Rapid Phenotypic Diversification Research Articles

Integrative taxonomy of an East Asian songbird indicates rapid dwarfism after island colonization

AbstractAnimals that colonize islands often undergo significant evolutionary changes in comparison with their continental counterparts as a response to specific island conditions. The pace of such changes can be relatively fast, which poses challenges in the evaluation of the taxonomic status of island taxa. The Japanese and Manchurian Bush Warbler species complex (Horornis diphone–canturians), which breeds in East Asia and the Japanese Archipelago, is such an avian example. This species complex exhibits significant morphological differentiation between different taxa, and the taxonomic status and phylogenetic relationships within the complex are debated. Here, we updated the taxonomy of this species complex and shed insight on its evolutionary history using multi‐locus phylogeographic and acoustic analyses. Our results support the conventional treatment of the two continental taxa borealis and canturians as subspecies of H. canturians, contrary to some recent proposals that they are affiliated to H. diphone. We also document a reduction in body size, that is dwarfism, and vocal divergence in the nominate subspecies H. d. diphone, which is endemic to the remote and isolated Ogasawara Islands. These changes may have happened following colonization of these islands, which was estimated to have taken place approximately 0.2 million years ago. Although H. d. diphone is clearly distinctive and deserves recognition as an evolutionarily significant unit, H. d. diphone and other H. diphone samples were not reciprocally monophyletic. Because of this lack of reciprocal monophyly and a relatively recent divergence time, we advocate maintaining its current subspecies status. We also detected reduced genetic diversity, measured as heterozygosity, in H. d. diphone. We suggest that conservation efforts in the Ogasawara Islands should prioritize the protection of this endemic subspecies. Collectively, our findings suggest that the separation between the populations on the East Asian continent and the Japanese Archipelago, followed by colonization of remote oceanic islands through long‐distance dispersal, underlie rapid phenotypic and genetic diversification of the Horornis diphone–canturians species complex.

Decoupling of sexual signals and their underlying morphology facilitates rapid phenotypic diversification.

How novel phenotypes evolve is challenging to imagine because traits are often underlain by numerous integrated phenotypic components, and changes to any one form can disrupt the function of the entire module. Yet novel phenotypes do emerge, and research on adaptive phenotypic evolution suggests that complex traits can diverge while either maintaining existing form-function relationships or through innovations that alter form-function relationships. How these alternate routes contribute to sexual signal evolution is poorly understood, despite the role of sexual signals in generating biodiversity. In Hawaiian populations of the Pacific field cricket, male song attracts both female crickets and a deadly acoustically orienting parasitoid fly. In response to this conflict between natural and sexual selection, male crickets have evolved altered wing morphologies multiple times, resulting in loss and dramatic alteration of sexual signals. More recently, we and others have observed a radical increase in sexual signal variation and the underlying morphological structures that produce song. We conducted the first combined analysis of form (wing morphology), function (emergent signal), and receiver responses to characterize novel variation, test alternative hypotheses about form-function relationships (Form-Function Continuity vs. Form-Function Decoupling), and investigate underlying mechanistic changes and fitness consequences of novel signals. We identified three sound-producing male morphs (one previously undescribed, named "rattling") and found that relationships between morphology and signals have been rewired (Form-Function Decoupling), rapidly and repeatedly, through the gain, loss, and alteration of morphological structures, facilitating the production of signals that exist in novel phenotypic space. By integrating across a hierarchy of phenotypes, we uncovered divergent morphs with unique solutions to the challenge of attracting mates while evading fatal parasitism.

Simulated evolution of mating signal diversification in a primate radiation.

Divergence in allopatry and subsequent diversification of mating signals on secondary contact (reinforcement) is a major driver of phenotypic diversity. Observing this evolutionary process directly is often impossible, but simulated evolution can pinpoint key drivers of phenotypic variation. We developed evolutionary simulations in which mating signals, modelled as points in phenotype space, evolve across time under varying evolutionary scenarios. We model mate recognition signals in guenons, a primate radiation exhibiting colourful and diverse face patterns hypothesized to maintain reproductive isolation via mate choice. We simulate face pattern evolution across periods of allopatry and sympatry, identifying the role of key parameters in driving evolutionary endpoints. Results show that diversification in allopatry and assortative mate choice on secondary contact can induce rapid phenotypic diversification, resulting in distinctive (between species) and stereotyped (within species) face patterns, similar to extant guenons. Strong selection against hybrids is key to diversification, with even low levels of hybrid fitness often resulting in merged populations on secondary contact. Our results support a key role for reinforcement by assortative mating in the maintenance of species diversity and support the long-proposed prehistorical scenario for how such striking diversity was produced and maintained in perhaps the most colourful of all mammalian clades.

