applications of molecular markers in in situ and ex situ conservation 1
DESCRIPTION
loTRANSCRIPT
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Case Studies on Conservation of Forest Genetic Resources in
Asia, Pacific and Oceania Asia, Pacific and Oceania Region
Contents
• Background – threats, conservation tools, species diversity, sampling strategies for genetic diversity studiesg y
• Case study on two allopatric species; Hopea odorata, Dryobalanops aromatica
• Case study on long-term and short-term effects of logging
Threats to Forest Genetic Resources
• Natural disasters – hurricanes, volcanic eruptions, earth quakes, tsunami, fire, floods, etc.,
• Anthropogenic factors – logging, land conversion, dams, highways, grazing, fire, collection of non-timber products, war, global warming, etc.
Conservation Tools
Genetic conservation areas for specific species (e.g. kapur gene pools)
Virgin Jungle Reserves
Gardens and arboreta (e.g. Rimba Ilmu, UM, Dipterocarp A b FRIM) Virgin Jungle Reserves
(Pasoh F.R., Bukit Bauk F.R.)
Wildlife Sanctuaries and National Parks (Taman Negara, Mulu National Park)
Arboretum, FRIM)
• Seed or gamete banks
• Clonal archives
• DNA archives
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60
80
100
f sp
ecie
s
0
20
40
Q1 Q1,2 Q1-3 Q1-4 Q1-5
Quadrat
no o
f
Unlogged stand
Regenerated stand 1
Regenerated stand 2
Sampling strategy for genetic diversity studies
P l ti t t• Population structure
• Species boundary
• Phylogeny
Sampling strategy for genetic diversity studies
• Population Structure• Genetic variation within and among populations
(geographic variation), breeding system, heterozygosity, relatedness among individualsamong individuals
Sample size (N)? 2N 1/GST ( 5-50 )Molecular marker? ISOZYMES, RFLPs, VNTRs,
SSRsNo. of markers/loci? N Type of tissue? SEED, POLLEN, LEAF,
INNER BARK, ROOT TIP
0.58
0.60
0.62
0.64
0.66
0.68
0.70
0.72
0.74
0.76
5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105
Expe
cted
het
eroz
ygos
ity, H
e
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ffec
tive
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les,
ne
He ne
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0.80
5 10 15 20 25 30
Sample size
Mea
n he
tero
zygo
sity
, He
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2.50
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3.50
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4.50
Mea
n ef
fect
ive
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le n
umbe
r, ne
He ne
Sample size
• SL & SP, n = 20 samples
• AT, n = 15 samples
Sampling strategy for genetic diversity studies
• Species Boundary– Interspecific hybridisation,
introgression
Sample size (N)? MIN. 2Molecular marker? FIXED ALLELENo. of marker/loci? NType of tissue? SEED, LEAF, INNER
BARK, ROOT TIP
3
Sampling strategy for genetic diversity studies
• Phylogeny– Species divergence
Sample size (N)? MIN 1Sample size (N)? MIN. 1Molecular marker? RFLP, PCR-RFLP,
SEQUENCINGNo. of marker/loci? NType of tissue? LEAF, INNER
BARK, ROOT TIP
SNP
ISOZYMES
Hopea odorata(Dipterocarpaceae)
• Local name – Merawan siput jantan (Malaysia), sao den (Vietnam), kok (Cambodia), kh’en (Laos), takhian-thong (Thailand)
• Distributed in Andaman Islands, Mynamar, Thailand, Indo-China and Peninsular Malaysia
• Occurs in lowlands (riparian) and hills up to 300 m altitude or higher (in Andaman Is.)
• Flowers – small, unisexual, pinkish petals with hairs.• Fruits – polyembryonic with up to 7 plantlets per fruit• Pollinator – small insects, inferred apomixis • Light hardwood - construction uses, furniture, veneer,
etc.
