Supplementary Materials and Methods

Sampling locations and bat capture

Bats were captured from locations in four provinces (Fig A): Wat Tham Phra Cave in Mueang Chiang Rai District, Chiang Rai Province; Sia Cave in Khlong Lan National Park, Khlong Lan District, Kamphaeng Phet Province; a cave in Phu Pha Man District, Khon Kaen Province; and Khao Chakan Cave, Mueang Sa Kaeo District, Sa Kaeo Province.

Bat capture followed the approach used previously (Kuzmin et al. 2008; M. Y. Kosoy et al. 2010; Bai et al. 2012). Briefly, bat sampling sites in each province were chosen based on available information about bat roosts and observations of bat activity in the area. Bats were collected using hand nets or manually in caves while mist nets were used to capture foraging bats. Captured bats were anesthetized by intramuscular injection of ketamine hydrochloride (0.05-0.1 mg/g body weight) and euthanized under sedation in accordance with the field protocol approved by the CDC Institutional Animal Care and Use Committee; the CDC IACUC also specifically approved this study. Bats were weighed, sexed, and identified phenotypically to species using available field keys; some individuals could only be identified to the genus level. Bats were exsanguinated by cardiac puncture and blood was stored in sterile plastic tubes. Blood samples were transported from the field on dry ice.

Fig A. Map of bat sampling locations in Thailand. Bats were sampled in four provinces: Chiang Rai, Kamphaeng Phet, Khon Kaen, and Sa Kaeo. Counts of bat species captured in each location are shown in Figure S2.

Bartonella spp. culturing

Blood samples from bats were cultured following previously published protocols for Bartonella bacteria (M. Y. Kosoy et al. 1997). Briefly, bat blood was diluted 1:4 in brain heart infusion broth with 5% fungizone (amphotericin B) and 100 µl of the sample was placed on agar plates supplemented with 10% rabbit blood. Plates were then incubated at 35 ºC with 5% \(\text{CO}_{2}\) for up to five weeks, checking periodically for growth. Bacterial colonies that resembling those typical for Bartonella were passaged onto new plates to obtain pure cultures. Morphologically unique colonies obtained from the same sample were subpassaged in an attempt to find possible Bartonella coinfections. All isolates were collected in 10% glycerol solution. Cultures were then sent to the CDC Division of Vector-Borne Diseases in Fort Collins, Colorado for genetic characterization.

Priors used in Bayesian phylogenetic analyses

For all phylogenetic analyses using BEAST v1.8.4 on the five genetic loci analyzed (ftsZ, gltA, nuoG, rpoB, and ITS), the following default, diffuse priors were used for the GTR+Γ+I and birth-death models:

  • A-C substitutions ~ gamma(0.05, 10), initial value = 1
  • A-G substitutions ~ gamma(0.05, 20), initial value = 1
  • A-T substitutions ~ gamma(0.05, 10), initial value = 1
  • C-G substitutions ~ gamma(0.05, 10), initial value = 1
  • G-T substitutions ~ gamma(0.05, 10), initial value = 1
  • Base frequences ~ uniform(0, 1), initial value = 0.25
  • Gamma shape parameter ~ exponential(0.5), initial value = 0.5
  • Proportion of invariant sites ~ uniform(0, 1), initial value = 0.5
  • Relative rates among partitions ~ uniform(0, 1E100), initial value = 1
  • Birth-death birth rate ~ uniform(0, 1E5), initial value = 0.01
  • Birth-death relative death rate ~ uniform(0, 1), initial value = 0.5
  • Proportion of taxa sampled from birth-death tree ~ beta(1, 1), initial = 0.01

Previous sensitivity analyses have determined that these priors are sufficiently diffuse to have little influence on the posterior distributions of the parameters. The strict clock rate was fixed at one so that the branch lengths of the phylogenetic trees are scaled as substitutions per site.

