Significant population genetic structure detected for a new and highly restricted species of Atriplex (Chenopodiaceae) from Western Australia, and implications for conservation management

Australian Journal of Botany

Volumn 60, Issue 1, 2012, Pages 32-41

  Clarke, Laurence J ^a   Jardine, Duncan I ^a   Byrne, Margaret ^b   Shepherd, Kelly ^b   Lowe, Andrew J ^a,c  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b Crop Variety Testing Group   (Australia)

^c State Herbarium of South Australia   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; CONSERVATION GENETICS; CONSERVATION MANAGEMENT; DICOTYLEDON; GENETIC MARKER; GENETIC STRUCTURE; GENETIC VARIATION; GEOGRAPHICAL DISTRIBUTION; MINERALIZATION; NEW SPECIES; SPECIES CONSERVATION; TAXONOMY; URANIUM;

AUSTRALIA; WESTERN AUSTRALIA;

AMARANTHACEAE; ATRIPLEX; ATRIPLEX NUMMULARIA; SARCOBATUS VERMICULATUS;

EID: 84857831860     PISSN: 00671924     EISSN: None     Source Type: Journal    
DOI: 10.1071/BT11223     Document Type: Article

References (53)

1. Allendorf FW, Luikart G (2007) 'Conservation and the genetics of populations.' (Blackwell Publishing: Malden, MA)
2. Becker U, Colling G, Dostal P, Jakobsson A, Matthies D (2006) Local adaptation in the monocarpic perennial Carlina vulgaris at different spatial scales across Europe. Oecologia 150, 506-518. doi:10.1007/s00442-006-0534-9 (Pubitemid 44748907)
3. BesnardG, HenryP, Wille L, Cooke D, Chapuis E(2007) On the origin of the invasive olives (Olea europaea L., Oleaceae). Heredity 99, 608-619. doi:10.1038/sj.hdy.6801037 (Pubitemid 350146919)
4. Blackwell WH, Powell MJ (1981) A preliminary note on pollination in the Chenopodiaceae. Annals of the Missouri Botanical Garden 68, 524-526. doi:10.2307/2398886
5. Broadhurst LM, Lowe A, Coates DJ, Cunningham SA, McDonald M, Vesk PA, Yates C (2008) Seed supply for broadscale restoration: maximising evolutionary potential. Evolutionary Applications 1, 587-597.
6. Bruvo R,Michiels NK, D'Souza TG, Schulenburg H(2004)Asimple method for the calculation of microsatellite genotype distances irrespective of ploidy level. Molecular Ecology 13, 2101-2106. doi:10.1111/j.1365-294X.2004.02209.x (Pubitemid 38847612)
7. Butcher PA, McNee SA, Krauss SL (2009) Genetic impacts of habitat loss on the rare ironstone endemic Tetratheca paynterae subsp. paynterae. Conservation Genetics 10(6), 1735-1746. doi:10.1007/s10592-008-9775-y
8. Clark LV, Jasieniuk M (2011) POLYSAT: an R package for polyploid microsatellite analysis. Molecular Ecology Resources 11(3), 562-566. doi:10.1111/j.1755-0998.2011.02985.x
9. Clarke LJ, Mackay DA, Whalen MA (2011) Isolation of microsatellites from Baumea juncea (Cyperaceae). Conservation Genetics Resources 3, 113-115. doi:10.1007/s12686-010-9303-5
10. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Heled J, Kearse M, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2010) Geneious version5.3. Availableathttp://www.geneious.com [Verified 13 December 2012]
11. 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.
12. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4), 783-791. doi:10.2307/2408678
13. Frankham R (2005) Genetics and extinction. Biological Conservation 126, 131-140. doi:10.1016/j.biocon.2005.05.002 (Pubitemid 41113239)
14. Frankham R, Ballou JD, Eldridge MDB, Lacy RC, Ralls K, Dudash MR, Fenster CB (2011) Predicting the probability of outbreeding depression. Conservation Biology 25(3), 465-475. doi:10.1111/j.1523-1739.2011.01662.x
15. Galloway LF, Fenster CB (2000) Population differentiation in an annual legume: local adaptation. Evolution 54, 1173-1181.
