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Dudzik A, Dedukh D, Crochet PA, Rozenblut-Kościsty B, Rybka H, Doniol-Valcroze P, Choleva L, Ogielska M, Chmielewska M. Cytogenetics of the Hybridogenetic Frog Pelophylax grafi and Its Parental Species Pelophylax perezi. Genome Biol Evol 2023; 15:evad215. [PMID: 38015654 PMCID: PMC10715190 DOI: 10.1093/gbe/evad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 11/30/2023] Open
Abstract
Hybrid taxa from the genus Pelophylax can propagate themselves in a modified way of sexual reproduction called hybridogenesis ensuring the formation of clonal gametes containing the genome of only one parental (host) species. Pelophylax grafi from South-Western Europe is a hybrid composed of P. ridibundus and P. perezi genomes and it lives with a host species P. perezi (P-G system). Yet it is unknown, whether non-Mendelian inheritance is fully maintained in such populations. In this study, we characterize P. perezi and P. grafi somatic karyotypes by using comparative genomic hybridization, genomic in situ hybridization, fluorescent in situ hybridization, and actinomycin D-DAPI. Here, we show the homeology of P. perezi and P. grafi somatic karyotypes to other Pelophylax taxa with 2n = 26 and equal contribution of ridibundus and perezi chromosomes in P. grafi which supports F1 hybrid genome constitution as well as a hemiclonal genome inheritance. We show that ridibundus chromosomes have larger regions of interstitial (TTAGGG)n repeats flanking the nucleolus organizing region on chromosome no. 10 and a high quantity of AT pairs in the centromeric regions. In P. perezi, we found species-specific sequences in metaphase chromosomes and marker structures in lampbrush chromosomes. Pericentromeric RrS1 repeat sequence was present in perezi and ridibundus chromosomes, but the blocks were stronger in ridibundus. Various cytogenetic techniques applied to the P-G system provide genome discrimination between ridibundus and perezi chromosomal sets. They could be used in studies of germ-line cells to explain patterns of clonal gametogenesis in P. grafi and broaden the knowledge about reproductive strategies in hybrid animals.
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Affiliation(s)
- Anna Dudzik
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Dmitrij Dedukh
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | | | - Beata Rozenblut-Kościsty
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Hanna Rybka
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | | | - Lukáš Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Maria Ogielska
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Magdalena Chmielewska
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
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Poyarkov NA, Nguyen TV, Pawangkhanant P, Yushchenko PV, Brakels P, Nguyen LH, Nguyen HN, Suwannapoom C, Orlov N, Vogel G. An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina. PeerJ 2022; 10:e12713. [PMID: 35047234 PMCID: PMC8757378 DOI: 10.7717/peerj.12713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023] Open
Abstract
Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the "upstream" colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.
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Affiliation(s)
- Nikolay A. Poyarkov
- Laboratory of Tropical Ecology, Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam,Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | - Tan Van Nguyen
- Department of Species Conservation, Save Vietnam’s Wildlife, Ninh Binh, Vietnam
| | - Parinya Pawangkhanant
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Platon V. Yushchenko
- Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | | | - Linh Hoang Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Ngoc Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Chatmongkon Suwannapoom
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Nikolai Orlov
- Department of Herpetology, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Gernot Vogel
- Society for Southeast Asian Herpetology, Heidelberg, Germany
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3
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Blackburn DC, Nielsen SV, Ghose SL, Burger M, Gonwouo LN, Greenbaum E, Gvoždík V, Hirschfeld M, Kouete MT, Kusamba C, Lawson D, McLaughlin PJ, Zassi-Boulou AG, Rödel MO. Phylogeny of African Long-Fingered Frogs (Arthroleptidae: Cardioglossa) Reveals Recent Allopatric Divergences in Coloration. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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4
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5
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Ashraf MR, Nadeem A, Smith EN, Javed M, Smart U, Yaqub T, Hashmi AS. Molecular phylogenetics of Black Cobra (Naja naja) in Pakistan. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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6
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Shibasaki S. The evolutionary game of interspecific mutualism in the multi-species model. J Theor Biol 2019; 471:51-58. [PMID: 30935957 DOI: 10.1016/j.jtbi.2019.03.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 11/30/2022]
Abstract
Mutualistic interspecific interactions, including Müllerian mimicry and division of labor, are common in nature. In contrast to antagonistic interactions, where faster evolution is favored, mutualism can favor slower evolution under certain conditions. This is called the Red King effect. Since Bergstrom and Lachmann (2003) proposed the Red King effect, it has been investigated only in two-species models. However, biological examples suggest that mutualism can include three or more species. Here, I modeled the evolutionary dynamics of mutualism in communities where involving two or more species, and in which all species mutually interact. Regardless of the number of species in the community, it is possible to derive conditions for stable equilibria. Although nonlinear relationships exist between the evolutionary rates and the evolutionary fate of each species in the multi-species communities, the model suggests that it is possible to predict whether faster evolution is favored or disfavored for the relatively rapidly evolving species; however, it is difficult to predict the evolutionary fate of species that evolve relatively slowly because their evolutionary dynamics are affected by the evolutionary fate of species evolving rapidly.
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Affiliation(s)
- Shota Shibasaki
- Department of General Systems Studies, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 1538902, Japan; Department of Fundamental Microbiology, University of Lausanne, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland.
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7
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Crottini A, Orozco-terWengel P, Rabemananjara FCE, Hauswaldt JS, Vences M. Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella. Genes (Basel) 2019; 10:E317. [PMID: 31018611 PMCID: PMC6523892 DOI: 10.3390/genes10040317] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 01/17/2023] Open
Abstract
Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantellamadagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first confirm the monophyly of this clade using DNA sequences of three nuclear and four mitochondrial genes, and subsequently investigate the population genetic differentiation and demography of the swamp forest species using one mitochondrial, two nuclear and a set of nine microsatellite markers. Our results confirm the occurrence of two main mitochondrial lineages, one dominated by Mantellaaurantiaca (a grouping supported also by our microsatellite-based tree) and the other by Mantellacrocea + Mantellamilotympanum. These two main lineages probably reflect an older divergence in swamp Mantella. Widespread mitochondrial introgression suggests a fairly common occurrence of inter-lineage gene flow. However, nuclear admixture seems to play only a limited role in this group, and the analyses of the RAG-1 marker points to a predominant incomplete lineage sorting scenario between all five species of the group, which probably diverged relatively recently. Our demographic analyses show a common, severe and recent demographic contraction, inferred to be in temporal coincidence with the massive deforestation events that took place in the past 1000 years. Current data do not allow to conclusively delimit independent evolutionary units in these frogs, and we therefore refrain to suggest any taxonomic changes.
