Bradbury, Tapper, Coates, Hankinson, McArthur and Byrne; “How does the post-fire facultative seeding strategy impact genetic variation
and phylogeographic history? The case of Bossiaea ornata (Fabaceae) in a fire-prone, mediterranean-climate ecosystem”; Supplementary
Files
How does the post-fire facultative seeding strategy impact genetic variation and phylogeographic
history? The case of Bossiaea ornata (Fabaceae) in a fire-prone, mediterranean-climate ecosystem.
Donna Bradbury, Sarah-Louise Tapper, David Coates, Maggie Hankinson, Shelley McArthur and
Margaret Byrne *
Journal of Biogeography
Appendix S1.
Methods and results of nuclear population structure analysis using STRUCTURE 2.3 (Pritchard et al.,
2000; Falush et al., 2003) and TESS 2.3.1 (Chen et al., 2007) in Bossiaea ornata using eight nuclear
microsatellite markers.
STRUCTURE:
Optimal K was determined based on the ΔK method of Evanno et al. (2005), implemented in
STRUCTURE HARVESTER 0.6.94 (Earl & vonHoldt, 2012), and by assessing the slope of lnP(K) with
increasing K value.
TESS:
The most likely K was determined by obtaining the deviance information criterion (DIC) scores for all
100 runs, and plotting the mean of the 10% of runs with the lowest DIC scores against Kmax. Optimal
K was determined when the graph reached a plateau. The Greedy algorithm within CLUMPP
(Jakobsson & Rosenberg, 2007) was used to determine congruence of results among runs (H’) and to
summarise the optimal alignment, and DISTRUCT (Rosenberg, 2004) was used to plot a bar graph of
individual and population membership q-values.
Bradbury, Tapper, Coates, Hankinson, McArthur and Byrne; “How does the post-fire facultative seeding strategy impact genetic variation
and phylogeographic history? The case of Bossiaea ornata (Fabaceae) in a fire-prone, mediterranean-climate ecosystem”; Supplementary
Files
Bradbury, Tapper, Coates, Hankinson, McArthur and Byrne; “How does the post-fire facultative seeding strategy impact genetic variation and phylogeographic history? The case of Bossiaea ornata (Fabaceae) in a
fire-prone, mediterranean-climate ecosystem”; Supplementary Files
Appendix S2. Genetic diversity characteristics of eight nuclear microsatellite loci used to genotype 290 individuals of Bossiaea ornata.
Locus
Bo6G8
BoAg3E2
BoAg1E12
Bo5A10
Bo1D6
BoAg3E4
Bo5D1
Bo3D2
All loci
a
AT
26
35
28
33
26
30
25
38
Size
150-210
246-312
116-222
215-269
205-243
266-326
185-239
226-275
HO
0.632 (0.044)
0.489 (0.036)
0.691 (0.034)
0.867 (0.020)
0.773 (0.031)
0.845 (0.026)
0.797 (0.032)
0.807 (0.027)
HE
0.795 (0.019)
0.804 (0.018)
0.737 (0.029)
0.842 (0.014)
0.734 (0.030)
0.873 (0.008)
0.831 (0.018)
0.853 (0.009)
F
0.209 (0.049)a
0.384 (0.051)a
0.056 (0.036)a
-0.032 (0.023)
-0.058 (0.020)
0.033 (0.027)
0.038 (0.038)a
0.055 (0.027)a
Significant heterozygote deficit (p<0.05)
Bootstrapped 95% confidence interval in parentheses
AT – total number of alleles
Size Range – allele size range (bp)
HO – observed heterozygosity
HE – expected heterozygosity
F – fixation index
S – private alleles
FST –locus specific population differentiation, corrected for the presence of null alleles by the ENA method
Null – mean null allele frequency, range in square parentheses.
Standard errors are in round parentheses unless otherwise indicated.
b
S
7
10
9
9
7
2
4
11
FST
0.044
0.067
0.100
0.059
0.105
0.039
0.040
0.043
0.062 (0.049-0.081)b
Null
0.09 [0.00-0.23]
0.18 [0.04-0.31]
0.04 [0.00-0.14]
0.00 [0.00-0.04]
0.00 [0.00-0.08]
0.02 [0.00-0.13]
0.03 [0.00-0.14]
0.03 [0.00-0.12]
Bradbury, Tapper, Coates, Hankinson, McArthur and Byrne; “How does the post-fire facultative seeding strategy impact genetic variation and phylogeographic history? The case of Bossiaea ornata (Fabaceae) in a
fire-prone, mediterranean-climate ecosystem”; Supplementary Files
Appendix S3. Pairwise FST values among 15 natural populations of Bossiaea ornata, based on eight nuclear microsatellite markers. Significant values are
highlighted in bold (p<0.05 after Bonferroni correction).
SADD
NORB
SADD
COLN
COLS
BEAU
KIRP
GREE
NANN
BAUD
MARG
MANN
SCRE
MANE
PEER
COLN
0.018
COLS
BEAU
KIRP
GREE
NANN
BAUD
MARG
MANN
SCRE
MANE
PEER
MUIR
0.035
0.032
0.046
0.026
0.017
0.024
0.097
0.087
0.062
0.082
0.032
0.065
0.085
0.032
0.044
0.060
0.042
0.037
0.034
0.099
0.090
0.073
0.092
0.045
0.085
0.097
0.046
0.055
0.023
0.036
0.049
0.121
0.103
0.083
0.100
0.053
0.089
0.107
0.038
0.027
0.016
0.043
0.108
0.108
0.074
0.103
0.036
0.080
0.108
0.045
0.026
0.057
0.122
0.114
0.105
0.117
0.060
0.104
0.123
0.017
0.023
0.103
0.094
0.067
0.083
0.037
0.068
0.096
0.029
0.082
0.070
0.056
0.068
0.023
0.056
0.078
0.073
0.064
0.045
0.063
0.027
0.042
0.068
0.015
0.065
0.046
0.058
0.060
0.047
0.070
0.020
0.062
0.041
0.065
0.086
0.020
0.057
0.036
0.065
0.012
0.085
0.042
0.040
0.072
Bradbury, Tapper, Coates, Hankinson, McArthur and Byrne; “How does the post-fire facultative seeding strategy impact genetic variation
and phylogeographic history? The case of Bossiaea ornata (Fabaceae) in a fire-prone, mediterranean-climate ecosystem”; Supplementary
Files
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