1
|
Tran DV, Vu TT, Fukutani K, Nishikawa K. Demographic and ecological niche dynamics of the Vietnam warty newt, Paramesotriton deloustali: Historical climate influences. PLoS One 2023; 18:e0290044. [PMID: 37594998 PMCID: PMC10437943 DOI: 10.1371/journal.pone.0290044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023] Open
Abstract
Quaternary climatic cycles strongly affected the genetic diversification and ranges of organisms, shaping current genetic structures and distribution patterns. Urodeles provide ideal examples for exploring these dynamics over time and across space. In this study, we integrated a phylogeographic approach and ensemble species distribution modeling (eSDM) to infer the historical demography and distribution patterns of the Vietnam warty newt, Paramesotriton deloustali. Mitochondrial data revealed two groups, West and East, which diverged approximately 1.92 million years ago (Mya). Diversification was likely driven by change in the climate during early stages of the Pleistocene, with increasing monsoon and drought intensities. Biogeographic analysis indicated that the newt's current distribution formed as a result of vicariance events. In addition, the two groups occupy distinct ecological niches. Demographic reconstruction showed signs of expansion in the effective population sizes of the two major groups beginning around 0.11 and 0.15 Mya, respectively. However, eSDM showed fluctuating predicted distributions during the last interglacial, last glacial maximum, mid-Holocene, and present. Mountain systems in northern Vietnam are likely to have served as climatic refuges and to have played a crucial role in safeguarding species from the effects of climate change.
Collapse
Affiliation(s)
- Dung Van Tran
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Wildlife Department, Vietnam National University of Forestry, Ha Noi, Vietnam
| | - Thinh Tien Vu
- Wildlife Department, Vietnam National University of Forestry, Ha Noi, Vietnam
| | - Kazumi Fukutani
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Kaya S, Kabasakal B, Erdoğan A. Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations. BIOLOGY 2023; 12:biology12030401. [PMID: 36979093 PMCID: PMC10045126 DOI: 10.3390/biology12030401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/19/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population.
Collapse
Affiliation(s)
- Sarp Kaya
- First and Emergency Aid Programme, Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur 15030, Turkey
| | - Bekir Kabasakal
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
- Anesthesia Programme, Department of Medical Services and Techniques, Vocational School of Health Services, Antalya Bilim University, Antalya 07190, Turkey
- Correspondence:
| | - Ali Erdoğan
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
| |
Collapse
|
4
|
Candan K, Ilgaz Ç, Kumlutaş Y, Yıldırım Caynak E, Gül S. Molecular data confirm the presence of the Southern Crested Newt Triturus karelinii (Strauch, 1870) in Anatolia. ZOOLOGY IN THE MIDDLE EAST 2023. [DOI: 10.1080/09397140.2023.2183634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- Kamil Candan
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Türkiye
- Fauna and Flora Research and Application Center, Dokuz Eylül University, Buca, İzmir, Türkiye
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Türkiye
- Fauna and Flora Research and Application Center, Dokuz Eylül University, Buca, İzmir, Türkiye
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Türkiye
- Fauna and Flora Research and Application Center, Dokuz Eylül University, Buca, İzmir, Türkiye
| | - Elif Yıldırım Caynak
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Türkiye
- Fauna and Flora Research and Application Center, Dokuz Eylül University, Buca, İzmir, Türkiye
| | - Serkan Gül
- Department of Biology, Faculty of Science and Arts, Recep Tayyip Erdoğan University, Rize, Türkiye
| |
Collapse
|
5
|
Dursun C, Özdemir N, Gül S. Easternmost distribution of Bufo bufo (Linnaeus, 1758) in Türkiye: implications for the putative contact zone between B. bufo and B. verrucosissimus. Genetica 2023; 151:11-27. [PMID: 36418607 DOI: 10.1007/s10709-022-00175-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022]
Abstract
The geographic range of a species is crucial for obtaining information on the exact distribution of the species. The geographic data are important for delimiting distinct species or exploring the degree of differentiation among different populations of a species. The local details of species boundaries facilitate the study of the importance of phylogeographic background, secondary contacts, and hybrid zones, along with the relations between the species and its extrinsic environmental factors. In the present study, the range boundaries of Bufo bufo and Bufo verrucosissimus in the north-eastern region of Türkiye were delineated using an integrative taxonomic approach that utilized a combination of molecular and morphological data. According to the mtDNA results of the present study, B. bufo inhabits a single distribution from İyidere town to Çayeli town in Rize, while B. verrucosissimus is distributed from Şavşat town of Artvin to Ardeşen town in Rize. In addition, the two species coexist in Pazar, Hemşin, and Çamlıhemşin towns in Rize. The demographic analyses indicated a distinct population expansion for the B. verrucosissimus species after the Last Glacial Maximum, while the same did not occur for B. bufo. The univariate and multivariate statistical analyses conducted for the morphological data of the two species corroborated the presence of a putative contact zone between B. bufo and B. verrucosissimus. In summary, the present study resolved the non-distinct geographic boundaries between B. bufo and B. verrucosissimus species and also revealed the easternmost distribution of B. bufo in Türkiye. In addition, important evidence on the putative contact zone between the two species was indicated using an integrative taxonomic approach.
Collapse
Affiliation(s)
- Cantekin Dursun
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Fener Mah., 53100, Rize, Turkey.
| | - Nurhayat Özdemir
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Fener Mah., 53100, Rize, Turkey
| | - Serkan Gül
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Fener Mah., 53100, Rize, Turkey
| |
Collapse
|
6
|
Niwa K, Tran DV, Nishikawa K. Differentiated historical demography and ecological niche forming present distribution and genetic structure in coexisting two salamanders (Amphibia, Urodela, Hynobiidae) in a small island, Japan. PeerJ 2022; 10:e13202. [PMID: 35505683 PMCID: PMC9057287 DOI: 10.7717/peerj.13202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/09/2022] [Indexed: 01/12/2023] Open
Abstract
Background The climatic oscillations in the Quaternary period considerably shaped the distribution and population genetic structure of organisms. Studies on the historical dynamics of distribution and demography not only reflect the current geographic distribution but also allow us to understand the adaption and genetic differentiation of species. However, the process and factors affecting the present distribution and genetic structure of many taxa are still poorly understood, especially for endemic organisms to small islands. Methods Here, we integrated population genetic and ecological niche modelling approaches to investigate the historical distribution and demographic dynamics of two co-existing salamanders on Tsushima Island, Japan: the true H. tsuensis (Group A), and Hynobius sp. (Group B). We also examined the hypothesis on the equivalency and similarity of niches of these groups by identity and background tests for ecological niche space. Results Our result showed that Group A is considered to have undergone a recent population expansion after the Last Glacial Maximum while it is unlikely to have occurred in Group B. The highest suitability was predicted for Group A in southern Tsushima Island, whereas the northern part of Tsushima Island was the potential distribution of Group B. The results also suggested a restricted range of both salamanders during the Last Interglacial and Last Glacial Maximum, and recent expansion in Mid-Holocene. The genetic landscape-shape interpolation analysis and historical suitable area of ecological niche modelling were consistent, and suggested refugia used during glacial ages in southern part for Group A, and in northern part of Tsushima Island for Group B. Additionally, we found evidence of nonequivalence for the ecological niche of the two groups of the salamanders, although our test could not show either niche divergence or conservatism based on the background tests. The environmental predictors affecting the potential distribution of each group also showed distinctiveness, leading to differences in selecting suitable areas. Finally, the combination of population genetics and ecological modeling has revealed the differential demographic/historical response between coexisting two salamanders on a small island.
