In recent years the growing interest in the conservation of Paraná River’s riparian forest led to the discovery of botanical novelties for Argentina. Populations of Calophyllum brasiliense Camb. (Calophyllaceae), a typically flooded lowlands species, were identified in the remaining hygrophile forest of northeast Argentina and southeast Paraguay. Deforestation and flooding, due to the construction of dams, have caused these populations to suffer intensive fragmentation. The aim of this work was to infer phylogeographic relationships among five populations of C. brasiliense, three from Argentina and two from Paraguay, which represent the southernmost points of species’ distribution. We also compared them with samples of a C. brasiliense population from Mexico, the northernmost edge of the species distribution. The chloroplast intergenic spacers petG-trnP, psbJ-petA and the trnL-UAA chloroplast intron were amplified from leaves’ DNA. A total of 2234 bp were characterized once the three regions were analyzed. The three chloroplast regions showed nucleotide differences, represented by InDels, inversions and a few SNPs; however, only the trnL intron was selected for further phylogeographic analysis due to the amount of the information obtained for all populations. Based on trnL intron, it was possible to estimate nucleotide and haplotype diversity (π = 0.00237 and Hd = 0.29600, respectively). Three haplotypes were identified, which allowed Argentinean, Paraguayan and Mexican populations to be differentiated. Based on the three haplotypes found, we discuss and propose a model for a C. brasiliense’ geographic dispersion and historical colonization routes, including an alternative new one to the well-known of the Paraná River.
| Published in | Journal of Plant Sciences (Volume 3, Issue 6) |
| DOI | 10.11648/j.jps.20150306.14 |
| Page(s) | 310-319 |
| Creative Commons |
This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited. |
| Copyright |
Copyright © The Author(s), 2015. Published by Science Publishing Group |
C. brasiliense, cpDNA, petG-trnP, psbJ-petA, trnL Intron
| [1] | Morrone JJ (2001) Biogeografía de América Latina y el Caribe. M&T – Manuales & Tesis SEA, Zaragoza. |
| [2] | Brieger FG (1969) Patterns of evolutionary and geographical distribution in neotropical orchids. Biol J Linn Soc 1(1-2):197-217. |
| [3] | Müller P (1973) The Dispersal Centers of Terrestrial Vertebrates in the Neotropical Realm: A Study in the Evolution of the Neotropical Biota and Its Native Landscapes. The Hague: Dr. W. Junk. |
| [4] | Leitão-Filho HF (1982) Aspectos taxonômicos das florestas do Estado de São Paulo. Silvicultura em São Paulo 16 A: 197-206. |
| [5] | Rodrigues RR (2001) Florestas ciliares? Uma discussão nomenclatural das formações ciliares. In: Rodrigues RR, Leitão Filho HF (ed) Matas Ciliares: conservação e recuperação, 2nd edn. Editorial Universidad de São Paulo, São Paulo. |
| [6] | Lobo PC, Joly CA (2001) Aspectos ecofisiológicos da vegetação de mata ciliar do sudeste do Brasil. In: Rodrigues RR, Leitão Filho HF(ed) Matas Ciliares: conservação e recuperação, 2nd ed. Universidad de São Paulo, São Paulo. |
| [7] | de Souza A (2006) Estrutura genética de populações naturais de Calophyllum brasiliense Camb. na bacia de Alto Río Grande. Dissertation, Universidad Federal de Lavras. |
| [8] | Fischer EA (1990) Distribuição de freqüência de clases de tamanho e estratégia reproductiva de Calophyllum brasiliense Camb. (Guttiferae) em mata ciliar na Estação Ecológica Estadual Juréia-Itatins, São Paulo. Anais do II Simpósio de ecossistemas da costa sul e sudeste brasileira, ACIESP 71-1. |
| [9] | Schiavini I (1992) Estrutura das comunidades de mata de galeria da Estação Ecológica do Panga (Uberlândia, MG). Dissertation. Universidad de Campinas, Brazil. |
| [10] | Marques MCM (1994) Estudos auto-ecológicos do guanandi (Calophyllum brasiliense Camb. Clusiaceae) em mata ciliar no município de Brotas, SP. Dissertation. Universidad de Campinas, SP, Brazil. |
| [11] | Kawaguici CB, Kageyama PY (2001) Diversidade genética de três grupos de indivíduos (adultos, jovens e plántulas) de Calophyllum brasiliense em uma população de mata de galeria. Sci For 59:131-143. |
