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Methods for delimiting species via population genetics and phylogenetics using genotype data

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Abstract

In species delimitation, a formidable goal in the discipline of systematic biology, we identify and describe species morphologically and ecologically based on phenotypic data. Efficient genotyping technologies produce genetic and genomic data with relative ease, which promotes species discovery and validation using genotype data. For the last two decades, we have seen the development of species delimitation methods based on genetic distances and phylogenetic trees using genotype data. However, speciation processes via evolutionary relationship among species were mostly divorced from species delimitation. Recent approaches to drawing species boundaries use multi-locus sequence data to account for evolutionary processes including speciation and gene flow. They allow us to learn of jointly speciation and species delimitation, leveraging computational and statistical techniques developed in population genetics and phylogenetics. Here, we review the recent progress in the development of species delimitation using genotype data and discuss the future outlook for the research of developing species delimitation methods.

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References

  • Agapow P-M, Bininda-Emonds ORP, Crandall KA, Gittleman JL, Mace GM, Marshall JC, Purvis A (2004) The impact of species concept on biodiversity studies. Q Rev Biol 79:161–179

    Article  PubMed  Google Scholar 

  • Aydin Z, Marcussen T, Ertekin AS, Oxelman B (2014) Marginal likelihood estimate comparisons to obtain optimal species delimitations in Silene sect. Cryptoneurae (caryophyllaceae). PLoS One 9:e106990

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Baum DA, Shaw KL (1995) Genealogical perspectives on the species problem. In: Hoch PC, Stephenson AG (eds) Experimental and molecular approaches to plant biosystematics. Missouri Botanical Garden, St. Louis, pp 289–303

    Google Scholar 

  • Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M et al (2010) In defence of model-based inference in phylogeography. Mol Ecol 19:436–446

    Article  CAS  Google Scholar 

  • Beerli P, Felsenstein J (1999) Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152:763–773

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Boykin LM, Armstrong KF, Kubatko L, De Barro P (2012) Species delimitation and global biosecurity. Evol Bioinform 8:1–37

    Article  Google Scholar 

  • Brooks TM, Helgen KM (2010) Biodiversity: a standard for species. Nature 467:540–541

    Article  CAS  PubMed  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

    Article  CAS  PubMed  Google Scholar 

  • Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol 29:1917–1932

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Camargo A, Morando M, Avila LJ, Sites JW (2012) 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 66:2834–2849

    Article  PubMed  Google Scholar 

  • Carson HL (1957) The species as a field for recombination. In: Mayr E (ed) The species problem. American Association for the Advancement of Science, Washington DC, pp 23–38

    Google Scholar 

  • Carstens BC, Dewey TA (2010) Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats. Syst Biol 59:400–414

    Article  PubMed  PubMed Central  Google Scholar 

  • Carstens BC, Pelletier TA, Reid NM, Satler JD (2013) How to fail at species delimitation. Mol Ecol 22:4369–4383

    Article  PubMed  Google Scholar 

  • Choi SC, Hey J (2011) Joint inference of population assignment and demographic history. Genetics 189:561–577

    Article  PubMed  PubMed Central  Google Scholar 

  • Collins RA, Cruickshank RH et al (2014) Known knowns, known unknowns, unknown unknowns and unknown knowns in DNA barcoding: a comment on Dowton et al. Syst Biol 63:1005–1009

    Article  PubMed  Google Scholar 

  • Corander J, Waldmann P, Sillanpää MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163:367–374

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cracraft J (1983) Species concepts and speciation analysis. In: Johnston RF (ed) Current ornithology. Springer, Boston, pp 159–187

    Chapter  Google Scholar 

  • Davis JI, Nixon KC (1992) Populations, genetic variation, and the delimitation of phylogenetic species. Syst Biol 41:421–435

    Article  Google Scholar 

  • Dayrat B (2005) Towards integrative taxonomy. Biol J Linn Soc 85:407–415

    Article  Google Scholar 

  • de Queiroz K (2005) Ernst Mayr and the modern concept of species. Proc Natl Acad Sci USA 102:6600–6607

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • de Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56:879–886

    Article  PubMed  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

    Article  PubMed  Google Scholar 

  • Doyle JJ (1995) The irrelevance of allele tree topologies for species delimitation, and a non-topological alternative. Syst Bot 20:574

    Article  Google Scholar 

  • Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Duminil J, Di Michele M (2009) Plant species delimitation: a comparison of morphological and molecular markers. Plant Biosyst 143:528–542

    Article  Google Scholar 

  • Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63:1–19

    Article  CAS  PubMed  Google Scholar 

  • Ence DD, Carstens BC (2011) SpedeSTEM: a rapid and accurate method for species delimitation. Mol Ecol Resour 11:473–480

    Article  PubMed  Google Scholar 

  • Flot J-F (2015) Species delimitation’s coming of age. Syst Biol 64:897–899

    Article  PubMed  Google Scholar 

  • Fujisawa T, Barraclough TG (2013) Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Syst Biol 62:707–724

