High levels of genetic diversity and population structure in an endemic and rare species: Implications for conservation

AoB PLANTS

Volumn 8, Issue , 2016, Pages

  Turchetto, Caroline ^a   Segatto, Ana Lúcia A ^a   Mäder, Geraldo ^a   Rodrigues, Daniele M ^a   Bonatto, Sandro L ^b   Freitas, Loreta B ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

Conservation; Genetic diversity; Microendemic; Microsatellites; Plant evolution; Plastid sequences

Indexed keywords

EID: 84986249682     PISSN: None     EISSN: 20412851     Source Type: Journal    
DOI: 10.1093/aobpla/plw002     Document Type: Article

References (96)

1. Ando T. 1996. Distribution of Petunia axillaris (Solanaceae) and its new subspecies in Argentina and Bolivia. Acta Phytotaxonomica et Geobotanica 47:19-30.
2. Ando T, Tida S, Kokubun H, Ueda Y, Marchesi E. 1995. Distribution of Petunia axillaris sensu lato in Uruguay as revealed by discriminant analysis of the live plants. Journal of the Japanese Society for Horticultural Science 64:381-391.
3. Ando T, Tsukamoto T, Akiba N, Kokubun H, Watanabe H, Ueda Y, Marchesi E. 1998. Differentiation in the degree of selfincompatibility in Petunia axillaris (Solanaceae) occurring in Uruguay. Acta Phytotaxonomica et Geobotanica 49:37-47.
4. Ando T, Nomura M, Tsukahara J, Watanabe H, Kokubun H, Tsukamoto T, Hashimoto G, Marchesi E, Kitching J. 2001. Reproductive isolation in a native population of Petunia sensu Jussieu (Solanaceae). Annals of Botany 88:403-413.
5. Ando T, Kokubun H, Watanabe H, Tanaka N, Yukawa T, Hashimoto G, Marchesi E, Suaréz E, Basualdo IL. 2005. Phylogenetic analysis of Petunia sensu Jussieu (Solanaceae) using chloroplast DNA RFLP. Annals of Botany 96:289-297.
6. Bachman S, Moat J, Hill AW, de la Torre J, Scott B. 2011. Supporting Red List threat assessments with GeoCAT: geospatial conservation assessment tool. ZooKeys 150:117-126.
7. Beerli P. 2006. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22: 341-345.
8. Beerli P. 2009. How to use migrate or why are Markov chain Monte Carlo programs difficult to use? In: Bertorelle G, Bruford MW, Hauffe HC, Rizzoli A, Vernesi C, eds. Population genetics for animal conservation, volume 17 of conservation biology. Cambridge: Cambridge University Press, 42-79.
9. Beerli P, Felsenstein J. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences of the USA 98:4563-4568.
10. Bekker RM, Kwak MM. 2005. Life history traits as predictors of plant rarity, with particular reference to hemiparasitic Orobanchaceae. Folia Geobotanica 40:231-242.
11. Bossolini E, Klahre U, Brandenburg A, Reinhardt D, Kuhlemeier C. 2011. High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato. Genome 54:327-340.
12. Brown JH. 1984. On the relationship between abundance and distribution of species. The American Naturalist 124:255-279.
13. Chen S, Matsubara K, Omori T, Kokubun H, Kodama H, Watanabe H, Hashimoto G, Marchesi E, Bullrich L, Ando T. 2007. Phylogenetic analysis of the genus Petunia (Solanaceae) based on the sequence of the HF1 gene. Journal of Plant Research 120:385-397.
14. Choo J, Juenger TE, Simpson BB. 2012. Consequences of frugivoremediated seed dispersal for the spatial and genetic structures of a neotropical palm. Molecular Ecology 21:1019-1031.
15. Cole CT. 2003. Genetic variation in rare and common plants. Annual Review of Ecology, Evolution, and Systematics 34:213-237.
16. Coppi A, Cecchi L, Mengoni A, Pustahija F, Tomović G, Selvi F. 2014. Low genetic diversity and contrasting patterns of differentiation in the two monotypic genera Halacsya and Paramoltkia (Boraginaceae) endemic to the Balkan serpentines. Flora-Morphology, Distribution, Functional Ecology of Plants 209:5-14.
17. Cornuet JM, Luikart G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001-2014.
18. Davies TJ, Smith GF, Bellstedt DU, Boatwright JS, Bytebier B, Cowling RM, Forest F, Harmon LJ, Muasya AM, Schrire BD, Steenkamp Y, Van der Bank M, Savolainen V. 2011. Extinction risk and diversification are linked in a plant biodiversity hotspot. PLoS Biology 9:e1000620.
