Diversifying into the branches: Species boundaries in African green and bush snakes, Philothamnus (Serpentes: Colubridae)

Molecular Phylogenetics and Evolution - Tập 130 - Trang 357-365 - 2019
Hanlie M. Engelbrecht1,2,3, William R. Branch4,5, Eli Greenbaum6, Graham J. Alexander7, Kate Jackson3, Marius Burger8,9, Werner Conradie4,10, Chifundera Kusamba11, Ange-Ghislain Zassi-Boulou12, Krystal A. Tolley1,13
1South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7, Claremont, 7735, South Africa
2Department of Botany & Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
3Department of Biology, Whitman College, 345 Boyer Ave, Walla Walla, WA 99362, USA
4Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa
5Department of Zoology, P. O. Box 77000, Nelson Mandela University, Port Elizabeth 6031, South Africa
6Department of Biological Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, TX 79968, USA
7School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, P.O. Wits, Johannesburg, 2050, South Africa
8African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
9Flora Fauna & Man, Ecological Services Ltd. Tortola, British Virgin Islands
10School of Natural Resource Management, George Campus, Nelson Mandela University, George 6530, South Africa
11Laboratoire d’Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, Lwiro, The Democratic Republic of the Congo
12Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), BP 2400 Brazzaville, The Democratic Republic of the Congo
13Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2000, South Africa

