Rates Of Phenotypic Change Research Articles

Oldest record of a crown anomaluroid rodent from sub-Saharan Africa: a new genus and species from the early Oligocene Topernawi formation of northern Kenya

ABSTRACT Anomaluroid rodents (i.e. Anomaluridae + Zenkerellidae) have a long evolutionary history in Africa dating back to at least the middle Eocene, but Palaeogene fossil members of the anomaluroid crown group have never been found south of the Sahara. Here, we describe the oldest crown anomaluroid from sub-Saharan Africa, Eliwourus topernawiensis (new genus and species) from the early Oligocene Topernawi Formation of northern Kenya. Bayesian phylogenetic tip-dating analysis of a combined molecular-morphological dataset places ~29.5 Ma Eliwourus as an advanced stem anomalurid, and suggests that crown Anomaluridae originated ~28.2 Ma. The gliding behaviour seen in all crown anomalurids had, therefore, likely evolved before the close of the early Oligocene. Bayesian geocoordinates analysis places the origin of crown Anomaluroidea (~47.2 Ma) in northern Africa, and identifies a stem anomalurid dispersal into equatorial eastern Africa in the latest Eocene or earliest Oligocene. We present the first quantitative analysis of the pace of anomaluroid dental evolution and confirm a remarkably slow or bradytelic rate of phenotypic change, despite significant transformations in postcranial morphology related to the evolution of gliding behaviour during the same interval. The Topernawi area was evidently sufficiently forested during the early Oligocene to support both arboreal rodents and primates.

Body size predicts the rate of contemporary morphological change in birds

Variation in evolutionary rates among species is a defining characteristic of the tree of life and may be an important predictor of species' capacities to adapt to rapid environmental change. It is broadly assumed that generation length is an important determinant of microevolutionary rates, and body size is often used as a proxy for generation length. However, body size has myriad biological correlates that could affect evolutionary rates independently from generation length. We leverage two large, independently collected datasets on recent morphological change in birds (52 migratory species breeding in North America and 77 South American resident species) to test how body size and generation length are related to the rates of contemporary morphological change. Both datasets show that birds have declined in body size and increased in wing length over the past 40y. We found, in both systems, a consistent pattern wherein smaller species declined proportionally faster in body size and increased proportionally faster in wing length. By contrast, generation length explained less variation in evolutionary rates than did body size. Although the mechanisms warrant further investigation, our study demonstrates that body size is an important predictor of contemporary variation in morphological rates of change. Given the correlations between body size and a breadth of morphological, physiological, and ecological traits predicted to mediate phenotypic responses to environmental change, the relationship between body size and rates of phenotypic change should be considered when testing hypotheses about variation in adaptive responses to climate change.

Deep phenotyping and lifetime trajectories reveal limited effects of longevity regulators on the aging process in C57BL/6J mice

Current concepts regarding the biology of aging are primarily based on studies aimed at identifying factors regulating lifespan. However, lifespan as a sole proxy measure for aging can be of limited value because it may be restricted by specific pathologies. Here, we employ large-scale phenotyping to analyze hundreds of markers in aging male C57BL/6J mice. For each phenotype, we establish lifetime profiles to determine when age-dependent change is first detectable relative to the young adult baseline. We examine key lifespan regulators (putative anti-aging interventions; PAAIs) for a possible countering of aging. Importantly, unlike most previous studies, we include in our study design young treated groups of animals, subjected to PAAIs prior to the onset of detectable age-dependent phenotypic change. Many PAAI effects influence phenotypes long before the onset of detectable age-dependent change, but, importantly, do not alter the rate of phenotypic change. Hence, these PAAIs have limited effects on aging.

