Table S2. Basic Description of Microsatellite Loci Used

Supplementary/Appendices

Table S1. Museum number with no prefix is the mammal collection of the Museum of Vertebrate Zoology, University of California, Berkeley, California. FMNH prefix is the Field Museum of Natural History, Chicago, Illinois. ABTC prefix is the South Australian Museum. CBGP refers to Centre de Biologie et de Gestion des Populations, Montpellier, France. MahaU refers to Mahasarakham University, Mahasarakham, Thailand. UKMNH refers to University of Kansas Museum of Natural History. The haplotype name where used by Aplin et al. (2011) is shown by the reference.

Museum Number / Cytochrome b Genbank # / Phylogenetic species group assignment / General Locality / Microsatellite genotyped? / DNAsp hap / Reference
OUTGROUPS
186533 / JQ824369 / Niviventer langbianis / Vietnam / 9 / this study
176530 / JQ814207 / andamensis / China / 55 / this study
176532 / JQ814208 / andamensis / China / 54 / this study
193095 / JN675485 / andamensis / China / 53 / Aplin et al. (2011) 100Ran_48
193096 / JQ814211 / andamensis / China / 55 / this study
FMNH168825 / JQ814249 / andamensis / Cambodia / 38 / this study
specimen voucher R3087 / HM217403 / andamensis / Thailand / 17 / Pagès et al. (2010)
186526 / JQ814264 / losea / Vietnam / Y / 41 / this study
226407 / JQ814283 / norvegicus / Oakland, California / 2 / this study
ABTC 48063 / EU349762 / Maxomys bartelsii / Indonesia / 23 / Rowe et al. (2008)
Sample R2953, no voucher / HM217396 / andamensis / Thailand / 16 / Pagès et al. (2010)
HS130/KT2832 / AB033701 / argentiventer / Indonesia / 31 / Suzuki et al. (2000)
CB0001 / HM217362 / argentiventer / Cambodia / 15 / Pagès et al. (2010)
CB0104 / HM217364 / argentiventer / Cambodia / 15 / Pagès et al. (2010)
Sample R3484, no voucher / HM217421 / Clade 5 - sakeratensis / Thailand / 13 / Pagès et al. (2010)
Sample R3510, no voucher / HM217423 / Clade 5 - sakeratensis / Thailand / 12 / Pagès et al. (2010)
ABTC 48025 / EF186514 / Clade 6 - tiomanicus / Indonesia / 25 / Robins et al. (2007)
Sample R1833, no voucher / HM217391 / Clade 6 - tiomanicus / Thailand / 14 / Pagès et al. (2010)
FMNH 142350 / DQ191485 / everetti / Philippines / 30 / Jansa et al. (2006)
Sample R5349, voucher at CBGP / HM217470 / exulans / Thailand / 18 / Pagès et al. (2010)
Sample R5447, voucher at CBGP / HM217472 / exulans / Thailand / 18 / Pagès et al. (2010)
ABTC 8615 / EF186438 / fuscipes / Australia / 29 / Robins et al. (2007)
ABTC 8605 / EF186439 / fuscipes / Australia / 28 / Robins et al. (2007)
ABTC 65754 / EF186441 / hoffmanni / Indonesia / 27 / Robins et al. (2007)
ABTC 65809 / EF186442 / hoffmanni / Indonesia / 27 / Robins et al. (2007)
ABTC 65753 / EF186443 / hoffmanni / Indonesia / 27 / Robins et al. (2007)
UKMNH 160771 / EU349781 / leucopus / Papua New Guinea / 22 / Rowe et al. (2008)
sample L0180, voucher at MahaU / HM217478 / nitidus / Laos / 20 / Pagès et al. (2010)
sample L0192, voucher at MahaU / HM217479 / nitidus / Laos / 19 / Pagès et al. (2010)
Sample Haiphong port #20, no voucher / AB355903 / norvegicus / Vietnam / 1 / Truong et al. (2009)
ABTC 41168 / EF186480 / sordidus / Australia / 26 / Robins et al. (2007)
ABTC 51688 / EF186518 / tunneyi / Australia / 24 / Robins et al. (2007)
ABTC 00549 / EU349783 / villosissimus / Australia / 21 / Rowe et al. (2008)
Non-North America R. rattus Lineage II, IV
MSB141265 / JQ814256 / Clade 2 - tanezumi / China / Y / 3 / this study
MSB141286 / JQ814260 / Clade 2 - tanezumi / China / Y / 4 / this study
MSB141293 / JQ814262 / Clade 2 - tanezumi / China / Y / 32 / this study
MSB141273 / JQ814258 / Clade 2 - tanezumi / China / Y / 33 / this study
MSB141295 / JQ814263 / Clade 2 - tanezumi / China / Y / 33 / this study
MSB141266 / JQ814257 / Clade 2 - tanezumi / China / Y / 33 / this study
MSB141289 / JQ814261 / Clade 2 - tanezumi / China / Y / 34 / this study
MSB141261 / JQ814255 / Clade 2 - tanezumi / China / 33 / this study
MSB141279 / JQ814259 / Clade 2 - tanezumi / China / Y / 33 / this study
176528 / JN675576 / Clade 2 - tanezumi / China / Y / 7 / Aplin et al. 99RrII_47
176526 / JN675575 / Clade 2 - tanezumi / China / Y / 56 / Aplin et al. 98RrII_47
176527 / JQ814205 / Clade 2 - tanezumi / China / Y / 56 / this study
176529 / JQ814206 / Clade 2 - tanezumi / China / Y / 56 / this study
JL1113/HS1734, table 1 in Suzuki et al. 2003 / AB096841 / Clade 2 - tanezumi / China / 60 / Suzuki et al. (2000)
