Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): Another star phylogeny?

Abstract

BackgroundThe family Pteropodidae comprises bats commonly known as megabats or Old World fruit bats. Molecular phylogenetic studies of pteropodids have provided considerable insight into intrafamilial relationships, but these studies have included only a fraction of the extant diversity (a maximum of 26 out of the 46 currently recognized genera) and have failed to resolve deep relationships among internal clades. Here we readdress the systematics of pteropodids by applying a strategy to try to resolve ancient relationships within Pteropodidae, while providing further insight into subgroup membership, by 1) increasing the taxonomic sample to 42 genera; 2) increasing the number of characters (to >8,000 bp) and nuclear genomic representation; 3) minimizing missing data; 4) controlling for sequence bias; and 5) using appropriate data partitioning and models of sequence evolution.ResultsOur analyses recovered six principal clades and one additional independent lineage (consisting of a single genus) within Pteropodidae. Reciprocal monophyly of these groups was highly supported and generally congruent among the different methods and datasets used. Likewise, most relationships within these principal clades were well resolved and statistically supported. Relationships among the 7 principal groups, however, were poorly supported in all analyses. This result could not be explained by any detectable systematic bias in the data or incongruence among loci. The SOWH test confirmed that basal branches' lengths were not different from zero, which points to closely-spaced cladogenesis as the most likely explanation for the poor resolution of the deep pteropodid relationships. Simulations suggest that an increase in the amount of sequence data is likely to solve this problem.ConclusionsThe phylogenetic hypothesis generated here provides a robust framework for a revised cladistic classification of Pteropodidae into subfamilies and tribes and will greatly contribute to the understanding of character evolution and biogeography of pteropodids. The inability of our data to resolve the deepest relationships of the major pteropodid lineages suggests an explosive diversification soon after origin of the crown pteropodids. Several characteristics of pteropodids are consistent with this conclusion, including high species diversity, great morphological diversity, and presence of key innovations in relation to their sister group.

Predicting Extinction Risk for Data Deficient Bats

“…The phlawd workflow first queries sequences from GenBank [19], compares the sequences to "known" gene segments of the taxa of interest and aligns the sequences based on the degree of relatedness depending on the degree of sequence saturation. We used five genes commonly sequenced for bats: One mitochondrial gene, CytB, two nuclear genes RAG2, Val, and two ribosomal genes, 12S, 16S [24][25][26]. The GenBank query returned 1024 taxonomic entries, and we removed entries with uncertain species identity or incomplete scientific names.…”

Karyotypic Evolution in Malagasy Flying Foxes (Pteropodidae, Chiroptera) and Their Hipposiderid Relatives as Determined by Comparative Chromosome Painting

“…Molecular studies have disputed the morphologically based divisions of the Rousettinae and Pteropodinae and have posed alternative hypotheses concerning the evolutionary relationships among pteropodids. Mitochondrial and nuclear DNA-based analyses are consistent in recognizing Rousettus and the Indomalayan Eonycteris as sister taxa, to the exclusion of other rousettine genera [Giannini and Simmons, 2005;Almeida et al, 2011]. R. madagascariensis is considered the most derived species within this abridged rousettine clade [Almeida et al, 2011] and to be the sister species to R .…”

“…Mitochondrial and nuclear DNA-based analyses are consistent in recognizing Rousettus and the Indomalayan Eonycteris as sister taxa, to the exclusion of other rousettine genera [Giannini and Simmons, 2005;Almeida et al, 2011]. R. madagascariensis is considered the most derived species within this abridged rousettine clade [Almeida et al, 2011] and to be the sister species to R . obliviosus of the nearby Comoros Archipelago [Goodman et al, 2010], but it is unclear if these are derived from Asian or African ancestors.…”

“…lutionary history of certain Malagasy pteropodid and hipposiderid taxa have largely remained ambiguous as phylogenies, in general, were not fully resolved at the generic and species levels for both families [Alvarez et al, 1999;Agnarsson et al, 2011;Almeida et al, 2011;Murray et al, 2011;Foley et al, 2015]. For example, based on morphology the 3 endemic Malagasy pteropodid species are classified into 2 subfamilies: Eidolon dupreanum , Rousettus madagascariensis in the subfamily Rousettinae, and Pteropus rufus in the subfamily Pteropodinae [Bergmans, 1997].…”

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

“…The separation of Stenonycteris from Rousettus was already suggested by Leche (1921) and Kingdon (1974) [in Bergmans (1994: 111)], but was only proven by genetic sequence analyses (Juste B. et al 1999;Almeida et al 2011;Nesi et al 2012). Using cytochrome b sequences, Nesi et al (2012) found that the genus Rousettus was paraphyletic, and that Stenonycteris should be considered as a separate genus, even constituting its own tribe: Stenonycterini.…”