Terrestrial reproduction and parental care drive rapid evolution in the trade-off between offspring size and number across amphibians

The trade-off between offspring size and number is central to life history strategies. Both the evolutionary gain of parental care or more favorable habitats for offspring development are predicted to result in fewer, larger offspring. However, despite much research, it remains unclear whether and how different forms of care and habitats drive the evolution of the trade-off. Using data for over 800 amphibian species, we demonstrate that, after controlling for allometry, amphibians with direct development and those that lay eggs in terrestrial environments have larger eggs and smaller clutches, while different care behaviors and adaptations vary in their effects on the trade-off. Specifically, among the 11 care forms we considered at the egg, tadpole and juvenile stage, egg brooding, male egg attendance, and female egg attendance increase egg size; female tadpole attendance and tadpole feeding decrease egg size, while egg brooding, tadpole feeding, male tadpole attendance, and male tadpole transport decrease clutch size. Unlike egg size that shows exceptionally high rates of phenotypic change in just 19 branches of the amphibian phylogeny, clutch size has evolved at exceptionally high rates in 135 branches, indicating episodes of strong selection; egg and tadpole environment, direct development, egg brooding, tadpole feeding, male tadpole attendance, and tadpole transport explain 80% of these events. By explicitly considering diversity in parental care and offspring habitat by stage of offspring development, this study demonstrates that more favorable conditions for offspring development promote the evolution of larger offspring in smaller broods and reveals that the diversity of parental care forms influences the trade-off in more nuanced ways than previously appreciated.

The pace of modern life, revisited.

Wild populations must continuously respond to environmental changes or they risk extinction. Those responses can be measured as phenotypic rates of change, which can allow us to predict contemporary adaptive responses, some of which are evolutionary. About two decades ago, a database of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this database to examine phenotypic responses to specific types of human disturbance. Here, we update the database by adding 5675 new estimates of phenotypic change. Using this newer version of the data base, now containing 7338 estimates of phenotypic change, we revisit the conclusions of four published articles. We then synthesize the expanded database to compare rates of change across different types of human disturbance. Analyses of this expanded database suggest that: (i) a small absolute difference in rates of change exists between human disturbed and natural populations, (ii) harvesting by humans results in higher rates of change than other types of disturbance, (iii) introduced populations have increased rates of change, and (iv) body size does not increase through time. Thus, findings from earlier analyses have largely held-up in analyses of our new database that encompass a much larger breadth of species, traits, and human disturbances. Lastly, we use new analyses to explore how various types of human disturbances affect rates of phenotypic change, and we call for this database to serve as a steppingstone for further analyses to understand patterns of contemporary phenotypic change.

Human face‐off: a new method for mapping evolutionary rates on three‐dimensional digital models

AbstractModern phylogenetic comparative methods allow us to estimate evolutionary rates of phenotypic change, how these rates differ across clades, and to assess whether the rates remained constant over time. Unfortunately, currently available phylogenetic comparative tools express the rate in terms of a scalar dimension, and do not allow us to determine rate variations among different parts of a single, complex phenotype, or chart realized rate variation directly onto the phenotype. We present a new method which allows the mapping of evolutionary rate variation directly onto three‐dimensional phenotypes, informing on the direction and magnitude of trait change automatically. Implemented using the function rate.map embedded in the R package RRphylo, this method is based on phylogenetic ridge regression rate estimates. Since the latter represent ridge regression slopes, they possess sign and magnitude. In RRphylo, different rates are calculated for different districts of the phenotype, which can then be visualized directly onto the phenotype itself. We present the application of rate.map to the evolution of facial skeleton in Hominoidea, the primate clade inclusive of Homo and the greater apes (including living and fossil taxa). We found that the highly derived, unique shape of the face in modern humans evolved through rapid phenotypic changes affecting the nasal bones, the brow ridge and the maxillary region. The canine fossa, a facial feature unique to Homo sapiens, did not belong to a region of rapid phenotypic change, and could be seen as the by‐product of midface evolution as suggested by previous studies.

Evolutionary and Plastic Phenotypic Change Can Be Just as Fast as Changes in Population Densities.

