Relaxed trait covariance in interspecific cichlid hybrids predicts morphological diversity in adaptive radiations

The Ecology of Hybrid Incompatibilities

Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from selection caused by epistatic Dobzhansky-Muller hybrid incompatibilities. Here, we show how selection against transgressive phenotypes in hybrids manifests as incompatibility. After outlining our logic, we summarize current approaches for studying ecology-based selection on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are typically polygenic. Next, we describe how verbal models of selection on hybrids translate to phenotypic and genetic fitness landscapes, highlighting emerging approaches for detecting polygenic incompatibilities. Finally, in a synthesis of published data, we report that trait transgression-and thus possibly extrinsic hybrid incompatibility in hybrids-escalates with the phenotypic divergence between parents. We discuss conceptual implications and conclude that studying the ecological basis of hybrid incompatibility will facilitate new discoveries about mechanisms of speciation.

Phenotypic covariation predicts diversification in an adaptive radiation of pupfishes

Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically tested this relationship. In this study, we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas (SSI). The radiation includes generalist, durophagous, and lepidophagous species. We compared phenotypic variation and covariation (i.e., the P matrix) between (1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, (2) SSI pupfish allopatric lake populations with only generalist pupfish, and (3) SSI lake populations containing the full radiation in sympatry. Additionally, we examine patterns observed in the P matrices of two independent lab-reared F2 hybrid crosses of the two most morphologically distinct members of the radiation to make inferences about the underlying mechanisms contributing to the variation in craniofacial traits in SSI pupfishes. We found that the P matrix of SSI allopatric generalist populations exhibited higher levels of mean trait correlation, constraints, and integration with simultaneously lower levels of flexibility compared to allopatric generalist populations on other Caribbean islands and sympatric populations of all three species on SSI. We also document that while many craniofacial traits appear to result from additive genetic effects, variation in key traits such as head depth, maxilla length, and lower jaw length may be produced via non-additive genetic mechanisms. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity.

Evaluating modularity in the hominine skull related to feeding biomechanics

OBJECTIVES

Modular architecture of traits in complex organisms can be important for morphological evolution at micro- and sometimes macroevolutionary scales as it may influence the tempo and direction of changes to groups of traits that are essential for particular functions, including food acquisition and processing. We tested several distinct hypotheses about craniofacial modularity in the hominine skull in relation to feeding biomechanics.

MATERIALS AND METHODS

First, we formulated hypothesized functional modules for craniofacial traits reflecting specific demands of feeding biomechanics (e.g., masseter leverage/gape or tooth crown mechanics) in Homo sapiens, Pan troglodytes, and Gorilla gorilla. Then, the pattern and strength of modular signal was quantified by the covariance ratio coefficient and compared across groups using covariance ratio effect size. Hierarchical clustering analysis was then conducted to examine whether a priori-defined functional modules correspond to empirically recovered clusters.

RESULTS

There was statistical support for most a priori-defined functional modules in the cranium and half of the functional modules in the mandible. Modularity signal was similar in the cranium and mandible, and across the three taxa. Despite a similar strength of modularity, the empirically recovered clusters do not map perfectly onto our priori functional modules, indicating that further work is needed to refine our hypothesized functional modules.

CONCLUSION

The results suggest that modular structure of traits in association with feeding biomechanics were mostly shared with humans and the two African apes. Thus, conserved patterns of functional modularity may have facilitated evolutionary changes to the skull during human evolution.

Rapid and biased evolution of canalization during adaptive divergence revealed by dominance in gene expression variability during Arctic charr early development

Adaptive evolution may be influenced by canalization, the buffering of developmental processes from environmental and genetic perturbations, but how this occurs is poorly understood. Here, we explore how gene expression variability evolves in diverging and hybridizing populations, by focusing on the Arctic charr (Salvelinus alpinus) of Thingvallavatn, a classic case of divergence between feeding habitats. We report distinct profiles of gene expression variance for both coding RNAs and microRNAs between the offspring of two contrasting morphs (benthic/limnetic) and their hybrids reared in common conditions and sampled at two key points of cranial development. Gene expression variance in the hybrids is substantially affected by maternal effects, and many genes show biased expression variance toward the limnetic morph. This suggests that canalization, as inferred by gene expression variance, can rapidly diverge in sympatry through multiple gene pathways, which are associated with dominance patterns possibly biasing evolutionary trajectories and mitigating the effects of hybridization on adaptive evolution.

