Models Of Phenotypic Evolution Research Articles

Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates.

Key innovations provide ecological opportunity by enabling access to new resources, colonization of new environments, and are associated with adaptive radiation. The most well-known pattern associated with adaptive radiation is an early burst of phenotypic diversification. Venoms facilitate prey capture and are widely believed to be key innovations leading to adaptive radiation. However, few studies have estimated their evolutionary rate dynamics. Here, we test for patterns of adaptive evolution in venom gene expression data from 52 venomous snake species. By identifying shifts in tempo and mode of evolution along with models of phenotypic evolution, we show that snake venom exhibits the macroevolutionary dynamics expected of key innovations. Namely, all toxin families undergo shifts in their rates of evolution, likely in response to changes in adaptive optima. Furthermore, we show that rapid-pulsed evolution modelled as a Lévy process better fits snake venom evolution than conventional early burst or Ornstein–Uhlenbeck models. While our results support the idea of snake venom being a key innovation, the innovation of venom chemistry lacks clear mechanisms that would lead to reproductive isolation and thus adaptive radiation. Therefore, the extent to which venom directly influences the diversification process is still a matter of contention.

Does assortative mating lead to a polymorphic population? A toy model justification

We consider a model of phenotypic evolution in populations with assortative mating of individuals. The model is given by a nonlinear operator acting on the space of probability measures and describes the relation between parental and offspring trait distributions. We study long-time behavior of trait distribution and show that it converges to a combination of Dirac measures. This result means that assortative mating can lead to a polymorphic population and sympatric speciation.

What defines an adaptive radiation? Macroevolutionary diversification dynamics of an exceptionally species-rich continental lizard radiation.

BackgroundAdaptive radiation theory posits that ecological opportunity promotes rapid proliferation of phylogenetic and ecological diversity. Given that adaptive radiation proceeds via occupation of available niche space in newly accessed ecological zones, theory predicts that: (i) evolutionary diversification follows an ‘early-burst’ process, i.e., it accelerates early in the history of a clade (when available niche space facilitates speciation), and subsequently slows down as niche space becomes saturated by new species; and (ii) phylogenetic branching is accompanied by diversification of ecologically relevant phenotypic traits among newly evolving species. Here, we employ macroevolutionary phylogenetic model-selection analyses to address these two predictions about evolutionary diversification using one of the most exceptionally species-rich and ecologically diverse lineages of living vertebrates, the South American lizard genus Liolaemus.ResultsOur phylogenetic analyses lend support to a density-dependent lineage diversification model. However, the lineage through-time diversification curve does not provide strong support for an early burst. In contrast, the evolution of phenotypic (body size) relative disparity is high, significantly different from a Brownian model during approximately the last 5 million years of Liolaemus evolution. Model-fitting analyses also reject the ‘early-burst’ model of phenotypic evolution, and instead favour stabilizing selection (Ornstein-Uhlenbeck, with three peaks identified) as the best model for body size diversification. Finally, diversification rates tend to increase with smaller body size.ConclusionsLiolaemus have diversified under a density-dependent process with slightly pronounced apparent episodic pulses of lineage accumulation, which are compatible with the expected episodic ecological opportunity created by gradual uplifts of the Andes over the last ~25My. We argue that ecological opportunity can be strong and a crucial driver of adaptive radiations in continents, but may emerge less frequently (compared to islands) when major events (e.g., climatic, geographic) significantly modify environments. In contrast, body size diversification conforms to an Ornstein-Uhlenbeck model with multiple trait optima. Despite this asymmetric diversification between both lineages and phenotype, links are expected to exist between the two processes, as shown by our trait-dependent analyses of diversification. We finally suggest that the definition of adaptive radiation should not be conditioned by the existence of early-bursts of diversification, and should instead be generalized to lineages in which species and ecological diversity have evolved from a single ancestor.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0435-9) contains supplementary material, which is available to authorized users.

Selection towards different adaptive optima drove the early diversification of locomotor phenotypes in the radiation of Neotropical geophagine cichlids