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Affiliation(s)
- Angelica Crottini
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Rua Padre Armando Quintas, N° 7, 4485-661 Vairão, Portugal.
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK.
| | - Falitiana C E Rabemananjara
- Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d'Antananarivo, BP 906, Antananarivo 101, Madagascar.
| | - J Susanne Hauswaldt
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
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8
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Andrade P, Pinho C, Pérez I de Lanuza G, Afonso S, Brejcha J, Rubin CJ, Wallerman O, Pereira P, Sabatino SJ, Bellati A, Pellitteri-Rosa D, Bosakova Z, Bunikis I, Carretero MA, Feiner N, Marsik P, Paupério F, Salvi D, Soler L, While GM, Uller T, Font E, Andersson L, Carneiro M. Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard. Proc Natl Acad Sci U S A 2019; 116:5633-5642. [PMID: 30819892 DOI: 10.1101/481895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.
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Affiliation(s)
- Pedro Andrade
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Catarina Pinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Guillem Pérez I de Lanuza
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Jindřich Brejcha
- Department of Philosophy and History of Science, Faculty of Science, Charles University, 128 00 Prague 2, Czech Republic
- Department of Zoology, National Museum, 193 00 Prague, Czech Republic
- Ethology Laboratory, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 469 80 Paterna, Spain
| | - Carl-Johan Rubin
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Ola Wallerman
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Paulo Pereira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Stephen J Sabatino
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Adriana Bellati
- Department of Earth and Environmental Sciences, University of Pavia, 27100 Pavia, Italy
| | | | - Zuzana Bosakova
- Department of Analytical Chemistry, Faculty of Science, Charles University, 128 43 Prague 2, Czech Republic
| | - Ignas Bunikis
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, 752 36 Uppsala, Sweden
| | - Miguel A Carretero
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | | | - Petr Marsik
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 21 Prague 6, Czech Republic
| | - Francisco Paupério
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Daniele Salvi
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Lucile Soler
- Science for Life Laboratory, National Bioinformatics Infrastructure Sweden (NBIS), 751 23 Uppsala, Sweden
| | - Geoffrey M While
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7005 Tasmania, Australia
- Department of Zoology, University of Oxford, OX1 3PS Oxford, United Kingdom
| | - Tobias Uller
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Enrique Font
- Ethology Laboratory, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 469 80 Paterna, Spain
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden;
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal;
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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9
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Klonoski K, Bi K, Rosenblum EB. Phenotypic and genetic diversity in aposematic Malagasy poison frogs (genus Mantella). Ecol Evol 2019; 9:2725-2742. [PMID: 30891212 PMCID: PMC6406014 DOI: 10.1002/ece3.4943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/07/2018] [Accepted: 01/02/2019] [Indexed: 12/17/2022] Open
Abstract
Intraspecific color variation has long fascinated evolutionary biologists. In species with bright warning coloration, phenotypic diversity is particularly compelling because many factors, including natural and sexual selection, contribute to intraspecific variation. To better understand the causes of dramatic phenotypic variation in Malagasy poison frogs, we quantified genetic structure and color and pattern variation across three closely related species, Mantella aurantiaca, Mantella crocea, and Mantella milotympanum. Although our restriction site-associated DNA (RAD) sequencing approach identified clear genetic clusters, they do not align with current species designations, which has important conservation implications for these imperiled frogs. Moreover, our results suggest that levels of intraspecific color variation within this group have been overestimated, while species diversity has been underestimated. Within major genetic clusters, we observed distinct patterns of variation including: populations that are phenotypically similar yet genetically distinct, populations where phenotypic and genetic breaks coincide, and populations that are genetically similar but have high levels of within-population phenotypic variation. We also detected admixture between two of the major genetic clusters. Our study suggests that several mechanisms-including hybridization, selection, and drift-are contributing to phenotypic diversity. Ultimately, our work underscores the need for a reevaluation of how polymorphic and polytypic populations and species are classified, especially in aposematic organisms.
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Affiliation(s)
- Karina Klonoski
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCalifornia
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
| | - Ke Bi
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3)University of California, BerkeleyBerkeleyCalifornia
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCalifornia
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
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10
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Montingelli GG, Grazziotin FG, Battilana J, Murphy RW, Zhang Y, Zaher H. Higher‐level phylogenetic affinities of the Neotropical genus
Mastigodryas
Amaral, 1934 (Serpentes: Colubridae), species‐group definition and description of a new genus for
Mastigodryas bifossatus. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Giovanna G. Montingelli
- Department of Life SciencesNatural History Museum London UK
- Museu de Zoologia da Universidade de São Paulo São Paulo Brazil
| | | | | | - Robert W. Murphy
- Royal Ontario MuseumCentre for Biodiversity and Conservation Biology Toronto Ontario Canada
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of Zoology Kunming China
| | - Ya‐Ping Zhang
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of Zoology Kunming China
- Laboratory for Conservation and Utilization of Bio‐ResourcesYunnan University Kunming China
| | - Hussam Zaher
- Museu de Zoologia da Universidade de São Paulo São Paulo Brazil
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11
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Briolat ES, Burdfield-Steel ER, Paul SC, Rönkä KH, Seymoure BM, Stankowich T, Stuckert AMM. Diversity in warning coloration: selective paradox or the norm? Biol Rev Camb Philos Soc 2018; 94:388-414. [PMID: 30152037 PMCID: PMC6446817 DOI: 10.1111/brv.12460] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 07/25/2018] [Accepted: 07/27/2018] [Indexed: 01/03/2023]
Abstract
Aposematic theory has historically predicted that predators should select for warning signals to converge on a single form, as a result of frequency‐dependent learning. However, widespread variation in warning signals is observed across closely related species, populations and, most problematically for evolutionary biologists, among individuals in the same population. Recent research has yielded an increased awareness of this diversity, challenging the paradigm of signal monomorphy in aposematic animals. Here we provide a comprehensive synthesis of these disparate lines of investigation, identifying within them three broad classes of explanation for variation in aposematic warning signals: genetic mechanisms, differences among predators and predator behaviour, and alternative selection pressures upon the signal. The mechanisms producing warning coloration are also important. Detailed studies of the genetic basis of warning signals in some species, most notably Heliconius butterflies, are beginning to shed light on the genetic architecture facilitating or limiting key processes such as the evolution and maintenance of polymorphisms, hybridisation, and speciation. Work on predator behaviour is changing our perception of the predator community as a single homogenous selective agent, emphasising the dynamic nature of predator–prey interactions. Predator variability in a range of factors (e.g. perceptual abilities, tolerance to chemical defences, and individual motivation), suggests that the role of predators is more complicated than previously appreciated. With complex selection regimes at work, polytypisms and polymorphisms may even occur in Müllerian mimicry systems. Meanwhile, phenotypes are often multifunctional, and thus subject to additional biotic and abiotic selection pressures. Some of these selective pressures, primarily sexual selection and thermoregulation, have received considerable attention, while others, such as disease risk and parental effects, offer promising avenues to explore. As well as reviewing the existing evidence from both empirical studies and theoretical modelling, we highlight hypotheses that could benefit from further investigation in aposematic species. Finally by collating known instances of variation in warning signals, we provide a valuable resource for understanding the taxonomic spread of diversity in aposematic signalling and with which to direct future research. A greater appreciation of the extent of variation in aposematic species, and of the selective pressures and constraints which contribute to this once‐paradoxical phenomenon, yields a new perspective for the field of aposematic signalling.
