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Megabats (Megachiroptera) Yinpterochiroptera and Microbats (Microchiroptera) Yangochiroptera


image: Higher level relationships among the major lineages of bats.

Molecular studies support microbat paraphyly (A) whereas morphological studies support microbat monophyly (B). Chiropteran taxa correspond to genera that were sampled in Tsagkogeorga et al.’s genomic analysis. Molecular phylogenies imply independent origins of laryngeal echolocation in yangochiropteran and rhinolophoid microbats, respectively, as shown in (A), or gain of echolocation in the common ancestor of bats followed by loss of echolocation in megabats (scenario not shown). Morphological phylogenies imply a single origin of laryngeal echolocation in the common ancestor of microbats (B). Megabat genera are highlighted in green boxes; microbat genera are highlighted in pink boxes. Megabat painting by Carl Buell.

Megabats (Megachiroptera) new name Yinpterochiroptera

Microbats (Microchiroptera) new name Yangochiroptera

Bats were traditionally divided into two suborders, Microchiroptera and Megachiroptera, based on morphological cladistics. However, molecular studies suggested that rhinolophoid microbats are more closely related to the megabat family Pteropodidae than to other microbats, rendering Microchiroptera paraphyletic. A new taxonomy divides bats into Yangochiroptera, including 12 microbat families, and Yinpterochiroptera, including four microbat families in Rhinolophoidea plus Old World fruit bats (Springer, 2013)

Some notable national sites eg Integrated Taxonomic Information System ( which ultimately informs the Catalogue of Life, and in turn the IUCN) and Mammal Species of the World, recognise the new
suborders, while others including the Australian Faunal Directory still recognise the old suborders. Note that the new names are not simply a name replacement but reflect the new understanding of the relationships among the families of bats.

Sue Churchill's 2nd edition of Australian Bats has a paragraph on this and this site itis.gov / Taxonomy and Nomenclature discusses it further with a reference to a paper in Current Biology in 2013 by Mark Springer "Phylogenetics: Bats United, Microbats Dividied".


Megachiroptera Dobson, 1875

Taxonomy and Nomenclature

Kingdom: Animalia
Taxonomic Rank: Suborder
Valid Name: Chiroptera Blumenbach, 1779
Reference for: Megachiroptera

Curator of North American mammals and Chief of Mammal Section, National Biological Service, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
Reference for: Megachiroptera

Author/Editor: Springer, Mark S.
Publication Date: 2013
Article/Chapter Title: Phylogenetics: Bats United, Microbats Divided
Journal/Book Name, Vol. No.: Current Biology, vol. 23, no. 22
Page(s): 999-1001
ISBN/ISSN: 0960-9822
Reference for: Megachiroptera

Notes: DOI: 10.1016/j.cub.2013.09.053; available online at http://www.sciencedirect.com/science/article/pii/S0960982213012001

Author/Editor: Wilson, Don E., and DeeAnn M. Reeder, eds.
Publication Date: 1993
Journal/Book Name, Vol. No.: Mammal Species of the World: A Taxonomic and Geographic Reference, 2nd ed., 3rd printing
Page(s): xviii + 1207
Publisher: Smithsonian Institution Press
Publication Place: Washington, DC, USA
ISBN/ISSN: 1-56098-217-9
Notes: Corrections were made to text at 3rd printing


Taxonomic Hierarchy

Kingdom Animalia – Animal, animaux, animals
Subkingdom Bilateria
Infrakingdom Deuterostomia
Phylum Chordata – cordés, cordado, chordates
Subphylum Vertebrata – vertebrado, vertébrés, vertebrates
Infraphylum Gnathostomata
Superclass Tetrapoda
Class Mammalia Linnaeus, 1758 – mammifères, mamífero, mammals
Subclass Theria Parker and Haswell, 1897
Infraclass Eutheria Gill, 1872
Order Chiroptera Blumenbach, 1779 – morcego, quiróptero, bats
Direct Children:
Suborder Yangochiroptera Koopman, 1984
Suborder Yinpterochiroptera Springer, Teeling, Madsen, Stanhope and Jong, 2001



Summary

Phylogenetic analyses on four new bat genomes provide convincing support for the placement of bats relative to other placental mammals, suggest that microbats are an unnatural group, and have important implications for understanding the evolution of echolocation.