ABTC 8489 / EF186440 / Clade 2 - tanezumi / China / 42 / Robins et al. (2007)
ABTC 47993 / EF186491 / Clade 2 - tanezumi / Indonesia / 46 / Robins et al. (2007)
ABTC 47981 / EF186493 / Clade 2 - tanezumi / Indonesia / 61 / Robins et al. (2007)
ABTC 47982 / EF186494 / Clade 2 - tanezumi / Indonesia / 62 / Robins et al. (2007)
ABTC 47983 / EF186495 / Clade 2 - tanezumi / Indonesia / 61 / Robins et al. (2007)
ABTC 47984 / EF186502 / Clade 2 - tanezumi / Indonesia / 7 / Robins et al. (2007)
ABTC 47985 / EF186503 / Clade 2 - tanezumi / Indonesia / 61 / Robins et al. (2007)
ABTC 47986 / EF186504 / Clade 2 - tanezumi / Indonesia / 7 / Robins et al. (2007)
ABTC 47987 / EF186505 / Clade 2 - tanezumi / Indonesia / 7 / Robins et al. (2007)
ABTC 47989 / EF186507 / Clade 2 - tanezumi / Indonesia / 7 / Robins et al. (2007)
sample HS2393, no voucher / AB211040 / Clade 2 - tanezumi / Japan / 42 / Chinen et al. (2005)
sample HS2211, no voucher / AB211041 / Clade 2 - tanezumi / Japan / 42 / Chinen et al. (2005)
ABTC 8487 / EF186508 / Clade 2 - tanezumi / Japan / 42 / Robins et al. (2007)
ABTC 8514 / EF186509 / Clade 2 - tanezumi / Japan / 42 / Robins et al. (2007)
ABTC 8562 / EF186510 / Clade 2 - tanezumi / Japan / 42 / Robins et al. (2007)
138636 / JN675595 / Clade 2 - tanezumi / Papua New Guinea / 42 / Aplin et al. 142RrII_72
FMNH178425 / JQ814251 / Clade 2 - tanezumi / Philippines / Y / 40 / this study
FMNH178426 / JQ814252 / Clade 2 - tanezumi / Philippines / Y / 40 / this study
186531 / JQ814267 / Clade 2 - tanezumi / Vietnam / Y / 5 / this study
186532 / JN675484 / Clade 2 - tanezumi / Vietnam / Y / 6 / Aplin et al. 97Ran_46
186534 / JQ814268 / Clade 2 - tanezumi / Vietnam / Y / 7 / this study
186541 / JQ814269 / Clade 2 - tanezumi / Vietnam / Y / 8 / this study
186542 / JQ814270 / Clade 2 - tanezumi / Vietnam / Y / 7 / this study
186527 / JQ814265 / Clade 2 - tanezumi / Vietnam / Y / 7 / this study
186529 / JQ814266 / Clade 2 - tanezumi / Vietnam / Y / 42 / this study
186530 / JN675483 / Clade 2 - tanezumi / Vietnam / Y / 43 / Aplin et al. 96Ran_46
186525 / JQ814209 / Clade 2 - tanezumi / Vietnam / Y / 7 / this study
186528 / JQ814210 / Clade 2 - tanezumi / Vietnam / Y / 51 / this study
sample Haiphong port #42, no voucher / AB355899 / Clade 2 - tanezumi / Vietnam / 42 / Truong et al. (2009)
sample Haiphong port #72, no voucher / AB355900 / Clade 2 - tanezumi / Vietnam / 42 / Truong et al. (2009)
sample Haiphong port #82, no voucher / AB355901 / Clade 2 - tanezumi / Vietnam / 7 / Truong et al. (2009)
FMNH145705 / JQ814243 / Clade 4 - tanezumi / Philippines / Y / 36 / this study
FMNH146916 / JQ814244 / Clade 4 - tanezumi / Philippines / Y / 36 / this study
FMNH147773 / JQ814245 / Clade 4 - tanezumi / Philippines / Y / 37 / this study
FMNH147779 / JQ814246 / Clade 4 - tanezumi / Philippines / Y / 37 / this study
FMNH166498 / JQ814247 / Clade 4 - tanezumi / Philippines / Y / 36 / this study
FMNH166503 / JQ814248 / Clade 4 - tanezumi / Philippines / Y / 36 / this study
FMNH168826 / JQ814250 / Clade 4 - tanezumi / Philippines / 39 / this study
FMNH198515 / JQ814253 / Clade 4 - tanezumi / Philippines / Y / 36 / this study
FMNH198519 / JQ814254 / Clade 4 - tanezumi / Philippines / Y / 36 / this study
FMNH 137032 / DQ191488 / Clade 4 - tanezumi / Philippines / 36 / Jansa et al. (2006)
Non-North American R. rattus Lineage I, III
192025 / JQ814271 / Clade 1 - rattus / Iran / 44 / this study
216971 / JQ814272 / Clade 1 - rattus / Madagascar / Y / 45 / this study
216972 / JQ814273 / Clade 1 - rattus / Madagascar / Y / 45 / this study
216973 / JQ814274 / Clade 1 - rattus / Madagascar / Y / 45 / this study
216978 / JQ814275 / Clade 1 - rattus / Madagascar / Y / 45 / this study
216979 / JQ814229 / Clade 1 - rattus / Madagascar / Y / 45 / this study
216980 / JQ814276 / Clade 1 - rattus / Madagascar / Y / 45 / this study
216983 / JQ814277 / Clade 1 - rattus / Madagascar / Y / 45 / this study
216989 / JQ814278 / Clade 1 - rattus / Madagascar / Y / 45 / this study
216991 / JQ814279 / Clade 1 - rattus / Madagascar / Y / 45 / this study
216999 / JQ814230 / Clade 1 - rattus / Madagascar / Y / 45 / this study
217008 / JQ814231 / Clade 1 - rattus / Madagascar / Y / 45 / this study
217031 / JQ814280 / Clade 1 - rattus / Madagascar / 45 / this study
221216 / JQ814236 / Clade 1 - rattus / Madagascar / Y / 45 / this study
