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Defourneaux É, Herranz M, Armenteros M, Sørensen MV, Norenburg JL, Park T, Worsaae K. Circumtropical distribution and cryptic species of the meiofaunal enteropneust Meioglossus (Harrimaniidae, Hemichordata). Sci Rep 2024; 14:9296. [PMID: 38654022 DOI: 10.1038/s41598-024-57591-0] [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: 12/18/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Hemichordata has always played a central role in evolutionary studies of Chordata due to their close phylogenetic affinity and shared morphological characteristics. Hemichordates had no meiofaunal representatives until the surprising discovery of a microscopic, paedomorphic enteropneust Meioglossus psammophilus (Harrimaniidae, Hemichordata) from the Caribbean in 2012. No additional species have been described since, questioning the broader distribution and significance of this genus. However, being less than a millimeter long and superficially resembling an early juvenile acorn worm, Meioglossus may easily be overlooked in both macrofauna and meiofauna surveys. We here present the discovery of 11 additional populations of Meioglossus from shallow subtropical and tropical coralline sands of the Caribbean Sea, Red Sea, Indian Ocean, and East China Sea. These geographically separated populations show identical morphology but differ genetically. Our phylogenetic reconstructions include four gene markers and support the monophyly of Meioglossus. Species delineation analyses revealed eight new cryptic species, which we herein describe using DNA taxonomy. This study reveals a broad circumtropical distribution, supporting the validity and ecological importance of this enigmatic meiobenthic genus. The high cryptic diversity and apparent morphological stasis of Meioglossus may exemplify a potentially common evolutionary 'dead-end' scenario, where groups with highly miniaturized and simplified body plan lose their ability to diversify morphologically.
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Affiliation(s)
- Éloïse Defourneaux
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark
| | - Maria Herranz
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark
- Area of Biodiversity and Conservation, Superior School of Experimental Science and Technology (ESCET), Rey Juan Carlos University, C/ Tulipán S/N, 28933, Mostoles, Madrid, Spain
| | - Maickel Armenteros
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Joel Montes Camarena S/N, 82040, Mazatlán, México
| | - Martin V Sørensen
- Natural History Museum Denmark, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Jon L Norenburg
- Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Taeseo Park
- Species Diversity Research Division, National Institute of Biological Resources, Hwangyeong-Ro 42, Incheon, 22689, South Korea
| | - Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark.
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Trillo MC, Aisenberg A, Herberstein ME, Bidegaray-Batista L. Amazons Are Back: Absence of Males in a Praying Mantis from Uruguayan Savannas. NEOTROPICAL ENTOMOLOGY 2024; 53:323-329. [PMID: 38305945 DOI: 10.1007/s13744-023-01114-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/04/2023] [Indexed: 02/03/2024]
Abstract
With a broad distribution throughout South America, Brunneria subaptera (Saussure) (Coptopterygidae) is the most abundant praying mantis species in Uruguay, mostly associated with grassland vegetation. Their body coloration can vary between green or brown sepia. The recent catalog of Uruguayan mantids showed that all specimens of B. subaptera from the collections in Uruguay were females, suggesting an absence of males in natural populations. The aim of this study was to determine the occurrence of female-only populations of B. subaptera in Uruguay. Moreover, we analyzed the genetic variation and estimated the time of the most recent common ancestor of the species. We performed bimonthly samplings in two localities in Uruguay for 1 year and we sexed the individuals. We extracted DNA from the abdominal tissue of adult females and sequenced a fragment of the mitochondrial cox1 gene to assess the genetic diversity and to estimate diversification times. We did not find any males in either of the studied localities. The age estimates revealed a recent origin of the species (2.33 Ma), and there was no genetic differentiation between the individuals from Uruguayan localities. This absence of males of B. subaptera documented in the sampled locations suggests that the species reproduces by thelytokous parthenogenesis. This study opens promising venues for future research into reproductive strategies and polymorphism in South-American praying mantises that inhabit one of the largest areas of grasslands in the world, currently under dramatic deterioration and reduction.
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Affiliation(s)
- Mariana C Trillo
- Depto de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay.
- Depto de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay.
- Sección Entomología, Facultad de Ciencias, Univ de la República, Montevideo, Uruguay.
| | - Anita Aisenberg
- Depto de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | | | - Leticia Bidegaray-Batista
- Depto de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay.
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Puillandre N, Miralles A, Brouillet S, Fedosov A, Fischell F, Patmanidis S, Vences M. Species Delimitation and Exploration of Species Partitions with ASAP and LIMES. Methods Mol Biol 2024; 2744:313-334. [PMID: 38683328 DOI: 10.1007/978-1-0716-3581-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these were not initially provided as user-friendly GUI-driven executables. In spite of their differences, most of these tools share the same goal, i.e., inferring de novo a partition of subsets, potentially each representing a distinct species. More recently, a proposed common exchange format for the resulting species partitions (SPART) has been implemented by several of these tools, paving the way toward developing an interoperable digital environment entirely dedicated to integrative and comparative species delimitation. In this chapter, we provide detailed protocols for the use of two bioinformatic tools, one for single locus molecular species delimitation (ASAP) and one for statistical comparison of species partitions resulting from any kind of species delimitation analyses (LIMES).
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Affiliation(s)
- Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Aurélien Miralles
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Sophie Brouillet
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Alexander Fedosov
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Frank Fischell
- Institute of Zoology, University of Cologne, Köln, Germany
| | - Stefanos Patmanidis
- School of Electrical and Computer Engineering, National Technical University of Athens, Athens, Greece
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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Janko K, Mikulíček P, Hobza R, Schlupp I. Sperm-dependent asexual species and their role in ecology and evolution. Ecol Evol 2023; 13:e10522. [PMID: 37780083 PMCID: PMC10534198 DOI: 10.1002/ece3.10522] [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: 01/11/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
Sexual reproduction is the primary mode of reproduction in eukaryotes, but some organisms have evolved deviations from classical sex and switched to asexuality. These asexual lineages have sometimes been viewed as evolutionary dead ends, but recent research has revealed their importance in many areas of general biology. Our review explores the understudied, yet important mechanisms by which sperm-dependent asexuals that produce non-recombined gametes but rely on their fertilization, can have a significant impact on the evolution of coexisting sexual species and ecosystems. These impacts are concentrated around three major fields. Firstly, sperm-dependent asexuals can potentially impact the gene pool of coexisting sexual species by either restricting their population sizes or by providing bridges for interspecific gene flow whose type and consequences substantially differ from gene flow mechanisms expected under sexual reproduction. Secondly, they may impact on sexuals' diversification rates either directly, by serving as stepping-stones in speciation, or indirectly, by promoting the formation of pre- and postzygotic reproduction barriers among nascent species. Thirdly, they can potentially impact on spatial distribution of species, via direct or indirect (apparent) types of competition and Allee effects. For each such mechanism, we provide empirical examples of how natural sperm-dependent asexuals impact the evolution of their sexual counterparts. In particular, we highlight that these broad effects may last beyond the tenure of the individual asexual lineages causing them, which challenges the traditional perception that asexual lineages are short-lived evolutionary dead ends and minor sideshows. Our review also proposes new research directions to incorporate the aforementioned impacts of sperm-dependent asexuals. These research directions will ultimately enhance our understanding of the evolution of genomes and biological interactions in general.
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Affiliation(s)
- Karel Janko
- Laboratory of Non‐Mendelian Evolution, Institute of Animal Physiology and GeneticsAcademy of Sciences of the Czech RepublicLiběchovCzech Republic
- Department of Biology and Ecology, Faculty of ScienceUniversity of OstravaOstravaCzech Republic
| | - Peter Mikulíček
- Department of Zoology, Faculty of Natural SciencesComenius University in BratislavaBratislavaSlovakia
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of BiophysicsAcademy of Sciences of the Czech RepublicBrnoCzech Republic
| | - Ingo Schlupp
- Department of BiologyUniversity of OklahomaOklahomaNormanUSA
- Department of BiologyInternational Stock Center for Livebearing FishesOklahomaNormanUSA
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Stick R, Peter A. CaaX-less lamins: Lophotrochozoa provide a glance at the playground of evolution. PROTOPLASMA 2023; 260:741-756. [PMID: 36102949 PMCID: PMC10125929 DOI: 10.1007/s00709-022-01809-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/01/2022] [Indexed: 05/05/2023]
Abstract
Nuclear lamins are the main components of the nuclear lamina in many eukaryotes. They are members of the intermediate filament (IF) protein family. Lamins differ from cytoplasmic IF proteins by the presence of a nuclear localisation sequence (NLS) and a C-terminal tetrapeptide, the CaaX motif. The CaaX motif is target of post-translational modifications including isoprenylation, proteolytic processing, and carboxyl-methylation. These modifications, in conjunction with the NLS, direct lamins to the inner nuclear membrane where they assemble into filaments. Lamins lacking a CaaX motif are unable to associate independently with nuclear membranes and remain in the nucleoplasm. So far, three species have been reported to exclusively express CaaX-less lamins. All three belong to the lophotrochozoan lineage. To find out whether they represent rare exceptions, we analysed lamins of representatives of 17 lophotrochozoan phyla. Here we report that all four clades of Rotifera as well as individual taxa of Mollusca and Annelida lack CaaX-lamins, but express lamins with alternative C-termini. Of note, the respective mollusc and annelid groups occupy very different phylogenetic ranks. Most of these alternative C-termini are rich in aromatic residues. A possible function of these residues in membrane association is discussed. Alternative splicing of terebellid lamin transcripts gives rise to two lamin variants, one with a CaaX motif and one with an alternative C-terminus. A similar situation is found in Arenicolidae, Opheliidae, Capitellidae, and Echiura. This points a way, how the switch from lamins carrying a CaaX motif to lamins with alternative C-termini may have occurred.
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Affiliation(s)
- Reimer Stick
- Department of Cell Biology, University of Bremen, P.O. Box 330440, 28334, Bremen, Germany.
| | - Annette Peter
- Department of Cell Biology, University of Bremen, P.O. Box 330440, 28334, Bremen, Germany
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Wang L, Deng Z, Blair D, Hu W, Yin M. Phylogeography and genetic diversity of the Scapholeberis kingii species complex (Cladocera: Daphniidae) in China. Mol Phylogenet Evol 2023; 181:107725. [PMID: 36736845 DOI: 10.1016/j.ympev.2023.107725] [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: 10/22/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
There is increasing interest in the diversity and phylogeography of aquatic invertebrate zooplankton in the Eastern Palearctic, yet this topic remains largely unexplored in China. Here, we investigated the lineage diversity and phylogeography of an important cladoceran taxon, the Scapholeberis kingii (Cladocera: Daphniidae) species complex, members of which live in the surface layers of freshwater ecosystems. We identified only the S. smirnovi morphospecies from this species complex in 29 of 491 Chinese water bodies examined. Its phylogenetic position was verified using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear large subunit ribosomal RNA gene; 28S). Pronounced geographical separation among three S. smirnovi mitochondrial lineages was observed in China: only a single lineage (Lineage A) was present in the Eastern Plain, whereas Lineages B and C were restricted to the Inner Mongolia-Xinjiang Plateau and the Qinghai-Tibetan Plateau respectively. This deep mtDNA divergence and the substantial genetic differentiation among S. smirnovi populations from different regions is likely a result of the rapid uplift of the Qinghai-Tibetan Plateau and associated ecological changes. This study contributes to an understanding of the genetic diversity of the S. kingii complex, a key component of neustonic zooplankton.
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Affiliation(s)
- Lugege Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - David Blair
- College of Science and Engineering, James Cook University, Townsville, Qld 4811, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China; Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.
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Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [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: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
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Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
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Deep mtDNA Sequence Divergences and Possible Species Radiation of Whip Spiders (Arachnida, Amblypygi, Phrynidae, Phrynus/Paraphrynus) among Caribbean Oceanic and Cave Islands. TAXONOMY 2023. [DOI: 10.3390/taxonomy3010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Islands—whether classic oceanic islands or habitat islands such as isolated thermal vents, mountain tops, or caves—often promote the diversification of lineages that colonize them. We examined CO1 mtDNA sequence divergences within the tailless whip spider genus Phrynus Lamarck, 1809 (Amblypygi: Phrynidae) among oceanic islands and among cave ’islands´ distributed across the Caribbean archipelago and on the continental mainland. The significance of this study lies in the extensive taxon sampling of a supposedly depauperate lineage (considering its age), over a large proportion of its geographical range, and the discovery of deep mtDNA sequence divergences. We sampled thousands of specimens—and sequenced 544, including six outgroup species—across 173 localities on 17 islands (135 localities) and five countries on the North to South American mainland (38 localities), including a total of 63 caves. Classical taxonomy identified ten named Phrynus and two Paraphrynus Moreno, 1940 species. Paraphrynus seems to be paraphyletic and nested in Phrynus. Uncorrected genetic distances within named species and among morphological species ranged up to 15% and 19%, respectively. Geographic distances explained a significant portion of genetic distances on islands (19%, among both subterranean and epigean specimens), and for epigean specimens on the mainland (27%). Species delimitation analyses indicated that the 12 named species harbored from 66 to well over 100 putative species. The highest number of species was indicated by the GMYC method (114 species) while the Bayesian Poisson tree processes (bPTP) and the BP&P relaying on the Markov chain Monte Carlo Bayesian Phylogenetic model estimated an upper level of 110 species. On the other hand, the recently recommended and relatively conservative distance-based (phylogeny free) ASAP model has the greatest support for 73 species. In either case, nearly all putative species are tightly limited to a single locality, often a small cave system, and sometimes to the surrounding epigean area. Caribbean Phrynus diversity has likely been vastly underestimated, likely due to both morphological crypsis and the ignorance of Caribbean cave fauna. Although mtDNA sequences can suggest species limits, nuclear DNA sequencing and detailed morphological research are necessary to corroborate them and explore whether this phenomenon constitutes species radiation or perhaps just mtDNA divergences as a consequence of, for example, stationary females and actively dispersing males.
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Grismer LL, Aowphol A, Yodthong S, Ampai N, Termprayoon K, Aksornneam A, Rujirawan A. Integrative taxonomy delimits and diagnoses cryptic arboreal species of the Cyrtodactylusbrevipalmatus group (Squamata, Gekkonidae) with descriptions of four new species from Thailand. Zookeys 2022; 1129:109-162. [PMID: 36761846 PMCID: PMC9836718 DOI: 10.3897/zookeys.1129.90535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
Species delimitation and species diagnosis must remain separate operations to avoid constructing taxonomies comprised of non-monophyletic species based on morphological similarity as opposed to phylogenetic propinquity. This is particularly true for highly specialized species such as the range-restricted upland taxa in the Cyrtodactylusbrevipalmatus group of Indochina where strong selection pressure for an arboreal lifestyle has contributed to morphologically similar but distantly related species. This in turn, has resulted in a history of erroneous taxonomies that have actually obscured rather than revealed the diversity within this group. A Bayesian phylogeny of the C.brevipalmatus group recovered at least 15 putative species-level lineages, at least seven of which are undescribed, and of which four are described herein. A total evidence morphological data set comprised of 16 normalized morphometric, 15 meristic, and seven categorical characters scored across 51 individuals was subjected to a multiple factor analysis (MFA) and an analysis of variance (ANOVA) to diagnose the putative species. These new species descriptions contribute to focusing attention to the unrealized diversity in upland tropical ecosystems, which due to climate change, are some of the most impearled ecosystems on the planet. Thus, it is paramount that taxonomies do not conflate species identities and underrepresent true diversity.
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Affiliation(s)
- L. Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, California 92505, USALa Sierra UniversityRiversideUnited States of America,Department of Herpetology, San Diego Natural History Museum, PO Box 121390, San Diego, California, 92112, USADepartment of Herpetology, San Diego Natural History MuseumSan DiegoUnited States of America
| | - Anchalee Aowphol
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandKasetsart UniversityBangkokThailand
| | - Siriporn Yodthong
- Department of Biology, Faculty of Science, Thaksin University, Pa Phayom, Phattalung 93210, ThailandThaksin UniversityPhattalungThailand
| | - Natee Ampai
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, ThailandSrinakharinwirot UniversityBangkokThailand
| | - Korkhwan Termprayoon
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandKasetsart UniversityBangkokThailand
| | - Akrachai Aksornneam
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandKasetsart UniversityBangkokThailand
| | - Attapol Rujirawan
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandKasetsart UniversityBangkokThailand
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10
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Novaes-e-Fagundes G, Lyra ML, Loredam VSA, Carvalho TR, Haddad CFB, Rodrigues MT, Baldo D, Barrasso DA, Loebmann D, Ávila RW, Brusquetti F, Prudente ALC, Wheeler WC, Goyannes Dill Orrico V, Peloso P. A tale of two bellies: systematics of the oval frogs (Anura: Microhylidae: Elachistocleis Parker, 1927). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac057] [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]
Abstract
Abstract
Oval frogs (Elachistocleis) have a broad geographic distribution covering nearly all of South America and parts of Central America. They also have a large inter- and intraspecific variation of the few morphological characters commonly used as diagnostic traits among species of the genus. Based on molecular data, we provide the most complete phylogeny of Elachistocleis to date, and explore its genetic diversity using distance-based and tree-based methods for putative species delimitation. Our results show that at least two of the most relevant traditional characters used in the taxonomy of this group (belly pattern and dorsal median white line) carry less phylogenetic information than previously thought. Based on our results, we propose some synonymizations and some candidate new species. This study is a first major step in disentangling the current systematics of Elachistocleis. Yet, a comprehensive review of morphological data is needed before any new species descriptions can be properly made.