Collapse
Affiliation(s)
- Keita Niwa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Akita Prefectural Office, Akita, Japan
| | - Dung Van Tran
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan,Wildlife Department, Faculty of Forest Resources and Environmental Management, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| |
Collapse
|
7
|
Olgun Karacan G, Çolak R, Çolak E. The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse ( Apodemus mystacinus). MAMMALIA 2021. [DOI: 10.1515/mammalia-2020-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.
Collapse
Affiliation(s)
- Gül Olgun Karacan
- Department of Medical Services and Techniques , Vocational School of Health Services, Aksaray University , Aksaray 68100 , Turkey
| | - Reyhan Çolak
- Department of Biology , Faculty of Science, Ankara University , Ankara , Turkey
| | - Ercüment Çolak
- Department of Biology , Faculty of Science, Ankara University , Ankara , Turkey
| |
Collapse
|
8
|
Avtzis DN, Markoudi V, Mizerakis V, Devalez J, Nakas G, Poulakakis N, Petanidou T. The Aegean Archipelago as cradle: divergence of the glaphyrid genus Pygopleurus and phylogeography of P. foina. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1884622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Dimitrios N. Avtzis
- Forest Research Institute, Hellenic Agricultural Organization Demeter, Vassilika, Thessaloniki GR-57006, Greece
| | - Vasiliki Markoudi
- Forest Research Institute, Hellenic Agricultural Organization Demeter, Vassilika, Thessaloniki GR-57006, Greece
| | - Vangelis Mizerakis
- Aquatic Systems Biology, Technical University of Munich, Mühlenweg 22, Freising D-85354, Germany
- Laboratory of Biogeography and Ecology, Department of Geography, University of the Aegean, Mytilene GR-81100, Greece
| | - Jelle Devalez
- Laboratory of Biogeography and Ecology, Department of Geography, University of the Aegean, Mytilene GR-81100, Greece
| | - Georgios Nakas
- Laboratory of Biogeography and Ecology, Department of Geography, University of the Aegean, Mytilene GR-81100, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio GR-71409, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio GR-71110, Greece
| | - Theodora Petanidou
- Laboratory of Biogeography and Ecology, Department of Geography, University of the Aegean, Mytilene GR-81100, Greece
| |
Collapse
|
9
|
Rato C, Stratakis M, Sousa‐Guedes D, Sillero N, Corti C, Freitas S, Harris DJ, Carretero MA. The more you search, the more you find: Cryptic diversity and admixture within the Anatolian rock lizards (Squamata,
Darevskia
). ZOOL SCR 2020. [DOI: 10.1111/zsc.12462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Catarina Rato
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Vila do Conde Portugal
| | - Manos Stratakis
- Department of Biology School of Sciences and Engineering University of Crete Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Diana Sousa‐Guedes
- Centro de Investigação em Ciências Geo‐Espaciais (CICGE) Faculdade de Ciências da Universidade do Porto Vila Nova de Gaia Portugal
| | - Neftali Sillero
- Centro de Investigação em Ciências Geo‐Espaciais (CICGE) Faculdade de Ciências da Universidade do Porto Vila Nova de Gaia Portugal
| | - Claudia Corti
- Museo di Storia Naturale dell'Università di Firenze Firenze Italy
| | - Susana Freitas
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - D. James Harris
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Vila do Conde Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
| | - Miguel A. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Vila do Conde Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
| |
Collapse
|
10
|
Demırtaş S, Silsüpür M, Searle JB, Bilton D, Gündüz İ. What should we call the Levant mole? Unravelling the systematics and demography of Talpa levantis Thomas, 1906 sensu lato (Mammalia: Talpidae). Mamm Biol 2020. [DOI: 10.1007/s42991-020-00010-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
11
|
Parvizi E, Keikhosravi A, Naderloo R, Solhjouy‐Fard S, Sheibak F, Schubart CD. Phylogeography of Potamon ibericum (Brachyura: Potamidae) identifies Quaternary glacial refugia within the Caucasus biodiversity hot spot. Ecol Evol 2019; 9:4749-4759. [PMID: 31031941 PMCID: PMC6476761 DOI: 10.1002/ece3.5078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 11/30/2022] Open
Abstract
Refugia are critical for the maintenance of biodiversity during the periods of Quaternary climatic oscillations. The long-term persistence of refugial populations in a large continuous refugium has resulted in a homogenous pattern of genetic structure among populations, while highly structured evolutionary lineages characterize the restriction of refugial populations to smaller subrefugia. These mechanisms have resulted in the identification of hot spots of biodiversity within putative glacial refugia. We studied phylogeography of Potamon ibericum (Brachyura: Potamidae) in the drainages of the western Caucasus biodiversity hot spot (i.e., Colchis and the Caucasus) to infer spatial genetic structure and potential refugia for a freshwater crab in this region. These areas have traditionally considered as a refugium due to the presence of Tertiary relict species. We integrated population genetic data and historical demographic analysis from cytochrome oxidase subunit I sequences and paleoclimatic data from species distribution modeling (SDM). The results revealed the lack of phylogeographic structure and provided evidence for demographic expansion. The SDM presented a rather homogenous and large refugium that extended from northeast Turkey to Colchis during the last glacial period. In contrast to these findings, previous phylogeographic study on P. ibericum of the eastern Caucasus biodiversity hot spot (i.e., Hyrcania) identified multiple independent refugia. By combining these results, we explain the significance of this important western Palearctic hot spot of biological diversity in shaping the geographic distribution of intraspecific genetic diversity in a freshwater taxon.
Collapse
Affiliation(s)
- Elaheh Parvizi
- School of Biology, College of ScienceUniversity of TehranTehranIran
- Present address:
Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | | | - Reza Naderloo
- School of Biology, College of ScienceUniversity of TehranTehranIran
| | - Samaneh Solhjouy‐Fard
- Department of Plant Protection, College of Agriculture and Natural ResourcesUniversity of TehranKarajIran
| | | | | |
Collapse
|
12
|
Reconstructing evolution at the community level: A case study on Mediterranean amphibians. Mol Phylogenet Evol 2019; 134:211-225. [PMID: 30797941 DOI: 10.1016/j.ympev.2019.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 02/14/2019] [Accepted: 02/16/2019] [Indexed: 11/22/2022]
Abstract
Reconstructing reliable timescales for species evolution is an important and indispensable goal of modern biogeography. However, many factors influence the estimation of divergence times, and uncertainty in the inferred time trees remains a major issue that is often insufficiently acknowledged. We here focus on a fundamental problem of time tree analysis: the combination of slow-evolving (nuclear DNA) and fast-evolving (mitochondrial DNA) markers in a single time tree. Both markers differ in their suitability to infer divergences at different time scales (the 'genome-timescale-dilemma'). However, strategies to infer shallow and deep divergences in a single time tree have rarely been compared empirically. Using Mediterranean amphibians as model system that is exceptional in its geographic and taxonomic completeness of available genetic information, we analyze 202 lineages of western Palearctic amphibians across the entire Mediterranean region. We compiled data of four nuclear and five mitochondrial genes and used twelve fossil calibration points widely acknowledged for amphibian evolution. We reconstruct time trees for an extensive lineage-level data set and compare the performances of the different trees: the first tree is based on primary fossil calibration and mitochondrial DNA, while the second tree is based on a combination of primary fossil and on secondary calibrations taken from a nuclear tree using mitochondrial DNA (two-step protocol). Focusing on a set of nodes that are most likely explained by vicariance, we statistically compare the reconstructed alternative time trees by applying a biogeographical plausibility test. Our two-step protocol outperformed the alternative approach in terms of spatial and temporal plausibility. It allows us to infer scenarios for Mediterranean amphibian evolution in eight geographic provinces. We identified several tectonic and climatic events explaining the majority of Mediterranean amphibian divergences, with Plio-Pleistocene climatic fluctuations being the dominant driver for intrageneric evolution. However, often more than one event could be invoked for a specific split. We give recommendations for the use of secondary calibrations in future molecular clock analyses at the community level.