221217 / JQ814237 / Clade 1 - rattus / Madagascar / Y / 48 / this study
221218 / JQ814238 / Clade 1 - rattus / Madagascar / Y / 45 / this study
221219 / JQ814281 / Clade 1 - rattus / Madagascar / Y / 45 / this study
221220 / JQ814282 / Clade 1 - rattus / Madagascar / Y / 45 / this study
221229 / JQ814239 / Clade 1 - rattus / Madagascar / Y / 45 / this study
198239 / JN675550 / Clade 1 - rattus / Brazil / 49 / Aplin et al. 161RrI_87
197639 / JN675551 / Clade 1 - rattus / Brazil / 47 / Aplin et al. 162RrI_87
192026 / JN675524 / Clade 1 - rattus / Iran / 44 / Aplin et al. 13RrI_11
193732 / JN675546 / Clade 1 - rattus / Brazil / 50 / Aplin et al. 157RrI_83
HS132/KT2833 / AB033702 / Clade 1 - rattus / Indonesia / 58 / Suzuki et al. (2000)
sample HS2343, no voucher / AB211039 / Clade 1 - rattus / Japan / 59 / Chinen et al. (2005)
sample RrHu1 / EF186469 / Clade 1 - rattus / French Polynesia / 44 / Robins et al. (2007)
sample RNZTitRr01 / EF186470 / Clade 1 - rattus / New Zealand / 44 / Robins et al. (2007)
ABTC 50177 / EF186472 / Clade 1 - rattus / Papua New Guinea / 44 / Robins et al. (2007)
sample RrRa18 / EF186474 / Clade 1 - rattus / French Polynesia / 44 / Robins et al. (2007)
sample RrSamoa2 / EF186475 / Clade 1 - rattus / Samoa / 44 / Robins et al. (2007)
sample HS2425, no voucher / AB211042 / Clade 1 - rattus / Japan / 44 / Chinen et al. (2005)
sample HS2435, no voucher / AB211043 / Clade 1 - rattus / Japan / 44 / Chinen et al. (2005)
specimen voucher R3029 / HM217399 / Clade 3 - rattus / Thailand / 10 / Pagès et al. (2010)
specimen voucher CB0028 / HM217363 / Clade 3 - rattus / Cambodia / 11 / Pagès et al. (2010)
FMNH 140468 / JQ814242 / Clade 3 - rattus / Pakistan / 35 / this study
181309 / JN675602 / Clade 3 - rattus / Pakistan / 52 / Aplin et al. 17RrIII_13
Bay Area/California R. rattus Lineage I
200062 / JN675541 / Clade 1 - rattus / Berkeley, California / 44 / Aplin et al. 149RrI_79
206385 / JQ814212 / Clade 1 - rattus / Berkeley, California / 44 / this study
208240 / JN675545 / Clade 1 - rattus / La Grange, California / 44 / Aplin et al. 156RrI_82
208241 / JQ814213 / Clade 1 - rattus / Snelling, California / 44 / this study
208242 / JQ814214 / Clade 1 - rattus / Snelling, California / 44 / this study
208904 / JQ814215 / Clade 1 - rattus / Orinda, California / Y / 44 / this study
208918 / JQ814216 / Clade 1 - rattus / Orinda, California / Y / 44 / this study
216789 / JQ814217 / Clade 1 - rattus / Dublin, California / 44 / this study
216793 / JQ814219 / Clade 1 - rattus / Oakland, California / 44 / this study
216796 / JQ814222 / Clade 1 - rattus / Orinda, California / Y / 44 / this study
216797 / JQ814223 / Clade 1 - rattus / Orinda, California / Y / 44 / this study
216798 / JQ814224 / Clade 1 - rattus / Orinda, California / Y / 44 / this study
216800 / JQ814226 / Clade 1 - rattus / Orinda, California / Y / 44 / this study
216801 / JQ814227 / Clade 1 - rattus / Orinda, California / Y / 44 / this study
216802 / JQ814228 / Clade 1 - rattus / Orinda, California / 44 / this study
226362 / JQ814176 / Clade 1 - rattus / Castro Valley, California / 44 / this study
226363 / JQ814184 / Clade 1 - rattus / Oakland, California / 44 / this study
226364 / JQ814185 / Clade 1 - rattus / Oakland, California / 44 / this study
226365 / JQ814188 / Clade 1 - rattus / Oakland, California / 44 / this study
226366 / JQ814151 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226368 / JQ814159 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226369 / JQ814153 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226370 / JQ814178 / Clade 1 - rattus / Oakland, California / 44 / this study
226371 / JQ814177 / Clade 1 - rattus / Oakland, California / 44 / this study
226372 / JQ814182 / Clade 1 - rattus / Oakland, California / 44 / this study
226373 / JQ814179 / Clade 1 - rattus / Oakland, California / 44 / this study
226374 / JQ814183 / Clade 1 - rattus / Oakland, California / 44 / this study
226375 / JQ814181 / Clade 1 - rattus / Oakland, California / 44 / this study
226376 / JQ814186 / Clade 1 - rattus / Oakland, California / 44 / this study
226377 / JQ814187 / Clade 1 - rattus / Oakland, California / 44 / this study
226378 / JQ814180 / Clade 1 - rattus / Oakland, California / 44 / this study
