Genome-wide Patterns of Adaptation and Speciation and Demographic Histories of Young Radiations of Cichlids

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Demographic Histories of Young Radiations of Cichlids

Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften

vorgelegt von

Andreas F. Kautt

an der

Mathematisch-Naturwissenschaftliche Sektion Fachbereich Biologie

Tag der mündlichen Prüfung: 10.03.2016 1. Referent: Prof. Axel Meyer, Ph.D.

2. Referent: Prof. Jon Slate, Ph.D.

Konstanz 2016

Konstanzer Online-Publikations-System (KOPS) URL: http://nbn-resolving.de/urn:nbn:de:bsz:352-0-327298

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Table of Contents ... i

List of Figures ... iii

List of Tables... iv

Summary ... v

Zusammenfassung ... vii

Chapter I - General Introduction ... - 1 -

Sympatric ecological speciation ... - 1 -

Population genomics ... - 2 -

Genome-wide differentiation and identifying signatures of selection ... - 3 -

Demographic inference ... - 5 -

Cichlid fishes as a model system for speciation research ... - 7 -

The Midas cichlid species complex ... - 7 -

Chapter summary ... - 12 -

Chapter II –Sympatric speciation... - 13 -

Introduction ... - 13 -

General Overviews ... - 14 -

Journals ... - 15 -

History ... - 16 -

Defining sympatric speciation ... - 18 -

Theoretical models ... - 19 -

Mechanisms ... - 21 -

Constraints and conducive conditions ... - 25 -

Support and evidence ... - 28 -

Estimating the frequency ... - 31 -

Hallmarks ... - 32 -

Chapter III – Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa ... - 34 -

Abstract ... - 34 -

Materials and Methods ... - 38 -

Results... - 44 -

Discussion ... - 50 -

Data Accessibility ... - 56 -

Acknowledgments ... - 56 -

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Chapter IV – Evidence for multispecies outcomes of sympatric speciation in two

radiations of Nicaraguan crater lake cichlids ... - 57 -

Abstract ... - 57 -

Author summary ... - 58 -

Results... - 61 -

Materials and Methods ... - 84 -

Chapter V – Incipient speciation driven by hypertrophied lips as a ‘magic trait’ in Midas cichlids ... - 92 -

Summary ... - 92 -

Results... - 95 -

Experimental Procedures ... - 104 -

Chapter VI - Differential use of the limnetic and benthic habitats without apparent population differentiation in Midas cichlid fish inhabiting crater lake Asososca Managua ... - 109 -

Abstract ... - 109 -

Materials & Methods ... - 112 -

Results... - 117 -

Data accessibility ... - 128 -

Chapter VII - General Discussion ... - 129 -

Main contributions ... - 129 -

The value of knowing the demographic history ... - 130 -

Challenges in identifying signatures of selection ... - 131 -

Future approaches and outlook ... - 131 -

References ... - 133 -

Acknowledgments ... - 152 -

Record of achievement ... - 153 -

Publications ... - 154 -

Appendix ... - 155 -

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Fig. 1.1 Dynamics of divergent selection and gene flow ... - 4 -

Fig. 1.2 Visualization of exemplary folded 2D site frequency spectra (SFS) ... - 6 -

Fig. 1.3 The Nicaraguan great lakes and crater lakes inhabited by Midas cichlids... - 8 -

Fig. 1.4 All lake populations form distinct evolutionary lineages ... - 9 -

Fig. 3.1 Map of the sampling locations in Lake Magadi, Kenya ... - 36 -

Fig. 3.2 Canonical Variance Analysis (CVA) based on geometric morphometrics ... - 45 -

Fig. 3.3 Stable isotope analyses ... - 47 -

Fig. 3.4 Schematic representation of the most supported demographic model ... - 49 -

Fig. 4.1 Lake populations form clearly distinct genetic clusters... - 62 -

Fig. 4.2 Sympatric species are genetically distinct, yet there is ongoing gene flow ... - 63 -

Fig. 4.3 Multispecies outcomes of sympatric speciation ... - 67 -

Fig. 4.4 Demographic history of sympatric speciation... - 70 -

Fig. 5.1 Thin- and thick-lipped populations in the Midas cichlid species complex ... - 94 -

Fig. 5.3 Assortative mating by ecotype... - 97 -

Fig. 5.4 Genetic relationship and differentiation between ecotypes ... - 100 -

Fig. 6.2 Stable isotope analyses ... - 118 -

Fig. 6.3 Structure analysis ... - 119 -

Fig. 6.4 Phenotypic plasticity experiment ... - 121 -

Fig. 6.5 Schematic depiction of the most supported demographic model ... - 122 -

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Table 1.1 Nicaraguan lakes and Midas cichlid diversity ... - 11 - Table 4.1 f3-statistics do not provide evidence for secondary contact and introgression. - 65 - Table 4.2 Support for five-population demographic models ... - 71 - Table 4.3 Inferred parameters under models of sympatric speciation and secondary contact ... - 74 -

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Even more than one and a half centuries since the publication of Darwin’s “The origin of species” (1859), elucidating the processes that drive population divergence and speciation remains a key objective in evolutionary biology. While the formation of species in geographic isolation (allopatric speciation) is reasonably well understood, how speciation can happen without the mediating effects of geographic barriers (i.e. sympatric speciation) is less clear. Much of speciation research has been performed on relatively highly diverged species in the laboratory. This has contributed substantially to our understanding of the evolution of hybrid sterility and inviability. Yet, the evolution of these intrinsic postzygotic reproductive barriers is unlikely to initiate speciation in populations that are exchanging genes; they are rather a consequence once populations have already been reproductively isolated. Theory predicts that some forms of divergent selection and assortative mating are necessary for sympatric speciation (except for instantaneous cases, such as polyploidization). This is also the central tenet of ecological speciation: populations become reproductively isolated due to ecologically-based divergent selection. Thus, traditional model systems, which have been essentially “removed” from their ecology, are of limited use in investigating ecological speciation. The shift of focus in speciation research towards extrinsic postzygotic isolation and pre-mating isolating barriers requires a combination of evolutionary genetics and knowledge about the natural history of organisms. Especially young systems, at the earliest stages of divergence and speciation, hold promise to provide insights into the processes that initially drive population divergence against the counteracting forces of gene flow and recombination.

An entire chapter of this thesis is dedicated to the literature on the process of sympatric speciation and provides a much more thorough review on the topic. In preparing this chapter it became clear that most of the empirical examples of sympatric speciation rest on an argument of phylogenetic monophyly. Yet, phylogenetic monophyly is merely consistent with sympatric speciation; complex histories of secondary contact and introgressive hybridization can make species appear to have resulted from sympatric speciation (i.e. lead to phylogenetic monophyly), although a phase of geographic isolation was necessary for speciation. Recent advances in sequencing technologies have made it possible to collect sufficient data to test these alternative scenarios. Indeed, one of the most convincing cases of sympatric speciation that was still featured in the review, Cameroonian crater lake cichlids, will likely have to be removed from the list of empirical examples due to recent evidence for complex histories of secondary gene flow.