Collapse
|
13
|
Minoudi S, Papapetridis I, Karaiskou N, Chatzinikos E, Triantaphyllidis C, Abatzopoulos TJ, Triantafyllidis A. Genetic analyses of brown hare (Lepus europaeus) support limited migration and translocation of Greek populations. PLoS One 2018; 13:e0206327. [PMID: 30379887 PMCID: PMC6209229 DOI: 10.1371/journal.pone.0206327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 10/10/2018] [Indexed: 11/18/2022] Open
Abstract
Numerous studies have shown that the phylogeography of many species, including European brown hare, has been affected by the climatic oscillations of the Pleistocene. During this period the Balkans acted as a major refugium offering habitable conditions for many species. However, few studies have focused on the specific role of the Greek peninsula in the phylogeographic history of species in this southernmost margin of Balkans. We, therefore analyzed a 528 bp fragment of the D-loop region of mitochondrial DNA in 154 wild brown hare individuals from unsampled areas from both mainland and island Greece and compared it to 310 available brown hare sequences (including 110 Greek samples). Newly identified haplotypes show characteristic distribution in specific Greek areas reinforcing the theory that Greece can be considered as a subrefuge within Balkans for a number of species, with several “refugia within refugia” spots, holding significant genetic diversity. No haplotypes from wild Greek individuals clustered with the Central and Western Europe group revealing a minimal contribution of this area to the colonization of central Europe. One hundred and ten reared brown hares were also analyzed to elucidate the impact of introductions on local populations. Most of these samples presented close genetic affinity with haplotypes from Central and Western Europe indicating that farms in Greece use breeders from those areas. Therefore, despite human translocation of individuals, the genetic structure of brown hare has mostly been influenced by paleoclimatic conditions and minimally by human actions.
Collapse
Affiliation(s)
- Styliani Minoudi
- Deparment of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Papapetridis
- Deparment of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikoleta Karaiskou
- Deparment of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Costas Triantaphyllidis
- Deparment of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Theodore J. Abatzopoulos
- Deparment of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Deparment of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail:
| |
Collapse
|
14
|
Wielstra B, Burke T, Butlin RK, Arntzen JW. A signature of dynamic biogeography: enclaves indicate past species replacement. Proc Biol Sci 2017; 284:20172014. [PMID: 29187631 PMCID: PMC5740283 DOI: 10.1098/rspb.2017.2014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
Understanding how species have replaced each other in the past is important to predicting future species turnover. While past species replacement is difficult to detect after the fact, the process may be inferred from present-day distribution patterns. Species with abutting ranges sometimes show a characteristic distribution pattern, where a section of one species range is enveloped by that of the other. Such an enclave could indicate past species replacement: when a species is partly supplanted by a competitor, but a population endures locally while the invading species moves around and past it, an enclave forms. If the two species hybridize and backcross, the receding species is predicted to leave genetic traces within the expanding one under a scenario of species replacement. By screening dozens of genes in hybridizing crested newts, we uncover genetic remnants of the ancestral species, now inhabiting an enclave, in the range of the surrounding invading species. This independent genetic evidence supports the past distribution dynamics we predicted from the enclave. We suggest that enclaves provide a valuable tool in understanding historical species replacement, which is important because a major conservation concern arising from anthropogenic climate change is increased species replacement in the future.
Collapse
Affiliation(s)
- B Wielstra
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Naturalis Biodiversity Center, PO Box 9517, Leiden, 2300 RA, The Netherlands
| | - T Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - R K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Marine Sciences, University of Gothenburg, Gothenburg 405 30, Sweden
| | - J W Arntzen
- Naturalis Biodiversity Center, PO Box 9517, Leiden, 2300 RA, The Netherlands
| |
Collapse
|
15
|
van Riemsdijk I, Arntzen JW, Bogaerts S, Franzen M, Litvinchuk SN, Olgun K, Wielstra B. The Near East as a cradle of biodiversity: A phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation. Mol Phylogenet Evol 2017; 114:73-81. [DOI: 10.1016/j.ympev.2017.05.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 04/04/2017] [Accepted: 05/31/2017] [Indexed: 01/04/2023]
|
16
|
Ficetola GF, Colleoni E, Renaud J, Scali S, Padoa-Schioppa E, Thuiller W. Morphological variation in salamanders and their potential response to climate change. GLOBAL CHANGE BIOLOGY 2016; 22:2013-2024. [PMID: 26910389 PMCID: PMC4972144 DOI: 10.1111/gcb.13255] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 01/09/2016] [Accepted: 02/04/2016] [Indexed: 05/30/2023]
Abstract
Despite the recognition that some species might quickly adapt to new conditions under climate change, demonstrating and predicting such a fundamental response is challenging. Morphological variations in response to climate may be caused by evolutionary changes or phenotypic plasticity, or both, but teasing apart these processes is difficult. Here, we built on the number of thoracic vertebrae (NTV) in ectothermic vertebrates, a known genetically based feature, to establish a link with body size and evaluate how climate change might affect the future morphological response of this group of species. First, we show that in old-world salamanders, NTV variation is strongly related to changes in body size. Secondly, using 22 salamander species as a case study, we found support for relationships between the spatial variation in selected bioclimatic variables and NTV for most of species. For 44% of species, precipitation and aridity were the predominant drivers of geographical variation of the NTV. Temperature features were dominant for 31% of species, while for 19% temperature and precipitation played a comparable role. This two-step analysis demonstrates that ectothermic vertebrates may evolve in response to climate change by modifying the number of thoracic vertebrae. These findings allow to develop scenarios for potential morphological evolution under future climate change and to identify areas and species in which the most marked evolutionary responses are expected. Resistance to climate change estimated from species distribution models was positively related to present-day species morphological response, suggesting that the ability of morphological evolution may play a role for species' persistence under climate change. The possibility that present-day capacity for local adaptation might help the resistance response to climate change can be integrated into analyses of the impact of global changes and should also be considered when planning management actions favouring species persistence.