19. Derepas A, Dulieu H. 1992. Inheritance of the capacity to transfer plastids by pollen parent in Petunia hybrida Hort. Journal of Heredity 83:6-10.
20. Dieringer D, Schlötterer C. 2003. Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes 3:167-169.
21. Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB. 1994. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the USA 91:3166-3170.
22. Di Rienzo A, Donnelly P, Toomajian C, Sisk B, Hill A, Petzl-Erler ML, Haines GK, Barch DH. 1998. Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories. Genetics 148:1269-1284.
23. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7:214.
24. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution 22:1185-1192.
25. Dun IS, Blattner FR. 1987. Charons 36 to 40: multi enzyone, high capacity, recombination deficient replacement vectors with polylinkers and polystuffers. Nucleic Acids Research 15:2677-2698.
26. Earl DA, Vonholdt BM. 2012. Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conservation Genetics Resources 4:359-361.
27. Edwards CE, Lindsay DL, Bailey P, Lance RF. 2014. Patterns of genetic diversity in the rare Erigeron lemmoni and comparison with its more widespread congener, Erigeron arisolius (Asteraceae). Conservation Genetics 15:419-428.
28. Ellis JR, Pashley CH, Burke JM, Mccauley DEM. 2006. High genetic diversity in a rare and endangered sunflower as compared to a common congener. Molecular Ecology 15:2345-2355.
29. Ellstrand NC, Elam DR. 1993. Population genetic consequences of small population size: implications for plant conservation. Annual Review of Ecology and Systematics 24:217-242.
30. Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611-2620.
31. Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10:564-567.
32. Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491.
33. Falush D, Tephens MS, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567-1587.
34. Felsenstein J. 1985. Phylogenies and the comparative method. The American Naturalist 125:1-15.
35. Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915-925.
36. Furches MS, Small RL, Furches A. 2013. Genetic diversity in three endangered pitcher plant species (Sarracenia; Sarraceniaceae) is lower than widespread congeners. American Journal of Botany 100:2092-2101.
37. Geyer CJ, Thompson EA. 1995. Annealing Markov Chain Monte Carlo with applications to ancestral inference. Journal of the American Statistical Association 90:909-920.
38. Gibson JP, Rice SA, Stucke CM. 2008. Comparison of population genetic diversity between a rare, narrowly distributed species and a common, widespread species of Alnus (Betulaceae). American Journal of Botany 95:588-596.
39. Gitzendanner MA, Soltis PS. 2000. Patterns of genetic variation in rare and widespread plant congeners. American Journal of Botany 87: 783-792.
40. Goudet J. 1995. FSTAT version 1.2: a computer program to calculate F-statistics. Journal of Heredity 86:485-486.
41. Gübitz T, Hoballah ME, Dell'olivo A, Kuhlemeier C. 2009. Petunia as a model system for the genetics and evolution of pollination syndromes. In: Gerats T, Strommer J, eds. Petunia evolutionary, developmental and physiological genetics. New York: Springer, 29-49.
42. Hamilton MB. 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8:521-523.
43. Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4:1-9.
44. Hamrick JL, Godt MJW. 1989. Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL,Weir BS, eds. Plant population genetics, breeding and genetic resources. Sunderland: Sinauer, 43-63.
45. IUCN. 2012. The IUCN Red List of Threatened Species, version 3.1. International Union for Conservation of Nature and Natural Resources. http://www.iucnredlist.org (6 January 2015).
46. Jakobsson M, Rosenberg NA. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806.
47. Jombart T. 2008. ADEGENET: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403-1405.
48. Jombart T, Devillard S, Balloux F. 2010. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11:94.
49. Kalinowski ST. 2005. HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Notes 5:187-189.
50. Kalinowski ST, Taper ML, Marshall TC. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16:1099-1106.
51. Kettle CJ, Hollingsworth PM, Jaffré T, Moran B, Ennos RA. 2007. Identifying the early genetic consequences of habitat degradation in a highly threatened tropical conifer, Araucaria nemorosa Laubenfels. Molecular Ecology 16:3581-3591.
52. Klahre U, Gurba A, Hermann K, Saxenhofer M, Bossolini E, Guerin PM, Kuhlemeier C. 2011. Pollinator choice in Petunia depends on two major genetic loci for floral scent production. Current Biology 21: 730-739.
53. Knapp S. 2011. Rarity, species richness, and the threat of extinction- are plants the same as animals? PLoS Biology 9:e1001067.
54. Kokubun H, Nakano M, Tsukamoto T, Watanabe H, Hashimoto G, Marchesi E, Bullrich L, Basualdo IL, Kao TH, Ando T. 2006. Distribution of self-compatible and self-incompatible populations of Petunia axillaris (Solanaceae) outside Uruguay. Journal of Plant Research 119:419-430.
55. Koopman MM, Carstens BC. 2010. Conservation genetic inferences in the carnivorous pitcher plant Sarracenia alata (Sarraceniaceae). Conservation Genetics 11:2027-2038.
56. Kulcheski FR, Muschner VC, Lorenz-Lemke AP, Stehmann JR, Bonatto SL, Salzano FM, Freitas LB. 2006. Molecular phylogenetic analysis of Petunia Juss. (Solanaceae). Genetica 126:3-14.
57. Lorenz-Lemke AP, Mäder G, Muschner VC, Stehmann JR, Bonatto SL, Salzano FM, Freitas LB. 2006. Diversity and natural hybridization in a highly endemic species of Petunia (Solanaceae): a molecular and ecological analysis. Molecular Ecology 15:4487-4497.
58. Lorenz-Lemke AP, Togni PD, Mäder G, Kriedt RA, Stehmann JR, Salzano FM, Bonatto SL, Freitas LB. 2010. Diversification of plant species in a subtropical region of eastern South American highlands: a phylogeographic perspective on native Petunia (Solanaceae). Molecular Ecology 19:5240-5251.
59. Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27:209-220.
60. Markham J. 2014. Rare species occupy uncommon niches. Scientific Reports 4:6012.
61. Marshall TC, Slate J, Kruuk LEB, Pemberton JM. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7:639-655.
62. Miller MP. 2005. Alleles In Space: computer software for the joint analysis of interindividual spatial and genetic information. Journal of Heredity 96:722-724.
63. Nicholas KB, Nicholas KBJ. 1997. GeneDoc: a tool for editing and annotating multiple sequences alignments. http://iubio.bio.indiana.edu/soft/molbio/ibmpc/genedoc-readme.html (6 January 2015).
64. Oleas NH, Von Wettber EJB, Negrón-Ortiz V. 2014. Population genetics of the Federally Threatened Miccosukee gooseberry (Ribes echinellum), an endemic North American species. Conservation Genetics 15:749-755.
65. Pérez de Paz J, Caujapé-Castells J. 2013. A review of the allozyme data set for the Canarian endemic flora: causes of the high genetic diversity levels and implications for conservation. Annals of Botany 111:1059-1073.
66. Phillips RD, Peakall R, Hutchinson HF, Linde CC, Xu T, Dixon KW, Hopper SD. 2014. Specialized ecological interactions and plant species rarity: the role of pollinators and mycorrhizal fungi across multiple spatial scales. Biological Conservation 169:285-295.
67. Piry S, Luikart G, Cornuet J-M. 1999. BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity 90:502-503.
68. Premoli AC, Souto CP, Allnutt TR, Newton AC. 2001. Effects of population disjunction on isozyme variation in the widespread Pilgerodendron uviferum. Heredity 87:337-343.
69. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
70. Rabinowitz D. 1981. Seven forms of rarity. In: Synge H, ed. The biological aspects of rare plant conservation. Chichester: John wiley, 205-217.
71. Rambaut A. 2008. FigTree, version 1.4: tree figure drawing tool. http://tree.bio.ed.ac.uk/software/figtree/ (6 January 2015).
72. Rambaut A, Suchard MA, Xie D, Drummond AJ. 2013. Tracer, version 1.5. http://beast.bio.ed.ac.uk/Tracer (6 January 2015).