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In one chapter of this thesis the likelihood of sympatric speciation in another prime example of sympatric speciation, Midas cichlid fishes inhabiting two crater lakes in Nicaragua was re-evaluated. By modelling demographic scenarios of sympatric speciation and secondary contact and evaluating their likelihoods this study is to my knowledge the first to provide evidence in favor of sympatric speciation and not merely results that do not contradict it.

Interestingly, several of the species in the two investigated radiations seem to have diverged simultaneously providing the first empirical evidence for a theoretical outcome of sympatric speciation.

Two more chapters in this thesis examine the possibility of sympatric speciation in Midas cichlids, albeit in different crater lakes and at earlier stages of divergence. In two crater lakes and the great lakes in Nicaragua, speciation seems to happen through an adaptive trait, hypertrophied lips, that is either closely linked or in itself the mating cue for assortative mating. The speciation process seems to have further progressed in the great lakes, where the two ecotypes (thin-lipped and thick-lipped) are formally described as different species, than in the young populations of the crater lakes in which genetic differentiation is very subtle or even absent.

In another crater lake, fish were captured for the first time in the middle of the lake in addition to the shore. This provided the opportunity to test if individuals differentially use the open-water and shore-associated habitats, a sign of disruptive selection that may directly lead to spatial segregation; a condition thought to facilitate sympatric speciation. Individuals do indeed differentially use the respective habitats, yet no genetic differentiation was apparent. A possible explanation for the lack of differentiation is a very recent onset of sufficient selective pressures to initiate population divergence, due to an only recent colonization by a very small population size.

Another chapter in this thesis is about the investigation of the earliest stages of ecological speciation in a different system of a young cichlid radiation, Lake Magadi tilapia (Kenya), inhabiting one of the most extreme freshwater environments (salinity 60%

seawater, pH ~10, and temperatures often exceeding 40 °C). Three populations exhibit signs of eco-morphological diversification and the most diverged population is geographically isolated from the other two. Gene flow between the other two populations was detected, yet uninhabitable water and solidified sodium carbonate seem to allow for only limited gene flow between these two lagoon populations.

In summary, this thesis contributes to our understanding of the processes involved in the early stages of sympatric speciation in ecological model systems: small-scale radiations of cichlid fishes.

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Die Erforschung der Prozesses die zur Aufspaltung von Populationen und Artbildung führen bleibt selbst mehr als eineinhalb Jahrhunderte seit der Veröffentlichung von Darwins

„The origin of species“ (1859) eines der Hauptziele in der Evolutionsbiologie. Während unser Verständnis der Bildung von Arten in geografischer Isolation (allopatrische Artbildung) relativ gut ist, bleibt es weitest gehend ungeklärt wie Artbildung ohne geografische Barrieren (sympatrische Artbildung) stattfinden kann. Ein Großteil der Forschung zu Artbildungsprozessen wurde an Arten im Labor durchgeführt, die evolutionär gesehen bereits relativ weit voneinander entfernt waren. Dies hat maßgeblich zu unserem Verständnis der Evolution von Hybridsterilität und Hybridsterblichkeit beigetragen. Es ist allerdings unwahrscheinlich, dass die Evolution dieser intrinsischen postzygotischen reproduktiven Barrieren Artbildungsprozesse einleitet. Vielmehr sind sie eine zu erwartende Konsequenz, wenn Populationen bereits reproduktiv isoliert sind. Theoretisch sind divergente Selektion und gerichtete Partnerwahl in irgendeiner Form für sympatrische Artbildung notwendig (abgesehen von augenblicklichen Fällen, wie der Polyploidisierung).

Dies ist auch der zentrale Grundsatz der ökologischen Artbildung: Populationen werden durch die Umwelt-induzierte divergente Selektion reproduktiv isoliert. Daher sind traditionelle Modelsysteme, die im Grunde genommen aus ihrer natürlichen Umgebung

„entfernt“ wurden, nur von begrenztem Nutzen um ökologische Artbildung zu untersuchen.

Die Verlagerung des Schwerpunkts in der Erforschung von Artbildungsprozessen auf extrinsische postzygotische Barrieren und solcher die vor der Paarung stattfinden benötigt eine Kombination aus evolutionärer Genetik und Wissen über die Naturgeschichte von Organismen. Besonders junge Systeme, die sich in den anfänglichen Stadien der Aufspaltung und Artbildung befinden, versprechen Erkenntnisse über die Prozesse zu liefern, welche die Aufspaltung von Population und Artbildungsprozesse gegenüber den entgegenwirkenden Kräften des Genflusses und der Rekombination einleiten.

Ein komplettes Kapitel dieser Doktorarbeit ist der Literatur über den Prozess der sympatrischen Artbildung gewidmet und bietet eine sehr viel umfassendere Abhandlung über das Thema. Während der Vorbereitung dieses Kapitels wurde es deutlich, dass die meisten empirischen Beispiele von sympatrischer Artbildung auf einem Argument der phylogenetischen Monophylie beruhen. Phylogenetische Monophylie ist allerdings lediglich konsistent mit sympatrischer Artbildung: komplexe Vorgeschichten aus sekundärem Kontakt und genetischer Introgression können Arten erscheinen lassen als wären sie durch sympatrische Artbildung entstanden (zu phylogenetischer Monophylie führen), obwohl eine

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Phase der geografischen Isolation notwendig war. Jüngste Fortschritte in Sequenzierungstechnologien machen es möglich ausreichend Daten zu erfassen um diese Szenarien zu testen. Eines der überzeugendsten Beispiele für sympatrische Artbildung, welches noch in der Abhandlung über sympatrische Artbildung aufgeführt wurde, Buntbarsche in Kraterseen in Kamerun, müssen in diesem Bezug auf Grund von neuen Nachweisen von sekundärem Genfluss wahrscheinlich von der Liste der empirischen Beispielen entfernt werden.

In einem Kapitel dieser Doktorarbeit wurde die Wahrscheinlichkeit von sympatrischer Artbildung in einem anderen herausragenden Beispiel von sympatrischer Artbildung neu beurteilt, Midas-Buntbarschen, die in zwei Kraterseen in Nikaragua vorkommen. Indem demografische Szenarien von sympatrischer Artbildung und sekundärem Kontakt modelliert und deren Wahrscheinlichkeit verglichen wurde, ist diese Studie meiner Erkenntnis nach die Erste, die Beweise zugunsten von sympatrischer Artbildung liefert und nicht nur Ergebnisse die sie nicht widerlegen. Interessanterweise scheinen mehrere der Arten in den zwei untersuchten Radiationen gleichzeitig entstanden zu sein. Dies liefert den ersten empirischen Nachweis eines theoretischen Ausgangs von sympatrischer Artbildung.

Zwei weitere Kapitel dieser Doktorarbeit untersuchen die Möglichkeit von sympatrischer Artbildung in Midas-Buntbarschen, wenn auch in anderen Kraterseen und in früheren Stadien der Aufspaltung. In zwei Kraterseen und den großen Seen in Nikaragua scheint Artbildung von einem adaptives Merkmal voran getrieben zu werden, stark ausgeprägten (hypertrophen) Lippen, welches direkt zu einer gerichteten Partnerwahl führt oder genetisch stark mit ihr gekoppelt ist. Der Artbildungsprozess scheint in den großen Seen, in denen die beiden Ökotypen (dick- und dünnlippig) formell als verschiedene Arten beschrieben sind, weiter fortgeschritten zu sein als in den jungen Populationen der Kraterseen, in denen genetische Differenzierung nur schwach oder gar nicht vorhanden ist.