Invasive fish retain plasticity of naturally selected, but diverge in sexually selected traits

Invasive alien species (IAS) have become a major threat to ecosystems worldwide. From an evolutionary ecological perspective, they allow teasing apart the relative contributions of plasticity and evolutionary divergence in driving rapid phenotypic diversification. When IAS spread across extensive geographic ranges, climatic variation may represent a source of strong natural selection through overwinter mortality and summer heat stress. This could favour local adaptation, i.e., evolutionary divergence of certain traits. IAS, however, are likely to show plasticity in survival-related traits, and environmental fluctuation in their new distribution range could favour the maintenance of this pre-existing phenotypic plasticity. By contrast, sexually selected traits are more likely to undergo evolutionary divergence when components of sexual selection differ geographically. Here, using data from a common-garden rearing experiment of Western mosquitofish (Gambusia affinis Baird and Girard, 1853) from five populations across the species' invasive range in China, we show that invasive mosquitofish have retained plasticity in key physiological (thermal tolerances), morphological and life-history traits even 100 years after their introduction to China, but exhibit heritable population differences in several sexually selected traits, including the shape of the male copulatory organ. Adaptive plasticity of traits linked to immediate survival in different thermal environments—while likely responsible for the species' extraordinary invasion success—could slow down genetic evolution. Several sexually selected traits could diverge geographically and show rapid evolutionary change, e.g., because climate alters selective landscapes arising from mate competition as an indirect consequence of variation in overwinter mortality.

Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes

Sexual selection drives rapid phenotypic diversification of mating traits. However, we know little about the causative genes underlying divergence in sexually selected traits. Here, we investigate the genetic basis of male mating trait diversification in the medaka fishes (genus Oryzias) from Sulawesi, Indonesia. Using linkage mapping, transcriptome analysis, and genome editing, we identify csf1 as a causative gene for red pectoral fins that are unique to male Oryzias woworae. A cis-regulatory mutation enables androgen-induced expression of csf1 in male fins. csf1-knockout males have reduced red coloration and require longer for mating, suggesting that coloration can contribute to male reproductive success. Contrary to expectations, non-red males are more attractive to a predatory fish than are red males. Our results demonstrate that integrating genomics with genome editing enables us to identify causative genes underlying sexually selected traits and provides a new avenue for testing theories of sexual selection.

Evolutionary divergence of novel open reading frames in cichlids speciation

Novel open reading frames (nORFs) with coding potential may arise from noncoding DNA. Not much is known about their emergence, functional role, fixation in a population or contribution to adaptive radiation. Cichlids fishes exhibit extensive phenotypic diversification and speciation. Encounters with new environments alone are not sufficient to explain this striking diversity of cichlid radiation because other taxa coexistent with the Cichlidae demonstrate lower species richness. Wagner et al. analyzed cichlid diversification in 46 African lakes and reported that both extrinsic environmental factors and intrinsic lineage-specific traits related to sexual selection have strongly influenced the cichlid radiation, which indicates the existence of unknown molecular mechanisms responsible for rapid phenotypic diversification, such as emergence of novel open reading frames (nORFs). In this study, we integrated transcriptomic and proteomic signatures from two tissues of two cichlids species, identified nORFs and performed evolutionary analysis on these nORF regions. Our results suggest that the time scale of speciation of the two species and evolutionary divergence of these nORF genomic regions are similar and indicate a potential role for these nORFs in speciation of the cichlid fishes.

Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids.