    Article  PubMed  PubMed Central  Google Scholar 

  • Fujita MK, Leaché AD, Burbrink FT, McGuire JA, Moritz C (2012) Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol Evol (Amst) 27:480–488

    Article  Google Scholar 

  • Gerard RW (1957) Units and concepts of biology. Science 125:429–433

    Article  CAS  PubMed  Google Scholar 

  • Gernhard T (2008) The conditioned reconstructed process. J Theor Biol 253:769–778

    Article  PubMed  Google Scholar 

  • Good DA, Wake DB (1992) Geographic variation and speciation in the Torrent Salamanders of the genus Rhyacotriton (Caudata: Rhyacotritonidae). Univ Calif Publ Zool 126:1–91

    Google Scholar 

  • Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A (2011) Bayesian inference of ancient human demography from individual genome sequences. Nat Genet 43:1031–1034

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grummer JA, Bryson RW, Reeder TW (2014) Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae). Syst Biol 63:119–133

    Article  PubMed  Google Scholar 

  • Guillot G, Estoup A, Mortier F, Cosson J-F (2005) A spatial statistical model for landscape genetics. Genetics 170:1261–1280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guillot G, Renaud S, Ledevin R, Michaux J, Claude J (2012) A unifying model for the analysis of phenotypic, genetic, and geographic data. Syst Biol 61:897–911

    Article  PubMed  Google Scholar 

  • Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97–109

    Article  Google Scholar 

  • Hausdorf B (2011) Progress toward a general species concept. Evolution 65:923–931

    Article  PubMed  Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc B 270:313–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Mol Biol Evol 27:570–580

    Article  CAS  PubMed  Google Scholar 

  • Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747–760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hey J, Pinho C (2012) Population genetics and objectivity in species diagnosis. Evolution 66:1413–1429

    Article  PubMed  Google Scholar 

  • Highton R (1998) Is Ensatina eschscholtzii a ring-species? Herpetologica 54:254–278

    Google Scholar 

  • Hoberg EP (2006) Phylogeny of Taenia: Species definitions and origins of human parasites. Parasitol Int 55:S23–S30

    Article  PubMed  Google Scholar 

  • Huelsenbeck JP, Andolfatto P (2007) Inference of population structure under a Dirichlet process model. Genetics 175:1787–1802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jones G (2016) Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. J Math Biol 1–21

  • Jones G, Aydin Z, Oxelman B (2015) DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics 31:991–998

    Article  CAS  PubMed  Google Scholar 

  • Kalinowski ST (2010) The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure. Heredity 106:625–632

    Article  PubMed  PubMed Central  Google Scholar 

  • Kass RE, Raftery AE (1995) Bayes factors. J Am Stat Assoc 90:773–795

    Article  Google Scholar 

  • Kingman JFC (1982) On the genealogy of large populations. J Appl Probab 19:27–43

    Article  Google Scholar 

  • Kubatko LS, Carstens BC, Knowles LL (2009) STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25:971–973

    Article  CAS  PubMed  Google Scholar 

  • Kuhner MK, Yamato J, Felsenstein J (1995) Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140:1421–1430

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kuhner MK, Yamato J, Felsenstein J (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149:429–434

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kuhner MK, Yamato J, Felsenstein J (2000) Maximum likelihood estimation of recombination rates from population data. Genetics 156:1393–1401

    CAS  PubMed  PubMed Central  Google Scholar 

  • Leaché AD, Fujita MK, Minin VN, Bouckaert RR (2014) Species delimitation using genome-wide SNP data. Syst Biol 63:534–542

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu L, Pearl DK (2007) Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol 56:504–514

    Article  CAS  PubMed  Google Scholar 

  • Lopes JS, Balding D, Beaumont MA (2009) PopABC: a program to infer historical demographic parameters. Bioinformatics 25:2747–2749

    Article  CAS  PubMed  Google Scholar 

  • Maddison WP (1997) Gene trees in species trees. Syst Biol 46:523–536

    Article  Google Scholar 

  • Maddison WP, Knowles LL (2006) Inferring phylogeny despite incomplete lineage sorting. Syst Biol 55:21–30

    Article  PubMed  Google Scholar 

  • Masters BC, Fan V, Ross HA (2011) Species delimitation—a geneious plugin for the exploration of species boundaries. Mol Ecol Resour 11:154–157

    Article  PubMed  Google Scholar 

  • Mayden RL (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Springer, Netherlands, pp 381–424

    Google Scholar 

  • Mayr E (1942) Systematics and the origin of species. Columbia University Press, New York

    Google Scholar 

  • McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT (2013) Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 66:526–538

    Article  CAS  PubMed  Google Scholar 

  • Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1092

    Article  CAS  Google Scholar 

  • Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46

    Article  CAS  PubMed  Google Scholar 

  • Nee S, May RM, Harvey PH (1994) The reconstructed evolutionary process. Philos Trans R Soc Lond B Biol Sci 344:305–311