In einem anderen Kratersee wurden Fische zusätzlich zum Uferbereich erstmalig auch in der Mitte des Sees gefangen. Dadurch ergab sich die Möglichkeit zu testen, ob Individuen die Habitate der Freiwasser- und Uferzone unterschiedlich nutzen. Dies ist ein Zeichen von disruptiver Selektion, welche direkt zu räumlicher Abgrenzung führen könnte;

eine Gegebenheit, die sympatrische Artbildung einfacher macht. Individuen nutzen in der Tat die verschiedenen Habitate, allerdings wurde keine genetische Differenzierung gefunden. Eine mögliche Erklärung für die fehlende Differenzierung ist, dass eine ausreichende Stärke an disruptiver Selektion erst kürzlich erreicht wurde, da der Kratersee erst vor kurzer Zeit und von nur sehr wenigen Individuen kolonisiert wurde.

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Ein anderes Kapitel zielt auf die Erforschung der anfänglichen Stadien von ökologischer Artbildung in einem anderen System einer jungen Radiation von Buntbarschen ab, den Tilapias im Magadi-See (Kenia) Dieser See stellt eine der extremsten Süsswasserumgebungen überhaupt dar (Salinität 60 % von Salzwasser, pH ~ 10, Temperaturen oftmals über 40°C). Drei Populationen zeigen Anzeichen von ökomorphologischer Diversifizierung, wobei die am weitesten divergierte Population von den anderen beiden geografisch getrennt ist. Genfluss zwischen diesen beiden war nachweisbar, aber unbewohnbares Wasser und festgewordenes Natriumkarbonat scheinen nur ein geringes Maß an Genfluss zwischen den beiden Populationen in den Lagunen zuzulassen.

Zusammenfassend trägt diese Doktorarbeit zu unserem Verständnis der Prozesse bei, die in den anfänglichen Stadien der sympatrischen Artbildung in ökologischen Modelsystemen wirken: kleinen Radiationen von Buntbarschen.

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Sympatric ecological speciation

One of the shortcomings of Darwin’s seminal work (1859) according to some of the founders of the modern synthesis was that he was ambiguous about the definition of biological species and the process of speciation itself (Coyne & Orr 2004). In Darwin’s view, natural selection was the main driving force of speciation and diverging populations would gradually transition from varieties to species, once enough distinct characteristics had evolved between them. For all practical purposes, this definition was too vague and only the focus on reproductive isolating mechanisms and the biological species concept, stimulated foremost by Dobzhansky (1937) and Mayr (1942), resulted in a clear agenda for speciation genetic research; one centered around the genetics of reproductive isolation (Turelli et al. 2001).

Since then, speciation genetic research has for a long time focused on the investigation of genes involved in hybrid incompatibility and sterility and was mainly, for pragmatic reasons, conducted in laboratory-amenable traditional model organisms (reviewed in Coyne & Orr 2004). Insights from these studies have been and continue to be highly valuable (Matute et al. 2010; Wang et al. 2015), yet are limited in providing only a retrospective picture of the speciation process which normally involved a phase of geographic separation between populations in these organisms (Via 2009).

Theoretical and empirical studies suggesting that divergence-with-gene-flow might be widespread (Nosil 2008) and speciation in sympatry possible (reviewed in Via 2001;

Bolnick & Fitzpatrick 2007; Bird et al. 2012) demand alternative explanations, since the evolution of intrinsic postzygotic barriers alone seems in most cases insufficient to explain the initiation of divergence between populations that are exchanging genetic material (Wolf et al. 2010). The concept of ecological speciation, which states that populations might become reproductively isolated due to ecologically-based divergent selection (Schluter 1996;

Schluter 2000; Schluter 2001), seems to offer a fruitful framework for the investigation of such scenarios (Nosil 2012). Indeed, most theoretical models have evidenced an essential role for disruptive/divergent selection and the evolution of some kind of non-random mating in sympatric speciation, which can be seen as the most extreme case of divergence-with- gene-flow (Gavrilets 2003; Gavrilets 2004). But note that ecological speciation can occur in any geographical context and includes all kinds of reproductive barriers, as long as they result from divergent natural selection (Rundle & Nosil 2005). Briefly, the rationale behind ecological speciation is: when populations adapt to ecologically divergent environments, hybrids and later-generation recombinants may harbor a genetic composition that renders

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them maladaptive to either of the parental ecological niches, thereby reducing their fitness and leading to extrinsic postzygotic isolation (Egan & Funk 2009; Martin & Wainwright 2013; Arnegard et al. 2014). Thus, divergent selection itself constitutes a form of reproductive isolation, if immigrants or their offspring have a lower fitness in their non-native habitat (Nosil et al. 2005). Consequently, if previously separated populations that have experienced divergent selection come together in secondary contact this can drive the evolution of pre- mating isolating barriers via the process of reinforcement (Butlin 1987; Servedio & Noor 2003). In sympatric divergence, the processes of ecological divergence and pre-mating isolation are thought to evolve in concert, as individuals that avoid mating with dissimilar individuals have a fitness advantage (Dieckmann & Doebeli 1999). Thus, certain cases of ecological sympatric speciation are also referred to as adaptive speciation (Dieckmann 2004).

Adaptation to divergent environments can lead directly (e.g. via pleiotropic allelic effects or one-allele assortment mechanisms) or indirectly (e.g. via linkage disequilibrium) to an association with prezygotic isolating barriers (Smadja & Butlin 2011). Generally, the fewer associations between traits under selection and those conferring pre-mating isolation (i.e. assortative mating) are needed the more likely population divergence and speciation are to occur (Servedio et al. 2011; Smadja & Butlin 2011). The most conducive scenarios for sympatric divergence are those, in which the adaptation to divergent environments leads to a spatial or temporal isolation of mating pools (e.g. Feder 1998; Savolainen et al. 2006), or when the traits under selection also serve as cues for non-random mating (e.g. McKinnon et al. 2004). Such traits are also referred to as magic traits (Gavrilets 2004; Servedio et al. 2011) or multiple-effect traits (Smadja & Butlin 2011). Despite considerable progress in the last years, identifying the factors that bring about and maintain the coupling of adaptive gene combinations and genes underlying different isolating mechanisms against the counteracting force of recombination (Felsenstein 1981) remains one of the main objectives in speciation research and more empirical studies are needed to test and refine the mostly theoretically arguments (Wolf et al. 2010).

Population genomics

Although the genetic bases in form of quantitative trait loci (QTL) or even quantitative trait nucleotides (QTN) of several ecologically relevant traits have now been identified, no generalities have emerged so far (Stapley et al. 2010) and it is debatable how realistic and relevant the findings of few major loci with large effect sizes are for our understanding of the evolution of most traits (Rockman 2012; Slate 2013). Apart from the genetic architecture of traits themselves, some of the outstanding questions concerning adaptive phenotypic

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evolution are: How frequently are the same genetic mechanisms responsible for parallel phenotypic evolution (Elmer & Meyer 2011)? Do genetic changes underlying adaptations occur more often in coding versus regulatory regions and do they mainly stem from standing variation or do they have to be, and typically are, acquired de-novo (Stapley et al. 2010)? Thus, there is still a dearth for more studies covering diverse taxonomic groups, life histories and ecological settings to get a more universal picture of these processes (Stinchcombe &

Hoekstra 2008; Nadeau & Jiggins 2010; Nosil 2012).

