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Vučić T, Drobnjaković M, Ajduković M, Bugarčić M, Wielstra B, Ivanović A, Cvijanović M. A staging table of Balkan crested newt embryonic development to serve as a baseline in evolutionary developmental studies. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38953174 DOI: 10.1002/jez.b.23269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/08/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024]
Abstract
There is an increased interest in the evolution and development of newts from the genus Triturus because: (1) morphological differentiation among the nine constituent species largely corresponds to different ecological preferences, (2) hybridization between different species pairs has various evolutionary outcomes in terms of life history traits and morphology, and (3) the genus expresses a balanced lethal system that causes arrested growth and death of half of the embryos. These features provide natural experimental settings for molecular, morphological, and life-history studies. Therefore, we produce a staging table for the Balkan crested newt (T. ivanbureschi). We provide detailed descriptions of 34 embryonic stages based on easily observable and interpretable external morphological characters, to ensure reproducibility. Compared with previous staging tables for Triturus, we include a vastly increased sample size and provide high-resolution photographs in lateral, ventral, and dorsal view, complemented by videos of specific developmental periods, and accompanied by detailed explanations on how to delineate the specific stages. Our staging table will serve as a baseline in comparative studies on Triturus newts: an emerging model system in evolutionary and developmental studies.
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Affiliation(s)
- Tijana Vučić
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Marija Drobnjaković
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Maja Ajduković
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marko Bugarčić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ben Wielstra
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ana Ivanović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Milena Cvijanović
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
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Safaei-Mahroo B, Ghaffari H, Niamir A. A synoptic review of the Amphibians of Iran: bibliography, taxonomy, synonymy, distribution, conservation status, and identification key to the eggs, larvae, and adults. Zootaxa 2023; 5279:1-112. [PMID: 37518755 DOI: 10.11646/zootaxa.5279.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Indexed: 08/01/2023]
Abstract
This study provides an illustrated account, a comprehensive update of the systematics, and a bibliography of the 15 species of anurans in five families, eight genera; and of the six species of urodeles in two families, four genera in Iran. Bufonidae, with eight species, is the most diverse family; Salamandridae has five species and Ranidae has four species. This study also presents updated identification keys for the eggs, larvae, and metamorphosed amphibians of Iran. We designated specimen NMW 19855.1 as neotype of Pelophylax persicus (Schneider, 1799) comb. nov.. Along with distribution maps obtained from all the reliable localities and museum specimens known at this time, the modelled habitat of species, and for the first time, the National Red List of amphibians based on the IUCN red list categories and criteria. Based on our evaluation we propose to categorize Bufo eichwaldi, Paradactylodon persicus, Neurergus derjugini, and N. kaiseri as Vulnerable at National Red List, and to move Bufotes (Calliopersa) luristanicus, B. (C.) surdus, Firouzophrynus olivaceus, and Rana pseudodalmatina from the category of Least Concern (LC) to Near Threatened (NT). The National Red List of amphibians that we propose has significant implications for endangered species management and conservation. Forty-one percent of amphibian species in Iran are endemic to the country, and more than forty percent of the Iranian amphibians are at risk of extinction. Zagros Mountain forest and Hyrcaniain forests have more than 80% (i.e. 18 species) of the diversity of Iranian amphibians. A considerable amount of scientific literature published on Iranian amphibians in Persian language is not easily accessible to researchers outside Iran. This monograph attempts to remedy the situation and provides broader access to international herpetology. We recognize that taxonomy is always in a state of flux, and the names and synonymies used here reflect our current view.
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Affiliation(s)
| | - Hanyeh Ghaffari
- Department of Environmental Sciences; Faculty of Natural Resources; University of Kurdistan; Sanandaj; Iran.
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Centre; Frankfurt am Main; Germany.
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3
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Ajduković M, Vučić T, Cvijanović M. Effects of thiourea on the skull of Triturus newts during ontogeny. PeerJ 2021; 9:e11535. [PMID: 34141485 PMCID: PMC8179219 DOI: 10.7717/peerj.11535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/07/2021] [Indexed: 11/20/2022] Open
Abstract
Background In amphibians, thyroid hormone (TH) has a profound role in cranial development, especially in ossification of the late-appearing bones and remodeling of the skull. In the present study, we explored the influence of TH deficiency on bone ossification and resulting skull shape during the ontogeny of Triturus newt hybrid larvae obtained from interspecific crosses between T. ivanbureschi and T. macedonicus. Methods Larvae were treated with two concentrations of thiourea (an endocrine disruptor that chemically inhibits synthesis of TH) during the midlarval and late larval periods. Morphological differences of the cranium were assessed at the end of the midlarval period (ontogenetic stage 62) and the metamorphic stage after treatment during the late larval period. Results There was no difference in the ossification level and shape of the skull between the experimental groups (control and two treatment concentrations) at stage 62. During the late larval period and metamorphosis, TH deficit had a significant impact on the level of bone ossification and skull shape with no differences between the two treatment concentrations of thiourea. The most pronounced differences in bone development were: the palatopterygoid failed to disintegrate into the palatal and pterygoid portions, retardation was observed in development of the maxilla, nasal and prefrontal bones and larval organization of the vomer was retained in thiourea-treated larvae. Conclusions This implies that deficiency of TH caused retardation in development and arrested metamorphic cranium skeletal reorganization, which resulted in divergent cranial shape compared to the control group. Our results confirmed that skull remodeling and ossification of late-appearing bones is TH–dependent, as in other studied Urodela species. Also, our results indicate that TH plays an important role in the establishment of skull shape during the ontogeny of Triturus newts, especially during the late larval period and metamorphosis, when TH concentrations reach their maximum.
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Affiliation(s)
- Maja Ajduković
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Tijana Vučić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Milena Cvijanović
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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Mačát Z, Rulík M, Jablonski D, Reiter A, Jeřábková L, Rada S, Mikulíček P. Species-specific habitat preferences do not shape the structure of a crested newt hybrid zone ( Triturus cristatus x T. carnifex). Ecol Evol 2019; 9:12446-12458. [PMID: 31788189 PMCID: PMC6875670 DOI: 10.1002/ece3.5683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/31/2019] [Accepted: 09/04/2019] [Indexed: 11/08/2022] Open
Abstract
Reproductive isolation barriers maintain the integrity of species by preventing interspecific gene flow. They involve temporal, habitat or behavioral isolation acting before fertilization, and postzygotic isolation manifested as hybrid mortality or sterility. One of the approaches of how to study reproductive isolation barriers is through the analysis of hybrid zones. In this paper, we describe the structure of a hybrid zone between two crested newt species (Triturus cristatus and T. carnifex) in the southern part of the Czech Republic using morphological, microsatellite, and mitochondrial (mtDNA) markers. Specifically, we tested the hypothesis that the structure of the hybrid zone is maintained by species-specific habitat preferences. Comparing the genetic structure of populations with geographical and ecological parameters, we found that the hybrid zone was structured primarily geographically, with T. cristatus-like populations occurring in the northeast and T. carnifex-like populations in the southwest. Despite T. cristatus tending to occur in deeper ponds and T. carnifex on localities with more shading, the effect of both ecological parameters on the structure of the zone was minimal. Next, we corroborated that T. carnifex individuals and some hybrids possess mtDNA of T. dobrogicus, whose nuclear background was not detected in the studied hybrid zone. Hybridization between T. carnifex and T. dobrogicus (resulting in unidirectional mtDNA introgression) had to predate subsequent formation of the hybrid zone between T. cristatus and T. carnifex. Populations of crested newts in the southern part of the Czech Republic thus represent a genetic mosaic of nuclear and mitochondrial genomes of three species.