73. Rannala B, Yang ZH. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution 43:304-311.
74. Raymond M, Rousset F. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86:248-249.
75. R Development Core Team. 2011. R: a language and environment for statistical computing. http://www.r-project.org/ (6 January 2015).
76. Reck-Kortmann M, Silva-Arias GA, Segatto ALA, Mäder G, Bonatto SL, De Freitas LB. 2014. Multilocus phylogeny reconstruction: new insights into the evolutionary history of the genus Petunia. Molecular Phylogenetics and Evolution 81:19-28.
77. Rosenberg NA. 2004. DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes 4:137-138.
78. Roy A, Frascaria N, Mackay J, Bousquet J. 1992. Segregating random amplified polymorphic DNAs (RAPDs) in Betula alleghaniensis. Theoretical and Applied Genetics 85:173-180.
79. Saitou N, Nei N. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
80. Sang T, Crawford DJ, Stuessy TF. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84:1120-1136.
81. Schwartz MW, Simberloff D. 2001. Taxon size predicts rates of rarity in vascular plants. Ecology Letters 4:464-469.
82. Segatto ALA, Cazé ALR, Turchetto C, Klahre U, Kuhlemeier C, Bonatto SL, Freitas LB. 2014a. Nuclear and plastid markers reveal the persistence of genetic identity: a new perspective on the evolutionary history of Petunia exserta. Molecular Phylogenetics and Evolution 70:504-512.
83. Segatto ALA, Ramos-Fregonezi AMC, Bonatto SL, Freitas LB. 2014b. Molecular insights into the purple-flowered ancestor of garden petunias. American Journal of Botany 101:119-127.
84. Sheth SN, Angert AL. 2014. The evolution of environmental tolerance and range size: a comparison of geographically restricted and widespread Mimulus. Evolution 68:2917-2931.
85. Slatyer RA, Hirst M, Sexton JP. 2013. Niche breadth predicts geographical range size: a general ecological pattern. Ecology Letters 16:1104-1114.
86. Stehmann JR, Lorenz-Lemke AP, Freitas LB, Semir J. 2009. The genus Petunia. In: Gerats T, Strommer J, eds. Petunia evolutionary, developmental and physiological genetics. New York: Springer, 1-28.
87. Stehmann JR, Semir J. 2005. New species of Calibrachoa and Petunia (Solanaceae) from subtropical South America. Systematic Botany Monographs 104:341-348.
88. Tajima F. 1989. Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
89. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis. Version 6.0. Molecular Biology and Evolution 30:2725-2729.
90. Turchetto C, Fagundes NJR, Segatto ALA, Kuhlemeier C, Solís Neffa VG, Speranza PR, Bonatto SL, Freitas LB. 2014a. Diversification in the South American Pampas: the genetic and morphological variation of the widespread Petunia axillaris complex (Solanaceae). Molecular Ecology 23:374-389.
91. Turchetto C, Segatto ALA, Telles MPC, Diniz-Filho JAF, Freitas LB. 2014b. Infraspecific classification reflects genetic differentiation in the widespread Petunia axillaris complex: a comparison among morphological, ecological, and genetic patterns of geographic variation. Perspectives in Plant Ecology, Evolution and Systematics 16:75-82.
92. Turchetto C, Lima JS, Rodrigues DM, Bonatto SL, Freitas LB. 2015a. Pollen dispersal and breeding structure in a hawkmothpollinated Pampa grasslands species Petunia axillaris (Solanaceae). Annals of Botany 115:939-948.
93. Turchetto C, Segatto ALA, Beduschi J, Bonatto SL, Freitas LB. 2015b. Genetic differentiation and hybrid identification using microsatellite markers in closely related wild species. AoB PLANTS 7: plv084; doi:10.1093/aobpla/plv084
94. Venail J, Dell'olivo A, Kuhlemeier C. 2010. Speciation genes in the genus Petunia. Philosophical Transactions of the Royal Society B: Biological Sciences 365:461-468.
95. Wang ZF, Hamrick JL, Godt MJW. 2004. High genetic diversity in Sarracenia leucophylla (Sarraceniaceae), a carnivorous wetland herb. Journal of Heredity 95:234-243.
96. Watanabe H, Ando T, Tsukamoto T, Hashimoto G, Marchesi E. 2001. Cross-compatibility of Petunia exserta with other petunia taxa. Journal of the Japanese Society for Horticultural Science 70: 33-40.