title: Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.).
abstract: In the Andes, humid-forest organisms frequently exhibit pronounced genetic structure and geographic variation in phenotype, often coincident with physical barriers to dispersal. However, phylogenetic relationships of clades have often been difficult to resolve due to short internodes. Consequently, even in taxa with well-defined genetic structure, the temporal and geographic sequences of dispersal and vicariance events that led to this differentiation have remained opaque, hindering efforts to test the association between diversification and earth history and to understand the assembly of species-rich communities on Andean slopes. Here, we use mitochondrial DNA and thousands of short-read sequences generated with genotyping by sequencing (GBS) to examine the geographic history of speciation in a lineage of passerine birds found in the humid forest of the Andes, the 'bay-backed' antpitta complex (Grallaria hypoleuca s. l). Mitochondrial DNA genealogies documented genetic structure among clade but were poorly resolved at nodes relevant for biogeographic inference. By contrast, relationships inferred from GBS loci were highly resolved and suggested a biogeographic history in which the ancestor originated in the northern Andes and dispersed south. Our results are consistent with a scenario of vicariant speciation wherein the range of a widespread ancestor was fragmented as a result of geologic or climatic change, rather than a stepping-stone series of dispersal events across pre-existing barriers. However, our study also highlights challenges of distinguishing dispersal-mediated speciation from static vicariance. Our results further demonstrate the substantial evolutionary timescale over which the diverse biota of the Andes was assembled.
authors.affiliation: Committee on Evolutionary Biology, The University of Chicago, Chicago, IL, 60637, USA.|Life Sciences Section, Integrative Research Center, The Field Museum of Natural History, Chicago, IL, 60605, USA.
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Winger
authors.affiliation: Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA.|Department of Biology, University of Florida, Gainesville, FL, 32603, USA.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Hosner
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.|Secão de Aves, Museu de Zoologia, Universidade de São Paulo (MZUSP), São Paulo, SP 04263-000, Brasil.
authors.forename: Gustavo A
authors.initials: GA
authors.lastname: Bravo
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.|Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA.
authors.forename: Andrés M
authors.initials: AM
authors.lastname: Cuervo
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.|Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-900, Brasil.
authors.forename: Natalia
authors.initials: N
authors.lastname: Aristizábal
authors.affiliation: Life Sciences Section, Integrative Research Center, The Field Museum of Natural History, Chicago, IL, 60605, USA.
authors.forename: Luis E
authors.initials: LE
authors.lastname: Cueto
authors.affiliation: Life Sciences Section, Integrative Research Center, The Field Museum of Natural History, Chicago, IL, 60605, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Bates
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D049810:Genetic Speciation; D005828:Genetics, Population; D005838:Genotype; D008957:Models, Genetic; D046109:Passeriformes / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013020:South America
chemical_list: D004272:DNA, Mitochondrial
keywords: allopatric speciation; genotyping by sequencing; introgression; leapfrog patterns; phylogenomics; tropical montane forest