Main Text

Bats (Order: Chiroptera) are extraordinary among mammals, both for their taxonomic diversity and novel adaptive features. Bats are the only mammals that are capable of powered flight, and along with birds and pterosaurs comprise one of three vertebrate clades that have evolved this transformative feature. Bats are traditionally divided into two suborders — Microchiroptera (microbats) and Megachiroptera (megabats). Microbats are generally smaller than megabats, are often characterized by poor vision, and make use of sophisticated sonar systems based on echolocation pulses emitted by the larynx for navigation and aerial prey capture. The smallest microbat, Kitti’s hog-nosed bat (Craseonycteris thonglongyai), weighs in at a meager two grams. Megabats comprise a single family (Pteropodidae) and are commonly known as ‘Old World fruit bats’. They can weigh as much as 1.5 kilograms, attain wingspans up to 1.5 meters, and have well developed vision as do many primates. A few megabats are known to echolocate, but by a different mechanism that involves tongue clicks rather than laryngeal echolocation as in microbats. In a new study in this issue of Current Biology, Tsagkogeorga et al. [1] assemble a comprehensive phylogenomic data set for bats that resolves relationships within bats and the position of bats relative to other mammalian orders.

Bats have played a leading role in several controversies in resolving the evolutionary relationships among mammals, including the relationship of bats to other placental orders [2, 3], the natural (monophyly) versus unnatural (paraphyly) association of microbats [4, 5, 6, 7], and even the monophyly of bats themselves [2]. The monophyly versus paraphyly of microbats is of particular interest and has implications for understanding the evolution of laryngeal echolocation (Figure 1). Microbat monophyly is rooted in morphological cladistics and posits that laryngeal echolocation evolved in the common ancestor of all living microbats [2]. Microbat paraphyly, in turn, is based on molecular studies [4, 5] and suggests that rhinolophoid microbats are more closely related to the megabat family Pteropodidae than to other microbats, rendering microbats an unnatural group. These results have been codified in a new taxonomy for bats: Yangochiroptera includes 12 microbat families, whereas Yinpterochiroptera comprises four microbat families in Rhinolophoidea plus Old World fruit bats [5](Figure 1A). Importantly, this arrangement implies that laryngeal echolocation evolved independently in two different groups of microbats or was lost in Old World fruit bats after evolving in the common ancestor of Chiroptera. Most recently, O’Leary et al. [7] rekindled this debate by assembling a morphological data set of unprecedented size (4541 characters), combining these data with previously published molecular sequences for 27 genes. Based on phylogenetic analyses of the combined data, they claimed that morphology overturns molecules to restore the monophyly of echolocating bats (Figure 1B).

With regard to their position in the mammalian evolutionary tree, cladistic analyses of morphological characters have positioned bats within the group Archonta along with primates, tree shrews, and flying lemurs [6]. However, phylogenetic analyses of molecular data sets place bats in the superorder Laurasiatheria along with true insectivores (e.g., shrews, moles, hedgehogs), carnivorans (e.g., dogs, cats), pangolins, odd-toed ungulates (horses, rhinos, tapirs), even-toed ungulates (e.g., camels, pigs, cows) and cetaceans (whales, dolphins, porpoises) [3]. However, the relationship of bats to other members of Laurasiatheria has proven difficult to resolve with molecular data, and different studies support a range of conflicting hypotheses [3, 6, 8, 9, 10, 11].

Previous genomic studies have addressed the phylogenetic position of bats, but with more limited taxon sampling that only included one or two bats [12, 13]. Tsagkogeorga et al. [1] have now included sequences from six bat genomes in their study and performed phylogenetic analyses with standard concatenation methods that combine all of the gene sequences into a single data matrix, coalescence methods that infer a species tree from individual gene trees and a hybrid ‘concatalescence’ approach that combines elements of concatenation and coalescence [14]. The authors found compelling support for a sister-group relationship between bats and a large clade composed of representative carnivorans (dog, cat), perissodactyls (horse), and cetartiodactyls (alpaca, bottlenose dolphin). This arrangement agrees with some previous analyses of molecular sequences [3, 6, 13], but disagrees with sequence-based results wherein bats have a more nested position within Laurasiatheria [6, 9, 10, 11, 12]. Tsagkogeorga et al.’s [1] results also conflict with retroposon insertions [8, 15] that support alternative relationships within Laurasiatheria.

