Journal of Biogeography
SUPPORTING INFORMATI ON
Prolonged isolation and persistence of a common endemic on granite outcrops in both
mesic and semi-arid environments in south-western Australia
Sarah-Louise Tapper, Margaret Byrne, Colin J. Yates, Gunnar Keppel, Stephen D. Hopper,
Kimberly Van Niel, Antonius G. T. Schut, Laco Mucina and Grant W. Wardell-Johnson
Appendix S1 Details of sequence amplification and alignment.
Amplification of chloroplast DNA (cpDNA) sequences was conducted in 50-µL reactions
with the following reagents: 40 ng template DNA, 10 µL of 5xPCR Buffer (50 mM KCl,
20 mM Tris–HCl pH 8.4, 0.2 mM dNTPs), 0.1 µM each primer, MgCl2 at 3 mM (trnQ–rs16),
2 mM (trnV–ndhC) or 1.5 mM (psbD–trnT), and 0.1 µL of Taq polymerase following the
protocols of Shaw et al. (2007). Amplification products were sequenced using Macrogen
EZ-seq service (Macrogen, Seoul, South Korea).
CpDNA sequences were edited in SEQUENCHER 5.0 (Genecodes, MI, USA) and
aligned in CLUSTALW in MEGA 5.05 (Tamura et al., 2007). CLUSTALW did not always reach
the most parsimonious alignment as a result of large indels, and sequence alignments
were manually adjusted in MESQUITE 2.74 (Maddison & Maddison, 2007). Sequences of
all three regions were concatenated in MESQUITE and indels coded in SEQSTATE 1.4.1
(Müller, 2005) under Simmons & Ochoterena’s (2000) simple coding scheme.
REFERENCES
Maddison, W.P. & Maddison, D.R. (2007) Mesquite: a modular system for evolutionary analysis. Version
2.75. Available at: http://mesquiteproject.org/.
Müller, K. (2005) SeqState – primer design and sequence statistics for phylogenetic DNA data sets. Applied
Bioinformatics, 4, 65–69.
Shaw, J., Lickey, E.B., Schilling, E.E. & Small, R.L. (2007) Comparison of whole chloroplast genome
sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and
the hare III. American Journal of Botany, 94, 275–288.
Simmons, M. & Ochoterena, H. (2000) Gaps as characters in sequence-based phylogenetic analyses.
Systematic Biology, 49, 369–381.
Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: molecular evolutionary genetics analysis
(MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596–1599.
Eaglestone
Rock*
Merredin
Peak*
Talgomine
Rock 1*
Talgomine
Rock 2*
Little
Frankland
Mehniup
Rock
Mountt
Chudalup
Mountt
Frankland
Muiralup
Rock
Porongurups
Shannon
Rock
Beacon Hill*
Eaglestone Rock*
Merredin Peak*
Talgomine Rock 1*
Talgomine Rock 2*
Little Frankland
Mehniup Rock
Mount Chudalup
Mount Frankland
Muiralup Rock
Porongurups
Shannon Rock
Beacon Hill*
Appendix S2 Genetic differentiation (FST) between pairs of populations of Stypandra glauca in south-western Australia. Bold values refer
to comparisons of populations from different regions (north versus south). Northern populations are marked with asterisks (*).
—
0.144
0.132
0.148
0.166
0.180
0.157
0.153
0.123
0.155
0.106
0.127
—
0.186
0.206
0.215
0.231
0.197
0.190
0.148
0.208
0.173
0.185
—
0.184
0.178
0.244
0.206
0.197
0.188
0.201
0.156
0.180
—
0.091
0.286
0.230
0.237
0.216
0.238
0.188
0.195
—
0.292
0.235
0.236
0.225
0.241
0.198
0.190
—
0.102
0.105
0.049
0.094
0.115
0.121
—
0.055
0.101
0.061
0.100
0.045
—
0.095
0.054
0.106
0.060
—
0.098
0.076
0.095
—
0.114
0.057
—
0.079
—
Appendix S3 Principal coordinates analysis (PCoA) of microsatellite diversity in Stypandra
glauca in south-western Australia, using (a) Bruvo et al. (2004) distances and (b) Euclidean
distances. Crosses mark samples from Little Frankland, Mount Frankland and the Porongurups;
open circles, samples from Beacon Hill, Eaglestone Rock, Merredin Peak, Talgomine Rock 1 and
Talgomine Rock 2; black squares, samples from Mehniup Hill, Mount Chudalup, Muiralup Rock
and Shannon Rock.