226380 / JQ814146 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226381 / JQ814149 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226382 / JQ814152 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226384 / JQ814150 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226385 / JQ814147 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226386 / JQ814148 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226387 / JQ814172 / Clade 1 - rattus / Dublin, California / 44 / this study
226388 / JQ814173 / Clade 1 - rattus / Dublin, California / 44 / this study
226389 / JQ814174 / Clade 1 - rattus / Dublin, California / 44 / this study
226391 / JQ814164 / Clade 1 - rattus / Oakland, California / Y / 44 / this study
226392 / JQ814155 / Clade 1 - rattus / Oakland, California / 44 / this study
226393 / JQ814165 / Clade 1 - rattus / Oakland, California / 44 / this study
226394 / JQ814154 / Clade 1 - rattus / Oakland, California / 44 / this study
226395 / JQ814156 / Clade 1 - rattus / Oakland, California / 44 / this study
226396 / JQ814157 / Clade 1 - rattus / Oakland, California / 44 / this study
226397 / JQ814158 / Clade 1 - rattus / Oakland, California / 44 / this study
226398 / JQ814166 / Clade 1 - rattus / Oakland, California / 44 / this study
226399 / JQ814167 / Clade 1 - rattus / Oakland, California / 44 / this study
226400 / JQ814168 / Clade 1 - rattus / Oakland, California / 44 / this study
226401 / JQ814169 / Clade 1 - rattus / Oakland, California / 44 / this study
226402 / JQ814162 / Clade 1 - rattus / Oakland, California / 44 / this study
226403 / JQ814171 / Clade 1 - rattus / Oakland, California / 44 / this study
226404 / JQ814160 / Clade 1 - rattus / Oakland, California / 44 / this study
226405 / JQ814161 / Clade 1 - rattus / Oakland, California / 44 / this study
226406 / JQ814163 / Clade 1 - rattus / Oakland, California / 44 / this study
226409 / JQ814170 / Clade 1 - rattus / Oakland, California / 44 / this study
148399 / JQ814189 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148400 / JQ814190 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148401 / JQ814191 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148404 / JN675542 / Clade 1 - rattus / San Lorenzo, California / 47 / Aplin et al. 150RrI_79
148405 / JQ814192 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148406 / JQ814193 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148407 / JQ814194 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148408 / JQ814195 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148409 / JQ814196 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148410 / JQ814197 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148411 / JQ814198 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148412 / JQ814199 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148419 / JQ814200 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148420 / JQ814201 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148421 / JQ814202 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148422 / JQ814203 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
148423 / JQ814204 / Clade 1 - rattus / San Lorenzo, California / 47 / this study
216792 / JQ814218 / Clade 1 - rattus / Oakland, California / 47 / this study
216794 / JQ814220 / Clade 1 - rattus / Oakland, California / 47 / this study
216795 / JQ814221 / Clade 1 - rattus / Oakland, California / 47 / this study
220308 / JQ814233 / Clade 1 - rattus / Hayward, California / Y / 47 / this study
220309 / JQ814234 / Clade 1 - rattus / Hayward, California / Y / 47 / this study
226361 / JQ814175 / Clade 1 - rattus / Castro Valley, California / 57 / this study
226383 / Clade 1 - rattus / Oakland, California / Y / *
Bay Area R. rattus Lineage II
216791 / JN675596 / Clade 2 - tanezumi / Hayward, California / Y / 40 / Aplin 152(RrT-80)
216790 / JN675597 / Clade 2 - tanezumi / Oakland, California / Y / 42 / Aplin 153(RrT-80)
226367 / JQ814144 / Clade 2 - tanezumi / Oakland, California / Y / 42 / this study
226379 / JQ814145 / Clade 2 - tanezumi / Oakland, California / Y / 42 / this study
216799 / JQ814225 / Clade 2 - tanezumi / Orinda, California / Y / 46 / this study
219647 / JQ814232 / Clade 2 - tanezumi / Orinda, California / Y / 46 / this study
225257 / JQ814240 / Clade 2 - tanezumi / Orinda, California / Y / 46 / this study
225267 / JQ814241 / Clade 2 - tanezumi / Orinda, California / Y / 46 / this study
220318 / JQ814235 / Clade 2 - tanezumi / Oakland, California / Y / 63 / this study