Is the new study the final word on the phylogenetic position of bats? Perhaps, but improved taxon sampling and new methods have a history of reviving old debates, as recently illustrated by a re-examination of the root of the placental mammal tree with novel phylogenetic methods and arrived at opposite conclusions [16]. Tsagkogeorga et al.’s [1] data set provides additional taxon sampling for bats, but there remain long, undivided branches elsewhere in the tree that may be susceptible to known artifacts of phylogeny reconstruction methods. Most notably the only representative of Perissodactyla in Tsagkogeorga et al.’s [1] analysis is the horse (Equus caballus). It will be important to include a second representative in future studies to determine if the phylogenetic placement of perissodactyls is stable relative to bats and other laurasiatherians.

Unlike the problem of resolving the phylogenetic position of bats relative to other laurasiatherian clades, where molecular studies have yielded a variety of conflicting results, molecular data have consistently supported microbat paraphyly [4, 5, 6]. The new results based on genome sequences provide additional, convincing support for this hypothesis. Among bats that Tsagkogeorga et al. [1] included in their study, the microbat families Rhinolophidae and Megadermatidae are more closely related to the megabat family Pteropodidae than to the microbat families Mormoopidae and Vespertilionidae, thus rendering microbats an unnatural group (Figure 1A). O’Leary et al. [7] reported that microbat monophyly is upheld by 57 unambiguous shared derived characters from the osteological partitions of their combined data set, but viewed from the lens of Tsagkogeorga et al.’s [1] new genomic analyses these ‘synapomorphies’ are instead a remarkable case of homoplasy, involving convergent evolution in microbats and/or evolutionary losses in megabats (Figure 1A). For now, it remains unclear if laryngeal echolocation evolved independently in yangochiropteran and rhinolophoid microbats or evolved in the common ancestor of Chiroptera with subsequent loss in Old World fruit bats in conjunction with their elaboration of visual systems.

Interestingly, the homoplastic signal in morphology that supports Microchiroptera [7] is also discernible in molecular data. This signal was first identified in the motor protein Prestin, which occurs in the outer hair cells of the mammalian cochlea and confers sensitivity to high frequencies [17]. Later, Liu et al. [18]reported a phylogenetic tree based on Prestin amino acid sequences and showed that not only echolocating bats, but also echolocating dolphins, group together based on convergent amino acid substitutions. In another paper Parker et al. [19]extended these comparisons across the genome and showed that there are genome-wide signatures of adaptive convergence in echolocating bats and the bottlenose dolphin (Tursiops truncatus). These adaptive signatures were detected in both hearing and vision genes [19] and demonstrate that widespread adaptive convergence can occur at both the molecular and morphological level. Importantly, however, the genomic data of Tsagkogeorga et al. [1] retain a much higher proportion of homologous (true) phylogenetic signal than convergent signal and correctly deploy echolocating mammals into three separate clades: Rhinolophoidea, Yangochiroptera, and Odontoceti.

Tsagkogeorga et al. [1] have firmly cemented microbats in paraphyly, but discriminating between convergent origins of laryngeal echolocation versus a single origin with subsequent loss remains a central question in bat biology. The new genome sequences from Tsagkogeorga et al. [1] are welcome additions to genomic databases that may ultimately help to decipher if laryngeal echolocation evolved independently in Rhinolophoidea and Yangochiroptera or was lost in Pteropodidae after evolving in the common ancestor of all bats. Some molecular studies favor the former hypothesis [17, 18], but the oldest and most primitive fossil bat (Onychonycteris finneyi) may have used laryngeal echolocation based on a possible articulation between the stylohyal and tympanic bones [20], which suggests that laryngeal echolocation evolved in the common ancestor of bats and was subsequently lost in megabats. There is much more to learn from both genomes and the fossil record.


Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats

Highlights
  • Bats are a sister group of a clade of carnivores, ungulates, and cetaceans
  • Genome-scale analyses show that echolocating bats are not a true group
  • Previous conflicting results likely stem from a mixed signal among loci
Summary

Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups [1, 2], yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) [3, 4, 5, 6]. Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic [7, 8, 9] or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes [4, 11], we show that—contrary to recent suggestions—bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era.

