The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck

Abstract

Simultaneous examination of evolutionary history in island forms and closely related mainland relatives can provide reciprocal insight into the evolution of island and mainland faunas. The Cocos Flycatcher (Nesotriccus ridgwayi) is a small tyrant flycatcher (Tyrannidae) endemic to Cocos Island, an oceanic island in the eastern Pacific Ocean. We first established its close relationship to the mainland species Mouse-colored Tyrannulet (Phaeomyias murina) using a phylogeny from genome-wide ultraconserved elements and exons. We then used mitochondrial DNA to explore the relationships between Nesotriccus and Phaeomyias populations from across its distribution in Central and South America. We found that Nesotriccus is nested within the Phaeomyias evolutionary tree, and that Phaeomyias represents a complex of at least four evolutionarily distinct species that differ in plumage, voice, and habitat association. Nesotriccus underwent a population bottleneck subsequent to its divergence from Central American and northern South American Phaeomyias populations in the middle Pleistocene. The 46 UCE loci containing alleles that are fixed between the two species are widely distributed across the genome, which suggests that selective or neutral processes responsible for divergence have occurred genome-wide. Overall, our simultaneous examination of Phaeomyias and Nesotriccus revealed divergent levels of genetic diversity and evolutionary histories between island and mainland forms.

Habitat Association Predicts Genetic Diversity and Population Divergence in Amazonian Birds

“…We modified existing sequence capture probe sets for UCEs (Faircloth et al 2012) to obtain additional sequence from the more variable UCE flanking regions that might be useful for inferring shallow population histories. The modified probe set is described in Zucker et al (2016). In brief, in UCE loci targeted with a single probe, we designed two probes extending 30 bp farther into the UCE flanks in each direction.…”

“…We cleaned reads with Illumiprocessor software (Faircloth 2013). We processed and assembled data sets following Zucker et al (2016) using the seqcap_pop pipeline (https:// github.com/mgharvey/seqcap_pop). In brief, we used Velvet (Zerbino and Birney 2008) and the wrapper program Velvet-Optimiser (Gladman 2009) to assemble reads across all individuals into contigs de novo.…”

Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds

“…Guided by taxonomy, by results of preliminary analyses of ND2 sequences, and by an ongoing study reconstructing a species-level phylogeny of the suborder Tyranni (M. Harvey et al, in prep), we selected 63 specimens representing 42 named species and 11 subspecies of Scytalopus (missing species were S. alvarezlopezi and S. simonsi), as well as four individuals in the genera Rhinocrypta, Merulaxis, Myornis, and Eugralla for multilocus assessments of relationships (Appendix 2). This strategy involved a sequence capture approach targeting ultraconserved elements (UCEs; Faircloth et al 2012) and conserved exons across the genome (Zucker et al 2016). After quality control, trimming, assembly, and filtering this dataset comprised a total of 1,246,332 bp distributed in 1,833 UCEs (1,201,528 bp) and 80 exons (44,804 bp).…”

Molecular phylogenetics of Doraditos (Aves, Pseudocolopteryx): Evolution of cryptic species, vocal and mechanical sounds

“…Tyrant flycatchers include a large number of genera containing very similar, cryptic or sibling, species that differ in vocalizations ( Empidonax : Stein, 1963; Johnson & Cicero, 2002; Zimmerius : Rheindt et al., 2008b; Phaeomyias / Nesotriccus : Kroodsma et al., 1987; Zucker et al., 2016; Cnemotriccus : Belton, 1984; Serpophaga : Straneck, 1993, 2007; Elaenia : Rheindt et al., 2015; Pseudocolopteryx : this work). This suggests that auditory modalities of communication may frequently be more important than visual ones in species recognition systems in the family.…”