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Affiliation(s)
- Emmanuelle S Briolat
- Centre for Ecology & Conservation, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, U.K
| | - Emily R Burdfield-Steel
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Sarah C Paul
- Centre for Ecology & Conservation, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, U.K.,Department of Chemical Ecology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Katja H Rönkä
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40014, Finland.,Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - Brett M Seymoure
- Department of Biology, Colorado State University, Fort Collins, CO 80525, U.S.A.,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80525, U.S.A
| | - Theodore Stankowich
- Department of Biological Sciences, California State University, Long Beach, CA 90840, U.S.A
| | - Adam M M Stuckert
- Department of Biology, East Carolina University, 1000 E Fifth St, Greenville, NC 27858, U.S.A
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12
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Nicolas V, Mataame A, Crochet PA, Geniez P, Fahd S, Ohler A. Phylogeography and ecological niche modeling unravel the evolutionary history of the African green toad,Bufotes boulengeri boulengeri(Amphibia: Bufonidae), through the Quaternary. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | | | - Pierre-André Crochet
- CEFE UMR 5175, CNRS; EPHE; Université de Montpellier; Université Paul-Valéry Montpellier EPHE; Montpellier France
| | - Philippe Geniez
- PSL Research University; CEFE UMR 5175; CNRS, Université de Montpellier, Université Paul-Valéry Montpellier; EPHE; Biogéographie et Ecologie des Vertébrés; Montpellier France
| | - Soumia Fahd
- Laboratoire “Ecologie, Biodiversité et Environnement”; Département de Biologie; Faculté des Sciences de Tétouan; Université Abdelmalek Essaâdi; Tétouan Morocco
| | - Annemarie Ohler
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
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Maia GF, Lima AP, Kaefer IL. Not just the river: genes, shapes, and sounds reveal population-structured diversification in the Amazonian frog Allobates tapajos (Dendrobatoidea). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Larson TR, Castro D, Behangana M, Greenbaum E. Evolutionary history of the river frog genus Amietia (Anura: Pyxicephalidae) reveals extensive diversification in Central African highlands. Mol Phylogenet Evol 2016; 99:168-181. [PMID: 27026115 PMCID: PMC4898062 DOI: 10.1016/j.ympev.2016.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 10/22/2022]
Abstract
The African river frog genus Amietia is found near rivers and other lentic water sources throughout central, eastern, and southern Africa. Because the genus includes multiple morphologically conservative species, taxonomic studies of river frogs have been relatively limited. We sampled 79 individuals of Amietia from multiple localities in and near the Albertine Rift (AR) of Burundi, Democratic Republic of the Congo, and Uganda. We utilized single-gene (16S) and concatenated (12S, 16S, cyt b and RAG1) gene-tree analyses and coalescent species-tree analyses to construct phylogenetic trees. Two divergence dating approaches were used in BEAST, including secondary calibration points with 12S, 16S, cyt b and RAG1, and a molecular clock with the 12S, 16S, and cyt b genes. All analyses recovered Amietia as monophyletic with strong support, and revealed several well-supported cryptic lineages, which is consistent with other recent phylogeography studies of AR amphibians. Dating estimates were similar, and Amietia diversification is coincident with global cooling and aridification events in the Miocene and Pliocene, respectively. Our results suggest additional taxonomic work is needed to describe multiple new species of AR Amietia, some of which have limited geographic distributions that are likely to be of conservation concern.
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Affiliation(s)
- Thornton R Larson
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA
| | - Delilah Castro
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA
| | | | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA.
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Chiari Y, Glaberman S, Tarroso P, Caccone A, Claude J. Ecological and evolutionary influences on body size and shape in the Galápagos marine iguana (Amblyrhynchus cristatus). Oecologia 2016; 181:885-94. [PMID: 27041683 DOI: 10.1007/s00442-016-3618-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 03/17/2016] [Indexed: 10/22/2022]
Abstract
Oceanic islands are often inhabited by endemic species that have undergone substantial morphological evolutionary change due to processes of multiple colonizations from various source populations, dispersal, and local adaptation. Galápagos marine iguanas are an example of an island endemic exhibiting high morphological diversity, including substantial body size variation among populations and sexes, but the causes and magnitude of this variation are not well understood. We obtained morphological measurements from marine iguanas throughout their distribution range. These data were combined with genetic and local environmental data from each population to investigate the effects of evolutionary history and environmental conditions on body size and shape variation and sexual dimorphism. Our results indicate that body size and shape are highly variable among populations. Sea surface temperature and island perimeter, but not evolutionary history as depicted by phylogeographic patterns in this species, explain variation in body size among populations. Conversely, evolutionary history, but not environmental parameters or island size, was found to influence variation in body shape among populations. Finally, in all populations except one, we found strong sexual dimorphism in body size and shape in which males are larger, with higher heads than females, while females have longer heads than males. Differences among populations suggest that plasticity and/or genetic adaptation may shape body size and shape variation in marine iguanas. This study will help target future investigations to address the contribution of plasticity versus genetic adaptation on size and shape variation in marine iguanas.
