Folmer Bokma

DETECTION OF “PUNCTUATED EQUILIBRIUM” BY BAYESIAN ESTIMATION OF SPECIATION AND EXTINCTION RATES, ANCESTRAL CHARACTER STATES, AND RATES OF ANAGENETIC AND CLADOGENETIC EVOLUTION ON A MOLECULAR PHYLOGENY

Abstract Algorithms are presented to simultaneously estimate probabilities of speciation and extinction, rates of anagenetic and cladogenetic phenotypic evolution, as well as ancestral character states, from a complete ultrametric species-level phylogeny with dates assigned to all bifurcations and one or more phenotypes in three or more extant species, using Metropolis–Hastings Markov Chain Monte Carlo sampling. The algorithms also estimate missing phenotypes of extant species and numbers of speciation events that occurred on all branches of the phylogeny. The algorithms are discussed and their performance is evaluated using simulated data. That evaluation shows that precise estimation of rates of evolution of one or a few phenotypes requires large phylogenies. Estimation accuracy improves with the number of species on the phylogeny.

Extant mammal body masses suggest punctuated equilibrium

Is gradual microevolutionary change within species simultaneously the source of macroevolutionary differentiation between species? Since its first publication, Darwins original idea that phenotypic differences between species develop gradually over time, as the accumulation of small selection-induced changes in successive generations has been challenged by palaeontologists claiming that, instead, new species quickly acquire their phenotypes to remain virtually unchanged until going extinct again. This controversy, widely known as the ‘punctuated equilibrium’ debate, remained unresolved, largely owing to the difficulty of distinguishing biological species from fossil remains. We analysed body masses of 2143 existing mammal species on a phylogeny comprising 4510 (i.e. nearly all) extant species to estimate rates of gradual (anagenetic) and speciational (cladogenetic) evolution. Our Bayesian estimates from mammals as well as separate sub-clades such as primates and carnivores suggest that gradual evolution is responsible for only a small part of body size variation between mammal species.

TESTING FOR EQUAL RATES OF CLADOGENESIS IN DIVERSE TAXA

Abstract Taxa differ widely in numbers of species, which may be due either to chance alone or to factors that cause differences in speciation and extinction rates between taxa. To test whether an observed distribution of species over taxa differs from the distribution expected from chance alone, one must take into account that neither speciation nor extinction rates are known. This paper introduces a way to estimate speciation and extinction probabilities from the distribution of extant species over families and to test whether the observed distribution is different from expected. Application of this procedure to the distributions of bird, hexapod, primate, and angiosperm species over taxa provides statistical evidence of differences in rates of cladogenesis between taxa.

Detection of punctuated equilibrium from molecular phylogenies

Abstract The theory of ‘punctuated equilibrium’ hypothesises that most morphological change in species takes place in rapid bursts triggered by speciation. Eldregde and Gould postulated the theory in 1972, as an alternative to the idea that morphological change slowly accumulates in the course of time, a then common belief they dubbed ‘phyletic gradualism’. Ever since its introduction the theory of punctuated equilibrium has been the subject of speculation rather than empirical validation. Here I present a method to detect punctuated evolution without reference to fossil data, based on the phenotypes of extant species and on their relatedness as revealed by molecular phylogeny. The method involves a general mathematical model describing morphological differentiation of two species over time. The two parameters in the model, the rates of punctual (cladogenetic) and gradual (anagenetic) change, are estimated from plots of morphological diversification against time since divergence of extant species.

On age and species richness of higher taxa.

Many studies have tried to identify factors that explain differences in numbers of species between clades against the background assumption that older clades contain more species because they have had more time for diversity to accumulate. The finding in several recent studies that species richness of clades is decoupled from stem age has been interpreted as evidence for ecological limits to species richness. Here we demonstrate that the absence of a positive age-diversity relationship, or even a negative relationship, may also occur when taxa are defined based on time or some correlate of time such as genetic distance or perhaps morphological distinctness. Thus, inferring underlying processes from distributions of species across higher taxa requires caution concerning the way in which higher taxa are defined. When this definition is unclear, crown age is superior to stem age as a measure of clade age.

Problems detecting density-dependent diversification on phylogenies

While various sources of evidence suggest that speciation and perhaps also extinction rates decline as a clade diversifies (summarized in [McPeek 2008][1]; [Rabosky & Lovette 2008 a ][2]), estimates of these rates from molecular phylogenies were for a long time limited to constant-rates processes ([

ESTIMATING SPECIATION AND EXTINCTION RATES FOR PHYLOGENIES OF HIGHER TAXA

Speciation and extinction rates can be estimated from molecular phylogenies. Recently, a number of methods have been published showing that these rates can be estimated even if the phylogeny is incomplete, that is, if not all extant species are included. We show that the accuracy of such methods strongly depends on making the correct assumptions about how the sampling process was performed. We focus on phylogenies that are incomplete because some subclades (e.g., genera and families) are each represented as a single lineage. We show that previous methods implicitly assumed that such subclades are defined by randomly (or in an extreme deterministic way) choosing the edges that define the subclades from the complete species phylogeny. We show that these methods produce biased results if higher taxa are defined in a different manner. We introduce strict higher level phylogenies where subclades are defined so that the phylogeny is fully resolved from its origin to time x(cut), and fully unresolved thereafter, so that for all subclades, stem age > x(cut) > crown age. We present estimates of speciation and extinction rates from a phylogeny of birds in which this subclade definition was applied. However, for most higher level phylogenies in the literature, it is unclear how higher taxa were defined, but often such phylogenies can be easily transformed into strict higher level phylogenies, as we illustrate by estimating speciation and extinction rates from a near-complete but only partly resolved species-level phylogeny of mammals. The accuracy of our methods is verified using simulations.