| [12] | Reitz R, Klein RM (1978) Projeto madeira de Santa Catarina. Sellowia 30: 28-30. |
| [13] | Rodríguez ME, Cardozo A, Krauczuk E (2009) Calophyllum brasiliense (CLUSIACEAE) nuevo registro para la flora de la Argentina. Bol Soc Argent Bot 44(3-4): 361-366. |
| [14] | Gasparotto Jr A, Benzan MA, Piloto IC et al (2005) Estudo fitoquímico da atividade moluscida do Calophyllum brasiliense Camb. (Clusiaceae). Química Nova 28: 575-578. |
| [15] | Dharmaratne HRW, Tan GT, Marasinghe GP et al (2002) Inhibition of HIV-1 reverse transcriptase and HIV-1 replication by Calophyllum coumarins and xanthones. Planta Med 68: 86-87. |
| [16] | Ito C, Itoigawa M, Mishina Y et al (2002) Chemical constituents of Calophyllum brasiliense: Structure elucidation of seven new xanthones and their cancer chemopreventive activity. J Natural Products 65: 267-27. |
| [17] | Huerta-Reyes M, Basualdo MC, Lozada L et al (2004) HIV-1 Inhibition by extracts of Clusiaceae species from Mexico. Biol Pharm Bull 27: 916-920. |
| [18] | Ito C, Itoigawa M, Mishina Y et al (2003) Chemical constituents of Calophyllum brasiliense. 2. Structure of three new coumarins and cancer chemopreventive activity of 4-substituted coumarins. J Natural Products 66(3): 368-371. |
| [19] | Kimura S, Ito C, Jyoko N et al (2005) Inhibition of Leukemic Cell Growth by a Novel Anti- Cancer Drug (GUT – 70) from Calophyllum brasiliense that acts by induction of apoptosis. Int J Cancer 113: 158-165. |
| [20] | Rea A, Tempone AG, Pinto EG et al (2014) Soulamarin Isolated from Calophyllum brasiliense (Clusiaceae) Induces Plasma Membrane Permeabilization of Trypanosoma cruzi and Mytochondrial Dysfunction. PLoS Negl Trop Dis 7(12): e2556. doi: 10.1371/journal.pntd. 0002556. |
| [21] | Pires CTA, Brenzan MA, de Lima Socorro RB et al (2014) Anti-Mycobacterium tuberculosis activity and cytotoxicity of Calophyllum brasiliense Cambess. (Clusiaceae) Mem Inst Oswaldo Cruz 109(3): 324-329. |
| [22] | Giraudo AR, Povedano H (2004) Avifauna de la región biogeográfica Paranaense o Atlántica Interior de Argentina: biodiversidad, estado del conocimiento y conservación. Miscelánea 12: 331–348. |
| [23] | Galindo-Leal C, de Gusmão Câmara I (2005) Status do hotspot Mata Atlântica: uma síntese. In: Galindo-Leal C, de Gusmão Câmara I (ed) Mata Atlântica: Biodiversidade, Ameaças e Perspectivas.Center for Applied Biodiversity Science at Conservation International, Brasil. |
| [24] | Galindo-Leal C, Jacobsen TM, Langhammer PF et al (2005) Estado dos hotspots: a dinâmica da perda de biodiversidade. In: Galindo-Leal C, de Gusmão Câmara I (ed) Mata Atlântica: Biodiversidade, Ameaças e Perspectivas. Center for Applied Biodiversity Science at Conservation International, Brasil. |
| [25] | Moritz C (1994) Defining ‘Evolutionarily Significant Units’ for conservation. Tree 9(10): 373-375. |
| [26] | Percuoco CB, Bich GA, Talavera Stéfani LN et al (2014) Assessment of genetic differentiation among relict populations of Calophyllum brasiliense Camb. (Calophyllaceae) from Northeast Argentina. JBES 5(6): 87-98. |
| [27] | Ritland K, Clegg MT (1987) Evolutionary analysis of plant DNA sequences. Am Nat S74-S100. |
| [28] | Chase MW, Soltis DE, Olmstead RG et al (1993) Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann Missouri Bot Gard: 528-580. |
| [29] | Olmstead RG, Palmer JD (1994) Chloroplast DNA systematics: a review of methods and data analysis. Am J Bot 81(9): 1205-1224. |
| [30] | Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE (2014) Another look at the root of the angiosperms reveals a familiar tale. Systematic Biology 63: 368–382. |
| [31] | Petit RJ, Duminil J, Fineschi S et al (2005) Invited review: comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14 (3): 689-701. |
| [32] | Palmer JD, Herbon LA (1988) Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence. J Mol Evol 28(1-2): 87-97. |
| [33] | Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16(3): 142-147. |