Furthermore, most studies have so far focused on one or few loci (Nosil & Schluter 2011) and we still lack an integrated view of how different evolutionary mechanisms and genomic features affect the build-up of genome-wide divergence (Nosil & Feder 2012). Is there typically a positive correlation between the number and/or size of diverging regions and the degree of phenotypic and neutral population genetic differentiation (Nadeau et al.

2012; Renaut et al. 2012; Roesti et al. 2012a)? And is multifarious selection on many loci or strong selection on only a few loci more likely to facilitate speciation and will this result in a gradual build-up of genomic divergence or rapid transitions (Nosil & Feder 2012; Flaxman et al. 2014)? Recent advances in sequencing technologies allow evolutionary biologists to now investigate the genetic bases of adaptation and speciation at a genome-wide scale in different taxonomic groups within an ecologically relevant context. Especially techniques that reduce the complexity of the genome, such as restrictions-site-associated sequencing (RAD-seq) (Miller et al. 2007), offer a cost- and time-efficient means to screen thousands of randomly distributed loci across the whole genome (Davey et al. 2011; Elshire et al. 2011).

These loci can then be used to detect regions putatively under selection and to infer the demographic history of populations.

Genome-wide differentiation and identifying signatures of selection

At a population genomic level, sympatric ecological speciation leads to the following expectation: divergent selection will differentially alter allele frequencies of adaptive loci and regions linked to them (via genetic hitchhiking (Barton 2000)), while differentiation at neutral loci will be impeded by the homogenizing effect of gene flow (Fig. 1.1) or by insufficient time for the random effect of genetic drift in recently diverged populations (Lewontin & Krakauer 1973; Barton 2000; Wu 2001; Storz 2005). This process has been termed ‘heterogeneous genomic divergence’ (Nosil et al. 2008; Nosil et al. 2009) or the

‘genetic mosaic of speciation’ (Via & West 2008).

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Fig. 1.1 Dynamics of divergent selection and gene flow. A) Gene flow around loci under divergent selection will be reduced or impeded and thus have a local effect, whereas gene flow occurs freely across the rest of the genome. B) This will lead to high levels of genetic differentiation at loci under selection and those linked to them via genetic hitchhiking. Adapted from Wu (2001) and Nosil et al.

(2009).

Consequently, population genomic data sets hold the promise to identify regions putatively under selection in so called genome scans (Nosil et al. 2009). Yet, processes other than divergent selection affect the levels and variance of genetic differentiation and it is important to be aware of these caveats (Noor & Bennett 2009; Roesti et al. 2013; Cruickshank & Hahn 2014). Nonetheless, genome scans have proved to be useful to detect regions under selection and, thus, to investigate the genetic bases underlying adaptation and ecological speciation (Butlin 2008; Nosil et al. 2009; Hohenlohe et al. 2010). It is important to note, however, that population genomic approaches are essentially phenotype-free and do not provide by themselves a valid approach to establish a relationship between phenotypes and genetic regions. Yet, combining forward genetic approaches, such as pedigree-based quantitative trait locus (QTL) mapping or population-based genome-wide-association-studies (GWAS) with population genomics provides a fruitful framework to investigate the evolution of adaptive traits (Stinchcombe & Hoekstra 2008). On the other hand, genome scans have the potential to identify regions harboring the genetic bases of traits that had not even been previously known to be involved in adaptation and speciation. Further characterization of these regions might elucidate genes with known functions and the actual phenotypic traits under selection may thus be identified post hoc; an approach that has been termed ‘reverse ecology’ (Li et al. 2008). Thus, population genomics has become an increasingly valuable approach to investigate the build-up of genomic divergence (Feder et al. 2012; Feder et al.

2013) and to identify loci that may be responsible for adaptation and ecological speciation (Nosil & Schluter 2011).

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Demographic inference

Apart from detecting regions putatively under selection, population genomic approaches are also useful in providing large sets of neutral markers, which can be used to infer the demographic correlates of a population’s history (Stinchcombe & Hoekstra 2008).

Knowledge about the demographic history can provide valuable information on how quickly and readily adaptation to new environments and speciation can progress (Barrett &

Schluter 2008), and how gene flow and the secondary contact of populations can affect speciation (e.g. Martin et al. 2015). Furthermore, demographic parameters can provide information on the expected variation of genetic differentiation due to neutral processes alone, against which regions putatively under selection can be compared. Ideally, inferences on regions under selection and the demographic history are made simultaneously, as they can inform on each other, however, the development of joint estimators is still in its infancy (Li et al. 2012; Bank et al. 2014). Nonetheless, the impact of (at least positive) selection across the whole-genome is often considered negligible and means for demographic inference have received considerable interest since the advent of next-generation sequencing (e.g. Cornuet et al. 2008; Gutenkunst et al. 2009; Li & Durbin 2011; Loh et al. 2013).

One of the recently developed methods is based on simulating data in a coalescent framework and comparing the fit of these simulations to the empirical data (Excoffier et al.

2013). This method is especially well suited for unlinked SNP markers, which can be efficiently generated by RAD-sequencing. Unlike many Approximate Bayesian Computation (ABC) methods, in which the summary statistics have to be chosen (Nunes &

Balding 2010; Aeschbacher et al. 2012), in this method the empirical data is effectively stored in the site frequency spectrum (SFS). The site frequency spectrum is a complete summary of the allelic configurations of one or several populations except for linkage among markers (Fig 1.2): it can be one-, two-, or multi-dimensional, depending on the number of considered populations. If information from one or more outgroups exists and the variation in mutational patterns (i.e. the trinucleotide substitution matrix (Hwang & Green 2004;

Hernandez et al. 2007)) is known, the state of the alleles (ancestral or derived) can be inferred with considerable confidence. If this information is not available the minor (folded) SFS can be used, in which no assumption about the states of alleles is made. The former, referred to as the derived site frequency spectrum (DSFS), is more powerful than the latter (MSFS), yet both usually contain a wealth of information about the populations’ histories (Gutenkunst et al. 2009; Excoffier et al. 2013). Several pre-defined demographic models can be modelled and support for different parameters (e.g. migration rates and population size changes) can be evaluated based on information-theory criteria (Anderson 2008). The parameter estimates

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themselves are obtained by an algorithm that updates the parameter values to maximize the likelihood of the respective models (Excoffier et al. 2013).

Fig. 1.2 Visualization of exemplary folded 2D site frequency spectra (SFS). The SFS is a complete summary of the data (except linkage) and contains the frequency of sites that have a certain allelic configuration. For example, the lower left corner (0,0) denotes monomorphic sites and the coordinate (5,5) indicates the number of sites in the data set where exactly five alternative alleles (out of 50 alleles in total; 25 individuals) were found in both populations. Coordinates (0,50) and (50,0) denote alternatively fixed sites. Thus, in recently diverged populations almost all sites will lie along the diagonal, but with time genetic drift will stochastically drive sites to deviate from this line and lead to the populating of allelic configurations across the whole spectrum. This process will be faster in small populations and is counteracted by gene flow. Consequently, the SFS holds a wealth of information about the populations’ histories, such as divergence times, effective population sizes, and the amount of gene flow. This attribute of the SFS is apparent in the comparison of two species of Midas cichlids from a great lake (left) and a species from the great lake versus a crater lake population (right): The great lake species have relatively large population sizes and presumably exchange genes, whereas the crater lake population is isolated and much smaller. The frequency of sites is indicated by the heatmap legend (bottom; logarithmic scale). Note that numbers less than one arise from a resampling approach that accounts for missing data, which can otherwise not be present in the SFS.

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Cichlid fishes as a model system for speciation research

Cichlid fishes are among the most species-rich vertebrate lineages and famous for their phenotypic diversity, parallel phenotypic evolution, and extremely rapid speciation rates (Stiassny & Meyer 1999; Salzburger & Meyer 2004; Seehausen 2006). Together with the fact that many of the species can be readily crossed in the laboratory and many are still diverging in the presence of gene flow, this has made cichlid fishes a model system for investigating the genetic bases of adaptive traits and speciation (Kocher 2004; Henning & Meyer 2014).

The most spectacular radiations of cichlids have undoubtedly unfolded in the Great East African Rift Lakes (Victoria, Malawi, and Tanganyika) (Stiassny & Meyer 1999) and a lot of research has focused on these radiations. Yet, the large spatial scale and taxonomic complexity of these radiations also makes it exceedingly difficult to encompass all relevant geological and ecological factors as well as interspecific interactions that may drive speciation. Thus, the relative importance of the processes that are thought to have contributed to the phenotypic diversity, such as geographic isolation, sexual and natural selection, and hybridization remain debated (reviewed in Stiassny & Meyer 1999; Kocher 2004; Seehausen et al. 2008; Brawand et al. 2014; Henning & Meyer 2014; Seehausen 2015).

Less species-rich radiations of cichlids confined to small and remote lakes provide a promising alternative to investigate the processes driving adaptation and speciation as their evolutionary trajectories are much more traceable (Elmer et al. 2010b). Examples of such systems are crater lake cichlids in Cameroon (Schliewen et al. 1994) and Uganda (Machado- Schiaffino et al. 2015), soda lake tilapia in Tanzania and Kenya (Seegers & Tichy 1999), and Midas cichlids in Nicaragua (Barlow 1976; Elmer et al. 2010b).

The Midas cichlid species complex

Nicaragua is located on top of a subduction zone of two tectonic plates. Strong tectonic activity and frequent volcanic eruptions have characteristically shaped Western Nicaragua (Kutterolf et al. 2007) Nicaragua not only houses the largest freshwater lakes in Central America, great lakes Nicaragua and Managua, but is also home to several crater lakes, which formed after the volcanic calderas had been filled with ground- and rain water (Fig. 1.3).

The independent colonization of these crater lakes by Midas cichlid fishes [Amphilophus citrinellus species complex (Günther 1864)] from the two great lakes Nicaragua and Managua can be seen as a system of repeated natural experiments of evolution. The young species complex of Midas cichlids comprises thirteen described species to date (Table 1.1) and its small-scale intralacustrine radiations have become a prime example for sympatric speciation and parallel evolution (Barluenga et al. 2006; Kautt et al. 2012; Elmer et al. 2014), although

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critics remain doubtful (Schliewen et al. 2006; Geiger et al. 2013). All populations of Midas cichlids inhabiting the six largest crater lakes (Fig 1.3) have been studied so far and, despite their young age and shared recent ancestry, they show a remarkable degree of similarities on the one hand (parallel evolution), but distinctiveness on the other hand (divergence along different phenotypic axes).

Fig. 1.3 The Nicaraguan great lakes and crater lakes inhabited by Midas cichlids. The two great lakes are intermittently connected by Rio Tipitapa which flows through Tisma Pond. The Las Canoas watershed is inhabited by Midas cichlids, but is not a crater lake. It had historically been connected to L. Nicaragua by Rio Malacatoya until the construction of a dam.

Crater lake Apoyo is the oldest and largest of the Nicaraguan crater lakes (ca. 23,900 y; 21.1 km²surface area; Table 1.1) and has the highest species-richness of Midas cichlids, with six endemic species described to date: A. zaliosus (Barlow & Munsey 1976), A. astorquii, A.

chancho, A. flaveolus (Stauffer et al. 2008), A. globosus, and A. supercilius (Geiger et al. 2010b).

The latter two have been described only recently and without genetic evidence, representing an example of the unresolved and ongoing classification in this species complex. Lake Xiloá contains to date four described endemic species: A. sagittae, A. amarillo, A. xiloaensis (Stauffer

& McKaye 2002), and A. viridis (Recknagel et al. 2013b). The Midas cichlid populations inhabiting crater lakes Masaya, Apoyeque, and Asososca León are referred to as A. cf.

citrinellus, yet population genetic (Barluenga & Meyer 2010; Kautt et al., unpublished data)

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and morphological data (Elmer et al. 2010b) suggest that they represent distinct evolutionary significant units (Fig 1.4). In fact, the population inhabiting crater lake Asososca Managua has been formally described as a distinct species, A. tolteca (Recknagel et al. 2013b).

Fig. 1.4 All lake populations form distinct evolutionary lineages. Phylogenetic neighbor-net network based on genetic distance at 19,064 loci (Kautt et al, unpublished data).

Being shallow and turbid, the great lakes represent a rather homogeneous habitat, which differs markedly from the deep and clear waters of the crater lakes (Barlow et al. 1976). In the crater lakes the water body is divided into a shore-associated (benthic) and open-water (limnetic) zone (Vivas & McKaye 2001; Barluenga et al. 2006). Similar to many taxa of freshwater fish inhabiting postglacial lakes in the temperature zone (Robinson & Wilson 1994), Midas cichlids have diverged along the benthic-limnetic axis in at least two crater lakes. The limnetic niche has been filled in L. Apoyo by A. zaliosus and in L. Xiloá by A.

sagittae: the limnetic species differ in several ecologically important attributes from the other species in their respective endemic radiations and demonstrate a parallel pattern of body

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shape differences (Barluenga et al. 2006; Elmer et al. 2010b; Elmer et al. 2014). In L. As.

Managua Midas cichlids individually specialize along the benthic-limnetic axis, yet no population genetic differentiation has been detected so far (Kusche et al. 2014).

In the great lakes, Midas cichlids have diverged along a different phenotypic axis;

hypertrophied lips and head shape. Individuals of A. labiatus are characterized by big, fleshy lips and a more narrow head shape compared to A. citrinellus (Günther 1864). Yet, despite this and other clear morphological differences (Barlow & Munsey 1976; Elmer et al. 2010b), the two species can hardly be distinguished based on neutral genetic markers (Barluenga &

Meyer 2010; Kautt et al. 2012). Fish with hypertrophied lips also occur in the two crater lakes Apoyeque and Masaya. In L. Apoyeque, about 20 % of individuals exhibit hypertrophied lips and the two morphs differ in body shape, diet and stable isotope signature, though genetic differentiation is only very low at mtDNA sequences and absent at nuclear microsatellite loci (Elmer et al. 2010c). Hence, it has been proposed that the population is at a stage of incipient sympatric speciation (Elmer et al. 2010c). In all four lakes where they occur (great lakes Nicaragua and Managua and crater lakes Apoyeque and Masaya) the two ecotypes show significant differences in body shapes, pharyngeal jaw types, stable isotope signatures, and gene expression profiles (Manousaki et al. 2013).

