HAO-CHIH KUO, SHIANG-FAN CHEN, YIN-PING FANG, JAMES A COTTON,
JOE D PARKER, GÁBOR CSORBA, BURTON K LIM, JUDITH L EGER,
CHIA-HONG CHEN, CHENG-HAN CHOU and STEPHEN J ROSSITER
Supplementary Information
Appendix S1 Materials and methods
Systematic notes on the focal species
Our focal species belong to the genus Murina , a speciose genus with more than 30 known species distributed in the eastern part of the Palearctic, the full range of the
Indo-Malaya and the northern part of the Australasia (see Soisook et al.
2013 who described the 34th species). Phylogenetic studies based on both mitochondrial and nuclear DNA (Kawai et al.
2002; Hoofer et al.
2003; Lack et al.
2010) supported close relationships among bat subfamilies Murininae (includes Murina ), Kerivoulinae and Myotinae, to the exclusion of all other subfamilies in the family Vespertilionidae.
Murina gracilis and M. recondita from Taiwan and M. eleryi from the SE Asian continent have similar body sizes, while M. eleryi from Southern China appears to be slightly smaller. For details of these sizes see Table S1. Furey et al.
(2009) emphasized differences between the colour of the dorsal fur of M. eleryi to that of the
Taiwanese species, while Eger and Lim (2011) noted that colour variation in the former species broadly overlaps with variation in M. gracilis and M. recondita as described by Kuo et al.
(2009). The only diagnostic difference between M. gracilis and M. recondita based on all specimens in Kuo et al.
(2009) and those examined during fieldwork (Kuo et al.
2014) was the pale grey middle portion of the tricolor dorsal fur in M. recondita , while this grey portion was absent in the bicolor dorsal pelage of M. gracilis . Interestingly this character can also be seen in the plate of M. eleryi provided by Furey et al.
(2009: fig. 1C) and was referred to as ‘pale grey-yellow mid-section’ by these authors. All three taxa have similar sized and shaped skulls (Furey et al.
2009; Kuo et al.
2009; Eger & Lim 2011), although Furey et al.
(2009) described minor qualitative differences in their teeth.
Using neighbor-joining, maximum parsimony and maximum likelihood methods, Kuo

(2004) reconstructed phylogenies separately with partial cytochrome b (Cytb ; 1128 bp) and complete NADH dehydrogenase subunit 1 (ND1; 957 bp) genes from up to
12 Murina species (covering the subgenera Harpiola and Murina ). These mitochondrial DNA (mtDNA) phylogenies consistently showed a well-supported sister relationship between M. gracilis and M. recondita . Later, Kuo (2013) used concatenated sequences of the above two genes (1140 bp of Cytb and 800 bp of ND1) to build a Bayesian phylogeny for a total of 44 taxa from the subfamilies Murininae,
Kerivoulinae and Myotinae by which he confirmed among 16 Murina taxa the sister relationship between M. gracilis and M. recondita . Kuo (2013) also included M. eleryi , and found strong evidence supporting a sister relationship between this taxon and the clade comprising M. gracilis and M. recondita . Furthermore, to date this latter phylogeny, Kuo (2013) employed two calibration points which corresponded to the root of all taxa analysed as well as to a split within Myotinae, and employed
Drummond et al.
’s (2006) uncorrelated lognormal relaxed clock algorithm to accommodate rate heterogeneity across the tree; priors in normal distributions for these two calibration points were taken from Lack et al.
(2010) who reconstructed a family-leveled phylogeny based on concatenated sequences of multiple mitochondrial and nuclear markers and used ancient fossil records to calibrate their phylogeny. The resultant dating in Kuo (2013) showed a median estimate for the split between M. eleryi and the common ancestor of M. gracilis and M. recondita as 2.62 (95% CI:
1.86-3.48) million years ago (Ma) and that for the origin of the stem branch leading to the whole clade comprising the three focal taxa as 10.90 (95% CI: 8.60-13.35) Ma.
Thus, molecular and morphological evidence together strongly indicate that M. gracilis , M. recondita and M. eleryi constitute a species complex.
In the last decade, the number of known species of Murina has rapidly increased as a result of the active reporting of new species from East and Southeast Asia (reviewed in Soisook et al.
2013). A full picture of the systematics of the complex containing M. gracilis and its relatives needs morphological and molecular data from more Murina taxa. For this purpose, we suggest, in light of our finding presented in this study, the use of nuclear DNA in addition to the more conventionally used mtDNA (e.g. Francis et al.
2010; Soisook et al.
2013).

