highly host-specific. Their accurate morphological identification is hampered by their reduced size and simplified bodies and by the existence of cryptic species complexes. Previous studies have demonstrated the urgency of applying multisource methods to accurate taxonomic identification of eriophyoid mites, especially species belonging to the genus Abacarus. This genus comprises 65 species, of which 37 are associated with grasses and four with sugarcane Saccharum (Poaceae). Recently, Abacarus specimens very similar to Abacarus sacchari were collected from the sugarcane crop in Brazil; however, their taxonomic placement was uncertain. In this study, we used an integrative approach to determine whether A. aff. sacchari specimens belong to A. sacchari or constitute a cryptic species. Morphological data were combined with molecular phylogeny based on the nucleotide sequences of three markers, one mitochondrial (COI) and two nuclear (D2 region of 28S and ITS). Morphological differences were observed between A. aff. sacchari, A. sacchari and A. doctus. The phylogenetic relationships among these three taxa and the genetic distances separating them revealed an interspecific divergence. The results of the morphological and molecular methods were congruent and supported the existence of a new species: Abacarus neosacchari n. sp. Duarte and Navia, herein described. This species belongs to the Abacarus cryptic species complex associated with sugarcane in the Americas. The results of this study, presenting the occurrence of multiple Abacarus species associated with sugarcane, contribute to the knowledge on plants and mites diversity by adding up one more clue highlighting that plant hybridization can be an important mechanism contributing to the speciation of plant-feeding arthropods.
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Affiliation(s)
- Mércia Elias Duarte
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, Distrito Federal, 70770-900, Brazil
| | - Renata Santos de Mendonça
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, 70297-400, Brazil
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Edmilson Santos Silva
- Universidade Federal de Alagoas, Campus Arapiraca, Arapiraca, 57309-005, Brazil
- Universidade Federal de Alagoas, Centro de Ciências Agrárias (CECA), Alagoas, 57100-000, Brazil
| | - Denise Navia
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, Distrito Federal, 70770-900, Brazil.
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16
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Camaiti M, Villa A, Wencker LCM, Bauer AM, Stanley EL, Delfino M. Descriptive osteology and patterns of limb loss of the European limbless skink Ophiomorus punctatissimus (Squamata, Scincidae). J Anat 2019; 235:313-345. [PMID: 31125128 DOI: 10.1111/joa.13017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2019] [Indexed: 11/26/2022] Open
Abstract
The limbless skink Ophiomorus punctatissimus is a cryptozoic species found in the Peloponnese region of Greece and on the Greek island Kythira. To provide the first thorough description of the cranial and postcranial osteology of this species, both disarticulated specimens and X-ray computed tomographies of wet-preserved specimens were examined in detail. Resulting from this, an anatomical atlas of this species is provided. Two separate considerations, an evolutionary and an ecomorphological one, are made based on the observed adaptations related to limb loss in this skink. The structure of the girdles shows a particular pattern of reduction: whereas the pelvic girdle is mostly vestigial, the pectoral girdle is instead well developed, with all the elements typical of limbed lizards except for the actual limbs. This led us to hypothesize an asynchronous pattern of limb reduction during the evolution of this species, in which the hindlimbs regressed earlier than the forelimbs. Furthermore, considerations based on overall body morphology, osteology and the structure of the inner ear led to the recognition of this species as a burrowing ecomorph. In contrast to the morphology normally displayed in this ecomorph, O. punctatissimus is characterized by the retention of autotomic vertebrae in its tail. This is consistent with the habitats in which it lives, where active burrowing would be difficult because of the hard, rocky terrain. Instead, this skink hides among rocks on the surface and is, therefore, subject to greater predation risk.
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Affiliation(s)
- Marco Camaiti
- Dipartimento di Scienze della Terra, Università di Torino, Turin, Italy.,School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Andrea Villa
- Dipartimento di Scienze della Terra, Università di Torino, Turin, Italy.,Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
| | | | - Aaron M Bauer
- Department of Biology, Villanova University, Villanova, PA, USA
| | - Edward L Stanley
- Department of Herpetology, Florida Museum of Natural History, Gainesville, FL, USA
| | - Massimo Delfino
- Dipartimento di Scienze della Terra, Università di Torino, Turin, Italy.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
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17
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Hofmann EP, Nicholson KE, Luque-Montes IR, Köhler G, Cerrato-Mendoza CA, Medina-Flores M, Wilson LD, Townsend JH. Cryptic Diversity, but to What Extent? Discordance Between Single-Locus Species Delimitation Methods Within Mainland Anoles (Squamata: Dactyloidae) of Northern Central America. Front Genet 2019; 10:11. [PMID: 30804976 PMCID: PMC6378269 DOI: 10.3389/fgene.2019.00011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 01/11/2019] [Indexed: 01/10/2023] Open
Abstract
Single-locus molecular barcoding is a useful method for identifying overlooked and undescribed biodiversity, providing the groundwork for further systematic study and taxonomic investigation. A variety of methods for delimiting species from barcoding libraries have been developed and applied, allowing for rapid estimates of species diversity in a broad range of taxa. However, tree-based and distance-based analyses can infer different group assignments, potentially over- or underestimating the number of putative species groups. Here, we explore diversity of mainland species of anole lizards from the Chortís Block biogeographical province of northern Central America using a DNA barcoding approach, generating and analyzing cytochrome oxidase subunit I (COI) sequences for over 400 samples assignable to 33 of 38 (86.8%) native and one introduced mainland species. We subsequently tested the effects different models of nucleotide substitution, different species-delimitation algorithms, and reducing our dataset had on species delimitation estimates. We performed of two distance-based (ABGD, RESL) and three tree-based (bPTP, mPTP, GMYC) analyses on both the full dataset and a dataset consisting only of unique halotypes. From 34 nominal taxa, analyses of the full dataset recovered between 34 and 64 operational taxonomic units (OTUs), while analyses of the reduced dataset inferred between 36 and 59. Reassigning individuals to either mPTP-inferred or ABGD clustered (7.2% threshold) groups improved the detection of a barcoding gap across three different models of nucleotide substitution, removing overlap between intra- and interspecific distances. Our results highlight the underestimated diversity of mainland Chortís Block anoles, but the lack of congruence between analyses demonstrates the importance of considering multiple analytical methods when dealing with single-locus datasets. We recommend future studies consider the effects of different models of nucleotide substitution on proposed barcoding gaps, as well as the effect reducing a dataset to unique haplotypes may have on proposed diversity estimates.
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Affiliation(s)
- Erich P. Hofmann
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
- Department of Biological Sciences, Clemson University, Clemson, SC, United States
| | - Kirsten E. Nicholson
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | | | - Gunther Köhler
- Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt, Germany
| | - César A. Cerrato-Mendoza
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Melissa Medina-Flores
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Larry David Wilson
- Centro Zamorano de Biodiversidad, Escuela Agrícola Panamericana Zamorano, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
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