Collapse
Affiliation(s)
- Gentile Francesco Ficetola
- Laboratoire d’Ecologie Alpine (LECA), Université Grenoble-Alpes. Grenoble 38000, France
- LECA, CNRS, Grenoble 38000, France
- Dipartimento di Scienze dell’Ambiente e del Territorio, e di Scienze della Terra, Università degli Studi di Milano-Bicocca. 20126 Milano, Italy
| | - Emiliano Colleoni
- Dipartimento di Scienze dell’Ambiente e del Territorio, e di Scienze della Terra, Università degli Studi di Milano-Bicocca. 20126 Milano, Italy
| | - Julien Renaud
- Laboratoire d’Ecologie Alpine (LECA), Université Grenoble-Alpes. Grenoble 38000, France
- LECA, CNRS, Grenoble 38000, France
| | - Stefano Scali
- Museo Civico di Storia Naturale di Milano, 20121 Milano, Italy
| | - Emilio Padoa-Schioppa
- Dipartimento di Scienze dell’Ambiente e del Territorio, e di Scienze della Terra, Università degli Studi di Milano-Bicocca. 20126 Milano, Italy
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine (LECA), Université Grenoble-Alpes. Grenoble 38000, France
- LECA, CNRS, Grenoble 38000, France
| |
Collapse
|
17
|
Jablonski D, Jandzik D, Mikulíček P, Džukić G, Ljubisavljević K, Tzankov N, Jelić D, Thanou E, Moravec J, Gvoždík V. Contrasting evolutionary histories of the legless lizards slow worms (Anguis) shaped by the topography of the Balkan Peninsula. BMC Evol Biol 2016; 16:99. [PMID: 27165497 PMCID: PMC4863322 DOI: 10.1186/s12862-016-0669-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/25/2016] [Indexed: 11/27/2022] Open
Abstract
Background Genetic architecture of a species is a result of historical changes in population size and extent of distribution related to climatic and environmental factors and contemporary processes of dispersal and gene flow. Population-size and range contractions, expansions and shifts have a substantial effect on genetic diversity and intraspecific divergence, which is further shaped by gene-flow limiting barriers. The Balkans, as one of the most important sources of European biodiversity, is a region where many temperate species persisted during the Pleistocene glaciations and where high topographic heterogeneity offers suitable conditions for local adaptations of populations. In this study, we investigated the phylogeographical patterns and demographic histories of four species of semifossorial slow-worm lizards (genus Anguis) present in the Balkan Peninsula, and tested the relationship between genetic diversity and topographic heterogeneity of the inhabited ranges. Results We inferred phylogenetic relationships, compared genetic structure and historical demography of slow worms using nucleotide sequence variation of mitochondrial DNA. Four Anguis species with mostly parapatric distributions occur in the Balkan Peninsula. They show different levels of genetic diversity. A signature of population growth was detected in all four species but with various courses in particular populations. We found a strong correlation between genetic diversity of slow-worm populations and topographic ruggedness of the ranges (mountain systems) they inhabit. Areas with more rugged terrain harbour higher genetic diversity. Conclusions Phylogeographical pattern of the genus Anguis in the Balkans is concordant with the refugia-within-refugia model previously proposed for both several other taxa in the region and other main European Peninsulas. While slow-worm populations from the southern refugia mostly have restricted distributions and have not dispersed much from their refugial areas, populations from the extra-Mediterranean refugia in northern parts of the Balkans have colonized vast areas of eastern, central, and western Europe. Besides climatic historical events, the heterogeneous topography of the Balkans has also played an important role in shaping genetic diversity of slow worms. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0669-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - David Jandzik
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia.,Department of Ecology and Evolutionary Biology (EBIO), University of Colorado, Ramaley N122, Campus, Box 334, 80309-0334, Boulder, CO, USA
| | - Peter Mikulíček
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Georg Džukić
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", 11060, Belgrade, Serbia
| | - Katarina Ljubisavljević
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", 11060, Belgrade, Serbia
| | - Nikolay Tzankov
- Department of Vertebrates, National Museum of Natural History, Tsar Osvoboditel Blvd. 1, 1000, Sofia, Bulgaria
| | - Dušan Jelić
- Croatian Institute for Biodiversity, Croatian Herpetological Society Hyla, I, Breznička 5a, 10000, Zagreb, Croatia
| | - Evanthia Thanou
- Department of Biology, Section of Animal Biology, School of Natural Sciences, University of Patras, GR-26500, Patras, Greece
| | - Jiří Moravec
- Department of Zoology, National Museum, 193 00, Prague, Czech Republic
| | - Václav Gvoždík
- Department of Zoology, National Museum, 193 00, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65, Brno, Czech Republic
| |
Collapse
|
18
|
Freitas S, Vavakou A, Arakelyan M, Drovetski SV, Crnobrnja-isailović J, Kidov AA, Cogălniceanu D, Corti C, Lymberakis P, Harris DJ, Carretero MA. Cryptic diversity and unexpected evolutionary patterns in the meadow lizard,Darevskia praticola(Eversmann, 1834). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2015.1111267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
19
|
Wielstra B, Bozkurt E, Olgun K. The distribution and taxonomy of Lissotriton newts in Turkey (Amphibia, Salamandridae). Zookeys 2015; 484:11-23. [PMID: 25829839 PMCID: PMC4361781 DOI: 10.3897/zookeys.484.8869] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/16/2015] [Indexed: 11/29/2022] Open
Abstract
Two and perhaps three taxa of Lissotriton newt occur in Turkey. Their species status is controversial. The distribution of these taxa and the taxonomic status of each are reviewed and discussed. A database of 128 Turkish Lissotriton localities was compiled and species distribution models were constructed. We reiterate that the presence of Lissotriton (vulgaris) lantzi in Turkey is disputed and needs confirmation. The range of Lissotriton (vulgaris) kosswigi is restricted to north-western Anatolia - given the small global range of this Turkey endemic, a closer look at its conservation status is warranted. The distribution of Lissotritonvulgarisschmidtleri covers western Asiatic and European Turkey. The findings support an allopatric distribution of the Turkish Lissotriton species. We reflect on the biological significance of previously reported morphological intermediates between Lissotriton (vulgaris) kosswigi and Lissotritonvulgarisschmidtleri in the light of the recent proposal to recognize kosswigi at the species level. The available data are in line with species status for Lissotriton (vulgaris) lantzi and Lissotriton (vulgaris) kosswigi. Although Lissotritonvulgarisschmidtleri is a genetically diverged taxon as well, the extent of gene flow with parapatric European Lissotriton taxa is as yet unknown.