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Affiliation(s)
- Zdeněk Mačát
- Department of Ecology and Environmental SciencesPalacky UniversityOlomoucCzech Republic
| | - Martin Rulík
- Department of Ecology and Environmental SciencesPalacky UniversityOlomoucCzech Republic
| | | | | | - Lenka Jeřábková
- Nature Conservation Agency of the Czech RepublicPrahaCzech Republic
| | - Stanislav Rada
- Department of Ecology and Environmental SciencesPalacky UniversityOlomoucCzech Republic
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5
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Amin OM, Heckmann RA, Fiser Z, Zaksek V, Herlyn H, Kostanjsek R. Description of Acanthocephalus anguillae balkanicus subsp. n. (Acanthocephala: Echinorhynchidae) from Proteus anguinus Laurenti (Amphibia: Proteidae) and the cave ecomorph of Asellus aquaticus (Crustacea: Asellidae) in Slovenia. Folia Parasitol (Praha) 2019; 66. [PMID: 31617498 DOI: 10.14411/fp.2019.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 08/06/2019] [Indexed: 01/22/2023]
Abstract
Acanthocephalus balkanicus Batchvarov et Combes, 1974 was incompletely described from the northern crested newt, Triturus cristatus (Laurenti) (Amphibia: Salamandridae), a possible synonym of the Balkan crested newt, Triturus ivanbureschi Arntzen et Wielstra, from a pond in village of Pesnopoy, southern Bulgaria. We provide a full description of adult males and females of the same taxon from the olm, Proteus anguinus Laurenti (Amphibia: Proteidae), the only exclusively aquatic cave-dwelling vertebrate in Europe, captured in Postojna-Planina Cave System in Slovenia. Cystacanths were also collected from the cave ecomorph of Asellus aquaticus (Linnaeus) (Crustacea: Asellidae) in the same location. Molecular analysis of specimens from Slovenia revealed that they are genetically almost identical to those of Acanthocephalus anguillae (Müller, 1780), a common parasite of European freshwater fishes. We propose to recognise the morphological and host differences by describing A. balkanicus as a new subspecies of A. anguillae. Acanthocephalus anguillae balkanicus is rather small and cylindrical with cylindrical proboscis having 10 rows of 6 hooks with simple roots each, long neck, large balloon-shaped lemnisci, small spherical anterior testis, and 6 club-shaped cement glands in 3 pairs. SEM images reveal more morphological details and the X-ray scans of gallium cut hooks shows considerably higher levels of phosphorus and calcium in adult hooks than in cystacanth hooks, especially in basal areas. Sulfur levels were higher in the arch and basal area of cystacanth hooks than adult hooks. Considering that both definitive and intermediate hosts of the Slovenian population of this acanthocephalan are bound to cave life, it is possible that its entire life cycle is uniquely completed underground.
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Affiliation(s)
- Omar M Amin
- Institute of Parasitic Diseases, Scottsdale, Arizona, USA; 2
| | | | - Ziga Fiser
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Valerija Zaksek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Holger Herlyn
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz, Germany
| | - Rok Kostanjsek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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6
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Nie R, Wei J, Zhang S, Vogler AP, Wu L, Konstantinov AS, Li W, Yang X, Xue H. Diversification of mitogenomes in three sympatric
Altica
flea beetles (Insecta, Chrysomelidae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rui‐E Nie
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jing Wei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Shou‐Ke Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- Research Institute of Subtropical Forestry Chinese Academy of Forestry Fuyang China
| | - Alfried P. Vogler
- Department of Life Sciences Natural History Museum London UK
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
| | - Ling Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences Hebei University Baoding China
| | | | - Wen‐Zhu Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Xing‐Ke Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Huai‐Jun Xue
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
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Cogălniceanu D, Stănescu F, Arntzen JW. Testing the hybrid superiority hypothesis in crested and marbled newts. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12322] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dan Cogălniceanu
- Faculty of Natural and Agricultural Sciences Ovidius University Constanţa Romania
- Chelonia Romania Bucharest Romania
| | - Florina Stănescu
- Faculty of Natural and Agricultural Sciences Ovidius University Constanţa Romania
- Chelonia Romania Bucharest Romania
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8
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Huang W, Luo H, Luo S, Huang A, Ni Q, Yao Y, Xu H, Zeng B, Li Y, Wei Z, Zhang M. The complete mitogenome of the splendid japalure Japalura splendida (Squamata, Agamidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2641-2642. [PMID: 33365662 PMCID: PMC7706609 DOI: 10.1080/23802359.2019.1643797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The complete mitogenome of Japalura splendida (16,673 bp in length) is determined and analyzed in this study. It contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and one non-coding regions. All the genes in J. splendida are distributed on the H-strand, except for the ND6 gene and seven tRNA genes which are encoded on the L-strand. The phylogenetic tree suggests that J. splendida and Japalura flaviceps formed a sister group and reveals the order ((((Acanthosaura lepidogaster, Acanthosaura armata), ((J. splendida, J. flaviceps), Pseudocalotes microlepis))), Calotes versicolor) with substantial support for the monophyly.
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Affiliation(s)
- Weiyi Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongdi Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Sangdawa Luo
- Forestry and Grassland Administration of Qushui County, Lhasa, China
| | - An Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhimin Wei
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
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9
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Wielstra B, McCartney-Melstad E, Arntzen J, Butlin R, Shaffer H. Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle. Mol Phylogenet Evol 2019; 133:120-127. [DOI: 10.1016/j.ympev.2018.12.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/30/2018] [Accepted: 12/30/2018] [Indexed: 11/29/2022]
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10
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Drillon O, Dufresnes G, Perrin N, Crochet PA, Dufresnes C. Reaching the edge of the speciation continuum: hybridization between three sympatric species of Hyla tree frogs. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly198] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Olivier Drillon
- Agence Française pour la Biodiversité, Service Départemental de la Charente, Champniers, France
| | | | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Pierre-André Crochet
- CEFE, CNRS, University of Montpellier, University Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Christophe Dufresnes
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, UK
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11
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Dufresnes C, Mazepa G, Rodrigues N, Brelsford A, Litvinchuk SN, Sermier R, Lavanchy G, Betto-Colliard C, Blaser O, Borzée A, Cavoto E, Fabre G, Ghali K, Grossen C, Horn A, Leuenberger J, Phillips BC, Saunders PA, Savary R, Maddalena T, Stöck M, Dubey S, Canestrelli D, Jeffries DL. Genomic Evidence for Cryptic Speciation in Tree Frogs From the Apennine Peninsula, With Description of Hyla perrini sp. nov. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00144] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Climate change produces winners and losers: Differential responses of amphibians in mountain forests of the Near East. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00471] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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13
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Veith M, Bogaerts S, Pasmans F, Kieren S. The changing views on the evolutionary relationships of extant Salamandridae (Amphibia: Urodela). PLoS One 2018; 13:e0198237. [PMID: 30067741 PMCID: PMC6070172 DOI: 10.1371/journal.pone.0198237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/16/2018] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic relationships among members of the family Salamandridae have been repeatedly investigated over the last 90 years, with changing character and taxon sampling. We review the changing composition and the phylogenetic position of salamandrid genera and species groups and add a new phylogeny based exclusively on sequences of nuclear genes. Salamandrina often changed its position depending on the characters used. It was included several times in a clade together with the primitive newts (Echinotriton, Pleurodeles, Tylototriton) due to their seemingly ancestral morphology. The latter were often inferred as a monophyletic clade. Respective monophyly was almost consistently established in all molecular studies for true salamanders (Chioglossa, Lyciasalamandra, Mertensiella, Salamandra), modern Asian newts (Cynops, Laotriton, Pachytriton, Paramesotriton) and modern New World newts (Notophthalmus, Taricha). Reciprocal non-monophyly has been established through molecular studies for the European mountain newts (Calotriton, Euproctus) and the modern European newts (Ichthyosaura, Lissotriton, Neurergus, Ommatotriton, Triturus) since Calotriton was identified as the sister lineage of Triturus. In pre-molecular studies, their respective monophyly had almost always been assumed, mainly because a complex courtship behaviour shared by their respective members. Our nuclear tree is nearly identical to a mito-genomic tree, with all but one node being highly supported. The major difference concerns the position of Calotriton, which is no longer nested within the modern European newts. This has implications for the evolution of courtship behaviour of European newts. Within modern European newts, Ichthyosaura and Lissotriton changed their position compared to the mito-genomic tree. Previous molecular trees based on seemingly large nuclear data sets, but analysed together with mitochondrial data, did not reveal monophyly of modern European newts since taxon sampling and nuclear gene coverage was too poor to obtain conclusive results. We therefore conclude that mitochondrial and nuclear data should be analysed on their own.
