Rates Of Phenotypic Evolution Research Articles

Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits.

Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to data sets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large-scale biodiversity dynamics. [Brownian motion; continuous characters; discrete characters; macroevolution; Markov process; rate heterogeneity.].

Analyzing Disparity and Rates of Morphological Evolution with Model-Based Phylogenetic Comparative Methods.

Understanding variation in rates of evolution and morphological disparity is a goal of macroevolutionary research. In a phylogenetic comparative methods framework, we present three explicit models for linking the rate of evolution of a trait to the state of another evolving trait. This allows testing hypotheses about causal influences on rates of phenotypic evolution with phylogenetic comparative data. We develop a statistical framework for fitting the models with generalized least-squares regression and use this to discuss issues and limitations in the study of rates of evolution more generally. We show that the power to detect effects on rates of evolution is low in that even strong causal effects are unlikely to explain more than a few percent of observed variance in disparity. We illustrate the models and issues by testing if rates of beak-shape evolution in birds are influenced by brain size, as may be predicted from a Baldwin effect in which presumptively more behaviorally flexible large-brained species generate more novel selection on themselves leading to higher rates of evolution. From an analysis of morphometric data for 645 species, we find evidence that both macro- and microevolution of the beak are faster in birds with larger brains, but with the caveat that there are no consistent effects of relative brain size.[Baldwin effect; beak shape; behavioral drive; bird; brain size; disparity; phylogenetic comparative method; rate of evolution.]

A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines

AbstractRhinoceroses are among the most endangered mammalian species today. Their past diversity is well documented from the Eocene onward, although their evolutionary history is far from being fully understood. Here, we elucidate the systematic affinities of a Pleistocene rhinoceros species represented by a partial skeleton from 709 ± 68 kya archaeological deposits in Luzon Island, Philippines. We perform a comprehensive phylogenetic analysis, including all living species and a wide array of extinct rhinocerotid species. We confirm the early split between Elasmotheriinae and Rhinocerotinae at c. 35.5 Mya and constrain the divergence between recent Asian and African rhinoceroses at c. 24 Mya, with contrasting phenotypic evolutionary rates in Diceroti and Rhinoceroti. Dental features reveal the existence of an unsuspected Asian Pleistocene clade, referred to as Nesorhinus gen. nov.. It includes the rhinoceros from the Philippines and another extinct species from Taiwan, N. hayasakai. Nesorhinus is the sister-group to a cluster comprising Dicerorhinus and Rhinoceros. Our phylogenetic results strongly suggest an island-hopping dispersal for Nesorhinus, from the Asian mainland towards Luzon via Taiwan by the Late Miocene or later, and Pleistocene dispersals for representatives of Rhinoceros. Nesorhinus philippinensis would be the first perissodactyl species supporting the island-rule hypothesis, with decreased body weight and limb-bone robustness.

Higher evolutionary rates in life-history traits in insular than in mainland palms

Isolated islands, due to the reduced interspecific competition compared to mainland habitats, present ecological opportunities for colonizing lineages. As a consequence, island lineages may be expected to experience higher rates of trait evolution than mainland lineages. However, island effects on key life-history traits of vascular plants remain underexplored at broad spatiotemporal scales, even for emblematic island clades such as palms. Here, we used phylogenetic comparative methods to evaluate potential differences in size and macroevolutionary patterns of height and fruit diameter among mainland, continental, and volcanic island palms. Further, phylogenetic beta-diversity was used to determine if lineage turnover supported an adaptive radiation scenario on volcanic islands. Volcanic island palms were taller than their continental island and mainland counterparts, whereas continental island palms exhibited smaller fruit size. Height and fruit size of palms evolved under evolutionary constraints towards an optimal value. However, scenarios of adaptive radiation and niche conservatism were not supported for the height and fruit size of volcanic and mainland palm clades, respectively, as expected. Instead, continental island palms exhibited higher evolutionary rates for height and fruit size. Insular palm assemblages (continental and volcanic) are composed of unique lineages. Beyond representing evolutionary sources of new palm lineages, our results demonstrate that insular habitats are important in shaping palm trait diversity. Also, the higher phenotypic evolutionary rates of continental island palms suggest disparate selection pressures on this habitat type, which can be an important driver of trait diversification over time. Taken together, these results stress the importance of insular habitats for conservation of functional, phylogenetic, and taxonomic diversity of palms.

Heterogeneous relationships between rates of speciation and body size evolution across vertebrate clades.

Several theories predict that rates of phenotypic evolution should be related to the rate at which new lineages arise. However, drawing general conclusions regarding the coupling between these fundamental evolutionary rates has been difficult due to the inconsistent nature of previous results combined with uncertainty over the most appropriate methodology with which to investigate such relationships. Here we propose and compare the performance of several different approaches for testing associations between lineage-specific rates of speciation and phenotypic evolution using phylogenetic data. We then use the best-performing method to test relationships between rates of speciation and body size evolution in five major vertebrate clades (amphibians, birds, mammals, ray-finned fish and squamate reptiles) at two phylogenetic scales. Our results provide support for the long-standing view that rates of speciation and morphological evolution are generally positively related at broad macroevolutionary scales, but they also reveal a substantial degree of heterogeneity in the strength and direction of these associations at finer scales across the vertebrate tree of life.