Results and Discussion

Phylogenetic Reconstruction of Position of Bats

Bats are an ancient and diverse group that originated ∼65 million years ago in the late Cretaceous/early Paleocene and underwent a rapid radiation in the Eocene [9]. However, the exact evolutionary relationship of bats to their closest mammalian relatives is poorly understood due to their unique morphological features associated with flight, a lack of intermediate forms, and a poor fossil record. Our phylogenomic analyses of 2,320 coding DNA sequence (CDS) alignments, each containing 14 to 22 species and including four new bats, allowed us to determine the position of bats within the superorder Laurasiatheria with high confidence. Maximum likelihood (ML) reconstructions undertaken separately for concatenated CDS alignments of nucleotides and amino acids (2.4 Mb and ∼7.9 × 105 residues, respectively) both yielded congruent and highly resolved trees (Figure 1). In both the nucleotide and amino acid trees, the bats formed a well-supported sister group with a clade of ungulates, cetaceans, and carnivores. Within this clade (sometimes called Fereuungulata), we find strong support for placing the order Cetartiodactyla in a monophyletic clade with the Perissodactyla as a sister group to the Carnivora. We also obtain very strong support for many of the proposed clades within Laurasiatheria (Table 1) as well as for the deepest relationships within the mammals (Figure 1).

Table 1 Recognized Orders and Proposed Higher Clades within Laurasiatheria


Recognized orders and proposed higher clades within Laurasiatheria, together with the common names of representative member taxa (representatives included in our phylogenomic data set are indicated by asterisks). The first three higher clades are recovered by our study (Figures 1 and S1).

It is now widely accepted that bats belong to the superorder Laurasiatheria [1, 2,6]; however, the relationships within this group have been strongly contended, with different studies proposing that bats are a sister group to a clade comprising carnivores and odd-toed ungulates [12, 13, 14] or to the Fereuungulata [1, 4, 6,13, 15, 16]. The former hypothesis, termed Pegasoferae, was supported by the results of recent phylogenomic analyses that included four bat species [5], as well as by analyses of retroposon insertions [17] and conserved noncoding elements [13]. Our new results contradict this arrangement and instead support the latter hypothesis, in agreement with earlier findings [1, 6].

Conflicting results might reflect noisy phylogenetic signal, differences in taxonomic sampling, and/or the extent to which studies have controlled for heterogeneous sequence evolution inherent in large data sets of concatenated gene sequences. To account for such potential heterogeneity in our analyses, we partitioned our data set by CDS, estimated model parameters independently for each partition, and, in the case of nucleotide data, also partitioned by codon position. When we repeated our ML phylogenetic reconstructions for the full data set without model partitioning, in line with the recent genome-scale analysis [5], we recovered Pegasoferae based on the nucleotide data set, but not the amino acid data set (see Supplemental Experimental Procedures and Figure S1available online). In both cases, the model fit was significantly worse than that of the respective partitioned model (see Supplemental Experimental Procedures). These results thus support previous studies showing that partitioning can outperform standard models of sequence evolution when phylogenetic reconstruction is based on concatenated data [11, 18, 19]. To further determine the likely cause of differences between our results, we reduced our data set by removing CDSs from taxa that were not sampled in the previous study; however, repeating the analyses still failed to robustly recover the clade Pegasoferae (Table S3).

Uncertainty surrounding the interordinal relationships within Laurasiatheria [1, 4,5, 6, 10, 13, 17, 20, 21, 22] may also be largely attributable to rapid diversification of the main lineages (illustrated by the very short branches connecting these in the phylogenetic tree) and associated incomplete lineage sorting [4, 6, 13, 17, 21]. To account for incomplete lineage sorting and other sources of tree discordance among loci, we analyzed our data using coalescent methods of species tree reconstruction [4]. Again, coalescent trees containing all taxa were highly consistent with those inferred from the partitioned methods, both strongly supporting a sister relationship between bats and the Fereuungulata within the Scrotifera (Figure 2). Finally, to ensure that our findings were robust to potential within-locus recombination, we repeated these coalescent-based analyses using individual exons, and we recovered the same results. Our results therefore suggest that disagreements in the literature may reflect model misspecification, long branches (e.g., Equus), and/or poor taxon sampling.