Table S2. Basic description of microsatellite loci used.

No. of Alleles
Locus / Range (bp) / Flourescent Label / PCR protocol / GenBank Accession or UniSTS # / Total
(N = 78) / SF Bay Area
(N = 29) / Madagascar
(N = 18) / China
(N = 11) / Vietnam
(N = 10) / Philippines
(N = 10)
Rr14 / 111-154 / HEX / TD60 / EU272138 / 21 / 9 / 7 / 8 / 10 / 8
Rr17 / 200-230 / HEX / TD60 / EU272136 / 14 / 9 / 6 / 5 / 2 / 6
Rr22 / 352-410 / HEX / M13 / EU272140 / 28 / 4 / 4 / 12 / 10 / 10
Rr54 / 306-345 / 6-FAM / AT60 / EU272141 / 17 / 12 / 5 / 5 / 5 / 6
Rr68 / 117-167 / HEX / M13 / EU272143 / 19 / 6 / 2 / 8 / 10 / 11
Rr114 / 332-403 / 6-FAM / TD60 / EU272137 / 30 / 8 / 10 / 13 / 14 / 9
D10Rat20 / 107-188 / HEX / M13 / UniSTS:118165 / 29 / 9 / 6 / 9 / 12 / 11
D12Rat76 / 80-131 / HEX / M13 / UniSTS:120857 / 13 / 4 / 3 / 8 / 7 / 6
D15Rat77 / 216-260 / HEX / TD60 / UniSTS:121095 / 32 / 12 / 12 / 14 / 11 / 10
D16Rat81 / 126-192 / 6-FAM / TD60 / UniSTS:226803 / 20 / 10 / 6 / 12 / 8 / 11
D5Rat83 / 155-207 / 6-FAM / AT60 / UniSTS:227970 / 20 / 10 / 8 / 14 / 9 / 9
D2Rat234 / 101-142 / HEX / M13 / UniSTS:227383 / 19 / 12 / 8 / 12 / 10 / 12