The effect of experimental hybridization on cognition and brain anatomy: Limited phenotypic variation and transgression in Poeciliidae

Hybridization can promote phenotypic variation and often produces trait combinations distinct from the parental species. This increase in available variation can lead to the manifestation of functional novelty when new phenotypes bear adaptive value under the environmental conditions in which they occur. Although the role of hybridization as a driver of variation and novelty in traits linked to fitness is well recognized, it remains largely unknown whether hybridization can fuel behavioral novelty by promoting phenotypic variation in brain morphology and/or cognitive traits. To address this question, we investigated the effect of hybridization on brain anatomy, learning ability, and cognitive flexibility in first- and second-generation hybrids of two closely related fish species (Poecilia reticulata and Poecilia wingei). Overall, we found that F1 and F2 hybrids showed intermediate brain morphology and cognitive traits compared to parental groups. Moreover, as phenotypic dispersion and transgression were low for both brain and cognitive traits, we suggest that hybridization is not a strong driver of brain anatomical and cognitive diversification in these Poeciliidae. To determine the generality of this conclusion, hybridization experiments with cognitive tests need to be repeated in other families.

Differences among reciprocal hybrids of Labeotropheus

Current evidence suggests that hybridization played a crucial role in the early evolution and diversification of the species flocks of cichlid fishes in the African Great Lakes. Nonetheless, evidence for hybridization in the extant cichlid fauna is scant, suggesting that hybridization is rare in the modern era, perhaps enforced by natural or sexual selection acting against F1 hybrids. Additionally, most experimental studies of hybridization perform a hybrid cross in one direction, ignoring the reciprocal hybrid. In this study, we perform reciprocal crosses between sympatric congeners from Lake Malaŵi, Labeotropheus fuelleborni and L. trewavasae, in order to compare the body shape and coloration of males of both of these hybrids, as well as to examine how these hybrids fare during both inter- and intrasexual interactions. We found that L. trewavasae-sired hybrid males are intermediate to the parental species both morphologically and chromatically, while the reciprocal L. fuelleborni-sired hybrids are likely transgressive hybrids. Males of these transgressive hybrids also fare poorly during our mate choice experiments. While female L. trewavasae reject them as possible mates, male L. trewavasae do not make a distinction between them and conspecific males. Selection against transgressive F1 hybrids as observed in our crossing experiments may help explain why contemporary hybridization in Lake Malaŵi cichlids appears to be rare.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10750-022-05092-4.

Genetic architecture of adaptive radiation across two trophic levels

Evolution of trophic diversity is a hallmark of adaptive radiation. Yet, transitions between carnivory and herbivory are rare in young adaptive radiations. Haplochromine cichlid fish of the African Great Lakes are exceptional in this regard. Lake Victoria was colonized by an insectivorous generalist and in less than 20 000 years, several clades of specialized herbivores evolved. Carnivorous versus herbivorous lifestyles in cichlids require many different adaptations in functional morphology, physiology and behaviour. Ecological transitions in either direction thus require many traits to change in a concerted fashion, which could be facilitated if genomic regions underlying these traits were physically linked or pleiotropic. However, linkage/pleiotropy could also constrain evolvability. To investigate components of the genetic architecture of a suite of traits that distinguish invertivores from algae scrapers, we performed quantitative trait locus (QTL) mapping using a second-generation hybrid cross. While we found indications of linkage/pleiotropy within trait complexes, QTLs for distinct traits were distributed across several unlinked genomic regions. Thus, a mixture of independently segregating variation and some pleiotropy may underpin the rapid trophic transitions. We argue that the emergence and maintenance of associations between the different genomic regions underpinning co-adapted traits that evolved and persist against some gene flow required reproductive isolation.