AbstractEvolution and plasticity can drive population-level phenotypic change (e.g., changes in the mean phenotype) on timescales comparable to changes in population densities. However, it is unclear whether phenotypic change has the potential to be just as fast as changes in densities or whether comparable rates of change occur only when densities are changing slow enough for phenotypes to keep pace. Moreover, it is unclear whether this depends on the mode of adaptation. Using scaling theory and fast-slow dynamical systems theory, we develop a method for comparing maximum rates of density and phenotypic change estimated from population-level time-series data. We apply our method to 30 published empirical studies where changes in morphological traits are caused by evolution, plasticity, or an unknown combination. For every study, the maximum rate of phenotypic change was between 0.5 and 2.5 times faster than the maximum rate of change in density. Moreover, there were no systematic differences between systems with different modes of adaptation. Our results show that plasticity and evolution can drive phenotypic change just as fast as changes in densities. We discuss the implications of our results in terms of the strengths of feedbacks between population densities and traits.

Taxon incompleteness and discrete time bins affect character change rates in simulated data.

Estimating how fast or slow morphology evolves through time (phenotypic change rate, PR) has become common in macroevolutionary studies and has been important for clarifying key evolutionary events. However, the inclusion of incompletely scored taxa (e.g. fossils) and variable lengths of discrete arbitrary time bins could affect PR estimates and potentially mask real PR patterns. Here, the impact of taxon incompleteness (unscored data) on PR estimates is assessed in simulated data. Three different time bin series were likewise evaluated: bins evenly spanning the tree length (i), a shorter middle bin and longer first and third bins (ii), and a longer middle bin and shorter first and third bins (iii). The results indicate that PR values decrease as taxon incompleteness increases. Statistically significant PR values, and the dispersion among PR values, depended on the time bins. These outcomes imply that taxon incompleteness can undermine our capacity to infer morphology evolutionary dynamics and that these estimates are also influenced by our choice of discrete time bins. More importantly, the present results stress the need for a better approach to deal with taxon incompleteness and arbitrary discrete time bins.

Recent spread of blue tits into the Barcelona urban environment: morphological differences and the role of balanced dispersal

Rates of phenotypic change are greater in cities than in any other habitat. Consequently, urban habitats are an ideal experimental area to study contemporary evolution and adaptation. A key question related to phenotypic changes in urban animals relates to the patterns of gene flow between the city and the natural habitats surrounding cities, but the results obtained thus far have been contradictory. The aim of this study was to analyze genetic differentiation and patterns of gene flow and size variation in urban blue tits Cyanistes caeruleus in Barcelona city, using a panel of 26 microsatellites. We compared birds from one locality at the city center, one at the suburban area, and one in a nearby forest. We found a significant genetic differentiation between the populations, which has evolved over a period of about 35 generations (50 years), based on historical data. There was significant gene flow between all populations. There was no significant asymmetric gene flow between the forest and the other two populations, which is consistent with balanced gene flow and dispersal. City birds were smaller than individuals from the forest. Simulations showed that the selection required to achieve these phenotypic differences would have to be high, which in turn suggests that phenotype-dependent dispersal may be involved.

Asymptotic analysis of selection-mutation models in the presence of multiple fitness peaks

We study the long-time behaviour of phenotype-structured models describing the evolutionary dynamics of asexual populations whose phenotypic fitness landscape is characterised by multiple peaks. First we consider the case where phenotypic changes do not occur, and then we include the effect of heritable phenotypic changes. In the former case the model is formulated as an integrodifferential equation for the phenotype distribution of the individuals in the population, whereas in the latter case the evolution of the phenotype distribution is governed by a non-local parabolic equation whereby a linear diffusion operator captures the presence of phenotypic changes. We prove that the long-time limit of the solution to the integrodifferential equation is unique and given by a measure consisting of a weighted sum of Dirac masses centred at the peaks of the phenotypic fitness landscape. We also derive an explicit formula to compute the weights in front of the Dirac masses. Moreover, we demonstrate that the long-time solution of the non-local parabolic equation exhibits a qualitatively similar behaviour in the asymptotic regime where the diffusion coefficient modelling the rate of phenotypic change tends to zero. However, we show that the limit measure of the non-local parabolic equation may consist of less Dirac masses, and we provide a sufficient criterion to identify the positions of their centres. Finally, we carry out a detailed characterisation of the speed of convergence of the integral of the solution (i.e. the population size) to its long-time limit for both models. Taken together, our results support a more in-depth theoretical understanding of the conditions leading to the emergence of stable phenotypic polymorphism in asexual populations.

