Phylogeny and biogeography of Ficedula flycatchers (Aves: Muscicapidae): Novel results from fresh source material Robert G. Moyle a,⇑ , Peter A. Hosner a , Andrew W. Jones b , Diana C. Outlaw c a Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, United States b Department of Ornithology, Cleveland Museum of Natural History, Cleveland, OH 44106, United States c Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, United States article info Article history: Received 11 February 2014 Revised 22 September 2014 Accepted 30 September 2014 Available online 13 October 2014 Keywords: Ficedula Flycatcher Contamination Toepad Biogeography Migration abstract The avian genus Ficedula has been a model system for studying speciation, genomics, biogeography, and the evolution of migratory behavior. However, no multi-locus molecular phylogenetic hypothesis exists for the genus. We expanded taxon and character sampling over previous studies and produced a robust hypothesis of relationships for the genus. Many previous findings, such as the inclusion of Muscicapella and exclusion of Ficedula monileger from the genus, were verified, but many relationships differed com- pared to previous work. Some of the differences were due to increased sampling, but others were due to problematic sequence data produced from DNA extracted from historical museum specimens. The new phylogenetic hypothesis resulted in a simpler biogeographic scenario with fewer transitions between regions and fewer transitions between seasonally migratory and resident character states. Notably, all species endemic to the Philippines and Wallacea formed a clade, which included Ficedula dumetoria of the Sunda Shelf and Lesser Sundas. In addition, Ficedula hyperythra was not monophyletic; samples from Philippine populations formed a clade distantly related to a clade that comprised all other sampled populations. Ó 2014 Elsevier Inc. All rights reserved. 1. Introduction The Old World flycatchers in the genus Ficedula constitute the largest genus in the taxon Muscicapidae, with around 30 recog- nized species (Gill and Donsker, 2013). They occupy much of the Old World and exhibit a variety of life history characteristics, mak- ing them an ideal subject for evolutionary studies. In particular, they show variation in migratory behavior and they span many biogeographic realms, so several phylogenetic studies have focused on Ficedula and its relatives (Outlaw and Voelker, 2006; Sangster et al., 2010; Zuccon and Ericson, 2010). Additionally, the European Ficedula species have emerged as a model system for studies of avian speciation and genomics (e.g., Backström et al., 2010; Ellegren et al., 2012; Qvarnström et al., 2010), further increasing interest in assessing the evolutionary history of the genus. Sangster et al. (2010) and Zuccon and Ericson (2010) included multiple Ficedula species in higher-level phylogenies of the chat- flycatcher complex, whereas Outlaw and Voelker (2006) included denser taxon sampling and focused on relationships within the genus. The three studies clarified membership in the genus and some broad phylogenetic patterns. For example, all three studies found that Ficedula (Anthipes) monileger was part of a different clade and should no longer be included in the genus. Furthermore, Outlaw and Voelker (2006) and Zuccon and Ericson (2010) found that Muscicapella hodgsoni was embedded within Ficedula. This relationship caused a nomenclatural conflict with Slaty-backed Flycatcher, Ficedula hodgsonii Verraux 1871. Hereafter we follow Zuccon (2011) in transferring M. hodgsoni to Ficedula and using Ficedula sordida Godwin-Austen 1874 for Slaty-backed Flycatcher. In general, basal relationships in the phylogenies were weakly sup- ported and characterized by short internodes. Because of the dense taxon sampling, the phylogenetic results of Outlaw and Voelker (2006) were used to reconstruct biogeographic history and the evolution of migratory behavior (Outlaw and Voelker, 2008). Their results indicated multiple transitions among migratory behaviors and frequent colonization and back-colonization of biogeographic regions, implicating long-distance dispersal as a primary driver of speciation. As part of ongoing research programs on Philippine phylogeog- raphy (e.g., Andersen et al., 2013; Hosner et al., 2013a,b; Jones and Kennedy, 2008a,b; Oliveros and Moyle, 2010; Sánchez-González http://dx.doi.org/10.1016/j.ympev.2014.09.029 1055-7903/Ó 2014 Elsevier Inc. All rights reserved. ⇑ Corresponding author. E-mail address: moyle@ku.edu (R.G. Moyle). Molecular Phylogenetics and Evolution 82 (2015) 87–94 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev