Phylogenies form the backbone of evolutionary biology and represent tools that underlie a broad spectrum of evolutionary and ecological studies [1] [2]. Phylogenetic work on any given group often first focuses on the ‘big picture’, that is the placement of, and relationship among, major groups, long before species level phylogenies become available. One simple reason for this focus is that general interest questions, such as where and how the major divisions of life fit together, can be answered through sampling relatively few taxa, in a relatively cost and time effective manner. Yet, more detailed species-level phylogenies, often lagging far behind, are the most useful tools for evolutionary and ecological analyses. The above is certainly true for mammalian phylogenetics, where higher level phylogenetics are intensely studied, with the few detailed species level studies for major groups lagging far behind (see e.g. [3] [4] [5] [6]).

The ultimate goal of phylogenetics must be detailed species level phylogenies of all of life, based on many data. However, achieving this goal will take much time and effort. In the meantime, species level phylogenies may be rapidly reconstructed with already available data using several approaches. One is the construction of phylogenetic supertrees where available trees and taxonomies are united into a summary cladogram [7]. Another is the creation of supermatrices based on available character data. Both approaches make available useful research tools, which may have different strengths.

The bats (Chiroptera) are one such group where many phylogenetic studies have focused either on understanding higher-level bat relationships (e.g. [8] [9]) or species-level relationships within specific groups (e.g. [10] [11] [12]). Available phylogenies have then been summarized in a supertree [13]. Here, we provide cytochrome b gene tree for over 50% of bat species (648 total taxa). Cytb not only is the most widely available marker for most mammals, but also has been shown to be a particularly reliable phylogenetic marker (e.g. [14]). Thus according with prior analyses of other mammal groups [3] [4] [5] [6], the cytb gene tree can be expected to at least roughly approximate the species-level phylogeny of Chiroptera. We provide this phylogeny simply as an alternative tool to super-tree phylogenies, until more detailed studies become available.


Cytochrome b sequences were downloaded from GenBank for 648 bats, including nearly 550 named species, and the remaining terminal taxa being subspecies or unidentified/undescribed species. As outgroups we selected 10 species representing other Pegasoferae [15]: Cetartidoactyla, Perissodactyla, Carnivora, Pholidota (pangolins), and Erinaceomorpha as the primary outgroup. Because many of the taxa have incomplete Cytb sequences, and missing data can cause problems in phylogenetic reconstruction (e.g. [16]), we also created a ‘pruned’ dataset where taxa with less than 30% of the full sequence were removed (‘pruned’ matrix), and another set where only 2 representatives of each family were retained (‘time’ matrix). The latter was used for analysis of divergence times. The sequences were aligned in Mesquite [17], a trivial task given that it is a protein-coding gene with no implied gaps. The appropriate model for the Bayesian analysis was selected with jModeltest [18] using the AIC criterion [19]. The best model was GTR+Γ+I [20] [21]. Bayesian analysis was performed using MrBayes V3.1.2 [22] with settings as in [3] [4] with separate model estimation for first, second, and third codon positions. The MCMC was run with one cold and three heated chains for 30,000,000 generations, sampling trees every 1,000 generations. The first 15,000,000 were then discarded as burnin, after which stationarity was reached. The data matrix and trees are available from the first author and data and trees will be submitted to Treebase ( Genbank accession numbers are listed in Table 1 (see Appendices).

The ‘time’ matrix was used to estimate divergence times using relaxed clock methods in BEAST 1.6.1. [23] [24]. For Emballonuridae we additionally retained two Taphozous species as these did not group with the other Emballonuridae in the full analysis. The analysis was calibrated using normally distributed priors reflecting: (1) the minimal age of 37 my for the split between Rhinolophidae and Hipposiderids based on the estimated age of the oldest rhinolophid and hipposiderid fossils [25] [26]; (2) the estimated age of Carnivora (split of cat plus dog) of 54 my (the age of Carnivora as estimated by [27]); the estimated age of Chiroptera as a normally distributed prior with mean of 54 my, also based on [27]; and (4) the minimal age of Emballonuridae of 48 my based on the oldest fossils that are with some certainty placed within that family [28]. Prior to the divergence time analysis Erinaceus (Erinaceomorpha) and Talpa (Eulipotyphla) were set as primary outgroups by enforcing the monophyly of the remaining taxa, and the monophyly of Rhinolopidae plus Hipposideridae was furthermore enforced. The resulting age estimates were then compared to the above mentioned fossil data in addition to the age of other known fossil bats [28].

Results and Discussion


The analysis of the full dataset supports the monophyly of bats, and the major division of Chiroptera into Megachiroptera (Pteropodidae) and Microchiroptera with Yangochiroptera contained within the latter group (Figures 1-2).

Fig. 1: Relationships among bat families according with the analysis of all data.

Numbers are posterior probabilities, above branches from the full analysis, below branches support from the pruned analysis.