Two new species of fossil Paratydeidae (Acari: Trombidiformes) from the late Eocene amber highlight ultraslow morphological evolution in a soil-inhabiting arthropod lineage

We describe two species of soil mite of the family Paratydeidae from the late Eocene Rovno amber: Scolotydaeus vlaskini sp. nov. and Tanytydeus pogrebnyaki sp. nov. This is the first formal description of fossils from the family Paratydeidae. These exceptionally well-preserved fossils have very similar morphologies compared to extant species, suggesting that Paratydeidae is a lineage that has experienced extremely slow rates of phenotypic evolution. To infer rates of morphological evolution in this group, we used a combination of tip dating (from the fossils) and internal node dating (based on molecular outgroup time-calibrated analysis) in a Bayesian phylogenetic framework. This analysis inferred Paratydeidae as an ancient lineage, originating 242 Ma (stem group) and diversifying 150 Ma (crown group), having ultraslow average rates of morphological evolution, i.e. 4.53e-04 changes per site per million years, which is equivalent to one change in any of the characters per 46.0 million years, per each branch of the tree. Based on our divergence time estimates, we suggest that the present global distribution of the group could be explained by their early evolution on the Pangaean supercontinent. Analysis of character state distributions in the fossil specimens suggests later extinction of ancestral taxa in the Palaearctic.http://zoobank.org/urn:lsid:zoobank.org:pub:265A36D2-B6AE-4150-B5B6-59054D33CEA0

Phenotools: An r package for visualizing and analysing phenomic datasets

Abstract Phenotypic data are crucial for understanding genotype–phenotype relationships, assessing the tree of life and revealing trends in trait diversity over time. Large‐scale description of whole organisms for quantitative analyses (phenomics) presents several challenges, and technological advances in the collection of genomic data outpace those for phenomic data. Reasons for this disparity include the time‐consuming and expensive nature of collecting discrete phenotypic data and mining previously published data on a given species (both often requiring anatomical expertise across taxa), and computational challenges involved with analysing high‐dimensional datasets. One approach to building approximations of organismal phenomes is to combine published datasets of discrete characters assembled for phylogenetic analyses into a phenomic dataset. Despite a wealth of legacy datasets in the literature for many groups, relatively few methods exist for automating the assembly, analysis, and visualization of phenomic datasets in phylogenetic contexts. Here, we introduce a new r package phenotools for integrating (fusing original or legacy datasets), curating (finding and removing duplicates) and visualizing phenomic datasets. We demonstrate the utility of the proposed toolkit with a morphological dataset for flightless birds and two morphological datasets for theropod dinosaurs and provide recommendations for character construction to maximize accessibility in future workflows. Visualization tools allow rapid identification of anatomical subregions with difficult or problematic histories of homology. We anticipate these tools aiding automation of the assembly and visualization of phenomic datasets to inform evolutionary relationships and rates of phenotypic evolution.

Rates of niche and phenotype evolution lag behind diversification in a temperate radiation

Environmental change can create opportunities for increased rates of lineage diversification, but continued species accumulation has been hypothesized to lead to slowdowns via competitive exclusion and niche partitioning. Such density-dependent models imply tight linkages between diversification and trait evolution, but there are plausible alternative models. Little is known about the association between diversification and key ecological and phenotypic traits at broad phylogenetic and spatial scales. Do trait evolutionary rates coincide with rates of diversification, are there lags among these rates, or is diversification niche-neutral? To address these questions, we combine a deeply sampled phylogeny for a major flowering plant clade-Saxifragales-with phenotype and niche data to examine temporal patterns of evolutionary rates. The considerable phenotypic and habitat diversity of Saxifragales is greatest in temperate biomes. Global expansion of these habitats since the mid-Miocene provided ecological opportunities that, with density-dependent adaptive radiation, should result in simultaneous rate increases for diversification, niche, and phenotype, followed by decreases with habitat saturation. Instead, we find that these rates have significantly different timings, with increases in diversification occurring at the mid-Miocene Climatic Optimum (∼15 Mya), followed by increases in niche and phenotypic evolutionary rates by ∼5 Mya; all rates increase exponentially to the present. We attribute this surprising lack of temporal coincidence to initial niche-neutral diversification followed by ecological and phenotypic divergence coincident with more extreme cold and dry habitats that proliferated into the Pleistocene. A lack of density-dependence contrasts with investigations of other cosmopolitan lineages, suggesting alternative patterns may be common in the diversification of temperate lineages.

Tempo and mode of mandibular shape and size evolution reveal mixed support for incumbency effects in two clades of island-endemic rodents (Muridae: Murinae).