Table S1 External measurements showing body sizes of Murina gracilis and its relatives.
Values are means ± standard deviations with the range in the next row. Standard deviation values for M. eleryi are not given due to small sample sizes of this species.
Sex Taxa M FA TIB Source
Males M. gracilis (46)
4.4 ± 0.3 29.2 ± 0.6 13.8 ± 0.4 This study *
3.8 - 5.0 27.9 - 30.4 13.1 - 14.8
M. recondita (34)
4.3 ± 0.3 28.7 ± 0.6 14.1 ± 0.5 This study *
M. eleryi
†
(5)
M. eleryi
‡
(5)
3.8 - 4.8 27.8 - 30.0 13.3 - 15.2
4.4 (4)
3.4
28.3
27
14
4.0 - 5.0 27.7 - 29.4 13.0 - 14.7
12.6
Furey et al.
(2009)
Eger & Lim
M. eleryi
M. eleryi
§
**
(3)
(1)
3.0 - 4.0 26.5 - 27.3 12.2 - 13.5
4
?
¶
28.7
?
¶
13.5
?
¶
(2011)
Eger & Lim
(2011)
4 28.3 14.2
Females M. gracilis (25)
5.3 ± 0.4 31.0 ± 0.7 14.3 ± 0.4
Eger & Lim
(2011)
This study
*
4.3 - 6.0 29.2 - 32.0 13.7 - 15.1
M. recondita (33)
5.1 ± 0.4 30.6 ± 0.6 14.4 ± 0.4 This study *
M. eleryi
†
(6)
4.3 - 6.0 29.1 - 31.7 13.8 - 15.3
4.7 29.9 13.6 Furey et al.
4.0 - 5.5 28.6 - 31.3 12.8 - 14.8 (2009)
M, body mass (g); FA, forearm length (mm); TIB, tibia length (mm).
*
From fieldwork undertaken by HCK (see Kuo et al.
2014); juveniles of both sexes and pregnant females excluded.
†
From three sites in Northern Vietnam.
‡
From Southern China.
§
From Central Vietnam.
¶
Not provided in the source reference.
**
From Central Laos.

Table S2 Details of 13 voucher specimens of Murina eleryi sampled for genetic analyses. GPS coordinates and the altitude are given in decimal degrees and metres above sea level, respectively.
Catalog No. Country Province Locality GPS-E GPS-N Altitude
HNHM
2007.28.2 Vietnam Bac Kan
ROM
111286 Vietnam Quang Nam
Bac Thong district of Kim Hy Nature Reserve
Ngoc Linh Base Camp, 10 km SW Nuoc Xa
22.247
15.200
105.973
108.033
735
830
111300
111308
111360
111399
Vietnam
Vietnam
Vietnam
Vietnam
Quang Nam
Quang Nam
Quang Nam
Quang Nam
Ngoc Linh Base Camp, 10 km SW Nuoc Xa
Ngoc Linh Base Camp, 10 km SW Nuoc Xa
Noc Ong Toan, Tran Don
8 km ENE Nuoc Xa
15.200 108.033 830
15.200 108.033 830
15.233 108.033
?
*
?
*
?
200
116071
116099
116124
116182
116190
116199
116200
China
China
China
China
China
China
China
Guangxi
Guangxi
Guangxi
Guangxi
Guangxi
Guangxi
Guangxi
Jingxi County Provincial Nature Reserve
Jingxi County Provincial Nature Reserve
Jingxi County Provincial Nature Reserve
Jingxi County Provincial Nature Reserve
Jingxi County Provincial Nature Reserve
Jingxi County Provincial Nature Reserve
Jingxi County Provincial Nature Reserve
23.117
23.117
23.117
23.117
23.117
23.117
23.117
105.967
105.967
105.967
105.967
105.967
105.967
105.967
978
978
978
978
978
978
978
HNHM, Hungarian Natural History Museum; ROM, Royal Ontario Museum.
*
Provided GPS coordinates (1.867ºE, 108.150ºN) are questionable with reference to the recorded locality.