Apart from limnetic and benthic species and thick- and thin-lipped species/ecotypes there is a widespread gold-dark polymorphism in the species complex. Midas cichlids owe their name to this color polymorphism in reference to the ancient Greek myth of King Midas who was doomed to die of starvation, as everything he touched turned into gold. While most Midas cichlids exhibit a grayish to black color with spotted, striped, and barred patterns, a golden morph (orange, yellow or even white colored) occurs at a low frequency in almost all lake populations. All fish are born dark (melanic) and the gold coloration (amelanic) results from the loss of melanocytes during ontogeny revealing the underlying yellow/orange xantophores (Dickman et al. 1988). Although there is some incomplete penetrance, being gold is under genetic control and follows a simple Mendelian inheritance with gold being dominant (Henning et al. 2010; Henning et al. 2013).

It has been shown that individuals from A. sagittae and A. xiloaensis in L. Xiloá mate assortatively by color in the wild (Elmer et al. 2009) and that gold and dark individuals in several populations differ in body shapes, pharyngeal jaws and stable isotope signatures (Kusche et al. 2015). Thus, incipient speciation of gold and dark morphs has been proposed.

Yet, population genomic data do not support this hypothesis and the gold and dark morphs are probably better understood as a trans-specific stable polymorphism that is unlikely to lead to speciation (Henning et al., in preparation). How genetic variation and polymorphisms in ecologically and sexually relevant traits are maintained remains an

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outstanding question in evolutionary biology (Hughes et al. 2013; Johnston et al. 2013). The fitness consequences of being gold seem complex and more work is needed to determine whether the presumed intraspecific advantage of being gold (Barlow 1973, 1983) and the potential disadvantage due to increased predation (Kusche & Meyer 2014; Torres-Dowdall et al. 2014) could lead to the maintenance of this polymorphism alone.

Table 1.1 Nicaraguan lakes and Midas cichlid diversity.

Lake Max age

[years]

Surface area [km²]

Midas cichlid species

Ecotypes / Color morphs

Great lakes

Nicaragua Early

Pleistocene 8,143 A. citrinellus

A. labiatus gold / dark gold / dark

Managua Early

Pleistocene 1,053 A. citrinellus

A. labiatus gold / dark gold / dark

Crater lakes

Apoyo 23,900 21.10

A. zaliosus A. astorquii A. chancho A. flaveolus A. globosus A. supercilius

Xiloá 6,100 3.75

A. amarillo A. viridis A. sagittae A. xiloaensis

gold / dark gold / dark Masaya 6,000 8.38 A. cf. citrinellus gold / dark

lippy / non-lippy Apoyeque 1,900 2.50 A. cf. citrinellus lippy / non-lippy

As. Managua 1,250 0.74 A. tolteca gold / dark

As. León 4,500 0.81 A. cf. citrinellus

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Chapter summary

The five main chapters of this thesis are all concerned with the process of speciation. Apart from Chapter II, which is a review article, all chapters are empirical studies on ecological speciation in young radiations of cichlid fishes. Chapters II and III have undergone full peer- review and have been published. Chapters IV, V, and VI are currently under review.

Chapter II is a review article on sympatric speciation that was written in form of a bibliography entry. The format was partly predefined by the publisher and the concept is to provide a concise and balanced overview on sympatric speciation by providing the key references on the topic and briefly describing their main contribution. The study in Chapter III provides evidence for eco-morphological diversification of three populations of Lake Magadi tilapia, which live in one of the most extreme freshwater environments inhabited by fish. Chapter IV was partly inspired by writing the review on sympatric speciation and is about explicitly testing the likelihood of sympatric speciation in Midas cichlid fish inhabiting crater lakes Apoyo and Xiloá and reconstructing the demographic history of the two radiations. The study in Chapter V suggests that hypertrophied lips act as a magic trait, which has led to speciation in the two great lakes of Nicaragua. This process may be repeating itself in the crater lakes Apoyeque and Masaya. The results in Chapter VI provide evidence that Midas cichlids in crater lake As. Managua differentially use the limnetic and benthic habitats of the crater lake, but that genetic differentiation is lacking possibly due to a very recent onset of disruptive selection.

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AXEL MEYER & ANDREAS F. KAUTT Oxford Bibliographies in Evolutionary Biology (2014)

Introduction

Speciation can be described as the process of the splitting of cohesive groups of organisms into distinct entities, i.e. the evolution of biological species (cladogenesis). In sexually reproducing organisms this distinctness can only come about and be maintained if the exchange of genetic material between groups is strongly reduced. That reproductive isolation should be the defining characteristic of species is the central tenet of the biological species concept, the most commonly used species concept in the field of evolutionary biology. Hence, speciation research is mainly concerned with understanding the nature and evolution of barriers to interbreeding between organismal groups. The role of geography and specifically, geographic isolation, in this regard has been subject to one of the most persistent debates in the field of speciation research. While (the initiation of) speciation in geographic isolation (i.e. allopatric speciation) is supported by both several lines of evidence and a compelling body of underlying theory, speciation without the mediating effect of geographic isolation (i.e. sympatric speciation) has long been controversial and has been considered as unlikely to occur at all or to play a substantial role in terms of the frequency of its occurrence.

Yet, the study of sympatric speciation has received renewed interest during the last three decades and empirical and theoretical support for its plausibility has accumulated. Thus, the reality of sympatric speciation is no longer in doubt. Nevertheless, its importance as a mode of speciation and the circumstances under which it happens continue to be debated.

Estimates of the frequency of different modes of speciation typically assign only a minor role to sympatric speciation, apart from examples from certain animal and plant taxa. But, the importance of sympatric speciation for evolutionary biology goes beyond its relative frequency in generating biodiversity. Its conceptual and empirical challenges have stimulated advances of broader importance for our understanding of the general mechanisms involved in the process of speciation. Thus, the study of speciation in a setting without geographic isolation, whether viewed from a geographical perspective as sympatric speciation or considered in a population genetic point of view as an extreme case of speciation-with-gene-flow, will likely continue to attract the attention of future generations of evolutionary biologists.

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General Overviews

A basic overview on geographic modes of speciation that is accessible to the broad readership can be found in the evolution textbook by Futuyma 2013. Entire books devoted to the topic of speciation usually discuss sympatric speciation and often provide a detailed discussion. Mayr’s 1963 classic was one of the first books concerned with the topic of speciation and, although now obviously outdated, it still makes for excellent reading in order to understand the early history of speciation research and the beginnings of the debate about sympatric speciation. Several papers compiled in the book edited by Otte and Endler 1989 deal with sympatric speciation and provide an overview of the subject. The book edited by Howard and Berlocher 1998 includes contributions by various authors in the field of speciation research. One section is devoted to mechanisms of speciation and emphasizes possible modes of sympatric speciation. A timely and lucid review on speciation is the book of Coyne and Orr 2004. In this book Coyne and Orr also define four criteria for inferring that a certain past speciation event in the wild is best explained by sympatric speciation: (i) contemporary species’ ranges are sympatric; (ii) there is substantial reproductive isolation between species; (iii) species are sister groups; and (iv) a past allopatric phase is unlikely.