Distribution of Hopea odorata in Peninsular MalaysiaMalaysia
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H. nervosa
H. dyeri
H. dryobalanoides
H. beccariana
H. pierrei
H. latifolia
H. mengerawan
H. myrtifolia
H. ferruginea
99
6267
8478
1
1
0
0
1
11
1
2
5
3
0
3
2
4
Subsection Dryobalanoides
Subsection SphaerocarpaeDryobalanoides
clade
Dryobalanoides
H. sangal
H. nutans
H. odorata
H. helferi
H. apiculata
H. wightiana
Neobalanocarpus heimii
58 60
89
11
41
12
3
4
0
0
Subsection Hopea
SubsectionPierreaHopea clade
Outgroup
72-bp deletionin the trnL-trnF H
opea
Phylogeny of Hopea based on the trnL-trnF and atpB-rbcL sequences.
Numbers above branches are bootstrap values (500 replicates); numbers below branches are branch lengths
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Dryobalanops aromatica(Dipterocarpaceae)
• Local name – Kapur• Distributed in Sumatra, Riau Archipelago,
Borneo and Peninsular Malaysia• Occurs in lowlands and hills up to 365 mOccurs in lowlands and hills up to 365 m
altitude• Flowers – small, white colour, hermaphrodite.• Pollinated by bees - Apis dorsata, A. indica var.
cerrana• Medium hardwood - construction uses, poles,
furniture, flooring and railway sleeper.
D. aromatica populations studied
Shc02, Sch03
Sch04, Sch07
Sch09, Sch11
Sch17
Genetic Diversity Parameters
Population N Ae Ho He F
Kanching 19.1 3.69 0.555 0.721 0.225
L 17 4 3 36 0 454 0 684 0 304Lenggor 17.4 3.36 0.454 0.684 0.304
Lesong 17.1 3.92 0.506 0.735 0.300
Bukit Sai 17.0 3.60 0.531 0.707 0.239
Ulu Sedili 18.7 3.60 0.407 0.700 0.428
Mean 17.9 3.63 0.491 0.709 0.300
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Genetic differentiation and gene flow between populations
• GST (+Kanching) = 0.067
• GST (- Sch07 & Sch11) = 0.062ST ( )
• GST (-Kanching) = 0.062
• RST (- Sch07 & Sch11) = 0.09
• Nm = 2.94
HARVESTING PRACTICES
• MALAYAN UNIFORM SYSTEM (MUS)
55 year cutting cycle– 55-year cutting cycle
– all trees 45cm dbh
– sufficient regenerants must be present
HARVESTING PRACTICES
• SELECTIVE MANAGEMENT SYSTEM (SMS)– 30-year cutting cycle30 year cutting cycle
– dipterocarps 50cm dbh
– non-dipterocarps 45cm dbh
– 32 adolescent trees or equivalent left after logging
Two Approaches Were Used:IMMEDIATE EFFECTS• TROPICAL RIDGE/HILL FOREST
– Serting Tambahan F.R., Negeri Sembilan• Logged in 1996 (SMS)
– Ulu Sedili F.R., Johor,• Logged in 2000 (SMS)
LONG TERM EFFECTS• LOWLAND/HILL MIXED DIPTEROCARP
FOREST– Pasoh F.R., Negeri Sembilan, Ulu Sedili F.R.,
Johor and Panti F.R., Johor• Logged in 1950s (MUS)
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Shorea curtisii(Dipterocarpaceae)
• Local name - meranti seraya• Distributed in Peninsular Malaysia, Thailand,
Sumatra and Borneo• Found in the ridges of hill dipterocarp forests
(300 850 m)(300 - 850 m)• Light hardwood of dark red meranti type -
furniture, high-class interior finishing, flooring, veneer, etc.
