Rates of evolution: Is there a conflict between neo-darwinian evolutionary theory and the fossil record?

Neo-darwinian and population genetics theory assumes that the necessary and sufficient set of conditions for all genetic, therefore evolutionary, change has been identified. Punctuationalists have assumed the opposite and cite the fossil record as evidence for change too rapid to be explained in neo-darwinian theory. Data is given here to provide estimates of the rate of evolution in hominid fossils, in living populations, and of that rate which would qualify as punctuational in the hominid fossil record. Evolution in living populations is orders of magnitude greater than that found in the fossil record and far greater than necessary to create apparently instantaneous saltations in the fossil record. It is suggested that such saltations may not represent more rapid rates of evolution but, rather, the persistence of evolutionary change in a given direction for a longer than normal period.     

Positive correlation between diversification rates and phenotypic evolvability can mimic punctuated equilibrium on molecular phylogenies

The hypothesis of punctuated equilibrium proposes that most phenotypic evolution occurs in rapid bursts associated with speciation events. Several methods have been developed that can infer punctuated equilibrium from molecular phylogenies in the absence of paleontological data. These methods essentially test whether the variance in phenotypes among extant species is better explained by evolutionary time since common ancestry or by the number of estimated speciation events separating taxa. However, apparent "punctuational" trait change can be recovered on molecular phylogenies if the rate of phenotypic evolution is correlated with the rate of speciation. Strong support for punctuational models can arise even if the underlying mode of trait evolution is strictly gradual, so long as rates of speciation and trait evolution covary across the branches of phylogenetic trees, and provided that lineages vary in their rate of speciation. Species selection for accelerated rates of ecological or phenotypic divergence can potentially lead to the perception that most trait divergence occurs in association with speciation events.     

Do arms races punctuate evolutionary stasis? Unified insights from phylogeny,phylogeography and microevolutionary processes

One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio , likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae , the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.     

Tempo, mode and phylogenetic associations of relative embryo size evolution in angiosperms

Relative embryo size (E : S, the ratio of embryo to seed) is a key trait related to germination ecology and seed plant evolution. A small, underdeveloped embryo is a primitive feature of angiosperms, which has led to the hypothesis that an evolutionary trend towards increasing E : S has occurred. Here, I examine first the tempo and mode of E : S evolution in angiosperms; then I test for phylogenetic associations of E : S with traits hypothetically related to anagenetic (germination time) and cladogenetic (number of species per family and differential speciation) change, and finally I test the existence of a directional increasing trend in E : S. The analysis of the evolutionary tempo suggests that E : S changed very fast early in evolutionary time and remained stable later, which is consistent with early radiations and fits well with the history of angiosperms consisting of rapid spread associated with great diversification rates soon after their origin. E : S evolution in angiosperms has not followed a punctuational mode of evolution but a scaled-gradualism evolution in which stasis has occurred in longer branches of the phylogeny. An evolutionary trend towards increasing E : S has not been actively driven by anagenesis nor cladogenesis, although large E : S is associated with high levels of diversification (i.e. number of species per family). This rapid ecological diversification occurring in the early radiation probably produced an increasing phenotypic variance in the E : S. Because the ancestral embryo was so small, an increase in variance might have produced a passive trend towards the only direction allowed for the ancestral embryo to evolve. Thus, a passive diffusion away from a lower bound may explain the average increase in E : S.     

Evolution of cytochromec investigated by the maximum parsimony method

Summary Rates of evolution for cytochromec over the past one billion years were calculated from a maximum parsimony dendrogram which approximates the phylogeny of 87 lineages. Two periods of evolutionary acceleration and deceleration apparently occurred for the cytochromec molecule. The tempo of evolutionary change indicated by this analysis was compared to the patterns of acceleration and deceleration in the ancestry of several other proteins The synchrony of these tempos of molecular change supports the notion that rapid genetic evolution accompanied periods of major adaptive radiations.Rates of change at different times in several structural-functional areas of cytochromec were also investigated in order to test the Darwinian hypothesis that during periods of rapid evolution, functional sites accumulate proportionately more substitutions than areas with no known function. Rates of change in four proposed functional groupings of sites were therefore compared to rates in areas of unknown function for several different time periods. This analysis revealed a significant increase in the rate of evolution for sites associated with the regions of cytochromec oxidase and reductase interaction during the period between the emergence of the eutherian ancestor to the emergence of the anthropoid ancestor.     