Collapse
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
| | - Emin Bozkurt
- Adnan Menderes University, Faculty of Science and Art, Department of Biology, 09010, Efeler, Aydın, Turkey
| | - Kurtuluş Olgun
- Adnan Menderes University, Faculty of Science and Art, Department of Biology, 09010, Efeler, Aydın, Turkey
| |
Collapse
|
20
|
Wielstra B, Babik W, Arntzen JW. The crested newtTriturus cristatusrecolonized temperate Eurasia from an extra-Mediterranean glacial refugium. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12446] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center; P.O. Box 9517 2300 RA Leiden The Netherlands
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Wiesław Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Jan W. Arntzen
- Naturalis Biodiversity Center; P.O. Box 9517 2300 RA Leiden The Netherlands
| |
Collapse
|
21
|
Tominaga A, Matsui M, Kokuryo Y. Occurrence and Evolutionary History of TwoCynops pyrrhogasterLineages on the Izu Peninsula. CURRENT HERPETOLOGY 2015. [DOI: 10.5358/hsj.34.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
22
|
Candan K, Kankılıç T, Güçlü Ö, Kumlutaş Y, Durmuş SH, Lymberakis P, Poulakakis N, Ilgaz Ç. First assessment on the molecular phylogeny of Anatololacerta (Squamata, Lacertidae) distributed in Southern Anatolia: insights from mtDNA and nDNA markers. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2285-92. [PMID: 25489775 DOI: 10.3109/19401736.2014.987238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The genus Anatololacerta (Lacertidae) occurs mainly in Anatolia (western and southern Turkey) and on the Aegean islands Samos, Ikaria, and Rhodos. Although its taxonomy has long been debated and is currently nascent, three morphological species have been attributed to this genus: Anatololacerta anatolica, Anatololacerta oertzeni, and Anatololacerta danfordi. Here, we investigated the evolutionary history of A. oertzeni and Anatololacerta danfordi based on both mitochondrial and nuclear markers (16S rRNA and cmos). In total, 34 Anatololacerta specimens were analyzed using maximum likelihood (ML) and Bayesian inference (BI) methods. Our results supported the presence of four well-supported lineages: two belongs to A. oertzeni and two to A. danfordi. The temporal diversification of these lineages probably started with the divergence of the first A. oertzeni lineage from western Antalya at 7.9 Mya. The other two major splits may have occurred in early Pliocene (4.4 Mya: the divergence of the second A. oertzeni from A. danfordi) and in late Pliocene (2.7 Mya: the divergence of the two lineages of A. danfordi). The phylogeographical scenario suggests that the major diversification events (from late Miocene to late Pliocene) could be related with climatic oscillations (such as the late Miocene aridification and the Messinian Salinity Crisis) and tectonic movements (such as the uplift of the central Taurus mountain).
Collapse
Affiliation(s)
- Kamil Candan
- a Department of Biology, Faculty of Science , Ege University , Bornova-İzmir , Turkey .,b Department of Biology, Faculty of Science , Dokuz Eylül University , Buca-İzmir , Turkey
| | - Tolga Kankılıç
- c Department of Biology, Faculty of Science and Arts , Aksaray University , Aksaray , Turkey
| | - Özgür Güçlü
- d Department of Plant and Animal Production , Güzelyurt Vocational School , Güzelyurt-Aksaray , Turkey
| | - Yusuf Kumlutaş
- b Department of Biology, Faculty of Science , Dokuz Eylül University , Buca-İzmir , Turkey
| | - Salih Hakan Durmuş
- e Department of Biology, Faculty of Education , Dokuz Eylül University , Buca-İzmir , Turkey
| | - Petros Lymberakis
- f Natural History Museum of Crete, University of Crete , Iraklio , Crete , Greece , and
| | - Nikos Poulakakis
- f Natural History Museum of Crete, University of Crete , Iraklio , Crete , Greece , and.,g Department of Biology , University of Crete , Iraklio , Crete , Greece
| | - Çetin Ilgaz
- b Department of Biology, Faculty of Science , Dokuz Eylül University , Buca-İzmir , Turkey
| |
Collapse
|
23
|
Cryptic diversity within the Anatololacerta species complex (Squamata: Lacertidae) in the Anatolian Peninsula: evidence from a multi-locus approach. Mol Phylogenet Evol 2014; 82 Pt A:219-33. [PMID: 25315886 DOI: 10.1016/j.ympev.2014.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 09/16/2014] [Accepted: 10/02/2014] [Indexed: 11/21/2022]
Abstract
The rapid development of innovative molecular tools for characterizing biodiversity is leading to an extensive and sometimes unexpected renovation of taxonomic classifications. Particularly, for species having allopatric or parapatric distributions or resulting from recent speciation processes, the absence of clear phenotypic differentiation may hinder the recognition of closely related taxa, while intraspecific polymorphism may be confused with the presence of more than one single species. In the present work, we apply different phylogenetic methods in order to infer relationships within the genus Anatololacerta, and to assess the taxonomy of this morphologically diversified group of lizards endemic to western and southern Anatolia and some neighboring Aegean islands. According to morphology, three species have been recognized (Anatololacerta anatolica, A. oertzeni and A. danfordi) as well as several subspecies, but small variation at immunological markers led some authors to join all the populations into one single taxon, A. danfordi. By selecting both mitochondrial and nuclear informative markers, we tested the effectiveness of classical "gene tree" (i.e. Bayesian Inference) vs. innovative (i.e. coalescent-based) "species tree" methods in resolving the Anatololacerta taxonomic enigma, as a case in point for similar studies on species complexes resulting from non-obvious and cryptic diversification patterns. According to our results, the gene tree method failed in resolving phylogenetic relationships among clades, whereas the multi-locus species tree approach, coupled with species delimitation methods, allowed the identification of four well distinct species. These species probably diversified in different allopatric refugia located in southern and western Anatolia, where isolated populations may have persisted during Pleistocene glacial cycles.
Collapse
|
24
|
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]
|
25
|
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
| |
Collapse
|
26
|
Stoelting RE, Measey GJ, Drewes RC. Population genetics of the São Tomé caecilian (Gymnophiona: Dermophiidae: Schistometopum thomense) reveals strong geographic structuring. PLoS One 2014; 9:e104628. [PMID: 25171066 PMCID: PMC4149351 DOI: 10.1371/journal.pone.0104628] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 07/15/2014] [Indexed: 11/18/2022] Open
Abstract
Islands provide exciting opportunities for exploring ecological and evolutionary mechanisms. The oceanic island of São Tomé in the Gulf of Guinea exhibits high diversity of fauna including the endemic caecilian amphibian, Schistometopum thomense. Variation in pigmentation, morphology and size of this taxon over its c. 45 km island range is extreme, motivating a number of taxonomic, ecological, and evolutionary hypotheses to explain the observed diversity. We conducted a population genetic study of S. thomense using partial sequences of two mitochondrial DNA genes (ND4 and 16S), together with morphological examination, to address competing hypotheses of taxonomic or clinal variation. Using Bayesian phylogenetic analysis and Spatial Analysis of Molecular Variance, we found evidence of four geographic clades, whose range and approximated age (c. 253 Kya – 27 Kya) are consistent with the spread and age of recent volcanic flows. These clades explained 90% of variation in ND4 (φCT = 0.892), and diverged by 4.3% minimum pairwise distance at the deepest node. Most notably, using Mismatch Distributions and Mantel Tests, we identified a zone of population admixture that dissected the island. In the northern clade, we found evidence of recent population expansion (Fu's Fs = −13.08 and Tajima's D = −1.80) and limited dispersal (Mantel correlation coefficient = 0.36, p = 0.01). Color assignment to clades was not absolute. Paired with multinomial regression of chromatic data, our analyses suggested that the genetic groups and a latitudinal gradient together describe variation in color of S. thomense. We propose that volcanism and limited dispersal ability are the likely proximal causes of the observed genetic structure. This is the first population genetic study of any caecilian and demonstrates that these animals have deep genetic divisions over very small areas in accordance with previous speculations of low dispersal abilities.
