The Mouse-Colored Tyrannulet (Phaeomyias Murina)
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Molecular Phylogenetics and Evolution 101 (2016) 294–302 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev 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 ⇑ Marc R. Zucker a, , Michael G. Harvey a,b, Jessica A. Oswald b, Andrés Cuervo c, Elizabeth Derryberry c, Robb T. Brumfield a,b a Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA b Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA c Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA article info abstract Article history: Simultaneous examination of evolutionary history in island forms and closely related mainland relatives Received 1 December 2015 can provide reciprocal insight into the evolution of island and mainland faunas. The Cocos Flycatcher Revised 19 April 2016 (Nesotriccus ridgwayi) is a small tyrant flycatcher (Tyrannidae) endemic to Cocos Island, an oceanic island Accepted 24 April 2016 in the eastern Pacific Ocean. We first established its close relationship to the mainland species Mouse- Available online 25 April 2016 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 Keywords: Phaeomyias populations from across its distribution in Central and South America. We found that Phylogeny Nesotriccus is nested within the Phaeomyias evolutionary tree, and that Phaeomyias represents a complex Cocos Island Phylogeography of at least four evolutionarily distinct species that differ in plumage, voice, and habitat association. Ultraconserved elements Nesotriccus underwent a population bottleneck subsequent to its divergence from Central American Exons and northern South American Phaeomyias populations in the middle Pleistocene. The 46 UCE loci contain- Coalescent methods ing alleles that are fixed between the two species are widely distributed across the genome, which sug- gests 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 diver- sity and evolutionary histories between island and mainland forms. Ó 2016 Elsevier Inc. All rights reserved. 1. Introduction Despite extensive study, our knowledge of the genetic diversities and evolutionary histories of many island species is limited Evolutionary biologists have long recognized the utility of (Barrett, 1996; Franks, 2010). Population genetic information from islands for studying the evolution of organisms (Wallace, 1880). island species can provide information on genetic diversity and Due to the discrete geographical nature of islands, populations population size (Frankham, 1997), demographic history including on islands are isolated from high levels of gene flow typical on con- bottlenecks and founder effects (Clegg et al., 2002a), adaptation tinents, providing unique opportunities to study adaptation and and natural selection (Barton, 1996), and the impacts of inbreeding speciation (Grant and Grant, 1996; Losos and Ricklefs, 2009). Island (Frankham, 1998). Comparative studies between closely related species have been used to examine modes of speciation (Barrett, island and mainland taxa are especially useful because the typi- 1996; Cameron et al., 1996; Gittenberger, 1991; McDonald and cally larger mainland populations provide a reference for patterns Smith, 1990; Stuessy et al., 1990), adaptive radiations (Carlquist, and processes inferred on islands (Barrett, 1996; Woolfit and 1995, 1974; Grant and Grant, 1994; Grant, 1984; Tarr and Bromham, 2005). Fleischer, 1995; Vincek et al., 1997), and taxon cycles Simultaneous examination of island and mainland relatives (Greenslade, 1968; Klein and Brown, 1994; Ricklefs and Cox, may also provide insight into the evolution of the continental spe- 1978, 1972; Roughgarden and Pacala, 1989; Wilson, 1961, 1959). cies. Particularly in tropical regions, continental species may have deep evolutionary histories and contain high levels of cryptic diversity (Bickford et al., 2007; Gehara et al., 2014; Hebert et al., ⇑ Corresponding author. 