Fig. 2: Relationship among bat species with major clade names.

Numbers are posterior probabilities. The results are detailed in Figure 4, see Appendices.

The analysis of the ‘time’ matrix, however, supports the now rather generally accepted split into Yinpterochiroptera and Yangochiroptera (see below) (e.g. [29] [30] [31] [32] [33] [34]).

The Macrochiroptera, or fruitbats (Pteropodidae), are in the main analysis sister to the remaining bats (Figures 2, 4a). Within Pteropodidae most genera are monophyletic, with the exception of Rousettus angolensis (synonym Lissonycterisangolensis ) nests with Myonycteris . Overall, these results are similar to results of previous studies on macrochiroptera phylogenetics (e.g. [10]).

The Microchiroptera is divided in two major clades, one is the Yangochiroptera including the families Emballonuridae, Furipteridae, Miniopteridae, Molossidae, Mormoopidae, Mystacinidae, Myzopodidae, Natalidae Noctilionidae, Phyllostomidae, Thyropteridae, and Vespertilionidae. The other major group, which we refer to as a modified “Rhinolophoidea” (Figures 1-2, 4), contains the remaining microbat families Craseonycteridae, Hipposideridae, Megadermatidae, Rhinolophidae, and Rhinopomatidae. Hipposideridae and Rhinolophidae are sister families as supported by previous studies (e.g., [13] [31] [34]). Only Hipposideridae here contains more than a single genus, and within that family Hipposiderus is paraphyletic, containing several small genera.

Overall most microchiropteran superfamilies are not supported as monophyletic, except Rhinopomatoidea (Figure 2). A modified Rhinolophoidea that contains Rhinopomatoidea is also supported, and the superfamily Vespertilionioidea is monophyletic except for containing a couple of apparently misplaced species (Figures 2, 4b). The relationships among the families, however, in general are poorly supported and differ among analyses (see Figures 1, 3-4). Taxonomic families are generally recovered either as strictly monophyletic, or approximately, as paraphyletic groups due to one or a couple of ‘misplaced’ taxa. In the full analysis, families that are strictly supported (i.e. monophyletic, or in the case of families represented by single species, not nesting within another family) are: Craseonycteridae, Furipteridae, Hipposideridae, Megadermatidae, Miniopteridae, Molossidae, Mystacinidae, Myzopodidae, Natalidae, Noctilionidae, Rhinolophidae, Rhinopomatidae, and Thyropteridae. Not monophyletic families are Phyllostomidae due to the placement of one Platalina species nesting within Vestpertilionidae, Emballonuridae is rendered polyphyletic by the placement of the genus Taphozous (2 species) and one species of Emballonura outside it. Vespertilionidae is paraphyletic in that within it are placed the above mentioned Platalina and Emballonura. Finally Mormoopidae forms two clades that are not sister, one including the genus Mormoops, the other the genus Pteronotus. These ‘minor’ deviations from family monophyly in most cases probably do not represent refutation of family clades; rather this seems to be mostly an issue of missing data. For example, when species with less than 30% of the sequence are removed, all families are recovered monophyletic, with two exceptions that may be taxonomically informative : (1) The genus Taphozous still groups outside Emballonuridae which contradicts previous studies (e.g., [32] [34] [35]) and (2) the Mormoopidae family still forms two separate clades, which agrees with Kennedy et al [36] (for contrasting topologies see e.g., [13] [31]). Finally, several genera of the family Phyllostomidae are not monophyletic, including Mimon, Mycronycteris, Rousettus, Vampyressa, and Artibeus. Within Molossidae Tadarida, Mops, Chaerephon are not monophyletic. Within Natalidae, Chilonatalus is non-monophyletic, and within Vespertilionidae, the large genera Pipistrellus and Myotis are not monophyletic.

Many taxa in the full analysis only have available a partial Cytb sequence, and notably clade support is low for many of the deeper clades of the phylogeny. Low support is unsurprising given missing data, and the use of only a single locus for both very many taxa and old divergences. Further, any given gene tree can be expected to differ from the species tree due to various processes including incomplete lineage sorting, introgression, and others. Thus, future effort should focus on resolving the species-level phylogeny of bats with a multi-locus approach. Nevertheless, the phylogeny, especially when the taxa with the highest % missing data are removed, is broadly congruent with prior knowledge, and should thus be a useful tool.

Divergence times

The analysis of divergence times (Figure 3) generally agrees with prior studies [27] [35] [37], though the estimated ages are rather lower in general than those estimated by Jones et al. [38].

Fig. 3: A calibrated phylogeny of bat families.