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Affiliation(s)
- Gabriel Novaes-e-Fagundes
- Tropical Herpetology Laboratory, PPG Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz , Ilhéus, Bahia , Brazil
| | - Mariana L Lyra
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Vinicius S A Loredam
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Thiago R Carvalho
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Célio F B Haddad
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo , São Paulo , Brazil
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical `Claudio Juan Bidau’ (CONICET-UNaM), Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones , Posadas, Misiones , Argentina
| | - Diego A Barrasso
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET) , Puerto Madryn, Chubut , Argentina
- Facultad de Ciencias Naturales y Ciencias de la Salud, Universidad Nacional de la Patagonia `San Juan Bosco’ , Puerto Madryn, Chubut , Argentina
| | - Daniel Loebmann
- Laboratório de Vertebrados, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande , Rio Grande, Rio Grande do Sul , Brazil
| | - Robson W Ávila
- Departamento de Biologia, Núcleo Regional de Ofiologia da UFC, Universidade Federal do Ceará , Fortaleza, Ceará , Brazil
| | - Francisco Brusquetti
- Instituto de Investigación Biológica del Paraguay , Del Escudo, Asunción , Paraguay
| | - Ana L C Prudente
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém, Pará , Brazil
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History , New York, NY , USA
| | - Victor Goyannes Dill Orrico
- Tropical Herpetology Laboratory, PPG Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz , Ilhéus, Bahia , Brazil
| | - Pedro Peloso
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém, Pará , Brazil
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11
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Ní Leathlobhair M, Lenski RE. Population genetics of clonally transmissible cancers. Nat Ecol Evol 2022; 6:1077-1089. [PMID: 35879542 DOI: 10.1038/s41559-022-01790-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly striking examples of these processes. These unusual cancers are clonal lineages that can spread through populations via physical transfer of living cancer cells from one host individual to another, and they have achieved long-term success in the colonization of at least eight different host species. Population genetic theory provides a useful framework for understanding the shift from a multicellular sexual animal into a unicellular asexual clone and its long-term effects on the genomes of these cancers. In this Review, we consider recent findings from transmissible cancer research with the goals of developing an evolutionarily informed perspective on transmissible cancers, examining possible implications for their long-term fate and identifying areas for future research on these exceptional lineages.
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Affiliation(s)
- Máire Ní Leathlobhair
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland.
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
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12
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Deng Z, Yao Y, Blair D, Hu W, Yin M. Ceriodaphnia (Cladocera: Daphniidae) in China: Lineage diversity, phylogeography and possible interspecific hybridization. Mol Phylogenet Evol 2022; 175:107586. [PMID: 35810974 DOI: 10.1016/j.ympev.2022.107586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/29/2022]
Abstract
The distribution and species/lineage diversity of freshwater invertebrate zooplankton remains understudied in China. Here, we explored the species/lineage diversity and phylogeography of Ceriodaphnia species across China. The taxonomy of this genus is under-explored. Seven morphospecies of Ceriodaphnia (C. cornuta, C. laticaudata, C. megops, C. pulchella, C. quadrangula, C. rotunda and C. spinata) were identified across 45 of 422 water bodies examined. Rather little morphological variation was observed within any single morphospecies regardless of country of origin. Nevertheless, we recognized that some or all of these morphospecies might represent species complexes. To investigate this, phylogenetic relationships within and among these morphospecies were investigated based on mitochondrial (partial cytochrome c oxidase subunit I gene) and nuclear (partial 28S rRNA gene) markers. The mitochondrial marker placed these populations in nine lineages corresponding to the morphospecies: C. laticaudata and C. pulchella were each represented by two lineages, suggesting that both are species complexes. The remaining five morphospecies were each represented by a single mtDNA lineage. Three of the nine mitochondrial lineages (belonging to C. pulchella, C. rotunda and C. megops) are newly reported and exhibited a restricted distribution within China. The nuclear-DNA phylogeny also recognized seven Ceriodaphnia taxa within China. We detected occasional mito-nuclear discordances in Ceriodaphnia taxa across China, suggesting interspecific introgression and hybridization. Our study contributes to an understanding of the species/lineage diversity of Ceriodaphnia, a genus with understudied taxonomy.
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Affiliation(s)
- Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Yiyang Yao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - David Blair
- College of Science and Engineering, James Cook University, Townsville, Qld 4811, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China; Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.
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13
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Delicado D, Hauffe T. Shell features and anatomy of the springsnail genus Radomaniola (Caenogastropoda: Hydrobiidae) show a different pace and mode of evolution over five million years. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Shell features are key factors for systematics and evolutionary biology studies of freshwater gastropods. Based mostly on shell morphology, 19 species of the springsnail genus Radomaniola (family Hydrobiidae) have been described. Although the scarce differentiation of various shell dimensions suggests morphological stasis, the evolutionary dynamics of shell and other anatomical structures have not yet been explored fully. By inferring a phylogeny and a time-calibrated species tree from mitochondrial (COI and 16S) and nuclear (28S) sequences of 15 recognized species, we initially examine the species diversity of the Radomaniola dataset and then, through phylogenetic comparative methods, assess the evolutionary correlation, pace and mode of 40 continuous shell and anatomical characters. By synthesizing the results of four species delimitation methods and through morphological examinations, we recognize 21 groups, for which taxonomy is discussed here. Seven new species are described. We reveal a high degree of correlated evolution between characters of the shell, which are constrained by a single morphological optimum, consistent with the morphological stasis model. Anatomical traits diverged rapidly in an unconstrained manner or toward multiple optima. These findings indicate that in order to understand the morphological evolution of springsnails, it is essential to examine different organs in detail.
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Affiliation(s)
- Diana Delicado
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, D-35392, Giessen, Germany
| | - Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
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14
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Grismer LL, del Pinto L, Quah ESH, Anuar S, Cota M, McGuire JA, Iskandar DT, Wood Jr PL, Grismer JL. Phylogenetic and multivariate analyses of Gekko smithii Gray, 1842 recover a new species from Peninsular Malaysia and support the resurrection of G. albomaculatus (Giebel, 1861) from Sumatra. VERTEBRATE ZOOLOGY 2022. [DOI: 10.3897/vz.72.e77702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abstract
An integrative taxonomic analysis of Sundaic populations of Gekko smithii from the Thai-Malaya Peninsula, Sumatra, and Borneo recovered four deeply divergent mitochondrial lineages that are separated by major geographic barriers (mountains and seaways). Furthermore, they bear a number of concordant statistically significant differences in meristic and morphometric features, morphospatial separation in multivariate space, and discrete differences in color pattern. Gekko smithiisensu stricto is restricted to southern Thailand south of the Isthmus of Kra and Peninsular Malaysia west of the Banjaran (mountain range) Titiwangsa, being that the type locality is on Penang Island, Penang. Gekko hulksp. nov. is a new species from extreme southern Thailand and Peninsular Malaysia east of the Banjaran Titiwangsa and five east coast islands—the type locality being Pulau (island) Tioman, Pahang. Gekko cf. albofasciolatus is tentatively used to include Bornean populations west of the Iran Mountains in Sabah and Sarawak which, in the absence of molecular data, cannot unequivocally be separated morphologically from G. albofasciolatus from the type locality at Banjarmasin, Kalimantan, Indonesia east of the Iran Mountains. In the absence of molecular data, G. albomaculatus is resurrected to include mainland Sumatran, Nias Island, and Banyak Islands populations which, based on their morphology, cannot be separated from descriptions of G. albomaculatus from the type locality of Bangka Island, 15 km off the southeast coast of mainland Sumatra. Further integrative analyses of all Sumatran and Bornean populations are currently underway as well as the enigmatic Wallacean populations from Sulawesi. Data are presented that strongly suggest all references to G. smithii from Java stem from a 151 year-old misidentification of a specimen of G. gecko of unknown provenance. Additionally, there are no vouchered records of G. smithii from Myanmar. The phylogeographic patterns of Sundaic populations of the G. smithii complex are concordant with those of a plethora of other Sundaic lineages.
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15
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van Steenderen C, Sutton G. SPEDE‐sampler: an R Shiny application to assess how methodological choices and taxon‐sampling can affect Generalised Mixed Yule Coalescent (GMYC) output and interpretation. Mol Ecol Resour 2022; 22:2054-2069. [PMID: 35094502 PMCID: PMC9306842 DOI: 10.1111/1755-0998.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/01/2022]
Abstract
Species delimitation tools are vital to taxonomy and the discovery of new species. These tools can make use of genetic data to estimate species boundaries, where one of the most widely used methods is the Generalized Mixed Yule Coalescent (GMYC) model. Despite its popularity, a number of factors are known to influence the performance and resulting inferences of the GMYC. Moreover, the few studies that have assessed model performance to date have been predominantly based on simulated data sets, where model assumptions are not violated. Here, we present a user‐friendly R Shiny application, ‘SPEDE‐sampler’ (SPEcies DElimitation sampler), that assesses the effect of computational and methodological choices, in combination with sampling effects, on the GMYC model. Output phylogenies are used to test the effect that (1) sample size, (2) BEAST and GMYC parameters (e.g. prior settings, single vs multiple threshold, clock model), and (3) singletons have on GMYC output. Optional predefined grouping information (e.g. morphospecies/ecotypes) can be uploaded in order to compare it with GMYC species and estimate percentage match scores. Additionally, predefined groups that contribute to inflated species richness estimates are identified by SPEDE‐sampler, allowing for the further investigation of potential cryptic species or geographical substructuring in those groups. Merging by the GMYC is also recorded to identify where traditional taxonomy has overestimated species numbers. Four worked examples are provided to illustrate the functionality of the program's workflow, and the variation that can arise when applying the GMYC model to empirical data sets. The R Shiny program is available for download at https://github.com/clarkevansteenderen/spede_sampler_R.
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Affiliation(s)
- C.J.M. van Steenderen
- Centre for Biological Control Department of Zoology and Entomology Rhodes University Grahamstown/Makhanda 6139 Eastern Cape South Africa
| | - G.F. Sutton
- Centre for Biological Control Department of Zoology and Entomology Rhodes University Grahamstown/Makhanda 6139 Eastern Cape South Africa
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16
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Poyarkov NA, Nguyen TV, Pawangkhanant P, Yushchenko PV, Brakels P, Nguyen LH, Nguyen HN, Suwannapoom C, Orlov N, Vogel G. An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina. PeerJ 2022; 10:e12713. [PMID: 35047234 PMCID: PMC8757378 DOI: 10.7717/peerj.12713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023] Open
Abstract
Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the "upstream" colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.
