Genetic structuring of Genetic structuring of spotted gums spotted gums Merv Shepherd Merv Shepherd Shabana Kasam Kasam Shabana Gary Ablett Ablett Gary Joel Ochieng Ochieng Joel Allison Crawford Allison Crawford Sub-tropical Forestry Centre
Overview Overview ► Spotted gums and C. torelliana ► Spotted gums and C. torelliana ► Structure analysis ► Structure analysis ► An application ► An application
Eucalypts – – 3 genera 3 genera Eucalypts Spotted • Free sepals and petals • Opposite adult leaves gums • Corymbiod conflorescences Angophora Corymbia • Fused sepals & petals • Alternate leaves Angophora and Eucalyptus photo & Eucalyptus ss diagram from Euclid
Corymbia - - Phylogram Phylogram Corymbia Angophora Spotted Gums Fundoria Apeteria torelliana Rufaria Politaria Cadagaria Ochraria Blakearia Morphometric study Hill and Johnson 1995
Spotted gum species complex Spotted gum species complex citriodora variegata henryi maculata
Corymbia torelliana Corymbia torelliana •Section (Cadagaria) • Nth Qld Rainforest margin tree •Planted widely as an ornamental & shade tree • Hybridises naturally with citriodora in NQ •Spontaneously hybrids with spotted gums in plantings in SEQ •Torelliana hybrid – Emerging taxa for plantations
Corymbia species - - distributions distributions Corymbia species Corymbia torelliana Corymbia citriodora Corymbia variegata Corymbia henryi Corymbia maculata Provided by D Lee QDPI&F
This study – – Structure analysis Structure analysis This study ► Structure software ► Structure software – – (Pritchard et al 2000) (Pritchard et al 2000) ► Bayesian modelling & MCMC methods Bayesian modelling & MCMC methods ► ► ► Model optimises a likelihood parameter by max. LE and Model optimises a likelihood parameter by max. LE and HWE within populations by introducing structure HWE within populations by introducing structure ► No predefined groupings No predefined groupings ► ► ► Test models where Population # (K) = 1 to 10 and 10 Test models where Population # (K) = 1 to 10 and 10 replicates at each K value replicates at each K value ► Plot Delta K ► Plot Delta K – – change in log probability of data vs K and change in log probability of data vs K and look for peak ( look for peak (Evanno Evanno et al 2005) et al 2005) ► ► Hierarchical analysis Hierarchical analysis - - peeling off of populations till no peeling off of populations till no further structure detected – – model detects the strongest model detects the strongest further structure detected structure first structure first
Sample sites for genetic classification Sample sites for genetic classification citriodora variegata henryi maculata Windsor Qld • 118 individuals Barron Qld • 5 Taxa Mt Garnet Qld • 31 sites Kirrama Qld • 1-12 per site Yeppoon Qld Duaringa Qld Gympie Qld Cashmere Qld Bunyaville Qld Bunyaville Qld BFP 172 Qld BFP1 Qld Mt Barney Qld Mt Barney Qld Cherry Tree Cherry Tree Candole Bungawalbin Wingello Wedding Bells Camira Bagawa Candole Kioloa Nelligen Bodalla Mumbulla Mottle Range Vic
Microsatellite Marker pre- -analysis analysis Microsatellite Marker pre ► Distilled 9 microsatellite markers out of 32 ► Distilled 9 microsatellite markers out of 32 ► No null alleles (identified in CT x CV cross) ► No null alleles (identified in CT x CV cross) ► Power to self assign and assign simulation ► Power to self assign and assign simulation sets sets ► Power to discriminate known hybrids ► Power to discriminate known hybrids ► Private alleles ► Private alleles
Structure among taxa is weak Structure among taxa is weak Pairwise Fst below diagonal – Av Gene diversity on diagonal CT CM CC CV CH CT 0.68 (0.36) CM 0.26 0.77 (0.41) CC 0.19 0.12 0.82 (0.43) CV 0.19 0.07 0.02 0.77 (0.41) CH 0.22 0.07 0.04 0.01 0.67 (0.36)
Structure – –5 Taxa 5 Taxa – – k= 2 k= 2 Structure ► 5 taxa 5 taxa – – torelliana + 4 torelliana + 4 ► spotted gums spotted gums 50 ► K = 2 optimum K = 2 optimum ► 40 ► Ancestry assignments ► Ancestry assignments Torelliana splits off Torelliana splits off 30 from spotted gums from spotted gums 20 10 0 Delta K -10 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 K
Structure – – 4 SG 4 SG – – k= 2 k= 2 Structure ► 4 taxa of ► 4 taxa of 14 spotted gums spotted gums 12 10 ► K = 2 optimum ► K = 2 optimum 8 ► Maculata splits ► Maculata splits 6 from northern from northern 4 taxa taxa 2 DELTA K 0 -2 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 K
