The ancestral range estimation for superfamily Rhinolophoidaea (Rhinolophidae, (Hipposideridae, Rhinonycteridae)) suggests that the ancestors of family were in the Oriental origin, then diversified to other biogeographic regions, colonized Africa through Sahara-Arabian regions to Madagascar and to other archipelagoes in Asia including the Philippines and Indonesia, then colonized Australian through Philippine, Greater Sunda Island, Wallacea and Oceania. Our study is congruent with the previous hypothesis that Rhinolophidae bats originated in the old world tropics in Asia [16, 24, 32, 70] then the range contracted and expanded to East Asia region including India, Africa and islands in the vicinity, but, in contrast with [13, 25] which hypothesized that the ancestral of Rhinolophus species were of African origin based on LAGRANGE biogeographic analysis. Rhinolophidae of Oriental-Oceanian-Australian lineages originated from the Indomalayan region, and the ancestral range of Afrotropical lineages were widespread in the Afro-Palearctic. Allozyme variability also suggests colonization from Eurasia toward North Africa and that subsequent diversification took place in Africa [71], and morphological studies suggest that plesiomorph Oriental rhinolopids were basal and Afro-Palearctic species were more derived [32]. The widespread ancestral and current distribution of taxa in best-fit model BAYAREALIKE indicated the ancestral ranges were similar to those occupied by their descendants, and suggests over-land range expansion in the past around Late Oligocene coincided with diversification of Afrotropical lineages at 27.68–24.38 Ma. The dispersal rate was constantly lower than extinction rate in Rhinolophidae (d < e). Similarly with Hipposideridae-Rhinonycteridae Afro-Palearctic lineages (d < e), but in contrast with Hipposideridae Oriental lineages where dispersal or range expansion is higher (d > e). The estimated rate of dispersal is low suggesting that species have mostly retained the same geographic ranges as their ancestors [37, 39].
The common ancestor of Hipposideridae originated from Oriental or Afrotropical regions (similar posterior probability, Fig. 2), suggesting a possible widespread ancestral ranges of this family. The ancestor of Hipposideridae Oriental-Oceania-Australian lineages originated from the Indomalayan region and the Philippines, which suggests multiple colonization may occured during range expansion. The common ancestor of Hipposideridae Afro-Palearctic lineages originated from Sahara-Arabian and Sudanian-Somalia-Ethiopia suggested the early colonization from northern part of Africa and Arabian Peninsula (Fig. 4b). Our results are in agreement with previous studies based on fossils which suggest that major the dispersal axis of Hipposideridae was from North Africa toward South Europe during the Middle Eocene [72]. The result also suggests that Rhinonycteridae in Madagascar split from their common ancestor (Hipposideridae Afrotropical lineages) around Middle Eocene (~ 40.55 Ma) and ancestral range originated from the Sudanian-Somalia-Ethiopia regions.
Even thought our result indicates a Oriental (Indomalayan) origin for the Rhinolophidae, there is lack of Paleogene fossil founds from the Indomalayan region, though variable taphonomy means that the majority of the fossil record is missing across taxa. The only known possible record of Eocene bats in this region is Megachiroptera from Krabi Mine in Thailand. However, fossil evidence of bats is relatively rare due to delicate skeletons and are therefore rarely preserved, thus, leaving only teeth and postcranial fragments for identifcation [73]. The latest finding of ancestral Rhinolophidae (Protorhinolophus shanghuangensis) was from Shanghuang fissure, Jiangsu (northern part of Asia; Discussed below) [70], although further research in the future may improve the knowledge in the fossil evidence of this group. The oldest bat fossils are from the early Eocene, and are known from North America, Europe, Africa and Australia [73, 74]. There are competing hypothesis of bats originating in Laurasia or Gondwana [75]. The initial explosive radiation of bats occurred in Eocene, the extinct families such as “Eochiroptera” sensu Van Valen (1977) found in most of continents except Antartica [74, 76]. Modern radiation of extant taxa appears to have begun at least by Middle Eocene or earlier, a period characterized by a significant global rise temperature after K-Pg (Cretaceous-Paleogene) mass extinction event [17, 73, 77], which coincided with 43.25 Ma divergence between Hipposideridae and Rhinolophidae.