Inferring evolutionary processes from phylogenies

Evolutionary processes shape the regular trends of evolution and are responsible for the diversity and distribution of contemporary species. They include correlated evolutionary change and trajectories of trait evolution, convergent and parallel evolution, differential rates of evolution, speciation and extinction, the order and direction of change in characters, and the nature of the evolutionary process itself—does change accumulate gradually, episodically, or in punctuational bursts. Phylogenies, in combination with information on species, contain the imprint of these historical evolutionary processes. By applying comparative methods based upon statistical models of evolution to well resolved phylogenies, it is possible to infer the historical evolutionary processes that must have existed in the past, given the patterns of diversity seen in the present. I describe a set of maximum likelihood statistical methods for inferring such processes. The methods estimate parameters of statistical models for inferring correlated evolutionary change in continuously varying characters, for detecting correlated evolution in discrete characters, for estimating rates of evolution, and for investigating the nature of the evolutionary process itself. They also anticipate the wealth of information becoming available to biological scientists from genetic studies that pin down relationships among organisms with unprecedented accuracy.     

Speciational Evolution: a Phylogenetic Test With Allozymes in Sceloporus (Reptilia)

Abstract— The potential role of speciation in accelerating evolutionary divergence remains controversial. Earlier tests based on genetic and morphologic distances which indicated an absence of speciational evolution rely on problematic assumptions. We provide a phylogenetic test in which amounts of discrete character change relative to an outgroup are compared between sister taxa. Although this test is constrained by a need to assume similar extinction rates in groups compared, it provides conceptual improvements regarding monophyly, equal age of taxa, and distribution of homoplasy. Based on analysis of 68 informative allozyme characters for 19 lizard species in the genus Sceloporus , significant speciational evolution and punctuational change is, at least, a viable explanation for the distribution of observed character changes.     

Episodic Evolution of Protein Hormones in Mammals

Pituitary growth hormone (GH) and prolactin have been shown previously to display a pattern of evolution in which episodes of rapid change are imposed on a low underlying basal rate (near-stasis). This study was designed to explore whether a similar pattern is seen in the evolution of other protein hormones in mammals. Seven protein hormones were examined (with the common α-subunit of the glycoprotein hormones providing an additional polypeptide for analysis)—those for which sequences from at least four eutherian orders are available with a suitable non-eutherian outgroup. Six of these (GH, prolactin, insulin, parathyroid hormone, glycoprotein hormone α-subunit, and luteinizing hormone β-subunit) showed markedly variable evolutionary rates in each case with a pattern of a slow basal rate and bursts of rapid change, the precise positions of the bursts varying from protein to protein. Two protein hormones (follicle-stimulating hormone β-subunit and thyroid-stimulating hormone β-subunit) showed no significant rate variation. Based on the sequences currently available, and pooling data from all eight proteins, the phase of slow basal change occupied about 85% of the sampled evolutionary time, but most evolutionary change (about 62% of the substitutions accepted) occurred during the episodes of rapid change. It is concluded that, in mammals at least, a pattern of prolonged periods of near-stasis with occasional episodes of rapid change provides a better model of evolutionary change for protein hormones than the one of constant evolutionary rates that is commonly favored. The mechanisms underlying this episodic evolution are not yet clear, and it may be that they vary from one group to another; in some cases, positive selection appears to underlie bursts of rapid change. Where gene duplication is associated with a period of accelerated evolution this often occurs at the end rather than the beginning of the episode. To what extent the type of pattern seen for protein hormones can be extended to other proteins remains to be established. Received: 10 October 2000 / Accepted: 18 December 2000     

How should we define 'fitness' for general ecological scenarios?