The genetic basis of a novel reproductive strategy in Sulawesi ricefishes: How modularity and a low number of loci shape pelvic brooding

The evolution of complex phenotypes like reproductive strategies is challenging to understand, as they often depend on multiple adaptations that only jointly result in a specific functionality. Sulawesi ricefishes (Adrianichthyidae) evolved a reproductive strategy termed as pelvic brooding. In contrast to the more common transfer brooding, female pelvic brooders carry an egg bundle connected to their body for weeks until the fry hatches. To examine the genetic architecture of pelvic brooding, we crossed the pelvic brooding Oryzias eversi and the transfer brooding Oryzias nigrimas (species divergence time: ∼3.6 my). We hypothesize, that a low number of loci and modularity have facilitated the rapid evolution of pelvic brooding. Traits associated to pelvic brooding, like rib length, pelvic fin length, and morphology of the genital papilla, were correlated in the parental species but correlations were reduced or lost in their F1 and F2 hybrids. Using the Castle-Wright estimator, we found that generally few loci underlie the studied traits. Further, both parental species showed modularity in their body plans. In conclusion, morphological traits related to pelvic brooding were based on a few loci and the mid-body region likely could evolve independently from the remaining body parts. Both factors presumably facilitated the evolution of pelvic brooding.

Multivariate analysis of morphology, behaviour, growth and developmental timing in hybrids brings new insights into the divergence of sympatric Arctic charr morphs

BACKGROUND

Studying the development of fitness related traits in hybrids from populations diverging in sympatry is a fundamental approach to understand the processes of speciation. However, such traits are often affected by covariance structures that complicate the comprehension of these processes, especially because the interactive relationships between traits of different nature (e.g. morphology, behaviour, life-history) remain largely unknown in this context. In a common garden setup, we conducted an extensive examination of a large suit of traits putatively involved in the divergence of two morphs of Arctic charr (Salvelinus alpinus), and investigated the consequences of potential patterns of trait covariance on the phenotype of their hybrids. These traits were measured along ontogeny and involved growth, yolk sac resorption, developmental timing (hatching and the onset of exogeneous feeding), head morphology and feeding behaviour.

RESULTS

Growth trajectories provided the strongest signal of phenotypic divergence between the two charr. Strikingly, the first-generation hybrids did not show intermediate nor delayed growth but were similar to the smallest morph, suggesting parental biases in the inheritance of growth patterns. However, we did not observe extensive multivariate trait differences between the two morphs and their hybrids. Growth was linked to head morphology (suggesting that morphological variations in early juveniles relate to simple allometric effects) but this was the only strong signal of covariance observed between all the measured traits. Furthermore, we did not report evidence for differences in overall phenotypic variance between morphs, nor for enhanced phenotypic variability in their hybrids.

CONCLUSION

Our study shed light on the multivariate aspect of development in a context of adaptive divergence. The lack of evidence for the integration of most traits into a single covariance structure suggested that phenotypic constraints may not always favour nor impede divergence toward ecological niches differing in numerous physical and ecological variables, as observed in the respective habitats of the two charr. Likewise, the role of hybridization as a disruptive agent of trait covariance may not necessarily be significant in the evolution of populations undergoing resource polymorphism.

Nonadditive genetic effects induce novel phenotypic distributions in male mating traits of F1 hybrids

Hybridization is a source of phenotypic novelty and variation because of increased additive genetic variation. Yet, the roles of nonadditive allelic interactions in shaping phenotypic mean and variance of hybrids have been underappreciated. Here, we examine the distributions of male-mating traits in F1 hybrids via a meta-analysis of 3208 effect sizes from 39 animal species pairs. Although additivity sets phenotypic distributions of F1s to be intermediate, F1s also showed recessivity and resemblance to maternal species. F1s expressed novel phenotypes (beyond the range of both parents) in 65% of species pairs, often associated with increased phenotypic variability. Overall, however, F1s expressed smaller variation than parents in 51% of traits. Although genetic divergence between parents did not impact phenotypic novelty, it increased phenotypic variability of F1s. By creating novel phenotypes with increased variability, nonadditivity of heterozygotic genome may play key roles in determining mating success of F1s, and their subsequent extinction or speciation.