Collapse
Affiliation(s)
- Ricka E. Stoelting
- Department of Herpetology, California Academy of Sciences, San Francisco, California, United States of America
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
| | - G. John Measey
- Centre for Invasion Biology, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Robert C. Drewes
- Department of Herpetology, California Academy of Sciences, San Francisco, California, United States of America
| |
Collapse
|
27
|
Poulakakis N, Kapli P, Lymberakis P, Trichas A, Vardinoyiannis K, Sfenthourakis S, Mylonas M. A review of phylogeographic analyses of animal taxa from the Aegean and surrounding regions. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12071] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nikos Poulakakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Paschalia Kapli
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | - Apostolos Trichas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | | | | | - Moisis Mylonas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| |
Collapse
|
28
|
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.
Collapse
Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | |
Collapse
|
29
|
Previšić A, Schnitzler J, Kučinić M, Graf W, Ibrahimi H, Kerovec M, Pauls SU. Microscale vicariance and diversification of Western Balkan caddisflies linked to karstification. FRESHWATER SCIENCE (PRINT) 2014; 33:250-262. [PMID: 27042385 PMCID: PMC4813752 DOI: 10.1086/674430] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The karst areas in the Dinaric region of the Western Balkan Peninsula are a hotspot of freshwater biodiversity. Many investigators have examined diversification of the subterranean freshwater fauna in these karst systems. However, diversification of surface-water fauna remains largely unexplored. We assessed local and regional diversification of surface-water species in karst systems and asked whether patterns of population differentiation could be explained by dispersal-diversification processes or allopatric diversification following karst-related microscale vicariance. We analyzed mitochondrial cytochrome c oxidase subunit I (mtCOI) sequence data of 4 caddisfly species (genus Drusus) in a phylogeographic framework to assess local and regional population genetic structure and Pliocene/Pleistocene history. We used BEAST software to assess the timing of intraspecific diversification of the target species. We compared climate envelopes of the study species and projected climatically suitable areas during the last glacial maximum (LGM) to assess differences in the species climatic niches and infer potential LGM refugia. The haplotype distribution of the 4 species (324 individuals from 32 populations) was characterized by strong genetic differentiation with few haplotypes shared among populations (16%) and deep divergence among populations of the 3 endemic species, even at local scales. Divergence among local populations of endemics often exceeded divergence among regional and continental clades of the widespread D. discolor. Major divergences among regional populations dated to 2.0 to 0.5 Mya. Species distribution model projections and genetic structure suggest that the endemic species persisted in situ and diversified locally throughout multiple Pleistocene climate cycles. The pattern for D. discolor was different and consistent with multiple invasions into the region. Patterns of population genetic structure and diversification were similar for the 3 regional endemic Drusus species and consistent with microscale vicariance after the onset of intensified karstification in the Dinaric region. Karstification may induce microscale vicariance of running surface-water habitats and probably promotes allopatric fragmentation of stream insects at small spatial scales.
Collapse
Affiliation(s)
- Ana Previšić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Jan Schnitzler
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt/Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
| | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology Management, University of Natural Resources and Applied Life Sciences, Max-Emanuel-Straße 17, 1180 Vienna, Austria
| | - Halil Ibrahimi
- Department of Biology, Faculty of Mathematics and Natural Sciences, University of Prishtina, Mother Theresa p.n., 10000 Prishtina, Kosovo
| | - Mladen Kerovec
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Steffen U Pauls
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt/Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Arntzen JW, Recuero E, Canestrelli D, Martínez-Solano I. How complex is the Bufo bufo species group? Mol Phylogenet Evol 2013; 69:1203-8. [PMID: 23880535 DOI: 10.1016/j.ympev.2013.07.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 11/30/2022]
Abstract
Species delineation remains one of the most challenging tasks in the study of biodiversity, mostly owing to the application of different species concepts, which results in contrasting taxonomic arrangements. This has important practical consequences, since species are basic units in fields like ecology and conservation biology. We here review molecular genetic evidence relevant to the systematics of toads in the Bufo bufo species group (Anura, Bufonidae). Two studies recently published in this journal (Recuero et al., MPE 62: 71-86 and García-Porta et al., MPE 63: 113-130) addressed this issue but reached opposing conclusions on the taxonomy of the group (four versus two species). In particular, allozyme data in the latter paper were interpreted as evidence for hybridization across species (between B. bufo-B. spinosus and B. bufo-B. verrucosissimus). We tested claims for hybridization through re-analysis of allozyme data for individuals instead of populations, to be able to distinguish between sympatry with and without admixture, and found no evidence of hybridization across taxa. We propose alternative explanations for the observed patterns that García-Porta et al. (2012) failed to consider. In the absence of unequivocal evidence for hybridization and introgression, we reject the proposal to downgrade Bufo spinosus and Bufo verrucosissimus to the subspecies level.
Collapse
Affiliation(s)
- Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | | | | | | |
Collapse
|
32
|
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]
|
33
|
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.
Collapse
Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, P, O, Box 9517, 2300 RA, Leiden, The Netherlands.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
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.
Collapse
|
35
|
Kaya S, Boztepe Z, Çiplak B. Phylogeography ofTroglophilus(Orthoptera: Troglophilinae) based on Anatolian members of the genus: radiation of an old lineage following the Messinian. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.02025.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarp Kaya
- Department of Biology; Faculty of Science; Akdeniz University; 07058; Antalya; Turkey
| | - Zehra Boztepe
- Department of Biology; Faculty of Science; Akdeniz University; 07058; Antalya; Turkey
| | - Battal Çiplak
- Department of Biology; Faculty of Science; Akdeniz University; 07058; Antalya; Turkey
| |
Collapse
|
36
|
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
| |
Collapse
|
37
|
Tominaga A, Matsui M, Yoshikawa N, Nishikawa K, Hayashi T, Misawa Y, Tanabe S, Ota H. Phylogeny and historical demography of Cynops pyrrhogaster (Amphibia: Urodela): taxonomic relationships and distributional changes associated with climatic oscillations. Mol Phylogenet Evol 2012; 66:654-67. [PMID: 23103571 DOI: 10.1016/j.ympev.2012.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/13/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
Abstract
We investigated the phylogenetic relationships and estimated the historical demography of the Japanese fire-bellied newt, Cynops pyrrhogaster, from Japanese mainlands using 1407-bp sequences of the mitochondrial DNA (NADH6, tRNAglu, cyt b) and 1208-bp sequences of nuclear DNA (Rag-1) genes. Phylogenetic trees based on mitochondrial DNA revealed four major haplotype clades (NORTHERN, CENTRAL, WESTERN, and SOUTHERN clades) within this species. Degree of genetic differentiation among major haplotype clades was very large for intraspecific variation, suggesting this species to be composed of four species lineages that replace each other geographically. Nuclear genetic variation presented no obvious patterns of geographic structure except for the distinctness of populations diagnosed by NORTHERN clade of mitochondrial haplotypes, suggesting results of incomplete lineage sorting. Current distribution and estimated divergence times for the genus Cynops suggest that the common ancestor of two Japanese species (C. pyrrhogaster and C. ensicauda from the Ryukyu Islands) had diverged at the edge of the continent corresponding to the present East China Sea and Central Ryukyus. Subsequent range expansion to Japanese mainland seems to have occurred in the middle Miocene. Population-genetic analyses indicated that all species lineages, except for the SOUTHERN one, experienced geographic population reductions and expansions associated with glacial and postglacial climatic oscillations.