Supplementary Results

Bat species distributions

The distribution of bat species among the sampled locations was highly variable (Fig B). Specifically, there was limited overlap in species among locations and most locations were dominated by one species. Stoliczka’s trident bats (Aselliscus stoliczkanus, Hipposideridae), a fulvus roundleaf bat (Hipposideros fulvus, Hipposideridae), horshoe bats (Rhinolophus sp., Rhinolophidae), and a black-bearded tomb bat (Taphozous melanopogon, Emballonuridae) were captured in Wat Tham Phra Cave in Chiang Rai. Sia Cave in Kamphaeng Phet was dominated by intermediate roundleaf bats (H. larvatus), with a few great roundleaf bats (H. armiger) and a single horshoe bat (Rhinolophus sp.). The bat cave in Khon Kaen produced mostly H. armiger, but also some wrinkle-lipped free-tailed bats (Chaerephon plicatus, Molossidae) and a single roundleaf bat (Hipposideros sp.). Khao Chakan Cave in Sa Kaeo produced only C. plicatus. Not all samples produced adequate blood samples for culturing, so the total counts per species were slightly different between Fig B and Table A.

Fig B. Counts of bat species captured in four provinces of Thailand. Species were identified as close to the species level as possible. Three individuals were only identified to the genus level (Hipposideros and Rhinolophus sp.).

Bartonella prevalence and distribution of genogroups

There was some variation in Bartonella spp. prevalence among bat species and capture locations (Table A). In Chiang Rai, no bartonellae were cultured from Rhinolophus sp. or A. stoliczkanus, however the one H. fulvus individual captured was positive for Bartonella genogroup H3 according to its gltA sequence (Fig 1). In Kamphaeng Phet, H. armiger and Rhinolophus sp. showed no infection while 52.2% (12/23) of H. larvatus individuals and the single T. melanopogon individual were harboring bartonellae. H. larvatus individuals were found to be carrying Bartonella genogroups H1, H2, and H3 and the T. melanopogon was carrying Bartonella genogroup Tm. In Sa Kaeo, 41.5% (17/41) of captured C. plicatus individuals were carrying bartonellae; Bartonella genogroups Cp1, Cp2, and Cp3 were found in these bats. In Khon Kaen, C. plicatus and Hipposideros sp. individuals were negative for bartonellae, while 21.4% (3/14) of captured H. armiger individuals were infected with Bartonella genogroups H1 and H3. Despite the observed variation in Bartonella spp. prevalence, the differences among locations (\(\chi^{2}\) = 4.94, p-value = 0.18) and species (\(\chi^{2}\) = 12.5, p-value = 0.09) were not statistically significant, most likely due to the small sample size of bat species from each location. Larger sample sizes will be required to find significant differences among bat species and locations.

The counts of genogroups are larger than to total number of infected individuals due to the presence of multiple cultures originating from the same individual bat (Table A). The T. melanopogon individual (KP283) from Kamphaeng Phet produced two cultures (KP283a and KP283b), both of which were Bartonella genogroup Tm according to gltA (Fig 1); due to this similarity, only culture KP283b was chosen for multi-locus characterization. One C. plicatus individual (SK198) from Sa Kaeo produced two cultures (SK198a and SK198b) which were both Bartonella genogroup Cp3, so only culture SK198a was chosen for multi-locus characterization. One H. armiger individual (KK200) produced two cultures (KK200a and KK200b) which were both Bartonella genogroup H1, so only culture KK200a was characterized with other loci. Two H. larvatus individuals from Kamphaeng Phet (KP216 and KP268) produced two cultures each of genogroup H1 (KP216a, KP216b, KP268a, and KP268b), so only KP216a and KP268a was further characterized. Another H. larvatus bat from Kamphaeng Phet (KP287) produced multiple cultures, but only one (KP287a) was confirmed as a Bartonella species. Finally, H. larvatus KP293 from Kamphaeng Phet produced one culture (KP293a) which was genogroup H1 and a second culture (KP293b) which was genogroup H2. Only culture (KP293a) was chosen for further characterization since KP293b was so similar to culture KP277 (genogroup H2). Additional isolates from C. plicatus in Sa Kaeo (SK137), H. armiger in Khon Kaen (KK209), H. larvatus in Kamphaeng Phet (KP239, KP261, KP263, and KP274) were left out of the multi-locus characterization because they represented genogroups (Cp3, H1, and H3) which had already been detected. In summary, from the total of 42 isolates obtained from the bats, we narrowed the number of isolates selected for multi-locus characterization to 30 which were representative of the 7 Bartonella genogroups identified by gltA sequences (Fig 1). As noted in the main text, Bartonella genogroups segregated strictly among bat genera (Table A): genogroups Cp1-3 were found only in C. plicatus, genogroups H1-3 were found only in Hipposideros spp., and genogroup Tm was only found in T. melanopogon. However, it should be noted that the small sample size and limited species overlap among locations in our study precludes us from accurately estimating the rate at which these bat species may share Bartonella genogroups, especially if exchanges are rare.

