Species detection and individual assignment in species delimitation: Can integrative data increase efficacy?

Proceedings of the Royal Society B: Biological Sciences

Volumn 281, Issue 1777, 2014, Pages

  Edwards, Danielle L ^a   Knowles, L Lacey ^b  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Ecology; Individual assignment; Morphology; Multilocus genetics; Species delimitation; Species detection

Indexed keywords

DATA SET; DETECTION METHOD; MORPHOLOGY; SPECIATION (BIOLOGY); TAXONOMY;

EID: 84891888928     PISSN: 09628452     EISSN: 14712954     Source Type: Journal    
DOI: 10.1098/rspb.2013.2765     Document Type: Article

References (48)

1. Wheeler QD, Raven PH, Wilson EO. 2004 Taxonomy: impediment or expedient? Science 303, 285. (doi:10.1126/science.303.5656.285)
2. Knowles LL, Carstens BC. 2007 Delimiting species without monophyletic gene trees. Syst. Biol. 56, 887-895. (doi:10.1080/ 10635150701701091)
3. 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. (doi:10.1093/sysbio/syq024)
4. Hausdorf B, Hennig C. 2010 Species delimitation using dominant and codominant multilocus markers. Syst. Biol. 59, 491-503. (doi:10.1093/ sysbio/syq039)
5. Leaché AD, Fujita MK. 2010 Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc. R. Soc. B277, 3071-3077.(doi:10.1098/rspb.2010.0662)
6. O'Meara BC. 2010 New heuristic methods for joint species delimitation and species tree inference. Syst. Biol. 59, 59-73. (doi:10.1093/ sysbio/syp077)
7. Ence DD, Carstens BC. 2011 SpedeSTEM: a rapid and accurate method for species delimitation. Mol. Ecol. Res. 11, 473-480. (doi:10.1111/j.1755-0998.2010. 02947.x)
8. Yeates DK, Seago A, Nelson L, Cameron SL, Joseph L, Trueman JWH. 2010 Integrative taxonomy, or iterative taxonomy? Syst. Entomol. 36, 209-217. (doi:10.1111/j.1365-3113.2010.00558.x)
9. Camargo A, Morando M, Avila LJ, Sites Jr JW. 2012 Species delimitation with ABC and other methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Syst. Biol. 66, 2834-3849.
10. de Queiroz K. 2007 Species concepts and species delimitation. Syst. Biol. 56, 879-886. (doi:10.1080/ 10635150701701083)
11. Hausdorf B. 2011 Progress toward a general species concept. Evolution 65, 923-931. (doi:10.1111/j. 1558-5646.2011.01231.x)
12. Fujita MK, Leaché AD, Burbrink FT, McGuire JA, Moritz C. 2012 Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol. Evol. 27, 480-488. (doi:10.1016/j.tree.2012.04.012)
13. Bauer AM et al. 2011 Availability of new Bayesian-delimited gecko names and the importance of character-based species descriptions. Proc. R. Soc. B 278, 490-492. (doi:10.1098/rspb.2010.1330)
14. Fujita MK, Leaché AD. 2011 A coalescent perspective on delimiting and naming species: a reply to Bauer et al. Proc. R. Soc. B 278, 493-495. (doi:10.1098/ rspb.2010.1864)
15. Wiens JJ, Penkrot TA. 2002 Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloperus). Syst. Biol. 51, 69-91. (doi:10.1080/106351502753475880)
16. 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.(doi:10.1080/10635150701703063)
17. Sistrom MJ, Donnellan SC, Hutchinson MN. 2013 Delimiting species in recent radiations with low levels of morphological divergence: a case study in Australian Gehyra geckos. Mol. Phyl. Evol. 68, 135-143. (doi:10.1016/j.ympev.2013.03.007)
18. Pardial JM, Miralles A, De la Riva I, Vences M. 2010 The integrative future of taxonomy. Front. Zool. 7, 16.(doi:10.1186/1742-9994-7-16)
19. Liu L. 2008 BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24, 2542-2543. (doi:10.1093/bioinformatics/btn484)
20. Kubatko LS, Carstens BC, Knowles LL. 2009 STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25, 971-973. (doi:10.1093/bioinformatics/btp079)
21. Heled J, Drummond AJ. 2010 Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27, 570-580. (doi:10.1093/molbev/msp274)
22. Yang Z, Rannala B. 2010 Bayesian species delimitation using multilocus sequence data. Proc. Natl Acad. Sci. USA 107, 9264-9269. (doi:10.1073/ pnas.0913022107)