Allopolyploidy is an important process in plant speciation, yet newly formed allopolyploid species typically suffer from extreme genetic bottlenecks. One escape from this impasse might be homoeologous meiotic pairing, during which homoeologous exchanges (HEs) generate phenotypically variable progeny. However, the immediate genome-wide patterns and resulting phenotypic diversity generated by HEs remain largely unknown. Here, we analyzed the genome composition of 202 phenotyped euploid segmental allopolyploid individuals from the fourth selfed generation following chromosomal doubling of reciprocal F1 hybrids of crosses between rice subspecies, using whole-genome sequencing. We describe rampant occurrence of HEs that, by overcoming incompatibility or conferring superiority of hetero-cytonuclear interactions, generate extensive and individualized genomic mosaicism across the analyzed tetraploids. We show that the resulting homoeolog copy number alteration in tetraploids affects known-function genes and their complex genetic interactions, in the process creating extraordinary phenotypic diversity at the population level following a single initial hybridization. Our results illuminate the immediate genomic landscapes possible in a tetraploid genomic environment, and underscore HE as an important mechanism that fuels rapid phenotypic diversification accompanying the initial stages of allopolyploid evolution.

Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis).

Colour plays a prominent role in species recognition; therefore, understanding the proximate basis of pigmentation can provide insight into reproductive isolation and speciation. Colour differences between taxa may be the result of regulatory differences or be caused by mutations in coding regions of the expressed genes. To investigate these two alternatives, we studied the pigment composition and the genetic basis of coloration in two divergent dark-eyed junco (Junco hyemalis) subspecies, the slate-coloured and Oregon juncos, which have evolved marked differences in plumage coloration since the Last Glacial Maximum. We used HPLC and light microscopy to investigate pigment composition and deposition in feathers from four body areas. We then used RNA-seq to compare the relative roles of differential gene expression in developing feathers and sequence divergence in transcribed loci under common-garden conditions. Junco feathers differed in eumelanin and pheomelanin content and distribution. Within subspecies, in lighter feathers melanin synthesis genes were downregulated (including PMEL, TYR, TYRP1, OCA2 and MLANA), and ASIP was upregulated. Feathers from different body regions also showed differential expression of HOX and WNT genes. Feathers from the same body regions that differed in colour between the two subspecies showed differential expression of ASIP and three other genes (MFSD12, KCNJ13 and HAND2) associated with pigmentation in other taxa. Sequence variation in the expressed genes was not related to colour differences. Our findings support the hypothesis that differential regulation of a few genes can account for marked differences in coloration, a mechanism that may facilitate the rapid phenotypic diversification of juncos.

Diversification across biomes in a continental lizard radiation.

Ecological opportunity is a powerful driver of evolutionary diversification, and predicts rapid lineage and phenotypic diversification following colonization of competitor-free habitats. Alternatively, topographic or environmental heterogeneity could be key to generating and sustaining diversity. We explore these hypotheses in a widespread lineage of Australian lizards: the Gehyra variegata group. This clade occurs across two biomes: the Australian monsoonal tropics (AMT), where it overlaps a separate, larger bodied clade of Gehyra and is largely restricted to rocks; and in the larger Australian arid zone (AAZ) where it has no congeners and occupies trees and rocks. New phylogenomic data and coalescent analyses of AAZ taxa resolve lineages and their relationships and reveal high diversity in the western AAZ (Pilbara region). The AMT and AAZ radiations represent separate radiations with no difference in speciation rates. Most taxa occur on rocks, with small geographic ranges relative to widespread generalist taxa across the vast central AAZ. Rock-dwelling and generalist taxa differ morphologically, but only the lineage-poor central AAZ taxa have accelerated evolution. This accords with increasing evidence that lineage and morphological diversity are poorly correlated, and suggests environmental heterogeneity and refugial dynamics have been more important than ecological release in elevating lineage diversity.

Rapid Phenotypic and Genotypic Diversification After Exposure to the Oral Host Niche in Candida albicans.