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Affiliation(s)
- Michael Veith
- Department of Biogeography, Trier University, Trier, Germany
- * E-mail:
| | | | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Sarah Kieren
- Department of Biogeography, Trier University, Trier, Germany
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14
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Arntzen JW, Üzüm N, Ajduković MD, Ivanović A, Wielstra B. Absence of heterosis in hybrid crested newts. PeerJ 2018; 6:e5317. [PMID: 30065885 PMCID: PMC6063215 DOI: 10.7717/peerj.5317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/04/2018] [Indexed: 11/27/2022] Open
Abstract
Relationships between phylogenetic relatedness, hybrid zone spatial structure, the amount of interspecific gene flow and population demography were investigated, with the newt genus Triturus as a model system. In earlier work, a bimodal hybrid zone of two distantly related species combined low interspecific gene flow with hybrid sterility and heterosis was documented. Apart from that, a suite of unimodal hybrid zones in closely related Triturus showed more or less extensive introgressive hybridization with no evidence for heterosis. We here report on population demography and interspecific gene flow in two Triturus species (T. macedonicus and T. ivanbureschi in Serbia). These are two that are moderately related, engage in a heterogeneous uni-/bimodal hybrid zone and hence represent an intermediate situation. This study used 13 diagnostic nuclear genetic markers in a population at the species contact zone. This showed that all individuals were hybrids, with no parentals detected. Age, size and longevity and the estimated growth curves are not exceeding that of the parental species, so that we conclude the absence of heterosis in T. macedonicus-T. ivanbureschi. Observations across the genus support the hypothesis that fertile hybrids allocate resources to reproduction and infertile hybrids allocate resources to growth. Several Triturus species hybrid zones not yet studied allow the testing of this hypothesis.
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Affiliation(s)
| | - Nazan Üzüm
- Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, Aydin, Turkey
| | - Maja D. Ajduković
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Ana Ivanović
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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15
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Vučić T, Vukov TD, Tomašević Kolarov N, Cvijanović M, Ivanović A. The study of larval tail morphology reveals differentiation between two Triturus species and their hybrids. AMPHIBIA-REPTILIA 2018. [DOI: 10.1163/15685381-17000190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In amphibians, morphological differentiation and disparity at the larval and post-metamorphic ontogenetic stages can diverge, owing to various contrasting environments and different selective pressures. In the monophyletic clade of nineTriturusnewt species, five different morphotypes can be recognized, but information on larval morphology is limited. Here we explore divergence of larval morphology inTriturus ivanbureschi,T. macedonicus, and their F1 hybrids. These two genetically and morphologically distinct crested newt species hybridize in nature and form a relatively wide hybrid zone in the central part of the Balkan Peninsula. Using a geometric morphometric approach and multivariate statistics, we evaluated differences of tail size and shape, colouration pattern, and the presence of a tail filament at the mid-larval stage in larvae reared under controlled laboratory conditions. We chose the tail as the main propulsive organ crucial for locomotion, feeding, and escaping predators. We found thatTriturus ivanbureschiandT. macedonicuslarvae differ in tail shape, but not in tail size. Two groups of F1 hybrid larvae (obtained from reciprocal crossing) were similar to each other, but differed from the parental species in size and shape of the tail, colouration pattern, and the presence of a tail filament. Our results indicate that, like adults, larvae diverge morphologically and hybrid larvae do not exhibit intermediate morphology of the parental species.
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Affiliation(s)
- Tijana Vučić
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Tanja D. Vukov
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia
| | - Nataša Tomašević Kolarov
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia
| | - Milena Cvijanović
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia
| | - Ana Ivanović
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
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Slijepčević MD, Ukropina M, Filipović B, Ivanović A. Ossification and development of vertebrae in the Balkan crested newt Triturus ivanbureschi (Salamandridae, Caudata). ZOOLOGY 2017; 126:164-171. [PMID: 29113765 DOI: 10.1016/j.zool.2017.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 10/01/2017] [Accepted: 10/01/2017] [Indexed: 11/30/2022]
Abstract
Vertebral morphology, development, and evolution have been investigated for many decades, especially in the recent evo-devo era. Nevertheless, comparative data on development and ossification modes within the major tetrapod groups are scarce and frequently suffer from the use of a simplistic approach, resulting in simplistic generalizations about the formation of tetrapod vertebrae. Here, we describe the development and ossification of trunk vertebrae in Triturus ivanbureschi (Salamandridae, Caudata) and compare the results with published data on other related taxa. In so doing, we focus on the modes of ossification and development of the centrum and neural arches by analysing three developmental stages defined by the degree of limb development: stages 47, 52, and 62 according to Glücksohn (1932). Our examination of histological sections through trunk vertebrae enabled us to identify three modes of ossification within single trunk vertebrae: (i) perichordal (direct ossification of the connective tissue surrounding the notochord); (ii) perichondrial (direct ossification of the perichondrium, consisting of cartilage-covering connective tissue), and (iii) endochondral (ossification within the preformed cartilage template). We also noted the presence of intravertebral or notochordal cartilage. Although our results indicate that this cartilage develops within the notochord surrounded by the continuous notochordal sheath, more detailed further studies could shed light on its origin and development.
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Affiliation(s)
- Maja D Slijepčević
- University of Belgrade, Institute for Biological Research "Siniša Stanković", 11000 Belgrade, Serbia.