Meta-analysis Shows That Rapid Phenotypic Change in Angiosperms in Response to Environmental Change Is Followed by Stasis.

The amount and rate of phenotypic change at ecological timescales varies widely, but there has not been a comprehensive quantitative synthesis of the patterns and causes of such variation for plants. Present knowledge is based predominantly on animals, whose differences with plants in the origin of germ cells and the level of modularity (among others) could make it invalid for plants. We synthesized data on contemporary phenotypic responses of angiosperms to environmental change and show that if extinction does not occur, quantitative traits change quickly in the first few years following the environmental novelty and then remain stable. This general pattern is independent from life span, growth form, spatial scale, or the type of trait. Our work shows that high amounts and rates of phenotypic change at contemporary timescales observed in plants are consistent with the pattern of stasis and bounded evolution previously observed over longer time frames. We also found evidence that may contradict some common ideas about phenotypic evolution: (1) the total amount of phenotypic change observed does not differ significantly according to growth form or life span; (2) greater and faster divergence tends to occur between populations connected at the local scale, where gene flow could be intense, rather than between distant populations; and (3) traits closely related to fitness change as much and as fast as other traits.

Genetic and environmental architecture of processing speed across midlife.

Processing Speed (PS) is an important domain in cognitive aging that is characterized by multiple related but nonidentical abilities. Few studies have directly investigated the relationships among PS measures, and none have used genetically informed methods. In this study, we examined the relationship between measures of PS at up to two time points during middle age. We examined data from 1,262 middle-aged men when the sample was at a mean age of 56 and a mean age 62 years. Participants completed 6 measures of PS from three different cognitive tests. We used a genetically informative, confirmatory factor analytic approach to evaluate the phenotypic and genetic relationships cross-sectionally at both single time points and across time. A higher-order common PS factor accounted for the covariance among three test-specific factors, and each test-specific factor accounted for the covariance between two observed measures. The general PS factor was explained primarily by genetic influences at both time points (a²age56 = .75, a²age62 = .64), and all test-specific factors were heritable (a² range: .45 to .65). Factor loadings from the test-specific factors to the general PS factor varied from λ = .46 to .82. The model was stable over time, although there were differing rates of phenotypic change among latent factors (.20 SD to .44 SD). Cross-time genetic correlations were near unity for all latent factors. These results suggest that PS is highly heritable when considered at a latent variable level, and that there are different rates of change in tests of PS within this sample. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 34 primate species

We conducted a comparative analysis of primate cerebral size and neocortical folding using magnetic resonance imaging data from 65 individuals belonging to 34 different species. We measured several neocortical folding parameters and studied their evolution using phylogenetic comparative methods. Our results suggest that the most likely model for neuroanatomical evolution is one where differences appear randomly (the Brownian Motion model), however, alternative models cannot be completely ruled out. We present estimations of the ancestral primate phenotypes as well as estimations of the rates of phenotypic change. Based on the Brownian Motion model, the common ancestor of primates may have had a folded cerebrum similar to that of a small lemur such as the aye-aye. Finally, we observed a non-linear relationship between fold wavelength and fold depth with cerebral volume. In particular, gyrencephalic primate neocortices across different groups exhibited a strikingly stable fold wavelength of about 12 mm (±20%), despite a 20-fold variation in cerebral volume. We discuss our results in the context of current theories of neocortical folding.