Structure – – Nth SG Nth SG – – K= 3 K= 3 Structure ► K= 3 optimum ► K= 3 optimum ► No further ► No further 20 substructure substructure detected within detected within 10 any of the 5 any of the 5 populations populations 0 identified so identified so DELTA K far. far. -10 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 K
Population ancestry (K= 5) Population ancestry (K= 5) Most Northerly Most Southerly Nth Qld Sth Qld Gympie site within site within torelliana torelliana Mt Barney (Qld) I ndividuals grouped by taxa then ordered by site and latitude within taxa
Latitudinal arrangement of Latitudinal arrangement of populations populations ► Geographic distribution ► Geographic distribution torelliana Nth ► Latitudinal ► Latitudinal ► Population divisions ► Population divisions align with disjunctions. align with disjunctions. Central Disjunction 1 – 300km in Central Queensland Sth Disjunction 2 - Border Range maculata
Poor alignment with Taxa Poor alignment with Taxa Taxa Genetic ► 4 taxa ► 4 taxa ► 4 genetic ► 4 genetic Nth Citriodora groups groups ► Poor Poor ► alignment Variegata alignment Central Henryi Sth maculata maculata
Stepping stone model Stepping stone model Nth 0.05 ► Geographic isolation Geographic isolation ► major factor in major factor in 0.09 Central structuring structuring 0.05 0.13 ► Adjacent Adjacent popn popn more more ► similar similar Sth ► One dimensional One dimensional ► 0.11 0.08 maculata Pairwise Fst
Is it an improvement? Is it an improvement? ► Success of self ► Success of self- -assignment assignment – – fewer ambiguous assignments fewer ambiguous assignments using genetic groupings because differentiation among using genetic groupings because differentiation among population was maximised population was maximised Taxonomic Genetic No. in No. in Gro Gro Group No. Amb. up Group No. Amb. up Admix 8 13 CC 4 25 Nth 2 19 CV 14 26 Ctl 2 18 CH 17 22 Sth 14 23 CM 4 24 CM 1 24 CT 0 21 CT 0 21 Totals 39 118 27 118 Percentage Ambiguous 33 23
Application – – spotted gums of spotted gums of Application unknown origins unknown origins ► Northern NSW planting ► Northern NSW planting – – species unknown species unknown ► Too young to flower and identify Too young to flower and identify ► ► Can they be classified into pop and taxa? ► Can they be classified into pop and taxa? • Structure analysis of Ref pop + case study samples • 2 populations was optimal • Case study samples = maculata
Further study Further study ► Maculata ► Maculata – –prob. 2 prob. 2 popn popn – – Nth Coast not Nth Coast not sampled sampled ► Variegata ► Variegata – – also poorly sampled in North also poorly sampled in North ► Variegata & henryi ► Variegata & henryi - - Joint study between J Joint study between J Ochieng and U of Qld. and U of Qld. Ochieng
Conclusions Conclusions ► At least 4 populations in spotted gums probably 5 ► At least 4 populations in spotted gums probably 5 with North Coast maculata with North Coast maculata ► ► Maculata most distinct Maculata most distinct – – 3 northern taxa 3 northern taxa – – 1 1 species? species? ► Origins of plantings with uncertain origins can be Origins of plantings with uncertain origins can be ► determined determined ► Intersectional hybrid ID and genealogical class Intersectional hybrid ID and genealogical class ► determined determined ► More powerful classification than taxonomic ► More powerful classification than taxonomic grouping grouping
Acknowledgements Acknowledgements ► Southern Cross University ► Southern Cross University ► Funding Funding ► ► Centre for Plant Conservation ► Centre for Plant Conservation � ARC Linkage � Genetics ARC Linkage Genetics UofTas/ ForestsNSW UofTas/ ForestsNSW � � Robert Henry Robert Henry � ARC Linkage � ARC Linkage – – � � Cathy Nock Cathy Nock SCU/ QDPI F - -Wood Wood SCU/ QDPI F ► ForestsNSW ► ForestsNSW Quality for Spotted Gum Quality for Spotted Gum � � Mike Henson & Tree Improv Improv. . Mike Henson & Tree � � Grafton Nursery Grafton Nursery ► QDPIF, Hort. & Forestry Sci. ► QDPIF, Hort. & Forestry Sci. � � David Lee David Lee � � Garth Nikles Nikles Garth ► Sunshine Coast Uni ► Sunshine Coast Uni � � Rhonda Stokoe Stokoe Rhonda ► David Kleinig ► David Kleinig
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