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Affiliation(s)
- Nikolay A. Poyarkov
- Laboratory of Tropical Ecology, Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam,Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | - Tan Van Nguyen
- Department of Species Conservation, Save Vietnam’s Wildlife, Ninh Binh, Vietnam
| | - Parinya Pawangkhanant
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Platon V. Yushchenko
- Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | | | - Linh Hoang Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Ngoc Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Chatmongkon Suwannapoom
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Nikolai Orlov
- Department of Herpetology, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Gernot Vogel
- Society for Southeast Asian Herpetology, Heidelberg, Germany
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17
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Gutiérrez-Rodríguez J, Zaldívar-Riverón A, Weissman DB, Vandergast AG. Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus Stenopelmatus (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data. INVERTEBR SYST 2022. [DOI: 10.1071/is21022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American Ammopelmatus, and the Mexican, and central and northern South American Stenopelmatus. The taxonomy of the latter genus was also revised, with 5, 13 and 14 species being respectively validated, declared as nomen dubium and described as new. Despite this effort, the systematics of Stenopelmatus is still far from complete. Here, we generated sequences of the mitochondrial DNA barcoding locus and performed two distinct DNA sequence-based approaches to assess the species’ limits among several populations of Stenopelmatus, with emphasis on populations from central and south-east Mexico. We reconstructed the phylogenetic relationships among representative species of the main clades within the genus using nuclear 3RAD data and carried out a molecular clock analysis to investigate its biogeographic history. The two DNA sequence-based approaches consistently recovered 34 putative species, several of which are apparently undescribed. Our estimates of phylogeny confirmed the recent generic update of Stenopelmatinae and revealed a marked phylogeographic structure within Stenopelmatus. Based on our results, we propose the existence of four species-groups within the genus (the faulkneri, talpa, Central America and piceiventris species-groups). The geographic distribution of these species-groups and our molecular clock estimates are congruent with the geological processes that took place in mountain ranges along central and southern Mexico, particularly since the Neogene. Our study emphasises the necessity to continue performing more taxonomic and phylogenetic studies on Stenopelmatus to clarify its actual species richness and evolutionary history in Mesoamerica.
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18
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Matsvay A, Dyachkova M, Mikhaylov I, Kiselev D, Say A, Burskaia V, Artyushin I, Khafizov K, Shipulin G. Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus. Microorganisms 2021; 10:31. [PMID: 35056480 PMCID: PMC8781740 DOI: 10.3390/microorganisms10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/03/2023] Open
Abstract
Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host's ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.
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Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - Marina Dyachkova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Ivan Mikhaylov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Daniil Kiselev
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, 34091 Montpellier, France
| | - Anna Say
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | | | - Ilya Artyushin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
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19
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Tan D, Parus A, Dunbar M, Espeland M, Willmott KR. Cytochrome c oxidase subunit I barcode species delineation methods imply critically underestimated diversity in ‘common’ Hermeuptychia butterflies (Lepidoptera: Nymphalidae: Satyrinae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
DNA ‘barcoding’ has contributed greatly to resolving species limits in rapidly diverging tropical insect groups. Here, we explored species diversity in the widespread, cryptic Neotropical butterfly genus Hermeuptychia by generating 601 new sequences of the cytochrome c oxidase I (COI) barcode, tripling available information. Our dataset focused in particular on Ecuador, a biogeographically pivotal country, with additional sequences from Brazil, Costa Rica, French Guiana, Guatemala, Mexico, Panama and Peru. We examined the performance of two phylogeny-based approaches for objectively delineating species, Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP), as well as a clustering-based approach, Automatic Barcode Gap Discovery (ABGD), on the combined dataset, including our data and 302 published sequences. In general, GMYC and PTP tended to cluster or split likely species as assessed from morphology, depending on model settings, whereas ABGD was less sensitive and produced a more plausible classification. Numerous sequences formed well-supported clades, putative species, that were unrepresented in previously published datasets. The average diversity across all methods was 45 species, in contrast to the 11 species recognized in the current taxonomy. The resulting COI dataset, in combination with ongoing genomic and morphological research, should significantly clarify our understanding of Hermeuptychia species diversity.
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Affiliation(s)
- Denise Tan
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Anamaria Parus
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Michelle Dunbar
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Marianne Espeland
- Arthropoda Department, Zoological Research Museum Alexander Koenig, Adenauer allee, Bonn, Germany
| | - Keith R Willmott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
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20
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Říčan O, Dragová K, Almirón A, Casciotta J, Gottwald J, Piálek L. MtDNA species-level phylogeny and delimitation support significantly underestimated diversity and endemism in the largest Neotropical cichlid genus (Cichlidae: Crenicichla). PeerJ 2021; 9:e12283. [PMID: 34820161 PMCID: PMC8588857 DOI: 10.7717/peerj.12283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/20/2021] [Indexed: 12/29/2022] Open
Abstract
Crenicichla is the largest and most widely distributed genus of Neotropical cichlids. Here, we analyze a mtDNA dataset comprising 681 specimens (including Teleocichla, a putative ingroup of Crenicichla) and 77 out of 105 presently recognized valid species (plus 10 out of 36 nominal synonyms plus over 50 putatively new species) from 129 locations in 31 major river drainages throughout the whole distribution of the genus in South America. Based on these data we make an inventory of diversity and highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using three methods of molecular species delimitation, we find between 126 and 168 species-like clusters, i.e., an average increase of species diversity of 65–121% with a range of increase between species groups. The increase ranges from 0% in the Missioneira and Macrophthama groups, through 25–40% (Lacustris group), 50–87% (Reticulata group, Teleocichla), 68–168% (Saxatilis group), 125–200% (Wallacii group), and 158–241% in the Lugubris group. We found a high degree of congruence between clusters derived from the three used methods of species delimitation. Overall, our results recognize substantially underestimated diversity in Crenicichla including Teleocichla. Most of the newly delimited putative species are from the Amazon-Orinoco-Guiana (AOG) core area (Greater Amazonia) of the Neotropical region, especially from the Brazilian and Guiana shield areas of which the former is under the largest threat and largest degree of environmental degradation of all the Amazon.
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Affiliation(s)
- Oldřich Říčan
- Faculty of Science, Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - Klára Dragová
- Faculty of Science, Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - Adriana Almirón
- División Zoología Vertebrados, UNLP, Facultad de Ciencias Naturales y Museo, La Plata, Buenos Aires Province, Argentina
| | - Jorge Casciotta
- CIC, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, Buenos Aires, Argentina.,UNLP, Facultad de Ciencias Naturales y Museo, División Zoología Vertebrados, Paseo del Bosque, La Plata, Buenos Aires Province, Argentina
| | - Jens Gottwald
- Heinrich-Lödding-Str. 14, 30823 Garbsen, Garbsen, Germany
| | - Lubomír Piálek
- Faculty of Science, Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
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21
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DNA barcoding in Dorcadionini (Coleoptera, Cerambycidae) uncovers mitochondrial-morphological discordance and the hybridogenic origin of several subspecies. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00531-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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22
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Gonnet V, Bidegaray-Batista L, Aisenberg A, Laborda Á, Hagopián D, Izquierdo MA, Piacentini LN, Simó M. A wolf spider from South American grasslands: phylogenetic placement and redescription of Paratrochosina amica (Mello-Leitão 1941). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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De Biase A, Colonnelli E, Baviera C, Bellò C, Casalini R, Corso A, La Marca A. Molecular analyses of flightless weevils Chiloneus from Sicily and adjoining islands revealed new synonymy (Coleoptera: Curculionidae). THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1960443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- A. De Biase
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza Rome University, Rome, Italy
| | | | - C. Baviera
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Messina, Italy
| | - C. Bellò
- World Biodiversity Association Onlus c/o Museo Civico di Storia Naturale, Verona, Italy
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Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N. SPART: A versatile and standardized data exchange format for species partition information. Mol Ecol Resour 2021; 22:430-438. [PMID: 34288531 DOI: 10.1111/1755-0998.13470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.
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Affiliation(s)
- Aurélien Miralles
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | | | - Sophie Brouillet
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomochika Fujisawa
- Center for Data Science Education and Research, Shiga University, Shiga, Japan
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - L Lacey Knowles
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, USA
| | - Sangeeta Kumari
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jeet Sukumaran
- Biology Department, LS 262, San Diego State University, San Diego, CA, USA
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Miguel Vences
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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Mazungula DN, Chakona A. An integrative taxonomic review of the Natal mountain catfish, Amphilius natalensis Boulenger 1917 (Siluriformes, Amphiliidae), with description of four new species. JOURNAL OF FISH BIOLOGY 2021; 99:219-239. [PMID: 33635552 DOI: 10.1111/jfb.14714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
An integrative taxonomic analysis combining mitochondrial cytochrome oxidase subunit I sequences, morphology, colour pattern and two species delimitation approaches revealed the existence of five lineages within the Natal mountain catfish, Amphilius natalensis, in southern Africa. These lineages are separated by substantial genetic divergences (1.6%-9.46%), and they can be consistently distinguished from one another based on a combination of morphology and colour pattern differences. Additionally, the lineages are allopatrically distributed and confined to isolated river systems draining discrete mountain ranges, which makes gene flow among them unlikely. One of these lineages is A. natalensis s.s., which is confined to the uMngeni and Tukela river systems in KwaZulu Natal (KZN) Province in South Africa. The other four lineages represent new species to science which are described as Amphilius zuluorum sp. nov., endemic to the uMkhomazi River system in KZN, Amphilius engelbrechti sp. nov., endemic to the Inkomati River system in Mpumalanga Province in South Africa, Amphilius marshalli sp. nov., endemic to the Pungwe and Lower Zambezi river systems in Zimbabwe and Mozambique, and Amphilius leopardus sp. nov., endemic to the Ruo River in Malawi. The results show that Amphilius laticaudatus which is endemic to the Buzi River system in Zimbabwe and Mozambique, belongs to the A. natalensis s.l. complex. A redescription of A. laticaudatus is presented and an updated identification key for the mountain catfishes of southern Africa is provided.
