Out of America to Africa or Asia: Inference of dispersal histories using nuclear and plastid DNA and the S-RNase self-incompatibility locus

Molecular Biology and Evolution

Volumn 28, Issue 1, 2011, Pages 793-801

  Miller, Jill S ^a   Kamath, Ambika ^a   Damashek, Julian ^a,b   Levin, Rachel A ^a  

^a AMHERST COLLEGE   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Bayesian estimation of species trees (BEST); biogeography; Lycium; molecular dating; S RNase; self incompatibility; Solanaceae

Indexed keywords

CELL NUCLEUS DNA; NUCLEAR CONSERVED ORTHOLOG SET II; NUCLEAR GRANULE BOUND STARCH SYNTHASE I; PLANT DNA; RIBONUCLEASE; SPACER DNA; STARCH SYNTHASE; UNCLASSIFIED DRUG;

AFRICA; ALLELE; ARTICLE; ASIA; ASIAN; BIOGEOGRAPHY; BOTTLENECK POPULATION; ENZYME ISOLATION; GENE LOCUS; GENEALOGY; LYCIUM; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PLASTID; POPULATION DISPERSAL; SELF INCOMPATIBILITY; WESTERN HEMISPHERE;

AFRICA; AMERICAS; ASIA; BIOLOGICAL EVOLUTION; CELL NUCLEUS; DNA, PLANT; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASTIDS; POLLINATION; RIBONUCLEASES; SEQUENCE ANALYSIS, DNA; SOLANACEAE;

LYCIUM; SOLANACEAE;

EID: 78650440382     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq253     Document Type: Article

References (56)

