Discussion of Phylogenetic Relationships
Monophyly of Microchiroptera is strongly supported. A variety of data have been analyzed to help resolve the relationships of families within this clade, including osteological characteristics (Smith, 1976; Van Valen, 1979), fetal membrane traits (Luckett, 1980), auditory region morphology (Novacek, 1980), hyoid region characteristics (Griffiths and Smith, 1991; Griffiths et al., 1992), transferrin immunological distance data (Pierson, 1986), rDNA restriction sites (Baker et al., 1991), and DNA hybridization data (Kirsch et al., In press). The most recent comprehensive analyses were those of Simmons (1998) and Simmons and Geisler (1998), who combined all of these data (with the exception of immunological and DNA-hybridization data). Analysis of this large data set produced a relatively well-resolved, well supported phylogeny of Microchiroptera. Interestingly, this tree is largely compatible with trees produced from distance data by Kirsch et al. (In press).
An early phylogentic hypothesis proposed by Smith (1976) indicated two clades within Microchiroptera: Yinochiroptera (Emballonuridae, Rhinolopoidea) and Yangochiroptera (Noctilionoidea and Vespertilionoidea). Other analyses, however, have not supported these clades. Van Valen’s (1979) tree suggests that neither Yinochiroptera nor Yangochiroptera are monophyletic due to a close relationship between Emballonuridae and Noctilionoidea. Pierson (1986) concluded that Yinochiroptera was monophyletic, but due to the close relationship between Vespertilioninae and Yinochiroptera, Yangochiroptera was not. Simmons (1998) and Simmons and Geisler’s (1998) analyses suggested the reverse, a monophyletic Yangochiroptera and a paraphyletic Yinochiroptera. The latter appears paraphyletic due to Emballonuridae placed as the basal branch in Microchiroptera.
| ==== Rhinoloppoidea
| === Noctilionoidea (Phyllostomoidea)
Van Valen (1979)
| ========= Rhinolophoidea
===| | === Emballonuridae
| ===| ===|
=====| ===| === Craseonycteridae
| ====== Noctilionoidea
| ============ Vespertilionoidea (including Mystacinidae)
============ Natalidae (including Thyropteridae and Natalidae)
| === Rhinolophidae
===| | === Hipposideridae
===| | | === Megadermatidae
===| | | ===|
===| | | | === Rhinopomatidae
=====| | | | |
| | | | ============ vespertilionids
| | | |
| | | =============== Molossidae
| | |
| | ================== Thyropteridae
| ===================== Noctilionoidea (including Mystacinidae)
The placement of Emballonuridae has been often debated. Smith placed Emballonuridae in a monophyletic group containing Craseonycteridae and Rhinopomatidae, while Van Valen’s analysis indicated that Emballonuridae and Craseonycteridae were more closely related to Noctilionoidea and Rhinolophoidea than to Rhinopomatidae. Pierson’s tree also indicated that Rhinopomatidae belongs in a clade with Rhinolophoidea, not grouped with Emballonuridae, and did not support a close relationship between Emballonuridae and Noctilionoidea.
The relationships of members of the Vespertilionoidea have long been unclear. Vespertilionidae has been treated as a clade by most authors (Smith, 1976; Van Valen, 1979; Novacek, 1991). However, the frequent appearance of this group in discussions of bats may be attributed to the common assumption of monophyly rather than strong phylogenetic support for this hypothesis. Pierson (1986), who did not assume Vespertilionidae monophyly, placed Tomopeatinae and Miniopterinae (usually found within Vespertilionidae) with Molossoidea and suggested the remaining vespertilionids form a clade with Yinochiroptera. Recent work (Simmons, 1998; Simmons and Geisler, 1998) has indicated that Vespertilionidae as traditionally recognized is paraphyletic. Instead, Antrozoinae (which Simmons  raised from subfamily to family rank) appears closely related to Molossidae and should therefore be placed in Molossoidea; Myzopodidae, Thyropteridae, Fruipteridae and Natalidae represent a clade and are here represented in the superfamily Nataloidea. With the removal of the preceding families, Vespertilionidae, limited to Vespertilioninae, Miniopterinae, Myotinae, Murininae and Kerivoulinae, is now monophyletic." One group which is fairly well supported is the clade containing Phyllostomidae, Noctilionidae, and Mormoopidae (= Noctilionoidea). Mystacinidae, traditionally linked with vespertilionids and molossids, now appears to be closely related to this group (Pierson, 1986; Kirsch et al., In press) and is therfore here included in the Noctilionoidea.
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