Numbers are in million years, and gray bars are 95% confidence intervals

In part this may relate to the different suggested relationships among bat families across these studies, though the error margins of many nodes estimated are rather wide and nearly always include age estimates found by prior studies. The results also in most cases are consistent with the available bat fossil record [28]. The age of crown bats, i.e. the split between Yinpterochiroptera and Yangochiroptera is estimated at 58.9 my, a value lying in between the estimates of Cao et al. [27], and Jones et al. [38] and Arnason et al. [37]. Other dates that were included as priors, as expected, also are consistent with the fossil record. The split between Hipposideridae and Rhinolophidae is estimated at 36.9 my, consistent with the oldest known Hipposideridae fossil dated at close to 40 my. Similarly the age of Molossidae estimated at 36.1 my is close to the oldest Molossidae fossil at near 40 my [28]. The split between Emballonuridae and its sister lineage is estimated at 49 my, right around the age of the oldest emballonurid fossil. Most other dates are also consistent with the fossil record. The genus Taphozous has a fossil record going up to 20.4 my, a date in between the estimated split between crown Taphozous (18.1 my) and the split between Taphozous and other Emballonuridae (44.2 my). The oldest Mystacinidae fossil dates from around 20 my [28] and the estimated split here between Mystacinidae and its sister lineage is 24.3 my. The oldest Phyllostomidae fossil dates from around 16 my [28], a date in between the split between crown Phyllostoma (14.4 my) and the split between Phyllostomidae and its sister lineage (28.5 my). In a few cases the estimates are younger than possible given current understanding the fossil record, e.g. the age of Megadermatidae at 23.6 my while the oldest fossil is at least 37 my. However, 95% confidence interval of this node estimate reaches over 40 my. The age of Natalidae, estimated at around 43 my, is younger than the oldest fossil thought to belong to that family, at over 50 my. Similarly one putative Vespertilionidae genus, Stehlinia, has a fossil record older (up to 48 my) than the estimated age of the family at 36.1 my. These mismatches may reflect simply erroneous age estimates, or could possibly indicate that some fossil bats are taxonomically misplaced. In most other cases the estimated ages are older than the oldest available fossils, which may reflect the incompleteness of the fossil record.

In sum, we provide a cytochrome b genealogy for Chiroptera, which we expect to crudely approximate the bat species tree. Until more detailed species-level phylogenies become available, this offers an alternative phylogenetic tool to super-tree phylogenies, for comparative evolutionary, ecological analyzes, and phylogenetic conservation assessment.


Thanks to PLoS Currents: Tree of Life board of reviewers, the editor, and two anonymous reviewers for comments that improved this manuscript.

Funding information

This research was funded, in part, by the University of Puerto Rico. Competing interests The authors have declared that no competing interests exist.


Figure 4. Results from Fig. 2 in standard tree format.

Figure 4a. Results from Figure 2, Pteropodidae. Numbers are posterior probabilities.

Figure 4b. Results from Figure 2, Megadermatidae, Craseonycteridae, Rhinopomatidae, Hipposideridae, and Rhinolophidae. Numbers are posterior probabilities.

Figure 4c. Results from Figure 2, Miniopteridae, Noctilionidae, Mormoopidae, Mystacinidae, Thyropteridae, Furipteridae, and Phyllostomidae in part. Numbers are posterior probabilities.

Figure 4d. Results from Figure 2, Phyllostomidae, in part. Numbers are posterior probabilities.

Figure 4e. Results from Figure 2, Molossidae,Emballonuridae, Myzopodidae, Natalidae, and Vespertilionidae in part. Numbers are posterior probabilities.

Figure 4f. Results from Figure 2, Vespertilionidae in part. Numbers are posterior probabilities.

Figure 4g. Results from Figure 2, Vespertilionidae in part. Numbers are posterior probabilities.

Table 1.