Patterns, Predictors, and Consequences of Dominance in Hybrids

AbstractCompared to those of their parents, are the traits of first-generation (F₁) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F₁ hybrids. We find that individual traits in F₁s are halfway between the parental midpoint and one parental value. Considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (parent bias) about 50% more than the other, while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that parent bias improves fitness, whereas mismatch reduces fitness. Our study has three major conclusions. First, hybrids are not phenotypically intermediate but rather exhibit substantial mismatch. Second, dominance is likely determined by the idiosyncratic evolutionary trajectories of individual traits and populations. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.

Intraspecific genomic variation and local adaptation in a young hybrid species

Hybridization increases genetic variation, hence hybrid species may have greater evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular their adaptive potential. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation, suggesting ongoing local adaptation. As found previously in other nonhybrid species, climatic differences appear to increase population differentiation. We also report strong population divergence in a gene known to affect beak morphology. Most of the strongly divergent loci among Italian sparrow populations do not seem to be differentiated between its parent species, the house and Spanish sparrows. Unlike in the hybrid, population divergence within each of the parental taxa has occurred mostly at loci with high allele frequency difference between the parental species, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

Ontogenetic divergence generates novel phenotypes in hybrid cichlids

Hybridization is suggested to contribute to ecomorphological and taxonomic diversity in lacustrine East African cichlids. This is supported by studies demonstrating that genetic diversity within lake radiations has been influenced by hybridization events, leading to extensive phenotypic differentiation of genetically closely related species. Hybrid persistence and speciation in sympatry with gene flow can be explained by pleiotropy in traits involved in reproductive isolation; however, little attention has been given to how trait differentiation is established during hybrid ontogeny, and how this may relate to trophic and locomotor specialization. This study compares body shape changes in a Lake Victoria cichlid hybrid throughout its post-hatch ontogeny to those of its parental species. Across the considered age/size categories, hybrids occupy a distinct and intermediate morphological space, yet where several transgressive traits emerge. A between-group principal component analysis on body shapes across size categories reveals axes of shape variation exclusive to the hybrids in the youngest/smallest size categories. Shape differences in the hybrids involved morphological traits known to be implicated in trophic and locomotor specializations in the parental species. Combined, our findings suggest that phenotypic divergence in the hybrid can lead to functional differences that may potentially release them to some degree from competition with the parental species. These findings agree with recent literature that addresses the potential importance of hybridization for the unusually recent origin of the Lake Victoria cichlid super-species flock.

Surprising spatiotemporal stability of a multi-peak fitness landscape revealed by independent field experiments measuring hybrid fitness

The effect of the environment on fitness in natural populations is a fundamental question in evolutionary biology. However, experimental manipulations of both environment and phenotype at the same time are rare. Thus, the relative importance of the competitive environment versus intrinsic organismal performance in shaping the location, height, and fluidity of fitness peaks and valleys remains largely unknown. Here, we experimentally tested the effect of competitor frequency on the complex fitness landscape driving adaptive radiation of a generalist and two trophic specialist pupfishes, a scale-eater and molluscivore, endemic to hypersaline lakes on San Salvador Island (SSI), Bahamas. We manipulated phenotypes, by generating 3407 F4/F5 lab-reared hybrids, and competitive environment, by altering the frequency of rare transgressive hybrids between field enclosures in two independent lake populations. We then tracked hybrid survival and growth rates across these four field enclosures for 3-11 months. In contrast to competitive speciation theory, we found no evidence that the frequency of hybrid phenotypes affected their survival. Instead, we observed a strikingly similar fitness landscape to a previous independent field experiment, each supporting multiple fitness peaks for generalist and molluscivore phenotypes and a large fitness valley isolating the divergent scale-eater phenotype. These features of the fitness landscape were stable across manipulated competitive environments, multivariate trait axes, and spatiotemporal heterogeneity. We suggest that absolute performance constraints and divergent gene regulatory networks shape macroevolutionary (interspecific) fitness landscapes in addition to microevolutionary (intraspecific) competitive dynamics. This interplay between organism and environment underlies static and dynamic features of the adaptive landscape.

Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids

The East African cichlid radiations are characterized by repeated and rapid diversification into many distinct species with different ecological specializations and by a history of hybridization events between nonsister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second-generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialized on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialized on sand sifting. We combined experimental behavioral and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behavior related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioral traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behavior in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behavior, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.

Hybridization and transgressive exploration of colour pattern and wing morphology in Heliconius butterflies

Hybridization can generate novel phenotypes distinct from those of parental lineages, a phenomenon known as transgressive trait variation. Transgressive phenotypes might negatively or positively affect hybrid fitness, and increase available variation. Closely related species of Heliconius butterflies regularly produce hybrids in nature, and hybridization is thought to play a role in the diversification of novel wing colour patterns despite strong stabilizing selection due to interspecific mimicry. Here, we studied wing phenotypes in first- and second-generation hybrids produced by controlled crosses between either two co-mimetic species of Heliconius or between two nonmimetic species. We quantified wing size, shape and colour pattern variation and asked whether hybrids displayed transgressive wing phenotypes. Discrete traits underlain by major-effect loci, such as the presence or absence of colour patches, generate novel phenotypes. For quantitative traits, such as wing shape or subtle colour pattern characters, hybrids only exceed the parental range in specific dimensions of the morphological space. Overall, our study addresses some of the challenges in defining and measuring phenotypic transgression for multivariate traits and our data suggest that the extent to which transgressive trait variation in hybrids contributes to phenotypic diversity depends on the complexity and the genetic architecture of the traits.

Triad hybridization via a conduit species

Introgressive hybridization can affect the evolution of populations in several important ways. It may retard or reverse divergence of species, enable the development of novel traits, enhance the potential for future evolution by elevating levels of standing variation, create new species, and alleviate inbreeding depression in small populations. Most of what is known of contemporary hybridization in nature comes from the study of pairs of species, either coexisting in the same habitat or distributed parapatrically and separated by a hybrid zone. More rarely, three species form an interbreeding complex (triad), reported in vertebrates, insects, and plants. Often, one species acts as a genetic link or conduit for the passage of genes (alleles) between two others that rarely, if ever, hybridize. Demographic and genetic consequences are unknown. Here we report results of a long-term study of interbreeding Darwin's finches on Daphne Major island, Galápagos. Geospiza fortis acted as a conduit for the passage of genes between two others that have never been observed to interbreed on Daphne: Geospiza fuliginosa, a rare immigrant, and Geospiza scandens, a resident. Microsatellite gene flow from G. fortis into G. scandens increased in frequency during 30 y of favorable ecological conditions, resulting in genetic and morphological convergence. G. fortis, G. scandens, and the derived dihybrids and trihybrids experienced approximately equal fitness. Especially relevant to young adaptive radiations, where species differ principally in ecology and behavior, these findings illustrate how new combinations of genes created by hybridization among three species can enhance the potential for evolutionary change.