BackgroundSimpson envisaged a conceptual model of adaptive radiation in which lineages diversify into “adaptive zones” within a macroevolutionary adaptive landscape. However, only a handful of studies have empirically investigated this adaptive landscape and its consequences for our interpretation of the underlying mechanisms of phenotypic evolution. In fish radiations the evolution of locomotor phenotypes may represent an important dimension of ecomorphological diversification given the implications of locomotion for feeding and habitat use. Neotropical geophagine cichlids represent a newly identified adaptive radiation and provide a useful system for studying patterns of locomotor diversification and the implications of selective constraints on phenotypic divergence in general.ResultsWe use multivariate ordination, models of phenotypic evolution and posterior predictive approaches to investigate the macroevolutionary adaptive landscape and test for evidence of early divergence of locomotor phenotypes in Geophagini. The evolution of locomotor phenotypes was characterized by selection towards at least two distinct adaptive peaks and the early divergence of modern morphological disparity. One adaptive peak included the benthic and epibenthic invertivores and was characterized by fishes with deep, laterally compressed bodies that optimize precise, slow-swimming manoeuvres. The second adaptive peak resulted from a shift in adaptive optima in the species-rich ram-feeding/rheophilic Crenicichla-Teleocichla clade and was characterized by species with streamlined bodies that optimize fast starts and rapid manoeuvres. Evolutionary models and posterior predictive approaches favoured an early shift to a new adaptive peak over decreasing rates of evolution as the underlying process driving the early divergence of locomotor phenotypes.ConclusionsThe influence of multiple adaptive peaks on the divergence of locomotor phenotypes in Geophagini is compatible with the expectations of an ecologically driven adaptive radiation. This study confirms that the diversification of locomotor phenotypes represents an important dimension of phenotypic evolution in the geophagine adaptive radiation. It also suggests that the commonly observed early burst of phenotypic evolution during adaptive radiations may be better explained by the concentration of shifts to new adaptive peaks deep in the phylogeny rather than overall decreasing rates of evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0348-7) contains supplementary material, which is available to authorized users.

Emergence of cytotoxic resistance in cancer cell populations*

We formulate an individual-based model and an integro-differential model of phenotypic evolution, under cytotoxic drugs, in a cancer cell population structured by the expression levels of survival-potential and proliferation-potential. We apply these models to a recently studied experimental system. Our results suggest that mechanisms based on fundamental laws of biology can reversibly push an actively-proliferating, and drug-sensitive, cell population to transition into a weakly-proliferative and drug-tolerant state, which will eventually facilitate the emergence of more potent, proliferating and drug-tolerant cells.

Effects of allometry, productivity and lifestyle on rates and limits of body size evolution

Body size affects nearly all aspects of organismal biology, so it is important to understand the constraints and dynamics of body size evolution. Despite empirical work on the macroevolution and macroecology of minimum and maximum size, there is little general quantitative theory on rates and limits of body size evolution. We present a general theory that integrates individual productivity, the lifestyle component of the slow-fast life-history continuum, and the allometric scaling of generation time to predict a clade's evolutionary rate and asymptotic maximum body size, and the shape of macroevolutionary trajectories during diversifying phases of size evolution. We evaluate this theory using data on the evolution of clade maximum body sizes in mammals during the Cenozoic. As predicted, clade evolutionary rates and asymptotic maximum sizes are larger in more productive clades (e.g. baleen whales), which represent the fast end of the slow-fast lifestyle continuum, and smaller in less productive clades (e.g. primates). The allometric scaling exponent for generation time fundamentally alters the shape of evolutionary trajectories, so allometric effects should be accounted for in models of phenotypic evolution and interpretations of macroevolutionary body size patterns. This work highlights the intimate interplay between the macroecological and macroevolutionary dynamics underlying the generation and maintenance of morphological diversity.

INTERACTING PHENOTYPES AND THE EVOLUTIONARY PROCESS: I. DIRECT AND INDIRECT GENETIC EFFECTS OF SOCIAL INTERACTIONS.

Interacting phenotypes are traits whose expression is affected by interactions with conspecifics. Commonly-studied interacting phenotypes include aggression, courtship, and communication. More extreme examples of interacting phenotypes-traits that exist exclusively as a product of interactions-include social dominance, intraspecific competitive ability, and mating systems. We adopt a quantitative genetic approach to assess genetic influences on interacting phenotypes. We partition genetic and environmental effects so that traits in conspecifics that influence the expression of interacting phenotypes are a component of the environment. When the trait having the effect is heritable, the environmental influence arising from the interaction has a genetic basis and can be incorporated as an indirect genetic effect. However, because it has a genetic basis, this environmental component can evolve. Therefore, to consider the evolution of interacting phenotypes we simultaneously consider changes in the direct genetic contributions to a trait (as a standard quantitative genetic approach would evaluate) as well as changes in the environmental (indirect genetic) contribution to the phenotype. We then explore the ramifications of this model of inheritance on the evolution of interacting phenotypes. The relative rate of evolution in interacting phenotypes can be quite different from that predicted by a standard quantitative genetic analysis. Phenotypic evolution is greatly enhanced or inhibited depending on the nature of the direct and indirect genetic effects. Further, unlike most models of phenotypic evolution, a lack of variation in direct genetic effects does not preclude evolution if there is genetic variance in the indirect genetic contributions. The available empirical evidence regarding the evolution of behavior expressed in interactions, although limited, supports the predictions of our model.

Pleiotropic overdominance and the maintenance of genetic variation in polygenic characters.

A model of selection is described in which optimizing phenotypic selection is combined with pleiotropic overdominance. Thus, the role that mutation commonly plays in models of phenotypic evolution is replaced by balancing selection. Expressions are provided for the equilibrium genetic variance in phenotype and for the heterozygosity. An approximate analysis of the transient properties of the model shows that, in certain circumstances, the behavior is quite similar to that of models based on the interaction of mutation and selection.