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Senczuk G, Castiglia R, Colangelo P, Delaugerre M, Corti C. The role of island physiography in maintaining genetic diversity in the endemic Tyrrhenian wall lizard (
Podarcis tiliguerta
). J Zool (1987) 2019. [DOI: 10.1111/jzo.12705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- G. Senczuk
- Sezione di Zoologia “La Specola” Museo di Storia Naturale dell'Università di Firenze Firenze Italia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin” Università di Roma “La Sapienza” Rome Italia
| | - R. Castiglia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin” Università di Roma “La Sapienza” Rome Italia
| | - P. Colangelo
- Istituto di Ricerca sugli Ecosistemi Terrestri (CNR‐IRET) Consiglio Nazionale delle Ricerche Rome Italia
| | | | - C. Corti
- Sezione di Zoologia “La Specola” Museo di Storia Naturale dell'Università di Firenze Firenze Italia
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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: 16] [Impact Index Per Article: 3.2] [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.
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Bisconti R, Tenchini R, Belfiore C, Nascetti G, Canestrelli D. Fast and accurate identification of cryptic and sympatric mayfly species of the Baetis rhodani group. BMC Res Notes 2018; 11:7. [PMID: 29310715 PMCID: PMC5759225 DOI: 10.1186/s13104-017-3115-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/21/2017] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Species of the Baetis rhodani group are among the most widespread mayflies of the Palearctic region. However, frequent occurrence of morphologically cryptic species complicates the identification of sympatric species. Here, we proposed and tested a method for the fast, accurate, and cost-effective assignment of a large number of individuals to their putative species, based on high resolution melting profiles of a standard mitochondrial gene fragment. We tested this method using a system of three recently identified cryptic species inhabiting the Tyrrhenian Islands (western Mediterranean basin). RESULTS Highly species-specific high resolution melting profiles were obtained, allowing the unequivocal attribution of each individual to the respective species. This assay provides a convenient and easily customizable alternative to traditional barcoding approaches, provided that the mayfly taxa occurring within the geographic area of interest have been previously identified and their high resolution melting profiles assessed.
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Affiliation(s)
- Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viale dell’Università s.n.c., 01100 Viterbo, Italy
| | - Roberta Tenchini
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viale dell’Università s.n.c., 01100 Viterbo, Italy
| | - Carlo Belfiore
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viale dell’Università s.n.c., 01100 Viterbo, Italy
| | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viale dell’Università s.n.c., 01100 Viterbo, Italy
| | - Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viale dell’Università s.n.c., 01100 Viterbo, Italy
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Quaternary history, population genetic structure and diversity of the cold-adapted Alpine newt Ichthyosaura alpestris in peninsular Italy. Sci Rep 2017; 7:2955. [PMID: 28592856 PMCID: PMC5462806 DOI: 10.1038/s41598-017-03116-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022] Open
Abstract
Mediterranean peninsulas are major biodiversity hotspots, and cold-adapted species are an important component of this biodiversity. However, cold-adapted species contributed surprisingly little to our knowledge of the intimate links between Quaternary environmental changes, species' responses to these changes, and current patterns of intraspecific biodiversity. Here, we investigated the genetic structure and evolutionary history of a cold-adapted amphibian, the Alpine newt Ichthyosaura alpestris, within the Italian peninsula. Nuclear and mitochondrial markers consistently identified three distinct genetic lineages, whose divergence dates to the Early Pleistocene (1.9 and 0.8 million years ago). Our results show that the Italian peninsula provided multiple Pleistocene refugia to this cold-adapted species, and suggest that allopatric fragmentation followed by secondary admixture have been key events in the formation of its current pattern of genetic diversity. Indeed, estimates of population genetic diversity clearly identified contact populations as those achieving the highest levels of diversity. Such concordance among cold-adapted and temperate species in terms of processes triggering the formation of regional patterns of genetic diversity provides strong support for the hypothesis that gene exchange between divergent lineages, rather than long-term stability of refugial populations, has been the main step toward the formation of hotspots of intraspecific biodiversity.