Ancestral Biogeography range of Horseshoe bats (Rhinolophidae)
Four subset analysis (Rhinolophoidea, Rhinolophidae Oriental-Oceanian-Australia lineages and Rhinolophidae-Afro-Palearctic lineage, and cryptic Rhinolophidae) suggests estimation of dispersal rate was lower than range constriction (d < e). The high e in best fit model demonstrated all range-changes effectively occurred anagenetically along the branches [39][82]. Thus, we assume the distribution of Rhinolophidae driven primarily by dispersal (i.e., over-land range expansion, land-bridge colonization, and stepping-stone events) mixture with vicariance events. Additionally, jump-dispersal or founder-events was not well supported for Rhinolophidae ancestral ranges especially when we used bigger biogeographic ranges. However, jump-dispersal events were chosen as the best fit model for explaining oceanic-dispersal pattern when we separate each islands as different biogeography units (i.e., Greater Sunda Island: Sumatra, Borneo and Java). This may indicate that founder-even speciation is not a dominant force for long-distance oceanic dispersal in major lineages. Hence, the ability of an organism to disperse and diversify seems to be related to specialization of ecological niches and phenotypic adaptation (where certain ecomorphologies are more or less suited to dispersal and colonization) [83]. Range expansion by dispersal, extinction, sympatry (subset and narrow) and vicariance events appears to be relevant in explaining the historical biogeography of Rhinolophidae in Oriental-Oceania-Australia lineages, however, ancestral range of Rhinolophidae Afro-Palearctic is a better fit with dispersal, extinction, sympatry (narrow and widespread) events (without vicariance). The understanding of how organisms came to be distributed as they are also related to historical events involving complex geological history, such as glacial-inter glaciation, continental drift, biotic turnover and long-distance colonization [30]. The main event in Cenozoic era that shapes the continent including collision between the Indias plate and the Eurasian plate, created mountain ranges in Himalaya regions and acted as physical barrier for species dispersal between Indochina and India in late Eocene (around 50 Ma till present). The continuation of India attachment to Eurasia hugely affects the movement of other plates and influenced the shape of continents, archipelago and affects climatic condition in the region (Fig. 7) [47, 51, 58, 59, 84, 85].
The rapid diversification during Miocene coincided with the Mid-Miocene Climatic Optimum (around 15–18 Ma) which may provide a favourable climate in support for the evolution [86] of the Rhinolophus lineages. The high diversification in Miocene not only occurred in bats, but also in the diversification of modern bird genera in Southeast Asia [62]. The basal position of two lineages in Rhinolophidae are the three species belong to trifoliatus group (R. trifoliatus, R. luctus, R. formosae) and R. hipposideros. The three trifoliatus species are Oriental species distributed from Indian sub-continent, Southeast Asia and Eastern Asia [4], and R. hipposideros is distributed throughout the Europe from Ireland in the northwest to Pakistan in the east, and south into northern regions of Africa and Saudi Arabia [20]. Phylogeographic studies suggests early colonization event of R. hipposideros and R. ferrumequinum from the east (west Asian refugium) and both of species used multiple glacial refugia across Mediteranean during the ice age [20, 87]. Last Glacial Maximum in late Pleistocene have impact on current distribution of R. ferrumequinum, with secondary contact was identified between Central/East China and East China/Japan [87].
Our results also show colonization of Rhinolophidae species toward Japanese archipelago may have occurred since the Middle Pliocene, which coincided with fossil from caves and fissure deposits of Middle Pleistocene, Late Pleistocene and Early Holocene in Honshu and Kyushu Island (see [88]). The colonization from continental population toward Japanese archipelago may occurred via a continuous Korean Peninsula-Japanese land bridge due to lower sea levels than at present [87], as similarly used as route for Asian black bear (Ursus thibetanus) [89].
Our result showed the colonization towards the Philippines appears to be multiple colonization events via different route originating from the Indomalayan region (which may via Palawan) and Wallacea region in late Miocene (Fig. 7). Similarly with Wallacean and Oceanian region, the ancestral range and colonization events in these region are complex. The thousands of island in these region have different continental, oceanic and volcanic origin, with many of them undergone rapid tectonic movement since Cenozoic [90, 91]. The archipelagoes (including Philippine and Indonesia) with the combination of tectonic movement, climatological oscillation and Pleistocene sea level fluctuations causing the changes of island size, connectivity and boundaries [92–94]. These important geological events may have contributed to current species distributions [95, 96], and as the effect of presence or absence of Pleistocene land-bridge connection [93]. In addition, current distribution of species in the archipelago may be a direct result of when bats reaching the older islands longer ago and younger island more recently which leading to allopatric and vicariance speciation [97].