Collapse
Affiliation(s)
- Atsushi Tominaga
- Department of Natural Sciences, Faculty of Education, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, Japan
| | | | | | | | | | | | | | | |
Collapse
|
38
|
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.
Collapse
Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands.
| | | | | | | | | | | |
Collapse
|
39
|
Mulcahy DG, Noonan BP, Moss T, Townsend TM, Reeder TW, Sites JW, Wiens JJ. Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles. Mol Phylogenet Evol 2012; 65:974-91. [PMID: 22982760 DOI: 10.1016/j.ympev.2012.08.018] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 08/21/2012] [Accepted: 08/22/2012] [Indexed: 11/16/2022]
Abstract
Recently, phylogenetics has expanded to routinely include estimation of clade ages in addition to their relationships. Various dating methods have been used, but their relative performance remains understudied. Here, we generate and assemble an extensive phylogenomic data set for squamate reptiles (lizards and snakes) and evaluate two widely used dating methods, penalized likelihood in r8s (r8s-PL) and Bayesian estimation with uncorrelated relaxed rates among lineages (BEAST). We obtained sequence data from 25 nuclear loci (∼500-1,000 bp per gene; 19,020bp total) for 64 squamate species and nine outgroup taxa, estimated the phylogeny, and estimated divergence dates using 14 fossil calibrations. We then evaluated how well each method approximated these dates using random subsets of the nuclear loci (2, 5, 10, 15, and 20; replicated 10 times each), and using ∼1 kb of the mitochondrial ND2 gene. We find that estimates from r8s-PL based on 2, 5, or 10 loci can differ considerably from those based on 25 loci (mean absolute value of differences between 2-locus and 25-locus estimates were 9.0 Myr). Estimates from BEAST are somewhat more consistent given limited sampling of loci (mean absolute value of differences between 2 and 25-locus estimates were 5.0 Myr). Most strikingly, age estimates using r8s-PL for ND2 were ∼68-82 Myr older (mean=73.1) than those using 25 nuclear loci with r8s-PL. These results show that dates from r8s-PL with a limited number of loci (and especially mitochondrial data) can differ considerably from estimates derived from a large number of nuclear loci, whereas estimates from BEAST derived from fewer nuclear loci or mitochondrial data alone can be surprisingly similar to those from many nuclear loci. However, estimates from BEAST using relatively few loci and mitochondrial data could still show substantial deviations from the full data set (>50 Myr), suggesting the benefits of sampling many nuclear loci. Finally, we found that confidence intervals on ages from BEAST were not significantly different when sampling 2 vs. 25 loci, suggesting that adding loci decreased errors but did not increase confidence in those estimates.
Collapse
Affiliation(s)
- Daniel G Mulcahy
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
| | | | | | | | | | | | | |
Collapse
|
40
|
Helvaci Z, Renaud S, Ledevin R, Adriaens D, Michaux J, Çolak R, Kankiliç T, Kandemir İ, Yiğit N, Çolak E. Morphometric and genetic structure of the edible dormouse (Glis glis): a consequence of forest fragmentation in Turkey. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01952.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Zeycan Helvaci
- Department of Biology; Faculty of Science and Letter; Aksaray University; Campus 68100 Aksaray Turkey
- Department of Biology; Faculty of Science; Ankara University; Tandoğan Campus 06100 Ankara Turkey
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive; UMR 5558; CNRS; University Lyon 1; Campus de la Doua 69622 Villeurbanne France
| | - Ronan Ledevin
- Anthropologisches Institut & Museum; Universität Zürich-Irchel; Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Dominique Adriaens
- Evolutionary Morphology of Vertebrates; Ghent University; K.L. Ledeganckstraat 35 B-9000 Ghent Belgium
| | - Johan Michaux
- Laboratoire de Génétique des micro-organismes; Université de Liège; Institut de Botanique (Bat. 22) 4000 Liège Belgium
- INRA; UMR CBGP 1062; Campus international de Baillarguet; CS 30016 F-34988 Montferrier-sur-Lez Cedex France
| | - Reyhan Çolak
- Department of Biology; Faculty of Science; Ankara University; Tandoğan Campus 06100 Ankara Turkey
| | - Teoman Kankiliç
- Department of Biology; Faculty of Arts and Science; Niğde University; Campus 51240 Niğde Turkey
| | - İrfan Kandemir
- Department of Biology; Faculty of Science; Ankara University; Tandoğan Campus 06100 Ankara Turkey
| | - Nuri Yiğit
- Department of Biology; Faculty of Science; Ankara University; Tandoğan Campus 06100 Ankara Turkey
| | - Ercüment Çolak
- Department of Biology; Faculty of Science; Ankara University; Tandoğan Campus 06100 Ankara Turkey
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Canestrelli D, Salvi D, Maura M, Bologna MA, Nascetti G. One species, three Pleistocene evolutionary histories: phylogeography of the Italian crested newt, Triturus carnifex. PLoS One 2012; 7:e41754. [PMID: 22848590 PMCID: PMC3406094 DOI: 10.1371/journal.pone.0041754] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 06/25/2012] [Indexed: 11/19/2022] Open
Abstract
Phylogeographic patterns of temperate species from the Mediterranean peninsulas have been investigated intensively. Nevertheless, as more phylogeographies become available, either unique patterns or new lines of concordance continue to emerge, providing new insights on the evolution of regional biotas. Here, we investigated the phylogeography and evolutionary history of the Italian crested newt, Triturus carnifex, through phylogenetic, molecular dating and population structure analyses of two mitochondrial gene fragments (ND2 and ND4; overall 1273 bp). We found three main mtDNA lineages having parapatric distribution and estimated divergence times between Late Pliocene and Early Pleistocene. One lineage (S) was widespread south of the northern Apennine chain and was further geographically structured into five sublineages, likely of Middle Pleistocene origin. The second lineage (C) was widespread throughout the Padano-Venetian plain and did not show a clear phylogeographic structure. The third lineage (N) was observed in only two populations located on western Croatia/Slovenia. Results of analysis of molecular variance suggested that partitioning populations according to the geographic distribution of these lineages and sublineages explains 76% of the observed genetic variation. The phylogeographic structure observed within T. carnifex and divergence time estimates among its lineages, suggest that responses to Pleistocene environmental changes in this single species have been as diverse as those found previously among several codistributed temperate species combined. Consistent with the landscape heterogeneity, physiographic features, and palaeogeographical evolution of its distribution range, these responses encompass multiple refugia along the Apennine chain, lowland refugia in large peri-coastal plains, and a 'cryptic' northern refugium.