16. Gardner MG, Fitch AJ, Bertozzi T, Lowe AJ (2011) Rise of the machines-recommendations for ecologists when using next generation sequencing for microsatellite development. Molecular Ecology Resources 11, 1093-1101. doi:10.1111/j.1755-0998.2011.03037.x
17. Gordon DR, Rice KJ (1998) Patterns of differentiation in wiregrass (Aristida beyrichiana): implications for restoration efforts. Restoration Ecology 6(2), 166-174. doi:10.1111/j.1526-100X.1998.00627.x (Pubitemid 28466356)
18. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52(5), 696-704. doi:10.1080/10635150390235520 (Pubitemid 37365050)
19. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2, 618-620. doi:10.1046/j.1471-8286.2002.00305.x (Pubitemid 35436766)
20. Hardy OJ, Charbonnel N, Fréville H, Heuertz M (2003) Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation. Genetics 163, 1467-1482. (Pubitemid 36523397)
21. Hedrén M, Nordström S, Bateman RM (2011) Plastid and nuclear DNA marker data support the recognition of four tetraploid marsh orchids (Dactylorhiza majalis s.l., Orchidaceae) in Britain and Ireland, but require their recircumscription. Biological Journal of the Linnaean Society 104, 107-128.
22. Hufford KM, Mazer SJ (2003) Plant ecotypes: genetic differentiation in the age of ecological restoration. Trends in Ecology & Evolution 18(3), 147-155. doi:10.1016/S0169-5347(03)00002-8 (Pubitemid 36391422)
23. Hutchison DW, Templeton AR (1999) Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution 53(6), 1898-1914. doi:10.2307/2640449 (Pubitemid 30044821)
24. KadereitG,GotzekD,JacobsS,FreitagH(2005)Origin andageofAustralian Chenopodiaceae. Organisms, Diversity & Evolution 5, 59-80. doi:10.1016/j.ode.2004.07.002 (Pubitemid 40451702)
25. KadereitG, Mavrodiev EV, Zacharias EH, SukhorukovAP (2010) Molecular phylogeny of Atripliceae (Chenopodioideae, Chenopodiaceae): implications for systematics, biogeography, flower and fruit evolution, and the origin of C4 photosynthesis. American Journal of Botany 97(10), 1664-1687. doi:10.3732/ajb.1000169
26. Klooster MR, Culley TM (2010) Population genetic structure of the mycoheterotroph Monotropa hypopitys L. (Ericaceae) and differentiation between red and yellow color forms. International Journal of Plant Sciences 171, 167-174. doi:10.1086/648989
27. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England) 23(21), 2947-2948. doi:10.1093/bioinformatics/btm404 (Pubitemid 350162903)
28. LeimuR,FischerM(2008)Ameta-analysisoflocaladaptationinplants.PLoS ONE 3(12), e4010. doi:10.1371/journal.pone.0004010
29. Léotard G, Saltmarsh A, Kjellberg F, McKey D (2008) Mutualism, hybrid inviability and speciation in a tropical ant-plant. Journal of Evolutionary Biology 21, 1133-1143. doi:10.1111/j.1420-9101.2008.01521.x (Pubitemid 351832262)
30. Lowe AJ, Harris SA, Ashton P (2004) 'Ecological genetics: design, analysis and application.' (Blackwell Publishing: Oxford, UK) pp. 326
31. Lowe AJ, Boshier D, Ward M, Bacles CFE, Navarro C (2005) Genetic resource loss following habitat fragmentation and degradation; reconciling predicted theory with empirical evidence. Heredity 95, 255-273. doi:10.1038/sj.hdy.6800725 (Pubitemid 41372104)
32. Lynch M (1990) The similarity index and DNA fingerprinting. Molecular Biology and Evolution 7, 478-484.
33. McGlaughlin ME, Friar EA (2011) Evolutionary diversification and geographical isolation in Dubautia laxa (Asteraceae), a widespread member of the Hawaiian silversword alliance. Annals of Botany 107, 357-370. doi:10.1093/aob/mcq252
34. Meglécz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, Martin JF (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics (Oxford, England) 26(3), 403-404. doi:10.1093/bioinformatics/btp670
