The utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference in Lycium (Solanaceae)

Molecular Phylogenetics and Evolution

Volumn 53, Issue 3, 2009, Pages 881-890

  Levin, Rachel A ^a   Whelan, Andrew ^a   Miller, Jill S ^a  

^a AMHERST COLLEGE   (United States)

Author keywords

Bayesian estimation of species trees (BEST); Concatenation; COSII; Fine scale relationships; GBSSI; Gene trees; Hybridization; Incongruence; ITS; Lycium; Multi locus; Phylogeny; Solanaceae; Species trees

Indexed keywords

LYCIUM; MAGNOLIOPHYTA; SOLANACEAE; SOLANUM;

CHLOROPLAST DNA; PLANT DNA; RIBOSOMAL SPACER DNA;

ALLELE; ARTICLE; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; GENETIC MARKER; GENETICS; INTRON; LYCIUM; MOLECULAR EVOLUTION; PHYLOGENY; PLANT GENOME; SEQUENCE ALIGNMENT;

ALLELES; CELL NUCLEUS; DNA, CHLOROPLAST; DNA, PLANT; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; GENETIC MARKERS; GENOME, PLANT; INTRONS; LYCIUM; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 73949149357     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.08.016     Document Type: Article

References (61)

1. Álvarez, I., Costa, A., Nieto Feliner, G., 2008. Selecting single-copy nuclear genes for plant phylogenetics: a preliminary analysis for the Senecioneae (Asteraceae). J. Mol. Evol. 66, 276-291.
2. Ames, M., Spooner, D.M., 2008. Phylogeny of Solanum Series Piurana and Putatively Related Series Based on Morphological and Molecular Data. Abstract, Botany 2008, Vancouver, BC, Canada.
3. Ané, C., Larget, B., Baum, D.A., Smith, S.D., Rokas, A., 2007. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 24, 412-426.
4. Barrett, M., Donoghue, M.J., Sober, E., 1991. Against consensus. Syst. Zool. 40, 486-493.
5. Belfiore, N.M., Liu, L., Moritz, C., 2008. Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Syst. Biol. 57, 294-310.
6. Bernardello, L.M., 1982. Estudios en Lycium (Solanaceae) II. Recuentos cromosomicos en entidades Argentinas. Hickenia 1, 321-328.
7. Bernardello, L.M., 1986. Revisión taxonómica de las especies sudamericanas de Lycium (Solanaceae). Bol. Acad. Nac. Cienc. Córdoba 57, 173-356.
8. Brumfield, R.T., Liu, L., Lum, D.E., Edwards, S.V., 2008. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Syst. Biol. 57, 719-731.
9. Carstens, B.C., Knowles, L.L., 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 56, 400-411.
10. Chapman, M.A., Change, J., Weisman, D., Kesseli, R.V., Burke, J.M., 2007. Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae. Theor. Appl. Genet. 115, 747-755.
11. Cronn, R.C., Small, R.L., Haselkorn, T., Wendel, J.F., 2002. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Am. J. Bot. 89, 707-725.
12. Degnan, J.H., Rosenberg, N.A., 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2, e68. doi:10.1371/journal.pgen.0020068.
13. Degnan, J.H., Rosenberg, N.A., 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24, 332-340.
14. Degnan, J.H., Salter, L.A., 2005. Gene tree distributions under the coalescent process. Evolution 59, 24-37.
15. Degnan, J.H., DeGiorgio, M., Bryant, D., Rosenberg, N.A., 2008. Properties of consensus methods for inferring species trees from gene trees. arxiv:/0802.2355v1 [q-bio.PE].
16. Eckert, A.J., Carstens, B.C., 2008. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol. Phylogenet. Evol. 49, 832-842.
17. Edwards, S.V., Liu, L., Pearl, D.K., 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 104, 5936-5941.
18. Fajardo, D., Spooner, D.M., 2008. Preliminary Phylogeny of Solanum Series Conicibaccata Based on Morphological and Molecular Data. Abstract, Botany 2008, Vancouver, BC, Canada.
19. Gatesy, J., Baker, R.H., 2005. Hidden likelihood support in genomic data: can forty-five wrongs make a right? Syst. Biol. 54, 483-492.
20. Howarth, D.G., Baum, D.A., 2002. Phylogenetic utility of a nuclear intron from nitrate reductase for the study of closely related plant species. Mol. Phylogenet. Evol. 23, 525-528.
21. Huelsenbeck, J.P., Ronquist, F., 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17, 754-755.
22. Kluge, A.G., 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7-25.
23. Kress, W.J., Erickson, D.L., 2007. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2, e508. doi:10.1371/journal.pone.0000508.
24. Kubatko, L.S., Degnan, J.H., 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56, 17-24.
25. Lahaye, R., van der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Maurin, O., Duthoit, S., Barraclough, T.G., Savolainen, V., 2008. DNA barcoding the floras of biodiversity hotspots. Proc. Natl. Acad. Sci. USA 105, 2923-2928.
26. Levin, R.A., Miller, J.S., 2005. Relationships within tribe Lycieae (Solanaceae):paraphyly of Lycium and multiple origins of gender dimorphism. Am. J. Bot. 92, 2044-2053.
27. Levin, R.A., Bernardello, G., Venter, A.M., Shak, J.R., Miller, J.S., 2007. Evolutionary relationships in tribe Lycieae (Solanaceae). Acta Hort. 745, 225-239.
28. Levin, R.A., Blanton, J., Miller, J.S., 2009. Phylogenetic utility of nuclear nitrate reductase: a multi-locus comparison of nuclear and chloroplast sequence data for inference of relationships among American Lycieae (Solanaceae). Mol. Phylogenet. Evol. 50, 608-617.