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Salvi D, Pinho C, Harris DJ. Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta. BMC Evol Biol 2017; 17:63. [PMID: 28253846 PMCID: PMC5335832 DOI: 10.1186/s12862-017-0899-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity. RESULTS We analysed DNA sequences of mitochondrial (12S and nd4) and nuclear (acm4 and mc1r) gene fragments in 174 individuals of P. tiliguerta from 81 localities across the full range of the species in a geographic and genealogical framework. We found surprisingly high genetic diversity both at mitochondrial and nuclear loci. Seventeen reciprocally monophyletic allopatric mitochondrial haplogroups were sharply divided into four main mitochondrial lineages (two in Corsica and two in Sardinia) of Miocene origin. In contrast, shallow divergence and shared diversity within and between islands was observed at the nuclear loci. We evaluated alternative biogeographic and evolutionary scenarios to explain such profound discordance in spatial and phylogenetic patterning between mitochondrial and nuclear genomes. While neutral models provided unparsimonious explanations for the observed pattern, the hypothesis of environmental selection driving mitochondrial divergence in the presence of nuclear gene flow is favoured. CONCLUSIONS Our study on the genetic variation of P. tiliguerta reveals surprising levels of diversity underlining a complex phylogeographic pattern with a striking example of mito-nuclear discordance. These findings have profound implications, not only for the taxonomy and conservation of P. tiliguerta. Growing evidence on deep mitochondrial breaks in absence of geographic barriers and of climatic factors associated to genetic variation of Corsican-Sardinian endemics warrants additional investigation on the potential role of environmental selection driving the evolution of diversity hotspots within Mediterranean islands.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 Coppito, L'Aquila, Italy. .,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
| | - Catarina Pinho
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
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6
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Ball SE, Bovero S, Sotgiu G, Tessa G, Angelini C, Bielby J, Durrant C, Favelli M, Gazzaniga E, Garner TWJ. Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus. Ecol Evol 2017; 7:1190-1211. [PMID: 28303189 PMCID: PMC5306002 DOI: 10.1002/ece3.2665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/21/2016] [Indexed: 12/04/2022] Open
Abstract
The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus. Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.
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Affiliation(s)
- Sarah E. Ball
- Institute of ZoologyThe Zoological Society of LondonLondonUK
| | - Stefano Bovero
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giuseppe Sotgiu
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giulia Tessa
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
- Dipartimento di Scienze della Vita e Biologia dei SistemiUniversita degli Studi di TorinoTorinoItaly
| | - Claudio Angelini
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Jon Bielby
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | | | - Marco Favelli
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Enrico Gazzaniga
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Trenton W. J. Garner
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
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Bisconti R, Canestrelli D, Tenchini R, Belfiore C, Buffagni A, Nascetti G. Cryptic diversity and multiple origins of the widespread mayfly species group Baetis rhodani (Ephemeroptera: Baetidae) on northwestern Mediterranean islands. Ecol Evol 2016; 6:7901-7910. [PMID: 30128138 PMCID: PMC6093170 DOI: 10.1002/ece3.2465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/17/2016] [Accepted: 08/24/2016] [Indexed: 01/30/2023] Open
Abstract
How the often highly endemic biodiversity of islands originated has been debated for decades, and it remains a fervid research ground. Here, using mitochondrial and nuclear gene sequence analyses, we investigate the diversity, phylogenetic relationships, and evolutionary history of the mayfly Baetis gr. rhodani on the three largest northwestern Mediterranean islands (Sardinia, Corsica, Elba). We identify three distinct, largely co‐distributed, and deeply differentiated lineages, with divergences tentatively dated back to the Eocene–Oligocene transition. Bayesian population structure analyses reveal a lack of gene exchange between them, even at sites where they are syntopic, indicating that these lineages belong to three putative species. Their phylogenetic relationships with continental relatives, together with the dating estimates, support a role for three processes contributing to this diversity: (1) vicariance, primed by microplate disjunction and oceanic transgression; (2) dispersal from the continent; and (3) speciation within the island group. Thus, our results do not point toward a prevailing role for any of the previously invoked processes. Rather, they suggest that a variety of processes equally contributed to shape the diverse and endemic biota of this group of islands.
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Affiliation(s)
- Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche Università della Tuscia Viterbo Italy
| | - Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche Università della Tuscia Viterbo Italy
| | - Roberta Tenchini
- Dipartimento di Scienze Ecologiche e Biologiche Università della Tuscia Viterbo Italy.,Water Research Institute CNR - IRSA Brugherio MB Italy
| | - Carlo Belfiore
- Dipartimento di Scienze Ecologiche e Biologiche Università della Tuscia Viterbo Italy
| | | | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche Università della Tuscia Viterbo Italy
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Salvi D, Schembri PJ, Sciberras A, Harris DJ. Evolutionary history of the Maltese wall lizardPodarcis filfolensis: insights on the ‘Expansion-Contraction’ model of Pleistocene biogeography. Mol Ecol 2014; 23:1167-87. [DOI: 10.1111/mec.12668] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniele Salvi
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão; 4485-661 Vairão Portugal
| | | | | | - D. James Harris
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão; 4485-661 Vairão Portugal
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Poncet V, Munoz F, Munzinger J, Pillon Y, Gomez C, Couderc M, Tranchant-Dubreuil C, Hamon S, de Kochko A. Phylogeography and niche modelling of the relict plantAmborella trichopoda(Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia. Mol Ecol 2013; 22:6163-78. [DOI: 10.1111/mec.12554] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Valérie Poncet