Hybridization increases population variation during adaptive radiation

Adaptive radiations are prominent components of the world's biodiversity. They comprise many species derived from one or a small number of ancestral species in a geologically short time that have diversified into a variety of ecological niches. Several authors have proposed that introgressive hybridization has been important in the generation of new morphologies and even new species, but how that happens throughout evolutionary history is not known. Interspecific gene exchange is expected to have greatest impact on variation if it occurs after species have diverged genetically and phenotypically but before genetic incompatibilities arise. We use a dated phylogeny to infer that populations of Darwin's finches in the Galápagos became more variable in morphological traits through time, consistent with the hybridization hypothesis, and then declined in variation after reaching a peak. Some species vary substantially more than others. Phylogenetic inferences of hybridization are supported by field observations of contemporary hybridization. Morphological effects of hybridization have been investigated on the small island of Daphne Major by documenting changes in hybridizing populations of Geospiza fortis and Geospiza scandens over a 30-y period. G. scandens showed more evidence of admixture than G. fortis Beaks of G. scandens became progressively blunter, and while variation in length increased, variation in depth decreased. These changes imply independent effects of introgression on 2, genetically correlated, beak dimensions. Our study shows how introgressive hybridization can alter ecologically important traits, increase morphological variation as a radiation proceeds, and enhance the potential for future evolution in changing environments.

Interspecific hybridization can generate functional novelty in cichlid fish

The role of interspecific hybridization in evolution is still being debated. Interspecific hybridization has been suggested to facilitate the evolution of ecological novelty, and hence the invasion of new niches and adaptive radiation when ecological opportunity is present beyond the parental species niches. On the other hand, hybrids between two ecologically divergent species may perform less well than parental species in their respective niches because hybrids would be intermediate in performance in both niches. The evolutionary consequences of hybridization may hence be context-dependent, depending on whether ecological opportunities, beyond those of the parental species, do or do not exist. Surprisingly, these complementary predictions may never have been tested in the same experiment in animals. To do so, we investigate if hybrids between ecologically distinct cichlid species perform less well than the parental species when feeding on food either parent is adapted to, and if the same hybrids perform better than their parents when feeding on food none of the species are adapted to. We generated two first-generation hybrid crosses between species of African cichlids. In feeding efficiency experiments we measured the performance of hybrids and parental species on food types representing both parental species niches and additional 'novel' niches, not used by either of the parental species but by other species in the African cichlid radiations. We found that hybrids can have higher feeding efficiencies on the 'novel' food types but typically have lower efficiencies on parental food types when compared to parental species. This suggests that hybridization can generate functional variation that can be of ecological relevance allowing the access to resources outside of either parental species niche. Hence, we provide support for the hypothesis of ecological context-dependency of the evolutionary impact of interspecific hybridization.

Evolutionary diversity as a catalyst for biological discovery

The tremendous diversity of animal behaviors has inspired generations of scientists from an array of biological disciplines. To complement investigations of ecological and evolutionary factors contributing to behavioral evolution, modern sequencing, gene editing, computational and neuroscience tools now provide a means to discover the proximate mechanisms upon which natural selection acts to generate behavioral diversity. Social behaviors are motivated behaviors that can differ tremendously between closely related species, suggesting phylogenetic plasticity in their underlying biological mechanisms. In addition, convergent evolution has repeatedly given rise to similar forms of social behavior and mating systems in distantly related species. Social behavioral divergence and convergence provides an entry point for understanding the neurogenetic mechanisms contributing to behavioral diversity. We argue that the greatest strides in discovering mechanisms contributing to social behavioral diversity will be achieved through integration of interdisciplinary comparative approaches with modern tools in diverse species systems. We review recent advances and future potential for discovering mechanisms underlying social behavioral variation; highlighting patterns of social behavioral evolution, oxytocin and vasopressin neuropeptide systems, genetic/transcriptional "toolkits," modern experimental tools, and alternative species systems, with particular emphasis on Microtine rodents and Lake Malawi cichlid fishes.