• Hermaphrodite flowers• Pollinator – thrips (genera Thrips &
Megalurothrips)
Basal area for S. curtisii
2.50
3.00
3.50
4.004.50
are
a pe
r ha
0.00
0.50
1.00
1.50
2.00
Mea
n ba
sal
<5cm 5-15cm 15-30cm 30-45cm >45cm
dbh classes
BF-C48 LS-C48
Tree density for S. curtisii
30
40
50
60
of tr
ees
per h
a
0
10
20
Mea
n no
. o
<5cm 5-15cm 15-30cm 30-45cm >45cm
dbh classes
BF-C48 LS-C48
Immediate effects (SMS)S. curtisii
Stand N A He V Vgam LP
BF-C118 Seedling 0.0 19.2 2.9 6.0 34.3 30.2
vs Sapling 2.5 -10.8 0.6 -0.4 37.3 -72.2p g
AF-C118 Adult 83.3 50.0 5.4 26.3 84.8 85.1
UL-C40 Seedling -400 -34.5 0.8 -14.8 -105.8 -136.5
vs Sapling -200 -27.3 3.0 -0.8 -73.4 -51.6
LS-C48 Adult 50.0 20.0 -4.8 8.8 43.4 47.4
Long term effects (MUS)S. curtisii
Stand N A He V Vgam LP
BF-C118 Seedling 18.0 14.9 0.6 0.9 -15.2 34.8BF C118 Seedling 18.0 14.9 0.6 0.9 15.2 34.8
vs Sapling 30.0 8.1 0.0 1.1 45.3 -14.8
RS-C69 Adult 76.7 37.5 2.0 16.5 71.3 63.4
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Scaphium macropodum(Sterculiaceae)
• Local name – Kembang Semangkok Jantong• Distributed in Malaysia, Southern Thailand,
Cambodia, Borneo and SumatraF d i l l d f id 1200 i• Found in lowland forests, on ridges <1200m, in swampy areas
• Light hardwood – veneer and plywood• Unisexual flowers, male and female flowers on
separate inflorescences on same tree• Pollinators – bees, flies, beetles and butterflies
Basal area for S. macropodum
0 30
0.40
0.50
0.60
l are
a pe
r ha
0.00
0.10
0.20
0.30
Mea
n ba
sal
<5cm 5-15cm 15-30cm 30-45cm >45cm
dbh classes
BF-C48 LS-C48
Tree density for S. macropodum
30.00
40.00
50.00
60.00
f tre
es p
er h
a
0.00
10.00
20.00
Mea
n no
. o
<5cm 5-15cm 15-30cm 30-45cm >45cm
dbh classes
BF-C48 LS-C48
Immediate effects (SMS)S. macropodum
Sampling time
Age cohort A H H Fis
Before Adults (33) 3.3 0.415 - 0.132logging 1.7 0.198 1.075 -
After logging
(57.5%)
Adults (22)
Poles(15)
3.0
1.7
3.5
0.390
0.212
0.318
-
0.978
-
-0.036
-
0.382Saplings(31)
Seedlings(33)3.0
3.0
0.337
0.396
-
-
0.076
0.235
Long term effects (MUS)S. macropodum
FMU A H H Fis
US 3.5 0.381 - -0.037
(30) 1.8 0.225 1.457 -0.041
RS1 - 13.5%
(11)
3.0
1.5*
0.541
0.163*
-
0.998*
0.155
0.073
RS2 - 40.7%
(18)
3.0
1.7*
0.498
0.218
-
1.400
0.175
0.143
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Conclusions
0 30
0.40
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al a
rea
per h
a
Before After
0.00
0.10
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0.30
<5cm 5-15cm 15-30cm 30-45cm >45cm
dbh classes
Mea
n ba
s
30.0
40.0
50.0
60.0
70.0
o. o
f tre
es p
er h
a
Before After
0.0
10.0
20.0
<5cm 5-15cm 15-30cm 30-45cm >45cm
dbh classes
Mea
n no
Reduction in genetic diversity measures:
Saplings < Seedlings < AdultsSaplings < Seedlings < Adults
• Assessment of genetic erosion should becarried out using more than onemolecular marker analysis if one of themshows no significant difference.
• Species’ vulnerability to the threat of• Species’ vulnerability to the threat ofgenetic erosion posed by selective loggingis highly correlated with its abundanceand heterogeneity in a particular FMU