Delimiting genetic units in Neotropical toads under incomplete lineage sorting and hybridization

BMC Evolutionary Biology

João Alexandrino¹  Célio F B Haddad³  Kelly R Zamudio²  Maria Tereza C Thomé³ 

[1] Departamento de Ciências Biológicas, UNIFESP - Univ Federal de São Paulo, Campus Diadema, Rua Professor Artur Riedel 275, 09972-270, Diadema, SP, Brazil;Department of Ecology and Evolutionary Biology, Cornell University, E209 Corson Hall, Ithaca, NY, 14853-2701, USA;Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Caixa Postal 19913506-900, Rio Claro, SP, Brazil

关键词: Taxonomy;    Bufonidae;    Species complex;    Rhinella crucifer group;   

Others  :  1139889
DOI  :  10.1186/1471-2148-12-242

 received in 2012-07-13, accepted in 2012-12-04,  发布年份 2012

【 摘 要 】

Background

Delimiting genetic units is useful to enhance taxonomic discovery and is often the first step toward understanding evolutionary mechanisms generating diversification. The six species within the Rhinella crucifer group of toads were defined under morphological criteria alone. Previous data suggest limited correspondence of these species to mitochondrial lineages, and morphological intergradation at transitions between forms suggests hybridization. Here we extensively sampled populations throughout the geographic distribution of the group and analyzed mitochondrial and nuclear sequence data to delimit genetic units using tree–based and allele frequency–based approaches.

Results

These approaches yielded complementary results, with allele frequency-based methods performing unexpectedly well given the limited number of loci examined. Both mitochondrial and nuclear markers supported a genetic structure of five units within the group, with three of the inferred units distributed within its main range, while two other units occur in separate isolates. The inferred units are mostly discordant with currently described forms: unequivocal association exists for only two of the six species in the group. Genetic evidence for hybridization exists for two pairs of units, with clear cyto–nuclear allele mixing observed in one case.

Conclusions

Our results confirmed that current taxonomy does not represent evolutionary units in the Rhinella crucifer group. Correspondence between genetically distinguishable units and the currently recognized species is only possible for Rhinella henseli and R. inopina. The recognition of other species relies on the reassessment of the geographic range of R. crucifer, the examination of the type series of R. ornata for hybrids, and on the use of additional markers to verify the genetic distinctiveness of R. abei. We state that R. pombali should not remain a valid species since its description appears to be based on hybrids, and that the name R. pombali should be considered a synonym of both R. crucifer and R. ornata. The fifth inferred but undescribed genetic unit may represent a new species. Our results underscore the potential of the R. crucifer species group to contribute to a better understanding of diversification processes and hybridization patterns in the Neotropics, and provide the basis for future evolutionary and taxonomic studies.

