Comparative analyses of species delimitation methods with molecular data in snappers (Perciformes: Lutjaninae)

References

• Aguila RN, Genaro JA, Peréz-Asso ARHA. 2017. A new species of the Hysius species-group of Calisto Hübner (Lepidoptera, Nymphalidae, Satyrinae) and insights into the status of different populations currently attributed to C. grannus Bates. Zootaxa. 4317:001–044.
   Web of Science ®Google Scholar
• Allen G-R. 1985. Snappers of the world. An annotated and illustrated catalogue of Lutjanid species known to date. Rome: FAO.
   Google Scholar
• Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu C, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 10:1–6.
   Web of Science ®Google Scholar
• Brower AVZ. 1999. Delimitation of phylogenetic species with DNA sequences: a critique of Davis and Nixon’s population aggregation analysis. Syst Biol. 48:199–213.
   PubMed Web of Science ®Google Scholar
• Butcher BA, Smith MA, Sharkey MJ, Quicke DL. 2012. A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadinae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species. Zootaxa. 3457:1–232.
   Google Scholar
• Carstens BC, Pelletier TA, Reid NM, Satler JD. 2013. How to fail at species delimitation. Mol Ecol. 22:4369–4383.
   PubMed Web of Science ®Google Scholar
• Ceccarelli FS, Sharkey MJ, Zaldívar-Riverón A. 2012. Species identification in the taxonomically neglected, highly diverse, neotropical parasitoid wasp genus Notiospathius (Braconidae: Doryctinae) based on an integrative molecular and morphological approach. Mol Phylogenet Evol. 62:485–495.
   PubMed Web of Science ®Google Scholar
• Correa C, Vásquez D, Castro-Carrasco C, Zúñiga-Reinoso Á, Ortiz JC, Palma RE. 2017. Species delimitation in frogs from South American temperate forests: the case of Eupsophus, a taxonomically complex genus with high phenotypic variation. PLoS ONE. 12:e0181026.
   PubMed Web of Science ®Google Scholar
• da Silva R, Veneza I, Sampaio I, Araripe J, Schneider H, Gomes G. 2015. High levels of genetic connectivity among populations of yellowtail snapper, Ocyurus chrysurus (Lutjanidae – Perciformes), in the Western South Atlantic revealed through multilocus analysis. PLoS One. 10:e0122173.
   PubMed Web of Science ®Google Scholar
• Davis JI, Nixon KC. 1992. Populations, genetic variation, and the delimitation of phylogenetic species. Syst Biol. 41:421–435.
   Web of Science ®Google Scholar
• Dentinger BTM, Suz LM. 2014. What’s for dinner? Undescribed species of porcini in a commercial packet. Peer J. 2:e570.
   PubMed Web of Science ®Google Scholar
• Dowton M, Meiklejohn K, Cameron SL, Wallman J. 2014. A preliminary framework for DNA barcoding, incorporating the multispecies coalescent. Syst Biol. 63:639–644.
   PubMed Web of Science ®Google Scholar
• Esselstyn JA, Evans BJ, Sedlock JL, Ali F, Khan A, Heaney LR. 2012. Single-locus species delimitation: a test of the mixed Yule – coalescent model, with an empirical application to Philippine round-leaf bats. Proc R Soc Lond B Biol Sci. 279:3678–3686.
   PubMed Web of Science ®Google Scholar
• Flot J-F. 2015. Species delimitation’s coming of age. Syst Biol. 64:897–899.
   PubMed Web of Science ®Google Scholar
• Frédérich B, Santini F. 2017. Macroevolutionary analysis of the tempo of diversification in snappers and fusiliers (Percomorpha: Lutjanidae). Belg J Zool. 147:17–35.
   Web of Science ®Google Scholar
• Fujisawa T, Barraclough TG. 2013. Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent (GMYC) approach: a revised method and evaluation on simulated datasets. Syst Biol. 44:1–49.
   Google Scholar
• Glez-Peña D, Gómez-Blanco D, Reboiro-Jato M, Fdez-Riverola F, Posada D. 2010. ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Res. 38:14–18.
   PubMed Web of Science ®Google Scholar
• Gold JR, Voelker G, Renshaw MA. 2011. Phylogenetic relationships of tropical western Atlantic snappers in subfamily Lutjaninae (Lutjanidae: Perciformes) inferred from mitochondrial DNA sequences. Biol J Linn Soc. 102:915–929.
   Web of Science ®Google Scholar
• Gold JR, Willis SC, Renshaw MA, Buentello A, Puritz JB, Hollenbeck CM, Voelker G. 2015. Phylogenetic relationships of tropical eastern Pacific snappers (Lutjanidae) inferred from mitochondrial DNA sequences. Syst Biodivers. 13:1–12.
   Web of Science ®Google Scholar
• Gomes G, Sampaio I, Schneider H. 2012. Population structure of Lutjanus purpureus (Lutjanidae – Perciformes) on the Brazilian coast: further existence evidence of a single species of red snapper in the western Atlantic. An Acad Bras Cienc. 84:979–999.
   PubMed Web of Science ®Google Scholar
• Gomes G, Schneider H, Vallinoto M, Santos S, Orti G, Sampaio I. 2008. Can Lutjanus purpureus (South red snapper) be “legally” considered a red snapper (Lutjanus campechanus)? Genet Mol Biol. 31:372–376.
   Web of Science ®Google Scholar
• Hajibabaei M, Shokralla S, Zhou X, Singer GA, Baird DJ. 2011. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One. 6:e17497.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Ratnasingham S, DeWaard JR. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B Biol Sci. 270:96–99.
   PubMed Web of Science ®Google Scholar
• Hennig W. 1966. Phylogenetic systematics. Urbana: University of Illinois Press.
   Google Scholar
• Hubert N, Hanner R. 2015. DNA barcoding, species delineation and taxonomy: a historical perspective. DNA Barcodes. 3:44–58.
   Google Scholar
• Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. 2017. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics. 33:1630–1638.
   PubMed Web of Science ®Google Scholar
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics. 23:2947–2948.
   PubMed Web of Science ®Google Scholar
• Lessios HA. 2008. The great American schism: divergence of marine organisms after the rise of the Central American Isthmus. Annu Rev Ecol Evol Syst. 39:63–91.
   Web of Science ®Google Scholar
• McCusker MR, Bentzen P. 2010. Positive relationships between genetic diversity and abundance in fishes. Mol Ecol. 19:4852–4862.
   PubMed Web of Science ®Google Scholar
• Monaghan MT, Wild R, Elliot M, Fujisawa T, Balke M, Inward DJG. 2009. Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Syst Biol. 58:298–311.
   PubMed Web of Science ®Google Scholar
• Nelson JS, Grande TC, Wilson MV. 2016. Fishes of the world. 5th ed. Hoboken (NJ): John Wiley & Sons.
   Google Scholar
• Pons J, Barraclough T, Gomez-Zurita J, Cardoso A, Duran DP, Hazzel S, Kamoun S, Sumlin WD, Vogler AP. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol. 55:595–609.
   PubMed Web of Science ®Google Scholar
• Puillandre N, Lambert A, Brouillet S, Achaz G. 2012. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol. 21:1864–1877.
   PubMed Web of Science ®Google Scholar
• R Core Team 2012. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
   Google Scholar
• Reid NM, Carstens BC. 2012. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evol Biol. 12:1471–2148.
   Web of Science ®Google Scholar
• Salzburger W, Ewing GB, Von Haeseler A. 2011. The performance of phylogenetic algorithms in estimating haplotype genealogies with migration. Mol Ecol. 20:1952–1963.
   PubMed Web of Science ®Google Scholar
• Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Chen W, Consortium FB. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA. 109:6241–6246.
   PubMed Web of Science ®Google Scholar
• Silva D, Martins K, Oliveira J, da Silva R, Sampaio I, Schneider H, Gomes G. 2018. Genetic differentiation in populations of lane snapper (Lutjanus synagris – Lutjanidae) from Western Atlantic as revealed by multilocus analysis. Fish Res. 198:138–149.
   Web of Science ®Google Scholar
• Sites JW, Jr, Marshall JC. 2003. Delimiting species: a renaissance issue in systematic biology. Trends Ecol Evol. 18:462–470.
   Web of Science ®Google Scholar
• Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30:1312–1313.
   PubMed Web of Science ®Google Scholar
• Talavera G, Dinca V, Vila R. 2013. Factors affecting species delimitations with the GMYC model: insights from a butterfly survey. Methods Ecol Evol. 4:1101–1110.
   Web of Science ®Google Scholar
• Tanabe AS. 2007. kakusan: a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data. Mol Ecol Notes. 7:962–964.
   Web of Science ®Google Scholar
• Tang CQ, Humphreys AM, Fontaneto D, Barraclough TG. 2014. Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data. Methods Ecol Evol. 5:1086–1094.
   PubMed Web of Science ®Google Scholar
• Vasconcellos AV, Vianna P, Paiva PC, Schama R, Solé-Cava A. 2008. Genetic and morphometric differences between yellowtail snapper (Ocyurus chrysurus, Lutjanidae) populations of the tropical West Atlantic. Genet Mol Biol. 31:308–316.
   Web of Science ®Google Scholar
• Veneza I, Felipe B, Oliveira J, Silva R, Sampaio I, Schneider H, Gomes G. 2014. A barcode for the authentication of the snappers (Lutjanidae) of the western Atlantic: rDNA 5S or mitochondrial COI? Food Control. 38:116–123.
   Web of Science ®Google Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B Biol Sci. 360:1847–1857.
   PubMed Web of Science ®Google Scholar
• Yang Z, Rannala B. 2016. Species identification by Bayesian fingerprinting: a powerful alternative to DNA barcoding. bioRxiv. 2016:041608.
   Google Scholar
• Zhang J, Kapli P, Pavlidis P, Stamatakis A. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. 29:2869–2876.
   PubMed Web of Science ®Google Scholar