29. Li, M., Wunder, J., Bissoli, G., Scarponi, E., Gazzani, S., Barbaro, E., Saedler, H., Varotto, C., 2008. Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species. Cladistics 24, 727-745.
30. Liu, L., 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24, 2542-2543.
31. Liu, L., Pearl, D.K., 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56, 504-514.
32. Liu, L., Pearl, D.K., Brumfield, R.T., Edwards, S.V., 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62, 2080-2091.
33. Maddison, W.P., Knowles, LL, 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55, 21-30.
34. Miller, J.S., 2002. Phylogenetic relationships and the evolution of gender dimorphism in Lycium (Solanaceae). Syst. Bot. 27, 416-428.
35. Miller, J.S., Venable, D.L., 2000. Polyploidy and the evolution of gender dimorphism in plants. Science 289, 2335-2338.
36. Miller, J.S., Kamath, A., Levin, R.A., 2009. Do multiple tortoises equal a hare? The utility of nine noncoding plastid regions for species-level phylogenetics in tribe Lycieae (Solanaceae). Syst. Bot. 34, in press.
37. Miller, J.S., Levin, R.A., Feliciano, N.M., 2008. A tale of two continents: Baker's rule and the maintenance of self-incompatibility in Lycium (Solanaceae). Evolution 62, 1052-1065.
38. Mueller, LA, Solow, T.H., Taylor, N., Skwarecki, B., Buels, R., Binns, J., Lin, C, Wright, M.H., Ahrens, R., Wang, Y., Herbst, E.V., Keyder, E.R., Menda, N., Zamir, D., Tanksley, S.D., 2005. The SOL Genomics Network. A comparative resource for Solanaceae biology and beyond. Plant Physiol. 138, 1310-1317.
39. Olmstead, R.G., Bohs, L., Abdel Migid, H., Santiago-Valentin, E., Garcia, V.F., Collier, S.M., 2008. A molecular phylogeny of the Solanaceae. Taxon 57,1159-1181.
40. Paithankar, K.R., Prasad, K.S.N., 1991. Precipitation of DNA by polyethylene glycol and ethanol. Nucleic Acids Res. 19,1346.
41. Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818.
42. Rambaut, A., 2002. Se-Al: sequence alignment editor, version 2.0. Available from:.
43. Rambaut, A., Drummond, A.J., 2007. Tracer v 1.4. Available from: .
44. Rodríguez, F., Spooner, D.M., 2007. Multi Nuclear Gene Phylogenetic Analyses of Potatoes and Tomatoes. Abstract, Botany & Plant Biology 2007, Chicago, IL, USA.
45. Rodríguez, F., Spooner, D.M., 2008. Do Potatoes and Tomatoes have a Single Evolutionary History? What Proportion of the Genome Supports this History? Abstract, Botany 2008, Vancouver, BC, Canada.
46. Rodríguez, F., Wu, F., Tanksley, S., Spooner, D., 2006. A Multiple Single-Copy Gene Phylogenetic Analysis of Wild Tomatoes (Solanum L. section Lycopersicon (Mill.) Wettst.) and their Outgroup Relatives. Abstract, Solanaceae 2006 Meeting, Madison, WI, USA.
47. Rokas, A., Williams, B.L, King, N., Carroll, S.B., 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798-804.
48. Ronquist, F., Huelsenbeck, J.P., 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19,1572-1574.
49. Rosenberg, N.A., Tao, R., 2008. Discordance of species trees with their most likely gene trees: the case of five taxa. Syst. Biol. 57,131-140.
50. Sang, T., 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit. Rev. Biochem. Mol. Biol. 37, 121-147.
51. Savage, A.E., Miller, J.S., 2006. Gametophytic self-incompatibility in Lycium parishii (Solanaceae): allelic diversity, genealogical structure, and patterns of molecular evolution. Heredity 96, 434-444.
52. Shaw, J., Lickey, E.B., Beck, J.T., Farmer, S.B., Liu, W., Miller, J., Sirpun, K.C., Winder, C.T., Schilling, E.E., Small, R.L, 2005. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot. 92, 142-166.
53. Shaw, J., Lickey, E.B., Schilling, E.E., Small, R.L., 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 94, 275-288.
54. Small, R.L, Cronn, R.C., Wendel, J.F., 2004. Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot. 17,145-170.
55. Steele, P.R., Guisinger-Bellian, M., Linder, C.R., Jansen, R.K., 2008. Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related fa *nilies of rosids. Mol. Phylogenet. Evol. 48,1013-1026.
56. Swofford, D.L., 2002. PAUP : phylogenetic analysis using parsimony (* and other methods), version 4. Sinauer, Sunderland, Massachusetts, USA.
57. Venter, A.M., 2000. Taxonomy of the genus Lycium L (Solanaceae) in Africa., Ph.D. dissertation, University of the Free State, Bloemfontein, South Africa.
58. Wu, F., Mueller, LA., Crouzillat, D., Pétiard, V., Tanksley, S.D., 2006. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174, 1407-1420.
59. Yeung, K., Miller, J.S., Savage, A.E., Husband, B.C., Igic, B., Kohn, J.R., 2005. Association of ploidy and sexual system in Lycium californicum (Solanaceae). Evolution 59, 2048-2055.
60. Yuan, Y.W., Olmstead, R.G., 2008. Evolution and phylogenetic utility of the PHOT gene duplicates in the Verbena complex (Verbenaceae): dramatic intron size variation and footprint of ancestral recombination. Am. J. Bot. 95, 1166-1176.
61. Yuan, Y.W., Liu, C, Marx, H.E., Olmstead, R.G., 2009. The pentatricopeptide repeat (PPR) gene family, a tremendous resource for plant phylogenetic studies. New Phytol. 182, 272-283.