【 授权许可】

   
2012 Thomé et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]De Queiroz K: The general lineage concept of species, species criteria, and the process of speciation: A conceptual unification and terminological recommendations. In Endless forms: species and speciation. 1st edition. Edited by Howard DJ, Berlocher SH. Oxford: Oxford University Press; 1998:57-75.
• [2]Agapow PM, Bininda‐Emonds ORP, Crandall KA, Gittleman JL, Mace GM, Marshall JC, Purvis A: The Impact of species concept on biodiversity studies. Q Rev Biol 2004, 79:161-179.
• [3]Hebert PDN, Cywinska A, Ball SL, de Waard JR, Hebert PDN, Cywinska A, Ball SL, de Waard JR: Biological identifications through DNA barcodes. Proc R Soc B 2003, 270:313-321.
• [4]DeSalle R, Egan MG, Siddall M: The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc Lond B Biol Sci 2005, 360:1905-1916.
• [5]Dayrat B: Towards integrative taxonomy. Zool J Linn Soc 2005, 85:407-415.
• [6]Padial JM, Miralles A, De la Riva I, Vences M: The integrative future of taxonomy. Front Zool 2010, 7:16. BioMed Central Full Text
• [7]Will KW, Mishler BD, Wheeler QD: The perils of DNA barcoding and the need for integrative taxonomy. Syst Biol 2005, 54:844-851.
• [8]Ryder OA: Species conservation and systematics: the dilemma of subspecies. Trends Ecol Evol 1986, 1:9-10.
• [9]Moritz C: Defining ‘evolutionary significant units’ for conservation. Trends Ecol Evol 1994, 9:373-375.
• [10]Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK: Considering evolutionary processes in conservation biology. Trends Ecol Evol 2000, 15:289-295.
• [11]De Queiroz K: Branches in the lines of descent: Charles Darwin and the evolution of the species concept. Biol J Linn Soc 2011, 103:19-35.
• [12]Global Taxonomy Initiative http://www.cbd.int/gti/ webcite
• [13]Ennos RA, Whitlock R, Fay MF, Jones B, Neaves LE, Payne R, Taylor I, De Vere N, Hollingsworth PM: Process-Based Species Action Plans: an approach to conserve contemporary evolutionary processes that sustain diversity in taxonomically complex groups. Bot J Linn Soc 2012, 168:194-203.
• [14]Edwards SV: Is a new and general theory of molecular systematics emerging? Evolution 2009, 63:1-19.
• [15]Yang Z, Rannala B: Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci USA 2010, 107:9264-9269.
• [16]Liu L, Pearl DK: Species trees from gene trees: peconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol 2007, 56:504-514.
• [17]Knowles L, Carstens B: Delimiting species without monophyletic gene trees. Syst Biol 2007, 56:887-895.
• [18]Heled J, Drummond AJ: Bayesian inference of species trees from multilocus data. Mol Biol Evol 2010, 27:570-580.
• [19]O’Meara BC: New heuristic methods for joint species delimitation and species tree inference. Syst Biol 2010, 59:59-73.
• [20]Carstens BC, Dewey TA: Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats. Syst Biol 2010, 59:400-414.
• [21]Camargo A, Morando M, Avila LJ, Sites JW Jr: Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution
• [22]Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959.
• [23]Dépraz A, Hausser J, Pfenninger M: A species delimitation approach in the Trochulus sericeus/hispidus complex reveals two cryptic species within a sharp contact zone. BMC Evol Biol 2009, 9:171. BioMed Central Full Text
• [24]Meudt HM, Lockhart PJ, Bryant D: Species delimitation and phylogeny of a New Zealand plant species radiation. BMC Evol Biol 2009, 9:111. BioMed Central Full Text
• [25]Larson SR, Culumber CM, Schweiger RN, Chatterton NJ: Species delimitation tests of endemic Lepidium papilliferum and identification of other possible evolutionarily significant units in the Lepidium montanum complex (Brassicaceae) of western North America. Conserv Genet 2010, 11:57-76.
• [26]Reeves PA, Richards CM: Species delimitation under the general lineage concept: An empirical example using wild North American hops (Cannabaceae: Humulus lupulus). Syst Biol 2011, 60:45-59.
• [27]Ross KG, Gotzek D, Ascunce MS, Shoemaker D: Species delimitation: a case study in a problematic ant taxon. Syst Biol 2010, 59:162-184.
