title: Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs.
abstract: The microhylid frog genus Kaloula is an adaptive radiation spanning the edge of the Asian mainland and multiple adjacent island archipelagos, with much of the clade's diversity associated with an endemic Philippine radiation. Relationships among clades from the Philippines, however, remain unresolved. With ultraconserved element (UCE) and mitogenomic data, we identified highly supported differences in topology and areas of poor resolution, for each marker set. Using the UCE data, we then identified possible instances of contemporary hybridization, past introgression, and incomplete lineage sorting (ILS) within the Philippine Kaloula. Using a simulation approach, and an estimate of the Philippine Kaloula clade origin (12.7-21.0 mya), we demonstrate that an evolutionary history including inferred instances of hybridization, introgression, and ILS leads to phylogenetic reconstructions that show concordance with results from the observed mitogenome and UCE data. In the process of validating a complex evolutionary scenario in the Philippine Kaloula, we provide the first demonstration of the efficacy of UCE data for phylogenomic studies of anuran amphibians.
authors.affiliation: Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045.
authors.forename: Alana M
authors.initials: AM
authors.lastname: Alexander
authors.affiliation: Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045.|Department of Biological Sciences, National University of Singapore, 117543, Singapore.
authors.forename: Yong-Chao
authors.initials: YC
authors.lastname: Su
authors.affiliation: Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045.|Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803.
authors.forename: Carl H
authors.initials: CH
authors.lastname: Oliveros
authors.affiliation: Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045.
authors.forename: Karen V
authors.initials: KV
authors.lastname: Olson
authors.affiliation: Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045.
authors.forename: Scott L
authors.initials: SL
authors.lastname: Travers
authors.affiliation: Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045.
authors.forename: Rafe M
authors.initials: RM
authors.lastname: Brown
mesh_terms: D000818:Animals; D001001:Anura / Q000235:genetics*; D002467:Cell Nucleus / Q000235:genetics; D049810:Genetic Speciation; D016678:Genome; D054629:Genome, Mitochondrial; D006824:Hybridization, Genetic; D010679:Philippines; D010802:Phylogeny; D017422:Sequence Analysis, DNA
keywords: Amphibians; Kaloula; Microhylidae; UCE; mitogenome; ultraconserved elements