Two hypothesis of species biogeography in Philippine including Pleistocene aggregate island complexes (PAICs) suggesting land exposure in the Pleistocene due to glaciation allowed species to expand their range inter five major islands [98]. Palawan Ark Hypothesis suggested species “rafted” with North Palawan block since the separation from mainland Asia by Early Oligocene 30 Ma [51], in contact with Borneo around 15 Ma [94] and then move northward toward present position [99, 100]. The multi-route colonization of Rhinolophidae species toward the Philippines is similar to other taxa, for instance Begonia [101], Cynopterus and Macroglossus [102, 103]. This coincided with theory of biotic colonization of Philippines, postulated as submerged land bridges, with many taxa known to have colonized Philippine through northern Philippines (from mainland Asia and Palawan) and through south route (via Sulu archipelago and Sulawesi) [104]. Previous study also suggested that colonization of the Philippines may taken place from the Sunda Shelf (Sumatra, Java and Borneo) and Wallacea [93].
Wallacea, including Sulawesi Island, and many small islands surrounding (i.e., Outer Banda Arc (Sumba, Timor, Babar, Yamdena, Kai, Seram), Inner Banda Arc (Bali, Lombok, Sumbawa, Flores, Alor and Wetar), Halmahera etc) result from complex tectonic plate movement from Australian and Asian plate. Some of the Island were never connected in the past (e.g. Inner and Outer Banda Arc), and Inner Banda Arc exposed the land above sea-level and therefore permitted the colonization in Lesser Sunda Islands around 3 Ma [105]. The current arrangement of the islands provides a series of stepping stones facilitating movement of terrestrial mammals, which may include volant mammals, to colonize the Australian region [48].
Furthermore, glacial and sea-level fluctuation repeatedly formed land bridges in Pleistocene [106] and the landmass between Asia, Sumatra, Borneo and Java islands (Sundaland) [51] allowed colonialization and range expansion of Rhinolophidae from Indochina towards Sumatra and Borneo, which is in line with our results here. The diversification of Rhinolophus species in Borneo Island may coincide with separation of Sundaic and Indochinese rainforests [54]. The rainforest refugia in some parts of Borneo and Sumatra may allowed populations of forest-species to diverge and adapted with local climatic conditions and environment [54, 107, 108]. The glaciation and interglacial events during Plio-Pleistocene caused dramatic changes in climate, forest cover and the connection between land areas allowed species to colonized different geographic ranges. Recent diversification within species groups in Pleistocene may coincide with climatic fluctuations which affects the vegetation transition in the region, and the possible savanna corridor in part of the region [107, 109], thus indirectly influencing diversification of forest-dwelling mammals [110] and insects [111]. The divergences of R. affinis and R. pusillus lineages in Malay Peninsula during Plio-Pleistocene may coincide with the major event in the peninsula. The possible flooding of Isthmus of Kra during Pliocene, the adaptation to specific climatic conditions and long term ecological differences, combined with the peninsula effect may cause the faunal transition between Indochinese taxa and Sundaic taxa, with major transitions at the Isthmus of Kra, and the Kangar Pattani line [108, 110, 112, 113] (Fig. 7). Furthermore, the sea-level rises during Pliocene isolated Sumatra, Borneo and Java Islands in Indonesia created physical barriers between Indochina and species from the islands [51, 62]. Borneo is the largest landmass of former Sundaland and has served as stable land for at least 20 million years and was less affected by sea-levels changes compared with Sumatra (which has come together as a stable from 5–10 Ma) and Java (2–5 Ma) [54, 62].
