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Genomics of Speciation and Introgression in Princess Cichlid fishes from Lake Tanganyika

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Genomics of Speciation and Introgression in Princess Cichlid fishes from Lake Tanganyika Molecular Ecology (2016) 25, 6143–6161 doi: 10.1111/mec.13767 Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika HUGO F. GANTE,* MICHAEL MATSCHINER,† MARTIN MALMSTRØM,† KJETILL S. JAKOBSEN,† SISSEL JENTOFT†‡ and WALTER SALZBURGER*† *Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland, †Department of Biosciences, CEES (Centre for Ecological and Evolutionary Synthesis), University of Oslo, 0316 Oslo, Norway, ‡Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway Abstract How variation in the genome translates into biological diversity and new species origi- nate has endured as the mystery of mysteries in evolutionary biology. African cichlid fishes are prime model systems to address speciation-related questions for their remarkable taxonomic and phenotypic diversity, and the possible role of gene flow in this process. Here, we capitalize on genome sequencing and phylogenomic analyses to address the relative impacts of incomplete lineage sorting, introgression and hybrid speciation in the Neolamprologus savoryi-complex (the ‘Princess cichlids’) from Lake Tanganyika. We present a time-calibrated species tree based on whole-genome sequences and provide strong evidence for incomplete lineage sorting in the early phases of diversification and multiple introgression events affecting different stages. Importantly, we find that the Neolamprologus chromosomes show centre-to-periphery biases in nucleotide diversity, sequence divergence, GC content, incomplete lineage sorting and rates of introgression, which are likely modulated by recombination den- sity and linked selection. The detection of heterogeneous genomic landscapes has strong implications on the genomic mechanisms involved in speciation. Collinear chro- mosomal regions can be protected from gene flow and harbour incompatibility genes if they reside in lowly recombining regions, and coupling can evolve between non- physically linked genomic regions (chromosome centres in particular). Simultaneously, higher recombination towards chromosome peripheries makes these more dynamic, evolvable regions where adaptation polymorphisms have a fertile ground. Hence, dif- ferences in genome architecture could explain the levels of taxonomic and phenotypic diversity seen in taxa with collinear genomes and might have contributed to the spec- tacular cichlid diversity observed today. Keywords: genomic landscapes, introgressive hybridization, linked selection, Neolamprologus, recombination bias, whole-genome sequencing Received 7 January 2016; revision received 30 May 2016; accepted 11 July 2016 emerged forms (sensu Mayr 1963; Coyne & Orr 2004). Introduction Once a topic of disagreement with botanists, the perva- The origin of new species – the process of speciation – siveness of introgressive hybridization, defined as the has traditionally been viewed as a strictly bifurcating effective flow of genes beyond species boundaries process, in which one biological species splits into two (Anderson 1949; Barton & Bengtsson 1986), is no longer distinct entities as a consequence of the evolution of disputed by zoologists. The detection of hybridization complete reproductive isolation between the newly and introgression between sister and nonsister species became commonplace with the introduction of molecu- Correspondence: Hugo F. Gante, Fax: +41 61 267 03 01; lar markers in evolutionary studies (Dowling & Secor E-mail: [email protected] 1997; Arnold 2006). In particular, advances in © 2016 John Wiley & Sons Ltd 6144 H. F. GANTE ET AL. genotyping methods and DNA sequencing have had a combinations of parental genes, a mechanistic role of major impact on our understanding of the nature of hybrid ‘filters’ shapes the properties of introgressed species boundaries. chromosomal segments [or chromosomal blocks (Han- Earlier views of reproductive isolation as a property son 1959; Martinsen et al. 2001)]. Therefore, the key fac- of species and, hence, of whole genomes gradually tor to effective interspecific gene flow is the ratio shifted towards a view where individual genes or speci- between selection and recombination in hybrids (Barton fic regions of the genome are responsible for keeping & Bengtsson 1986; Baird 1995). species’ distinctiveness (Wu 2001; Baack & Rieseberg Detection of introgression vs. incomplete lineage sorting 2007; Smadja & Butlin 2011; Feder et al. 2012). Further- and the characterization of hybridization remain major more, empirical studies are making it increasingly clear challenges (Abbott et al. 2013). Recent advances in that interspecific gene flow is an integral part of the genome-wide typing and whole-genome sequencing