| | - Mirela Ukropina
- University of Belgrade, Institute of Zoology, Faculty of Biology, 11000 Belgrade, Serbia
| | - Branko Filipović
- University of Belgrade, Institute for Biological Research "Siniša Stanković", 11000 Belgrade, Serbia
| | - Ana Ivanović
- University of Belgrade, Institute of Zoology, Faculty of Biology, 11000 Belgrade, Serbia
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17
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Kornilios P. Polytomies, signal and noise: revisiting the mitochondrial phylogeny and phylogeography of the Eurasian blindsnake species complex (Typhlopidae, Squamata). ZOOL SCR 2017. [DOI: 10.1111/zsc.12243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panagiotis Kornilios
- Section of Animal Biology; Department of Biology; School of Natural Sciences; University of Patras; GR-26500 Patras Greece
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18
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Urošević A, Slijepčević MD, Arntzen JW, Ivanović A. Vertebral shape and body elongation in Triturus newts. ZOOLOGY 2016; 119:439-446. [DOI: 10.1016/j.zool.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/18/2016] [Accepted: 05/18/2016] [Indexed: 12/29/2022]
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19
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Zieliński P, Nadachowska-Brzyska K, Dudek K, Babik W. Divergence history of the Carpathian and smooth newts modelled in space and time. Mol Ecol 2016; 25:3912-28. [PMID: 27288862 DOI: 10.1111/mec.13724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 12/24/2022]
Abstract
Information about demographic history is essential for the understanding of the processes of divergence and speciation. Patterns of genetic variation within and between closely related species provide insights into the history of their interactions. Here, we investigated historical demography and genetic exchange between the Carpathian (Lissotriton montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an extensive geographical sampling and multilocus nuclear sequence data with the approximate Bayesian computation framework to test alternative scenarios of divergence and reconstruct the temporal and spatial pattern of gene flow between species. A model of recent (last glacial period) interspecific gene flow was favoured over alternative models. Thus, despite the relatively old divergence (4-6 mya) and presumably long periods of isolation, the species have retained the ability to exchange genes. Nevertheless, the low migration rates (ca. 10(-6) per gene copy per generation) are consistent with strong reproductive isolation between the species. Models allowing demographic changes were favoured, suggesting that the effective population sizes of both species at least doubled as divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv. We found asymmetry in rates of interspecific gene flow between Lm and one evolutionary lineage of Lv. We suggest that intraspecific polymorphism for hybrid incompatibilities segregating within Lv could explain this pattern and propose further tests to distinguish between alternative explanations. Our study highlights the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.
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Affiliation(s)
- P Zieliński
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - K Nadachowska-Brzyska
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - K Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - W Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
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20
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Leaché AD, Banbury BL, Linkem CW, de Oca ANM. Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)? BMC Evol Biol 2016; 16:63. [PMID: 27000803 PMCID: PMC4802581 DOI: 10.1186/s12862-016-0628-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/29/2016] [Indexed: 01/25/2023] Open
Abstract
Background Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. Results The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20–25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Conclusions Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0628-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA. .,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195, USA.
| | - Barbara L Banbury
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA.,Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail Stop M4-B402, Seattle, 98109, Washington, USA
| | - Charles W Linkem
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - Adrián Nieto-Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, México
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21
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Massive genetic introgression in threatened northern crested newts (Triturus cristatus) by an invasive congener (T. carnifex) in Western Switzerland. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0825-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Strzała T, Grochowalska R, Najbar B, Mikulíček P, Jandzik D, Lymberakis P, Jablonski D. Complete mitochondrial genome of the endemic legless lizard Anguis cephallonica Werner, 1894 and its comparison with mitogenome of Anguis fragilis Linnaeus, 1758. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:83-85. [PMID: 33473417 PMCID: PMC7800002 DOI: 10.1080/23802359.2015.1137834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Complete mitochondrial genome of the Peloponnese endemic lizard species Anguis cephallonica is presented in this study. The complete sequence is 17 208 bp long and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The gene order is same as in the relative species Anguis fragilis. Length of the 22 tRNA genes varies from 64 bp to 73 bp. The Anguis cephallonica mitogenome base composition is: A (30.5%), T (24.2%), C (30.5%), G (14.8%), with an A + T bias (54.7%). Six protein coding genes have incomplete stop codons. This is the first complete mitogenome described in this species as well as in any endemic Peloponnese lizard. Presented complete mitochondrial genome will form a basis for future comparative analysis within the genus Anguis.
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Affiliation(s)
- Tomasz Strzała
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Renata Grochowalska
- Nature Museum, Faculty of Biological Sciences, University of Zielona Góra, Zielona Góra, Poland
| | - Bartłomiej Najbar
- Nature Museum, Faculty of Biological Sciences, University of Zielona Góra, Zielona Góra, Poland
| | - Peter Mikulíček
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Bratislava, Slovakia
| | - David Jandzik
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Bratislava, Slovakia.,Department of Ecology and Evolutionary Biology (EBIO), University of Colorado at Boulder, Boulder, CO, USA
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Crete, Greece
| | - Daniel Jablonski
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Bratislava, Slovakia
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23
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Mamos T, Wattier R, Burzyński A, Grabowski M. The legacy of a vanished sea: a high level of diversification within a European freshwater amphipod species complex driven by 15 My of Paratethys regression. Mol Ecol 2016; 25:795-810. [DOI: 10.1111/mec.13499] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 11/19/2015] [Accepted: 11/24/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology; University of Lodz; Banacha 12/16, 90-237 Lodz Poland
| | - Remi Wattier
- Equipe Ecologie Evolutive; UMR CNRS 6282 Biogéosciences; Université de Bourgogne; 6 Boulevard Gabriel 21000 Dijon France
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology; Institute of Oceanology, Polish Academy of Sciences; Powstańców Warszawy 55 81-712 Sopot, Poland
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology; University of Lodz; Banacha 12/16, 90-237 Lodz Poland
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24
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Landscape as a determinant of dispersal patterns and population connectivity in a newt species. ECOL INFORM 2015. [DOI: 10.1016/j.ecoinf.2015.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Jiang Y, Li Z, Liu J, Li Y, Ni Q, Yao Y, Xu H, Li Y, Zhang M. The complete mitochondrial genome sequence of Tylototriton taliangensis (Amphibia: Caudata). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2639-40. [PMID: 26024138 DOI: 10.3109/19401736.2015.1041132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tylototriton taliangensis was listed as a Near Threatened amphibian in IUCN red list. In this study, we sequenced the complete mitochondrial (mt) genome of this species (GenBank: KP979646) and found it contains 16,265 base pairs, which encode 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA) and 1 control region (CR). We also found that almost all PCGs and tRNA genes are located on the H-strand, except for ND6 subunit gene and eight tRNA genes, which were distributed on the L-strand. The PCGs used "ATG" and "GTG" as the start codon, while used four types of stop codons. Almost all tRNA genes were folded into typical cloverleaf secondary structures. The L-strand replication origin (OL) and a non-coding region were also found. The new mitogenomic phylogenetic tree confirms the reciprocally monophyly of the genus Tylototriton, Echinotriton and Pleurodeles with high bootstrap value. The present study will provide information for future studies on the conservation genetics and phylogeny of this species and its relatives.
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Affiliation(s)
- Ye Jiang
- a College of Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , P.R. China and
| | - Ziyuan Li
- a College of Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , P.R. China and
| | - Jiabin Liu
- a College of Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , P.R. China and
| | - Yan Li
- a College of Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , P.R. China and
| | - Qingyong Ni
- a College of Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , P.R. China and
| | - Yongfang Yao
- a College of Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , P.R. China and
| | - Huailiang Xu
- a College of Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , P.R. China and
| | - Ying Li
- b Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , P.R. China
| | - Mingwang Zhang
- a College of Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , P.R. China and
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26
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Brede E. Beam Brook revisited: a molecular study of a historically introduced non-native amphibian (Triturus carnifex) and its limited introgression into native UK Triturus cristatus populations. AMPHIBIA-REPTILIA 2015. [DOI: 10.1163/15685381-00003006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human mediated introductions of non-native species can pose a major threat to global biodiversity on several accounts i.e. through competition, the introduction of novel pathogens, and genetic pollution. Where hybridization occurs between two closely related species the F1 offspring are usually phenotypically discernible whereas F2 hybrid, backcrossed or admixed individuals become more difficult to separate. At this point the utilization of molecular methods is required in conservation efforts to differentiate and manage populations. This study demonstrated how a possible threat of hybridization from an introduced non-native (T. carnifex) with a protected native newt species (T. cristatus) could be investigated with molecular tools, and examined the current extent of its genetic introgression over an 80 years period. The results confirmed that hybridization had taken place at the site of introduction (and continues to do so), and that historically limited local dispersal of both non-natives and/or hybrids had occurred sometime in the past. However, the data suggests that although dispersal of hybrids into a local satellite site may still be occuring, hybridization with native species appears limited.
