How and Why Overcome the Impediments to Resolution: Lessons from rhinolophid and hipposiderid Bats

Abstract

The phylogenetic and taxonomic relationships among the Old World leaf-nosed bats (Hipposideridae) and the closely related horseshoe bats (Rhinolophidae) remain unresolved. In this study, we generated a novel approximately 10-kb molecular data set of 19 nuclear exon and intron gene fragments for 40 bat species to elucidate the phylogenetic relationships within the families Rhinolophidae and Hipposideridae. We estimated divergence times and explored potential reasons for any incongruent phylogenetic signal. We demonstrated the effects of outlier taxa and genes on phylogenetic reconstructions and compared the relative performance of intron and exon data to resolve phylogenetic relationships. Phylogenetic analyses produced a well-resolved phylogeny, supporting the familial status of Hipposideridae and demonstrated the paraphyly of the largest genus, Hipposideros. A fossil-calibrated timetree and biogeographical analyses estimated that Rhinolophidae and Hipposideridae diverged in Africa during the Eocene approximately 42 Ma. The phylogram, the timetree, and a unique retrotransposon insertion supported the elevation of the subtribe Rhinonycterina to family level and which is diagnosed herein. Comparative analysis of diversification rates showed that the speciose genera Rhinolophus and Hipposideros underwent diversification during the Mid-Miocene Climatic Optimum. The intron versus exon analyses demonstrated the improved nodal support provided by introns for our optimal tree, an important finding for large-scale phylogenomic studies, which typically rely on exon data alone. With the recent outbreak of Middle East respiratory syndrome, caused by a novel coronavirus, the study of these species is urgent as they are considered the natural reservoir for emergent severe acute respiratory syndrome (SARS)-like coronaviruses. It has been shown that host phylogeny is the primary factor that determines a virus’s persistence, replicative ability, and can act as a predictor of new emerging disease. Therefore, this newly resolved phylogeny can be used to direct future assessments of viral diversity and to elucidate the origin and development of SARS-like coronaviruses in mammals.

The bats of the Congo and of Rwanda and Burundi revisited (Mammalia: Chiroptera)

“…This key is primarily modified from Hayman et al (1966), with additional information from Hayman & Hill (1971), Bergmans (1997), Cotterill (2001b), , Kerbis Peterhans et al (2013) and Foley et al (2014 …”

New records of bat species using Gatkop Cave in the maternal season

“…Skulls and mandibles of Miniopterus natalensis and the various Rhinolophus species were also measured using measure ments indicated in Goodman et al (2007) and Csorba et al (2003). The nomenclature used follows ACR (2015) and Foley et al (2014).…”

A New Family of Large Omnivorous Bats (Mammalia, Chiroptera) from the Late Eocene of the Fayum Depression, Egypt, with Comments on Use of the Name “Eochiroptera”

“…Abundant, fairly complete, unabraded jaws and postcranial bones of arboreal primates are also found in the same deposit, suggesting that the area around BQ-2 was densely forested (Seiffert et al, 2003(Seiffert et al, , 2005(Seiffert et al, , 2009Boyer et al, 2010). Pteropodidae F X X X X X X Gray, 1821; Aguilar et al, 1986;Qui et al, 1985;Ducrocq et al, 1993;Simmons, 2005b;Gunnell, 2010 Rhinolophidae X X X X X X Gray, 1825;Simmons, 2005b Hipposideridae F X X X X X X Flower and Lydekker, 1891;McKenna and Bell, 1997;Simmons, 2005b Rhinonycteridae F X X X X Gray, 1866a; Foley et al, 2014 Megadermatidae X X X X X Allen, 1864; Simmons, 2005b Rhinopomatidae F X X X X Bonaparte, 1838;Simmons, 2005b;Hulva et al, 2007Craseonycteridae X Hill, 1974Simmons, 2005b Emballonuridae X X F X X X X X X Gervais, 1855; Storch et al, 2002;Simmons, 2005b Nycteridae F X X X X Van der Hoeven, 1855; Simmons, 2005b;Sigé, 2011b In 2006 excavations at BQ-2 resulted in discovery of a maxilla fragment with two teeth that appears to be a fossil bat but one that does not fit within the diagnosis of any previously described family of bats from Africa or any other continent. This specimen is herein described as representing a new bat family and its significance is discussed below.…”