High rhinolophids diversity in Asia compared to the other biogeographic regions may be expected as many species are restricted to islands or group of islands, for instance four endemic species in Japan (i.e., R. cornutus, R. pumilus, R. perditus, R.imaizumii) (Ohdachi et al. 2015) and four endemic in the Philippine (i.e., R. inops, R. rufus, R. subrufus, R. virgo) and various species endemic in Indonesia islands (i.e., R. nereis, R. madurensis, R, keyensis, R. montanus, R. euryotis, R. celebensis, R. canuti [114], which represents physical barriers for bat dispersal such as water and mountain range. In contrast, Palearctic regions was influenced with repeated glaciation and in Africa, much of relatively flat landscape that may cause high species turn-over and high rates of gene flow which decelerating speciation compared to complex biogeographic areas in Asia [71]. The dispersal of Rhinolophidae species to Africa may be via forest corridors that appeared during middle Eocene because of the warm climate [115], and disperse the ancient species throughout southern Palearctic and Mediterranean, through Sahara Arabian and eventually into Africa [16]. The basal lineages within African radiation are R. landeri and R. alcyone, which occur in in rainforest and may indicate early colonization around late Oligocene (~ 20 Ma) through forest affinities as predicted in [18]. The closure of Tethys Ocean estimated around the Oligocene (around 27) Ma to Miocene [78, 116, 117] formed a land bridge in Arabian Peninsula which connecting Asia and Africa, and may facilitate dispersal of many animals lineages in the Miocene such as lizards [118], frogs [119], chameleons [120], and butterflies [121, 122]. As the consequences of shrinkage of Tethys sea, desert and arid conditions expanded across North Africa in the Late Miocene (around 7 Ma), marking the origin of Sahara Desert and the Middle East Desert and the Arabian Peninsula [79]. Arid adapted species colonized Africa and currently successfully inhabited most of savanna region in Sudanian, Somalia, Ethiopia and deciduous woodland in Southern Africa [19, 32].
Unlike Hipposideridae, currently there are no records of Rhinolophidae species in Madagascar. Madagascar + India + Africa are ancient fragments of Gondwana and has been separated from Gondwana since 120 Ma and, and Madagascar separated from India by 90 Ma [83]. Madagascar started to break away from Africa around 165 Ma [123] and to become isolated in Cretaceous [124], and the invasion from Africa continent toward the island may not occurred due to broad watergaps as physical barriers for dispersal as Rhinolophidae are weak fliers [32]. Additionally, higher diversity richness and endemism in Madagascar appears as a result of dispersal from Africa and followed with diversification [125, 126], and typically reflects more recent events around Plio-Pleistocene [127].
Compared with previous study implementing BioGeoBEARS for bats, the d parameter (for dispersal rate in anagenetic) shown higher than e parameter (for extinction or range contraction rate) in Pteropodidae family across the oceanic island systems, and may explained peripatric speciation within Pteropodidae species [128]. Therefore, we assumed the historical biogeography in bats varied between families which strongly relates to flight performance between species and differences in dispersal ability For instance bat colonization to Madagascar (Pteropodidae, Emballonuridae, Hipposideridae, Vespertillionidae, Nycteridae, Molossidae and Myzopodidae), with a notable of absence Rhinolophidae species (Racey et al., 2009). Wing-loading, wing-span, aspect ratio and wing shape are the main aerodynamic variables in determining the flight performance and flight efficiency of species. Rhinolophid bats generally possess broad and short, low wing loading and aspect ratio adapted for good maneuverability in foraging as slow aerial hawkers, perch hunters and gleaners (Norberg and Rayner 1987; Amador et al. 2020). However, flight would be expensive for a long distance flight and therefore limiting the ability for dispersal. Contrary to Rhinolophidae, most Pteropodidae possess high wing loading and large wing spans, with low aspect ratios that support for long distance travel but are less maneuverable [3], as a consequence many Pteropodids are restricted to various oceanic islands where they are often the only native mammal species.
True-flight abilities together with echolocation has been long considered as remarkable evolutionary features which have driven the success of bat species and enables them to occupy wide range of ecological niches, but the morphological features have evolved into current form from a common ancestor [2]. Other factors such as dispersal filters (isolation, geologic history), environmental filters (present and past climate, and environmental heterogeneity) which influence the diversity of vascular plants [129] may also have contributed in shaping the current biogeographic ranges of Rhinolophidae.
The Systematic and Ancestral Biogeography range of Hipposideridae and Rhinonycteridae.
Hipposideridae and Rhinonycteridae are the sister families within Rhinolophoidea superfamily.. Amador et al (2018), suggested the phylogenetic tree for superfamily as (Rhinonycteridae, (Hipposideridae, Rhinolophidae)) but Foley et al (2015) resolved the relationship as (Rhinolophidae, (Hipposideridae, Rhinonycteridae)), similar with species tree in this study [44]. Foley et al (2015) suggested the African species of H. abae, H. caffer and H. jonesi were within Asian Hipposideros, and Coelops frithii, Aselliscus stoliczkanus were sister to Hipposideros African species (H. commersoni and H. vittatus). Nevertheless, this arrangement has low branch support, and low taxonomic coverage which only includes total of 13 species of Hipposideridae Asian lineages and Afrotropical lineages. In the species tree use in this study, [44] resolved the relationship and H. jonesi (Afrotropical species) species fall within Oriental-Australian lineages, similar with tree topology of Amador et al (2018), paraphyly with Aselliscus sp, Coelops frithii and Anthops ornatus in the same lineage, which is in agreement with [130]. H. abae and H. caffer as Afrotropical species are within Afrotropical lineages (in contrast with Foley et al, 2015, but in concordance with [61]) with Asellia tridens in the basal of Afrotropical and Oriental-Australian tree.