In vitro studies suggest that stress may generate random standing variation and that different cellular and ploidy states may evolve more rapidly under stress. Yet this idea has not been tested with pathogenic fungi growing within their host niche in vivo Here, we analyzed the generation of both genotypic and phenotypic diversity during exposure of Candida albicans to the mouse oral cavity. Ploidy, aneuploidy, loss of heterozygosity (LOH), and recombination were determined using flow cytometry and double digest restriction site-associated DNA sequencing. Colony phenotypic changes in size and filamentous growth were evident without selection and were enriched among colonies selected for LOH of the GAL1 marker. Aneuploidy and LOH occurred on all chromosomes (Chrs), with aneuploidy more frequent for smaller Chrs and whole Chr LOH more frequent for larger Chrs. Large genome shifts in ploidy to haploidy often maintained one or more heterozygous disomic Chrs, consistent with random Chr missegregation events. Most isolates displayed several different types of genomic changes, suggesting that the oral environment rapidly generates diversity de novo In sharp contrast, following in vitro propagation, isolates were not enriched for multiple LOH events, except in those that underwent haploidization and/or had high levels of Chr loss. The frequency of events was overall 100 times higher for C. albicans populations following in vivo passage compared with in vitro These hyper-diverse in vivo isolates likely provide C. albicans with the ability to adapt rapidly to the diversity of stress environments it encounters inside the host.

Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus) \u2014 towards understanding gene function and regulatory evolution in an ecological model system for rapid phenotypic diversification

BackgroundThe Midas cichlid species complex (Amphilophus spp.) is widely known among evolutionary biologists as a model system for sympatric speciation and adaptive phenotypic divergence within extremely short periods of time (a few hundred generations). The repeated parallel evolution of adaptive phenotypes in this radiation, combined with their near genetic identity, makes them an excellent model for studying phenotypic diversification. While many ecological and evolutionary studies have been performed on Midas cichlids, the molecular basis of specific phenotypes, particularly adaptations, and their underlying coding and cis-regulatory changes have not yet been studied thoroughly.ResultsFor the first time in any New World cichlid, we use Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus). By adapting existing microinjection protocols, we established an effective protocol for transgenesis in Midas cichlids. Embryos were injected with a Tol2 plasmid construct that drives enhanced green fluorescent protein (eGFP) expression under the control of the ubiquitin promoter. The transgene was successfully integrated into the germline, driving strong ubiquitous expression of eGFP in the first transgenic Midas cichlid line. Additionally, we show transient expression of two further transgenic constructs, ubiquitin::tdTomato and mitfa::eGFP. Transgenesis in Midas cichlids will facilitate further investigation of the genetic basis of species-specific traits, many of which are adaptations.ConclusionTransgenesis is a versatile tool not only for studying regulatory elements such as promoters and enhancers, but also for testing gene function through overexpression of allelic gene variants. As such, it is an important first step in establishing the Midas cichlid as a powerful model for studying adaptive coding and non-coding changes in an ecological and evolutionary context.

Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice.

Allopolyploidization, that is, concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genomewide transcriptome dynamics, a phenomenon referred to as "transcriptomic shock." However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain underinvestigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic and homoeologous gene expression status in two tissues (leaf and root) of a set of randomly chosen individuals from populations of parental rice subspecies (indica and japonica), invitro "hybrids" (parental mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5th-selfed generation (S5). We show that hybridization and whole genome duplication (WGD) have opposing effects on allelic and homoeologous expression in the F1 hybrids and tetraploids, respectively. Whereas hybridization exerts strong attenuating effects on allelic expression differences in diploid hybrids, WGD augments the intrinsic parental differences and generates extensive and variable homoeolog content which triggers diversification in expression patterning among the tetraploid plants. Coupled with the vast phenotypic diversity observed among the tetraploid individuals, our results provide experimental evidence in support of the notion that allopolyploidy catalyses rapid phenotypic diversification in higher plants. Our data further suggest that largely stochastic homoeolog content reshuffling rather than alteration in total expression level may be an important feature of evolution in young segmental allopolyploids, which underlies rapid expression diversity at the population level.

Population genomics reveals a candidate gene involved in bumble bee pigmentation.