Beginners in life history theory or evolutionary ecology seemingly face a variety of almost unrelated approaches. Yet the biomathematical literature of the last 10-20 years reflects the implicit acceptance of a common evolutionary framework, the core idea being that there exists a unique general fitness measure that concisely summarizes the overall time course of potential invasions by initially rare mutant phenotypes. Using such an invasion criterion to characterize fitness implicitly presupposes a scenario in which, during periods o f clear evolutionary change, the rate of evolution is set primarily by the random occurrence (and initial establishment) of favourable mutations. Evolutionarily stable life history strategies (ESSs) may then be regarded as traps for the evolutionary random walk.     

Assessing rapid evolution in a changing environment

Climate change poses a serious threat to species persistence. Effective modelling of evolutionary responses to rapid climate change is therefore essential. In this review we examine recent advances in phylogenetic comparative methods, techniques normally used to study adaptation over long periods, which allow them to be applied to the study of adaptation over shorter time scales. This increased applicability is largely due to the emergence of more flexible models of character evolution and the parallel development of molecular technologies that can be used to assess adaptive variation at loci scattered across the genome. The merging of phylogenetic and population genetic approaches to the study of adaptation has significant potential to advance our understanding of rapid responses to environmental change.     

Rapid evolution and the convergence of ecological and evolutionary time

Recent studies have documented rates of evolution of ecologically important phenotypes sufficiently fast that they have the potential to impact the outcome of ecological interactions while they are underway. Observations of this type go against accepted wisdom that ecological and evolutionary dynamics occur at very different time scales. While some authors have evaluated the rapidity of a measured evolutionary rate by comparing it to the overall distribution of measured evolutionary rates, we believe that ecologists are mainly interested in rapid evolution because of its potential to impinge on ecological processes. We therefore propose that rapid evolution be defined as a genetic change occurring rapidly enough to have a measurable impact on simultaneous ecological change. Using this definition we propose a framework for decomposing rates of ecological change into components driven by simultaneous evolutionary change and by change in a non‐evolutionary factor (e.g. density dependent population dynamics, abiotic environmental change). Evolution is judged to be rapid in this ecological context if its contribution to ecological change is large relative to the contribution of other factors. We provide a worked example of this approach based on a theoretical predator–prey interaction [ Abrams, P. & Matsuda, H. (1997) . Evolution, 51, 1740], and find that in this system the impact of prey evolution on predator per capita growth rate is 63% that of internal ecological dynamics. We then propose analytical methods for measuring these contributions in field situations, and apply them to two long‐term data sets for which suitable ecological and evolutionary data exist. For both data sets relatively high rates of evolutionary change have been found when measured as character change in standard deviations per generation (haldanes). For Darwin's finches evolving in response to fluctuating rainfall [ Grant, P.R. & Grant, B.R. (2002) . Science, 296, 707], we estimate that evolutionary change has been more rapid than ecological change by a factor of 2.2. For a population of freshwater copepods whose life history evolves in response to fluctuating fish predation [ Hairston, N.G. Jr & Dillon, T.A. (1990) . Evolution, 44, 1796], we find that evolutionary change has been about one quarter the rate of ecological change – less than in the finch example, but nevertheless substantial. These analyses support the view that in order to understand temporal dynamics in ecological processes it is critical to consider the extent to which the attributes of the system under investigation are simultaneously changing as a result of rapid evolution.     

Tempo does not correlate with mode in the fossil record

The dominating view of evolution based on the fossil record is that established species remain more or less unaltered during their existence. Substantial evolution is on the other hand routinely reported for contemporary populations, and most quantitative traits show high potential for evolution. These contrasting observations on long‐ and short‐time scales are often referred to as the paradox of stasis, which rests on the fundamental assumption that periods of morphological stasis in the fossil record represent minimal evolutionary change. Investigating 450 fossil time series, I demonstrate that the nonaccumulating morphological fluctuations during stasis travel similar distances in morphospace compared to lineages showing directional change. Hence, lineages showing stasis are commonly undergoing considerable amounts of evolution, but this evolution does not accumulate to produce large net evolutionary changes over time. Rates of evolutionary change across modes in the fossil record may be more homogenous than previously assumed and advocated, supporting the claim that substantial evolution is not exclusively or causally linked to the process of speciation. Instead of exemplifying minimal evolution, stasis likely represents information on the dynamics of the adaptive landscape on macroevolutionary time scales, including the persistence of adaptive zones and ecological niches over millions of years.     