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Affiliation(s)
- Edward Brede
- School of Biological Sciences, Museum Avenue, Cardiff University, CF10 3AX, UK
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27
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Poortvliet M, Olsen JL, Croll DA, Bernardi G, Newton K, Kollias S, O'Sullivan J, Fernando D, Stevens G, Galván Magaña F, Seret B, Wintner S, Hoarau G. A dated molecular phylogeny of manta and devil rays (Mobulidae) based on mitogenome and nuclear sequences. Mol Phylogenet Evol 2014; 83:72-85. [PMID: 25462995 DOI: 10.1016/j.ympev.2014.10.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 09/07/2014] [Accepted: 10/08/2014] [Indexed: 12/24/2022]
Abstract
Manta and devil rays are an iconic group of globally distributed pelagic filter feeders, yet their evolutionary history remains enigmatic. We employed next generation sequencing of mitogenomes for nine of the 11 recognized species and two outgroups; as well as additional Sanger sequencing of two mitochondrial and two nuclear genes in an extended taxon sampling set. Analysis of the mitogenome coding regions in a Maximum Likelihood and Bayesian framework provided a well-resolved phylogeny. The deepest divergences distinguished three clades with high support, one containing Manta birostris, Manta alfredi, Mobula tarapacana, Mobula japanica and Mobula mobular; one containing Mobula kuhlii, Mobula eregoodootenkee and Mobula thurstoni; and one containing Mobula munkiana, Mobula hypostoma and Mobula rochebrunei. Mobula remains paraphyletic with the inclusion of Manta, a result that is in agreement with previous studies based on molecular and morphological data. A fossil-calibrated Bayesian random local clock analysis suggests that mobulids diverged from Rhinoptera around 30 Mya. Subsequent divergences are characterized by long internodes followed by short bursts of speciation extending from an initial episode of divergence in the Early and Middle Miocene (19-17 Mya) to a second episode during the Pliocene and Pleistocene (3.6 Mya - recent). Estimates of divergence dates overlap significantly with periods of global warming, during which upwelling intensity - and related high primary productivity in upwelling regions - decreased markedly. These periods are hypothesized to have led to fragmentation and isolation of feeding regions leading to possible regional extinctions, as well as the promotion of allopatric speciation. The closely shared evolutionary history of mobulids in combination with ongoing threats from fisheries and climate change effects on upwelling and food supply, reinforces the case for greater protection of this charismatic family of pelagic filter feeders.
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Affiliation(s)
- Marloes Poortvliet
- Department of Marine Benthic Ecology and Evolution, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, USA; Faculty of Biosciences and Aquaculture, Universitetet i Nordland, Universitetsalleen 11, 8049 Bodø, Norway.
| | - Jeanine L Olsen
- Department of Marine Benthic Ecology and Evolution, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
| | - Donald A Croll
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, USA.
| | - Giacomo Bernardi
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, USA.
| | - Kelly Newton
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, USA.
| | - Spyros Kollias
- Faculty of Biosciences and Aquaculture, Universitetet i Nordland, Universitetsalleen 11, 8049 Bodø, Norway.
| | - John O'Sullivan
- Monterey Bay Aquarium, 886 Cannery Row, Monterey, CA 93940, USA.
| | - Daniel Fernando
- Department of Biology and Environmental Science, Linnaeus University, SE 39182 Kalmar, Sweden; The Manta Trust, Catemwood House, Corscombe, Dorchester, Dorset DT2 0NT, United Kingdom.
| | - Guy Stevens
- The Manta Trust, Catemwood House, Corscombe, Dorchester, Dorset DT2 0NT, United Kingdom.
| | - Felipe Galván Magaña
- Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, Av. IPN s/n, La Paz, Baja California Sur 23096, Mexico.
| | - Bernard Seret
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, CP 51, rue Buffon, 75231 Paris cedex 05, France.
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, 1A Herrwood Drive, Umhlanga Rocks 4320, South Africa; Biomedical Resource Unit, University of KwaZulu-Natal, Westville Campus, University Road, Westville 3600, South Africa.
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Universitetet i Nordland, Universitetsalleen 11, 8049 Bodø, Norway.
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28
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Wielstra B, Arntzen JW, van der Gaag KJ, Pabijan M, Babik W. Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts. PLoS One 2014; 9:e111011. [PMID: 25337997 PMCID: PMC4206468 DOI: 10.1371/journal.pone.0111011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/22/2014] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.
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Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
| | | | | | - Maciej Pabijan
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
- Institute of Zoology, Jagiellonian University, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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29
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Extending the natural range of a declining species: genetic evidence for native great crested newt (Triturus cristatus) populations in the Scottish Highlands. EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0863-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Vukov TD, Cvijanović M, Wielstra B, Kalezić ML. The Roles of Phylogeny and Climate in Shaping Variation in Life-History Traits of the Newt GenusTriturus(Caudata, Salamandridae). ANN ZOOL FENN 2014. [DOI: 10.5735/086.051.0505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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31
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Arntzen JW, Wielstra B, Wallis GP. The modality of nineTriturusnewt hybrid zones assessed with nuclear, mitochondrial and morphological data. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12358] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jan W. Arntzen
- Naturalis Biodiversity Center; PO Box 9517 2300 RA Leiden the Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center; PO Box 9517 2300 RA Leiden the Netherlands
- Department of Animal and Plant Sciences; University of Sheffield; S10 2TN Sheffield UK
| | - Graham P. Wallis
- Naturalis Biodiversity Center; PO Box 9517 2300 RA Leiden the Netherlands
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
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32
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Cvijanović M, Ivanović A, Kalezić ML, Zelditch ML. The ontogenetic origins of skull shape disparity in theTriturus cristatusgroup. Evol Dev 2014; 16:306-17. [DOI: 10.1111/ede.12093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Milena Cvijanović
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”; University of Belgrade; 11060 Belgrade Serbia
| | - Ana Ivanović
- Institute of Zoology, Faculty of Biology; University of Belgrade; 11000 Belgrade Serbia
| | - Miloš L. Kalezić
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”; University of Belgrade; 11060 Belgrade Serbia
- Institute of Zoology, Faculty of Biology; University of Belgrade; 11000 Belgrade Serbia
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Pons J, Bauzà-Ribot MM, Jaume D, Juan C. Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea). BMC Genomics 2014; 15:566. [PMID: 24997985 PMCID: PMC4112215 DOI: 10.1186/1471-2164-15-566] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/26/2014] [Indexed: 11/16/2022] Open
Abstract
Background Comparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012). Results We present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure. Conclusions Next-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (-) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to those of the few crustaceans studied at present. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-566) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, c/Miquel Marquès 21, 07190 Esporles, Spain.