Table S3 Primer pairs for amplification of flanking regions of 10 microsatellite loci.
Locus Pirmer pair
Target length
*
(bp)
A4
A9
F: TCCACTAGCCACATCTCTGT
R: TTTTCAGTAACCACCAGAGG
F: TTAGGGGAGTCTGAAAAAGG
R: TCCCAGATCCACTTTACAGG
A104 F: CTCTCAGACCTGGCTTGC
R: GGGCCTAATGCCAAAGTT
A109 F: TTGAACCTGGGCTTAATCTT
R: CGGTGGACCTTGTTTGTT
A118 F: TCTCAGAGTCAGCCGGAAT
R: ACATTCTGGATTTGCAACAA
A122 F: TTCTAAATTCCATCCAACTCC
R: CTCACTAGGCACAGAGTCCA
B5 F: TCAGTCTAGCGCAGTTCTCA
R: TCCACAGTGGTGTCCCTTA
B114 F: GGCCTCAGGATTGGATAAG
R: GGAATCGAACCAGTGACCT
B124 F: TCATTAGCAAAACTCCGACTC
R: TTCCTAATCTGATCACCCATT
D117 F: GCATCCTTATGGGCATGAT
R: GAAAAGGGGCTGCTGTAAC
*
Priming sites removed.
181
194
286
321
225
106
197
140
251
238

Selection of a demographic model for the ncDNA *BEAST analysis.
In order to select between two demographic models for the the ncDNA *BEAST analysis - the piecewise-constant (PC) model versus piecewise-linear and constant root (PLCR) model - we calculated the Bayes factor (BF). The latter model assumes that populations change size linearly through time between divergence events and the size of each ancestral population is equal to the sum of those of its corresponding pair of descendant populations. To estimate the marginal likelihood under each of the two demographic models, which was used in turn to calculate the BF, we adopted both path sampling (PS, Ogata 1989; Gelman & Meng 1998) and stepping-stone sampling
(SS, Xie et al.
2011) estimators. Simulation studies suggested improved accuracies in model selection based on these estimators compared to competing ones (Baele et al.
2012; Baele et al.
2013).
To perform these marginal likelihood estimators, we built two independent MCMC chains in the program BEAST, each comprising a path made of 200 steps of power posteriors. These chains had directly followed those constructed for the standard
*BEAST analysis (see Methods) and, therefore, no further burn-in was specified. We specified a length of 0.5 million iterations for each of the 200 steps (1,000 iterations per sample). From the generated samples of power posteriors, we estimated target marginal likelihood values via Baele et al.
’s (2012) BEAST-implemented scripts for the PS and SS methods.
We obtained consistent estimates both across chains and across methods. When combined across chains, the BF values derived using PS and SS methods for PLCR over PC were 0.038 and 0.026, respectively, indicative of favoring the PC model
(Jeffreys 1961).

Table S4 Estimated proportions of ‘foreign’ genetic composition for four individual bats of Murina recondita as inferred from
STRUCTURE analyses. Labels of individuals follow Figure 1. Values are shown for the analysis based on all 14 microsatellite loci and also for a reduced dataset of 13 loci when each locus was in turn removed.
Locus removed
Individual
14 loci
A4 A9 A10 A104 A109 A118 A122 B5 B9 B114 B121 B124 D110 D117
RA
RB
RC
RD
0.37 0.23 0.06 0.70 0.48 0.29 0.27 0.35 0.41 0.48 0.34 0.53 0.43 0.42 0.30
0.11 0.07 0.08 0.11 0.07 0.09 0.17 0.05 0.09 0.13 0.08 0.12 0.04 0.13 0.17
0.11 0.13 0.20 0.03 0.11 0.07 0.21 0.04 0.07 0.05 0.08 0.11 0.04 0.12 0.09
0.27 0.24 0.09 0.24 0.27 0.23 0.26 0.32 0.26 0.22 0.16 0.25 0.16 0.19 0.19

Figure S1 Median-joining networks built for the Murina gracilis complex based on 10 microsatellite flanking regions. Unique haplotypes are colour-coded for M. gracilis (yellow), M. recondita (dark blue), M. eleryi 1 (light blue), and M. eleryi 2 (pink). Dashed lines and ellipses indicate haplotypes (for loci A104 and B124) and branches (for loci A4 and A109), respectively, that were removed by the IMgc software in order to avoid violations of the four gamete test and thus ensure suitability for downstream coalescent-based analyses.