Table A. Counts of bat species captured and Bartonella genogroups cultured in four provinces of Thailand. Total infected bats are recorded for each location. The counts of Bartonella genogroups for some species are larger than the number of infected bats because multiple cultures were isolated from some individuals, including some coinfections of multiple genogroups. Exact 95% binomial confidence intervals for prevalence were estimated using the Clopper-Pearson method.

Province Species Family Count Positive Prevalence (%) 95% confidence interval (%) gltA genogroups (count)
Chiang Rai Aselliscus stoliczkanus Hipposideridae 3 0 0 [0, 70.8]
Hipposideros fulvus Hipposideridae 1 1 100 [2.5, 100] H3 (1)
Rhinolophus sp. Rhinolphidae 1 0 0 [0, 97.5]
5 1 20 [0.5, 71.6]
Kamphaeng Phet Hipposideros armiger Hipposideridae 4 0 0 [0, 60.2]
Hipposideros larvatus Hipposideridae 23 12 52.2 [30.6, 73.2] H1 (10), H2 (2), H3 (3)
Rhinolophus sp. Rhinolophidae 1 0 0 [0, 97.5]
Taphozous melanopogon Emballonuridae 1 1 100 [2.5, 100] Tm (2)
29 13 44.8 [26.4, 64.3]
Sa Kaeo Chaerephon plicatus Molossidae 41 17 41.5 [26.3, 57.9] Cp1 (10), Cp2 (2), Cp3 (6)
Khon Kaen Chaerephon plicatus Molossidae 3 0 0 [0, 70.8]
Hipposideros armiger Hipposideridae 14 3 21.4 [4.7, 50.8] H1 (3), H3 (1)
Hipposideros sp. Hipposideridae 1 0 0 [0, 97.5]
18 3 16.7 [3.6, 41.4]
Total 93 34 36.6 [26.8, 47.2]
Separate gene trees for MLST loci

Maximum likelihood (ML) phylogenies generated for each locus (ftsZ, gltA, nuoG, rpoB, and ITS) separately using RAxML v8.2.10 (Stamatakis 2014) showed that most cultures clustered into the same genogroups as identified by gltA sequences (Figs C-G). The two exceptions were isolates KP174 and KP287a. Isolate KP174 from a Hipposideros sp. bat in Kamphaeng Phet was identified as genogroup H1 by all loci except nuoG where it clustered with genogroup H3. Isolate KP287a from a H. larvatus individual in Kamphaeng Phet was identified as genogroup H1 by all loci except rpoB where it clustered with genogroup H2.

Fig C. Maximum likelihood phylogeny for ftsZ sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Fig C. Maximum likelihood phylogeny for ftsZ sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Fig D. Maximum likelihood phylogeny for gltA sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Fig D. Maximum likelihood phylogeny for gltA sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Fig E. Maximum likelihood phylogeny for nuoG sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Fig E. Maximum likelihood phylogeny for nuoG sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Fig F. Maximum likelihood phylogeny for rpoB sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Fig F. Maximum likelihood phylogeny for rpoB sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Fig G. Maximum likelihood phylogeny for ITS sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Fig G. Maximum likelihood phylogeny for ITS sequences from Thai bats. The phylogeny was created with RAxML using the GTRCAT model with 25 per site rate categories. Node support was estimated with 1000 bootstrap replicates and is indicated by the size and color of circles at each node. Tip labels for recombinant strains are colored red.