Species included and Genbank accession numbers

Genus Species sub sp or voucher Accession Number
Acerodon jubatus EU330962
Aethalops alecto AY629006
Ametrida centurio AY604446
Anoura caudifer L19506
Anoura geoffroyi FJ155495
Antrozous dubiaquercus EF222381
Antrozous pallidus EF222382
Ardops nichollsi AY572337
Ariteus flavescens AY604436
Artibeus amplus EU160947
Artibeus anderseni U66509
Artibeus aztecus U66510
Artibeus cf.jamaicensis DQ985486
Artibeus cf.obscurus DQ903818
Artibeus cinereus EU805599
Artibeus concolor U66519
Artibeus fimbriatus U66498
Artibeus fraterculus U66499
Artibeus fuliginosus L19505
Artibeus glaucus watsoni FJ179259
Artibeus glaucus U66512
Artibeus glaucus bogotensis EU805596
Artibeus glaucus gnomus EU805594
Artibeus hartii EU160972
Artibeus hirsutus U66500
Artibeus inopinatus U66501
Artibeus intermedius FJ179231
Artibeus jamaicensis aequatorialis DQ869450
Artibeus jamaicensis jamaicensis DQ869518
Artibeus jamaicensis parvipes DQ869474
Artibeus jamaicensis paulus DQ869456
Artibeus jamaicensis richardsoni DQ869454
Artibeus jamaicensis trinitatis DQ003028
Artibeus jamaicensis triomylus AY382782
Artibeus jamaicensis yucatanicus DQ869484
Artibeus lituratus EU160813
Artibeus obscurus U66507
Artibeus phaeotis FJ376727
Artibeus planirostris fallax DQ869426
Artibeus planirostris grenadensis DQ869439
Artibeus planirostris hercules DQ869421
Artibeus planirostris planirostris DQ869396
Artibeus planirostris trinitatis DQ869433
Artibeus schwartzi DQ869531
Artibeus sp.FURB DQ985497
Artibeus toltecus U66515
Asellia tridens FJ457617
Aselliscus stoliczkanus EU434954
Aselliscus tricuspidatus DQ888679
Balantiopterys infusca EF584151
Balantiopterys io EF584153
Balantiopterys plicata EF584154
Balionycteris maculata AF044636
Barbastella barbastellus EU360700
Barbastella beijingensis EF534762
Barbastella leucomelas EF534766
Brachyphylla cavernarum AY572383
Brachyphylla nana EU521680
Brachyphylla pumila EU521678
Carollia benkeithi DQ177282
Carollia brevicauda FJ154120
Carollia castanea DQ888289
Carollia sowelli AF511973
Carollia subrufa AF187024
Centronycteris centralis EF584155
Centronycteris maximiliani EF584157
Centurio senex greenhalli AY604445
Centurio senex AY604444
Chaerephon ansorgei AY377967
Chaerephon chapini AY591329
Chaerephon jobensis AY591331
Chaerephon leucogaster EU716041
Chaerephon nigeriae AY591330
Chaerephon pumila AY614756
Chalinolobus tuberculatus NC_002626
Chilonatalus micropus AY621026
Chilonatalus tumidifrons AY621028
Chiroderma improvisum L28938
Chiroderma doriae AY169958
Chiroderma salvini L28939
Chiroderma trinitatum DQ312413
Chiroderma villosum FJ154121
Chironax melanocephalus AY629005
Chrotopterus auritus FJ155481
Cloeotis percivali FJ457616
Coelops frithii EU434955
Cormura brevirostris EF584159
Craseonycteris thonglongyai EF035012
Cynomops paranus AY675219
Cynopterus brachyotis EF201644
Cynopterus horsfieldii EF201643
Cynopterus sphinx DQ445703
Cyttarops aleco EF584162
Dermanura bogotensis FJ376714
Dermanura rava FJ179252
Dermanura rosenbergi FJ179254
Dermanura incomitata FJ376718
Desmalopex leucopterus EU330965
Desmalopex microleucopterus EU330976
Desmodus rotundus FJ155477
Diaemus youngi FJ155475
Diclidurus albus EF584163
Diclidurus ingens EF584164
Diclidurus isabellus EF584166
Diclidurus scutatus EF584167
Diphylla ecaudata FJ155476
Dobsonia inermis DQ445704
Dobsonia minor DQ445705
Dobsonia moluccensis AF144064
Dyacopterus spadiceus EF105531
Ectophylla alba DQ312404
Emballonura alecto AY426101
Emballonura atrata DQ178261
Emballonura beccarrii EF584222
Emballonura monticola EF584223
Emballonura raffrayana EF584224
Emballonura semicaudata EF635553
Emballonura serii EF635544
Emballonura tiavato DQ178285
Eonycteris spelaea AB062476
Epomophorus wahlbergi DQ445706
Epomops franqueti DQ445707
Eptesicus andersoni andersoni EU786850
Eptesicus andersoni pallescens EU786841
Eptesicus bottae anatolicus EU786812
Eptesicus bottae hingstoni EU786819
Eptesicus bottae innesi EU786815
Eptesicus bottae ogveni EU786876
Eptesicus bottae taftanimontis EU786814
Eptesicus diminutus EU786864
Eptesicus fuscus EU786866
Eptesicus hottentotus EU786823
Eptesicus isabellinus boscai EU786838
Eptesicus isabellinus isabellinus EU786831
Eptesicus nasutus EU786840
Eptesicus nilssoni AF376836
Eptesicus regulus AY007531
Eptesicus serotinus mirza EU786861
Eptesicus serotinus turcomanus EU786875
Erophylla bombifrons AY620438
Erophylla sezekorni AY620439
Eumops glaucinus floridanus EU350026
Eumops perotis EU349991
Eumops sp. MMM-2008 EU349999
Eumops underwoodi EU349989
Furipterus horrens AY621004
Glossophaga commissarisi AF382886
Glossophaga leachi AF382878
Glossophaga longirostris AF382875
Glossophaga morenoi AF382882
Glossophaga soricina FJ392516
Glyphonycteris daviesi AY380747
Glyphonycteris sylvestris AY380746
Haplonycteris fischeri AY817881
Harpiocephalus mordax AJ841971
Harpyionycteris whiteheadi DQ445708
Hipposideros abae EU934448
Hipposideros armiger EU434946
Hipposideros ater DQ054807
Hipposideros beatus FJ347976
Hipposideros bicolor DQ054808
Hipposideros caffer FJ347980
Hipposideros calcaratus DQ054806
Hipposideros cervinus DQ054805
Hipposideros cineraceus DQ054809
Hipposideros coxi EF108148
Hipposideros cyclops EU934466
Hipposideros diadema DQ219421
Hipposideros dyacorum EF108151
Hipposideros fuliginosus EU934468
Hipposideros gigas EU934470
Hipposideros jonesi EU934473
Hipposideros khaokhouayensis DQ054816
Hipposideros larvatus EU434949
Hipposideros pomona EU434950
Hipposideros pratti EU434952
Hipposideros ridleyi DQ054812
Hipposideros rotalis DQ054814
Hipposideros ruber FJ347996
Hipposideros sp.1KS-2008 EU434948
Hipposideros speoris DQ680823
Hypsugo cardonae DQ318883
Hypsugo savii DQ120866
Hypsugo sp.C1 EU360677
Hypsugo sp.C2 EU360678
Hypsugo sp.C4 EU360679
Ia io DQ302094
Idionycteris phyllotis IINMTCYTB
Kerivoula cf.papillosa AJ841970
Laephotis wintoni AJ841964
Lasionycteris noctivagans LSNMTCYTBZ
Lasiurus cinereus DQ421825
Lasiurus ega DQ421826
Lasiurus xanthinus AF369549
Leptonycteris curasoae AF382889
Lionycteris spurrelli AF423100
Lonchophylla chocoana AF423092
Lonchophylla handleyi AF423094
Lonchophylla mordax AF423095
Lonchophylla robusta AF423091
Lonchophylla thomasi AF423086
Lonchorhina aurita FJ155494
Lophostoma silvicola FJ155493
Lophostoma brasiliense FJ155486
Lophostoma evotis FJ155491
Lophostoma schulzi FJ155485
Macroglossus minimus AY926645
Macroglossus sobrinus FJ226494
Macrophyllum macrophyllum FJ155484
Macrotus californicus AY380744
Macrotus waterhousii AY380745
Megaderma lyra DQ888678
Megaderma spasma AY057942
Megaerops ecaudatus EF201645
Megaerops niphanae AF044647
Megaerops wetmorei EF105537
Megaloglossus woermanni DQ445710
Melonycteris fardoulisi fardoulisi AY847251
Melonycteris fardoulisi maccoyi AY847254
Melonycteris fardoulisi mengermani AY847241
Melonycteris fardoulisi schouteni AY847236
Melonycteris melanops AF044645
Melonycteris woodfordi woodfordi AY847234
Mesophylla macconnelli FJ154122
Micronycteris brachyotis AY380748
Micronycteris brosseti AY380771
Micronycteris cf.schmidtorum DQ077407
Micronycteris giovanniae AY380750
Micronycteris hirsuta DQ077415
Micronycteris homezi AY380754
Micronycteris matses DQ077419
Micronycteris megalotis DQ077429
Micronycteris microtis AY380756
Micronycteris minuta DQ077405
Micronycteris schmidtorum DQ077442
Micronycteris sp.TK136752 DQ077420
Micronycteris nicefori AY380749
Micropteropus pusillus AF044648
Mimon crenulatum FJ155478
Mimon bennettii DQ903832
Miniopterus africanus EF363524
Miniopterus australis AY614735
Miniopterus fraterculus AJ841975
Miniopterus fuliginosus AB085735
Miniopterus gleni FJ383146
Miniopterus griveaudi FJ232802
Miniopterus griveaudi griveaudi FJ383143
Miniopterus inflatus AY614737
Miniopterus macrocneme AY614734
Miniopterus magnater EF517308
Miniopterus majori DQ899776