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Affiliation(s)
- Daniel Nkosinathi Mazungula
- National Research Foundation - South African Institute for Aquatic Biodiversity, Makhanda (Grahamstown), South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Albert Chakona
- National Research Foundation - South African Institute for Aquatic Biodiversity, Makhanda (Grahamstown), South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda (Grahamstown), South Africa
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Vakhrusheva OA, Mnatsakanova EA, Galimov YR, Neretina TV, Gerasimov ES, Naumenko SA, Ozerova SG, Zalevsky AO, Yushenova IA, Rodriguez F, Arkhipova IR, Penin AA, Logacheva MD, Bazykin GA, Kondrashov AS. Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga. Nat Commun 2020; 11:6421. [PMID: 33339818 PMCID: PMC7749112 DOI: 10.1038/s41467-020-19614-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 10/23/2020] [Indexed: 01/08/2023] Open
Abstract
Sexual reproduction is almost ubiquitous among extant eukaryotes. As most asexual lineages are short-lived, abandoning sex is commonly regarded as an evolutionary dead end. Still, putative anciently asexual lineages challenge this view. One of the most striking examples are bdelloid rotifers, microscopic freshwater invertebrates believed to have completely abandoned sexual reproduction tens of Myr ago. Here, we compare whole genomes of 11 wild-caught individuals of the bdelloid rotifer Adineta vaga and present evidence that some patterns in its genetic variation are incompatible with strict clonality and lack of genetic exchange. These patterns include genotype proportions close to Hardy-Weinberg expectations within loci, lack of linkage disequilibrium between distant loci, incongruent haplotype phylogenies across the genome, and evidence for hybridization between divergent lineages. Analysis of triallelic sites independently corroborates these findings. Our results provide evidence for interindividual genetic exchange and recombination in A. vaga, a species previously thought to be anciently asexual.
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Affiliation(s)
- Olga A Vakhrusheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation.
| | - Elena A Mnatsakanova
- Department of General Ecology and Hydrobiology, Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Yan R Galimov
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
| | - Tatiana V Neretina
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Evgeny S Gerasimov
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, 119435, Russian Federation
| | - Sergey A Naumenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, 02115, USA
| | - Svetlana G Ozerova
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
- Medkvadrat, Moscow, 115409, Russian Federation
| | - Arthur O Zalevsky
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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Qi S, Grismer LL, Lyu ZT, Zhang L, Li PP, Wang YY. A definition of the Goniurosaurus yingdeensis group (Squamata, Eublepharidae) with the description of a new species. Zookeys 2020; 986:127-155. [PMID: 33223883 PMCID: PMC7661482 DOI: 10.3897/zookeys.986.47989] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/08/2020] [Indexed: 11/12/2022] Open
Abstract
A definition of the Goniurosaurusyingdeensis group is presented in this study, on the basis of morphological and phylogenetic analyses based on a series of additional specimens. Moreover, a new species of this group, Goniurosaurusvariussp. nov., is proposed for northern Guangdong Province, China. The new species can be distinguished from the other two congeners of this group by the following unique characters: one or two internasals; enlarged supraorbital tubercles absent; paravertebral tubercles between limb insertions 27–29; dorsal tubercle rows at midbody 21–24; ten precloacal pores in males and absent in females; body bands with black spots; iris orange-red.
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Affiliation(s)
- Shuo Qi
- State Key Laboratory of Biocontrol/ The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China Sun Yat-sen University Guangzhou China.,Institute of Herpetology, Shenyang Normal University, Shenyang, Liaoning 110034, China Shenyang Normal University Shenyang China
| | - L Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, California 92515, USA La Sierra University Riverside United States of America
| | - Zhi-Tong Lyu
- State Key Laboratory of Biocontrol/ The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China Sun Yat-sen University Guangzhou China
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization/ Guangdong Public Laboratory of Wild Animal Conservation and Utilization/ Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou, Guangdong 510275, China Guangdong Academy of Science Guangzhou China
| | - Pi-Peng Li
- Institute of Herpetology, Shenyang Normal University, Shenyang, Liaoning 110034, China Shenyang Normal University Shenyang China
| | - Ying-Yong Wang
- State Key Laboratory of Biocontrol/ The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China Sun Yat-sen University Guangzhou China
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García-Morales AE, Domínguez-Domínguez O. Cryptic species within the rotifer Lecane bulla (Rotifera: Monogononta: Lecanidae) from North America based on molecular species delimitation. REV MEX BIODIVERS 2020. [DOI: 10.22201/ib.20078706e.2020.91.3116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Launay C, Félix MA, Dieng J, Delattre M. Diversification and hybrid incompatibility in auto-pseudogamous species of Mesorhabditis nematodes. BMC Evol Biol 2020; 20:105. [PMID: 32811433 PMCID: PMC7433073 DOI: 10.1186/s12862-020-01665-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/27/2020] [Indexed: 01/16/2023] Open
Abstract
Background Pseudogamy is a reproductive system in which females rely on the sperm of males to activate their oocytes, generally parasitizing males of other species, but do not use the sperm DNA. The nematode Mesorhabditis belari uses a specific form of pseudogamy, where females produce their own males as a source of sperm. Males develop from rare eggs with true fertilization, while females arise by gynogenesis. Males thus do not contribute their genome to the female offspring. Here, we explored the diversity of reproductive mode within the Mesorhabditis genus and addressed species barriers in pseudogamous species. Results To this end, we established a collection of over 60 Mesorhabditis strains from soil and rotting vegetal matter. We found that males from pseudogamous species displayed a reduced size of their body, male tail and sperm cells compared to males of sexual Mesorhabditis species, as expected for males that face little competition. Using rDNA sequences and crosses, we could define 11 auto-pseudogamous biological species, with closely related species pairs and a possible single origin of pseudogamy in the Mesorhabditis genus. Most crosses between males and females of different species did not even produce female progeny. This surprising species barrier in pseudogamous egg activation was pre or postcopulatory depending on the species pair. In the latter case, when hybrid embryos were produced, most arrested before the first embryonic cell division. Hybrid incompatibility between auto-pseudogamous species was due to defective interaction between sperm and oocyte as well as defective reconstitution of zygotic centrosomes. Conclusions We established a collection of sexual and pseudo-sexual species which offer an ideal framework to explore the origin and consequences of transition to asexuality. Our results demonstrate that speciation occurs in the pseudogamous state. Whereas genomic conflicts are responsible for hybrid incompatibility in sexual species, we here reveal that centrosomes constitute key organelles in the establishment of species barrier.
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Affiliation(s)
- Caroline Launay
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Inserm, UCBL, 69007, Lyon, France
| | - Marie-Anne Félix
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005, Paris, France
| | - Joris Dieng
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Inserm, UCBL, 69007, Lyon, France
| | - Marie Delattre
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Inserm, UCBL, 69007, Lyon, France.
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Astrop TI, Park Boush L, Weeks SC. Testing Weissman's Lineage Selection Model for the Maintenance of Sex: The Evolutionary Dynamics of Clam Shrimp Reproduction over Geologic Time. Zool Stud 2020; 59:e34. [PMID: 33262856 PMCID: PMC7689051 DOI: 10.6620/zs.2020.59-34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 11/18/2022]
Abstract
One of the most perplexing questions within evolutionary biology is: "why are there so many methods of reproduction?" Contemporary theories assume that sexual reproduction should allow long term survival as dispersal and recombination of genetic material provides a population of organisms with the ability to adapt to environmental change. One of the most frustrating aspects of studying the evolution of reproductive systems is that we have not yet been able to utilize information locked within the fossil record to assess breeding system evolution in deep time. While the fossil record provides us with information on an organism's living environment, as well as some aspects of its ecology, the preservation of biological interactions (reproduction, feeding, symbiosis, communication) is exceedingly rare. Using both information from extant taxa uncovered by a plethora of biological and ecological studies and the rich representation of the Spinicaudata (Branchiopoda: Crustacea) throughout the fossil record (from the Devonian to today), we address two hypotheses of reproductive evolutionary theory: (1) that unisexual species should be short lived and less speciose than their outcrossing counterparts and (2) that androdioecy (mixtures of males and hermaphrodites) is an unstable, transitionary system that should not persist over long periods of time. We find no evidence of all-unisexual spinicaudatan taxa (clam shrimp) in the fossil record, but do find evidence of both androdioecious and dioecious clam shrimp. We find that clades with many androdioecious species are less speciose but persist longer than their mostly dioecious counterparts. These data suggest that all-unisexual lineages likely do not persist long whereas mixtures of unisexual and sexual breeding can persist for evolutionarily long periods but tend to produce fewer species than mostly sexual breeding.