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Ivanović A, Arntzen JW. Evolution of skull and body shape inTriturusnewts reconstructed from three-dimensional morphometric data and phylogeny. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12314] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Ana Ivanović
- Faculty of Biology; Institute for Zoology; University of Belgrade; Studentski trg 16 11000 Belgrade Serbia
- Naturalis Biodiversity Center; PO Box 9517 2300 RA Leiden The Netherlands
| | - Jan W. Arntzen
- Naturalis Biodiversity Center; PO Box 9517 2300 RA Leiden The Netherlands
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Wielstra B, Arntzen JW. Exploring the effect of asymmetric mitochondrial DNA introgression on estimating niche divergence in morphologically cryptic species. PLoS One 2014; 9:e95504. [PMID: 24743746 PMCID: PMC3990694 DOI: 10.1371/journal.pone.0095504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/27/2014] [Indexed: 11/18/2022] Open
Abstract
If potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species. However, mitochondrial DNA introgression hampers the correct estimation of ecological divergence. We test the hypothesis that estimated niche divergence differs when considering nuclear DNA composition or mitochondrial DNA type as representing the true species range. We use empirical data of two crested newt species (Amphibia: Triturus) which possess introgressed mitochondrial DNA from a third species in part of their ranges. We analyze the data in environmental space by determining Fisher distances in a principal component analysis and in geographical space by determining geographical overlap of species distribution models. We find that under mtDNA guidance in one of the two study cases niche divergence is overestimated, whereas in the other it is underestimated. In the light of our results we discuss the role of estimated niche divergence in species delineation.
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Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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Wielstra B, Duijm E, Lagler P, Lammers Y, Meilink WRM, Ziermann JM, Arntzen JW. Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform. Mol Ecol Resour 2014; 14:1080-9. [PMID: 24571307 PMCID: PMC4285185 DOI: 10.1111/1755-0998.12242] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/15/2014] [Accepted: 02/19/2014] [Indexed: 11/28/2022]
Abstract
Next-generation sequencing is a fast and cost-effective way to obtain sequence data for nonmodel organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptome data of a single Triturus species and design 96 primer pairs that amplify c. 180 bp fragments positioned in 3-prime untranslated regions. Next, these markers are tested with uniplex PCR for a set of species spanning the taxonomical width of the genus Triturus. The 52 markers that consistently show a single band of expected length at gel electrophoreses for all tested crested newt species are then amplified in five multiplex PCRs (with a plexity of ten or eleven) for 132 individual newts: a set of 84 representing the seven (candidate) species and a set of 48 from a presumed hybrid population. After pooling multiplexes per individual, unique tags are ligated to link amplicons to individuals. Subsequently, individuals are pooled equimolar and sequenced on the Ion Torrent next-generation sequencing platform. A bioinformatics pipeline identifies the alleles and recodes these to a genotypic format. Next, we test the utility of our markers. baps allocates the 84 crested newt individuals representing (candidate) species to their expected (candidate) species, confirming the markers are suitable for species delineation. newhybrids, a hybrid index and hiest confirm the 48 individuals from the presumed hybrid population to be genetically admixed, illustrating the potential of the markers to identify interspecific hybridization. We expect the set of markers we designed to provide a high resolving power for analysis of hybridization in Triturus.
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Affiliation(s)
- B Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300, RA Leiden, The Netherlands; Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK
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Wielstra B, Sillero N, Vörös J, Arntzen JW. The distribution of the crested and marbled newt species (Amphibia: Salamandridae: Triturus) – an addition to the New Atlas of Amphibians and Reptiles of Europe. AMPHIBIA-REPTILIA 2014. [DOI: 10.1163/15685381-00002960] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the recently published New Atlas of Amphibians and Reptiles of Europe (Sillero et al., 2014a), the distribution of the newt genusTrituruswas not resolved at the level of the species. The main reason for this was the lack of high quality distribution data from in and around the parapatric contact zones between species, where interspecific hybridization occurs. We are working extensively onTriturusand the (particularly genetic) data we have accumulated allow us to map the individualTriturusspecies at the appropriate scale. We here provide a database composed of distribution data for the individual species, at generally high resolution, particularly from in and around contact zones. Based on this database we produce maps at the 50 × 50 km UTM grid resolution as used in the new atlas and highlight those grid cells in which more than oneTriturusspecies occurs.
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Affiliation(s)
- Ben Wielstra
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN Sheffield, UK
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Neftalí Sillero
- Centro de Investigação em Ciências Geo-Espaciais, Observatório Astronómico Prof. Manuel de Barros, Alameda do Monte da Virgem, 4430-146 Vila Nova de Gaia, Portugal
| | - Judit Vörös
- Department of Zoology, Hungarian Natural History Museum, 1088 Budapest, Hungary
| | - Jan W. Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
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Sillero N, Campos J, Bonardi A, Corti C, Creemers R, Crochet PA, Crnobrnja Isailović J, Denoël M, Ficetola GF, Gonçalves J, Kuzmin S, Lymberakis P, de Pous P, Rodríguez A, Sindaco R, Speybroeck J, Toxopeus B, Vieites DR, Vences M. Updated distribution and biogeography of amphibians and reptiles of Europe. AMPHIBIA-REPTILIA 2014. [DOI: 10.1163/15685381-00002935] [Citation(s) in RCA: 225] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A precise knowledge of the spatial distribution of taxa is essential for decision-making processes in land management and biodiversity conservation, both for present and under future global change scenarios. This is a key base for several scientific disciplines (e.g. macro-ecology, biogeography, evolutionary biology, spatial planning, or environmental impact assessment) that rely on species distribution maps. An atlas summarizing the distribution of European amphibians and reptiles with 50 × 50 km resolution maps based on ca. 85 000 grid records was published by the Societas Europaea Herpetologica (SEH) in 1997. Since then, more detailed species distribution maps covering large parts of Europe became available, while taxonomic progress has led to a plethora of taxonomic changes including new species descriptions. To account for these progresses, we compiled information from different data sources: published in books and websites, ongoing national atlases, personal data kindly provided to the SEH, the 1997 European Atlas, and the Global Biodiversity Information Facility (GBIF). Databases were homogenised, deleting all information except species names and coordinates, projected to the same coordinate system (WGS84) and transformed into a 50 × 50 km grid. The newly compiled database comprises more than 384 000 grid and locality records distributed across 40 countries. We calculated species richness maps as well as maps of Corrected Weighted Endemism and defined species distribution types (i.e. groups of species with similar distribution patterns) by hierarchical cluster analysis using Jaccard’s index as association measure. Our analysis serves as a preliminary step towards an interactive, dynamic and online distributed database system (NA2RE system) of the current spatial distribution of European amphibians and reptiles. The NA2RE system will serve as well to monitor potential temporal changes in their distributions. Grid maps of all species are made available along with this paper as a tool for decision-making and conservation-related studies and actions. We also identify taxonomic and geographic gaps of knowledge that need to be filled, and we highlight the need to add temporal and altitudinal data for all records, to allow tracking potential species distribution changes as well as detailed modelling of the impacts of land use and climate change on European amphibians and reptiles.