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Affiliation(s)
- Ylenia Chiari
- Department of Biology, University of South Alabama, 5871 USA Drive North, Mobile, AL, 36688, USA.
| | - Scott Glaberman
- Department of Biology, University of South Alabama, 5871 USA Drive North, Mobile, AL, 36688, USA
| | - Pedro Tarroso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Julien Claude
- Institut des Sciences de l'Evolution, UMR 5554, CNRS/IRD/UM/EPHE, Université de Montpellier II, 2 Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
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Miralles A, Jono T, Mori A, Gandola R, Erens J, Köhler J, Glaw F, Vences M. A new perspective on the reduction of cephalic scales in fossorial legless skinks (Squamata, Scincidae). ZOOL SCR 2016. [DOI: 10.1111/zsc.12164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aurélien Miralles
- Division of Evolutionary Biology; Zoological Institute; Technical University of Braunschweig; Mendelssohnstr. 4 Braunschweig 38106 Germany
| | - Teppei Jono
- Department of Zoology; Graduate School of Science; Kyoto University; Kyoto 606-8502 Japan
- Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu 610041 China
| | - Akira Mori
- Department of Zoology; Graduate School of Science; Kyoto University; Kyoto 606-8502 Japan
| | - Robert Gandola
- Ocean and Earth Sciences; National Oceanography Centre; University of Southampton; European Way Southampton SO13 3ZH UK
| | - Jesse Erens
- Division of Evolutionary Biology; Zoological Institute; Technical University of Braunschweig; Mendelssohnstr. 4 Braunschweig 38106 Germany
- Biosystematics Group; Wageningen University; Droevendaalsesteeg 1 Wageningen 6708PB The Netherlands
| | - Jörn Köhler
- Hessisches Landesmuseum Darmstadt; Friedensplatz 1 Darmstadt 64283 Germany
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB); Münchhausenstr. 21 München 81247 Germany
| | - Miguel Vences
- Division of Evolutionary Biology; Zoological Institute; Technical University of Braunschweig; Mendelssohnstr. 4 Braunschweig 38106 Germany
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Rato C, Harris DJ, Carranza S, Machado L, Perera A. The taxonomy of the Tarentola mauritanica species complex (Gekkota: Phyllodactylidae): Bayesian species delimitation supports six candidate species. Mol Phylogenet Evol 2016; 94:271-8. [DOI: 10.1016/j.ympev.2015.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 07/29/2015] [Accepted: 09/08/2015] [Indexed: 12/15/2022]
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Individual and Geographic Variation of Skin Alkaloids in Three Swamp-Forest Species of Madagascan Poison Frogs (Mantella). J Chem Ecol 2015; 41:837-47. [PMID: 26329921 DOI: 10.1007/s10886-015-0616-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/14/2015] [Accepted: 08/10/2015] [Indexed: 10/23/2022]
Abstract
Seventy skins of three mantellid frog species from Madagascan swamp-forest habitats, Mantella aurantiaca, M. crocea, and M. milotympanum, were individually examined for skin alkaloids using GC/MS. These poison frogs were found to differ significantly in their alkaloid composition from species of Mantella originating from non-flooded rainforest in eastern Madagascar, which were examined in earlier work. Only 16 of the previously detected 106 alkaloids were represented among the 60 alkaloids from the swamp-forest frogs of the present study. We hypothesize this difference is related mainly to habitat but cannot exclude a phylogenetic component as the three swamp-forest species are a closely related monophyletic group. The paucity of alkaloids with unbranched-carbon skeletons (ant-derived) and the commonness of alkaloids with branched-carbon skeletons (mite-derived) indicate that oribatid mites are a major source of alkaloids in these species of mantellids. Furthermore, most of the alkaloids have an oxygen atom in their formulae. Differences in alkaloids were observed among species, populations of the same species, and habitats. In M. aurantiaca, small geographic distances among populations were associated with differences in alkaloid profiles, with a remote third site illustrating even greater differences. The present study and an earlier study of three other mantellid species suggest that oribatid mites, and not ants, are the major source of alkaloids in the species of mantellids examined thus far.
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de Sá FP, Canedo C, Lyra ML, Haddad CF. A New Species of Hylodes (Anura, Hylodidae) and its Secretive Underwater Breeding Behavior. HERPETOLOGICA 2015. [DOI: 10.1655/herpetologica-d-13-00053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Fábio P. de Sá
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Clarissa Canedo
- Setor de Herpetologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 20940-040, Brazil
| | - Mariana L. Lyra
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Célio F.B. Haddad
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
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Nicolas V, Mataame A, Crochet PA, Geniez P, Ohler A. Phylogeographic patterns in North African water frog Pelophylax saharicus
(Anura: Ranidae). J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12094] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité; ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE; Muséum national d'Histoire naturelle; Sorbonne Universités; Paris France
| | | | | | | | - Annemarie Ohler
- Institut de Systématique, Évolution, Biodiversité; ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE; Muséum national d'Histoire naturelle; Sorbonne Universités; Paris France
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21
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Portillo F, Greenbaum E, Menegon M, Kusamba C, Maximilian Dehling J. Phylogeography and species boundaries of Leptopelis (Anura: Arthroleptidae) from the Albertine Rift. Mol Phylogenet Evol 2015; 82 Pt A:75-86. [DOI: 10.1016/j.ympev.2014.09.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/24/2014] [Accepted: 09/27/2014] [Indexed: 11/25/2022]
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22
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A New Species of theLeptopelis modestusComplex (Anura: Arthroleptidae) from the Albertine Rift of Central Africa. J HERPETOL 2014. [DOI: 10.1670/13-043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Zaher H, de Oliveira L, Grazziotin FG, Campagner M, Jared C, Antoniazzi MM, Prudente AL. Consuming viscous prey: a novel protein-secreting delivery system in neotropical snail-eating snakes. BMC Evol Biol 2014; 14:58. [PMID: 24661572 PMCID: PMC4021269 DOI: 10.1186/1471-2148-14-58] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Efficient venom delivery systems are known to occur only in varanoid lizards and advanced colubroidean snakes among squamate reptiles. Although components of these venomous systems might have been present in a common ancestor, the two lineages independently evolved strikingly different venom gland systems. In snakes, venom is produced exclusively by serous glands in the upper jaw. Within the colubroidean radiation, lower jaw seromucous infralabial glands are known only in two distinct lineages-the basal pareatids and the more advanced Neotropical dipsadines known as "goo-eating snakes". Goo-eaters are a highly diversified, ecologically specialized clade that feeds exclusively on invertebrates (e.g., gastropod molluscs and annelids). Their evolutionary success has been attributed to their peculiar feeding strategies, which remain surprisingly poorly understood. More specifically, it has long been thought that the more derived Dipsadini genera Dipsas and Sibynomorphus use glandular toxins secreted by their infralabial glands to extract snails from their shells. RESULTS Here, we report the presence in the tribe Dipsadini of a novel lower jaw protein-secreting delivery system effected by a gland that is not functionally related to adjacent teeth, but rather opens loosely on the oral epithelium near the tip of the mandible, suggesting that its secretion is not injected into the prey as a form of envenomation but rather helps control the mucus and assists in the ingestion of their highly viscous preys. A similar protein-secreting system is also present in the goo-eating genus Geophis and may share the same adaptive purpose as that hypothesized for Dipsadini. Our phylogenetic hypothesis suggests that the acquisition of a seromucous infralabial gland represents a uniquely derived trait of the goo-eating clade that evolved independently twice within the group as a functionally complex protein-secreting delivery system. CONCLUSIONS The acquisition by snail-eating snakes of such a complex protein-secreting system suggests that the secretion from the hypertrophied infralabial glands of goo-eating snakes may have a fundamental role in mucus control and prey transport rather than envenomation of prey. Evolution of a functional secretory system that combines a solution for mucus control and transport of viscous preys is here thought to underlie the successful radiation of goo-eating snakes.