Predicting the evolutionary consequences of trophy hunting on a quantitative trait

ABSTRACTSome ecologists suggest that trophy hunting (e.g., harvesting males with a desirable trait above a certain size) can lead to rapid phenotypic change, which has led to an ongoing discussion about evolutionary consequences of trophy hunting. Claims of rapid evolution come from the statistical analyses of data, with no examination of whether these results are theoretically plausible. We constructed simple quantitative genetic models to explore how a range of hunting scenarios affects the evolution of a trophy such as horn length. We show that trophy hunting does lead to trophy evolution defined as change in the mean breeding value of the trait. However, the fastest rates of phenotypic change attributable to trophy hunting via evolution that are theoretically possible under standard assumptions of quantitative genetics are 1–2 orders of magnitude slower than the fastest rates of phenotypic change reported from statistical analyses. Our work suggests a re‐evaluation of the likely evolutionary consequences of trophy hunting would be appropriate when setting policy. Our work does not consider the ethical or ecological consequences of trophy hunting. © 2017 The Wildlife Society.

The combined effects of temporal autocorrelation and the costs of plasticity on the evolution of plasticity.

Adaptive phenotypic plasticity is an important source of intraspecific variation, and for many plastic traits, the costs or factors limiting plasticity seem cryptic. However, there are several different factors that may constrain the evolution of plasticity, but few models have considered costs and limiting factors simultaneously. Here we use a simulation model to investigate how the optimal level of plasticity in a population depends on a fixed maintenance fitness cost for plasticity or an incremental fitness cost for producing a plastic response in combination with environmental unpredictability (environmental fluctuation speed) limiting plasticity. Our model identifies two mechanisms that act, almost separately, to constrain the evolution of plasticity: (i) the fitness cost of plasticity scaled by the nonplastic environmental tolerance, and (ii) the environmental fluctuation speed scaled by the rate of phenotypic change. That is, the evolution of plasticity is constrained by the high cost of plasticity in combination with high tolerance for environmental variation, or fast environmental changes in combination with slow plastic response. Qualitatively similar results are found when maintenance and incremental fitness costs of plasticity are incorporated, although a larger degree of plasticity is selected for with an incremental cost. Our model highlights that it is important to consider direct fitness costs and phenotypic limitations in relation to nonplastic environmental tolerance and environmental fluctuations, respectively, to understand what constrains the evolution of phenotypic plasticity.

Global urban signatures of phenotypic change in animal and plant populations.

Humans challenge the phenotypic, genetic, and cultural makeup of species by affecting the fitness landscapes on which they evolve. Recent studies show that cities might play a major role in contemporary evolution by accelerating phenotypic changes in wildlife, including animals, plants, fungi, and other organisms. Many studies of ecoevolutionary change have focused on anthropogenic drivers, but none of these studies has specifically examined the role that urbanization plays in ecoevolution or explicitly examined its mechanisms. This paper presents evidence on the mechanisms linking urban development patterns to rapid evolutionary changes for species that play important functional roles in communities and ecosystems. Through a metaanalysis of experimental and observational studies reporting more than 1,600 phenotypic changes in species across multiple regions, we ask whether we can discriminate an urban signature of phenotypic change beyond the established natural baselines and other anthropogenic signals. We then assess the relative impact of five types of urban disturbances including habitat modifications, biotic interactions, habitat heterogeneity, novel disturbances, and social interactions. Our study shows a clear urban signal; rates of phenotypic change are greater in urbanizing systems compared with natural and nonurban anthropogenic systems. By explicitly linking urban development to traits that affect ecosystem function, we can map potential ecoevolutionary implications of emerging patterns of urban agglomerations and uncover insights for maintaining key ecosystem functions upon which the sustainability of human well-being depends.

Why are estimates of the strength and direction of natural selection from wild populations not congruent with observed rates of phenotypic change?

