Habibollah IJBARI, Masoud SHEIDAI, Ahmad-reza MEHRABIAN, Zahra NOORMOHAMMADI

K-means clustering and STRUCTURE analyses of genetic diversity in Tamarix L. accessions

Tamarix L. accessions were collected from Sistan and Baluchestan Province of Iran, covering an area of about 60 km located in the southeast of Iran. The present investigation was performed to study the genetic structure of Tamarix populations in this province and present some information about gene flow among these populations. Forty-two tree specimens were randomly collected and studied for molecular and morphological diversity. Based on morphological descriptions we recognized 3 species that were confirmed by detailed morphometric and genetic analysis. The studied tree specimens were separated in 3 distinct clusters by UPGMA clustering and principal coordinate analysis and multidimensional scaling ordination methods. Clustering of molecular (ISSR) data showed some degree of genetic variation within each species. Similarly, STRUCTURE analysis and K-means clustering revealed some degree of genetic admixture among the studied accessions. NeighborNet and reticulograms revealed some degree of gene exchange among the studied populations. AMOVA and the Hickory test showed significant genetic differences of the studied populations and the Mantel test showed significant correlation between genetic distance and geographical distance of these populations.

Anahtar Kelimeler:

Genetic variation, species relationship, Tamarix

K-means clustering and STRUCTURE analyses of genetic diversity in Tamarix L. accessions

Keywords:

Genetic variation, species relationship, Tamarix,

PDF

___

Allred KW (2002). Identification and taxonomy of Tamarix (Tamaricaceae) in New Mexico. Desert Plants 18: 26–29.
Baum BR (1967). Introduced and naturalized tamarisks in the United States and Canada [Tamaricaceae]. Baileya 15: 19–25.
Baum BR (1978). The Genus Tamarix. Jerusalem, Israel: Israel Academy of Sciences and Humanities.
Brotherson JD, Winkel V (1986). Habitat relationships of saltcedar (Tamarix ramosissima). The Great Basin Natural 46: 535–541.
Bryant D, Moulton V (2004). NeighborNet: an agglomerative algorithm for the construction of planar phylogenetic networks. Mol Biol Evol 21: 255–265.
Buerkle CA (2005). Maximum-likelihood estimation of a hybrid index based on molecular markers. Mol Ecol Notes 5: 684–687.
Caliński R, Harabasz J (1974). A dendrite method for cluster analysis. Commun Stat 3: 1–27.
Earl DA, von Holdt BM (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resources 4: 359–361.
Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611–2620.
Falush D, Stephens M, Pritchard JK (2007). Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7: 574–578.
Friedman JM, Roelle JE, Cade BS (2012). Genetic and environmental influences on cold hardiness of native and introduced riparian trees. In: Haase DL, Pinto JR, Riley LE, technical coordinators. National Proceedings: Forest and Conservation Nursery Associations, 2011. Fort Collins, CO, USA: USDA Forest Service, Rocky Mountains Research Station, pp. 82–85.
Gaskin JF, Kazmer DJ (2009). Introgression between invasive saltcedars (Tamarix chinensis and T. ramosissima) in the USA. Biol Invasions 11: 1121–1130.
Gaskin JF, Schaal BA (2002) Hybrid Tamarix widespread in US invasion and undetected in native Asian range. P Natl Acad Sci USA 99:11256–11259.
Gaskin JF, Shafroth PB (2005) Hybridization of Tamarix ramosissima and T. chinensis (saltcedars) with T. aphylla (athel) (family Tamaricaceae) in the southwestern USA determined from DNA sequence data. Madrono 52: 1–10.
Gilpin ME, Soule ME (1986). Minimum variable populations: process of species extinction. In: Soule ME, editor. Conservation Biology: The Science of Scarcity and Diversity. Sunderland, MA, USA: Sinauer Associates, pp. 19–34.
Gitzendanner MA, Soltis PS (2000). Patterns of genetic variation in rare and widespread plant congeners. Am J Bot 87: 783–792.
Godt MJW, Hamrick JL (1998). Allozyme diversity in the endangered pitcher plant Sarracenia rubra ssp. alabamensis (Sarraceniaceae) and its close relative S. rubra ssp. rubra. Am J Bot 85: 802–810.
Hamrick JL, Godt MJW (1996a). Conservation genetics of endemic plant species. In: Avise JL, Hamrick JL, editors. Conservation Genetics Case Histories from Nature. London, UK: Chapman and Hall, pp. 281–304.
Hamrick JL, Godt MJW (1996b). Effects of life history traits on genetic diversity in plant species. Philos Trans R Soc Lond B 351: 1291–1298.
Hedrick PW (2005). A standardized genetic differentiation measure. Evol 59: 1633–1658.
Jost L (2008). GST and its relatives do not measure differentiation. Mol Ecol 17: 4015–4026.
Holsinger KE, Mason-Gamer RJ, Whitton J (1999). Genes, demes, and plant conservation. In: Landweber LF, Dobson AP, editors. Genetics and the Extinction of Species: DNA and the Conservation of Biodiversity. Princeton, NJ, USA: Princeton University Press, pp. 23–46.
Huson DH, Bryant D (2006). Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267.
Križman M, Jakse J, Baricevic D, Javornik B, Prosek M (2006) Robust CTAB-activated charcoal protocol for plant DNA extraction. Acta Agri Slov 87: 427–433.
Lande R (1999). Extinction risks from anthropogenic, ecological, and genetic factors. In: Landweber LF, Dobson AP. editors. Genetics and the Extinction of Species: DNA and the Conservation of Biodiversity. Princeton, NJ, USA: Princeton University Press, pp. 1–22.
Legendre P, Makarenkov V (2002). Reconstruction of biogeographic and evolutionary networks using reticulograms. Syst Biol 51: 199–216.
McClintock E (1951). Studies in California ornamental plants: 3. The tamarisks. J California Hort Soci 12: 76–83.
Meirmans PG, Van Tienderen PH (2004). GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4: 792–794.
Moerman DE (1998). Native American Ethno-Botany. Portland, OR, USA: Timber Press.
Parsons WT, Cuthbertson EG (1992). Noxious Weeds of Australia. Melbourne, Australia: Inkata Press, pp. 620–622.
Peakall R, Smouse PE (2006). GENALEX 6: Genetic Analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288–295.
Podani J (2000). Introduction to the Exploration of Multivariate Data (English translation). Leiden, the Netherlands: Backhuys.
Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype Data. Genetics 155: 945– 959.
Rodman J (1989). Reflections on tamarisk bashing. In: Hughes HG, Bonnicksen TM, editors. Papers from the First Annual Meeting of the Society for Ecological Restoration. Madison, WI, USA: Society for Ecological Restoration, pp. 59–68.
Schwarz GE (1978). Estimating the dimension of a model. Ann Stat 6: 461–464.
Sexton JP, McKay JK, Sala A (2002). Plasticity and genetic diversity may allow saltcedar to invade cold climates in North America. Ecol Appl 12: 1652–1660.
Stevens LE (1989) The status of ecological research on tamarisk (Tamaricaceae: Tamarix ramosissima) in Arizona. In: Kunzmann MR, Johnson RR, Bennett P, technical coordinators. Tamarisk Control in Southwestern United States: Proceedings, 2–3 September 1987. Tucson, AZ, USA: National Park Service, pp. 99–105.
Sudbrock A (1993). Tamarisk control-fighting back: an overview of the invasion, and a low-impact way of fighting it., Restor Manage Notes 11: 31–34.
Tykač J (1990). The Illustrated Guide to Ornamental Shrubs. London, UK: Treasure Press.
Weising K, Nybom H, Wolf K, Kahl G (2005). DNA Finger Printing in Plants. 2nd ed. Boca Raton, FL, USA: CRC Press.