Genetic structuring of Genetic structuring of spotted gums spotted - - PowerPoint PPT Presentation

Genetic structuring of Genetic structuring of spotted gums spotted gums

Merv Shepherd Merv Shepherd Shabana Shabana Kasam Kasam Gary Gary Ablett Ablett Joel Joel Ochieng Ochieng 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 Eucalypts – – 3 genera 3 genera

Angophora Eucalyptus ss

• Fused sepals & petals
• Alternate leaves
• Free sepals and petals
• Opposite adult leaves
• Corymbiod conflorescences

Spotted gums

Corymbia

Angophora and Eucalyptus photo & diagram from Euclid

Corymbia Corymbia -

• Phylogram

Phylogram

Apeteria Rufaria Blakearia Angophora Fundoria Cadagaria Politaria Ochraria

Hill and Johnson 1995

Spotted Gums torelliana

Morphometric study

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
• rnamental & shade tree
• Hybridises naturally with

citriodora in NQ

• Spontaneously hybrids with

spotted gums in plantings in SEQ

• Torelliana hybrid –

Emerging taxa for plantations

Corymbia variegata

Corymbia species Corymbia species -

• distributions

distributions

Corymbia henryi Corymbia maculata Corymbia torelliana Corymbia citriodora Provided by D Lee QDPI&F

This study This study – – Structure analysis Structure analysis

► ► 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 further structure detected – – model detects the strongest model detects the strongest structure first structure first

Sample sites for genetic classification Sample sites for genetic classification

maculata Wingello Kioloa Nelligen Bodalla Mumbulla Mottle Range Vic citriodora Windsor Qld Barron Qld Mt Garnet Qld Kirrama Qld Yeppoon Qld Duaringa Qld variegata Gympie Qld Bunyaville Qld BFP 172 Qld Mt Barney Qld Cherry Tree Candole Wedding Bells Bagawa henryi Cashmere Qld Bunyaville Qld BFP1 Qld Mt Barney Qld Cherry Tree Bungawalbin Camira Candole

• 118 individuals
• 5 Taxa
• 31 sites
• 1-12 per site

Microsatellite Marker pre Microsatellite Marker pre-

• analysis

analysis

► ►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

0.67 (0.36) 0.01 0.04 0.07 0.22 CH 0.77 (0.41) 0.02 0.07 0.19 CV 0.82 (0.43) 0.12 0.19 CC 0.77 (0.41) 0.26 CM 0.68 (0.36) CT CH CV CC CM CT

Pairwise Fst below diagonal – Av Gene diversity on diagonal

Structure Structure – –5 Taxa 5 Taxa – – k= 2 k= 2

► ► 5 taxa

5 taxa – – torelliana + 4 torelliana + 4 spotted gums spotted gums

► ► K = 2 optimum

K = 2 optimum

► ► Ancestry assignments

Ancestry assignments Torelliana splits off Torelliana splits off from spotted gums from spotted gums

K

10.00 9.00 8.00 7.00 6.00 5.00 4.00 3.00 2.00 1.00

Delta K

50 40 30 20 10

• 10

Structure Structure – – 4 SG 4 SG – – k= 2 k= 2

► ►4 taxa of

4 taxa of spotted gums spotted gums

► ►K = 2 optimum

K = 2 optimum

► ►Maculata splits

Maculata splits from northern from northern taxa taxa

K

10.00 9.00 8.00 7.00 6.00 5.00 4.00 3.00 2.00 1.00

DELTA K

14 12 10 8 6 4 2

• 2

Structure Structure – – Nth SG Nth SG – – K= 3 K= 3

► ►K= 3 optimum

K= 3 optimum

► ►No further

No further substructure substructure detected within detected within any of the 5 any of the 5 populations populations identified so identified so far. far.