Analyses of Bat Subordinal Relationships

Our phylogenomic reconstructions provide an equally clear and statistically robust picture of the evolutionary relationship between echolocating and nonecholocating bats, providing unequivocal support for the reciprocal monophyly of the proposed suborders Yinpterochiroptera and Yangochiroptera (bootstrap percentages [BP] = 100%; see Figure 1). Contrary to this result, a recent large-scale analysis that combined 27 genes plus morphological characters recovered the traditional subordinal split of bats into Microchiroptera, members of which are all capable of laryngeal echolocation, and Megachiroptera (Old World fruit bats), members of which are usually larger, do not possess laryngeal echolocation, and instead exhibit well-developed visual systems [23] (Figure 3B). By including bat species encompassing both proposed systems of subordinal systematics in our analyses (see Experimental Procedures), we were able to firmly reject this traditional systematic division of Microchiroptera and Megachiroptera, and this finding was also strongly corroborated by coalescent analyses (Figure 2). Within the Yinpterochiroptera, we also recovered full support for both the clades of Old World fruit bats, represented by the taxa Eidolon helvum and Pteropus vampyrus, and the laryngeal echolocators, represented byRhinolophus ferrumequinum and Megaderma lyra (BP = 100% in both cases).

Our data therefore support most other genetic analyses that have suggested some echolocating bats are more closely related to nonecholocating Old World fruit bats than to the remaining echolocating bats [2, 7, 8, 9]. By moving from a few tens of loci to over 2,000 loci, our findings prove without doubt that the evolution of laryngeal echolocation in bats has involved either multiple acquisitions or an evolutionary loss in Old World fruit bats [7, 8, 9, 24, 25, 26,27].

Locus-wise Phylogenetic Support and Selection

To dissect the phylogenetic signal in our data, we assessed the relative support of each locus for the two competing hypotheses of bat subordinal systematics, each in the context of eight different recently described phylogenetic proposals that vary in the position of the bats within Laurasiatheria (Figure 3; Table S4). Comparisons of 16 candidate topologies across 2,320 loci revealed clear and consistently greater genomic signal favoring the paraphyly of echolocating bats regardless of the relationship of bats with respect to other laurasiatherian clades (Figure 3; Table S4). Nonetheless, inspection of individual loci revealed remarkably few cases of unambiguous signal: based on approximately unbiased tests of amino acid tree selection, just 121 loci (5%) significantly rejected the Microchiroptera-Megachiroptera hypothesis in favor of the Yinpterochiroptera-Yangochiroptera division (Table S5C), whereas 19 loci (<1%) showed the opposite signature and thus favored the traditional taxonomy (Table S5B). However, these analyses did not clearly distinguish among alternative hypotheses for the placement of bats within mammals. This result highlights the common difficulties of using individual genes for recovering the species phylogeny, in this case likely due in part to the rapid early emergence of the main lineages [9], molecular convergence [28], and other factors contributing to the mixed signal in the data.

We assessed whether differential support among loci for the alternative subordinal divisions is likely due to selection by using codon-based models of molecular evolution to test for heterogeneous selection regimes in these groups (see Supplemental Experimental Procedures). These models estimate the ratio of the rate of nucleotide substitutions that result in amino acid replacements (dN) to the rate of synonymous substitutions (dS), where separate dN/dS ratios can be separately inferred for different clades in the phylogeny. Among loci supporting the Microchiroptera-Megachiroptera hypothesis, we identified three genes showing evidence of divergent selection in fruit bats: LEF1 (lymphoid enhancer-binding factor 1), BECN1 (beclin 1, autophagy related), and RPE65(retinal pigment epithelium-specific protein 65 kDa) (Table S5B). Similarly, among 161 loci supporting the Yinpterochiroptera-Yangochiroptera hypothesis, several loci (TMED8, SPOK2, SMC3, KLHDC10, PARP6, ACVRL1, P14KB, LIN7C,BUB3, CCDC64B, C19orf55, and LINGO1) showed divergent selection in these bats (Table S5C), but neither set of loci showed evidence for different selection pressure between bat lineages, suggesting that selection was not responsible for the support for these groupings (see Supplemental Experimental Procedures).