Miniopterus manavi FJ383130
Miniopterus minor FJ232805
Miniopterus natalensis AY614744
Miniopterus newtonii EF363521
Miniopterus petersoni EU091258
Miniopterus pusillus DQ837650
Miniopterus schreibersii EF530348
Miniopterus schreibersii bassanii AY614733
Miniopterus schreibersii blepotis AF217444
Miniopterus schreibersii oceanensis AF130123
Miniopterus schreibersii orianae AY614732
Miniopterus schreibersii pallidus AY614736
Miniopterus sp. BBRA-2009b FJ383134
Miniopterus sp. Comoros clade 2 FJ232800
Miniopterus sp. FMNH 167450 FJ383132
Miniopterus sp. FMNH 172602 FJ383133
Miniopterus sp. sororculus DQ899771
Molossus molossus L19724
Monophyllus plethodon AF382887
Monophyllus redmani AF382888
Mops condylurus EF474030
Mops leucostigma EF474029
Mops midas EF474049
Mormoops blainvillii AY604462
Mormoops megalophylla AF330808
Mormopterus kalinowskii L19725
Mosia nigrescens EF635558
Murina cf.cyclotis AJ841974
Murina leucogaster AB085733
Murina sp. GGJ-2006 DQ435071
Murina sp. hn1151 EF570883
Myonycteris brachycephala AF044644
Myonycteris relicta AF044649
Myonycteris torquata AF044650
Myotis adversus AB106587
Myotis albescens AF376839
Myotis alcathoe AJ841955
Myotis altarium FJ215677
Myotis annectans AJ841956
Myotis atacamensis AM261882
Myotis aurascens AY665161
Myotis auriculus AM261884
Myotis austroripari AM261885
Myotis bechsteinii AF376843
Myotis blythii DQ120906
Myotis blythii ancilla AM284170
Myotis blythii blythii AF376840
Myotis blythii omari DQ288853
Myotis blythii oxygnathus AF376841
Myotis blythii punicus AF376842
Myotis bocagei AJ504408
Myotis bombinus EF555240
Myotis bombinus amurensis AM284169
Myotis brandtii AM261886
Myotis californicus AM261887
Myotis capaccinii AF376845
Myotis cf.nipalensis kukunorensis AY699845
Myotis cf.pequinius AM284173
Myotis cf.punicus AF246252
Myotis chiloensis AM261888
Myotis chinensis AB106588
Myotis ciliolabrum AM261889
Myotis dasycneme AF376846
Myotis daubentoni AY665137
Myotis daubentoni nathalinae AF376862
Myotis daubentoni daubentonii EU153105
Myotis davidii AB106591
Myotis dominicensis AF376848
Myotis elegans AM261891
Myotis emarginatus AF376849
Myotis escalerai FJ460363
Myotis evotis AJ841949
Myotis fimbriatus EF555226
Myotis formosus AJ841950
Myotis formosus flavus EU434932
Myotis formosus watasei EU434933
Myotis frater AB106593
Myotis goudoti AJ504451
Myotis gracilis AB243029
Myotis grisescens AM261892
Myotis hajastanicus AY665138
Myotis hasseltii AF376850
Myotis horsfieldii AF376851
Myotis ikonnikovi AB106602
Myotis keaysi AF376852
Myotis keenii AM262329
Myotis laniger EF555229
Myotis latirostris AM262330
Myotis leibii AM262331
Myotis lesueuri AY485687
Myotis levis AF376853
Myotis longipes FJ215678
Myotis lucifugus AF376854
Myotis lucifugus alascensis DQ503483
Myotis lucifugus carissima AF294512
Myotis lucifugus lucifugus DQ503488
Myotis lucifugus relictus DQ503558
Myotis macrodactylus EF555238
Myotis macropus AJ841959
Myotis macrotarsus AJ841960
Myotis martiniquensis AM262332
Myotis montivagus AM262333
Myotis muricola AY665144
Myotis muricola browni AF376859
Myotis myotis AM261883
Myotis myotis myotis AF246246
Myotis mystacinus AY665167
Myotis nattereri AB106606
Myotis nattereri escalerae EU360649
Myotis nattereri tschuliensis AM284171
Myotis nigricans AF376864
Myotis nipalensis AY699844
Myotis oxyotus AF376865
Myotis pequinius AM284172
Myotis petax EF555236
Myotis pruinosus AB106607
Myotis punicus EU360640
Myotis ricketti AJ504452
Myotis riparius AF376866
Myotis ruber AF376867
Myotis schaubi AF376868
Myotis scotti AJ841958
Myotis seabrai AJ841962
Myotis septentrionalis AM262335
Myotis sicarius AJ841951
Myotis siligorensis FJ215679
Myotis simus AM262336
Myotis sodalis AM262337
Myotis sp. 1 ZZ-2009 FJ215680
Myotis sp. 2 ZZ-2009 FJ215681
Myotis sp. AM_M15111 AY007527
Myotis sp. C1 EU360644
Myotis sp. C2 EU360645
Myotis sp. C3 EU360646
Myotis sp. C4 EU360647
Myotis sp. C5 EU360648