Figure S2 Marginal densities for demographic parameters from a four-taxon IM analysis of the Murina gracilis complex, including (a) split times (Ma), (b) migration rates scaled by the mutation rate and (c) effective population sizes (thousand individuals). These are based on the 4PM2 prior. See Figure 4 for the abbreviations of taxon names and split times. Only plots for migration rates with nonzero peaks are presented in (b).

Table S5 IM estimates based on all four taxa from the Murina gracilis complex.
Values are obtained with 4PM2 and 4PME0.5 priors and are presented as modes with corresponding 95% confidence intervals in row directly below. Parameters include the split time (T, Ma), population migration rates (2NM, per generation) and effective population sizes (N, thousand individuals). See Figure 4 for the abbreviations of taxon names and split times. Asterisks denote significant results from Nielsen and Wakeley’s
(2001) tests based on 2NM (*, P < 0.05).
Parameter
T1
T2
T3
2NM
2NM
2NM
2NM
2NM
2NM
G→R
R→G
G→E1
E1→G
G→E2
E2→G
4PM2 4PME0.5
1.36
0.174-2.086
1.807
1.221
0.142-2.026
1.863
1.119-2.542 1.105-2.574
2.291 2.3
1.830-4.649 1.728-4.649
0 0
0-0.039 0-0.031
0 0
0-0.075 0-0.063
0 0
0-0.202 0-0.179
0 0
0-0.086 0-0.072
0 0
0-0.168 0-0.145
0 0
0-0.077
2NM
R→E1
* 0.322*
2NM
2NM
E1→R
R→E2
0.007-1.037
0.036
0-0.106
0.08
0-0.501
0-0.065
* 0.212*
0-0.757
0.017
0-0.084
0.071
0-0.419
2NM
E2→R
0 0
0-0.067 0-0.047
2NM
E1→E2
0.063 0.028
0-0.825 0-0.613
Parameter
2NM
E2→E1
* 0.347* * 0.245*
0-0.987 0-0.805
2NM
G→A1
2NM
A1→G
2NM
E2→A1
2NM
A1→E2
2NM
G→A2
2NM
A2→G
N
G
N
R
N
E1
N
E2
N
A1
N
A2
N
A3
4PM2 4PME0.5
0
0
0
0
0
0.279
27
0
2
0
0-2.911 0-1.384
0
0-0.496 0-0.378
0
0-3.456 0-2.144
0
0-1.32 0-0.935
0
0-2.201 0-1.234
0
0-0.525 0-0.496
126 132
72-203 78-211
33
9-63 12-76
322 348
159-617 171-677
319 349
172-563 197-598
483
0-1453 129-1453
2
0-1193 0-1265
2 2
0-1255 0-1100

Figure S3 Marginal densities for demographic parameters from IM analyses for the 6 two-taxon pairs of the Murina gracilis complex, including (a) split times (Ma), (b) migration rates scaled by the mutation rate and (c) effective population sizes
(thousand individuals). These are based on the 2PM2 prior. See Figure 4 for the abbreviations of taxon names.