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Affiliation(s)
- Neftali Sillero
- 1Centro de Investigação em Ciências Geo-Espaciais, Alameda do Monte da Virgem, 4430-146 Vila Nova de Gaia, Portugal
| | - João Campos
- 1Centro de Investigação em Ciências Geo-Espaciais, Alameda do Monte da Virgem, 4430-146 Vila Nova de Gaia, Portugal
| | - Anna Bonardi
- 2Department of Earth and Environmental Sciences, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Claudia Corti
- 3Museo di Storia Naturale dell’Università di Firenze, Sezione di Zoologia “La Specola”, Via Romana 17, 50125 Firenze, Italia
| | | | - Pierre-Andre Crochet
- 5CNRS-UMR5175 CEFE, Centre d’Ecologie Fonctionnelle et Evolutive, 1919, route de Mende, 34293 Montpellier, France
| | - Jelka Crnobrnja Isailović
- 6Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Serbia
- 7Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Despota Stefana 142, 11000 Beograd, Serbia
| | - Mathieu Denoël
- 8F.R.S. – FNRS Research Associate, Behavioural Biology Unit, University of Liège, 22 Quai van Beneden, 4020 Liege, Belgium
| | - Gentile Francesco Ficetola
- 2Department of Earth and Environmental Sciences, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - João Gonçalves
- 9CIBIO, University of Porto, R. Campo Alegre 687, 4169-007 Porto, Portugal
| | - Sergei Kuzmin
- 10Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 117071, Russia
| | - Petros Lymberakis
- 11Natural History Museum of Crete, University of Crete, Knossou Ave., P.O. Box 2208, 71409 Heraklion Crete, Greece
| | - Philip de Pous
- 12Faculty of Life Sciences and Engineering, Universitat de Lleida, Av. Rovira Roura 191, 25198 Lleida, Spain
- 13Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Animal Phylogeny and Systematics, Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Ariel Rodríguez
- 14Technische Universität Braunschweig, Division of Evolutionary Biology, Zoological Institute, Mendelssohnstr. 4, 38108 Braunschweig, Germany
| | - Roberto Sindaco
- 15c/o Museo Civico di Storia Naturale, via San Francesco di Sales 88, 10022 Carmagnola (TO), Italia
| | - Jeroen Speybroeck
- 16Research Institute for Nature and Forest, Kliniekstraat 25, 1070 Brussels, Belgium
| | - Bert Toxopeus
- 17University of Twente, Faculty of Geo-Information Science and Earth Observation (ITC), P.O. Box 217, 7500 AA Enschede, The Netherlands
| | - David R. Vieites
- 18Museo Nacional de Ciencias Naturales and Consejo Superior de Investigaciones Científicas, c/José Gutierrez Abascal 2, 28006 Madrid, Spain
- 19REFER Biodiversity Chair, University of Porto, CIBIO, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Miguel Vences
- 14Technische Universität Braunschweig, Division of Evolutionary Biology, Zoological Institute, Mendelssohnstr. 4, 38108 Braunschweig, Germany
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Pabijan M, Wandycz A, Hofman S, Węcek K, Piwczyński M, Szymura JM. Complete mitochondrial genomes resolve phylogenetic relationships within Bombina (Anura: Bombinatoridae). Mol Phylogenet Evol 2013; 69:63-74. [PMID: 23707701 DOI: 10.1016/j.ympev.2013.05.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 02/14/2013] [Accepted: 05/08/2013] [Indexed: 11/25/2022]
Abstract
A highly resolved and time-calibrated phylogeny based on nucleotide variation in 18 complete mitochondrial genomes is presented for all extant species and major lineages of fire-bellied toads of the genus Bombina (Bombinatoridae). Two sets of divergence time estimates are inferred by applying alternative fossil constraints as minima. Divergence time estimates from both analyses differed for the two oldest nodes. The earliest phylogenetic split occurred between small- and large-bodied Bombina (subgenera Bombina and Grobina, respectively) either in the Middle Oligocene or the Early Miocene. East Asian B. orientalis and European B. bombina+B. variegata diverged in the early or Middle Miocene. Divergence times inferred using the alternative fossil calibration strategies converged for the younger nodes, with broadly overlapping HPD intervals. The split between Bombina bombina and B. variegata occurred in the Late Miocene of Europe and somewhat preceded another deep mtDNA division between the Balkan B. v. scabra and B. v. variegata inhabiting the Carpathian Mts. Concurrently, the genetically distinct B. maxima diverged from other Grobina in southeast Asia in the Late Miocene or Pliocene. Our mtDNA phylogeny and a new species-tree analysis of published data (nuclear and mtDNA) suggest that B. fortinuptialis, B. lichuanensis and B. microdeladigitora may be conspecific geographic forms that separated due to Pleistocene climatic fluctuations in southeastern Asia. In the western Palearctic, the Late Pliocene to Pleistocene climatic vagaries most probably induced vicariant events in the evolutionary history of B. variegata that led to the formation of the two Balkan B. v. scabra lineages and the allopatric B. v. pachypus in the Apennine Peninsula. Divergence among B. bombina mtDNA lineages is low, with an Anatolian Turkey lineage as the sister group to the European mtDNA clades. In sum, Miocene diversification in the genus Bombina established six allopatrically distributed major mtDNA lineages that diversified during the Pliocene and Pleistocene and have survived until the present. The narrow habitat requirements of fire-bellied toads and extensive environmental changes throughout the Palearctic in the Neogene may have contributed to a putatively high extinction rate in these anurans resulting in the current east/west disjunction of their ranges.
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Affiliation(s)
- Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland.
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Ivanović A, Üzüm N, Wielstra B, Olgun K, Litvinchuk SN, Kalezić ML, Arntzen JW. Is mitochondrial DNA divergence of Near Eastern crested newts (Triturus karelinii group) reflected by differentiation of skull shape? ZOOL ANZ 2013. [DOI: 10.1016/j.jcz.2012.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Wielstra B, Crnobrnja-Isailović J, Litvinchuk SN, Reijnen BT, Skidmore AK, Sotiropoulos K, Toxopeus AG, Tzankov N, Vukov T, Arntzen JW. Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling. Front Zool 2013; 10:13. [PMID: 23514662 PMCID: PMC3608019 DOI: 10.1186/1742-9994-10-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 03/11/2013] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION The major climatic oscillations during the Quaternary Ice Age heavily influenced the distribution of species and left their mark on intraspecific genetic diversity. Past range shifts can be reconstructed with the aid of species distribution modeling and phylogeographical analyses. We test the responses of the different members of the genus Triturus (i.e. the marbled and crested newts) as the climate shifted from the previous glacial period (the Last Glacial Maximum, ~21 Ka) to the current interglacial. RESULTS We present the results of a dense mitochondrial DNA phylogeography (visualizing genetic diversity within and divergence among populations) and species distribution modeling (using two different climate simulations) for the nine Triturus species on composite maps. CONCLUSIONS The combined use of species distribution modeling and mitochondrial phylogeography provides insight in the glacial contraction and postglacial expansion of Triturus. The combined use of the two independent techniques yields a more complete understanding of the historical biogeography of Triturus than both approaches would on their own. Triturus newts generally conform to the 'southern richness and northern purity' paradigm, but we also find more intricate patterns, such as the absence of genetic variation and suitable area at the Last Glacial Maximum (T. dobrogicus), an 'extra-Mediterranean' refugium in the Carpathian Basin (T. cristatus), and areas where species displaced one another postglacially (e.g. T. macedonicus and western T. karelinii). We provide a biogeographical scenario for Triturus, showing the positions of glacial refugia, the regions that were postglacially colonized and the areas where species displaced one another as they shifted their ranges.
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Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, P, O, Box 9517, 2300 RA, Leiden, The Netherlands.