For Rhinonycteridae, here we provide seven species out of nine species within family, belonging to four genera, Triaenops, Paratriaenops, Cloeotis, distributed in Madagascar and Afrotropical, and Rhinonycteris endemic to Australia with tree topology as ((Cloeotis, Paratriaenops), (Rhinonycteris, Triaenops)). This arrangement also in contrasts with Foley et al (2015) with tree topology as ((Paratriaenops, ((Triaenops, Cloeotis), Rhinonycteris)) while using six species, and Amador et al (2018) (Paratriaenops, (Triaenops, Cloeotis)) with absence of genus Rhinonycteris. Certainly, missing taxa and gene choice compromise these result, thus the tree generated in Álvarez-Carretero et al. 2021 using supermatrix genome-scale of 182 genes may assume as the latest update tree with smaller uncertainties which facilitates precise testing of historical biogeographic analysis.
The historical biogeography of family Hipposideridae is also related to complex historical geology of the Old-World regions (see discussion above) (Fig. 7). The ancestral ranges of Hipposideridae suggests an Oriental and African origin, the Oriental-Oceania-Australia lineages supports the jump-dispersal for species colonization. This explains how new lineages colonized between regions (such as island), and allowed inter-continental disjunction or oceanic-dispersal pattern (dispersal without range expansion) (Matzke 2014).
In contrast with Rhinolophidae, their dispersal rate is higher than range constriction in Hipposideridae. This indicates that ancestor Hipposideridae are able to disperse across water bodies or using land-bridges and stepping stones. The colonization of Hipposideridae toward Greater Sunda Island may have occurred when the land was connected with Peninsula since early Miocene, followed with multiple fluctuation of sea level until the Sunda Island formed separately at 5 Ma [51, 58, 59, 85], similarly with Rhinolophidae. The Wallacea region might have played an important role as a stepping stone to colonize Oceania and Australia regions, but migration, population exchanges and secondary contact may have occurred in the past between Oceanian-Wallacean region. In concordance with Rhinolophidae ancestral ranges, the range expansion of Hipposideridae to Africa may also occurs via Arabian Peninsula and Sahara-Arabian around Oligocene periods (27–30 Ma). Even though the Gomphoterium landbridge and Tethys Ocean closed around the Late Miocene, the marine barriers did not totally prevent mammalia exchanges between Eurasia and Afro-Arabian, for example for proboscideans [131]. Ancestral Hipposideridae were widespread in Eurasia and Africa since the end of Early Eocene with the evidence of fossils records in Africa and Arabia [72].
The colonization of Hipposideridae toward the Philippines, Wallacea, Oceania and Australia coincided with acceleration of the orogeny of Philippine archipelago, Wallacea with the orogeny of Sulawesi and the main stages of the New Guinean orogeny in Oligocene [51, 85, 121]. Our result suggests Oceanian colonization since early Miocene (~ 20 Ma), similarly with passerine birds by [132]. However, central range of present day of Papua New-Guinea likely did not begin to appear as land until the early-middle Miocene (14–16 Ma) [133] and the present form is predicted since 4–5 Ma. Therefore, founder-events may have involved in island-hopping across the final fragments of a proto-Papuan archipelago in Hipposideridae [134].