Sequence References

Sequences representing reference strains of Bartonella species and also previously identified Bartonella strains from bats or other mammal hosts were used to reconstruct the gltA phylogeny (Fig 1) and multi-locus phylogeny (Fig 2) in the main text. GenBank accession numbers for these sequences are listed in Table B.

Table B. GenBank accession numbers for ftsZ, gltA, nuoG, rpoB, and ITS sequences from Bartonella reference strains and Bartonella genogroups from mammal hosts. Blank references for some strains indicate that no sequence for that locus has been listed on GenBank. References for some Bartonella strains from bats and other mammals are listed.

Species Strain ftsZ gltA nuoG rpoB ITS Reference
Bartonella acomydis KS2-1 AB602545 AB444979 AB529942 AB602563
Bartonella alsatica IBS382 NZ_JH725020 NZ_JH725020 NZ_JH725020 NZ_JH725020 AF312506
Bartonella ancashensis 20.00 NZ_CP010401 NZ_CP010401 NZ_CP010401 NZ_CP010401 KP720644
Bartonella antechini MU1-F19 GU168958 GU168962 GU168961 GU168959
Bartonella apis PEB0122 NZ_LXYU00000000 NZ_LXYU00000000 NZ_LXYU00000000 NZ_LXYU00000000 NZ_LXYU00000000
Bartonella australis Aust-NH1 NC_020300 NC_020300 NC_020300 NC_020300 DQ538396
Bartonella bacilliformis Ver097 NZ_KL503805 NZ_KL503803 NZ_KL503804 NZ_KL503803 DQ200883
Bartonella bandicootii BA1 HQ444163 HQ444165 HQ444164 HQ444162
Bartonella birtlesii IBS325 NZ_CM001557 NZ_CM001557 NZ_CM001557 NZ_CM001557 AY116640
Bartonella bovis 91-4 NZ_CM001844 NZ_CM001844 NZ_CM001844 NZ_CM001844 KM371094
Bartonella callosciuri BR1-1 AB602541 AB444977 AB529929 AB602559
Bartonella capreoli IBS193 AB290192 AF293392 AB290188 AB498009
Bartonella chomelii A828 KM215688 KM215690 KM215699 KM215705 KM215713
Bartonella clarridgeiae ATCC51734 NZ_JADC01000017 NZ_JADC01000010 NZ_JADC01000010 NZ_JADC01000010 AF312497
Bartonella coopersplainsensis AUST-NH20 EU111781 EU111803 EU111792 EU111770
Bartonella davousti BvS14 KU859898 KU859878 KU859888 KU859908
Bartonella doshiae NCTC12862 NZ_JH725095 NZ_JH725094 NZ_JH725094 NZ_JH725094 AF442954
Bartonella elizabethae F9251 NZ_JH725034 NZ_JH725033 NZ_JH725033 NZ_JH725033 L35103
Bartonella florenciae R4 NZ_HE997451 NZ_HE997451 NZ_HE997451 NZ_HE997451 HM622140
Bartonella grahamii as4aup NC_012846 NC_012846 NC_012846 NC_012846 JN810847
Bartonella henselae Houston-1 NC_005956 NC_005956 NC_005956 NC_005956 L35101
Bartonella jaculi OY2-1 AB602539 AB444975 AB529934 AB602557
Bartonella japonica Fuji_18-1 AB440633 AB242289 AB242288 AB498007
Bartonella koehlerae C-29 NZ_KL407334 NZ_KL407334 NZ_KL407334 NZ_KL407334 AF312490
Bartonella lascolai C102 KP715476 KP715477 KP715478 (Davoust et al. 2016)
Bartonella mastomydis 205-2 KR107234 KP997021 KT895985
Bartonella mayotimonensis EYL-2008 FJ376734 FJ376732 FJ376736 FJ376735 (E. Y. Lin et al. 2010)