Tài liệu tham khảo

Alexander, 1990, Reptiles and amphibians of Durban, Durban Museum Novitates, 15, 1 Aljanabi, 1997, Universal and rapid salt-extraction of high quality genomic DNA for PCR based techniques, Nucleic Acids Res., 25, 4692, 10.1093/nar/25.22.4692 Andersson, 1901, Some new species of snakes from Cameroon and South America, belonging to the collections of the Royal Museum in Stockholm, Bihang till Kongliga Svenska Vet. Akad. Handlingar, 27, 1 Arévalo, 1994, Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in central Mexico, Syst. Biol., 43, 387, 10.1093/sysbio/43.3.387 2014 Bocage, J.V., du B., 1882. Notice sur les espèces du genre “Philothamnus” qui se trouvent au Muséum de Lisbonne. Jornal de Sciencias, Mathematicas, Physicas e Naturaes, Lisboa 9:1–19. Broadley, 1966, A review of the Natal green snake, Philothamnus natalensis (A. Smith), with a description of a new subspecies, Ann. Natal Museum, 18, 417 Bryson, 2007, A phylogeny of the Lampropeltis mexicana complex (Serpentes: Colubridae) based on mitochondrial DNA sequences suggests evidence for species-level polyphyly within Lampropeltis, Mol. Phylogenet. Evol., 43, 674, 10.1016/j.ympev.2006.11.025 Burbrink, 2000, Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept, Evolution, 54, 2107, 10.1111/j.0014-3820.2000.tb01253.x Carstens, 2013, How to fail at species delimitation, Mol. Ecol., 22, 4369, 10.1111/mec.12413 Chen, 2013, Understanding the formation of ancient intertropical disjunct distributions using Asian and Neotropical hinged-teeth snakes (Sibynophis and Scaphiodontophis: Serpentes: Colubridae), Mol. Phylogenet. Evol., 66, 254, 10.1016/j.ympev.2012.09.032 Chippaux, 2006 Cogger, 1998 Criscuolo, 2010, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BioMed Central Evolut. Biol., 10, 210, 10.1186/1471-2148-10-210 de Queiroz, 1998, The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations, 57 de Queiroz, 2007, Species concepts and species delimitation, Syst. Biol., 56, 879, 10.1080/10635150701701083 Farris, 1994, Testing significance of incongruence, Cladistics, 10, 315, 10.1111/j.1096-0031.1994.tb00181.x Flot, 2015, Species delimitation’s coming of age, Syst. Biol., 64, 897, 10.1093/sysbio/syv071 Fontaneto, 2015, Guidelines for DNA taxonomy, with a focus on the meiofauna, Mar. Biodivers., 45, 433, 10.1007/s12526-015-0319-7 Glaw, 2013, Resolving an enigma by integrative taxonomy: Madagascarophis fuchsi (Serpentes: Lamprophiidae), a new opisthoglyphous and microendemic snake from northern Madagascar, Zootaxa, 3630, 317, 10.11646/zootaxa.3630.2.7 Groth, 1999, Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene, Mol. Phylogenet. Evol., 12, 115, 10.1006/mpev.1998.0603 Hudson, 1990, Gene genealogies and the coalescent process, Oxford Surv. Evolut. Biol., 7, 1 Hughes, 1985, Progress on a taxonomic revision of the African green tree snakes (Philothamnus spp.), 511 Jesus, 2009, Phylogenetic relationships of African green snakes (genera Philothamnus and Hapsidophrys) from São Tomé, Príncipe and Annobón islands based on mtDNA sequences, and comments on their colonization and taxonomy, Herpetol. J., 19, 41 Kapli, 2017, Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo, Bioinformatics, 33, 1630, 10.1093/bioinformatics/btx025 Kearse, 2012, Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, 28, 1647, 10.1093/bioinformatics/bts199 Lanfear, 2014, Selecting optimal partitioning schemes for phylogenomic datasets, BioMed Central Evolut. Biol., 14, 82, 10.1186/1471-2148-14-82 Lawson, 2005, Phylogeny of the Colubroidea (Serpentes): new evidence from mitochondrial and nuclear genes, Mol. Phylogenet. Evol., 37, 581, 10.1016/j.ympev.2005.07.016 Lefébure, 2006, Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation, Mol. Phylogenet. Evol., 40, 435, 10.1016/j.ympev.2006.03.014 Loveridge, 1958, Revision of five African snake genera, Bull. Museum Comparat. Zool., Harvard, 119, 1 Meier, 2006, DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success, Syst. Biol., 55, 715, 10.1080/10635150600969864 Meier, 2008, The use of mean instead of smallest interspecific distances exaggerates the size of the “barcoding gap” and leads to misidentification, Syst. Biol., 57, 809, 10.1080/10635150802406343 Meyer, 2005, DNA barcoding: error rates based on comprehensive sampling, PLoS Biol., 3, 10.1371/journal.pbio.0030422 Mezzasalma, 2015, A sisters’ story: comparative phylogeography and taxonomy of Hierophis viridiflavus and H. gemonensis (Serpentes, Colubridae), Zool. Scripta, 44, 495, 10.1111/zsc.12115 Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments workshop (GCE), New Orleans, LA, pp. 1–8. Mucina, 2006 Padial, 2010, The integrative future of taxonomy, Front. Zool., 7, 16, 10.1186/1742-9994-7-16 Palumbi, 1996, Nucleic acids II: the polymerase chain reaction, 205 Pante, 2015, Species are hypotheses: avoid connectivity assessments based on pillars of sand, Mol. Ecol., 24, 525, 10.1111/mec.13048 Paradis, 2004, APE: analyses of phylogenetics and evolution in R language, Bioinformatics, 20, 289, 10.1093/bioinformatics/btg412 Pons, 2006, Sequence-based species delimitation for the DNA taxonomy of undescribed insects, Syst. Biol., 55, 595, 10.1080/10635150600852011 Pook, 2009, When continents collide: phylogeny, historical biogeography and systematics of the medically important viper genus Echis (Squamata: Serpentes: Viperidae), Mol. Phylogenet. Evol., 53, 792, 10.1016/j.ympev.2009.08.002 Puillandre, 2012, Large-scale species delimitation method for hyperdiverse groups, Mol. Ecol., 21, 2671, 10.1111/j.1365-294X.2012.05559.x Pyron, 2011, The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees, Mol. Phylogenet. Evol., 58, 329, 10.1016/j.ympev.2010.11.006 Pyron, 2013, A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes, BioMed Central Evolut. Biol., 13, 93, 10.1186/1471-2148-13-93 Pyron, 2014, Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia), Mol. Phylogenet. Evolut., 81, 221, 10.1016/j.ympev.2014.08.023 Rambaut, A., Drummond, A., 2007. Tracer version 1.6 computer program. Available: <http://tree.bio.ed.ac.uk/software/> [accessed 20 April 2017]. Reid, 2012, Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model, BioMed Central Evolut. Biol., 12, 196, 10.1186/1471-2148-12-196 Ronquist, 2012, MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst. Biol., 61, 539, 10.1093/sysbio/sys029 Schlick-Steiner, 2010, Integrative taxonomy: a multisource approach to exploring biodiversity, Annu. Rev. Entomol., 55, 421, 10.1146/annurev-ento-112408-085432 Schliep, 2011, Phangorn: phylogenetic analysis in R, Bioinformatics, 27, 592, 10.1093/bioinformatics/btq706 Shimodaira, 1999, Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Mol. Biol. Evol., 16, 1114, 10.1093/oxfordjournals.molbev.a026201 Simpson, 1951, The species concept, Evolution, 5, 285, 10.1111/j.1558-5646.1951.tb02788.x Smith, 1840 Stamatakis, 2006, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446 Swofford, 2001 Team, R., 2013. R Development Core Team. R: a language and environment for statistical computing. Available: <http://www.r.project.org/> [accessed December 2013]. Tonini, 2015, Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status, Biol. Conserv., 204, 23, 10.1016/j.biocon.2016.03.039 Trape, 2014, A checklist of the snake fauna of Guinea, with taxonomic changes in the genera Philothamnus and Dipsadoboa (Colubridae) and a comparison with the snake fauna of some other West African countries, Zootaxa, 3900, 301, 10.11646/zootaxa.3900.3.1 Trape, 2015, The snakes of Niger, Amphibian Reptile Conserv., 9, 39 Trape, 1990, Note sur une collection de serpents du Congo avec description d’une espéce nouvelle, J. Afric. Zool., 104, 375 Uetz, P., Freed, P., Hošek, J., (Eds.), 2018. The Reptile Database. Available: <http://www.reptile-database.org> [Accessed: 21 August 2018]. Vidal, 2007, The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes, C.R. Biol., 330, 182, 10.1016/j.crvi.2006.10.001 Wallach, 2014 Wiemers, 2007, Does the DNA barcoding gap exist?–a case study in blue butterflies (Lepidoptera: Lycaenidae), Front. Zool., 4, 8, 10.1186/1742-9994-4-8 Wilcox, 2002, Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support, Mol. Phylogenet. Evol., 25, 361, 10.1016/S1055-7903(02)00244-0 Wiley, 1980, Is the evolutionary species fiction? – A consideration of classes, individuals and historical entities, Syst. Zool., 29, 76, 10.2307/2412628 Yule, 1925, A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F.R.S, Philos. Trans. R. Soc. Lond. B Biol. Sci., 213, 21, 10.1098/rstb.1925.0002 Zheng, 2016, Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species, Mol. Phylogenet. Evol., 94, 537, 10.1016/j.ympev.2015.10.009