Myotis sp. KK0005 AB106609
Myotis sp. PH-2006 DQ337479
Myotis sp. XT-2007 EF555233
Myotis thysanodes AF376869
Myotis tricolor AJ841952
Myotis velifer AF376870
Myotis vivesi AJ504406
Myotis volans AF376871
Myotis welwitschii AF376874
Myotis yanbarensis AB106610
Myotis yumanensis AF376875
Mystacina tuberculata AY960981
Myzopoda aurita EF432190
Myzopoda schliemanni EF432213
Natalus jamaicensis AY621023
Natalus major AY621021
Natalus saturatus AY621014
Natalus stramineus AY621019
Natalus tumidirostris AY621008
Neoromicia brunneus EU786868
Neoromicia capensis AJ841966
Neoromicia somalicus EU786869
Noctilio albiventris AF330806
Nyctalus azoreum DQ887590
Nyctalus lasiopterus DQ120871
Nyctalus leisleri AF376832
Nyctalus noctula AJ841967
Nyctalus plancyi DQ435073
Nycteris leporinus AF330802
Nycticeius humeralis L19727
Nyctiellus lepidus AY621007
Nyctimene albiventer DQ314264
Nyctimene cephalotes DQ314268
Nyctimene major AF044652
Nyctimene robinsoni AF144066
Nyctimene vizcaccia DQ445711
Nyctinomops aurispinosus L19728
Nyctinomops laticaudatus L19729
Otomops cf.formosus EF504252
Otomops madagascariensis EF216381
Otomops martiensseni EF216441
Otomops wroughtoni EF504251
Otopteropus cartilagonodus AY974770
Penthetor lucasi EF105542
Peropteryx kappleri EF584169
Peropteryx leucoptera EF584175
Peropteryx macrotis EF584180
Peropteryx spvoucherROM104396 EF584170
Peropteryx spvoucherRSV2330 EF584171
Peropteryx trinitatis EF584182
Phylloderma stenops FJ155480
Phyllonycteris aphylla AF187033
Phyllops falcatus DQ211651
Phyllostomus hastatus FJ155479
Pipistrellus abramus AJ504448
Pipistrellus cf.javanicus AJ504447
Pipistrellus hesperidus AJ841968
Pipistrellus hesperus DQ421823
Pipistrellus kuhli AJ504444
Pipistrellus maderensis AJ426632
Pipistrellus nathusii AJ504446
Pipistrellus pipistrellus AJ504443
Pipistrellus pygmaeus DQ120856
Pipistrellus pygmaeusxmediterraneus AJ504442
Pipistrellus sp. Be_2136_8 AY426091
Pipistrellus sp. Be_2137_9 AY426092
Pipistrellus sp. Be_2142_10 AY426089
Pipistrellus sp. Be_2145 AY316334
Pipistrellus sp. Be_2151_13 AY426090
Pipistrellus sp. Be_2152 AY316332
Pipistrellus sp. CO1 EU420890
Pipistrellus sp. CO2 EU420891
Pipistrellus sp. CO3 EU420892
Pipistrellus sp. PH-2007 EF370417
Pipistrellus sp. Be_2129 AY316333
Pipistrellus subflavus AJ504449
Platalina genovensium AF423101
Platyrrhinus albericoi FJ154124
Platyrrhinus helleri FJ154141
Platyrrhinus helleri incarum FJ154146
Platyrrhinus masu FJ154164
Platyrrhinus matapalensis FJ154168
Platyrrhinus aurarius FJ154127
Platyrrhinus brachycephalus FJ154132
Platyrrhinus dorsalis FJ154139
Platyrrhinus lineatus FJ154160
Platyrrhinus recifinus FJ154176
Platyrrhinus vittatus FJ154178
Plecotus auritus EF570882
Plecotus austriacus EU360707
Plecotus balensis AF513798
Plecotus cf.kolombatovici AF513783
Plecotus christii EU743801
Plecotus kolombatovici AF513785
Plecotus macrobullaris AF513805
Plecotus mexicanus AY776038
Plecotus rafinesquii AY776084
Plecotus sp. JJJ-2003 AF513791
Plecotus teneriffae EU360704
Promops centralis L19732
Ptenochirus jagori AB046325
Ptenochirus minor AY974702
Pteralopex acrodonta FJ561376
Pteronotus davyi AF338672
Pteronotus gymnonotus AF338675
Pteronotus macleayii AY604461
Pteronotus parnellii AY604456
Pteronotus personatus AF338680
Pteronotus pusillus AY604455
Pteronotus quadridens AY604460
Pteronotus rubiginosus AY604457
Pteropus rufus AB085732
Pteropus aldabrensis FJ561394
Pteropus alecto AF144065
Pteropus conspicillatus FJ561380
Pteropus giganteus FJ561381
Pteropus hypomelanus FJ561383
Pteropus livingstonii FJ561384
Pteropus lylei EF584229
Pteropus niger FJ561385
Pteropus poliocephalus FJ561387
Pteropus pumilus FJ561390
Pteropus rodricensis FJ561392
Pteropus scapulatus FJ561377
Pteropus seychellensis seychellensis FJ561399
Pteropus seychellensis comoroensis FJ561398
Pteropus speciosus AB062474
Pteropus tonganus AF044656
Pteropus vampyrus FJ561401
Pteropus voeltzkowi FJ561405