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Affiliation(s)
- Timothy I Astrop
- Fossil Forest Project, Blast Road, Brymbo, Wales, United Kingdom, LI11 5BT. E-mail: (Astrop)
| | - Lisa Park Boush
- Department of Geosciences, University of Connecticut, Storrs, CT 06269-1045, USA. E-mail: (Park Boush)
| | - Stephen C Weeks
- Department of Biology, The University of Akron, Akron, OH 44325-3908, USA. E-mail: (Weeks)
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Ramos-Rodríguez E, Moreno E, Conde-Porcuna JM. Intraspecific variation in sensitivity to food availability and temperature-induced phenotypic plasticity in the rotifer Keratella cochlearis. J Exp Biol 2020; 223:jeb209676. [PMID: 32107306 DOI: 10.1242/jeb.209676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 02/23/2020] [Indexed: 11/20/2022]
Abstract
Organisms with wide environmentally induced morphological plasticity and cosmopolitan distribution, e.g. the common freshwater rotifer Keratella cochlearis, are ideal models to study the evolution of plastic polymorphisms and the capacity of zooplankton to adapt to local selection conditions. We investigated population-level differences (population-by-environment interaction) in sensitivity to food availability and temperature-induced phenotypic plasticity between two clones of K. cochlearis isolated from neighboring populations in Ruidera Natural Park (Spain) with different trophic statuses: Tinaja lake (mesotrophic) and Cueva Morenilla lake (eutrophic). Using common-garden experiments, each clone proved to have a different sensitivity to food availability, with substantial phenotypic differences between them. When rotifers grew at moderate temperature (15.6°C), low food levels were more efficiently used by the Tinaja versus Cueva Morenilla clone, whereas high food levels were more efficiently used by the Cueva Morenilla versus Tinaja clone. The posterior spine was much longer and the lorica wider in the Tinaja versus Cueva Morenilla clone, with no difference in lorica length. Phylogenetic analysis based on cytochrome c oxidase subunit I (COI) gene sequences showed that the two populations have the same haplotype. This is the first study to show possible local adaptation by a rotifer species to habitats that consistently differ in food availability. We also detected an intriguing deviation from the expected negative relationship between posterior spine length and temperature. Our experimental results indicate that intermediate temperatures may activate the gene responsible for spine elongation in K. cochlearis This suggests that rotifers in nature could use water temperature as proxy signal of a change in predation risk before defense is needed.
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Affiliation(s)
- Eloísa Ramos-Rodríguez
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
- Instituto del Agua, Universidad de Granada, 18003 Granada, Spain
| | - Emilio Moreno
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
- Instituto del Agua, Universidad de Granada, 18003 Granada, Spain
| | - José María Conde-Porcuna
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
- Instituto del Agua, Universidad de Granada, 18003 Granada, Spain
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Chambers EA, Hillis DM. The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa. Syst Biol 2020; 69:184-193. [PMID: 31180508 DOI: 10.1093/sysbio/syz042] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/14/2022] Open
Abstract
Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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Zhao Z, Heideman N, Grobler P, Jordaan A, Bester P, Hofmeyr MD. Unraveling the diversification and systematic puzzle of the highly polymorphic Psammobates tentorius(Bell, 1828) complex (Reptilia: Testudinidae) through phylogenetic analyses and species delimitation approaches. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Neil Heideman
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Paul Grobler
- Department of Genetics University of the Free State Bloemfontein South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Phillip Bester
- Department of Virology University of the Free State and National Health Laboratory Service (NHLS) Bloemfontein South Africa
| | - Margaretha D. Hofmeyr
- Chelonian Biodiversity and Conservation Department of Biodiversity and Conservation Biology University of the Western Cape Bellville South Africa
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Postiglioni R, Bidegaray-Batista L, Simó M, Arnedo MA. Move to stay: genetic structure and demographic history of a wolf spider inhabiting coastal sand dunes of southern South America. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1689197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Rodrigo Postiglioni
- Departamento de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo, CP 11600, Uruguay
- Sección Entomología. Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
| | - Leticia Bidegaray-Batista
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo, CP 11600, Uruguay
| | - Miguel Simó
- Departamento de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo, CP 11600, Uruguay
- Sección Entomología. Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
| | - Miquel A. Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, Barcelona, CP 08028, Spain
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Fungal species boundaries in the genomics era. Fungal Genet Biol 2019; 131:103249. [PMID: 31279976 DOI: 10.1016/j.fgb.2019.103249] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/21/2019] [Accepted: 06/28/2019] [Indexed: 12/30/2022]
Abstract
Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.
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Dalstein V, Eberle J, Fabrizi S, Etzbauer C, Ahrens D. COI-based species delimitation in Indochinese Tetraserica chafers reveal hybridisation despite strong divergence in male copulation organs. ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00398-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Alonso F, Terán GE, Aguilera G, Říčan O, Casciotta J, Serra WS, Almirón A, Benítez MF, García I, Mirande JM. Description of a new species of the Neotropical cichlid genus Gymnogeophagus Miranda Ribeiro, 1918 (Teleostei: Cichliformes) from the Middle Paraná basin, Misiones, Argentina. PLoS One 2019; 14:e0210166. [PMID: 30759109 PMCID: PMC6374015 DOI: 10.1371/journal.pone.0210166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/14/2019] [Indexed: 12/04/2022] Open
Abstract
Gymnogeophagus jaryi, new species, is described from Southern tributaries of the Middle Paraná basin in Misiones. It can be distinguished from all other members of the genus, except from G. australis and G. caaguazuensis, by the presence of a hyaline to grey anterior portion of the dorsal fin. Gymnogeophagus jaryi differs from G. caaguazuensis by a longer caudal peduncle, caudal fin not lyrate, central portion of scales on dorsal portion of trunk light iridescent blue and by white spots in soft portion of dorsal fin in adult males, and from G. australis by the light iridescent blue coloration of central portion of scales on the dorsal portion of trunk and tail, and by the lack of scales on the soft portion of the dorsal fin. Additionally, it can be diagnosed by the following unique combination of characters: 10-11 dorsal-fin branched rays, 27-30 E1 scales, absence of lips thickening, and, in males, by the possession of a hump in adults, caudal fin not lyrate, presence of large white spots forming transversal stripes distally and in anterior area of the dorsal fin's soft portion, central area of scales on the dorsal portion of the trunk light iridescent blue, lack of scales on the base of the dorsal fin's soft portion, absence of a conspicuous and oblique dark band from the eye to the anterior border of the head, anterior portion of dorsal fin hyaline to grey, scales of the midlateral spot each bearing a semicircular light blue blotch, head hump starting at the horizontal through the eyes, concave anterior profile in lateral view, base of unpaired fins yellow, and whitish hyaline spots on caudal fin. The new species, based on mtDNA phylogeny, is the sister species of G. caaguazuensis from the Paraguay basin and is closely related to G. australis.
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Affiliation(s)
- Felipe Alonso
- Instituto de Bio y Geociencias del NOA (IBIGEO-CONICET), CCT-Salta, Rosario de Lerma, Salta, Argentina
| | - Guillermo E. Terán
- Unidad Ejecutora Lillo (CONICET), Fundación Miguel Lillo, San Miguel de Tucumán, Tucumán, Argentina
| | - Gastón Aguilera
- Unidad Ejecutora Lillo (CONICET), Fundación Miguel Lillo, San Miguel de Tucumán, Tucumán, Argentina
| | - Oldřich Říčan
- University of South Bohemia, Faculty of Science, Department of Zoology, České Budějovice, Czech Republic
| | - Jorge Casciotta
- Universidad Nacional de La Plata, Facultad de Ciencias Naturales y Museo, División Zoología Vertebrados, La Plata, Buenos Aires, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Buenos Aires, Argentina
| | - Wilson Sebastián Serra
- Sección Ictiología, Dpto. de Zoología, Museo Nacional de Historia Natural, Montevideo, Uruguay
- Centro Universitario Regional del Este (CURE) Sede Rocha, Rocha, Uruguay
- Sección Zoología de Vertebrados, Facultad de Ciencias de la UdelaR, Montevideo, Uruguay
| | - Adriana Almirón
- Universidad Nacional de La Plata, Facultad de Ciencias Naturales y Museo, División Zoología Vertebrados, La Plata, Buenos Aires, Argentina
| | | | - Ignacio García
- Instituto de Limnología "Dr. Raúl A. Ringuelet" (ILPLA-CONICET), La Plata, Buenos Aires, Argentina
| | - Juan Marcos Mirande
- Unidad Ejecutora Lillo (CONICET), Fundación Miguel Lillo, San Miguel de Tucumán, Tucumán, Argentina
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Steiner FM, Csősz S, Markó B, Gamisch A, Rinnhofer L, Folterbauer C, Hammerle S, Stauffer C, Arthofer W, Schlick-Steiner BC. Turning one into five: Integrative taxonomy uncovers complex evolution of cryptic species in the harvester ant Messor “structor”. Mol Phylogenet Evol 2018; 127:387-404. [DOI: 10.1016/j.ympev.2018.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 03/02/2018] [Accepted: 04/04/2018] [Indexed: 11/25/2022]
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Waddell EH, Crotti M, Lougheed SC, Cannatella DC, Elmer KR. Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group, the Neotropical Pristimantis leaf litter frogs. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1503202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Emily H. Waddell
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- Centre for Ecology and Hydrology, Bush Estate, Penicuik, EH26 0QB, UK
| | - Marco Crotti
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Stephen C. Lougheed
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - David C. Cannatella
- Section of Integrative Biology and Texas Memorial Museum, University of Texas, Austin, TX 78712, USA
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada
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Grismer LL, Wood PL, Quah ES, Murdoch ML, Grismer MS, Herr MW, Espinoza RE, Brown RM, Lin A. A phylogenetic taxonomy of the Cyrtodactylus peguensis group (Reptilia: Squamata: Gekkonidae) with descriptions of two new species from Myanmar. PeerJ 2018; 6:e5575. [PMID: 30258710 PMCID: PMC6151117 DOI: 10.7717/peerj.5575] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/10/2018] [Indexed: 11/21/2022] Open
Abstract
A phylogenetic taxonomy of species in the Cyrtodactylus peguensis group from the Ayeyarwady Basin of Myanmar is constructed based on color pattern, morphology, and molecular systematic analyses using the mitochondrial gene NADH dehydrogenase subunit 2. Newly collected samples from the type locality of C. peguensis and other localities indicate that this clade is endemic to central Myanmar and contains at least seven species, four of which are undescribed. Three species, including C. peguensis occur in the low hills of the Bago Yoma Range within the central portion of the Ayeyarwady Basin. Two of these, C. myintkyawthurai sp. nov. from the northern and central Bago Yoma and C. meersi sp. nov. which is syntopic with C. peguensis in the southern Bago Yoma are described herein. As more lowland hilly areas bordering, and within the Ayeyarwady Basin are surveyed, more new species of this group are likely to be discovered. These discoveries continue the recent surge of descriptions of new species of Cyrtodactylus that are being discovered in Myanmar.