K

10.00 9.00 8.00 7.00 6.00 5.00 4.00 3.00 2.00 1.00

DELTA K

20 10

• 10

Population ancestry (K= 5) Population ancestry (K= 5)

I ndividuals grouped by taxa then ordered by site and latitude within taxa

Most Northerly site within torelliana Most Southerly site within torelliana Gympie Mt Barney (Qld) Nth Qld Sth Qld

Latitudinal arrangement of Latitudinal arrangement of populations populations

► ►Geographic distribution

Geographic distribution

► ►Latitudinal

Latitudinal

► ►Population divisions

Population divisions align with disjunctions. align with disjunctions.

maculata Nth Central Sth

Disjunction 1 – 300km in Central Queensland Disjunction 2 - Border Range

torelliana

Poor alignment with Taxa Poor alignment with Taxa

► ► 4 taxa

4 taxa

► ► 4 genetic

4 genetic groups groups

► ► Poor

Poor alignment alignment

Taxa Genetic

maculata Nth Central Sth

Citriodora Variegata Henryi maculata

Stepping stone model Stepping stone model

maculata Nth Central Sth 0.05 0.05 0.08 0.13 0.09

Pairwise Fst

0.11

► ► Geographic isolation

Geographic isolation major factor in major factor in structuring structuring

► ► Adjacent

Adjacent popn popn more more similar similar

► ► One dimensional

One dimensional

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

23 33 Percentage Ambiguous 118 27 118 39 Totals 21 CT 21 CT 24 1 CM 24 4 CM 23 14 Sth 22 17 CH 18 2 Ctl 26 14 CV 19 2 Nth 25 4 CC 13 8 Admix

• No. in

Gro up

• No. Amb.

Group

• No. in

Gro up

• No. Amb.

Group Genetic Taxonomic

Application Application – – spotted gums of spotted gums of 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 Ochieng and U of Qld. and U of Qld.

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

► ► Centre for Plant Conservation

Centre for Plant Conservation Genetics Genetics

• Robert Henry

Robert Henry

• Cathy Nock

Cathy Nock

► ► ForestsNSW

ForestsNSW

• Mike Henson & Tree

Mike Henson & Tree Improv Improv. .

• Grafton Nursery

Grafton Nursery

► ► QDPIF, Hort. & Forestry Sci.

QDPIF, Hort. & Forestry Sci.

• David Lee

David Lee

• Garth

Garth Nikles Nikles

► ► Sunshine Coast Uni

Sunshine Coast Uni

• Rhonda

Rhonda Stokoe Stokoe

► ► David Kleinig

David Kleinig ► ► Funding

Funding

• ARC Linkage

ARC Linkage UofTas/ ForestsNSW UofTas/ ForestsNSW

• ARC Linkage

ARC Linkage – – SCU/ QDPI F SCU/ QDPI F -

• Wood

Wood Quality for Spotted Gum Quality for Spotted Gum

Application Application – – torelliana hybrids torelliana hybrids

► ►It isn’t always

It isn’t always this easy this easy

F1

Application Application – – torelliana hybrids torelliana hybrids

• BC to torelliana
• Torelliana
• F1

Application Application – – torelliana hybrids torelliana hybrids

► ► 22 putative hybrids

22 putative hybrids from amenity from amenity plantings plantings

► ► 4 controlled

4 controlled-

• cross

cross F1 F1

► ► New Hybrids

New Hybrids – – genealogical genealogical assignments assignments

► ► Botanist two

Botanist two putative putative F1 and 1 F1 and 1 BC BC

0.08437 0.00840 0.06489 0.84232 0.00000 0.00002 CT?10152 0.92045 0.00000 0.07870 0.00000 0.00085 0.00000 CT?10148 0.00519 0.00000 0.00023 0.00000 0.99458 0.00000 CT?10147 0.10271 0.00787 0.06085 0.82850 0.00000 0.00007 CT?10146 0.00221 0.00000 0.00016 0.00000 0.99763 0.00000 CT?10140 0.57776 0.00000 0.32658 0.00000 0.09566 0.00000 CT?10139 0.00632 0.00000 0.00102 0.00000 0.99265 0.00001 CT?10138 0.01799 0.00000 0.79962 0.00000 0.18238 0.00001 CT?10131 0.00370 0.01031 0.01125 0.97470 0.00000 0.00004 F17836* 0.05269 0.07600 0.69892 0.17235 0.00000 0.00004 F17835* 0.02911 0.00256 0.01818 0.95015 0.00001 0.00000 F17834* 0.02961 0.00494 0.02845 0.93700 0.00000 0.00001 F17833* F1xCT F1xSG F2 F1 CT SG

