Journal of Biogeography
SUPPORTING INFORMATION
Discordant population expansions in four species of coral-associated Pacific hermit crabs (Anomura: Diogenidae)
linked to habitat availability resulting from sea-level change
Iliana B. Baums, L. Scott Godwin, Erik C. Franklin, Dave B. Carlon and Robert J. Toonen
Appendix S1 Cytochrome c oxidase subunit I sequence variation in four Pacific species of Calcinus. Tajima’s D tests whether a
population is stable and evolving under neutrality. Fu’s FS is a powerful test for detecting population growth and hitchhiking
(Fu, 1997).
C. haigae
C. hazletti
C. laevimanus
C. seurati
Mean (SD)
Haplotypes
Number
120
67
88
89
91 (21.83)
Polymorphic sites
First codon position
Second codon position
Third codon position
Total
18
4
98
120
13
2
54
69
21
0
89
110
15
0
91
106
16.75 (2.50)
1.50 (1.91)
83 (19.71)
101.25 (22.29)
All sites
Parsimony-informative
Singleton variable sites
Synonymous changes
Replacement changes
Haplotype diversity (SD)
Nucleotide diversity, π
k (variance)
Fu’s FS
Tajima’s D
69
51
103
17
0.957 (0.01)
0.008
4.570 (5.085)
−24.614***
−2.437 **
28
41
63
6
0.685 (0.00)
0.002
1.196 (0.592)
−25.922***
−2.765***
81
29
106
7
0.989 (0.00)
0.016
8.850 (16.857)
−24.260***
−1.870 ***
79
27
101
10
0.983 (0.00)
0.018
10.114 (21.592)
−24.112**
−1.489*
64.25 (24.73)
37 (11.20)
93.25 (20.27)
10 (4.97)
0.90 (0.15)
0.01 (0.01)
6.18 (4.08)
−24.73 (0.82)
−2.36 (0.39)
**P < 0.01; *P < 0.05. Variance of k estimated under assumption of no recombination. Total length of alignments is 568 bp. SD, standard
deviation; k, average number of nucleotide differences (calculated by DNASP 5 and ARLEQUIN 3.1.1 using all sites).
Appendix S2 Neighbourjoining tree of COI sequences from Pacific Calcinus
species, produced by
FASTTREE assuming a
GTRnt model (Price et al.,
2009). To account for the
varying rates of evolution
across sites, FASTTREE
uses a single rate for each
site. Phylogenetic trees
were built using the
neighbour-joining
(NJ)
algorithm. We chose to
use NJ to depict population structure because it
performs reasonably well
over a broad range of evolutionary histories (Kalinowski, 2009). The scale bar is in substitutions per site. The reliability of each split in the tree is estimated by computing local
support values with the Shimodaira–Hasegawa test (Shimodaira & Hasegawa, 1999). Clades as designated by Malay & Paulay
(2010) are given above the branches (Roman numerals). Red indicates clades with different positions than in Malay & Paulay
(2010). The focal species are in blue. Sequences for most groups outside the focal taxa are from Malay & Paulay (2010). Taxa
with number codes are probable cryptic species; 07_4283 (C. haigae aff.) was collected from Palmyra Atoll. Tree available in
TreeBase. All sequences available in GenBank.
Appendix S3 Species-level neighbour-joining tree of COI sequences for (a) Calcinus
haigae, (b) C. hazletti, and (c) C. laevimanus and C. seurati.
(a)
(a) Calcinus haigae neighbour-joining tree of COI sequences, produced by FASTTREE,
assuming a GTRnt model. Local support values > 0.80 are shown. The outgroups are Calcinus
minutae, Calcinus nitidus and Calcinus rosaceus, based on the phylogeny of the genus (Malay
& Paulay, 2010). Colours indicate sampling sites. The scale bar is in substitutions per site.
The tree is available in TreeBase.
(b)
(b) Calcinus hazletti neighbour-joining tree of COI sequences. Produced by FASTTREE assuming a GTRnt model. Given are local support
values > 0.80. Outgroups are C. hazletti aff. and C. haigae based on the phylogeny of the genus (Malay & Paulay, 2010). Colour indicates
sampling sites. The scale bar is in substitutions per site. Tree available in TreeBase.
(c)
(c) Calcinus laevimanus
and C. seurati neighbourjoining tree of COI
sequences. Produced by
FASTTREE assuming a
GTR/NT model. Branches
with local support values
> 0.80 are indicated.
Calcinus laevimanus and
Calcinus seurati are sister
taxa and Calcinus
explorator is the outgroup
to both based on the
phylogeny of the genus
(Malay & Paulay, 2010).
Colour indicates sampling
sites. The scale bar is in
substitutions per site. The
tree is available in
TreeBase.
REFERENCES
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hitchhiking and background selection. Genetics, 147, 915–925.
Kalinowski, S.T. (2009) How well do evolutionary trees describe genetic relationships
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634–662.
Price, M.N., Dehal, P.S. & Arkin, A.P. (2009) FastTree: computing large minimum evolution
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Shimodaira, H. & Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114–1116.