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Affiliation(s)
- Hussam Zaher
- Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré 481, São Paulo, SP CEP 04263-000, Brazil
| | - Leonardo de Oliveira
- Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré 481, São Paulo, SP CEP 04263-000, Brazil
- Programa de Pós Graduação em Zoologia, Universidade Estadual Paulista, Avenida 24A 1515, Rio Claro, SP CEP 13506-900, Brazil
| | - Felipe G Grazziotin
- Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré 481, São Paulo, SP CEP 04263-000, Brazil
| | - Michelle Campagner
- Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré 481, São Paulo, SP CEP 04263-000, Brazil
- Museu Biológico, Instituto Butantan, Avenida Vital Brazil 1500, São Paulo, SP CEP 05503-900, Brazil
| | - Carlos Jared
- Laboratório de Biologia Celular, Instituto Butantan, Avenida Vital Brazil 1500, São Paulo, SP CEP 05503-900, Brazil
| | - Marta M Antoniazzi
- Laboratório de Biologia Celular, Instituto Butantan, Avenida Vital Brazil 1500, São Paulo, SP CEP 05503-900, Brazil
| | - Ana L Prudente
- Museu Paraense Emílio Goeldi, Avenida Magalhães Barata 376, Belém, PA CEP 66040-170, Brazil
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24
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Portillo F, Greenbaum E. At the Edge of a Species Boundary: A New and Relatively Young Species of Leptopelis (Anura: Arthroleptidae) from the Itombwe Plateau, Democratic Republic of the Congo. HERPETOLOGICA 2014. [DOI: 10.1655/herpetologica-d-12-00087] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Frank Portillo
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA
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25
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Fusinatto LA, Alexandrino J, Haddad CFB, Brunes TO, Rocha CFD, Sequeira F. Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic forest. PLoS One 2013; 8:e79504. [PMID: 24223956 PMCID: PMC3815154 DOI: 10.1371/journal.pone.0079504] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/22/2013] [Indexed: 12/02/2022] Open
Abstract
Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing “Terrarana” frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.
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Affiliation(s)
- Luciana A. Fusinatto
- Departamento de Ecologia, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
- * E-mail:
| | - João Alexandrino
- Departamento de Ciências Biológicas, UNIFESP - Universidade Federal de São Paulo, Campus Diadema, Diadema, São Paulo, Brasil
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brasil
| | - Célio F. B. Haddad
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brasil
| | - Tuliana O. Brunes
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Carlos F. D. Rocha
- Departamento de Ecologia, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Fernando Sequeira
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
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Ongoing speciation in the Tibetan plateau Gymnocypris species complex. PLoS One 2013; 8:e71331. [PMID: 23977018 PMCID: PMC3744573 DOI: 10.1371/journal.pone.0071331] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/28/2013] [Indexed: 11/30/2022] Open
Abstract
Local adaptation towards divergent ecological conditions often results in genetic differentiation and adaptive phenotypic divergence. To illuminate the ecological distinctiveness of the schizothoracine fish, we studied a Gymnocypris species complex consisting of three morphs distributed across four bodies of water (the Yellow River, Lake Qinghai, the Ganzi River and Lake Keluke) in the Northeast Tibetan Plateau. We used a combination of mitochondrial (16S rRNA and Cyt b) and nuclear (RAG-2) genetic sequences to investigate the phylogeography of these morphs based on a sample of 277 specimens. Analysis of gill rakers allowed for mapping of phenotypic trajectories along the phylogeny. The phylogenetic and morphological analyses showed that the three sparsely rakered morphs were present at two extremes of the phylogenetic tree: the Yellow River morphs were located at the basal phylogenetic split, and the Lake Keluke and Ganzi River morphs at the peak, with the densely rakered Lake Qinghai morphs located between these two extremes. Age estimation further indicated that the sparsely rakered morphs constituted the oldest and youngest lineages, whereas the densely rakered morph was assigned to an intermediate-age lineage. These results are most compatible with the process of evolutionary convergence or reversal. Disruptive natural selection due to divergent habitats and dietary preferences is likely the driving force behind the formation of new morphs, and the similarities between their phenotypes may be attributable to the similarities between their forms of niche tracking associated with food acquisition. This study provides the first genetic evidence for the occurrence of convergence or reversal in the schizothoracine fish of the Tibetan Plateau at small temporal scales.