Variation in bumble bee color patterns is well‐documented within and between species. Identifying the genetic mechanisms underlying such variation may be useful in revealing evolutionary forces shaping rapid phenotypic diversification. The widespread North American species Bombus bifarius exhibits regional variation in abdominal color forms, ranging from red‐banded to black‐banded phenotypes and including geographically and phenotypically intermediate forms. Identifying genomic regions linked to this variation has been complicated by strong, near species level, genome‐wide differentiation between red‐ and black‐banded forms. Here, we instead focus on the closely related black‐banded and intermediate forms that both belong to the subspecies B. bifarius nearcticus. We analyze an RNA sequencing (RNAseq) data set and identify a cluster of single nucleotide polymorphisms (SNPs) within one gene, Xanthine dehydrogenase/oxidase‐like, that exhibit highly unusual differentiation compared to the rest of the sequenced genome. Homologs of this gene contribute to pigmentation in other insects, and results thus represent a strong candidate for investigating the genetic basis of pigment variation in B. bifarius and other bumble bee mimicry complexes.

Eco-evolutionary Model of Rapid Phenotypic Diversification in Species-Rich Communities

Evolutionary and ecosystem dynamics are often treated as different processes –operating at separate timescales– even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field experiment has explicitly shown that communities of competing plant species can experience very fast phenotypic diversification, and that this gives rise to enhanced complementarity in resource exploitation and to enlarged ecosystem-level productivity. Here, we build on progress made in recent years in the integration of eco-evolutionary dynamics, and present a computational approach aimed at describing these empirical findings in detail. In particular we model a community of organisms of different but similar species evolving in time through mechanisms of birth, competition, sexual reproduction, descent with modification, and death. Based on simple rules, this model provides a rationalization for the emergence of rapid phenotypic diversification in species-rich communities. Furthermore, it also leads to non-trivial predictions about long-term phenotypic change and ecological interactions. Our results illustrate that the presence of highly specialized, non-competing species leads to very stable communities and reveals that phenotypically equivalent species occupying the same niche may emerge and coexist for very long times. Thus, the framework presented here provides a simple approach –complementing existing theories, but specifically devised to account for the specificities of the recent empirical findings for plant communities– to explain the collective emergence of diversification at a community level, and paves the way to further scrutinize the intimate entanglement of ecological and evolutionary processes, especially in species-rich communities.

Long-term phenotypic evolution of bacteria.

For many decades comparative analyses of protein sequences and structures have been used to investigate fundamental principles of molecular evolution. In contrast, relatively little is known about the long-term evolution of species' phenotypic and genetic properties. This represents an important gap in our understanding of evolution, as exactly these proprieties play key roles in natural selection and adaptation to diverse environments. Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. Overall, bacterial phenotypic evolution can be described by a two-stage process with a rapid initial phenotypic diversification followed by a slow long-term exponential divergence. The observed average divergence trend, with approximately similar fractions of phenotypic properties changing per unit time, continues for billions of years. We experimentally confirm the predicted divergence trend using the phenotypic profiles of 40 diverse bacterial species across more than 60 growth conditions. Our analysis suggests that, at long evolutionary distances, gene essentiality is significantly more conserved than the ability to utilize different nutrients, while synthetic lethality is significantly less conserved. We also find that although a rapid phenotypic evolution is sometimes observed within the same species, a transition from high to low phenotypic similarity occurs primarily at the genus level.

Transfer of noncoding DNA drives regulatory rewiring in bacteria

Understanding the mechanisms that generate variation is a common pursuit unifying the life sciences. Bacteria represent an especially striking puzzle, because closely related strains possess radically different metabolic and ecological capabilities. Differences in protein repertoire arising from gene transfer are currently considered the primary mechanism underlying phenotypic plasticity in bacteria. Although bacterial coding plasticity has been extensively studied in previous decades, little is known about the role that regulatory plasticity plays in bacterial evolution. Here, we show that bacterial genes can rapidly shift between multiple regulatory modes by acquiring functionally divergent nonhomologous promoter regions. Through analysis of 270,000 regulatory regions across 247 genomes, we demonstrate that regulatory "switching" to nonhomologous alternatives is ubiquitous, occurring across the bacterial domain. Using comparative transcriptomics, we show that at least 16% of the expression divergence between Escherichia coli strains can be explained by this regulatory switching. Further, using an oligonucleotide regulatory library, we establish that switching affects bacterial promoter architecture. We provide evidence that regulatory switching can occur through horizontal regulatory transfer, which allows regulatory regions to move across strains, and even genera, independently from the genes they regulate. Finally, by experimentally characterizing the fitness effect of a regulatory transfer on a pathogenic E. coli strain, we demonstrate that regulatory switching elicits important phenotypic consequences. Taken together, our findings expose previously unappreciated regulatory plasticity in bacteria and provide a gateway for understanding bacterial phenotypic variation and adaptation.