These criteria have become the conservative “gold standard” in evolutionary biology. The review articles by Via 2001 and Bolnick and Fitzpatrick 2007 focus specifically on the mode of sympatric speciation and offer excellent overviews. A concise overview on speciation in plants is given in Rieseberg and Willis 2007.

Futuyma 2013: Evolution is an introductory textbook in evolutionary biology. An overview of the different geographic modes of speciation can be found in Chapter 18.

Mayr 1963: One of Mayr’s most influential books. In a section of Chapter 15 the evidence for sympatric speciation is critically assessed.

Otte and Endler 1989: This volume arose from a symposium on speciation and consists of twenty-five papers and a concluding review. Several contributions are primarily concerned with sympatric speciation.

Howard and Berlocher 1998: The contributions in this book resulted from a symposium in honor of Guy Bush, who was a strong advocate of the plausibility of sympatric speciation, especially in insects. Bush’s interests in sympatric speciation are reflected in a number of chapters in the book.

Coyne and Orr 2004: Written by two authorities in the field of speciation research, this book represents the most comprehensive contemporary treatise on speciation and has become a must-read for those interested in speciation. Sympatric speciation and the evidence for it from theoretical models, experimental work and natural populations.

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Via 2001: This review is part of a special issue on speciation and begins with a brief recapitulation of the history of sympatric speciation and then moves on to describe the underlying mechanisms of, and favorable conditions for, sympatric speciation. This discussion is based on both empirical and theoretical work.

Bolnick and Fitzpatrick 2007: This review paper begins with a brief general introduction, followed by a discussion of the empirical evidence for sympatric speciation and its frequency in nature. Subsequent sections provide an overview on the multitude of existing theoretical models and evaluate the justification of assumptions with respect to empirical data.

Rieseberg and Willis 2007: In this brief review the authors describe several aspects of speciation in plants. One section is devoted to hybrid and polyploid speciation, which is an important mode of sympatric speciation in plants. A list of case studies on sympatric speciation in plants is provided in the supplementary materials.

Journals

Since the process of speciation is a central aspect of evolutionary research, almost any journal that focuses on evolutionary pattern and process will publish articles on sympatric speciation. Examples of journals with a focus on evolution include Evolution and the Journal of Evolutionary Biology, the journals of the two most influential societies for the study of evolutionary biology. The topic of sympatric speciation is also regularly featured in Molecular Ecology, a journal that promotes the use of molecular genetic techniques to study various aspects of ecology and evolution. Another journal that highlights integrative and interdisciplinary work on broad biological principles, including sympatric speciation, is the American Naturalist. Articles on sympatric speciation are also occasionally published in Nature or Science, which are among the most prestigious journals in the natural and life sciences. The journals Trends in Ecology and Evolution and Annual Reviews of Ecology, Evolution and Systematics publish articles that aim to synthesize past work and to highlight new directions in the field; these journals periodically publish papers on speciation in general or on sympatric speciation.

Evolution: Published on behalf of the Society for the Study of Evolution (SSE), Evolution or The International Journal for Organic Evolution is one of the leading journals in the field of evolutionary biology. Besides empirical and theoretical papers it publishes review articles and commentaries, which regularly address speciation research.

Journal of Evolutionary Biology: The journal’s scope includes all aspects of evolutionary biology, from an empirical and theoretical point of view. Naturally, speciation research

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is regularly published in JEB, the journal of the European Society for Evolutionary Biology.

Molecular Ecology: The journal publishes papers that use molecular genetics to study aspects of ecology, evolution, behavior and conservation. Because ecological and behavioral isolation can be important in sympatric speciation, studies of sympatric speciation are regularly featured.

American Naturalist: The American Naturalist has maintained its position as a highly influential journal for more than one hundred years. The primary objective of the journal of the American Society of Naturalists is to advance our knowledge of broad biological concepts, promoting integrative empirical work as well as evolutionary theory.

Nature: Nature publishes articles spanning all fields of the natural and life sciences and has one of the highest impacts among all scientific journals, including in the field of evolutionary biology. Models and empirical studies on sympatric speciation are occasionally presented here.

Science: Science has a broad readership and features original articles from a variety of scientific fields and disciplines. Due its controversial nature, the topic of sympatric speciation has a great appeal and appears from time to time in this journal.

Trends in Ecology and Evolution: TREE is a distinguished journal that publishes review articles and opinion letters rather than original studies and has been highly influential in directing and shaping the focus of the field of evolutionary biology. Sympatric speciation, either alone or as part of a focus on speciation in general, is featured occasionally.

Annual Review of Ecology, Evolution and Systematics: This journal is one publication of the Annual Reviews series and provides some of the most comprehensive and insightful review articles in the field of ecology, evolution and systematics. Various aspects of speciation have been covered in the past decades.

History

The notion that speciation can occur without geographic isolation dates at least back to Darwin 1859, although Darwin was not entirely explicit about the role of geography in speciation. After Darwin the plausibility of sympatric speciation was not considered particularly controversial, but attempts to demonstrate its occurrence were often followed by rebuttals from strong proponents of geographic (allopatric) speciation. A brief account of these exchanges can be found in Mayr 1963. In this book, Mayr critically evaluated the evidence in favor of sympatric speciation and argued strongly that the concept of sympatric speciation was neither necessary nor supported by the facts. His arguments had a substantial

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influence on the next generations of evolutionary biologists. Yet, Mayr’s forceful opinion also stimulated further research on the topic, and some of the earliest theoretical models, experiments and empirical cases of sympatric speciation were published within a few years following the publication of Mayr’s 1963 book. However, the controversy persisted and only a few convincing empirical examples of sympatric speciation were published. The debate about sympatric speciation continued. Bush 1975 stated that geographic isolation may not be required for speciation in many animals and White 1978 concluded his chapter on sympatric models of speciation with the statement that the reality of sympatric speciation, at least in certain groups of insects, could not be denied. In stark contrast, Futuyma and Mayer 1980 stated that they were unable to find any convincing evidence for sympatric speciation. Research on speciation in the last decades has yielded compelling evidence for the occurrence and possibility of sympatric speciation. In this respect, Bush 1994 concluded that it was no longer possible to dismiss the mode of sympatric speciation, and even Mayr 2001 (late in his life, in 2001 he was already 95 years old!) accepted some of the more recent findings that support sympatric speciation. Thus, as stated in Jiggins 2006, in the last years the debate on sympatric speciation has mainly shifted away from the issue of its existence towards questions about its frequency in nature and the conditions under which it is likely to occur.

Darwin 1859: An enormous compilation of evidence on organismal evolution and an account of the action of natural selection in driving evolutionary change. Numerous re- prints of The Origin have been published and the complete work can be freely accessed online [http://darwin-online.org.uk/].

Mayr 1963: Following a thorough discussion of the evidence for sympatric speciation, Mayr argues that none of it is convincing and advocates the necessity of geographic isolation for speciation. This opinion influenced subsequent generations of evolutionary biologists.