Bartonella melophagi K-2C NZ_JH725081 NZ_JH725083 NZ_JH725082 NZ_JH725083 JF834886
Bartonella pachyuromydis FN15-2 AB602543 AB444978 AB602555 AB602561
Bartonella phoceensis 16120 AY515135 AY515126 AY515132 AY515123
Bartonella queenslandensis AUST-NH15 NZ_HE997987 NZ_HE998003 NZ_HE997985 NZ_HE998003 EU111769
Bartonella quintana Toulouse NC_005955 NC_005955 NC_005955 NC_005955 L35100
Bartonella rattaustraliani AUST-NH4 NZ_CALW02000009 NZ_CALW02000061 NZ_CALW02000050 NZ_CALW02000063 EU111760
Bartonella rattimassiliensis 15908 NZ_JH725069 NZ_JH725064 NZ_JH725064 NZ_JH725065 AY515121
Bartonella rochalimae ATCCBAA-1498 NZ_KL407337 NZ_KL407337 NZ_KL407337 NZ_KL407337 DQ683199
Bartonella rolaini C65 KP715472 KP715473 KP715475 KP715474 (Davoust et al. 2016)
Bartonella rondoniensis clone-1-2 KX377404 KX377405
Bartonella rudakovii St490 EF682092 EF682090 EF682088 EF682087
Bartonella schoenbuchensis R1 FN645509 FN645507 FN645509 FN645507 EF418055
*Bartonella senegalensis OSO2 NZ_HE997541 NZ_HE997540 NZ_HE997542 NZ_HE997540 HM636451
Bartonella silvatica Fuji_23-1 AB440637 AB242287 AB242292 AB498008
Bartonella silvicola Cul-9 EF616479 EF616477 EF616480 unpublished
Bartonella tamiae Th239 NZ_JH725147 NZ_JH725147 NZ_JH725147 NZ_JH725147 DQ395180
Bartonella taylorii 8TBB NZ_JH725051 NZ_JH725052 NZ_JH725052 NZ_JH725052 AJ269784
Bartonella thailandensis Bthai FJ411481 FJ411482 FJ411483 FJ411485
Bartonella tribocorum BM1374166 NZ_HG969192 NZ_HG969192 NZ_HG969192 NZ_HG969192 AF312505
Bartonella vinsonii subsp. vinsonii Baker AF467757 Z70015 EF659944 AF165997 L35102
Bartonella washoensis Sb944nv NZ_JH725024 NZ_JH725022 NZ_JH725025 NZ_JH725022 AB674253
Bartonella woyliei WC1 HQ444150 HQ444152 HQ444151 HQ444149
Brucella abortus Biovar-3 NZ_DS999886 NZ_DS999886 NZ_DS999883 NZ_DS999886 X95889
Coleura afra C-583 HQ832883 HM545136 MF288100 KM382256 (M. Y. Kosoy et al. 2010)
Corynorhinus townsendii ZAG01 JX416236 (Morse et al. 2012)
Dog BK11 FJ946847 (Bai et al. 2010)
Dog BK62 FJ946848 (Bai et al. 2010)
Dog KK48 FJ946850 (Bai et al. 2010)
Dog KK49 FJ946851 (Bai et al. 2010)
Dog KK61 FJ946852 (Bai et al. 2010)
Dog KK14 FJ946853 (Bai et al. 2010)
Dog KK20 FJ946854 (Bai et al. 2010)
Dog KK45 FJ946855 (Bai et al. 2010)
Eidolon dupreanum 1_CycDub KT751146 (Wilkinson et al. 2016)
Eidolon dupreanum 4_CycDub KT751148 (Wilkinson et al. 2016)
Eidolon dupreanum 5_CycDub KT751149 (Wilkinson et al. 2016)
Eidolon dupreanum 6_CycDub KT751150 (Wilkinson et al. 2016)
Eidolon dupreanum 7_CycDub KT751151 (Wilkinson et al. 2016)
Eidolon helvum E1-105 HM363770 HM363765 MF288093 HM363775 MF288105 (M. Y. Kosoy et al. 2010)
Eidolon helvum E2-114 HM363771 HM363766 MF288094 HM363776 MF288106 (M. Y. Kosoy et al. 2010)
Eidolon helvum E3-106 HM363772 HM363767 MF288095 HM363777 MF288107 (M. Y. Kosoy et al. 2010)