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Affiliation(s)
- N. Tomašević Kolarov
- Department of Evolutionary Biology Institute for Biological Research ‘Siniša Stanković’ University of Belgrade Belgrade Serbia
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Hancock‐Hanser BL, Frey A, Leslie MS, Dutton PH, Archer FI, Morin PA. Targeted multiplex next‐generation sequencing: advances in techniques of mitochondrial and nuclear
DNA
sequencing for population genomics. Mol Ecol Resour 2013; 13:254-68. [DOI: 10.1111/1755-0998.12059] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 11/30/2012] [Accepted: 12/06/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Brittany L. Hancock‐Hanser
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Amy Frey
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Matthew S. Leslie
- Scripps Institution of Oceanography University of California San Diego 9500 Gilman Drive, MC 0202 La Jolla CA 92093 USA
| | - Peter H. Dutton
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Frederick I. Archer
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Phillip A. Morin
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
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A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species. Mol Phylogenet Evol 2013; 67:167-75. [PMID: 23353071 DOI: 10.1016/j.ympev.2013.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 01/09/2013] [Accepted: 01/10/2013] [Indexed: 11/21/2022]
Abstract
The crested newt Triturus cristatus superspecies is composed of five recognized species. One of these, T. karelinii sensu lato, comprises three geographically structured mitochondrial DNA lineages: 'eastern', 'central' and 'western T. karelinii'. Genetic divergence among these lineages is comparable to that of recognized crested newt species, but morphologically they are indistinguishable. Here, we conduct a multimarker phylogeographical survey to explore the evolutionary independence of these mitochondrial DNA lineages and we include representatives of the other species to guide our interpretation of the results. All markers show distinct patterns when analyzed singly (as a phylogeny or haplotype network) and none of them sort haplotypes fully in line with species or mitochondrial DNA lineage. A multilocus approach (BAPS and *BEAST) on the other hand shows that not only the recognized species, but also the three mitochondrial DNA lineages represent discrete nuclear DNA gene pools. A mismatch is found in the northwest of Asiatic Turkey, where several populations identified as 'central T. karelinii' based on nuclear DNA possesses 'western T. karelinii' mitochondrial DNA. We invoke asymmetric mitochondrial DNA introgression to explain this pattern and support this with a historical biogeographical scenario. The three spatial groups in T. karelinii sensu lato should be regarded as distinct species.
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Affiliation(s)
- Lumír Gvoždík
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic
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Mikulíček P, Horák A, Zavadil V, Kautman J, Piálek J. Hybridization between three crested newt species (Triturus cristatussuperspecies) in the Czech Republic and Slovakia: comparison of nuclear markers and mitochondrial DNA. FOLIA ZOOLOGICA 2012. [DOI: 10.25225/fozo.v61.i3.a4.2012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Peter Mikulíček
- Comenius University, Faculty of Natural Sciences, Department of Zoology, Mlynská dolina B-1, 842 15 Bratislava, Slovak Republic
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65 Brno, Czech Republic
| | - Aleš Horák
- Biology Centre of Academy of Sciences of the Czech Republic, v.v.i., Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Sciences, Department of Molecular Biology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Vít Zavadil
- ENKI, o.p.s., Dukelská 145, 379 01 Třeboň, Czech Republic
| | - Ján Kautman
- Slovak National Museum — Museum of Natural History, Department of Zoology, Vajanského nábrežie 2, 814 36 Bratislava, Slovak Republic
| | - Jaroslav Piálek
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65 Brno, Czech Republic
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Evolution of Sexual Dimorphism in the Number of Tail Vertebrae in Salamanders: Comparing Multiple Hypotheses. Evol Biol 2012. [DOI: 10.1007/s11692-012-9203-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Wielstra B, Beukema W, Arntzen JW, Skidmore AK, Toxopeus AG, Raes N. Corresponding mitochondrial DNA and niche divergence for crested newt candidate species. PLoS One 2012; 7:e46671. [PMID: 23029564 PMCID: PMC3460878 DOI: 10.1371/journal.pone.0046671] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 09/06/2012] [Indexed: 11/18/2022] Open
Abstract
Genetic divergence of mitochondrial DNA does not necessarily correspond to reproductive isolation. However, if mitochondrial DNA lineages occupy separate segments of environmental space, this supports the notion of their evolutionary independence. We explore niche differentiation among three candidate species of crested newt (characterized by distinct mitochondrial DNA lineages) and interpret the results in the light of differences observed for recognized crested newt species. We quantify niche differences among all crested newt (candidate) species and test hypotheses regarding niche evolution, employing two ordination techniques (PCA-env and ENFA). Niche equivalency is rejected: all (candidate) species are found to occupy significantly different segments of environmental space. Furthermore, niche overlap values for the three candidate species are not significantly higher than those for the recognized species. As the three candidate crested newt species are, not only in terms of mitochondrial DNA genetic divergence, but also ecologically speaking, as diverged as the recognized crested newt species, our findings are in line with the hypothesis that they represent cryptic species. We address potential pitfalls of our methodology.
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Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands.
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Wielstra B, Arntzen JW. Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models. BMC Evol Biol 2012; 12:161. [PMID: 22935041 PMCID: PMC3520116 DOI: 10.1186/1471-2148-12-161] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/25/2012] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND If the geographical displacement of one species by another is accompanied by hybridization, mitochondrial DNA can introgress asymmetrically, from the outcompeted species into the invading species, over a large area. We explore this phenomenon using the two parapatric crested newt species, Triturus macedonicus and T. karelinii, distributed on the Balkan Peninsula in south-eastern Europe, as a model. RESULTS We first delimit a ca. 54,000 km(2) area in which T. macedonicus contains T. karelinii mitochondrial DNA. This introgression zone bisects the range of T. karelinii, cutting off a T. karelinii enclave. The high similarity of introgressed mitochondrial DNA haplotypes with those found in T. karelinii suggests a recent transfer across the species boundary. We then use ecological niche modeling to explore habitat suitability of the location of the present day introgression zone under current, mid-Holocene and Last Glacial Maximum conditions. This area was inhospitable during the Last Glacial Maximum for both species, but would have been habitable at the mid-Holocene. Since the mid-Holocene, habitat suitability generally increased for T. macedonicus, whereas it decreased for T. karelinii. CONCLUSION The presence of a T. karelinii enclave suggests that T. karelinii was the first to colonize the area where the present day introgression zone is positioned after the Last Glacial Maximum. Subsequently, we propose T. karelinii was outcompeted by T. macedonicus, which captured T. karelinii mitochondrial DNA via introgressive hybridization in the process. Ecological niche modeling suggests that this replacement was likely facilitated by a shift in climate since the mid-Holocene. We suggest that the northwestern part of the current introgression zone was probably never inhabited by T. karelinii itself, and that T. karelinii mitochondrial DNA spread there through T. macedonicus exclusively. Considering the spatial distribution of the introgressed mitochondrial DNA and the signal derived from ecological niche modeling, we do not favor the hypothesis that foreign mitochondrial DNA was pulled into the T. macedonicus range by natural selection.
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Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Faculty of Geo-Information Science and Earth Observation – ITC, University of Twente, P.O. Box 6, 7500 AA, Enschede, The Netherlands
| | - Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
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A Phenotypic Point of View of the Adaptive Radiation of Crested Newts (Triturus cristatus Superspecies, Caudata, Amphibia). INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:740605. [PMID: 22315697 PMCID: PMC3270399 DOI: 10.1155/2012/740605] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/06/2011] [Accepted: 10/11/2011] [Indexed: 11/18/2022]
Abstract
The divergence in phenotype and habitat preference within the crested newt Triturus cristatus superspecies, examined across different ontogenetic stages, provides an excellent setting to explore the pattern of adaptive radiation. The crested newts form a well-supported monophyletic clade for which at least the full mitochondrial DNA phylogeny is resolved. Here we summarise studies that explored the variation in morphological (larval and adult body form, limb skeleton, and skull shape) and other phenotypic traits (early life history, developmental sequences, larval growth rate, and sexual dimorphism) to infer the magnitude and direction of evolutionary changes in crested newts. The phenotypic traits show a high level of concordance in the pattern of variation; there is a cline-like variation, from T. dobrogicus, via T. cristatus, T. carnifex, and T. macedonicus to the T. karelinii group. This pattern matches the cline of ecological preferences; T. dobrogicus is relatively aquatic, followed by T. cristatus. T. macedonicus, T. carnifex, and the T. karelinii group are relatively terrestrial. The observed pattern indicates that phenotypic diversification in crested newts emerged due to an evolutionary switch in ecological preferences. Furthermore, the pattern indicates that heterochronic changes, or changes in the timing and rate of development, underlie the observed phenotypic evolutionary diversification.
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