Plastid DNA variation of the endemic species Oxytropis glandulosa Turcz. (Fabaceae)

Plastid DNA variation of the endemic species Oxytropis glandulosa Turcz. (Fabaceae)

Oxytropis glandulosaTurcz. (Fabaceae) is a rare perennial plant endemic to Buryatia (Russia). We sequenced three intergenicspacers (thepsbA trnH ,trnL trnF , andtrnS trnG ) of chloroplast DNA (cpDNA) in specimens of four populations from two geographicregions (Barguzin and Yeravna depressions) within this species range. The levels of haplotype and nucleotide diversity varied in the rangeof 0.133 0.911 and 0.0002 0.0059, respectively. The highest values of these parameters are characteristic of populations located in theBarguzin depression. Variable sites detected within the intergenic spacers allowed the identification of eleven haplotypes; nine of themwere found in the populations from the Barguzin depression and only two haplotypes were found in the populations from the Yeravnadepression. No common haplotypes for all four populations were found. A high level of population differentiation ( Φ ST= 0.758, P

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  • Artyukova EV, Kholina AB, Kozyrenko MM, Zhuravlev YuN (2004). Analysis of genetic variation in rare endemic species Oxytropis chankaensis Jurtz. (Fabaceae) using RAPD markers. Russ J Genet 40: 710-716.
  • Artyukova EV, Kozyrenko MM (2012). Phylogenetic relationships of Oxytropis chankaensis Jurtz. and Oxytropis oxyphylla (Pall.) DC. (Fabaceae) inferred from the data of sequencing of the ITS region of the nuclear ribosomal DNA operon and intergenic spacers of the chloroplast genome. Russ J Genet 48: 163-169.
  • Artyukova EV, Kozyrenko MM, Boltenkov EV, Gorovoy PG (2014). One or three species in Megadenia (Brassicaceae): insight from molecular studies. Genetica 142: 337-350.
  • Artyukova EV, Kozyrenko MM, Kholina AB, Zhuravlev YuN (2011). High chloroplast haplotype diversity in the endemic legume Oxytropis chankaensis may result from independent polyploidization events. Genetica 139: 221-232.
  • Bandelt HJ, Forster P, Röhl A (1999). Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37-48.
  • Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker K, Ingram KK, Das I (2006). Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22: 148-155.
  • Bonfeld JK, Smith KF, Staden R (1995). A new DNA sequence assembly program. Nucleic Acids Res 23: 4992-4999.
  • Britton MN, Hedderson TA, Verboom GA (2014). Topography as a driver of cryptic speciation in the high elevation cape sedge Tetraria triangularis (Boeck.) C. B. Clarke (Cyperaceae: Schoeneae). Mol Phylogenet Evol 77: 96-109.
  • Corander J, Marttinen P, Sirén J, Tang J (2008). Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9: 539.
  • De Queiroz K (2007). Species concepts and species delimitation. Syst Biol 56: 879-886.
  • Doyle JJ, Doyle JL, Rauscher JT, Brown AHD (2004). Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans ( Glycine subgenus Glycine ). New Phytol 161: 121-132.
  • Ellstrand NC, Elam DR (1993). Population genetic consequences of small population size: implication for plant conservation. Annu Rev Ecol Syst 24: 217-242.
  • Eriksson JS, Blanco-Pastor JL., Sousa F, Bertrand YJK, Pfeil BE (2017). A cryptic species produced by autopolyploidy and subsequent introgression involving Medicago prostrata (Fabaceae). Mol Phylogenet Evol 107: 367-381.
  • Excoffier L, Lischer HEL (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564-567.
  • Fujii N, Ueda K, Watano Y, Shimizu T (2001). Two genotypes of Pedicularis chamissonis (Scrophulariaceae) distributed at Mt. Gassan, Japan: additional genetic and morphological studies. J Plant Res 114: 133-140.
  • Gielly L, Taberlet P (1994). The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Mol Biol Evol 11: 769-777.
  • Gonzales E, Hamrick JL, Chang SM (2008). Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum . J Biogeogr 35: 844-852.
  • Gouy M, Guindon S, Gascuel O (2010). SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27: 221-224.
  • Govindaralulu R, Hughes CE, Bailey CD (2011). Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation. Am J Bot 98: 2049-2063.
  • Guo YP, Tong XY, Wang LW, Vogl C (2013). A population genetic model to infer allotetraploid speciation and long-term evolution applied to two yarrow species. New Phytol 199: 609-621.
  • Kholina AB, Kozyrenko MM, Artyukova EV, Sandanov DV, Andrianova EA (2016). Phylogenetic Relationships of the species of Oxytropis DC. subg. Oxytropis and Phacoxytropis (Fabaceae) from Asian Russia inferred from the nucleotide sequence analysis of the intergenic spacers of the chloroplast genome. Russ J Genet 52: 780-793.