PHYLOGENETIC ANALYSES OF THE CORRELATED EVOLUTION OF CONTINUOUS CHARACTERS: A SIMULATION STUDY

We use computer simulation to compare the statistical properties of several methods that have been proposed for estimating the evolutionary correlation between two continuous traits, and define alternative evolutionary correlations that may be of interest. We focus on Felsenstein's (1985) method and some variations of it and on several “minimum evolution” methods (of which the procedure of Huey and Bennett [1987] is a special case), as compared with a nonphylogenetic correlation. The last, a simple correlation of trait values across the tips of a phylogeny, virtually always yields inflated Type I error rates, relatively low power, and relatively poor estimates of evolutionary correlations. We therefore cannot recommend its use. In contrast, Felsenstein's (1985) method yields acceptable significance tests, high power, and good estimates of what we term the input correlation and the standardized realized evolutionary correlation, given complete phylogenetic information and knowledge of the rate and mode of character change (e.g., gradual and proportional to time [“Brownian motion”] or punctuational, with change only at speciation events). Inaccurate branch length information may affect any method adversely, but only rarely does it cause Felsenstein's (1985) method to perform worse than do the others tested. Other proposed methods generally yield inflated Type I error rates and have lower power. However, certain minimum evolution methods (although not the specific procedure used by Huey and Bennett [1987]) often provide more accurate estimates of what we term the unstandardized realized evolutionary correlation, and their use is recommended when estimation of this correlation is desired. We also demonstrate how correct Type I error rates can be obtained for any method by reference to an empirical null distribution derived from computer simulations, and provide practical suggestions on choosing an analytical method, based both on the evolutionary correlation of interest and on the availability of branch lengths and knowledge of the model of evolutionary change appropriate for the characters being analyzed. Computer programs that implement the various methods and that will simulate (correlated) character evolution along a known phylogeny are available from the authors on request. These programs can be used to test the effectiveness of any new methods that might be proposed, and to check the generality of our conclusions with regard to other phylogenies.     

Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo,Evo-Eco and Evolutionary Transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.     

Evolutionary rescue can prevent extinction following environmental change

The ubiquity of global change and its impacts on biodiversity poses a clear and urgent challenge for evolutionary biologists. In many cases, environmental change is so widespread and rapid that individuals can neither accommodate to them physiologically nor migrate to a more favourable site. Extinction will ensue unless the population adapts fast enough to counter the rate of decline. According to theory, whether populations can be rescued by evolution depends upon several crucial variables: population size, the supply of genetic variation, and the degree of maladaptation to the new environment. Using techniques in experimental evolution we tested the conditions for evolutionary rescue (ER). Hundreds of yeast populations were exposed to normally lethal concentrations of salt in conditions, where the frequency of rescue mutations was estimated and population size was manipulated. In a striking match with theory, we show that ER is possible, and that the recovery of the population may occur within 25 generations. We observed a clear threshold in population size for ER whereby the ancestral population size must be sufficiently large to counter stochastic extinction and contain resistant individuals. These results demonstrate that rapid evolution is an important component of the response of small populations to environmental change.     

Episodic Evolution of Protein Hormones: Molecular Evolution of Pituitary Prolactin

Previous studies have shown that pituitary growth hormone displays an episodic pattern of evolution, with a slow underlying evolutionary rate and occasional sustained bursts of rapid change. The present study establishes that pituitary prolactin shows a similar pattern. During much of tetrapod evolution the sequence of prolactin has been strongly conserved, showing a slow basal rate of change (approx 0.27 × 10⁹ substitutions/amino acid site/year). This rate has increased substantially (∼12- to 38-fold) on at least four occasions during eutherian evolution, during the evolution of primates, artiodactyls, rodents, and elephants. That these increases are real and not a consequence of inadvertant comparison of paralogous genes is shown (for at least the first three groups) by the fact that they are confined to mature protein coding sequence and not apparent in sequences coding for signal peptides or when synonymous substitutions are examined. Sequences of teleost prolactins differ markedly from those of tetrapods and lungfish, but during the course of teleost evolution the rate of change of prolactin has been less variable than that of growth hormone. It is concluded that the evolutionary pattern seen for prolactin shows long periods of near-stasis interrupted by occasional bursts of rapid change, resembling the pattern seen for growth hormone in general but not in detail. The most likely basis for these bursts appears to be adaptive evolution though the biological changes involved are relatively small. Received: 31 August 1999 / Accepted: 9 February 2000     