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
| | - François Munoz
- UM2 and IRD; UMR AMAP; Boulevard de la Lironde, PS 2 34398 Montpellier France
| | - Jérôme Munzinger
- UM2 and IRD; UMR AMAP; Boulevard de la Lironde, PS 2 34398 Montpellier France
- IRD; UMR AMAP; Herbarium NOU 98848 Nouméa New Caledonia
| | - Yohan Pillon
- IRD; UMR DIADE; 98848 Nouméa New Caledonia
- Tropical Conservation Biology and Environmental Science; University of Hawai'i at Hilo; 200 West Kawili St. Hilo HI 96720 USA
| | - Céline Gomez
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
- IRD; UMR DIADE; 98848 Nouméa New Caledonia
| | - Marie Couderc
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
| | | | - Serge Hamon
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
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Zhang ZY, Wu R, Wang Q, Zhang ZR, López-Pujol J, Fan DM, Li DZ. Comparative phylogeography of two sympatric beeches in subtropical China: Species-specific geographic mosaic of lineages. Ecol Evol 2013; 3:4461-72. [PMID: 24340187 PMCID: PMC3856746 DOI: 10.1002/ece3.829] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/29/2013] [Accepted: 09/09/2013] [Indexed: 11/05/2022] Open
Abstract
In subtropical China, large-scale phylogeographic comparisons among multiple sympatric plants with similar ecological preferences are scarce, making generalizations about common response to historical events necessarily tentative. A phylogeographic comparison of two sympatric Chinese beeches (Fagus lucida and F. longipetiolata, 21 and 28 populations, respectively) was conducted to test whether they have responded to historical events in a concerted fashion and to determine whether their phylogeographic structure is exclusively due to Quaternary events or it is also associated with pre-Quaternary events. Twenty-three haplotypes were recovered for F. lucida and F. longipetiolata (14 each one and five shared). Both species exhibited a species-specific mosaic distribution of haplotypes, with many of them being range-restricted and even private to populations. The two beeches had comparable total haplotype diversity but F. lucida had much higher within-population diversity than F. longipetiolata. Molecular dating showed that the time to most recent common ancestor of all haplotypes was 6.36 Ma, with most haplotypes differentiating during the Quaternary. [Correction added on 14 October 2013, after first online publication: the timeunit has been corrected to '6.36'.] Our results support a late Miocene origin and southwards colonization of Chinese beeches when the aridity in Central Asia intensified and the monsoon climate began to dominate the East Asia. During the Quaternary, long-term isolation in subtropical mountains of China coupled with limited gene flow would have lead to the current species-specific mosaic distribution of lineages.
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Affiliation(s)
- Zhi-Yong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University Nanchang, Jiangxi, 330045, China
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Pavesi L, Tiedemann R, De Matthaeis E, Ketmaier V. Genetic connectivity between land and sea: the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea. Front Zool 2013; 10:21. [PMID: 23618554 PMCID: PMC3640956 DOI: 10.1186/1742-9994-10-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/03/2013] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces. RESULTS Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set. CONCLUSIONS We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.
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Affiliation(s)
- Laura Pavesi
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, D-14476, Germany.
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Xia X. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol 2013; 30:1720-8. [PMID: 23564938 PMCID: PMC3684854 DOI: 10.1093/molbev/mst064] [Citation(s) in RCA: 739] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank, and the new NeXML format for interoperability, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony, and maximum-likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot, and many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly, and intuitive interface and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16, 2013).
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Affiliation(s)
- Xuhua Xia
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada
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Bisconti R, Canestrelli D, Nascetti G. Has living on islands been so simple? Insights from the insular endemic frog Discoglossus montalentii. PLoS One 2013; 8:e55735. [PMID: 23393599 PMCID: PMC3564813 DOI: 10.1371/journal.pone.0055735] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 12/30/2012] [Indexed: 11/21/2022] Open
Abstract
Island populations have been extensively used as model systems in ecology, biogeography, conservation and evolutionary biology, owing to the several simplifying assumptions that they allow. Nevertheless, recent findings from intra-island phylogeographic studies are casting doubts on the generality of some of these underlying assumptions. We investigated the phylogeography, historical demography, and population genetic structure of the Corsican endemic frog, Discoglossus montalentii. In contrast with expectations based on its insular, restricted and continuous distribution, we found evidence of 3 phylogroups, whose rather ancient divergence (Early-Middle Pleistocene) was likely primed by climatic changes that occurred during the ‘middle Pleistocene revolution’. Furthermore, their differentiation explained most (68%) of the overall genetic diversity that was observed. These results and the growing evidence from intra-island phylogeographies, suggest that island populations frequently may not conform to some long-standing assumptions, including long-term stability, range-wide panmixia and the correlation of effective population size to the island size. As a consequence, both for theoretical and for applied purposes, the extensive use of these assumptions in the study of island populations warrants a careful re-examination.
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Affiliation(s)
- Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
| | - Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
- * E-mail:
| | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
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