See Loiseau et al. (2008) for more details on Rr14 through Rr114, and Jacob et al. (1995) for D10Rat20 through D2Rat234.

Table S3. Null allele frequency by locus and population. With bootstrap re-sampling (number of replicates = 10,000)

Locus / SF Bay Area / Madagascar / China / Vietnam / Philippines / Locus mean
Rr14 / 0.257 / 0.032 / 0.252 / 0.233 / 0.148 / 0.184
Rr17 / 0.110 / 0.000 / 0.274 / 0.285 / 0.286 / 0.191
Rr22 / 0.149 / 0.000 / 0.113 / 0.000 / 0.000 / 0.052
Rr54 / 0.027 / 0.044 / 0.250 / 0.279 / 0.286 / 0.177
Rr68 / 0.048 / 0.187 / 0.303 / 0.256 / 0.178 / 0.194
Rr114 / 0.012 / 0.000 / 0.000 / 0.000 / 0.047 / 0.012
D10Rat20 / 0.037 / 0.000 / 0.047 / 0.000 / 0.000 / 0.017
D12Rat76 / 0.000 / 0.041 / 0.000 / 0.028 / 0.200 / 0.054
D15Rat77 / 0.054 / 0.000 / 0.041 / 0.000 / 0.113 / 0.042
D16Rat81 / 0.000 / 0.042 / 0.000 / 0.000 / 0.000 / 0.008
D5Rat83 / 0.048 / 0.136 / 0.000 / 0.000 / 0.049 / 0.047
D2Rat234 / 0.074 / 0.000 / 0.176 / 0.000 / 0.019 / 0.054
Population mean / 0.068 / 0.040 / 0.121 / 0.090 / 0.111 / 0.086

Table S4. Analysis of Molecular Variance results (Excoffier et al. 1992)

Source of Variation / d.f. / Sum of squares / Variance components / % of Total
Among populations / 4 / 116.032 / 0.82275 / 16.63
Among individuals within populations / 73 / 347.327 / 0.63216 / 12.77
Within individuals / 78 / 272.5 / 3.49359 / 70.6
Total / 155 / 735.859 / 4.94296 / 100

Table S5. Population pair-wise FST after correction for potential null alleles using the EMA algorithm in FreeNA (Chapuis & Estoup 2007)

Populations / SF Bay Area / Madagascar / China / Vietnam / Philippines
San Francisco / ---- / ---- / ---- / ---- / ----
Madagascar / 0.180 / ---- / ---- / ---- / ----
China / 0.155 / 0.145 / ---- / ---- / ----
Vietnam / 0.171 / 0.174 / 0.031 / ---- / ----
Philippines / 0.176 / 0.170 / 0.040 / 0.059 / ----