• [28]Yang B, Zhao H, Kranzler HR, Gelernter J: Practical population group assignment with selected informative markers: characteristics and properties of Bayesian clustering via STRUCTURE. Genet Epidemiol 2005, 28:302-312.
• [29]Ribeiro MC, Metzger JP, Martensen AC, Ponzoni FJ, Hirota MM: The Brazilian Atlantic forest: how much is left, and how is the remaining forest distributed? Implications for conservation. Biol Conserv 2009, 142:1141-1153.
• [30]Baldissera FA, Caramaschi U, Haddad CFB: Review of the Bufo crucifer species group, with descriptions of two new related species (Amphibia, Anura, Bufonidae). Arq Mus Nac 2004, 62:255-282.
• [31]Frost DR: Amphibian species of the world: An Online reference Version 55. http://research.amnh.org/vz/herpetology/amphibia/ webcite. American Museum of Natural History, New York, USA
• [32]Lima AMX, Rodrigues RG, Bittencourt S, Condrati LH, Machado RA: Bufo henseli First record. Herpetol Rev 2005, 36:198.
• [33]Silveira AL, Salles ROL, Pontes RC: Primeiro registro de Rhinella pombali e novos registros de R crucifer e R ornata no Estado do Rio de Janeiro, Brasil (Amphibia, Anura, Bufonidae). Biotemas 2009, 22:231-235.
• [34]Vaz-Silva W, Valdujo PH, Pombal JP Jr: New species of the Rhinella crucifer group (Anura, Bufonidae) from the Brazilian Cerrado. Zootaxa 2012, 3265:57-65.
• [35]Thomé MTC, Zamudio KR, Giovanelli JGR, Haddad CFB, Baldissera FA Jr, Alexandrino J: Phylogeography of endemic toads and post-Pliocene persistence of the Brazilian Atlantic Forest. Mol Phylogenet Evol 2010, 55:1018-1031.
• [36]Leaché AD, Fujita MK: Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc R Soc B 2010, 277:3071-3077.
• [37]Beebee TJC: Conservation genetics of amphibians. Heredity 2005, 95:423-427.
• [38]Masta SE, Sullivan BK, Lamb T, Routmana EJ: Molecular systematics, hybridization, and phylogeography of the Bufo americanus complex in Eastern North America. Mol Phylogenet Evol 2002, 24:302-314.
• [39]Stöck M, Moritz C, Hickerson M, Frynta D, Dujsebayeva T, Eremchenko V, Macey JR, Papenfuss TJ, Wake DB: Evolution of mitochondrial relationships and biogeography of Palearctic green toads (Bufo viridis subgroup) with insights in their genomic plasticity. Mol Phylogenet Evol 2006, 41:663-689.
• [40]Cunningham M, Cherry MI: Molecular systematics of African 20-chromosome toads (Anura: Bufonidae). Mol Phylogenet Evol 2004, 32:671-685.
• [41]Yamazaki Y, Kouketsu S, Fukuda T, Araki Y, Nambu H: Natural hybridization and directional introgression of two species of japanese toads Bufo japonicus formosus and Bufo torrenticola (Anura: Bufonidae) resulting from changes in their spawning habitat. J Herpetol 2008, 42:427-436.
• [42]Malone JH, Fontenot BE: Patterns of reproductive isolation in toads. PLoS One 2008, 3:e3900.
• [43]Blair WF: Evolution in the genus. Bufo. Austin: University of Texas Press; 1972:459.
• [44]Evans BJ, Kelley DB, Tinsley RC, Melnick DJ, Cannatella DC: A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution. Mol Phylogenet Evol 2004, 33:197-213.
• [45]Crawford AJ: Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. Mol Ecol 2003, 12:2525-2540.
• [46]Colliard C, Sicilia A, Turrisi GF, Arculeo M, Perrin N, Stöck M: Strong reproductive barriers in a narrow hybrid zone of West-Mediterranean green toads (Bufo viridis subgroup) with Plio-Pleistocene divergence. BMC Evol Biol 2010, 10:232. BioMed Central Full Text
• [47]Bokermann WCA: Lista anotada das localidades tipo de anfíbios brasileiros. São Paulo: Serviço de Documentação RUSP; 1966.
• [48]Lourenço ACC, Baêta D, Abreu ACL, Pombal JP Jr: Tadpole and advertisement call of Rhinella pombali (Baldissera, Caramaschi & Haddad, 2004) (Amphibia, Anura, Bufonidae). Zootaxa 2010, 2370:65-68.
• [49]Fontenot BE, Makowsky R, Chippindale PT: Nuclear-mitochondrial discordance and gene flow in a recent radiation of toads. Mol Phylogenet Evol 2011, 59:66-80.
• [50]ICZN: International Code of Zoological Nomenclature. 4th edition. London: International Trust for Zoological Nomenclature; 1999.
• [51]Dubois A, Ohler A: Frogs of the subgenus Pelophylax (Amphibia, Anura, genus Rana): a catalogue of available and valid scientific names, with comments on name-bearing types, complete synonymies, proposed common names, and maps showing all type localities. Zool Polon 1994, 39:139-204.