  • Konichenko ES, Selyutina IYu (2013). Chromosome numbers of rare and endemic species of the genus Oxytropis (Fabaceae). Botanicheskii Zhurnal 98: 647-651 (in Russian with abstract in English).
  • Kozyrenko MM, Artyukova EV, Zhuravlev YuN (2009). Independent species status of Iris vorobievii N.S. Pavlova, Iris mandshurica Maxim., and Iris humilis Georgi (Iridaceae): Evidence from the nuclear and chloroplast genomes. Russ J Genet 45: 1394-1402.
  • Lewke Bandara N, Papini A, Mosti S, Brown T, Smith LMJ (2013). A phylogenetic analysis of genus Onobrychis and its relationships within the tribe Hedysareae (Fabaceae). Turk J Bot 37: 981-992.
  • Librado P, Rozas J (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451- 1452.
  • Liu J, Moller M, Provan J, Gao LM, Poudel RC, Li DZ (2013). Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot. New Phytol 199: 1093-1108.
  • Ma XG, Zhao C, Wang CB, Liang QL, He XJ (2015). Phylogenetic analyses and chromosome counts reveal multiple cryptic species in Bupleurum commelynoideum (Apiaceae). J Syst Evol 53: 104-116.
  • Malyshev LI (2008). Diversity of the genus Oxytropis in the Asian part of Russia. Turczaninowia 11: 5-141 (in Russian with abstract in English). Martin E, Karaman Erkul S, Aytaç Z (2015). Karyological studies on Oxytropis (Fabaceae) from Turkey. Caryologia 68: 357-362.
  • Peshkova GA (2008). Glandulous locoweed – Oxytropis glandulosa Turcz. In: Trutnev YuP, editor. Red Data Book of Russian Federation (Plants and Fungi). Moscow, Russia: KMK Scientific Press, p. 253 (in Russian).
  • Pleines T, Jakob SS, Blattner FR (2009). Application of non-coding DNA regions in intraspecific analyses. Plant Syst Evol 282: 281- 294.
  • Posada D, Crandall KA (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
  • Ramos ACS, Lemos-Filho JP, Ribeiro RA, Santos FCR, Lovato MB (2007). Phylogeography of the tree Hymenaea stigonocarpa (Fabaceae: Caesalpinioideae) and the influence of quaternary climate changes in the Brazilian Cerrado. Ann Bot-London 100: 1219-1228.
  • Raubeson LA, Jansen RK (2005). Chloroplast genomes of plants. In: Henry RJ, editor. Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants. Cambridge, MA, USA: CABI, pp. 45-68.
  • Ribeiro RA, Lemos-Filho JP, Ramos ACS, Lovato MB (2011). Phylogeography of the endangered rosewood Dalbergia nigra (Fabaceae): insights into the evolutionary history and conservation of the Brazilian Atlantic Forest. Heredity 106: 46-57.
  • Sandanov DV, Chimitov DG (2013). Glandulous locoweed – Oxytropis glandulosa Turcz. In: Pronin NM, editor. Red Data Book of Republic of Buryatia: Rare and Endangered Species of Animals, Plants and Fungi. 3rd ed. Ulan-Ude, Russia: Buryat Scientific Center SB RAS Publisher, p. 526 (in Russian).
  • Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (2005). The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92: 142-166.
  • Shneyer VS, Kotseruba VV (2015). Cryptic species in plants and their detection by genetic differentiation between populations. Russ J Genet Appl Res 5: 528-541.
  • Simmons MP, Ochoterena H (2000). Gaps as characters in sequence- based phylogenetic analyses. Syst Biol 49: 369-381.
  • Soltis DE, Buggs RJA, Doyle JJ, Soltis PS (2010). What we still don’t know about polyploidy. Taxon 59: 1387-1403.
  • Soltis DE, Soltis PS, Schemske DW, Hancock JF, Thompson JN, Husband BC, Walter S, Judd WS (2007). Autopolyploidy in angiosperms: have we grossly underestimated the number of species? Taxon 56: 13-30.
  • Sotuyo S, Delgado-Salinas A, Chase MW, Lewis JP, Oyama K (2007). Cryptic speciation in the Caesalpinia hintonii complex (Leguminosae: Caesalpinioideae) in a seasonally dry Mexican Forest. Ann Bot-London 100: 1307-1314.
  • Su Z, Pan B, Zhang M, Shi W (2016). Conservation genetics and geographic patterns of genetic variation of endangered shrub Ammopiptanthus (Fabaceae) in northwestern China. Conserv Genet 17: 485-496.
  • Swofford DL (2002). PAUP* Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.0b10. Sunderland, MA, USA: Sinauer Associates, Inc.
  • Taberlet P, Gielly L, Pautou G, Bouvet J (1991). Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105-1109.
  • Wang FY, Gong X, Hu CM, Hao G (2008). Phylogeography of an alpine species Primula secundiflora inferred from the chloroplast DNA sequence variation. J Syst Evol 46: 13-22.
  • Wojciechowski MF (2005). Astragalus (Fabaceae): a molecular phylogenetic perspective. Brittonia 57: 382-396.
  • Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Riesebergb LH (2009). The frequency of polyploid speciation in vascular plants. P Natl Acad Sci USA 106: 13875-13879.
  • Zhukova PG (1983). Chromosome numbers of some species of the Family Fabaceae from North-East Asia. Botanicheskii Zhurnal 68: 925-932 (in Russian with abstract in English).