have speciation process, with manifold potential evolutionary provided unprecedented resolution to identify polymor- impacts (Abbott et al. 2013). For instance, while phisms for adaptation to different niches or characterize hybridization may lead to the fusion of species, it has the patterns of interspecific gene flow, including the detec- been suggested that interspecific gene flow may in fact tion of hybrid speciation, adaptive introgression and fuel rapid diversification by providing an abundant incomplete lineage sorting in a number of systems (Pollard source of potentially adaptive genetic variation (See- et al. 2006; Kulathinal et al. 2009; Pardo-Diaz et al. 2012; hausen 2004; Berner & Salzburger 2015). In addition, Heliconius Genome Consortium 2012; Cui et al. 2013; Pease new alleles introduced by introgression may not only & Hahn 2013; Keller et al. 2013; Nadeau et al. 2013; Martin be more abundant than alleles originating by mutation, et al. 2013; Poelstra et al. 2014; Roesti et al. 2014, 2015; Gom- but could also be more beneficial. This is likely because pert et al. 2014; Huerta-Sanchez et al. 2014; Berg et al. 2015; – in contrast to alleles arising de novo by mutation – Eaton et al. 2015; Fontaine et al. 2015; Lamichhaney et al. introgressed alleles have already been exposed to natu- 2015; Liu et al. 2015; Malinsky et al. 2015; Norris et al. 2015; ral selection, albeit in the genomic background of the but see Cruickshank & Hahn 2014). Rapidly diversifying introgression donor (Sætre 2013). Finally, introgression groups are particularly prone to incomplete lineage sort- can also lead to the establishment of stable hybrid lin- ing, and they are also the ones with the largest potential eages that are reproductively isolated from parental for consequential introgression and hybrid speciation, species, following distinct evolutionary and ecological because of incipient isolation and exploitation of empty trajectories (Arnold 2006). Hybrid speciation through ecological niches. Therefore, the application of genomic polyploidization has been shown to be particularly data to study these groups will be of major importance for common in flowering plants and ferns, but a number of understanding the mechanisms of speciation and factors cases of homoploid hybrid species have also been docu- affecting interspecific gene flow. mented, both in animals and in plants (DeMarais et al. Here, we employ whole-genome sequencing in combi- 1992; Rieseberg et al. 2003; Baack & Rieseberg 2007; nation with phylogenomic analyses to examine the inter- Mallet 2007; Mavarez & Linares 2008; Paun et al. 2009; play between genome architecture, speciation, and Nolte & Tautz 2010; Salazar et al. 2010; Hermansen et al. interspecific gene flow (isolation vs. introgression vs. 2014; Sousa-Santos et al. 2014; Trier et al. 2014). incomplete lineage sorting) in a group of East African Cline theory and hybrid zone studies have been cichlid fishes. African cichlids constitute the largest extremely influential to our understanding of the extant vertebrate radiation, with several hundreds of spe- dynamics of introgression. Coupling operating between cies inhabiting lakes and associated river drainages isolation loci is maintained by linkage disequilibrium (Turner et al. 2001; Salzburger 2009; Salzburger et al. and contributes to limit gene flow when related species 2014). Cichlids have thus become favourite model organ- come into contact, whereas recombination acts in the isms for studying speciation mechanisms and factors that opposite direction, eroding the association between promote or retard diversification (Kocher 2004; See- physically linked loci (e.g. Haldane 1948; Barton 1983; hausen 2006; Gante & Salzburger 2012; Santos & Salzbur- Barton & Bengtsson 1986; Baird 1995; Gavrilets 2004; ger 2012; Wagner et al. 2012). In addition, five species of Bierne et al. 2011; Flaxman et al. 2014). Breaking down African cichlids from different lineages and geographical linkage with genes under negative selection allows origins have had their genomes recently sequenced (Bra- introgression of neutral or positively selected loci that wand et al. 2014). One of these lineages, the tribe Lam- would otherwise be prevented from crossing species prologini, comprises almost half of the entire cichlid boundaries due to Hill–Robertson interference (Hill & diversity in Lake Tanganyika (Gante & Salzburger 2012; Robertson 1966; Barton & Bengtsson 1986; Charlesworth Wagner et al. 2012). Lamprologines show complex eco- 2009). Because selection acts particularly strongly on logical, morphological, trophic and behavioural attri- early-generation hybrids that carry maladaptive butes, representing a radiation within the cichlid © 2016 John Wiley & Sons Ltd SPECIATION AND GENE FLOW IN NEOLAMPROLOGUS 6145 radiation (Stiassny 1997). Unlike other highly diverse
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