    Article  CAS  PubMed  Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106:283–292

    Article  Google Scholar 

  • Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885–896

    CAS  PubMed  PubMed Central  Google Scholar 

  • O’Meara BC (2010) New heuristic methods for joint species delimitation and species tree inference. Syst Biol 59:59–73

    Article  PubMed  Google Scholar 

  • Pella J, Masuda M (2006) The Gibbs and split-merge sampler for population mixture analysis from genetic data with incomplete baselines. Can J Fish Aquat Sci 63:576–596

    Article  Google Scholar 

  • Pons J, Barraclough T, Gomez-Zurita J, Cardoso A, Duran D, Hazell S, Kamoun S, Sumlin W, Vogler A (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55:595–609

    Article  PubMed  Google Scholar 

  • Porter AH (1990) Testing nominal species boundaries using gene flow statistics: the taxonomy of two hybridizing admiral butterflies (Limenitis: Nymphalidae). Syst Biol 39:131–147

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  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

    Article  CAS  PubMed  Google Scholar 

  • Rannala B (2015) The art and science of species delimitation. Curr Zool 61:846–853

    Article  Google Scholar 

  • Rannala B, Yang Z (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645–1656

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rasmussen RS, Morrissey MT (2008) DNA-based methods for the identification of commercial fish and seafood species. Compr Rev Food Sci Food Saf 7:280–295

    Article  CAS  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 12:196

    Article  PubMed  PubMed Central  Google Scholar 

  • Rissler LJ, Apodaca JJ (2007) Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus). Syst Biol 56:924–942

    Article  PubMed  Google Scholar 

  • Rittmeyer EN, Austin CC (2012) The effects of sampling on delimiting species from multi-locus sequence data. Mol Phylogenet Evol 65:451–463

    Article  CAS  PubMed  Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  CAS  PubMed  Google Scholar 

  • Rosenberg NA (2007) Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution 61:317–323

    Article  PubMed  Google Scholar 

  • Sites JJ, Camargo A (2013) Species delimitation: a decade after the Renaissance. In: Pavlinov IY (ed) The species problem—ongoing issues. InTech, Rijeka, pp 225–247

    Google Scholar 

  • Sites JW Jr, Marshall JC (2003) Delimiting species: a Renaissance issue in systematic biology. Trends Ecol Evol (Amst) 18:462–470

    Article  Google Scholar 

  • Solís-Lemus C, Knowles LL, Ané C (2015) Bayesian species delimitation combining multiple genes and traits in a unified framework. Evolution 69:492–507

    Article  PubMed  Google Scholar 

  • Takahata N, Satta Y, Klein J (1995) Divergence time and population size in the lineage leading to modern humans. Theor Popul Biol 48:198–221

    Article  CAS  PubMed  Google Scholar 

  • Tattersall I (1989) The roles of ecological and behavioral observation in species recognition among primates. Hum Evol 4:117–124

    Article  Google Scholar 

  • Taylor HR, Harris WE (2012) An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol Ecol Resour 12:377–388

    Article  CAS  PubMed  Google Scholar 

  • Templeton AR (2001) Using phylogeographic analyses of gene trees to test species status and processes. Mol Ecol 10:779–791

    Article  CAS  PubMed  Google Scholar 

  • Wheeler QD, Meier R (2000) Species concepts and phylogenetic theory: a debate. Columbia University Press, New York

    Google Scholar 

  • Wiens JJ (2007) Species delimitation: new approaches for discovering diversity. Syst Biol 56:875–878

    Article  PubMed  Google Scholar 

  • Wiens JJ, Penkrot TA (2002) Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Syst Biol 51:69–91

    Article  PubMed  Google Scholar 

  • Wiley EO (1978) The evolutionary species concept reconsidered. Syst Biol 27:17–26

    Google Scholar 

  • Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wright S (1943) Isolation by distance. Genetics 28:114–138

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci USA 107:9264–9269

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Z, Rannala B (2014) Unguided species delimitation using DNA sequence data from multiple loci. Mol Biol Evol 31:3125–3135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Z, Rannala B (2016) Species identification by Bayesian fingerprinting: a powerful alternative to DNA barcoding. bioRxivorg. doi: 10.1101/041608

  • Yule UG (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 213:21–87

    Article  Google Scholar 

  • Zhang C, Zhang D-X, Zhu T, Yang Z (2011) Evaluation of a Bayesian coalescent method of species delimitation. Syst Biol 60:747–761

    Article  PubMed  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

I thank the reviewer and the reviews editor for improving the manuscript. This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2015R1D1A1A02062381/1).

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  1. Department of Biology, A342, Sungshin Women’s University, 55, Dobong-ro 76ga-gil, Gangbuk-gu, Seoul, 01133, Republic of Korea

    Sang Chul Choi

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Choi, S.C. Methods for delimiting species via population genetics and phylogenetics using genotype data. Genes Genom 38, 905–915 (2016). https://doi.org/10.1007/s13258-016-0458-7

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