Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae Markos A. Alexandrou a , Brian A. Swartz b,c , Nicholas J. Matzke b , Todd H. Oakley a,⇑ a Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA b Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, CA 94720, USA c Millennium Alliance for Humanity and the Biosphere, Stanford University, Stanford, CA 94305, USA article info Article history: Received 23 April 2013 Revised 21 July 2013 Accepted 26 July 2013 Available online xxxx Keywords: Evolution Ancestral states Phylogenetics Time trees Anadromy Genome duplication Salmon abstract Multiple rounds of whole genome duplication have repeatedly marked the evolution of vertebrates, and correlate strongly with morphological innovation. However, less is known about the behavioral, physio- logical and ecological consequences of genome duplication, and whether these events coincide with major transitions in vertebrate complexity. The complex behavior of anadromy – where adult fishes migrate up rivers from the sea to their natal site to spawn – is well known in salmonid fishes. Some hypotheses suggest that migratory behavior evolved as a consequence of an ancestral genome duplica- tion event, which permitted salinity tolerance and osmoregulatory plasticity. Here we test whether anadromy evolved multiple times within salmonids, and whether genome duplication coincided with the evolution of anadromy. We present a method that uses ancestral character simulation data to plot the frequency of character transitions over a time calibrated phylogenetic tree to provide estimates of the absolute timing of character state transitions. Furthermore, we incorporate extinct and extant taxa to improve on previous estimates of divergence times. We present the first phylogenetic evidence indi- cating that anadromy evolved at least twice from freshwater salmonid ancestors. Results suggest that genome duplication did not coincide in time with changes in migratory behavior, but preceded a transi- tion to anadromy by 55–50 million years. Our study represents the first attempt to estimate the absolute timing of a complex behavioral trait in relation to a genome duplication event. Ó 2013 Elsevier Inc. All rights reserved. 1. Introduction Multiple rounds of whole genome duplication have character- ized the evolution of vertebrates (Jaillon et al., 2004). Specifically, in actinopterygians (ray-finned fishes), genome duplication events correlate with bursts of morphological change in extant lineages (Ohno, 1970; Taylor et al., 2001, 2003; Van de Peer et al., 2003, 2009; Braasch et al., 2009a,b) but see (Heimberg et al., 2008). How- ever, incorporating fossil taxa into these analyses demonstrates that morphological complexity accumulated more continuously through time (Donoghue and Purnell, 2005). Whether episodic or periodic, little is known about the behavioral consequences of gen- ome duplication in vertebrates, and if duplication events coincide with transitions in behavior and physiology (Novak et al., 2006). The ecophysiological consequences of genome duplication re- main understudied (Mable, 2004; Soltis et al., 2010; Mable et al., 2011), but evidence from plants suggests that polyploids are able to inhabit a greater diversity of environments compared to their diploid progenitors (Otto and Whitton, 2000). Generally speaking, duplication events trigger morphological and physiological changes in size and ecological tolerance (Adams and Wendel, 2005; Hu et al., 2012). For example, recent work suggests that newly formed polyploid populations are more resistant to para- sites (Oswald and Nuismer, 2007). Furthermore, polyploidy affects cellular physiology by altering cell size and enhancing photosyn- thetic capacity (Warner and Edwards, 1993); it may even change cellular metabolic rates (Comai, 2005). Less is known about the ecophysioloical consequences of genome duplication in verte- brates. In one notable example, mating calls in gray tree frogs fol- low directly from changes in ploidy, which leads to reproductive isolation via female mate choice (Mable et al., 2011). The link be- tween genome duplication and the evolution of complex traits has also been hypothesized for salmonid fishes (Ohno, 1970). Salmonids (salmon, trout, char, whitefishes, and graylings) are one of the most well studied vertebrate groups that have under- gone genomic duplication. Their migratory behaviors require ma- jor physiological plasticity, which are known popularly in Atlantic and Pacific salmon. These fishes are capable of overcoming tremendous obstacles to return from distant oceans to natal streams for spawning. This behavior has inspired centuries of re- search into the evolution of salmon migrations and the origin(s) 1055-7903/$ - see front matter Ó 2013 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.ympev.2013.07.026 ⇑ Corresponding author. Fax: +1 805 893 4714. E-mail address: oakley@lifesci.ucsb.edu (T.H. Oakley). Molecular Phylogenetics and Evolution xxx (2013) xxx–xxx Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Please cite this article in press as: Alexandrou, M.A., et al. Genome duplication and multiple evolutionary origins of complex migratory behavior in Sal- monidae. Mol. Phylogenet. Evol. (2013), http://dx.doi.org/10.1016/j.ympev.2013.07.026