| [34] | Ebert D, Peakall ROD (2009) Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol Ecol Resour 9(3): 673-690. |
| [35] | Huang S, Hwang S, Wang J et al (2004) Phylogeography of Trochodendron aralioides (Trochodendraceae) in Taiwan and its adjacent areas. J Biogeography 31: 1251–1259. |
| [36] | Shaw J, Lickey EB, Beck JT et al (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92(1): 142-166. |
| [37] | Shaw J, Lickey EB, Schilling EE et al (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(3): 275-288. |
| [38] | Huang H, Shi C, Liu Y, Mao S, Gao L (2014) Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evolutionary Biology 14: 151. |
| [39] | Köppen W, Geiger R (1954) Klima der Erde (Climate of the Earth). Wall Map 1:16 Mill. Klett-Perthes, Gotha. |
| [40] | Stange C, Prehn D, Arce-Johnson P (1998) Isolation of Pinus radiate genomic DNA suitable for RAPD analysis. Plant Mol Biol Rep 16: 1-8. |
| [41] | Palmer JD (1987) Chloroplast DNA and biosystematic uses of chloroplast DNA variation. Am Nat 130: S6-S29. |
| [42] | Shimada H, Sugiura M (1991) Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucleic Acids Res 19: 983-995. |
| [43] | Taberlet P, Gielly L, Pautou G et al (1991) Universal primers for amplifications of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105-1109. |
| [44] | Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23(10): 1289-91. |
| [45] | Untergrasser A, Cutcutache I, Koressaar T et al (2012) Primer3 - new capabilities and interfaces. Nucleic Acids Res 40(15): e115. |
| [46] | Sambrook J, Fritsch E, Maniatis T (1989) Molecular clonning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, New York. |
| [47] | Zheng Z, Schwartz L, Wagner L et al (2000) A greedy algorithm for aligning DNA sequence. J Comput Biol 7(1-2): 203-214. |
| [48] | Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98. |
| [49] | Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York. |
| [50] | Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595. |
| [51] | Fu Y (1997) Statistical tests of neutrality of mutations against population growth hitchhiking and background selection. Genetics 147(2): 915-925. |
| [52] | Rozas J, Rozas R (1995) DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data. CABIOS 11(6) 621-625. |
| [53] | Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37-48. |
| [54] | Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10): 2731-2739. |
| [55] | Grivet D, Heinze B, Vendramin GG et al (2001) Genome walking with consensus primers: application to the large single copy region of chloroplast DNA. Mol Ecol Notes 1: 345-349. |
| [56] | Shaw J, Shafer HL, Leonard OR et al (2014) Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV. Am J Bot 101(11):1987-2004. |
| [57] | Hwang SY, Lin TP, Ma CS et al (2003) Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation. Mol Ecol 12(10): 2689-2695. |
| [58] | Lihová J, Kudoh H, Marhold K (2010) Genetic structure and phylogeography of a temperate-boreal herb, Cardamine scutata (Brassicaceae), in northeast Asia inferred from AFLPs and cpDNA haplotypes. Am J Bot 97(6): 1058-1070. |
| [59] | Wheeler GL, Dorman HA, Buchanan A, Challagundla L, Wallace LE (2014) A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology. Appl Plant Sci 2: 1400059. |
| [60] | Bang SW, Chung S (2015) One size does not fit all: the risk of using amplicon size of chloroplast SSR marker for genetic relationship studies. Plant Cell Rep 34: 1681–1683. |
| [61] | Petit RJ, Vendramin GG (2007) Plant phylogeography based on organelle genes: an introduction. In: Weiss S, Ferrand N (ed) Phylogeography of southern European refugia. Springer, Netherlands. |
| [62] | Kelchner SA, Wendel JF (1996) Hairpins create minute inversions in non-coding regions of chloroplast DNA Curr Genet 30: 259-262. |
| [63] | Byrne M, MacDonald B, Coates D (2002) Phylogeographical patterns in chloroplast DNA variation within the Acacia acuminata (Leguminosae: Mimosoideae) complex in Western Australia. J Evol Biol 15: 576–587. |
| [64] | Borsch T, Quandt D (2009) Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Syst Evol 282(3-4): 169-199. |