35. Meirmans PG, Van Tienderen PH (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes 4, 792-794. doi:10.1111/j.1471-8286.2004.00770.x (Pubitemid 39569241)
36. Millar MA, Byrne M, Coates DJ (2010) The maintenance of disparate levels of clonality, genetic diversity and genetic differentiation in disjunct subspecies of the rare Banksia ionthocarpa. Molecular Ecology 19, 4217-4227. doi:10.1111/j.1365-294X.2010.04817.x
37. Moody ME, Mueller LD, Soltis DE (1993) Genetic variation and random drift in autotetraploid populations. Genetics 134, 649-657. (Pubitemid 23156957)
38. Moritz C (2002) Strategies to protect biological diversity and the evolutionary processes that sustain it. Systematic Biology 51(2), 238-254. doi:10.1080/10635150252899752 (Pubitemid 35180707)
39. Nobs MA (1980) Chromosome numbers in Australian species of Atriplex. Carnegie Institute Yearbook 79, 164-169.
40. Ortíz-Dorda J, Martínez-Mora C, Correal E, Simón B, Cenis JL (2005) Genetic structure of Atriplex halimus populations in the Mediterranean basin. Annals of Botany 95, 827-834. doi:10.1093/aob/mci086 (Pubitemid 41238670)
41. Parr-Smith GA (1982) Biogeography and evolution in the shrubby Australian species ofAtriplex (Chenopodiaceae). In 'Evolution of the flora and fauna of arid Australia'. (Eds WR Barker, PJM Greenslade) pp. 291-299. (Peacock Publications: Frewville, SA)
42. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6(1), 288-295. doi:10.1111/j.1471-8286.2005.01155.x (Pubitemid 43373825)
43. Posada D (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25, 1253-1256. doi:10.1093/molbev/msn083 (Pubitemid 351882013)
44. Robertson A, Rich TCG, Allen AM, Houston L, Roberts C, Bridle JR, Harris SA, Hiscock SJ (2010) Hybridization and polyploidy as drivers of continuing evolution and speciation in Sorbus. Molecular Ecology 19, 1675-1690. doi:10.1111/j.1365-294X.2010.04585.x
45. Sampson JF, Byrne M (2012) Genetic diversity and the origins of polyploid Atriplex nummularia Lindl. (Chenopodiaceae). Biological Journal of the Linnaean Society 105, 218-230. doi:10.1111/j.1095-8312.2011.01787.x
46. Sgrò CM, Lowe AJ, Hoffmann AA (2011) Building evolutionary resilience for conserving biodiversity under climate change. Evolutionary Applications 4, 326-337. doi:10.1111/j.1752-4571.2010.00157.x
47. Soltis PS, Soltis DE (2000) The role of genetic and genomic attributes in the success of polyploids. Proceedings of the National Academy of Sciences of the United States of America 97(13), 7051-7057. doi:10.1073/pnas.97.13.7051 (Pubitemid 30431415)
48. Stutz HC, Pope CL, Sanderson SC (1979) Evolutionary studies of Atriplex: adaptive products from the natural hybrid, 6N A. tridentata x 4N A. canescens. American Journal of Botany 66(10), 1181-1193. doi:10.2307/2442217
49. Swofford DL (2002) 'PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods).' (Florida State University: Tallahassee, FL)
50. Taschereau PM (1988) Taxonomy, morphology and distribution of Atriplex hybrids in the British Isles. Watsonia 17, 247-264.
51. VergilinoR, Markova S, Ventura M, Manca M,Dufresne F (2011) Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers. Molecular Ecology 20, 1191-1207. doi:10.1111/j.1365-294X.2011.05004.x
52. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38, 1358-1370. doi:10.2307/2408641 (Pubitemid 16277759)
53. Western Australian Herbarium (1998) 'FloraBase-The Western Australian Flora.' (Department of Environment and Conservation: Perth, WA) Available at http://florabase.dec.wa.gov.au/[Verified 5 August 2011]