Genome-wide scans reveal cryptic population structure in a dry-adapted eucalypt
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Genome-wide DArTseq scans of 268 individuals of Eucalyptus salubris, distributed along an aridity gradient in southwestern Australia, revealed cryptic population structure that appears to signal hitherto unappreciated ecotypic differentiation and barriers to gene flow. Genome-wide scans were undertaken on 30 wild-sampled individuals from each of nine populations; 10 individuals per population were measured for habit and functional traits. DArTseq generated 16,122 high-quality markers, of which 56.3 % located to E. grandis chromosomes. Genetic affinities of the nine populations were only weakly correlated with geographic distances. Rather, populations appeared to form two distinct molecular lineages that maintained their distinctiveness in an area of geographic overlap. Twenty-four outlier markers signalled divergent selection and differentiation of the two putative lineages. Populations from the two lineages were phenotypically differentiated in leaf thickness, specific leaf area (SLA) and leaf nitrogen per unit mass (Nmass). The more northerly lineage (with thinner leaves) occurred in hotter, drier conditions with higher radiation. Populations of the more southerly lineage occurred on soils that were relatively low in phosphorus; the trees had thicker leaves, lower SLA and lower leaf Nmass, consistent with general responses to low nutrient levels. While historic isolation and drift may have contributed to the cryptic population structure observed, there is evidence of ecotypic adaptation, which may provide an exogenous barrier to gene flow. This study highlights the power of new molecular technologies to provide novel insights into the genetic architecture of wild populations.
KeywordsEcotypic variation Soil phosphorus Eucalyptus Outlier analysis DArTseq Population genetics
This work was funded by a grant from the Australian National Climate Change Adaptation Research Facility (TB11 03) with additional support through the Great Western Woodlands Supersite of Australia’s Terrestrial Ecosystem Research Network and ARC Discovery Grant DP130104220. We thank: Craig Macfarlane, Nat Raisbeck-Brown, Georg Wiehl, Didier Alanoix (CSIRO Land and Water Flagship) and Anne Rick for assistance with field work; Bronwyn MacDonald, Rachel Binks and Donna Bradbury (Department of Parks and Wildlife, Western Australia), Carl Gosper (CSIRO Land and Water Flagship and Department of Parks and Wildlife, Western Australia), Paul Tilyard and Chris Burridge (University of Tasmania) for technical assistance; the project’s end-user advisory group, David Freudenberger, Gary Howling, Neil Riches and Richard Mazanec; the Western Australian Herbarium for accession of samples and assistance with and access to FloraBase data; and the Tasmanian Partnership for Advanced Computing (TPAC).
Data archiving statement
Data relating to this study is available from Dryad: doi: 10.5061/dryad.h06r3. These include Climate data, soil data, isotope data (relating to physiology), morphometric data and dominant (presence/absence) DArTseq data (including DNA sequences of each DArTseq marker).
- Anderson MJ, Gorley RN, Clarke KR (2008) Permanova + for primer: guide to software and statistical methods. PRIMER-E, PlymouthGoogle Scholar
- Australian Plant Name Index (2014) Eucalyptus salubris F. Muell. Centre for Plant Biodiversity Research, Australian GovernmentGoogle Scholar
- Byrne M (2008) Phylogeny, diversity and evolution of eucalypts. In: Ch. 11 in Sharma AK and Sharma A (eds) Plant genome biodiversity and evolution. Part E. phanerogams - angiosperms. Science Publishers, Berlin. pp 303–346Google Scholar
- Byrne M, Moran GF, Tibbits WN (1993) Restriction map and maternal inheritance of chloroplast DNA in Eucalyptus nitens. J Hered 84:218–220Google Scholar
- Clarke KR, Gorley RN (2006) Primer v6: user manual/tutorial. PRIMER-E, PlymouthGoogle Scholar
- Esau K (1960) Anatomy of seed plants. Wiley, New YorkGoogle Scholar
- French M (ed) (2012) Eucalypts of Western Australia’s wheatbelt. Malcolm French, PadburyGoogle Scholar
- Leavitt SD, Fankhauser JD, Leavitt DH, Porter LD, Johnson LA, St Clair LL (2011) Complex patterns of speciation in cosmopolitan “rock posy” lichens—discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota). Mol Phylogenet Evol 59:587–602. doi: 10.1016/j.ympev.2011.03.020 PubMedCrossRefGoogle Scholar
- Lousada JM, Lovato MB, Borba EL (2013) High genetic divergence and low genetic variability in disjunct populations of the endemic Vellozia compacta (Velloziaceae) occurring in two edaphic environments of Brazilian campos rupestres. Braz J Bot 36:45–53. doi: 10.1007/s40415-013-0001-x CrossRefGoogle Scholar
- Medina R, Lara F, Goffinet B, Garilleti R, Mazimpaka V (2012) Integrative taxonomy successfully resolves the pseudo-cryptic complex of the disjunct epiphytic moss Orthotrichum consimile s.l. (Orthotrichaceae). Taxon 61:1180–1198Google Scholar
- Sansaloni CP, Petroli CD, Jaccoud D, Carling J, Detering F, Grattapaglia D, Kilian A (2011) Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proc 5:P54PubMedCentralCrossRefGoogle Scholar
- Sarkinen TE, Marcelo-Pena JL, Yomona AD, Simon MF, Pennington RT, Hughes CE (2011) Underestimated endemic species diversity in the dry inter-Andean valley of the Rio Maranon, northern Peru: an example from Mimosa (Leguminosae, Mimosoideae). Taxon 60:139–150Google Scholar
- Schimper AFW (1903) Plant geography upon a physiological basis (English translation by W.R. Fisher). Clarendon, OxfordGoogle Scholar
- Sotuyo S, Lewis GP (2007) A new species of Caesalpinia from the Rio Balsas Depression, Mexico, and an updated taxonomic circumscription of the Caesalpinia hintonii complex (Leguminosae: Caesalpinioideae: Caesalpinieae: Poincianella Group). Brittonia 59:33–36. doi: 10.1663/0007-196x(2007)59[33:ansocf]2.0.co;2 CrossRefGoogle Scholar
- Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods), 4th edn. Sinauer Associates, SunderlandGoogle Scholar
- Xu T, Hutchinson M (2011) ANUCLIM version 6.1 user guide. The Australian National University, Fenner School of Environment and Society, CanberraGoogle Scholar