Bush 1975: A review of the classic classification of modes of speciation based on geography.

The section on sympatric speciation emphasizes phytophagous and parasitoid insects.

White 1978: Discusses various models of speciation, including the geographic modes, but also other modes like chromosomal and polyploid speciation. Chapter seven is devoted to sympatric speciation and the evidence presented comes mainly from phytophagous insects.

Futuyma and Mayer 1980: In this review the authors respond to claims that challenged allopatric speciation as being the primary or exclusive mode of speciation. They conclude that sympatric speciation is unlikely.

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Bush 1994: A short review on evidence for sympatric speciation, with an emphasis on scenarios where mate choice is linked to host or resource use, i.e. habitat isolation.

Mayr 2001: A very general and easily accessible popular science book on evolution. The topic of speciation is the focus of Chapter Nine. In the section on sympatric speciation Mayr acknowledges certain cases of sympatric speciation in the wild.

Jiggins 2006: A short commentary article on the state of speciation research with particular focus on the importance (or not) of geographic isolation.

Defining sympatric speciation

The term sympatric – being derived from the Greek words “sym” and “patra” meaning

“together” and ”country” – was coined by Poulton 1903 and originally used to describe the pattern of geographically overlapping species ranges. With the development of the biological species concept (by Dobzhansky and Mayr) Mayr 1942 thought of sympatric speciation as the evolution of reproductive barriers within a single interbreeding unit. Yet, stating that the process of “sympatric speciation” had not yet been properly defined, Mayr 1947 argued that it was usually characterized by the assumption of the establishment of new populations within the normal cruising range (dispersal distance) of members of the parental population;

moreover, in this process gene flow must be inhibited by intrinsic (biological) rather than extrinsic (geographic) factors. After Mayr, numerous definitions of sympatric speciation have been provided, most of which are based on either biogeographic (spatial) or population genetic (demic) criteria. An overview of definitions is provided by Fitzpatrick et al. 2008.

For example, arguing that previous definitions had not been exact enough for modelling purposes, Gavrilets 2003 defined speciation as being sympatric if mating were random with regard of the birthplace of mates. Following Gavrilets, this translates to an initial migration rate of m=0.5 or complete panmixia. In contrast, cases without any gene flow between two demes (m=0) would be considered as allopatric and everything in between might be called parapatric speciation. Although precise and unambiguous, this classification has been criticized as being not useful for application to natural populations, because it would be virtually impossible to demonstrate sympatric – or strictly allopatric - speciation in nature.

Thus, empiricists, on the whole, have tended to invoke a rather biogeographic and theoreticians a more population genetic framework. In an attempt to reconcile the spatial and demic definitions, Mallet et al. 2009 proposed a composite spatial population genetic definition based on the geographic distance and dispersal distance of diverging populations.

Yet, this approach has in turn been criticized by Fitzpatrick et al. 2009 and to date there has been no consensus on a universally accepted definition of sympatric speciation. Recognizing that a simple classification of speciation events as sympatric, parapatric or allopatric will

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always remain ambiguous, several authors, such as Butlin et al. 2008, have advocated focusing instead on the quantitative impact of spatial, ecological and genetic factors and mechanisms driving divergence.

Mayr 1999: Originally published in 1942. According to Mayr, a lack of data and adequate definitions precluded a more elaborate discussion of sympatric speciation. His definition of sympatric speciation given in Chapter XIII (nongeographical speciation) has been the basis of many subsequent definitions of sympatric speciation.

Mayr 1947: The main argument of this classic paper is to reconcile the apparent conflict between the roles of ecological versus geographic factors in speciation. Yet, this work may be equally prominent for coining a definition of sympatric speciation with respect to the cruising range of individuals.

Fitzpatrick et al. 2008: Several definitions of sympatric speciation and their inherent inconsistencies are reviewed. The authors strongly question the usefulness of the discrete

‘geographic’ classification of speciation events.

Gavrilets 2003: A review of models of speciation. The definition of sympatric speciation given here is considered as one of the most exact by many researchers.

Mallet et al. 2009: In this response to Fitzpatrick et al. 2008, the authors defend the value of a geographic classification of speciation modes and propose a novel composite definition.

Fitzpatrick et al. 2009: This short communication is in turn a reply to Mallet et al. 2009.

This exchange of ideas and opinions between empiricists and theoreticians highlights the controversy and the debates surrounding sympatric speciation.

Butlin et al. 2008: A critique of the simplistic traditional geographic classification scheme.

The authors argue that it may be more fruitful to focus on the current dynamics of selection and gene flow rather than aiming to infer how divergence was initiated in the past or how it might proceed in the future.

Theoretical models

The majority of modelling work in speciation research has been on sympatric speciation.

These theoretical models have largely contributed to our basic understanding of the conditions for sympatric speciation and several models have demonstrated that sympatric speciation is indeed possible. However, most models have been numerical and only prove that sympatric speciation may happen under specific conditions. In contrast, analytical models, which can provide more general quantitative results, have been rare. This argument is elaborated in the paper by Gavrilets 2003, which also provides a brief recapitulation of the

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early history as well as a synthesis of previous models. A much more extensive treatise of theoretical models in speciation research is given in the book by Gavrilets 2004. Probably the first theoretical model that dealt explicitly with sympatric speciation is Maynard Smith 1966. This work stimulated the further development of theoretical models. By now, the number of models of sympatric speciation has grown enormously. An overview is provided by Bolnick and Fitzpatrick 2007. Supplementary Table 2 in that paper is noteworthy; it lists a multitude of theoretical models and provides information on their key assumptions. A common feature of basically all models of sympatric speciation is the presence of a genetic basis for a trait under disruptive/divergent selection and some sort of nonrandom mating.

One of the most influential papers was published by Felsenstein 1981. An important step in the theoretical development was the extension of the prevailing informative, yet rather simple, models to incorporate a quantitative genetic framework and invoke stochastic processes. This progress was spear-headed by the simultaneous publication of work by Dieckmann and Doebeli 1999, and Kondrashov and Kondrashov 1999. While most models are concerned with only one bifurcating event, the work by Bolnick 2006 investigates an outcome of multiple species.

Gavrilets 2003: In the section about sympatric speciation two basic models are discussed - the “Udovic model” and a model based on sexual conflict. In these models the conditions for sympatric speciation were found analytically. The author advocates a shift towards more analytical research, which may help to identify more general rules Gavrilets 2004: The most comprehensive account on theoretical models in speciation

research including those models dealing with sympatric speciation. Although a certain mathematical background is required, this book is clearly written not only for theoreticians and Gavrilets generally succeeds to make the content of this book accessible to the empirical evolutionary biologist.

Maynard Smith 1966: Although this pioneering work is mainly concerned with the maintenance of a polymorphism and not speciation per se, it stimulated much of the theoretical work. The four proposed mechanisms, potentially leading to reproductive isolation in the presence of gene flow, have provided the foundation for almost all other models.

Bolnick and Fitzpatrick 2007: A general overview on models of sympatric speciation and their key assumptions.

Felsenstein 1981: A classic paper that demonstrates the antagonism between selection and recombination in scenarios of divergence-with-gene-flow. It is also here that the