Impact of the huge 2011 Tohoku-oki tsunami on the phenotypes and genotypes of Japanese coastal threespine stickleback populations

On March 11, 2011, a large earthquake occurred, causing a tsunami which struck the Pacific coast of northeast Japan. We investigated the ecological and genetic effects of the large tsunami on the threespine stickleback (genus Gasterosteus) populations in Otsuchi Town, which was one of the most severely damaged areas after the tsunami. Our environmental surveys showed that spring water may have contributed to the habitat recovery. Morphological analysis of the stickleback before and after the tsunami showed morphological shifts in the gill raker number, which is a foraging trait. Genetic analyses revealed that the allelic richness of one population was maintained after the tsunami, whereas that of another decreased in 2012 and then started to recover in 2013. Additionally, we found that the large tsunami and ground subsidence created new spring water-fed pools with sticklebacks, suggesting that the tsunami brought sticklebacks into these pools. Genetic analysis of this population showed that this population might be derived from hybridization between freshwater Gasterosteus aculeatus and anadromous G. nipponicus. Overall, our data indicate that tsunamis can influence morphologies and genetic structures of freshwater fishes. Furthermore, spring water may play important roles in the maintenance and creation of fish habitats, faced with environmental disturbance.

Biological action in Read-Write genome evolution

Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

Body shape differences in a pair of closely related Malawi cichlids and their hybrids: Effects of genetic variation, phenotypic plasticity, and transgressive segregation

Phenotypic differences may have genetic and plastic components. Here, we investigated the contributions of both for differences in body shape in two species of Lake Malawi cichlids using wild-caught specimens and a common garden experiment. We further hybridized the two species to investigate the mode of gene action influencing body shape differences and to examine the potential for transgressive segregation. We found that body shape differences between the two species observed in the field are maintained after more than 10 generations in a standardized environment. Nonetheless, both species experienced similar changes in the laboratory environment. Our hybrid cross experiment confirmed that substantial variation in body shape appears to be genetically determined. The data further suggest that the underlying mode of gene action is complex and cannot be explained by simple additive or additive-dominance models. Transgressive phenotypes were found in the hybrid generations, as hybrids occupied significantly more morphospace than both parentals combined. Further, the body shapes of transgressive individuals resemble the body shapes observed in other Lake Malawi rock-dwelling genera. Our findings indicate that body shape can respond to selection immediately, through plasticity, and over longer timescales through adaptation. In addition, our results suggest that hybridization may have played an important role in the diversification of Lake Malawi cichlids through creating new phenotypic variation.

Mechanical Transgressive Segregation and the Rapid Origin of Trophic Novelty

Hybrid phenotypes are often intermediate between those of parental species. However, hybridization can generate novel phenotypes when traits are complex. For instance, even when the morphologies of individual musculo-skeletal components do not segregate outside the parental range in hybrid offspring, complex functional systems can exhibit emergent phenotypes whose mechanics exceed the parental values. To determine if transgression in mechanics could facilitate divergence during an adaptive radiation, we examined three functional systems in the trophic apparatus of Lake Malawi cichlid fishes. We conducted a simulation study of hybridization between species pairs whose morphology for three functional systems was empirically measured, to determine how the evolutionary divergence of parental species influences the frequency that hybridization could produce mechanics that transgress the parental range. Our simulations suggest that the complex mechanical systems of the cichlid trophic apparatus commonly exhibit greater transgression between more recently diverged cichlid species. Because (1) all three mechanical systems produce hybrids with transgressive mechanics in Lake Malawi cichlids, (2) hybridization is common, and (3) single hybrid crosses often recapitulate a substantial diversity of mechanics, we conclude that mechanical transgressive segregation could play an important role in the rapid accumulation of phenotypic variation in adaptive radiations.

Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization

Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.