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Affiliation(s)
- L. Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Perry L. Wood
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Evan S.H. Quah
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Penang, Malaysia
| | | | - Marta S. Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Mark W. Herr
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Robert E. Espinoza
- Department of Biology, California State University, Northridge, Northridge, CA, USA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Aung Lin
- Department of Biology, Fauna and Flora International, Yangon, Myanmar
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Cross-Contamination Explains "Inter and Intraspecific Horizontal Genetic Transfers" between Asexual Bdelloid Rotifers. Curr Biol 2018; 28:2436-2444.e14. [PMID: 30017483 DOI: 10.1016/j.cub.2018.05.070] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/07/2017] [Accepted: 05/23/2018] [Indexed: 11/22/2022]
Abstract
A few metazoan lineages are thought to have persisted for millions of years without sexual reproduction. If so, they would offer important clues to the evolutionary paradox of sex itself [1, 2]. Most "ancient asexuals" are subject to ongoing doubt because extant populations continue to invest in males [3-9]. However, males are famously unknown in bdelloid rotifers, a class of microscopic invertebrates comprising hundreds of species [10-12]. Bdelloid genomes have acquired an unusually high proportion of genes from non-metazoans via horizontal transfer [13-17]. This well-substantiated finding has invited speculation [13] that homologous horizontal transfer between bdelloid individuals also may occur, perhaps even "replacing" sex [14]. In 2016, Current Biology published an article claiming to supply evidence for this idea. Debortoli et al. [18] sampled rotifers from natural populations and sequenced one mitochondrial and four nuclear loci. Species assignments were incongruent among loci for several samples, which was interpreted as evidence of "interspecific horizontal genetic transfers." Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more highly divergent mitochondrial and ribosomal sequences, revealing cross-contamination with DNA from multiple animals of different species. Other chromatograms indicate contamination with DNA from conspecific animals, explaining genetic and genomic evidence for "intraspecific horizontal exchanges" reported in the same study. Given the clear evidence of contamination, the data and findings of Debortoli et al. [18] provide no reliable support for their conclusions that DNA is transferred horizontally between or within bdelloid species.
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Thézé J, Lopez-Vaamonde C, Cory JS, Herniou EA. Biodiversity, Evolution and Ecological Specialization of Baculoviruses: A Treasure Trove for Future Applied Research. Viruses 2018; 10:E366. [PMID: 29997344 PMCID: PMC6071083 DOI: 10.3390/v10070366] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 11/16/2022] Open
Abstract
The Baculoviridae, a family of insect-specific large DNA viruses, is widely used in both biotechnology and biological control. Its applied value stems from millions of years of evolution influenced by interactions with their hosts and the environment. To understand how ecological interactions have shaped baculovirus diversification, we reconstructed a robust molecular phylogeny using 217 complete genomes and ~580 isolates for which at least one of four lepidopteran core genes was available. We then used a phylogenetic-concept-based approach (mPTP) to delimit 165 baculovirus species, including 38 species derived from new genetic data. Phylogenetic optimization of ecological characters revealed a general pattern of host conservatism punctuated by occasional shifts between closely related hosts and major shifts between lepidopteran superfamilies. Moreover, we found significant phylogenetic conservatism between baculoviruses and the type of plant growth (woody or herbaceous) associated with their insect hosts. In addition, we found that colonization of new ecological niches sometimes led to viral radiation. These macroevolutionary patterns show that besides selection during the infection process, baculovirus diversification was influenced by tritrophic interactions, explained by their persistence on plants and interactions in the midgut during horizontal transmission. This complete eco-evolutionary framework highlights the potential innovations that could still be harnessed from the diversity of baculoviruses.
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Affiliation(s)
- Julien Thézé
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, 37200 Tours, France.
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
| | - Carlos Lopez-Vaamonde
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, 37200 Tours, France.
- INRA, UR633 Zoologie Forestière, 45075 Orléans, France.
| | - Jenny S Cory
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, 37200 Tours, France.
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43
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Okamiya H, Sugawara H, Nagano M, Poyarkov NA. An integrative taxonomic analysis reveals a new species of lotic Hynobius salamander from Japan. PeerJ 2018; 6:e5084. [PMID: 29942708 PMCID: PMC6015758 DOI: 10.7717/peerj.5084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/05/2018] [Indexed: 11/20/2022] Open
Abstract
We examine the phylogenetic structure and morphological differentiation within the Hynobius kimurae–H. boulengeri species complex—a widely-distributed group of stream-breeding hynobiid salamanders, inhabiting montane areas of western, central and eastern parts of Honshu Island, Japan. Phylogenetic relationships were assessed based on analyses of mitochondrial (mtDNA) and nuclear (nuDNA) gene fragments for a total of 51 samples representing 23 localities covering the entire range of the species complex. Morphological study included one-way analysis of variance (ANOVA) and principal components analysis (PCA) analyses of 26 morphometric and six meristic characters for 38 adult specimens of H. kimurae and three adult specimens of H. boulengeri. MtDNA genealogy supported monophyly of the H. kimurae–H. boulengeri complex, which is sister to all other Hynobius except H. retardatus. The complex is subdivided into three major clades, corresponding to the Eastern (Clade I) and Western (Clade II) populations of H. kimurae sensu lato, and to H. boulengeri (Clade III). Monophyly of H. kimurae sensu lato is only moderately supported by mtDNA, while nuDNA suggested that the Western form of H. kimurae is closer to H. boulengeri than to the eastern form. The time of the split of the H. kimurae–H. boulengeri complex is estimated as late Miocene and coincides with intensive crust movement in western Japan. Divergence between Clades I and II took place in early Pliocene and was likely influenced by the uplift of Central Japanese Highlands. All three clades were found to be different in a number of morphological characters, allowing us to describe the eastern form of H. kimurae as a new species, Hynobius fossigenussp. nov.
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Affiliation(s)
- Hisanori Okamiya
- Department of Biology, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Hirotaka Sugawara
- Department of Biology, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Masahiro Nagano
- Faculty of Science and Technology, Oita University, Dannoharu, Oita, Japan
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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44
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Lorén JG, Farfán M, Fusté MC. Species Delimitation, Phylogenetic Relationships, and Temporal Divergence Model in the Genus Aeromonas. Front Microbiol 2018; 9:770. [PMID: 29731747 PMCID: PMC5920023 DOI: 10.3389/fmicb.2018.00770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/05/2018] [Indexed: 11/16/2022] Open
Abstract
The definition of species boundaries constitutes an important challenge in biodiversity studies. In this work we applied the Generalized Mixed Yule Coalescent (GMYC) method, which determines a divergence threshold to delimit species in a phylogenetic tree. Based on the tree branching pattern, the analysis fixes the transition threshold between speciation and the coalescent process associated with the intra-species diversification. This approach has been widely used to delineate eukaryote species and establish their diversification process from sequence data. Nevertheless, there are few examples in which this analysis has been applied to a bacterial population. Although the GMYC method was originally designed to assume a constant (Yule) model of diversification at between-species level, it was later evaluated simulating other conditions. Our aim was therefore to determine the species delineation in Aeromonas using the GMYC method and asses which model best explains the speciation process in this bacterial genus. The application of the GMYC method allowed us to clearly delineate the Aeromonas species boundaries, even in the controversial groups, such as the A. veronii or A. media species complexes.