Pygoderma bilabiatum AY604438
Rhinolophus acumiatus EF108155
Rhinolophus affinis EU434934
Rhinolophus blasii EU436669
Rhinolophus blythi DQ865344
Rhinolophus borneensis EF108162
Rhinolophus clivosus EU436674
Rhinolophus cornutus DQ297594
Rhinolophus creaghi EF108164
Rhinolophus darlingi EU436675
Rhinolophus eloquens EU436677
Rhinolophus eurvale EU436671
Rhinolophus ferrumequinum EU436673
Rhinolophus formosae NC_011304
Rhinolophus fumigatus EU436678
Rhinolophus hildebrandti EU436676
Rhinolophus hipposideros EU360631
Rhinolophus landeri FJ457612
Rhinolophus lepidus AF451338
Rhinolophus luctus EF544422
Rhinolophus macrotis EU434957
Rhinolophus marshalli EU434938
Rhinolophus mehelyi EU436672
Rhinolophus monocerus EF555788
Rhinolophus pearsonii EU434940
Rhinolophus perditus AY141039
Rhinolophus philippinensis EF108169
Rhinolophus pumilus NC_005434
Rhinolophus pusillus EF217392
Rhinolophus rex EU075216
Rhinolophus sedulus EF108174
Rhinolophus simulator EU436670
Rhinolophus sinicus EU434941
Rhinolophus sp.1KS-2008 EU434937
Rhinolophus sp.2KS-2008 EU434942
Rhinolophus stheno EF108175
Rhinolophus thomasi EU434943
Rhinolophus trifoliatus EF108177
Rhinolophus xinanzhongguoensis EU750753
Rhinophylla alethina AF187028
Rhinophylla fischerae AF187032
Rhinophylla pumilio AF187031
Rhinopoma hardwickei AY056462
Rhinopoma microphyllum AM931063
Rhinopoma muscatellum DQ337500
Rhogeessa aeneus EF222359
Rhogeessa genowaysi EF222326
Rhogeessa gracilis EF222412
Rhogeessa io EF222392
Rhogeessa mira EF222336
Rhogeessa parvula EF222355
Rhogeessa tumida EF222367
Rhogeessa velilla EF222341
Rhynchonycteris naso EF584192
Rousettus aegyptiacus EU624124
Rousettus aegyptiacus aegyptiacus AF044658
Rousettus aegyptiacus princeps AF044659
Rousettus amplexicaudatus AB046329
Rousettus angolensis AF044643
Rousettus lanosus AF044661
Rousettus leschenaultii FJ549331
Rousettus madagascariensis AF044663
Rousettus spinalatus EF105523
Saccopterix bilineata EF584202
Saccopterix canescens EF584206
Saccopterix gymnura EF584208
Saccopterix leptura EF584216
Scotomanes ornatus DQ435069
Scotophilus borbonicus DQ459067
Scotophilus dinganii EU750999
Scotophilus heathii EU750946
Scotophilus kuhlii EU750931
Scotophilus leucogaster EU750940
Scotophilus marovaza EU750943
Scotophilus nigrita EU750955
Scotophilus nux EU750939
Scotophilus robustus EU750948
Scotophilus tandrefana EU750941
Scotophilus viridis EU750991
Scotophilus viridis nigritellus EU750976
Sphaeronycteris toxophyllum AY604452
Stenoderma rufum AY604431
Sturnira luisi serotinus AF435170
Sturnira luisi thomasi AF435250
Sturnira luisi vulcanensis AF435251
Sturnira aratathomasi AF435252
Sturnira bidens AF435201
Sturnira bogotensis AF435248
Sturnira erythromos FJ154179
Sturnira ludovici AF435235
Sturnira luisi angeli AF435158
Sturnira luisi paulsoni AF435162
Sturnira luisi zygomaticus AF435159
Sturnira magna AF435180
Sturnira mordax AF435212
Sturnira nana AF435253
Sturnira oporaphilum AF435210
Sturnira sp.CAI-2003A AF435203
Sturnira sp.CAI-2003B AF435204
Sturnira lilium AF187035
Sturnira tildae AF435185
Syconycteris sp. AF044665
Tadarida brasiliensis L19734
Tadarida fulminans EU760911
Tadarida teniotis EU360721
Taphozous longimanes EF584219
Taphozous melanopogon EF584221
Thyroptera tricolor AY621005
Tomopeas ravus L19735
Tonatia bidens FJ155490
Tonatia saurophila FJ155488
Trachops cirrhosus FJ155483
Triaenops afer EU798750
Triaenops auritus DQ005794
Triaenops furculus DQ005845
Triaenops persicus EU798758
Triaenops rufus DQ005771
Triaenops sp.PPV-2008 EU798756
Tylonycteris pachypus EF517315
Uroderma bilobatum AY169955
Uroderma magnirostrum FJ154180
Vampyressa bidens AY157055
Vampyressa melissa FJ154185
Vampyressa pusilla DQ312428
Vampyressa thyone DQ312431
Vampyressa brocki DQ312421
Vampyressa nymphaea DQ312418
Vampyrodes caraccioli FJ154184
Vampyrum spectrum FJ155482
Vespertilio murinus AB287359
Vespertilio sinensis AB287362