G - E1
Table S6 IM estimates for six pairs of two taxa from the Murina gracilis complex. Values are obtained under 2PM2 and 2PME0.5 priors and are presented in the format as in Table S4 (Supporting information). modes with 95% confidence intervals given in the row directly below. Units of different demographic parameters are also as in Table S4. See Figure 4 for the abbreviations of taxon names (‘A’ refers to the ancestral population for each taxon pair). Asterisks mark significant results from Nielsen and Wakeley’s
(2001) tests based on 2NM (*, P < 0.05; **, P < 0.01).
Taxon pair Parameter 2PM2
Prior
2PME0.5
Taxon pair Parameter 2PM2
Prior
2PME0.5
G - R T
2NM
G→E2
2NM
E2→G
N
N
N
T
N
N
N
G
E2
A
R
E1
A
2NM
2NM
R→E1
E1→R
1.556 1.612
0.747-3.514 0.788-3.142
0 0
0-0.340 0-0.251
0 0
0-0.097 0-0.075
130 134
72-214 76-217
361 374
194-649 207-664
225 219
0-761 0-649
1.105 1.077
0.226-4.644 0.212-2.560
* 0.367* * 0.229*
0-1.607 0-1.111
** 0.046** ** 0.026**
0.006-0.122 0-0.096
28 34
11-68 12-78
451 475
211-1028 232-1059
0 2
0-636 0-405
T
2NM
2NM
N
N
N
T
N
N
N
G
R
A
G
E1
A
G→R
R→G
2NM
G→E1
2NM
E1→G
1.156 1.16
0.640-4.649 0.444-4.644
0.035 0
0-0.098 0-0.072
0 0
0-0.085 0-0.069
98 108
47-180 55-191
33 40
11-79 14-89
0 191
0-1334 0-1233
1.565 1.495
0.840-2.793 0.867-2.733
0 0
0-0.236 0-0.196
0 0
0-0.095 0-0.074
132 133
73-213 76-216
434 441
241-786 248-793
169 166
0-497 0-476
G - E2
R - E1

Table S6 Continued.
Taxon pair Parameter 2PM2
Prior
2PME0.5
R - E2
E1 - E2
T
2NM
2NM
N
N
N
T
N
N
N
R
E2
A
E1
E2
A
R→E2
E2→R
2NM
E1→E2
2NM
E2→E1
1.453 1.402
0.588-4.644 0.398-4.649
0.114 0.085
0-0.617 0-0.461
** 0.040** ** 0.023**
0.004-0.111 0.001-0.086
30 37
11-72 14-84
291 326
145-588 166-630
36 0
0-1059 0-687
1.374 1.398
0.681-2.644 0.663-2.495
0.4 * 0.214*
0-1.067 0-0.842
0.3373 * 0.239*
0-1.137 0-0.881
403 424
209-777 227-803
335 366
178-626 194-660
130 133
0-377 0-372

Tests of positive selection
We screened for signatures consistent with positive selection on several branches of the gene tree, each of which corresponded to a different scenario (see Fig S4). Specifically, positive selection could have acted before secondary contact, possibly on the Taiwanese lineage (in M. gracilis ), on the continental lineage (in the common ancestor of M. recondita and M. eleryi ) or on both lineages then, leaving mitochondrial genomes better adapted to their surrounding environments than to more distant ones. It followed that we expected signatures of positive selection on the stem branch of M. gracilis and M. recondita (labeled as branch I in Fig S4), on the stem branch of the two M. eleryi taxa
(branch II) or on both these branches along the reconstructed mitochondrial gene tree. To infer natural selection, we thus examined the ratio of the rates of nonsynonymous to synonymous codon substitutions, termed ω, for the proposed branches; a value of ω =
1 suggested a neutrally evolving gene while values of >1 and <1 indicated positive selection and purifying selection, respectively (Yang et al.
2000). For estimating ω values, we fitted codon substitution models to coding regions of our focal mitochondrial genes (1404 bp) and conducted maximum likelihood analyses in PAML
4.7 (Yang 2007). Given that the approaches implemented in PAML estimate ω values based on phylogenetic tree which is unsuitable for modeling the intra-specific genealogy (Posada & Crandall 2001), we selected for each of the four focal taxa the most abundant haplotype as a representative while we kept inter-taxon relationships as those estimated from *BEAST. Concatenated mitochondrial sequences for two outgroup taxa, Murina puta and Murina tiensa , were included so that codon substitutions on branches I and II can be estimated separately. See Table S7 for further information of all sequences used.
We first investigated whether the two proposed branches (foreground branches) had ω values that differed from each other, or from the background ω value. We compared this to a null model in in which a single ω was fitted across the tree, and performed a likelihood ratio test (LRT) for model selection (Yang 1998). The LRT suggested no better performance of the hypothesized branch model than the null model (2∆ = 3.020, df = 2, P = 0.221).
We also screened for evidence of positive selection acting on a subset of sites on these key branches, using the branch-site model. We compared a model in which ω was allowed to exceed one on the foreground branch only (Zhang et al.
2005) to a null model in which it was fixed at 1. The LRT provided no support for the alternative models over corresponding null models (2∆ = 0, df = 1, P = 1 in both cases). The two