23. Huelsenbeck JP, Andolfatto P. 2007 Inference of population structure under a Dirichlet process model. Genetics 175, 1787-1802. (doi:10.1534/ genetics.106.061317)
24. Zapata F, Jiménez I. 2012 Species delimitation: inferring gaps in morphology across geography. Syst. Biol. 61, 179 -194. (doi:10.1093/sysbio/ syr084)
25. Sobel JM, Chen GF, Watt LR, Schemske DW. 2010 The biology of speciation. Evolution 64, 295-315. (doi:10.1111/j.1558-5646.2009.00877.x)
26. Carstens BC, Pelletier TA, Reid NM, Salter JD. 2013 How to fail at species delimitation. Mol. Ecol. 22, 4369-4383. (doi:10.1111/mec.12413)
27. Elmer KR, Lehtonen TK, Kautt AF, Harrod C, Meyer A. 2010 Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times. BMC Biol. 8, 60.(doi:10.1186/1741-7007-8-60)
28. Harrington RC, Near TJ. 2012 Phylogenetic and coalescent strategies of species delimitation in Snubnose Darters (Percidae: Etheostoma). Syst. Biol. 61, 63-79.(doi:10.1093/sysbio/syr077)
29. Wagner CE, Keller I, Wittwer S, Selz OM, Mwaiko S, Greuter L, Sivasundar A, Seehausen O. 2013 Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol. Ecol. 22, 787-798.(doi:10.1111/ mec.12023)
30. Edwards DL, Melville J, Joseph L, Keogh JS. In revision. Ecological divergence, adaptive radiation and the evolution of sexual signaling traits in a complex of Australian agamid lizards. Evolution.
31. Gower JC. 1971 A general coefficient of similarity and some of its properties. Biometrics 27, 857-871. (doi:10.2307/2528823)
32. Maechler M. 2010 Cluster 1.13.2. See http://cran. r-project.org/web/packages/cluster/index.html.
33. Tamura K, Peterson D, Peterson N, Stecher G, Neo M, Kumar S. 2011 Mega5: Molecular evolutionary genetic analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739. (doi:10. 1093/molbev/msr121)
34. Jukes TH, Cantor CR. 1969 Evolution of protein molecules. In Mammalian protein metabolism (ed. HN Munro), pp. 21-123. New York, NY: Academic Press.
35. Venables WN, Ripley BD. 2002 Modern applied statistics with S, 4th edn. New York, NY: Springer.
36. Zhang C, Zhang D-X, Zhu T, Yang Z. 2011 Evaluation of a Bayesian coalescent method of species delimitation. Syst. Biol. 60, 747-761. (doi:10.1093/ sysbio/syr071)
37. Drummond AJ, Rambaut A. 2007 BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. (doi:10.1186/1471-2148-7-214)
38. Fraley C, Raftery AE. 2002 Model-based clustering, discriminant analysis, and density estimation. J. Am. Stat. Assoc. 97, 611-631. (doi:10.1198/ 016214502760047131)
39. Storr GM. 1965 The Amphibolurus maculatus species group (Lacertilia, Agamidae) in Western Australia. J. Roy. Soc. West. Aust. 48, 45-54.
40. Olave M, Solá E, Knowles LL. 2014 Upstream analyses create problems with DNA-based species delimitation. Syst. Biol. In press.
41. Petit RJ, Excoffier L. 2009 Gene flow and species delimitation. Trends Ecol. Evol. 24, 386-393. (doi:10.1016/j.tree.2009.02.011)
42. Degnan JH, Rosenberg NA. 2009 Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24, 332-340. (doi:10.1016/j.tree.2009.01.009)
43. Knowles LL. 2009 Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 58, 463-467. (doi:10.1093/ sysbio/syp061)
44. Vähä JP, Primmer CR. 2006 Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Mol. Ecol. 15, 63-72. (doi:10.1111/j.1365-294X.2005.02773.x)
45. Kerr JT, Ostrovsky M. 2003 From space to species: ecological applications for remote sensing. Trends Ecol. Evol. 18, 299-305. (doi:10.1016/S0169-5347(03)00071-5)
46. Isaac NJ, Mallet J, Mace GM. 2004 Taxonomic inflation: its influence on macroecology and conservation. Trends Ecol. Evol. 19, 464-469. (doi:10.1016/j.tree.2004.06.004)
47. Huang H, He Q, Kubatko LS, Knowles LL. 2010 Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing different methods. Syst. Biol. 59, 573-583. (doi:10.1093/sysbio/syq047)
48. Tänzler R, Sagata K, Surbakti S, Balke M, Reidel A. 2012 DNA barcoding for community ecology - How to tackle a hyperdiverse, mostly undescribed Melanesian fauna. PLoS ONE 7, e28832. (doi:10. 1371/journal.pone.0028832)