Evidence of Adaptive Evolutionary Divergence during Biological Invasion

Rapid phenotypic diversification during biological invasions can either arise by adaptation to alternative environments or by adaptive phenotypic plasticity. Where experimental evidence for adaptive plasticity is common, support for evolutionary diversification is rare. Here, we performed a controlled laboratory experiment using full-sib crosses between ecologically divergent threespine stickleback populations to test for a genetic basis of adaptation. Our populations are from two very different habitats, lake and stream, of a recently invaded range in Switzerland and differ in ecologically relevant morphological traits. We found that in a lake-like food treatment lake fish grow faster than stream fish, resembling the difference among wild type individuals. In contrast, in a stream-like food treatment individuals from both populations grow similarly. Our experimental data suggest that genetically determined diversification has occurred within less than 140 years after the arrival of stickleback in our studied region.

Concordant female mate preferences in the cichlid fish Tropheus moorii

Discriminating female mate preferences enhance the variance in reproductive success among males of a population and create a potential for sexual selection, which can account for trait evolution and diversification. Fish color patterns are among the prime targets of mate choice-driven sexual selection. Populations of the cichlid Tropheus from Lake Tanganyika display remarkable geographic color pattern variation, but the role of female choice in their rapid and rich phenotypic diversification is unclear. Males and females establish a pair bond prior to spawning monogamously, but as brood care is strictly maternal, female investment in reproduction is high and the operational sex ratio is male-biased. Therefore, variance in male reproductive success can accrue if individual males succeed repeatedly in securing a mate. To test this prediction in the red colored Tropheus moorii “Chimba”, four pairs of males were presented to a series of females and female mate preferences were inferred from pairwise interactions. There was a significant difference in mating success between the males of each pair (P < 0.001 over all trials), as—with one exception—females shared preferences for the same males. Male courtship activity was strongly correlated with female choice. Our experiment suggests that female choice contributes to the variance in male reproductive success in the tested population.

Non‐random infection across individuals and populations supports that parasites can change morphology within an adaptive radiation

Adaptive radiation is characterized by rapid phenotypic diversification as a result of utilizing different environments. Red crossbills (Loxia curvirostra Linnaeus – complex) have diversified in bill size and shape, and overall size, in response to differences in the conifer cones that hold the seeds they almost exclusively feed upon. However, a recent study showed how a bill of suboptimal size for foraging has evolved due to antagonistic selection by scaly leg mites Knemidokoptes jamaicensis. This suggests that the current variation in morphology within the adaptive radiation of crossbills may not be exclusively the result of adaptation to alternative resources. Using an independent set of populations, we found that the surprising and little-understood relationship between crossbill morphology and infection with mites is repeatable. Assuming mites depress survival, this relationship would result in directional, not stabilizing selection on morphology. We also find that the rates of infection can differ dramatically between populations, potentially depending on their ecologies. These findings suggest that morphological evolution within the adaptive radiation of crossbills may partly occur for reasons unrelated to resource use.

Diversity versus disparity and the radiation of modern cetaceans

Modern whales are frequently described as an adaptive radiation spurred by either the evolution of various key innovations (such as baleen or echolocation) or ecological opportunity following the demise of archaic whales. Recent analyses of diversification rate shifts on molecular phylogenies raise doubts about this interpretation since they find no evidence of increased speciation rates during the early evolution of modern taxa. However, one of the central predictions of ecological adaptive radiation is rapid phenotypic diversification, and the tempo of phenotypic evolution has yet to be quantified in cetaceans. Using a time-calibrated molecular phylogeny of extant cetaceans and a morphological dataset on size, we find evidence that cetacean lineages partitioned size niches early in the evolutionary history of neocetes and that changes in cetacean size are consistent with shifts in dietary strategy. We conclude that the signature of adaptive radiations may be retained within morphological traits even after equilibrium diversity has been reached and high extinction or fluctuations in net diversification have erased any signature of an early burst of diversification in the structure of the phylogeny.