• [52]Casola C, Marracci S, Bucci S, Ragghianti M, Mancino G, Hotz H, Uzzell T, Guex GD: A hAT-related family of interspersed repetitive elements in genomes of western Palaearctic water frogs. J Zool Syst Evol Res 2004, 42:234-244.
• [53]Álvarez-Presas M, Carbayo F, Rozas J, Riutort M: Land planarians (Platyhelminthes) as a model organism for fine-scale phylogeographic studies: Understanding patterns of biodiversity in the Brazilian Atlantic Forest hotspot. J Evol Biol 2011, 24:887-896.
• [54]D’Horta FM, Cabanne GS, Meyer D, Miyaki CY: The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine. Mol Ecol 2011, 20:1923-1935.
• [55]Carnaval AC, Hickerson MJ, Haddad CFB, Rodrigues MT, Moritz C: Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot. Science 2009, 323:785-789.
• [56]Vogel LS, Johnson SG: Estimation of hybridization and introgression frequency in toads (genus: Bufo) using Dna sequence variation at mitochondrial and nuclear loci. J Herpetology 2008, 42:61-75.
• [57]Dixo M: Diversidade de sapos e lagartos de serrapilheira numa paisagem fragmentada do Planalto Atlântico de São Paulo. São Paulo, Brazil: University of São Paulo; 2005. Ph.D. Thesis
• [58]Haddad CFB, Cardoso AJ, Castanho LM: Hibridação natural entre Bufo ictericus e Bufo crucifer (Amphibia: Anura). Rev Brasil Biol 1990, 50:739-744.
• [59]Azevedo MFC, Foresti F, Ramos PRR, Jim J: Comparative cytogenetic studies of Bufo ictericus, B. paracnemis (Amphibia, Anura) and an intermediate form in sympatry. Genet Mol Biol 2003, 26:289-294.
• [60]Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J: Biodiversity hotspots for conservation priorities. Nature 2000, 403:853-858.
• [61]The IUCN Red List of Threatened Species: Amphibians. http://www.iucnredlist.org/amphibians webcite
• [62]Bell RC, MacKenzie JB, Hickerson M, Chavarría K, Cunningham M, Williams SE, Moritz C: Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs. Proc R Soc B 2011.
• [63]Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: ClustalW and ClustalX version 2. Bioinformatics 2007, 23:2947-2948.
• [64]Duellman W, Schulte R: Description of a new species of Bufo from northern Peru with comments on phenetic groups of South American toads (Anura: Bufonidae). Copeia 1992, 1992:162-172.
• [65]Maxson LR: Molecular probes of phylogeny and biogeography in toads of the widespread genus Bufo. Mol Biol Evo 1984, 1:345-356.
• [66]Pramuk JB: Phylogeny of South American Bufo (Anura: Bufonidae) inferred from combined evidence. Zool J Linn Soc 2006, 146:407-452.
• [67]Stamatakis A: RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
• [68]Stamatakis A: Phylogenetic models of rate heterogeneity: a high performance computing perspective. IPDPS 2006, 3745:283-293.
• [69]Nei M: Molecular Evolutionary Genetics. NewYork: Colombia University Press; 1987.
• [70]Librado P, Rozas J: DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452.
• [71]Stephens M, Smith N, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001, 68:978-989.
• [72]Lewontin RC: The interaction of selection and linkage I Genetic considerations; heterotic models. Genetics 1964, 49:49-67.
• [73]Hudson RR, Kaplan NL: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 1985, 111:147-164.
• [74]Wilson DJ, McVean G: Estimating diversifying selection and functional constraint in the presence of recombination. Genetics 2006, 172:1411-1425.
• [75]Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF, Wright F: TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 2008, 25:126-127.
• [76]Jakobsson M, Rosenberg NA: CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 2007, 23:1801-1806.
• [77]Evanno G, Regnaut S, Goudet J: Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol 2005, 14:2611-2620.
• [78]Earl DA: Structure harvester v061. https://github.com/dentearl/structureHarvester webcite
• [79]Benzécri JP: L'analyse des correspondances. Paris: Dunod; 1973.
• [80]Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F: GENETIX 405, logiciel sous Windows TM pour la génétique des populations. Montpellier (France): Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II; 1996. 2004