Eidolon helvum Ew-111 HM363773 HM363768 MF288096 HM363778 MF288108 (M. Y. Kosoy et al. 2010)
Eidolon helvum B39301 KJ999687 KM030516 KM030541 KM215201 MF288109 (Bai et al. 2015)
Eidolon helvum B40014 KJ999689 KM030520 KM030542 KM215202 KM233479 (Bai et al. 2015)
Eptesicus nilssoni 1157-3 KF003121 KF003115 KF003118 KF003117 (Veikkolainen et al. 2014)
Eptesicus serotinus 44722 KX300199 KX300200 KX300202 KX300203 MF288110 (Urushadze et al. 2017)
Harpyionycteris whiteheadi JAE1033 JX416239 (Morse et al. 2012)
Hipposideros armiger B095 KP100356 (Anh et al. 2015)
Hipposideros armiger B096 KP100357 (Anh et al. 2015)
Hipposideros larvatus B081 KP100354 (Anh et al. 2015)
Hipposideros larvatus B087 KP100355 (Anh et al. 2015)
Hipposideros larvatus B110 KP100360 (Anh et al. 2015)
Hipposideros sp. Mala15 JX416238 (Morse et al. 2012)
Hipposideros vittatus (formerly H. commersoni) H-556 KM382254 HM545137 KM382252 KM382258 (M. Y. Kosoy et al. 2010)
Human G19 HM116784 (Podsiadly et al. 2010)
Human G10 HM116785 (Podsiadly et al. 2010)
Human G14 HM116786 (Podsiadly et al. 2010)
Megaderma lyra B109 KP100359 (Anh et al. 2015)
Megaderma spasma B005 KP100341 (Anh et al. 2015)
Meriones libycus B29881 KT327035 KT327028 KT327037 KT327041 JF766260 (Malania et al. 2016)
Meriones libycus B29771 KT327034 KT327027 KT327036 KT327040 JF766255 (Malania et al. 2016)
Miniopterus aelleni 11c_PenLep KT751143 (Wilkinson et al. 2016)
Miniopterus gleni Gr16_NycSty KT751152 (Wilkinson et al. 2016)
Miniopterus griveaudi Gr20_PenLep KT751153 (Wilkinson et al. 2016)
Miniopterus griveaudi Gr6_NycSty KT751155 (Wilkinson et al. 2016)
Miniopterus minor M1-44 MF288090 HM545139 MF288097 MF288101 MF288111 (M. Y. Kosoy et al. 2010)
Miniopterus natalensis M3-373 MF288091 HM545141 MF288098 MF288102 MF288112 (M. Y. Kosoy et al. 2010)
Miniopterus schreibersii No.05 JF500495 JF500511 JF500543 (J.-W. Lin et al. 2012)
Miniopterus schreibersii 44530 KX300175 KX300183 KX300185 KX300186 MF288113 (Urushadze et al. 2017)
Miniopterus schreibersii 44608 KY679153 KX300195 KX300197 KX300198 MF288114 (Urushadze et al. 2017)
Miniopterus schreibersii 44599 KX300191 KX300192 KX300193 KX300194 MF288115 (Urushadze et al. 2017)
Miniopterus schreibersii 44593 KX300187 KY679154 KX300190 KX300188 MF288116 (Urushadze et al. 2017)
Miniopterus sp. M2-491 HM545140 (M. Y. Kosoy et al. 2010)
Miniopterus sp. 12_PenLep KT751144 (Wilkinson et al. 2016)
Miniopterus sp. 13b_PenLep KT751145 (Wilkinson et al. 2016)
Myotis blythii 44731 KX300139 KX300140 KX300142 KX300143 MF288117 (Urushadze et al. 2017)
Myotis blythii 44602 KX300116 KX300117 KX300119 KX300120 MF288118 (Urushadze et al. 2017)
Myotis blythii 44601 KX300111 KX300112 KX300114 KX300115 MF288119 (Urushadze et al. 2017)
Myotis blythii 44622 KX300121 KX300123 KX300125 KX300122 MF288120 (Urushadze et al. 2017)