Rhinonycteridae split earlier from the common ancestor Hipposideridae Afrotropical lineage around Middle Miocene 40.55 Ma (95% HPD = 36.98–44.14 Ma), but species diversification occurred since 21.88 Ma (95% HPD = 16.54–28.48 Ma) with most of extant species distributed in Madagascar, except Rhinonycteris aurantia which is distributed in Australia. Our result suggests the origin of Rhinonycteridae in Madagascar was Sudanian + Somalia + Ethiopia with Paratriaenops and Triaenops was recently emerged in Plio-Pleistocene epoch (1–3 Ma). This coincided with previous study, stated that most the present-day organism in Madagascar is predominantly of African origin [125]. Dispersal over-water may explained the colonization of ancient Rhinonycteridae in Madagascar, followed with diversification and in-situ radiation, which coincided with Plio-Pleistocene climate cycles [127]. The ancestral Cloeotis percivali may have high dispersal ability allowed the ancestor to exchange from Madagascar to Southern Africa. This associated with our result that suggests the higher extinction rate in this lineages, indicates that the extinction on species in ancestral range followed with colonization of descendants to the new area. The endemic species in Australia belong to Rhinonycteridae, Rhinonycteris aurantia is the only species that currently distributed outside Africa continent [14]. The colonization event of this species toward Australia is challenging to explain, our result shows the African origin but it is almost impossible to explain range extension from Africa to Australia with diversification around Miocene. Some possible hypothesis maybe long distance dispersal over water barrier from Africa to Australia, however the dispersal mechanisms are unknown considering the species is weak fliers. Some of hypothesis suggests that bats colonized Australia by storm-blown to continental shore, for example red flying foxes (Pteropus scapulatus) [135], though landbridges between North Australia and Papua existed for extended periods of time. Ancestral Rhinonycteris may have entered Australia before the Miocene, with fossil evidence of Rhinonycteris tedfordi dating around Miocene from Riversleigh, Northwestern Queensland [136]. Alternative hypothesis suggest waif dispersal and stepping stone through Asia, Sundaland, Wallacea and Oceania [135], therefore, how this species colonized the region still debatable, but low diversity means that species in intermediate regions may have become extinct.
The evolutionary history of species divergence in potential cryptic Rhinolophidae and the comparisons with previous study
Indomalaya is the region with particularly high species diversity of Rhinolophidae and Hipposideridae. However, many species are cryptic suggest the number of species currently underestimate [137]. Chornelia et al. (2022) identify around 40% of potential cryptic species within complex species based on integrative taxonomic approaches, with estimated around 44 potential cryptic species from total of 10 Rhinolophus species sensu lato. In order to estimate the time of divergence between Rhinolophidae sensu-lato species and between potential cryptic species, we ran Bayesian Evolutionary Analysis using Sampling Trees (BEAST) as described in Materials and Methods section.
Our posterior ages estimated Rhinolophidae and Hipposideridae split about 40.26 Ma (95% HPD = 37–43.5 Ma, Middle Eocene) falling within the range of time divergence from previous publications 39–45 Ma [13, 24, 25, 44, 112], similarly, R. shameli and R. creaghi were predicted to split around 3.99 Ma and Foley et al (2015) predicted the time split between two species around 4 Ma (95% HPD = 3–5 Ma), and Álvarez-Carretero et al. (2021) estimated the time divergences as 4.15 Ma (95% HPD = 1.94–7.08 Ma). Our analysis shows the diversification of bats in Southeast Asia was rapid at 24 Ma (95% HPD = 18–31 Ma), in concordance with Álvarez-Carretero et al. (2021) at 22.77 Ma (95% HPD = 19.25–26.51), while Foley et al 2015 predicted the diversification within Rhinolophidae was slightly lower at 17 Ma generated from nuclear exons and introns. The robustness of nodes time estimates in BEAST were related to the choice of clock model and tree priors. A poor choice of tree prior may reduce accuracy of node time estimation [67]. Relaxed clock log normal was the best fit to our data considering the database where it represents a wider geographic region [66, 138]. The birth-death tree prior was selected for our dataset as it consistently provides precise result and were a better choice for mixed dataset. Thus, we expected this analysis to provide a better estimation of dating divergence for cryptic Rhinolophus in the region, to complement the analysis from previous studies when some species are missing.
However, comparison of time divergence estimation across the genes is challenging because of the limited number of species used in previous studies, and the paucity of the bat fossil records. We acknowledge the disconcordance of time tree in this study with other study, which also due to differences in systematic taxa coverage and gene being used (as described in the “Introduction” section). Although we found some discordance between tree topologies we generated in this study and previous studies, we attained similar result across subset analysis related to ancestral range estimation. In terms of species coverage from South China and the Southeast Asia region, we covered most of the described species representing geographical regions. Our results suggest current species sensu lato started to diverge in the late Oligocene and Miocene, meanwhile the potential cryptic species in the region diverged in the Plio-Pleistocene epoch. This analysis indicates that geological events during the epoch contributed in shaping current cryptic diversity patterns seen today. Future directions should aim to include all Rhinolophoid species distributed in the Old-World tropics, as we currently cover around 108 (52%) species of total species identified to date (210 species; Rhinolophidae = 110, Hipposideridae = 90, Rhinonycteridae = 9 species) (Simmons and Cirranello, 2021).