Collapse
Affiliation(s)
- Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy.
| | | | | | | | | |
Collapse
|
43
|
Kornilios P, Ilgaz Ç, Kumlutaş Y, Lymberakis P, Moravec J, Sindaco R, Rastegar-Pouyani N, Afroosheh M, Giokas S, Fraguedakis-Tsolis S, Chondropoulos B. Neogene climatic oscillations shape the biogeography and evolutionary history of the Eurasian blindsnake. Mol Phylogenet Evol 2012; 62:856-73. [DOI: 10.1016/j.ympev.2011.11.035] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 11/23/2011] [Accepted: 11/30/2011] [Indexed: 11/16/2022]
|
44
|
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.
Collapse
|
45
|
Gómez-Zurita J, Sassi D, Cardoso A, Balke M. Evolution of Cryptocephalus leaf beetles related to C. sericeus (Coleoptera: Chrysomelidae) and the role of hybridization in generating species mtDNA paraphyly. ZOOL SCR 2011. [DOI: 10.1111/j.1463-6409.2011.00500.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
46
|
Sexual dimorphism in the skull geometry of newt species of Ichthyosaura, Triturus and Lissotriton (Salamandridae, Caudata, Amphibia). ZOOMORPHOLOGY 2011. [DOI: 10.1007/s00435-011-0143-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
47
|
Recuero E, Canestrelli D, Vörös J, Szabó K, Poyarkov NA, Arntzen JW, Crnobrnja-Isailovic J, Kidov AA, Cogălniceanu D, Caputo FP, Nascetti G, Martínez-Solano I. Multilocus species tree analyses resolve the radiation of the widespread Bufo bufo species group (Anura, Bufonidae). Mol Phylogenet Evol 2011; 62:71-86. [PMID: 21964513 DOI: 10.1016/j.ympev.2011.09.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 09/07/2011] [Accepted: 09/11/2011] [Indexed: 11/19/2022]
Abstract
New analytical methods are improving our ability to reconstruct robust species trees from multilocus datasets, despite difficulties in phylogenetic reconstruction associated with recent, rapid divergence, incomplete lineage sorting and/or introgression. In this study, we applied these methods to resolve the radiation of toads in the Bufo bufo (Anura, Bufonidae) species group, ranging from the Iberian Peninsula and North Africa to Siberia, based on sequences from two mitochondrial and four nuclear DNA regions (3490 base pairs). We obtained a fully-resolved topology, with the recently described Bufo eichwaldi from the Talysh Mountains in south Azerbaijan and Iran as the sister taxon to a clade including: (1) north African, Iberian, and most French populations, referred herein to Bufo spinosus based on the implied inclusion of populations from its type locality and (2) a second clade, sister to B. spinosus, including two sister subclades: one with all samples of Bufo verrucosissimus from the Caucasus and another one with samples of B. bufo from northern France to Russia, including the Apennine and Balkan peninsulas and most of Anatolia. Coalescent-based estimations of time to most recent common ancestors for each species and selected subclades allowed historical reconstruction of the diversification of the species group in the context of Mediterranean paleogeography and indicated a long evolutionary history in this region. Finally, we used our data to delimit the ranges of the four species, particularly the more widespread and historically confused B. spinosus and B. bufo, and identify potential contact zones, some of which show striking parallels with other co-distributed species.
Collapse
Affiliation(s)
- E Recuero
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Bilgin R. Back to the suture: the distribution of intraspecific genetic diversity in and around anatolia. Int J Mol Sci 2011; 12:4080-103. [PMID: 21747726 PMCID: PMC3131610 DOI: 10.3390/ijms12064080] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 06/10/2011] [Indexed: 11/16/2022] Open
Abstract
The effect of ice ages in speciation and diversification is well established in the literature. In Europe, the Iberian, the Italian and the Balkan peninsulas comprise the main glacial refugia, where the subsequent re-population of Europe started. Though not studied as extensively, Anatolia has also been hinted to be a potential glacial refugium for Europe, and with its proximity to the Caucasus and the Middle East at the same time, has potential to exhibit high levels of intraspecific diversity. The more ubiquitous use and cheaper availability of molecular methods globally now makes it possible to better understand molecular ecology and evolution of the fauna and flora in the genetically understudied regions of the world, such as Anatolia. In this review, the molecular genetic studies undertaken in Anatolia in the last decade, for 29 species of plants and animals, are examined to determine general phylogeographic patterns. In this regard, two major patterns are observed and defined, showing genetic breaks within Anatolia and between Anatolia and the Balkans. A third pattern is also outlined, which suggests Anatolia may be a center of diversity for the surrounding regions. The patterns observed are discussed in terms of their relevance to the location of suture zones, postglacial expansion scenarios, the effect of geographic barriers to gene flow and divergence time estimates, in order to better understand the effect of the geological history of Anatolia on the evolutionary history of the inhabitant species. In view of the current state of knowledge delineated in the review, future research directions are suggested.
Collapse
Affiliation(s)
- Rasit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek 34342, Istanbul, Turkey; E-Mail: ; Tel.: +90-537-988-4734
| |
Collapse
|
49
|
Wielstra B, Arntzen JW. Unraveling the rapid radiation of crested newts (Triturus cristatus superspecies) using complete mitogenomic sequences. BMC Evol Biol 2011; 11:162. [PMID: 21672214 PMCID: PMC3224112 DOI: 10.1186/1471-2148-11-162] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Accepted: 06/14/2011] [Indexed: 12/03/2022] Open
Abstract
Background The rapid radiation of crested newts (Triturus cristatus superspecies) comprises four morphotypes: 1) the T. karelinii group, 2) T. carnifex - T. macedonicus, 3) T. cristatus and 4) T. dobrogicus. These vary in body build and the number of rib-bearing pre-sacral vertebrae (NRBV). The phylogenetic relationships of the morphotypes have not yet been settled, despite several previous attempts, employing a variety of molecular markers. We here resolve the crested newt phylogeny by using complete mitochondrial genome sequences. Results Bayesian inference based on the mitogenomic data yields a fully bifurcating, significantly supported tree, though Maximum Likelihood inference yields low support values. The internal branches connecting the morphotypes are short relative to the terminal branches. Seen from the root of Triturus (NRBV = 13), a basal dichotomy separates the T. karelinii group (NRBV = 13) from the remaining crested newts. The next split divides the latter assortment into T. carnifex - T. macedonicus (NRBV = 14) versus T. cristatus (NRBV = 15) and T. dobrogicus (NRBV = 16 or 17). Conclusions We argue that the Bayesian full mitochondrial DNA phylogeny is superior to previous attempts aiming to recover the crested newt species tree. Furthermore, our new phylogeny involves a maximally parsimonious interpretation of NRBV evolution. Calibrating the phylogeny allows us to evaluate potential drivers for crested newt cladogenesis. The split between the T. karelinii group and the three other morphotypes, at ca. 10.4 Ma, is associated with the separation of the Balkan and Anatolian landmasses (12-9 Ma). No currently known vicariant events can be ascribed to the other two splits, first at ca. 9.3 Ma, separating T. carnifex - T. macedonicus, and second at ca. 8.8 Ma, splitting T. cristatus and T. dobrogicus. The crested newt morphotypes differ in the duration of their annual aquatic period. We speculate on the role that this ecological differentiation could have played during speciation.
Collapse
Affiliation(s)
- Ben Wielstra
- Netherlands Centre for Biodiversity-NCB Naturalis, Leiden, The Netherlands.
| | | |
Collapse
|