GRADUAL VERSUS PUNCTUATED EQUILIBRIUM EVOLUTION IN THE TURKANA BASIN MOLLUSCS: EVOLUTIONARY EVENTS OR BIOLOGICAL INVASIONS?

A running controversy in evolutionary thought was Eldredge and Gould's punctuated equilibrium model, which proposes long periods of morphological stasis interspersed with rapid bursts of dramatic evolutionary change. One of the earliest and most iconic pieces of research in support of punctuated equilibrium is the work of Williamson on the Plio-Pleistocene molluscs of the Turkana Basin. Williamson claimed to have found firm evidence for three episodes of rapid evolutionary change separated by long periods of stasis in a high-resolution sequence. Most of the discussions following this report centered on the topics of (eco)phenotype versus genotype and the possible presence of preservational and temporal artifacts. The debate proved inconclusive, leaving Williamson's reports as one of the empirical foundations of the paradigm of punctuated equilibrium. Here we conclusively show Williamson's original interpretations to be highly flawed. The supposed rapid bursts of punctuated evolutionary change represent artifacts resulting from the invasion of extrabasinal faunal elements in the Turkana palaeolakes during wet phases well known from elsewhere in Africa.     

Genes,culture, and the human niche: An overview

The sharp distinction between biological traits and culturally based traits, which had long been standard in evolutionary approaches to behavior, was blurred in the early 1980s by mathematical models that allowed a co‐dependent evolution of genetic transmission and cultural information. Niche‐construction theory has since added another contrast to standard evolutionary theory, in that it views niche construction as a cause of evolutionary change rather than simply a product of selection. While offering a new understanding of the coevolution of genes, culture, and human behavior, niche‐construction models also invoke multivariate causality, which require multiple time series to resolve. The empirical challenge lies in obtaining time‐series data on causal pathways involved in the coevolution of genes, culture, and behavior. This is a significant issue in archeology, where time series are often sparse and causal behaviors are represented only by proxies in the material record.     

Digest: Disentangled bank: Less diverse urban environments modify the shape and magnitude of natural selection*

Urbanization provides a natural experiment for biologists to test how anthropogenic environmental change affects evolution in real time and frames predictions for anticipated evolutionary outcomes worldwide. Start et al. ( 2018 ) found that changes in species interactions (herbivore abundance and avian predation) along urbanization gradients predictably alter the shape and magnitude of natural selection on gall size (a defensive trait), suggesting that rapid global environmental change can alter species interactions, which may have foreseeable evolutionary consequences.     

THE ACCURACY OF PHYLOGENETIC ESTIMATION USING THE NEIGHBOR-JOINING METHOD

We studied the factors affecting the accuracy of the neighbor-joining (NJ) method for estimating phylogenies by simulating character change under different evolutionary models applied to twenty different 8-OTU tree topologies that varied widely with respect to tree imbalance and stemminess. The models incorporated three evolutionary rates—constant, varying among lineages, varying among characters—and three evolutionary contexts concerning patterns of character change relative to speciation events—phyletic, speciational, and punctuational. All combinations of the rate and context models were studied. In addition, three different absolute rates of change were investigated. To measure the accuracy, the strict consensus index was computed between the estimated tree and the tree topology along which the data had been generated. The results were analyzed by analysis of variance and compared to a previous study that evaluated UPGMA clustering and maximum parsimony (MP) as phylogenetic estimation techniques. We found evolutionary context and tree imbalance to be the most important factors affecting the accuracy of the NJ method. NJ was more accurate than UPGMA or MP in terms of the average strict consensus index over all treatments. However, no one method was more accurate than the other two for all combinations of treatments. Higher absolute rate of change generally resulted in higher accuracy for all three methods.