| [65] | Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PloS one 6(5): e19254. |
| [66] | Mustapha SB, Tamarzizt HB, Baraket G, Abdallah D, Salhi-Hannachi A (2015) Cytoplasmic polymorphism and evolutionary history of plum cultivars: Insights from chloroplast DNA sequence variation of trnL-trnF spacer and aggregated trnL intron & trnL-trnF spacer. Genetics and Molecular Research 14 (2): 3964-3979. |
| [67] | Choulak S, Rhouma-Chatti S, Marzouk Z, Said K, Chatti N, Chatti K (2015) Chloroplast DNA analysis of Tunisian pistachio (Pistacia vera L.): Sequence variations of the intron trnL (UAA). Scientia Horticulturae 191: 57-64. |
| [68] | Taberlet P, Coissac E, Pompanon F et al (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35: e14. |
| [69] | Valentini A, Miquel C, Nawaz MA et al (2009) New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Mol Ecol Resour 9: 1–60. |
| [70] | Hale ML, Borland AM, Gustafsson MH (2004) Causes of Size Homoplasy Among Chloroplast Microsatellites in Closely Related Clusia Species. J Mol Evol 58: 182-190. |
| [71] | Schaal BA, Leverich WJ, Rogstad SH (1991) A comparison of methods for assessing genetic variation in plant conservation biology. In: Falk DA, Holsinger KE (ed) Genetics and Conservation of Rare Plants. Oxford University Press, New York. |
| [72] | Lu HP, Cai YW, Chen XY et al (2006) High RAPD but no cpDNA sequence variation in the endemic and endangered plant, Heptacodium miconioides Rehd. (Caprifoliaceae). Genetica 128(1-3): 409-417. |
| [73] | Pons O, Petit RJ (1995) Estimation, variance and optimal sampling of gene diversity. Theor Appl Genet 90(3-4):462-470. |
| [74] | Pluzhnikov A, Donnelly P (1996) Optimal sequencing strategies for surveying molecular genetic diversity. Genetics 144(3): 1247-1262. |
| [75] | Felsenstein J (2006) Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Mol Biol Evol 23(3): 691-700. |
| [76] | Sanjurjo MD (1994) El arary, un árbol en extinción en el Paraguay. Revista Crítica 9: 51-55. |
| [77] | Salgueiro F, Neri J, Alves-Ferreira M (2011) Phylogeographic patterns of Calophyllum brasiliense Camb. (Calophyllaceae) based on the psbA-trnH cpDNA locus. BMC Proceedings 5(Suppl 7): P17. |
APA Style
Cecilia Beatriz Percuoco, Liliana Noelia Talavera Stéfani, Manuela Edith Rodríguez, Naiké Lucía González, Juan Fernando Crivello, et al. (2015). Looking Inside Non-coding Chloroplast Regions of Calophyllum brasiliense (Calophyllaceae) to Understand Its Southernmost Population Distribution. Journal of Plant Sciences, 3(6), 310-319. https://doi.org/10.11648/j.jps.20150306.14
ACS Style
Cecilia Beatriz Percuoco; Liliana Noelia Talavera Stéfani; Manuela Edith Rodríguez; Naiké Lucía González; Juan Fernando Crivello, et al. Looking Inside Non-coding Chloroplast Regions of Calophyllum brasiliense (Calophyllaceae) to Understand Its Southernmost Population Distribution. J. Plant Sci. 2015, 3(6), 310-319. doi: 10.11648/j.jps.20150306.14
AMA Style
Cecilia Beatriz Percuoco, Liliana Noelia Talavera Stéfani, Manuela Edith Rodríguez, Naiké Lucía González, Juan Fernando Crivello, et al. Looking Inside Non-coding Chloroplast Regions of Calophyllum brasiliense (Calophyllaceae) to Understand Its Southernmost Population Distribution. J Plant Sci. 2015;3(6):310-319. doi: 10.11648/j.jps.20150306.14
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author = {Cecilia Beatriz Percuoco and Liliana Noelia Talavera Stéfani and Manuela Edith Rodríguez and Naiké Lucía González and Juan Fernando Crivello and Jorge Víctor Crisci and Carina Francisca Argüelles},
title = {Looking Inside Non-coding Chloroplast Regions of Calophyllum brasiliense (Calophyllaceae) to Understand Its Southernmost Population Distribution},
journal = {Journal of Plant Sciences},
volume = {3},
number = {6},
pages = {310-319},
doi = {10.11648/j.jps.20150306.14},
url = {https://doi.org/10.11648/j.jps.20150306.14},
eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.jps.20150306.14},