null models gave consistent estimates, with ω = 0.005 for 96.7% of the total sequence and ω = 1 for the rest 3.3%.
Apart from the above ω-based tests, we also performed the McDonald-Kreitman test
(MKT, McDonald & Kreitman 1991) in which information on intra-specific polymorphism was used in addition to that of inter-specific divergence for inferring action of natural selection. More specifically, when standardized respectively by inter- and intra-specific synonymous variation, a higher level of inter-specific nonsynonymous variation than intra-specific nonsynonymous variation suggested positive selection; purifying selection would be inferred when an opposite trend between these two sorts of nonsynonymous variation was observed. We applied MKT, implemented in DnaSP 5.10.01 (Librado & Rozas 2009), to four possible sets of pairwise comparisons each of which contain one Taiwanese and one continental taxon.
All available sequences for the comparing taxa were used (see Table 1 of the main text), with Cytb and COI analysed separately as well as in concatenation. The results of these MKTs failed to detect positive selection or purifying selection regardless of taxa compared and gene analysed (Fisher’s exact tests, P = 0.101-1.000).
Figure S4 A mitochondrial gene tree used in tests of positive selection. The gene tree was obtained from the *BEAST analysis applied to concatenated cytochrome b (Cytb ) and cytochrome c oxidase subunit 1 (COI) sequences (see Results of the main text for details); genealogies within four clades representing the four focal taxa of this study were collapsed into triangles with heights indicating medians of time to the most recent common ancestor (TMRCA).

Table S7 Sources of mitochondrial sequences used in maximum likelihood analyses in
PAML to test for signatures of positive selection.
Accession no.
Taxon Cytb COI Voucher Reference
M. gracilis KJ198046 KJ198484 No voucher
M. recondita KJ198165 KJ198593 No voucher
M. eleryi 1 KT762300 HM540937 ROM 116071
M. eleryi 2
M. puta
M. tiensa
KT762296
KJ198364
GQ168913
HM540933
KT982277
KT982278
ROM 111300
No voucher
HNHM 2007.28.1
Kuo
Kuo
Kuo et al.
et al.
Francis
Francis et al.
this study
(2014)
(2014) this study; et al. this study; et al.
(2010)
(2010)
(2014);
NCBI unpublished data; this study

Tests for sex-biased dispersal in Murina gracilis and M. recondita
In our previous study of range-wide we typed 106 M. gracilis and 144 M. recondita , at 17 microsatellite loci (Kuo et al.
2014). Here we used these datasets and applied both ‘population-level’ and ‘individual-level’ analyses to test for evidence of sex-biased dispersal within each species. For the population-level analyses, we performed permutation tests described in Goudet et al.
(2002) based on the following four statistics: F
IS
and F
ST
(Weir & Cockerham 1984) as well as mean and variance of the Assignment Index - an expression of how likely an individual’s genotypes were born in the population where it is sampled (Paetkau et al.
1995; Favre et al.
1997).
These methods detect differences between sexes in the level of instantaneous dispersers among populations (before such dispersers equally transmit carried genes to both sexes in the next generation), with expectations that the less philopatric sex will show a higher level of within-population F
IS
and variance of the Assignment
Index (vAI), and a lower level of within-population mean of the Assignment Index
(mAI) than the more philopatric sex.
Figure S5 Samples of (a) Murina gracilis and (b) Murina recondita analysed for sex-biased dispersal.
(a) (b)
N
F
N
M
= 11
= 8
N
F
N
M
= 10
= 6
N
F
N
M
= 13
= 29
N
F
N
M
= 10
= 33
N
F
N
M
= 8
= 8
N
F
N
M
= 5
= 23 N
F
N
M
= 8
= 8
N
F
N
M
= 3
= 8
N
F
N
M
= 22
= 19
N
F
N
M
= 8
= 10
As shown in the above maps (Fig. S5), four and six populations of M. gracilis and
M. recondita , respectively, were delimited according to our previous analyses (Kuo et al.
2014) via the Bayesian clustering method implemented in STRUCTURE
(Pritchard et al.
2000); N
F
and N
M
denoted sample sizes of females and males in the corresponding populations in the maps. One population of M. recondita (delimited by dashed lines) was excluded from analyses due to a small sample size (<5 individuals)