Myotis blythii 44711 KX300126 KX300127 KX300128 KX300129 MF288121 (Urushadze et al. 2017)
Myotis blythii 44719 KX300134 KX300136 KX300138 KX300135 MF288122 (Urushadze et al. 2017)
Myotis blythii 44715 KX300130 KX300131 KX300132 KX300133 MF288123 (Urushadze et al. 2017)
Myotis blythii 44591 KX300106 KX300107 KX300109 KX300110 MF288124 (Urushadze et al. 2017)
Myotis daubentonii 1160-1 KF003128 KF003122 KF003125 KF003124 (Veikkolainen et al. 2014)
Myotis daubentonii 2574-1 KF003135 KF003129 KF003132 KF003131 (Veikkolainen et al. 2014)
Myotis daubentonii bat2053_2034 KR822802 (Lilley, Veikkolainen, and Pulliainen 2015)
Myotis daubentonii M406 AJ871613 (Concannon et al. 2005)
Myotis emarginatus 44617 KX300148 KX300149 KX300151 KX300152 MF288125 (Urushadze et al. 2017)
Myotis emarginatus 44724 KX300153 KX300154 KX300156 KX300157 MF288126 (Urushadze et al. 2017)
Myotis emarginatus 44544 KX300176 KX300145 KX300144 KX300147 MF288127 (Urushadze et al. 2017)
Myotis fimbriatus SD-73 KX655821 (Han et al. 2017)
Myotis fimbriatus SD-74-2 KX655808 (Han et al. 2017)
Myotis fimbriatus SD-72 KX655834 (Han et al. 2017)
Myotis fimbriatus SD-75 KX655822 (Han et al. 2017)
Myotis fimbriatus SD-70 KX655829 (Han et al. 2017)
Myotis fimbriatus SD-78 KX655839 (Han et al. 2017)
Myotis fimbriatus SD-74-1 KX655827 (Han et al. 2017)
Myotis fimbriatus SD-76 KX655843 (Han et al. 2017)
Myotis fimbriatus SD-62 KX655832 (Han et al. 2017)
Myotis grisescens UTK0803 KX807176 (Lilley et al. 2017)
Myotis grisescens UTK1106 KX807175 (Lilley et al. 2017)
Myotis keaysi SJ126 KJ816667 (Judson, Frank, and Hadly 2015)
Myotis keaysi SJ125 KJ816669 (Judson, Frank, and Hadly 2015)
Myotis keaysi SJ132 KJ816689 (Judson, Frank, and Hadly 2015)
Myotis lucifugus DMR02097 KX807171 (Lilley et al. 2017)
Myotis lucifugus DMR02036 KX807174 (Lilley et al. 2017)
Myotis lucifugus DMR02098 KX807173 (Lilley et al. 2017)
Myotis lucifugus DMR02005 KX807178 KX807183 KX807186 (Lilley et al. 2017)
Myotis lucifugus DMR02028 KX807179 KX807184 KX807187 (Lilley et al. 2017)
Myotis lucifugus DMR02051 KX807177 KX807182 KX807185 (Lilley et al. 2017)
Myotis lucifugus DMR02050 KX807172 (Lilley et al. 2017)
Myotis myotis AS048 JQ695836 unpublished
Myotis myotis AS036 JQ695837 unpublished
Myotis myotis AS033 JQ695838 unpublished
Myotis myotis AS025 JQ695839 unpublished
Myotis myotis AS067 JQ695840 unpublished
Myotis myotis AS071 JQ695834 unpublished
Myotis myotis AS050 JQ695835 unpublished
Myotis mystacinus M62 AJ871612 (Concannon et al. 2005)
Myotis nattererei ZAG03 JX416241 (Morse et al. 2012)
Myotis pequinius SD-123 KX655815 (Han et al. 2017)
Myotis pequinius SD-119 KX655825 (Han et al. 2017)
Myotis pequinius SD-120-2 KX655816 (Han et al. 2017)
Myotis pequinius SD-109 KX655842 (Han et al. 2017)