New Hybrids Results New Hybrids Results

Reference population Reference population

► ►5 taxa

5 taxa -

• CT; CC; CV; CH and CM

CT; CC; CV; CH and CM

► ►118 individuals ~ 25 per taxa

118 individuals ~ 25 per taxa

► ►31 sites 1

31 sites 1-

• 12 individuals per site

12 individuals per site

► ►Latitude 16 to 37

Latitude 16 to 37 – – but some gaps but some gaps – –ie

• ie. Nth

. Nth Coast region CM Coast region CM

Congruence in genetic structure Congruence in genetic structure

► ►3 marker systems (reanalysis of

3 marker systems (reanalysis of isozymes, isozymes, cpDNA cpDNA and microsatellites) and microsatellites)

Corymbia maculata Corymbia henryi Corymbia citriodora subsp. citriodora Corymbia citriodora subsp. variegata

King 2003

(cpDNA + reanalysis

• f isozymes

Corymbia maculata Corymbia henryi Corymbia citriodora subsp. citriodora Corymbia citriodora subsp. variegata

Shepherd et al 2007

(microsatellites)

Stepping Stone 2 D element Stepping Stone 2 D element

► ►Additional dimension to

Additional dimension to Cental and Southern Cental and Southern populations of populations of variegata variegata

► ►Gene flow restricted in

Gene flow restricted in West of distribution by West of distribution by Border Ranges Border Ranges

► ►Not evident in henryi?

Not evident in henryi?

Eastern Central Eastern Sth Western Central Western Sth Border Range Nth maculata

Why a genetic classification? Why a genetic classification?

1. 1.

Taxonomic difficulties Taxonomic difficulties

2. 2.

Gene pool management Gene pool management

3. 3.

Tree improvement Tree improvement

Revolving Taxonomy Revolving Taxonomy

Eucalyptus citriodora Eucalyptus maculata Corymbia citriodora Corymbia variegata Corymbia henryi Corymbia maculata Corymbia citriodora subsp. citriodora Corymbia citriodora subsp. variegata Corymbia henryi Corymbia maculata

Pre 1995 Hill & Johnson 1995 McDonald & Bean 2000

(morpho + isozymes)

Corymbia maculata Corymbia henryi Corymbia citriodora subsp. citriodora Corymbia citriodora subsp. variegata

King 2003

(cpDNA + reanalysis

• f isozymes

Full circle - back to a 2 pronged model?

Taxonomic difficulties Taxonomic difficulties

► ► Taxonomic

Taxonomic classification often classification often relies on knowing an relies on knowing an

• rigin
• rigin

► ► Difficult ID in

Difficult ID in sympatry sympatry – – segregating characters segregating characters

► ► Once classified does it

Once classified does it relate to genetic relate to genetic structure determined structure determined by evolutionary past by evolutionary past and interbreeding? and interbreeding?

Gene pool management Gene pool management

► ►Spotted gums are not endangered but…

Spotted gums are not endangered but…

► ►Are there unique populations vulnerable?

Are there unique populations vulnerable?

► ►What will be the impact of plantations on

What will be the impact of plantations on any structure due to mixing of historically any structure due to mixing of historically isolated populations isolated populations

► ►Introgression from

Introgression from C. torelliana

• C. torelliana an

an environmental weed in many shires in Qld environmental weed in many shires in Qld and Nth NSW and Nth NSW

► ►Tools to monitor gene flow

Tools to monitor gene flow

Plantations adjacent to Native Plantations adjacent to Native forest forest

Map produced by Rob Kirkwood ForestsNSW

Improvement Improvement

• Efficiently formulating

Efficiently formulating breeding populations breeding populations

• Provenance of plantings

Provenance of plantings

• f uncertain origin
• f uncertain origin
• ID of intersectional and

ID of intersectional and interpopulational interpopulational hybrids hybrids

• Pollen mixing in

Pollen mixing in

• rchards
• rchards
• Association studies

Association studies

Corymbia (Bloodwoods) Corymbia (Bloodwoods)