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From widespread to microendemic: molecular and acoustic analyses show that Ischnocnema guentheri (Amphibia: Brachycephalidae) is endemic to Rio de Janeiro, Brazil. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0488-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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Engleder A, Haring E, Kirchhof S, Mayer W. Multiple nuclear and mitochondrial DNA sequences provide new insights into the phylogeny of South African Lacertids (Lacertidae, Eremiadinae). J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anja Engleder
- Central Research Laboratories; Museum of Natural History Vienna; Vienna Austria
- Department of Intagrative Zoology; University of Vienna; Vienna Austria
| | - Elisabeth Haring
- Central Research Laboratories; Museum of Natural History Vienna; Vienna Austria
- Department of Intagrative Zoology; University of Vienna; Vienna Austria
| | - Sebastian Kirchhof
- Museum für Naturkunde - Leibniz Institute for Research on Evolution and Biodiversity; Berlin Germany
| | - Werner Mayer
- Central Research Laboratories; Museum of Natural History Vienna; Vienna Austria
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29
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Arbuckle K, Brockhurst M, Speed MP. Does chemical defence increase niche space? A phylogenetic comparative analysis of the Musteloidea. Evol Ecol 2013. [DOI: 10.1007/s10682-013-9629-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Species limits in the Andean toad genus Osornophryne (Bufonidae). Mol Phylogenet Evol 2012; 65:805-22. [DOI: 10.1016/j.ympev.2012.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 08/01/2012] [Accepted: 08/02/2012] [Indexed: 11/19/2022]
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31
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Velo-Antón G, Godinho R, Harris D, Santos X, Martínez-Freiria F, Fahd S, Larbes S, Pleguezuelos J, Brito J. Deep evolutionary lineages in a Western Mediterranean snake (Vipera latastei/monticola group) and high genetic structuring in Southern Iberian populations. Mol Phylogenet Evol 2012; 65:965-73. [DOI: 10.1016/j.ympev.2012.08.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 08/14/2012] [Accepted: 08/21/2012] [Indexed: 11/24/2022]
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Wang B, Jiang J, Xie F, Li C. Postglacial colonization of the Qinling Mountains: phylogeography of the swelled vent frog (Feirana quadranus). PLoS One 2012; 7:e41579. [PMID: 22848532 PMCID: PMC3405020 DOI: 10.1371/journal.pone.0041579] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/22/2012] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The influence of Pleistocene climatic fluctuations on intraspecific diversification in the Qinling-Daba Mountains of East Asia remains poorly investigated. We tested hypotheses concerning refugia during the last glacial maximum (LGM) in this region by examining the phylogeography of the swelled vent frog (Feirana quadranus; Dicroglossidae, Anura, Amphibia). METHODOLOGY/PRINCIPAL FINDINGS We obtained complete mitochondrial ND2 gene sequences of 224 individuals from 34 populations of Feirana quadranus for phylogeographic analyses. Additionally, we obtained nuclear tyrosinase gene sequences of 68 F. quadranus, one F. kangxianensis and three F. taihangnica samples to test for mitochondrial introgression among them. Phylogenetic analyses based on all genes revealed no introgression among them. Phylogenetic analyses based on ND2 datasets revealed that F. quadranus was comprised of six lineages which were separated by deep valleys; the sole exception is that the Main Qinling and Micang-Western Qinling lineages overlap in distribution. Analyses of population structure indicated restricted gene flow among lineages. Coalescent simulations and divergence dating indicated that the basal diversification within F. quadranus may be associated with the dramatic uplifts of the Tibetan Plateau during the Pliocene. Coalescent simulations indicated that Wuling, Daba, and Western Qinling-Micang-Longmen Mountains were refugia for F. quadranus during the LGM. Demographic analyses indicated that the Daba lineage experienced population size increase prior to the LGM but the Main Qinling and the Micang-Western Qinling lineages expanded in population size and range after the LGM, and the other lineages almost have stable population size or slight slow population size decline. CONCLUSIONS/SIGNIFICANCE The Qinling-Daba Mountains hosted three refugia for F. quadranus during the LGM. Populations that originated in the Daba Mountains colonized the Main Qinling Mountains after the LGM. Recent sharp expansion of the Micang-Western Qinling and Main Qinling lineages probably contribute to their present-day secondary contact.
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Affiliation(s)
- Bin Wang
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Feng Xie
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
| | - Cheng Li
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, China
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Crottini A, Brown JL, Mercurio V, Glaw F, Vences M, Andreone F. Phylogeography of the poison frogMantella viridis(Amphibia: Mantellidae) reveals chromatic and genetic differentiation across ecotones in northern Madagascar. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00665.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Castalanelli MA, Baker AM, Munyard KA, Grimm M, Groth DM. Molecular phylogeny supports the paraphyletic nature of the genus Trogoderma (Coleoptera: Dermestidae) collected in the Australasian ecozone. BULLETIN OF ENTOMOLOGICAL RESEARCH 2012; 102:17-28. [PMID: 21749736 DOI: 10.1017/s0007485311000319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
To date, a molecular phylogenetic approach has not been used to investigate the evolutionary structure of Trogoderma and closely related genera. Using two mitochondrial genes, Cytochrome Oxidase I and Cytochrome B, and the nuclear gene, 18S, the reported polyphyletic positioning of Trogoderma was examined. Paraphyly in Trogoderma was observed, with one Australian Trogoderma species reconciled as sister to all Dermestidae and the Anthrenocerus genus deeply nested within the Australian Trogoderma clade. In addition, time to most recent common ancestor for a number of Dermestidae was calculated. Based on these estimations, the Dermestidae origin exceeded 175 million years, placing the origins of this family in Pangaea.
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Affiliation(s)
- M A Castalanelli
- Cooperative Research Centre for National Plant Biosecurity, Deakin, ACT, Australia.
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Rato C, Carranza S, Harris DJ. Evolutionary history of the genus Tarentola (Gekkota: Phyllodactylidae) from the Mediterranean Basin, estimated using multilocus sequence data. BMC Evol Biol 2012; 12:14. [PMID: 22289419 PMCID: PMC3298722 DOI: 10.1186/1471-2148-12-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 01/30/2012] [Indexed: 11/26/2022] Open
Abstract
Background The pronounced morphological conservatism within Tarentola geckos contrasted with a high genetic variation in North Africa, has led to the hypothesis that this group could represent a cryptic species complex, a challenging system to study especially when trying to define distinct evolutionary entities and address biogeographic hypotheses. In the present work we have re-examined the phylogenetic and phylogeographic relationships between and within all Mediterranean species of Tarentola, placing the genealogies obtained into a temporal framework. In order to do this, we have investigated the sequence variation of two mitochondrial (12S rRNA and 16S rRNA), and four nuclear markers (ACM4, PDC, MC1R, and RAG2) for 384 individuals of all known Mediterranean Tarentola species, so that their evolutionary history could be assessed. Results Of all three generated genealogies (combined mtDNA, combined nDNA, and mtDNA+nDNA) we prefer the phylogenetic relationships obtained when all genetic markers are combined. A total of 133 individuals, and 2,901 bp of sequence length, were used in this analysis. The phylogeny obtained for Tarentola presents deep branches, with T. annularis, T. ephippiata and T. chazaliae occupying a basal position and splitting from the remaining species around 15.38 Mya. Tarentola boehmei is sister to all other Mediterranean species, from which it split around 11.38 Mya. There are also two other major groups: 1) the T. mauritanica complex present in North Africa and Europe; and 2) the clade formed by the T. fascicularis/deserti complex, T. neglecta and T. mindiae, occurring only in North Africa. The cladogenesis between these two groups occurred around 8.69 Mya, coincident with the late Miocene. Contrary to what was initially proposed, T. neglecta and T. mindiae are sister taxa to both T. fascicularis and T. deserti. Conclusions At least in the Iberian Peninsula and Northwest Africa, the lineages obtained have some geographic coherency, whilst the evolutionary history of the forms from Northeast Africa remains unclear, with a paraphyletic T. fascicularis with respect to T. deserti. The separation between the T. mauritanica complex and the clade formed by the T. fascicularis/deserti complex, T. neglecta and T. mindiae is coincident with the uplift of the Atlas Mountain chain, and the establishment of two distinct bioclimatic regions on each side of the barrier.