Observing adaptive evolution is difficult. In the fossil record, phenotypic evolution happens much more slowly than in artificial selection experiments or in experimental evolution. Yet measures of selection on phenotypic traits, with high heritabilities, suggest that phenotypic evolution should also be rapid in the wild, and this discrepancy often remains even after accounting for correlations between different traits (i.e. making predictions using the multivariate version of the breeder's equation). Are fitness correlations with quantitative traits adequate measures of selection in the wild? We should instead view fitnesses as average properties of genotypes, while acknowledging that they can be environment-dependent. Populations will tend to remain at fitness equilibria, once these are attained, and phenotypes will then be stable. Thus, studying the causes of adaptive change at a genotypic rather than phenotypic level may reveal that, typically, it is occurring too slowly to be easily observed.

Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli

The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By sampling the solution space of E. coli's metabolic network, we show that empirical growth rate distributions recently obtained in experiments at single-cell resolution can be explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the higher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of a large bacterial population that captures this trade-off. The scaling relationships observed in experiments encode, in such frameworks, for the same distance from the maximum achievable growth rate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being grounded on genome-scale metabolic network reconstructions, these results allow for multiple implications and extensions in spite of the underlying conceptual simplicity.

Stability and acceleration of phenotypic evolution in spiny rats (Trinomys, Echimyidae) across different environments

Trinomys is a very diverse mammalian genus of eastern Brazil, comprising ten species. Eight of them have remained in their original biome, the Atlantic Forest, while two others occupy the semi-arid Caatinga. One of the species from the Atlantic Forest, T. eliasi, also inhabits adjacent restingas, an open vegetation ecosystem on sandy sediments of marine origin. Here we assess the impact of colonization of very different environments on the rates of phenotypic change in Trinomys. Multivariate analyses showed that species that had remained in the Atlantic Forest maintained a strong cohesion in skull shape and size. By contrast, colonization of the Caatinga was associated with remarkable differentiation and a strong increase in the rates of phenotypic change, 7–17 times higher than in the Atlantic Forest. Trinomys eliasi from restinga differed from forest samples and other species by a recent change in morphology. Our findings showed that occupation of remarkably different ecosystems had a significant impact in the phenotypic evolution of Trinomys.

Trajectories of the healthy ageing phenotype among middle-aged and older Britons, 2004–2013

ObjectivesSince the ageing population demands a response to ensure older people remain healthy and active, we studied the dynamics of a recently proposed healthy ageing phenotype. We drew the phenotype’s trajectories and tested whether their levels and rates of change are influenced by health behaviours, comorbidities and socioeconomic positions earlier in the life course. Design and outcomesThe English Longitudinal Ageing Study, a prospective, nationally representative sample of people aged ≥50 years, measured a set of eight biomarkers which make up the outcome of the healthy ageing phenotype three times over nearly a decade (N2004=5009, N2008=5301, N2013=4455). A cluster of health behaviours, comorbidities and socioeconomic positions were also measured repeatedly. We assessed the phenotype’s distribution non-parametrically, then fitted linear mixed models to phenotypic change and further examined time interactions with gender and socioeconomic position. We ran additional analyses to test robustness. ResultsWomen had a wider distribution of the healthy ageing phenotype than men had. The phenotype declined annually by −0.242 (95% confidence interval [CI]: −0.352, −0.131). However, there was considerable heterogeneity in the levels and rates of phenotypic change. Women started at higher levels, then declined more steeply by −0.293 (CI: −0.403, −0.183) annually, leading to crossover in the trajectories. Smoking and physical activity assessed on the Allied Dunbar scale were strongly associated with the trajectories. ConclusionThough marked by secular decline, the trajectories of the healthy ageing phenotype showed distinct socioeconomic gradients. The trajectories were also susceptible to variations in health behaviours, strengthening the case for serial interventions to attain healthy and active ageing.