1. Aguilar R, Bernardello G. 2001. The breeding system of Lycium cestroides: a Solanaceae with ovarian self-incompatibility. Sex Plant Reprod. 13:273-277.
2. Aguilar A, Roemer G, Debenham S, Binns M, Garcelon D, Wayne RK. 2004. High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. Proc Natl Acad Sci USA. 101:3490-3494.
3. Benton MJ. 1993. The fossil record 2. London: Chapman and Hall.
4. Bianchi MB, Gibbs PE, Prado DE, Vesprini JL. 2000. Studies on the breeding systems of understorey species of a Chaco woodland in NE Argentina. Flora 195:339-348.
5. Bos DH, Gopurenko D, Williams RN, DeWoody JA. 2008. Inferring population history and demography using microsatellites, mitochondrial DNA, and major histocompatibility complex (MHC) genes. Evolution 62:1458-1468.
6. Castric V, Bechsgaard J, Schierup MH, Vekemans X. 2008. Repeated adaptive introgression at a gene under multiallelic balancing selection. PLoS Genet. 4:e1000168.
7. Clarkson JJ, Lim KY, Kovarik A, Chase MW, Knapp S, Leitch AR. 2005. Long-term genome diploidization in allopolyploid Nicotiana-section Repandae(Solanaceae). New Phytol. 168:241-252.
8. de Bellocq JG, Delarbre C, Gachelin G, Morand S. 2005. Allelic diversity at the M hc-DQA locus of woodmouse populations (Apodemus sylvaticus) present in the islands and mainland of the northern Mediterranean. Glob Ecol Biogeogr. 14:115-122.
9. Dillon MO, Tu T, Xie L, Quipuscoa Silvestre V, Wen J. 2009. Biogeographic diversification in Nolana (Solanaceae), a ubiquitous member of the Atacama and Peruvian Deserts along the western coast of South America. J Syst Evol. 47:457-476.
10. Drummond AJ, Ho SYW, Rawlence N, Rambaut A. 2007. A rough guide to BEAST 1.4. [cited 2010 Oct 1]. Available from: http:// beast-mcmc.googlecode.com/ files/BEAST14-Manual-6July2007. pdf.
11. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
12. Hartley AJ, Chong G. 2002. Late Pliocene age for the Atacama Desert: implications for the desertification of western South America. Geology 30:43-46.
13. Igic B, Bohs L, Kohn JR. 2004. Historical inferences from the self-incompatibility locus. New Phytol. 161:97-105.
14. Igic B, Lande R, Kohn JR. 2008. Loss of self-incompatibility and its evolutionary consequences. Int J Plant Sci. 169:93-104.
15. Igic B, Smith WA, Robertson KA, Schaal BA, Kohn JR. 2007. Studies of self-incompatibility in wild tomatoes: I. S-allele diversity in Solanum chilense Dun. (Solanaceae). Heredity. 99:553-561.
16. Ioerger TR, Clark AG, Kao T. 1990. Polymorphism at the self-incompatibility locus in Solanaceae predates speciation. Proc Natl Acad Sci USA. 87:9372-9375.
17. Ioerger TR, Gohlke JR, Xu B, Kao TH. 1991. Primary structural features of the self-incompatibility protein in Solanaceae. Sex Plant Reprod. 4:81-87.
18. Lawrence MJ. 2000. Population genetics of the homomorphic self-incompatibility polymorphisms in flowering plants. Ann Bot. 85:221-226.
19. Levin RA, Miller JS. 2005. Relationships within tribe Lycieae (Solanaceae): paraphyly of Lycium and multiple origins of gender dimorphism. Am J Bot. 92:2044-2053.
20. Levin RA, Shak JR, Bernardello G, Venter AM, Miller JS. 2007. Evolutionary relationships in tribe Lycieae (Solanaceae). Acta Hortic. 745:225-239.
21. Levin RA, Whelan A, Miller JS. 2009. The utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference in Lycium (Solanaceae). Mol Phylogenet Evol. 53:881-890.
22. Liu L. 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics. 24:2542-2543.
23. Lu Y. 2001. Roles of lineage sorting and phylogenetic relationship in the genetic diversity at the self-incompatibility locus of Solanaceae. Heredity 86:195-205.
24. Maddison WP, Maddison DR. 2009. Mesquite: a modular system for evolutionary analysis. Version 2.72. [cited 2010 Oct 1]. Available from: http://mesquiteproject.org.
25. Miller JS, Kamath A, Levin RA. 2009. Do multiple tortoises equal a hare? The utility of nine noncoding plastid regions for species-level phylogenetics in tribe Lycieae (Solanaceae). Syst Bot. 34:796-804.
26. Miller JS, Levin RA, Feliciano NM. 2008. A tale of two continents: Baker's rule and the maintenance of self-incompatibility in Lycium (Solanaceae). Evolution 62:1052-1065.
27. Miller JS, Venable DL. 2002. The transition to gender dimorphism on an evolutionary background of self-incompatibility: an example from Lycium (Solanaceae). Am J Bot. 89:1907-1915.
28. Newbigin E, Uyenoyama MK. 2005. The evolutionary dynamics of self-incompatibility systems. Trends Genet. 21:500-504.
29. Olmstead RG, Bohs L, Migid HA, Santiago-Valentin E, Garcia VF, Collier SM. 2008. A molecular phylogeny of the Solanaceae. Taxon 57:1159-1181.
30. Paape T, Igic B, Smith SD, Olmstead R, Bohs L, Kohn JR. 2008. A 15-myr-old genetic bottleneck. Mol Biol Evol. 25:655-663.
31. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
32. Rambaut A. 1996-2002. Se-Al: sequence alignment editor. Version 2.0a11. [cited 2010 Oct 1]. Available from: http://tree.bio.ed .ac.uk/software/seal/.
33. Rambaut A. 2006-2009. FigTree: tree figure drawing tool. Version 1.3.1. [cited 2010 Oct 1]. Available from: http://tree.bio.ed.ac.uk/ software/figtree/
34. Rambaut A, Drummond AJ. 2003-2009. Tracer: MCMC trace analysis tool. Version 1.5.0. [cited 2010 Oct 1]. Available from: http://tree.bio.ed.ac.uk/ software/tracer/.
35. Richman AD, Kohn JR. 1999. Self-incompatibility alleles from Physalis: implication for historical inference from balanced genetic polymorphisms. Proc Natl Acad Sci USA. 96:168-172.
36. Richman AD, Kohn JR. 2000. Evolutionary genetics of self-incompatibility in the Solanaceae. Plant Mol Biol. 42:169-179.
37. Ronquist F, Huelsenbeck JP. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
38. Sanderson MJ. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302.
39. Savage AE, Miller JS. 2006. Gametophytic self-incompatibility in Lycium parishii (Solanaceae): allelic diversity, genealogical structure, and patterns of molecular evolution at the S-RNase locus. Heredity 96:434-444.
40. Schnabel A, Wendel JF. 1998. Cladistic biogeography of Gleditsia (Leguminosae) based on ndhF and rpl16 chloroplast gene sequences. Am J Bot. 85:1753-1765.
41. Spies JJ, Minne L, Venter HJT, Venter AM. 1993. A cytogenetic study of the functionally dioecious species in the genus Lycium (Solanaceae). S Afr J Bot. 59:535-540.
42. Surbanovski N, Tobutt KR, Konstantinovic M, Maksimovic V, Sargent DJ, Stevanovic V, Ortega E, Boskovic RI. 2007. Self-incompatibility of Prunus tenella and evidence that reproduc-tively isolated species of Prunus have different SFB alleles coupled with an identical S-RNase allele. Plant J. 50:723-734.
43. Sutherland BG, Tobutt KR, Robbins TP. 2008. Trans-specific S-RNase and SFB alleles in Prunus self-incompatibility haplotypes. Mol Genet Genomics. 279:95-106.
44. Swofford DL. 2002. PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sunderland (MA): Sinauer Associates.
45. Takebayashi N, Brewer PB, Newbigin E, Uyenoyama MK. 2003. Patterns of variation within self-incompatibility loci. Mol Biol Evol. 20:1778-1794.
46. Uyenoyama MK, Zhang Y, Newbigin E. 2001. On the origin of self-incompatibility haplotypes: transition through self-compatible intermediates. Genetics 157:1805-1817.
47. Venter AM. 2000. Taxonomy of the genus Lycium L. (Solanaceae) in Africa. [Ph.D. dissertation]. [Bloemfontein (South Africa)]: University of the Orange Free State.
48. Vieira J, Fonseca NA, Santos RAM, Habu T, Tao R, Vieira CP. 2008. The number, age, sharing and relatedness of S-locus specificities in Prunus. Genet Res. 90:17-26.
49. Vieira J, Morales-Hojas R, Santos RAM, Vieira CP. 2007. Different positively selected sites at the gametophytic self-incompatibility pistil S-RNase gene in the Solanaceae and Rosaceae (Prunus, Pyrus, and Malus). J Mol Evol. 65:175-185.
50. Wikström N, Savolainen V, Chase MW. 2001. Evolution of the angiosperms: calibrating the family tree. Proc R Soc B. 268: 2211-2220.
51. Wong WSW, Yang Z, Goldman N, Nielsen R. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051.
52. Wright S. 1939. The distribution of self-sterility alleles in populations. Genetics 24:538-552.
53. Yang Z. 2007. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
54. Yang Z, Nielsen R, Goldman N, Pedersen AM. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
55. Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol. 7:203-214.
56. Zhang ZY, Lu AM, D'Arcy WG. 1994. Solanaceae. In: Wu ZY, Raven PH, editors. Flora of China. Vol. 17. St. Louis (MO): Missouri Botanical Garden Press. p.300-332