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Affiliation(s)
- Catarina Rato
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Portugal.
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Vences M, Gehara M, Köhler J, Glaw F. Description of a new Malagasy treefrog (Boophis) occurring syntopically with its sister species, and a plea for studies on non-allopatric speciation in tropical amphibians. AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/15685381-00002856] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Based on concordant differences in male advertisement call, tadpole morphology, and absence of haplotype sharing in mitochondrial and nuclear DNA markers, we describe a new species of treefrog from Ranomafana National Park in the southern central east of Madagascar. In its adult stage Boophis narinsi sp. n. is highly similar to its sister species, Boophis majori, but appears to differ in having longer hindlimbs. The genetic divergences between these two species (2.5-3.3% in a fragment of the 16S rRNA gene, depending on fragment length and individual haplotype analyzed) are below the threshold typically characterizing distinct species of anurans. Together with their relatively small and largely overlapping ranges and their sympatric occurrence in Ranomafana National Park, this indicates that they potentially could have originated rather recently by adaptive speciation under parapatric or sympatric conditions. Most studies on amphibian speciation have so far by default assumed vicariant speciation. We suggest that alternative speciation scenarios should be considered in future works and characterize settings in which more reliable assessments of adaptive parapatric or sympatric speciation could be carried out.
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Affiliation(s)
- Miguel Vences
- 1Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Marcelo Gehara
- 1Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Jörn Köhler
- 2Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany
| | - Frank Glaw
- 3Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany
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Bisconti R, Canestrelli D, Colangelo P, Nascetti G. Multiple lines of evidence for demographic and range expansion of a temperate species (Hyla sarda) during the last glaciation. Mol Ecol 2011; 20:5313-27. [PMID: 22097966 DOI: 10.1111/j.1365-294x.2011.05363.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Many temperate species experienced demographic and range contractions in response to climatic changes during Pleistocene glaciations. In this study, we investigate the evolutionary history of the Tyrrhenian tree frog Hyla sarda, a species inhabiting the Corsica-Sardinia island system (Western Mediterranean basin). We used sequence analysis of two mitochondrial (overall 1229 bp) and three nuclear (overall 1692 bp) gene fragments to assess the phylogeography and demographic history of this species, and species distribution modelling (SDM) to predict its range variation over time. Phylogeographic, historical demographic and SDM analyses consistently indicate that H. sarda does not conform to the scenario generally expected for temperate species but rather underwent demographic and range expansion mostly during the last glacial phase. Palaeogeographic data and SDM analyses suggest that such expansion was driven by the glaciation-induced increase in lowland areas during marine regression. This unusual scenario suggests that at least some temperate species may not have suffered the adverse effects of glacial climate on their population size and range extent, owing to the mitigating effects of other glaciations-induced palaeoenvironmental changes. We discuss previous clues for the occurrence of such a scenario in other species and some possible challenges with its identification. Early phylogeographic literature suggested that responses to the Pleistocene glacial-interglacial cycles were expected to vary among species and regions. Our results point out that such variation may have been greater than previously thought.
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Affiliation(s)
- Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università snc, I-01100 Viterbo, Italy
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van der Meijden A, Crottini A, Tarrant J, Turner A, Vences M. Multi-locus phylogeny and evolution of reproductive modes in the Pyxicephalidae, an African endemic clade of frogs. AFR J HERPETOL 2011. [DOI: 10.1080/21564574.2010.523904] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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When selection deceives phylogeographic interpretation: The case of the Mediterranean house gecko, Hemidactylus turcicus (Linnaeus, 1758). Mol Phylogenet Evol 2011; 58:365-73. [DOI: 10.1016/j.ympev.2010.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/08/2010] [Accepted: 12/10/2010] [Indexed: 11/22/2022]
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Miralles A, Vasconcelos R, Perera A, Harris DJ, Carranza S. An integrative taxonomic revision of the Cape Verdean skinks (Squamata, Scincidae). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00453.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rato C, Carranza S, Perera A, Carretero M, Harris D. Conflicting patterns of nucleotide diversity between mtDNA and nDNA in the Moorish gecko, Tarentola mauritanica. Mol Phylogenet Evol 2010; 56:962-71. [DOI: 10.1016/j.ympev.2010.04.033] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 04/16/2010] [Accepted: 04/23/2010] [Indexed: 10/19/2022]
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Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast Asia. Proc Natl Acad Sci U S A 2010; 107:13765-70. [PMID: 20643945 DOI: 10.1073/pnas.1008415107] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Asian frogs of the tribe Paini (Anura: Dicroglossidae) range across several first-order tectono-morphological domains of the Cenozoic Indo-Asian collision that include the Tibetan Plateau, the Himalayas, and Indochina. We show how the tectonic events induced by the Indo-Asian collision affected the regional biota and, in turn, how the geological history of the earth can be viewed from a biological perspective. Our analysis of a concatenated dataset comprising four nuclear gene sequences of Paini revealed two main radiations, corresponding to the genera Nanorana (I) and Quasipaa (II). Five distinct clades are recognized: Tibetan plateau clade (I-1), Himalaya clade (I-2), environs of Himalaya-Tibetan plateau clade (I-3), South China clade (II-1), and Indochina clade (II-2). This pattern of relationships highlights the significance of geography in shaping evolutionary history. Building on our molecular dating, ancestral region reconstruction, and distributional patterns, we hypothesize a distinct geographic and climatic transition in Asia beginning in the Oligocene and intensifying in the Miocene; this stimulated rapid diversification of Paini. Vicariance explains species formation among major lineages within Nanorana. Dispersal, in contrast, plays an important role among Quasipaa, with the southern Chinese taxa originating from Indochina. Our results support the tectonic hypothesis that an uplift in the Himalaya-Tibetan plateau region resulting from crustal thickening and lateral extrusion of Indochina occurred synchronously during the transition between Oligocene and Miocene in reaction to the Indo-Asian collision. The phylogenetic history of Paini illuminates critical aspects of the timing of geological events responsible for the current geography of Southeast Asia.