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Affiliation(s)
- J G Lorén
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Maribel Farfán
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - M C Fusté
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
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45
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Lucid M, Rankin A, Espíndola A, Chichester L, Ehlers S, Robinson L, Sullivan J. Taxonomy and biogeography of Hemphillia (Gastropoda: Pulmonata: Arionidae) in North American rainforests, with description of a new species (Skade’s jumping-slug, Hemphillia skadei sp. nov.). CAN J ZOOL 2018. [DOI: 10.1139/cjz-2017-0260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Species diversity of the genus Hemphillia Bland and W.G. Binney, 1872 (jumping-slugs) was studied across its range in western North America’s inland temperate rainforests. The taxonomic relationships among jumping-slug populations were clarified by integrating morphological, molecular, and biogeographic approaches. A new species, Skade’s jumping-slug (Hemphillia skadei sp. nov.), was discovered in this process and is described herein. We base this taxonomic decision on molecular comparison of representatives from other Hemphillia species and four morphological characters that distinguish H. skadei from its sister species, the pale jumping-slug (Hemphillia camelus Pilsbry and Vanatta, 1897). The distribution of H. skadei and H. camelus is described along with the notable lack of detection of the marbled jumping-slug (Hemphillia danielsi Vanatta, 1914) within the primary survey area.
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Affiliation(s)
- M.K. Lucid
- Idaho Department of Fish and Game, 2885 Kathleen Avenue, Coeur d’Alene, ID 83815, USA
| | - A. Rankin
- Department of Biological Sciences, Life Sciences South 252, 875 Perimeter Drive MS 3051, University of Idaho, Moscow, ID 83844-3051, USA
| | - A. Espíndola
- Department of Biological Sciences, Life Sciences South 252, 875 Perimeter Drive MS 3051, University of Idaho, Moscow, ID 83844-3051, USA
| | - L. Chichester
- 209 Chestnut Springs Way, Williamston, SC 29697, USA
| | - S. Ehlers
- Idaho Department of Fish and Game, 2885 Kathleen Avenue, Coeur d’Alene, ID 83815, USA
| | - L. Robinson
- Idaho Department of Fish and Game, 2885 Kathleen Avenue, Coeur d’Alene, ID 83815, USA
| | - J. Sullivan
- Department of Biological Sciences, Life Sciences South 252, 875 Perimeter Drive MS 3051, University of Idaho, Moscow, ID 83844-3051, USA
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Camelier P, Menezes NA, Costa-Silva GJ, Oliveira C. Molecular and morphological data of the freshwater fish Glandulocauda melanopleura (Characiformes: Characidae) provide evidences of river captures and local differentiation in the Brazilian Atlantic Forest. PLoS One 2018; 13:e0194247. [PMID: 29579069 PMCID: PMC5868800 DOI: 10.1371/journal.pone.0194247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/27/2018] [Indexed: 01/16/2023] Open
Abstract
The current distribution of freshwater fishes across multiple basins along Eastern Brazil can be associated to two main events: river captures or temporary paleoconnections. Apparently, river captures had a more significant role on distribution and structuring of species from upland areas, such as Glandulocauda melanopleura. Populations of this species are found in contiguous drainages in presently isolated upper parts of Rio Tietê and the coastal basins of Guaratuba, Itatinga, Itanháem, and Ribeira de Iguape, in the Atlantic Forest domain. The allopatric and disjoint distribution of G. melanopleura associated with variation of morphological characters detected among geographically isolated populations stimulated this study. Thus, an integrative approach was undertaken, including morphological and molecular data, to better understand the evolutionary history of the species and the area where it occurs. Molecular analyses based on two mitochondrial markers revealed a strong genetic structure within G. melanopleura, that allowed recognition of two lineages, one distributed in both the upper Tietê and Itanhaém and the other in the Guaratuba. Overall, morphological data revealed some intraspecific overlapping variation, indicating that all samples are conspecific. Phylogenetic and phylogeographic analyses allied to divergence times and geomorphological information indicate that the current distribution of G. melanopleura is a result of relatively recent river captures involving the Tietê and some other coastal drainages. Although of recent origin, they occurred long enough to completely isolate these populations, since there are no haplotypes sharing between them. The conservation status of this species is also discussed, and our results corroborate the need to understand population structure for conservation planning.
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Affiliation(s)
- Priscila Camelier
- Museu de Zoologia da Universidade de São Paulo, CEP, São Paulo, SP, Brazil
| | | | - Guilherme José Costa-Silva
- Universidade Santo Amaro, Rua Prof. Enéas de Siqueira Neto, Jardim das Imbuias, CEP, São Paulo, SP, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito Rubião Jr., CEP, Botucatu, SP, Brazil
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Wang B, Nishikawa K, Matsui M, Nguyen TQ, Xie F, Li C, Khatiwada JR, Zhang B, Gong D, Mo Y, Wei G, Chen X, Shen Y, Yang D, Xiong R, Jiang J. Phylogenetic surveys on the newt genus Tylototriton sensu lato (Salamandridae, Caudata) reveal cryptic diversity and novel diversification promoted by historical climatic shifts. PeerJ 2018; 6:e4384. [PMID: 29576937 PMCID: PMC5853667 DOI: 10.7717/peerj.4384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
Global climatic transitions and Tibetan Plateau uplifts are hypothesized to have profoundly impacted biodiversity in southeastern Asia. To further test the hypotheses related to the impacts of these incidents, we investigated the diversification patterns of the newt genus Tylototriton sensu lato, distributed across the mountain ranges of southeastern Asia. Gene-tree and species-tree analyses of two mitochondrial genes and two nuclear genes revealed five major clades in the genus, and suggested several cryptic species. Dating estimates suggested that the genus originated in the early-to-middle Miocene. Under different species delimitating scenarios, diversification analyses with birth-death likelihood tests indicated that the genus held a higher diversification rate in the late Miocene-to-Pliocene era than that in the Pleistocene. Ancestral area reconstructions indicated that the genus originated from the northern Indochina Peninsula. Accordingly, we hypothesized that the Miocene Climatic Transition triggered the diversification of the genus, and the reinforcement of East Asian monsoons associated with the stepwise uplifts of the Tibetan Plateau promoted the radiation of the genus in southeastern Asia during the Miocene-to-Pliocene period. Quaternary glacial cycles likely had limited effects on speciation events in the genus, but mainly had contributions on their intraspecific differentiations.
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Affiliation(s)
- Bin Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Feng Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Cheng Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Janak Raj Khatiwada
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Baowei Zhang
- College of Life Science, Anhui University, Hefei, China
| | - Dajie Gong
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Yunming Mo
- Natural History Museum of Guangxi, Nanning, China
| | - Gang Wei
- Biodiversity Conservation Key Laboratory, Guiyang College, Guiyang, China
| | - Xiaohong Chen
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Youhui Shen
- College of Life Science, Hunan Normal University, Changsha, China
| | - Daode Yang
- Institute of Wildlife Conservation, Central South University of Forestry & Technology, Changsha, China
| | - Rongchuan Xiong
- Department of Life Science, Liupanshui Normal University, Liupanshui, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
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48
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Impact of tree priors in species delimitation and phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae). Mol Phylogenet Evol 2018; 119:1-12. [DOI: 10.1016/j.ympev.2017.10.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 09/23/2017] [Accepted: 10/27/2017] [Indexed: 11/22/2022]
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Carvalho ML, Costa Silva GJD, Melo S, Ashikaga FY, Shimabukuro-Dias CK, Scacchetti PC, Devidé R, Foresti F, Oliveira C. The non-monotypic status of the neotropical fish genus Hemiodontichthys (Siluriformes, Loricariidae) evidenced by genetic approaches. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1224-1230. [DOI: 10.1080/24701394.2018.1431230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Margarida Lima Carvalho
- Laboratório de Citogenética e Genética Molecular – LABGENE, Universidade Federal do Acre, Rio Branco, Acre, Brazil
| | - Guilherme José da Costa Silva
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
- Departamento de Biologia, Universidade Santo Amaro São Paulo, Brazil
| | - Silvana Melo
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Fernando Yuldi Ashikaga
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Cristiane Kioko Shimabukuro-Dias
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Priscilla Cardim Scacchetti
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Renato Devidé
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Fausto Foresti
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Claudio Oliveira
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
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Prantoni AL, Belmonte-Lopes R, Lana PC, Erséus C. Genetic diversity of marine oligochaetous clitellates in selected areas of the South Atlantic as revealed by DNA barcoding. INVERTEBR SYST 2018. [DOI: 10.1071/is17029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Marine oligochaetous clitellates are poorly investigated in the South Atlantic Ocean, especially along the east coast of South America. Closely related species are often difficult to distinguish based on morphology. The lack of specialists and modern identification guides have been pointed out as the main reasons for the scarcity of studies in the South Atlantic Ocean as a whole. To increase the knowledge of this group in the South Atlantic, the genetic diversity of a sample of marine oligochaetous clitellates from Brazil, South Africa and Antarctica was assessed by the Automatic Barcode Gap Discovery (ABGD) and the generalised mixed Yule coalescent (GMYC) approaches. In total, 80 cytochrome c oxidase subunit I (COI) sequences were obtained, each with ~658bp, estimated to represent 32 distinct putative species. ABGD established a barcoding gap between 3% and 14% divergence for uncorrected p-distances and the estimates of GMYC were largely concordant. All the clusters or putative species were genetically associated with previously known species or genera. This study thus confirms the adequacy of the COI barcoding approach combined with a genetic divergence threshold at the order of 10% for marine oligochaetous clitellates.
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