of females. To test for significance, we conducted 2,000 permutations (on the sex within populations) to obtain null distributions of the difference (for F
IS
, F
ST
and mAI) or the ratio (vAI) of the focal statistics between sexes (see Goudet et al.
2002 for further explanation). One-tailed tests were performed under the anticipation that the female is the more philopatric sex, as seen in several species of the genus Myotis
(Castella et al.
2001; Kerth et al.
2002; Arnold 2007), a close relative to Murina
(Kawai et al.
2002; Hoofer et al.
2003; Lack et al.
2010). All above analyses were carried out with the program FSTAT 2.9.3.2 (Goudet 2001).
For individual-level analyses, we used the bootstrap method described in Banks and
Peakall (2012) for detecting sex-differences in the the extent of genetic spatial autocorrelation. Both empirical (e.g. Banks et al.
2005; Double et al.
2005) and simulation (Banks & Peakall 2012) studies suggest within-population genetic spatial autocorrelation is significantly higher, in the more philopatric sex, and that this can be conveniently shown in a correlogram. For each focal species, we estimated pairwise individual-by-individual geographic distances based on Euclidean distances (derived from GPS coordinates, see Dryad entry doi:10.5061/dryad.f5th5) and these were then related to genetic distance based on Smouse and Peakall’s (1999). We calculated the autocorrelation coefficient (r) for the ‘first geographic distance class’ (see below) and performed bootstrap resampling of 10,000 replicates to estimate the 95% CI of r for each sex. Following Banks and Peakall (2012), we inferred significant sex-differences on the basis of zero overlap of the 95% CIs.
Because our sample sizes corresponding to short distance classes were small, which can reduce statistical power (Peakall et al.
2003; Banks & Peakall 2012), we performed spatial autocorrelation analyses using the following larger geographic distance class: 0-10 km, 0-20 km, 0-30 km and 0-40 km. These analyses were carried out with the program GENALEX 6.501 (Peakall & Smouse 2012).
Results from the population-level analyses are shown in Table S8. Male-biased dispersal was supported in M. gracilis based on F
IS
and mAI, but not in any of the metrics in M. recondita .
Results from the individual-level analyses are shown in Figure S6. We found that females showed higher observed r values than did males. In M. gracilis sex-differences were significantly different within 40 km, while for M. recondita sex-differences were seen within 20 km. To summarize, both population- and individual-level analyses suggested male-biased dispersal in M. gracilis while only

the latter analyses suggested so in M. recondita .
Figure S6 Correlograms of individual-level analyses of sex-biased dispersal for (a)
Murina gracilis and (b) Murina recondita . In each plot, r values and associated 95 %
CIs are coloured black for females and grey for males. Sample sizes of pairwise comparisons are given in the parentheses.
(a)
0.10
0.08
0.06
0.04
0.02
(b)
0.00
0.16
(106)
(359)
(118)
(537)
(118)
(688)
(138)
(871)
0 to 10 0 to 20 0 to 30
Geographic distance class (km)
0 to 40
0.12
0.08
0.04
0.00
(125)
(220)
(137)
(314)
(207)
(428)
(290)
(524)
0 to 10 0 to 20 0 to 30
Geographic distance class (km)
0 to 40

Table S8 Predictions and results of the population-level tests - based on four statistics - for evidence of male-biased dispersal in Murina gracilis and Murina recondita . The four statistics include F
IS
and F
ST
(Weir & Cockerham 1984) as well as mean and variance of the Assignment Index (mAI and vAI, respectively, Paetkau et al.
1995; Favre et al.
1997). For each species, values presented in consecutive rows are estimates of testing statistics for females and males and associated p-values obtained from 2,000 permutations for one-tailed tests under corresponding predictions.
Prediction
F
IS
F < M
F
ST
F > M mAI
F > M vAI
F < M
M. gracilis :
Females
Males p-value
M. recondita :
Females
Males p-value
-0.023
0.032
0.014
0.014
0.008
0.610
0.044
0.038
0.286
0.053
0.046
0.210
1.019
-0.481
0.044
0.623
-0.528
0.075
20.170
15.948
0.724
21.353
19.646
0.709

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