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Randrianavelona R, Rakotonoely H, Ratsimbazafy J, Jenkins RKB. Conservation assessment of the critically endangered frog Mantella aurantiaca in Madagascar. AFR J HERPETOL 2010. [DOI: 10.1080/04416651.2010.481761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Roma Randrianavelona
- a Madagasikara Voakajy , B.P. 5181, Antananarivo, 101, Madagascar
- b Département de Biologie Animale, Faculté des Sciences , Université d' Antananarivo , Antananarivo, Madagascar
| | - Harisoa Rakotonoely
- c Ecole Supérieure des Sciences Agronomiques, Département des Eaux et Forets , Université d' Antananarivo , Antananarivo, Madagascar
| | - Jonah Ratsimbazafy
- c Ecole Supérieure des Sciences Agronomiques, Département des Eaux et Forets , Université d' Antananarivo , Antananarivo, Madagascar
| | - Richard K. B. Jenkins
- a Madagasikara Voakajy , B.P. 5181, Antananarivo, 101, Madagascar
- d School of Biological Sciences , University of Aberdeen , Aberdeen, UK
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Wu Y, Wang Y, Jiang K, Chen X, Hanken J. Homoplastic evolution of external colouration in Asian stout newts (Pachytriton) inferred from molecular phylogeny. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2009.00400.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Chiari Y, van der Meijden A, Madsen O, Vences M, Meyer A. Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates. Front Zool 2009; 6:32. [PMID: 20015384 PMCID: PMC2803162 DOI: 10.1186/1742-9994-6-32] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 12/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Recombination Activating Proteins, RAG1 and RAG2, play a crucial role in the immune response in vertebrates. Among the nuclear markers currently used for phylogenetic purposes, Rag1 has especially enjoyed enormous popularity, since it successfully contributed to elucidating the relationships among and within a large variety of vertebrate lineages. We here report on a comparative investigation of the genetic variation, base composition, presence of indels, and selection in Rag1 in different vertebrate lineages (Actinopterygii, Amphibia, Aves, Chondrichthyes, Crocodylia, Lepidosauria, Mammalia, and Testudines) through the analysis of 582 sequences obtained from Genbank. We also analyze possible differences between distinct parts of the gene with different type of protein functions. RESULTS In the vertebrate lineages studied, Rag1 is over 3 kb long. We observed a high level of heterogeneity in base composition at the 3(rd )codon position in some of the studied vertebrate lineages and in some specific taxa. This result is also paralleled by taxonomic differences in the GC content at the same codon position. Moreover, positive selection occurs at some sites in Aves, Lepidosauria and Testudines. Indels, which are often used as phylogenetic characters, are more informative across vertebrates in the 5' than in the 3'-end of the gene. When the entire gene is considered, the use of indels as phylogenetic character only recovers one major vertebrate clade, the Actinopterygii. However, in numerous cases insertions or deletions are specific to a monophyletic group. CONCLUSIONS Rag1 is a phylogenetic marker of undoubted quality. Our study points to the need of carrying out a preliminary investigation on the base composition and the possible existence of sites under selection of this gene within the groups studied to avoid misleading resolution. The gene shows highly heterogeneous base composition, which affects some taxa in particular and contains sites under positive selection in some vertebrate lineages in the 5'-end. The first part of the gene (5'-end) is more variable than the second (3'-end), and less affected by a heterogeneous base composition. However, in some vertebrate lineages the 5'-end of the gene is not yet widely used for phylogenetic studies.
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Affiliation(s)
- Ylenia Chiari
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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46
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Nine microsatellite loci for the Malagasy Poison Frogs (Mantella). CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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47
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Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered 2009; 100:659-74. [PMID: 19892720 PMCID: PMC2877544 DOI: 10.1093/jhered/esp086] [Citation(s) in RCA: 371] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 09/21/2009] [Accepted: 09/22/2009] [Indexed: 01/13/2023] Open
Abstract
The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.
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Stöck M, Ustinova J, Lamatsch DK, Schartl M, Perrin N, Moritz C. A VERTEBRATE REPRODUCTIVE SYSTEM INVOLVING THREE PLOIDY LEVELS: HYBRID ORIGIN OF TRIPLOIDS IN A CONTACT ZONE OF DIPLOID AND TETRAPLOID PALEARCTIC GREEN TOADS (BUFO VIRIDIS SUBGROUP)*. Evolution 2009; 64:944-59. [DOI: 10.1111/j.1558-5646.2009.00876.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Conway Morris S. The predictability of evolution: glimpses into a post-Darwinian world. Naturwissenschaften 2009; 96:1313-37. [PMID: 19784612 DOI: 10.1007/s00114-009-0607-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 08/17/2009] [Accepted: 08/27/2009] [Indexed: 01/01/2023]
Abstract
The very success of the Darwinian explanation, in not only demonstrating evolution from multiple lines of evidence but also in providing some plausible explanations, paradoxically seems to have served to have stifled explorations into other areas of investigation. The fact of evolution is now almost universally yoked to the assumption that its outcomes are random, trends are little more than drunkard's walks, and most evolutionary products are masterpieces of improvisation and far from perfect. But is this correct? Let us consider some alternatives. Is there evidence that evolution could in anyway be predictable? Can we identify alternative forms of biological organizations and if so how viable are they? Why are some molecules so extraordinarily versatile, while others can be spoken of as "molecules of choice"? How fortuitous are the major transitions in the history of life? What implications might this have for the Tree of Life? To what extent is evolutionary diversification constrained or facilitated by prior states? Are evolutionary outcomes merely sufficient or alternatively are they highly efficient, even superb? Here I argue that in sharp contradistinction to an orthodox Darwinian view, not only is evolution much more predictable than generally assumed but also investigation of its organizational substrates, including those of sensory systems, which indicates that it is possible to identify a predictability to the process and outcomes of evolution. If correct, the implications may be of some significance, not least in separating the unexceptional Darwinian mechanisms from underlying organizational principles, which may indicate evolutionary inevitabilities.
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Affiliation(s)
- Simon Conway Morris
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, UK.
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Arnold EN, Vasconcelos R, Harris DJ, Mateo JA, Carranza S. Systematics, biogeography and evolution of the endemicHemidactylusgeckos (Reptilia, Squamata, Gekkonidae) of the Cape Verde Islands: based on morphology and mitochondrial and nuclear DNA sequences. ZOOL SCR 2008. [DOI: 10.1111/j.1463-6409.2008.00351.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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