Our results show that although phylogenetic signals from single loci fail to determine bat phylogenetic affinities among laurasiatherian groups, aggregating information across loci provides compelling evidence for the phylogenetic relationship of bats to some other groups of mammals. Moreover, by providing robust statistical support for the paraphyly of laryngeal echolocating bats, this study provides the most concrete evidence to date toward resolving the long-standing debate regarding bat evolutionary history. Our results further emphasize the extraordinary phenotypic convergence seen across echolocating members of the two suborders, including the possible independent origin of laryngeal echolocation itself, a hypothesis supported by several studies of molecular evolution of sensory genes (e.g., [28, 29, 30]).

Acknowledgments

We thank Kate Baker, Liliana Davalos, David Hayman, Emmanuvel Koilmani, Yang Liu, Alison Peel, Roger Ransome, and Armando Rodriguez for providing tissue for high-throughput sequencing. We are grateful to staff at BGI for laboratory work and to Anna Terry (Barts and the London Genome Centre) and Chris Walker (Queen Mary GridPP High Throughput Cluster) for providing access to computing facilities. This study was funded by grant BB/H017178/1 awarded by the Biotechnology and Biological Sciences Research Council (UK) to S.J.R., J.A.C., and E.S.

Supplemental Information

Document S1. Figure S1, Tables S1–S3, and Supplemental Experimental Procedures

Document S2. Tables S4 and S5



Figure 1 Evolutionary Relationships of Bats

RAxML tree inferred from the maximum likelihood (ML) analysis of the phylogenomic data set in nucleotides (2,394,810 sites) under the GTR + Γ4 + I model of sequence evolution, partitioned by coding DNA sequence (CDS) data set (n = 2,320) and by first, second, and third codon position. ML analyses of amino acid data sets (collectively containing 787,713 sites) yielded an identical topology. Node values represent RAxML bootstrap percentages (BPs) obtained for the nucleotide and amino acid data sets, respectively. The same analyses without model partitioning recovered the clade Pegasoferae based on the nucleotide data set (see Figure S1), but not the amino acid data set.


Figure 2 Evolutionary Relationships of Bats Inferred from Coalescent Model Analyses

The % bootstrap values at nodes are based on 100 bootstrap replicates of the CDS nucleotide (nuc) and amino acid (aa) data sets, shown for STAR and MP-EST methods, respectively (seeExperimental Procedures). Black filled circles indicate maximal statistical support (BPnuc = 100/100; BPaa = 100/100). All four analyses yielded identical topologies with respect to the sister group relationship between Chiroptera and Fereuungulata, as well as the intraordinal subdivision of the bats into the suborders Yinpterochiroptera and Yangochiroptera. The remaining taxa relationships were also identical, with the exception of the MP-EST tree based on amino acid trees, in which Perissodactyla (represented here by Equus caballus) was more closely related to Carnivora than to Cetartiodactyla (not shown).


Figure 3 Relative Per-Locus Support Scores Based on Amino Acids and Nucleotides for Sixteen Alternative Species Tree Hypotheses

These hypotheses comprise eight alternative Laurasiatheria phylogenies H1–H8 that differ in the placement of bats [1, 4, 5,6, 10, 13, 17, 20, 21, 22], and for each of the eight, the two bat subordinal hypotheses of (A) Yinpterochiroptera-Yangochiroptera (blue bars) and (B) Microchiroptera-Megachiroptera (yellow-brown bars). Details of these hypotheses are provided in Table S4. Phylogenomic analyses in RAxML based on both the concatenation and coalescent methods recovered H1. In contrast, recent genome-wide analyses based on six mammals recovered H5 [5], whereas a large-scale analysis combining morphological and molecular data recovered H4 with strong support for the Microchiroptera-Megachiroptera hypothesis [10]. The number of loci supporting a given hypothesis is the sum of weighted proportions: each proportion ranges from 1, where a single hypothesis could not be rejected, to 0.0625, where none of the 16 was rejected. Details of genes supporting the two bat subordinal hypotheses are given in Tables S5B and S5C.


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