► ► Blakearia

Blakearia – – Ghost Gums Ghost Gums

► ► Ochraria

Ochraria – – Yellow Bloodwoods Yellow Bloodwoods

► ► Cadagaria

Cadagaria – – Cadagi Cadagi

► ► Politaria

Politaria – – Spotted gums Spotted gums

► ► Rufaria

Rufaria – – Red bloodwoods Red bloodwoods

► ► Apteria

Apteria -

• unispecific

unispecific

► ► Fundoria

Fundoria -

• unispecific

unispecific

Yellow bloodwood alliance Red bloodwood assemblage

Hill and Johnson 1995 Telopea v6 p185

– – 7 sections 7 sections – – 29 series 29 series -

• 113 species

113 species

The odd Tree The odd Tree

Photo John Forster – Story Jane Mu http://www.abc.net.au/northcoast/stories/s1883990.htmnro – ABC website

Spotted Gums Spotted Gums – – plantations plantations

► ►Species and hybrids very

Species and hybrids very promising for 700 promising for 700-

• 1000

1000 mm MAR zone mm MAR zone

► ►> 30% of young

> 30% of young plantations in the north plantations in the north

► ►Highly prised saw log

Highly prised saw log – – flooring; furniture flooring; furniture

Corymbia hybrids Corymbia hybrids

Intersectional hybrid Intersectional hybrid

► ► C. torelliana x C. variegata

• C. torelliana x C. variegata

► ► Potential for plantations

Potential for plantations

► ► Hybrid vigour

Hybrid vigour

► ► Good form

Good form

► ► Coppicing of

Coppicing of variegata variegata but but Rooting of Rooting of torelliana torelliana

► ► Ramularia resistance

Ramularia resistance

► ► Site capture

Site capture

► ► Environmental plasticity

Environmental plasticity

► ► Frost tolerance

Frost tolerance

Improvement

PGM2 PGM2 – – Allele Frequencies Allele Frequencies

Kindly provided by Rachel King – See King 2004 PhD Griffith Uni – Based on McDonald et al 2000

0 .0 0 0 .10 0 .2 0 0 .3 0 0 .4 0 0 .50 0 .6 0 0 .70 0 .8 0 0 .9 0 1.0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 2 0 2 1 2 2 2 3 2 4 2 5 2 6 2 7 2 8 p o p ulatio n allele A allele B allele C allele D

citriodora variegata henryi maculata

Diversity at 9 SSR Diversity at 9 SSR

0.0857 0.0696 0.1242 0.1067 0.1212 0.1008 0.2662 (SD) 0.7283 0.7587 0.8035 0.6985 0.7722 0.7705 0.5958 Mean 0.8316 0.8378 0.9091 0.7917 0.8667 0.8333 0.8095 EMCRC 46 0.7876 0.7500 0.5600 0.8696 0.8095 0.7826 0.9524 EMCRC 35 0.6847 0.7033 0.7273 0.6667 0.7000 0.7200 0.6000 EMCRC 34 0.8053 0.8370 0.8400 0.7917 0.8000 0.9130 0.6667 EMCRC 36 0.7368 0.7419 0.9167 0.5833 0.6000 0.8400 0.7143 EMCRC 40 0.6396 0.6444 0.7727 0.5833 0.5789 0.6400 0.6190 EMCRC 37 0.7568 0.8111 0.8261 0.6667 0.9000 0.8696 0.5238 EMCRC 38 0.7500 0.8105 0.9600 0.7500 0.9048 0.6400 0.4762 EMCRC 93 0.5625 0.6923 0.7200 0.5833 0.7895 0.6957 0.0000 EMCRC 27 all taxa all SG CV CM CH CC CT Ho* Locus

torelliana maculata Nth Central Sth 0.21 0.22 0.19 0.05 0.05 0.26 0.08

Relationship to torelliana Relationship to torelliana

• Torelliana hybrids with

citriodora in Nature – D Lee

• Not an ideal outgroup

13 15 21 14 16

PGM2 allele PGM2 allele distribution distribution by location by location

19 20 17 18 variegata henryi maculata Allele frequency aligns with geographic location as much as taxon? ? What would henryi from north look like?