Hind Wing Shape Evolves Faster than Front Wing Shape in Calopteryx Damselflies

Wing shape has been shown in a variety of species to be influenced by natural and sexual selection. In damselflies, front- and hind wings can beat independently, and functional differentiation may occur. Males of Calopteryx damselflies show species-specific nuptial flights that differ in colour signalling with the hind wings. Therefore, hind wing shape and colour may evolve in concert to improve colour display, independent of the front wings. We predicted that male hind wing shape evolves faster than front wing shape, due to sexual selection. Females do not engage in sexual displays, so we predicted that females do not show differences in divergence between front- and hind wing shape. We analysed the non-allometric component of wing shape of five European Calopteryx taxa using geometric morphometrics. We found a higher evolutionary divergence of hind wing shape in both sexes. Indeed, we found no significant differences in rate of evolution between the sexes, despite clear sex-specific differences in wing shape. We suggest that evolution of hind wing shape in males is accelerated by sexual selection on pre-copulatory displays and that this acceleration is reflected in females due to genetic correlations that somehow link the rates of wing shape evolution in the two sexes, but not the wing shapes themselves.

Morphological and genetic divergence in Swedish postglacial stickleback (Pungitius pungitius) populations

BackgroundAn important objective of evolutionary biology is to understand the processes that govern phenotypic variation in natural populations. We assessed patterns of morphological and genetic divergence among coastal and inland lake populations of nine-spined stickleback in northern Sweden. Coastal populations are either from the Baltic coast (n = 5) or from nearby coastal lakes (n = 3) that became isolated from the Baltic Sea (< 100 years before present, ybp). Inland populations are from freshwater lakes that became isolated from the Baltic approximately 10,000 ybp; either single species lakes without predators (n = 5), or lakes with a recent history of predation (n = 5) from stocking of salmonid predators (~50 ybp).ResultsCoastal populations showed little variation in 11 morphological traits and had longer spines per unit of body length than inland populations. Inland populations were larger, on average, and showed greater morphological variation than coastal populations. A principal component analysis (PCA) across all populations revealed two major morphological axes related to spine length (PC1, 47.7% variation) and body size (PC2, 32.9% variation). Analysis of PCA scores showed marked similarity in coastal (Baltic coast and coastal lake) populations. PCA scores indicate that inland populations with predators have higher within-group variance in spine length and lower within-group variance in body size than inland populations without predators. Estimates of within-group PST (a proxy for QST) from PCA scores are similar to estimates of FST for coastal lake populations but PST > FST for Baltic coast populations. PST > FST for PC1 and PC2 for inland predator and inland no predator populations, with the exception that PST < FST for body size in inland populations lacking predators.ConclusionsBaltic coast and coastal lake populations show little morphological and genetic variation within and between groups suggesting that these populations experience similar ecological conditions and that time since isolation of coastal lakes has been insufficient to demonstrate divergent morphology in coastal lake populations. Inland populations, on the other hand, showed much greater morphological and genetic variation characteristic of long periods of isolation. Inland populations from lakes without predators generally have larger body size, and smaller spine length relative to body size, suggesting systematic reduction in spine length. In contrast, inland populations with predators exhibit a wider range of spine lengths relative to body size suggesting that this trait is responding to local predation pressure differently among these populations. Taken together the results suggest that predation plays a role in shaping morphological variation among isolated inland populations. However, we cannot rule out that a causal relationship between predation versus other genetic and environmental influences on phenotypic variation not measured in this study exists, and this warrants further investigation.

Little evidence for Cope's rule from Bayesian phylogenetic analysis of extant mammals

According to Cope’s rule, lineages tend to evolve towards larger body size, possibly because of selective advantages of being large. The status of Cope’s ‘rule’ remains controversial as it is supported in some but not all large‐scale fossil studies. Here, we test for Cope’s rule by Bayesian analyses of average body masses of 3253 extant mammal species on a dated phylogenetic tree. The data favour a model that does not assume Cope’s rule. When Cope’s rule is assumed, the best estimate of its strength is an average ancestor‐descendant increase in body size of only 0.4%, which sharply contrasts with the 9% bias estimated from fossil mammals. Thus, we find no evidence for Cope’s rule from extant mammals, in agreement with earlier analyses of existing species, which also did not find support for Cope’s rule.