Myotis pequinius SD-142 KX655830 (Han et al. 2017)
Myotis pequinius SD-93 KX655828 (Han et al. 2017)
Myotis pequinius SD-111 KX655841 (Han et al. 2017)
Myotis pequinius SD-91 KX655812 (Han et al. 2017)
Myotis pequinius SD-99 KX655823 (Han et al. 2017)
Myotis pequinius SD-120-1 KX655814 (Han et al. 2017)
Myotis pequinius SD-122 KX655820 (Han et al. 2017)
Myotis pequinius SD-138 KX655836 (Han et al. 2017)
Myotis pequinius SD-96 KX655833 (Han et al. 2017)
Myotis pequinius SD-117 KX655835 (Han et al. 2017)
Myotis ricketti SD-83 KX655811 (Han et al. 2017)
Myotis sp. B32942 JQ071390 (Bai et al. 2012)
Nyctalus noctula M451 AJ871615 (Concannon et al. 2005)
Pipistrellus pygmaeus 44718 KX300177 KX300179 KX300178 KX300181 MF288128 (Urushadze et al. 2017)
Pipistrellus sp. M409 AJ871611 (Concannon et al. 2005)
Pipistrellus sp. M207 AJ871614 (Concannon et al. 2005)
Ptenochirus jagori P2874 JX416255 (Morse et al. 2012)
Pteropus hypomelanus E7 JX416257 (Morse et al. 2012)
Pteropus hypomelanus E5 JX416256 (Morse et al. 2012)
Rattus norvegicus 1-1C FN645499 FN645496 FN645496 FN645496 EU551157 (Engel et al. 2011)
Rhinolophus acuminatus B003 KP100340 (Anh et al. 2015)
Rhinolophus acuminatus B006 KP100342 (Anh et al. 2015)
Rhinolophus acuminatus B050 KP100345 (Anh et al. 2015)
Rhinolophus acuminatus B055 KP100347 (Anh et al. 2015)
Rhinolophus acuminatus B056 KP100348 (Anh et al. 2015)
Rhinolophus acuminatus B063 KP100349 (Anh et al. 2015)
Rhinolophus acuminatus B064 KP100350 (Anh et al. 2015)
Rhinolophus acuminatus B068 KP100351 (Anh et al. 2015)
Rhinolophus euryale 44528 KX300105 KX300158 KX300160 KX300161 MF288129 (Urushadze et al. 2017)
Rhinolophus ferrumequinum SD-3 KX655838 (Han et al. 2017)
Rhinolophus ferrumequinum 44706 KX300168 KX300169 KX300172 KX300173 MF288130 (Urushadze et al. 2017)
Rhinolophus ferrumequinum 44658 KX300174 KX300165 KX300167 KX300170 MF288131 (Urushadze et al. 2017)
Rhinolophus ferrumequinum 44552 KX300182 KY679155 KX300163 KX300164 MF288132 (Urushadze et al. 2017)
Rhinolophus pearsoni 05_01_07 JX416252 (Morse et al. 2012)
Rhinolophus pusillus SD-19 KX655824 (Han et al. 2017)
Rhinolophus pusillus SD-16 KX655818 (Han et al. 2017)
Rhinolophus sinicus B049 KP100344 (Anh et al. 2015)
Rousettus aegyptiacus R-191 HM363769 HM363764 KM387321 HM363774 KM382255 (M. Y. Kosoy et al. 2010)
Scotophilus marovaza SC1_Basilia KT751157 (Wilkinson et al. 2016)
Scotophilus robustus 1b_Basilia KT751147 (Wilkinson et al. 2016)
Sorex araneus DB5-6 NZ_JH725120 NZ_JH725114 NZ_JH725119 NZ_JH725114 unpublished
Tamiasciurus hudsonicus AR-15-3 FN645482 FN645480 FN645479 FN645480 (Engel et al. 2011)
Triaenops persicus T-837 KM382253 HM545138 KM382251 MF288104 KM382257 (M. Y. Kosoy et al. 2010)
Tylonycteris sp. Mala11 JX416246 (Morse et al. 2012)

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