abstract = {In recent years the growing interest in the conservation of Paraná River’s riparian forest led to the discovery of botanical novelties for Argentina. Populations of Calophyllum brasiliense Camb. (Calophyllaceae), a typically flooded lowlands species, were identified in the remaining hygrophile forest of northeast Argentina and southeast Paraguay. Deforestation and flooding, due to the construction of dams, have caused these populations to suffer intensive fragmentation. The aim of this work was to infer phylogeographic relationships among five populations of C. brasiliense, three from Argentina and two from Paraguay, which represent the southernmost points of species’ distribution. We also compared them with samples of a C. brasiliense population from Mexico, the northernmost edge of the species distribution. The chloroplast intergenic spacers petG-trnP, psbJ-petA and the trnL-UAA chloroplast intron were amplified from leaves’ DNA. A total of 2234 bp were characterized once the three regions were analyzed. The three chloroplast regions showed nucleotide differences, represented by InDels, inversions and a few SNPs; however, only the trnL intron was selected for further phylogeographic analysis due to the amount of the information obtained for all populations. Based on trnL intron, it was possible to estimate nucleotide and haplotype diversity (π = 0.00237 and Hd = 0.29600, respectively). Three haplotypes were identified, which allowed Argentinean, Paraguayan and Mexican populations to be differentiated. Based on the three haplotypes found, we discuss and propose a model for a C. brasiliense’ geographic dispersion and historical colonization routes, including an alternative new one to the well-known of the Paraná River.},
year = {2015}
}
TY - JOUR T1 - Looking Inside Non-coding Chloroplast Regions of Calophyllum brasiliense (Calophyllaceae) to Understand Its Southernmost Population Distribution AU - Cecilia Beatriz Percuoco AU - Liliana Noelia Talavera Stéfani AU - Manuela Edith Rodríguez AU - Naiké Lucía González AU - Juan Fernando Crivello AU - Jorge Víctor Crisci AU - Carina Francisca Argüelles Y1 - 2015/11/19 PY - 2015 N1 - https://doi.org/10.11648/j.jps.20150306.14 DO - 10.11648/j.jps.20150306.14 T2 - Journal of Plant Sciences JF - Journal of Plant Sciences JO - Journal of Plant Sciences SP - 310 EP - 319 PB - Science Publishing Group SN - 2331-0731 UR - https://doi.org/10.11648/j.jps.20150306.14 AB - In recent years the growing interest in the conservation of Paraná River’s riparian forest led to the discovery of botanical novelties for Argentina. Populations of Calophyllum brasiliense Camb. (Calophyllaceae), a typically flooded lowlands species, were identified in the remaining hygrophile forest of northeast Argentina and southeast Paraguay. Deforestation and flooding, due to the construction of dams, have caused these populations to suffer intensive fragmentation. The aim of this work was to infer phylogeographic relationships among five populations of C. brasiliense, three from Argentina and two from Paraguay, which represent the southernmost points of species’ distribution. We also compared them with samples of a C. brasiliense population from Mexico, the northernmost edge of the species distribution. The chloroplast intergenic spacers petG-trnP, psbJ-petA and the trnL-UAA chloroplast intron were amplified from leaves’ DNA. A total of 2234 bp were characterized once the three regions were analyzed. The three chloroplast regions showed nucleotide differences, represented by InDels, inversions and a few SNPs; however, only the trnL intron was selected for further phylogeographic analysis due to the amount of the information obtained for all populations. Based on trnL intron, it was possible to estimate nucleotide and haplotype diversity (π = 0.00237 and Hd = 0.29600, respectively). Three haplotypes were identified, which allowed Argentinean, Paraguayan and Mexican populations to be differentiated. Based on the three haplotypes found, we discuss and propose a model for a C. brasiliense’ geographic dispersion and historical colonization routes, including an alternative new one to the well-known of the Paraná River. VL - 3 IS - 6 ER -
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