2004; Janzen et al., 2005; Lecocq et al., 2013; Willig et al., 2003). E-mail address: [email protected] (M.R. Zucker). http://dx.doi.org/10.1016/j.ympev.2016.04.031 1055-7903/Ó 2016 Elsevier Inc. All rights reserved. M.R. Zucker et al. / Molecular Phylogenetics and Evolution 101 (2016) 294–302 295 Island forms can serve as evidence of historical diversity and distri- 2. Methods butions for closely related populations or taxa on the mainland (Gotelli and Graves, 1990; Olson, 1997, 1993; Snow, 1985). Genetic 2.1. Sampling and DNA isolation information from island populations can be used to assess the monophyly of mainland populations (Crews et al., 2010; We sampled 46 individuals from across the distribution of the Fernández-Mazuecos and Vargas, 2011; Phillimore et al., 2008; Mouse-colored Tyrannulet (Phaeomyias murina; Table S1), includ- Wilson et al., 2015). In cases where the geological history of the ing all named subspecies (Fitzpatrick, 2004). All genetic samples island is well-known, island populations can be used to calibrate were obtained from fresh tissue, with the exception of one toe divergence time estimates among mainland populations pad from a study skin from Colombia. We also sampled toe pads (Almeida et al., 2005; Runemark et al., 2012; Smith and Klicka, from two individuals of Cocos Flycatcher (Nesotriccus ridgwayi) 2013; Tollis and Boissinot, 2014), and infer histories of selection from Cocos Island (Table S1) and single tissues from the closely (Blondel et al., 1999; Clegg et al., 2002b; Edwards, 1993; Griffith related Capsiempis flaveola and Planalto Tyrannulet (Phyllomyias et al., 1999) or demographic or distributional changes in the main- fasciatus). Genomic DNA was extracted using the Qiagen DNeasy land populations. Reciprocal insight into both mainland and island Blood & Tissue extraction kit (Qiagen, Valencia, California), follow- evolution is therefore possible by examining closely related insular ing the manufacturer’s protocol. Extractions from toe pads of and mainland taxa simultaneously. museum study skins were conducted in a lab space separate from Cocos Island is a 24 km2 oceanic island roughly 550 km off the other tissue extractions to minimize contamination risk. We Pacific coast of Costa Rica. Like the Galápagos Islands, Cocos arose obtained an ND2 sequence of Capsiempis flaveola (DQ294563) from volcanically as recently as 2 Mya and probably was never con- Genbank for use as an outgroup for mitochondrial analyses. nected with the mainland by a land bridge (Castillo et al., 1988; Dalrymple and Cox, 1968). A few phylogenetic studies provide 2.2. PCR amplification and mitochondrial DNA sequencing insight into the relationships and biogeographic history of terres- trial organisms on Cocos Island. The plant species found on the We used polymerase chain reaction (PCR) to amplify the entire island arrived via independent colonizations from other regions, second subunit of the NADH dehydrogenase mitochondrial gene mostly Central America and northwestern South America (Igea (ND2; 1041 bp). Target DNA fragments were amplified using pri- et al., 2015). Both the Yellow Warbler (Setophaga petechia) and mers L5215 (Hackett, 1996) and H6313 (Johnson and Sorenson, the Cocos Finch (Pinaroloxis inornata), however, are most closely 1998) for fresh tissues, and 3 pairs of internal primers (Table S2) related to populations on the Galápagos Islands, and the finch for toe pad samples. We designed the custom PCR primers using especially appears to represent a colonization from that archipe- an alignment of existing Phaeomyias sequences from GenBank lago (Petren et al., 1999; Chaves et al., 2012). More detailed studies and the PrimerQuest Tool from Integrated DNA Technologies of the population and demographic history of Cocos Island’s terres- (http://www.idtdna.com/primerquest). Each pair covers a frag- trial species, however, are lacking. ment of about 200 bp, and they are staggered so as to potentially The Cocos Flycatcher (Nesotriccus ridgwayi) is the only member recover a 600 bp region. PCR amplifications were performed in of its genus, and is endemic to Cocos Island. Nesotriccus is a small, 25 lL reactions using the following protocol: denaturation at brownish member of the Tyrannidae (flycatchers) with a curiously 94 °C for 2:15 min, 34 cycles of 94 °C for 30 s, 50 °C for 30 s, and long bill, and its taxonomic affinities were historically unclear 72 °C for 1 min, followed by 7 min elongation at 72 °C. DNA from (Fitzpatrick, 2004; Stiles and Skutch, 1989). Similarities of the toe pads was similarly amplified, via polymerase chain reaction nasal septum and of the supporting elements of the syrinx, how- (PCR) in 25 lL reactions. However, we used Qiagen hot-start plus ever, led Lanyon (1984) to suggest the nearest relatives of Nesotric- Taq (Qiagen, Valencia, California) and the following protocol: cus are two other flycatcher species, Mouse-colored Tyrannulet denaturation at 95 °C for 5 min, 34 cycles of 94 °C for 45 s, 50 °C (Phaeomyias murina) and Yellowish Tyrannulet (Capsiempis flave- for 45 s, and 72 °C for 1 min, followed by 10 min elongation at ola). Phaeomyias murina