Bayesian phylogenetics

Bats are extraordinary among mammals, having uniquely evolved powered flight and laryngeal echolocation, along with disease resistance, extended healthspans and the ability to hibernate1. However, the evolutionary history of bats and the understanding of these adaptations remain unresolved. We analysed chromosome-level, long-read genome assemblies from 103 bat species, including 42 new assemblies, representing all 21 bat families. This dataset, expanded in scope and assembly quality, yielded a new bat phylogeny. We placed Myzopodidae as the earliest branch within Vespertilionoidea, and resolved yangochiropteran relationships, identifying Emballonuroidea and Vespertilionoidea as sister groups. Our analysis revealed a mosaic evolutionary history across bats and explained why previous phylogenetic studies were misled. Chromosomal ancestral-state reconstructions supported 26 ancestral bat chromosomes. We integrated a morphological dataset of 699 characters for 65 species, including 44 pre-Quaternary fossils and representatives of most living bat families, with neutrally evolving genomic sites. Fossilized birth–death and dispersal–extinction cladogenesis analyses showed that bats, and thus powered flight, probably originated in Europe in the late Palaeocene, refuting African and North American origins. Placement of the fossil †Vielasia in the oldest ‘Eochiroptera’ clade indicates that laryngeal echolocation predates crown-bat diversification. Total evidence dating, including the fossil taxa, significantly reduced unrepresented basal branch lengths compared with molecular-only divergence estimates. By integrating comprehensive genomic and morphological datasets, analysed using innovative methods, we resolve long-standing controversies in bat biology and provide new insights into the evolutionary history and trait diversification of bats.

Previous phylogenies of extant short‐faced bats (Chiroptera Stenodermatina) supported either two colonization events from the mainland …

Paleontological and neontological systematics seek to answer evolutionary questions with different data sets. Phylogenies inferred for …

The mechanisms underlying the high extant biodiversity in the Neotropics have been controversial since the 19th century. Support for …

Morphological characters are indispensable in phylogenetic analyses for understanding the pattern, process, and tempo of evolution. If …

Symbiosis is well known to influence bacterial symbiont genome evolution and has recently been shown to shape eukaryotic host genomes. …

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. …

How ecological opportunity relates to diversification is a central question in evolutionary biology. However, there are few empirical …

Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous song- birds endemic to South America. We delimited species based on examination of >600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsi- mony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underesti- mated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recov- ered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America.

Aim To test the hypothesis that Caribbean Short‐faced bats descended from a single recent ancestor that originated in the continental Neotropics (Mexico, Central America and/or South America). Location The Neotropics, including the West Indies. Methods New mitochondrial cytochrome b and nuclear Rag2 sequences were combined with published molecular data to estimate phylogenetic relationships and sequence divergence among Short‐faced bats. The resulting phylogenies were compared with those compatible with the single‐origin hypothesis using two model‐based statistical tests. Confidence limits on sequence divergence were estimated using a parametric bootstrap. Results All molecular phylogenies revealed two independent Caribbean lineages and showed that continental Short‐faced bats share a recent common ancestor. Morphology‐based trees compatible with the single‐origin hypothesis were significantly worse at explaining the molecular data than any molecular phylogeny. Main conclusions The ancestor of all Short‐faced bats reached the Antilles in the Miocene, too recently to have used a proposed Oligocene land bridge, and well before the Pleistocene glaciations that are thought to have facilitated dispersal for many bats. After a long period of isolation, Short‐faced bats diversified quickly on the Caribbean islands. A single Short‐faced lineage then reached the continent and subsequently expanded its range and diversified into the four extant genera. Among bats, independent lineages of aerial insectivores and nectarivores have also recolonized the continent after evolving in the West Indies. The evidence for an insular origin of the short‐faced frugivorous radiation completes a dynamic model of Caribbean biogeography that encompasses an entire biological community.