Environmental change explains cichlid adaptive radiation at Lake Malawi over the past 1.2 million years

Long paleoecological records are critical for understanding evolutionary responses to environmental forcing and unparalleled tools for elucidating the mechanisms that lead to the development of regions of high biodiversity. We use a 1.2-My record from Lake Malawi, a textbook example of biological diversification, to document how climate and tectonics have driven ecosystem and evolutionary dynamics. Before ∼800 ka, Lake Malawi was much shallower than today, with higher frequency but much lower amplitude water-level and oxygenation changes. Since ∼800 ka, the lake has experienced much larger environmental fluctuations, best explained by a punctuated, tectonically driven rise in its outlet location and level. Following the reorganization of the basin, a change in the pacing of hydroclimate variability associated with the Mid-Pleistocene Transition resulted in hydrologic change dominated by precession rather than the high-latitude teleconnections recorded elsewhere. During this time, extended, deep lake phases have abruptly alternated with times of extreme aridity and ecosystem variability. Repeated crossings of hydroclimatic thresholds within the lake system were critical for establishing the rhythm of diversification, hybridization, and extinction that dominate the modern system. The chronology of these changes closely matches both the timing and pattern of phylogenetic history inferred independently for the lake's extraordinary array of cichlid fish species, suggesting a direct link between environmental and evolutionary dynamics.

Shallow genetic divergence and species delineations in the endemic Labeobarbus species flock of Lake Tana, Ethiopia

To assess whether the species distinctions of Lake Tana's Labeobarbus spp. are supported by genetic information, microsatellite markers were used. A total of 376 Labeobarbus spp., belonging to 24 populations of 11 species from three regions of the lake (north, south and east), were sampled. Eight microsatellite markers were analysed. In general, differences between conspecific populations were smaller than differences between populations of different species. For six species, conspecific populations from different regions in the lake were consistently more similar than populations of other species from the same region. For four species this was not the case, while for one species two populations were similar, but different from the third population. River-spawning species appeared to be more distinct than presumed lake spawners. On the species level, there was a significant correlation between genetic and morphological differentiation, especially in morphological aspects associated with ecological functioning. This suggests that genetic differentiation arose together with adaptive radiation, although the overall genetic differentiation among the Lake Tana Labeobarbus spp. is small.

Secondary contact seeds phenotypic novelty in cichlid fishes

Theory proposes that genomic admixture between formerly reproductively isolated populations can generate phenotypic novelty for selection to act upon. Secondary contact may therefore be a significant promoter of phenotypic novelty that allows species to overcome environmental challenges and adapt to novel environments, including during adaptive radiation. To date, this has largely been considered from the perspective of interspecific hybridization at contact zones. However, it is also possible that this process occurs more commonly between natural populations of a single species, and thus its importance in adaptive evolution may have been underestimated. In this study, we tested the consequences of genomic introgression during apparent secondary contact between phenotypically similar lineages of the riverine cichlid fish Astatotilapia calliptera. We provide population genetic evidence of a secondary contact zone in the wild, and then demonstrate using mate-choice experiments that both lineages can reproduce together successfully in laboratory conditions. Finally, we show that genomically admixed individuals display extreme phenotypes not observed in the parental lineages. Collectively, the evidence shows that secondary contact can drive the evolution of phenotypic novelty, suggesting that pulses of secondary contact may repeatedly seed genetic novelty, which when coupled with ecological opportunity could promote rapid adaptive evolution in natural circumstances.

Process and pattern in cichlid radiations - inferences for understanding unusually high rates of evolutionary diversification

The cichlid fish radiations in the African Great Lakes differ from all other known cases of rapid speciation in vertebrates by their spectacular trophic diversity and richness of sympatric species, comparable to the most rapid angiosperm radiations. I review factors that may have facilitated these radiations and compare these with insights from recent work on plant radiations. Work to date suggests that it was a coincidence of ecological opportunity, intrinsic ecological versatility and genomic flexibility, rapidly evolving behavioral mate choice and large amounts of standing genetic variation that permitted these spectacular fish radiations. I propose that spatially orthogonal gradients in the fit of phenotypes to the environment facilitate speciation because they allow colonization of alternative fitness peaks during clinal speciation despite local disruptive selection. Such gradients are manifold in lakes because of the interaction of water depth as an omnipresent third spatial dimension with other fitness-relevant variables. I introduce a conceptual model of adaptive radiation that integrates these elements and discuss its applicability to, and predictions for, plant radiations.

Genomics and the origin of species

Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.