Existing radiations in a spatially limited system such as an oceanic island may limit the ecological opportunity experienced by later colonists, resulting in lower macroevolutionary rates for secondary radiations. Additionally, potential colonists may be competitively excluded by these incumbent (resident) species, unless they are biologically distinct (biotic filtering). The extant phenotypic diversity of secondary colonists may thus be impacted by lower rates of phenotypic evolution, exclusion from certain phenotypes, and transitions to new morphotypes to escape competition from incumbent lineages. We used geometric morphometric methods to test whether the rates and patterns of mandibular evolution of the Luzon "old endemic" rodent clades, Phloeomyini and Chrotomyini, are consistent with these predictions. Each clade occupied nearly completely separate shape space and partially separate size space. We detected limited support for decelerating and clade-specific evolutionary rates for both shape and size, with strong evidence for a shift in evolutionary mode within Chrotomyini. Our results suggest that decelerating phenotypic evolutionary rates are not a necessary result of incumbency interactions; rather, incumbency effects may be more likely to determine which clades can become established in the system. Nonincumbent clades that pass a biotic filter can potentially exhibit relatively unfettered evolution.

Phylogenetic non-independence in rates of trait evolution.

Statistical non-independence of species' biological traits is recognized in most traits under selection. Yet, whether or not the evolutionary rates of such biological traits are statistically non-independent remains to be tested. Here, we test the hypothesis that phenotypic evolutionary rates are non-independent, i.e. contain phylogenetic signal, using empirical rates of evolution in three separate traits: body mass in mammals, beak shape in birds and bite force in amniotes. Specifically, we test if evolutionary rates are phylogenetically interdependent. We find evidence for phylogenetic signal in evolutionary rates in all three case studies. While phylogenetic signal diminishes deeper in time, this is reflective of statistical power owing to small sample and effect sizes. When effect size is large, e.g. owing to the presence of fossil tips, we detect high phylogenetic signals even in deeper time slices. Thus, we recommend that rates be treated as being non-independent throughout the evolutionary history of the group of organisms under study, and any summaries or analyses of rates through time-including associations of rates with traits-need to account for the undesired effects of shared ancestry.

High extinction rates and non-adaptive radiation explains patterns of low diversity and extreme morphological disparity in North American blister beetles (Coleoptera, Meloidae)

Untangling the relationship between morphological evolution and lineage diversification is key to explain global patterns of phenotypic disparity across the Tree of Life. Few studies have examined the relationship between high morphological disparity and extinction. In this study, we infer phylogenetic relationships and lineage divergence times within Eupomphini (Meloidae), a tribe of blister beetles endemic to the arid zone of North America, which exhibits a puzzling pattern of very low species richness but wild variation in morphological diversity across extant taxa. Using Bayesian and maximum likelihood inference, we estimate diversification and phenotypic evolutionary rates and infer the time and magnitude of extinction rate shifts and mass extinction events. Our results suggest that Eupomphini underwent an event of ancient radiation coupled with rapid morphological change, possibly linked to the loss of the evolutionary constraint in the elytral shape. A high extinction background associated to the Miocene-Pliocene transition decimated the diversity within each major clade, resulting in the species-poor genera observed today. Our study supports a connection between high extinction rates and patterns of decoupled phenotypic evolution and lineage diversification, and the possibility of a radiation in the absence of ecological release.

History is written by the victors: The effect of the push of the past on the fossil record.

Survivorship biases can generate remarkable apparent rate heterogeneities through time in otherwise homogeneous birth‐death models of phylogenies. They are a potential explanation for many striking patterns seen in the fossil record and molecular phylogenies. One such bias is the “push of the past”: clades that survived a substantial length of time are likely to have experienced a high rate of early diversification. This creates the illusion of a secular rate slow‐down through time that is, rather, a reversion to the mean. An extra effect increasing early rates of lineage generation is also seen in large clades. These biases are important but relatively neglected influences on many aspects of diversification patterns in the fossil record and elsewhere, such as diversification spikes after mass extinctions and at the origins of clades; they also influence rates of fossilization, changes in rates of phenotypic evolution and even molecular clocks. These inevitable features of surviving and/or large clades should thus not be generalized to the diversification process as a whole without additional study of small and extinct clades, and raise questions about many of the traditional explanations of the patterns seen in the fossil record.

Phylogeny, Macroevolutionary Trends and Historical Biogeography of Sloths: Insights From a Bayesian Morphological Clock Analysis.

Sloths, like other xenarthrans, are an extremely interesting group of mammals that, after a long history of evolution and diversification in South America, became established on islands in the Caribbean and later reached North America during the Great American Biotic Interchange. In all three regions, they were part of the impressive Pleistocene megafauna. Most taxa became extinct and only two small, distantly related tree-dwelling genera survived. Here, we incorporate several recently described genera of sloths into an assembled morphological data supermatrix and apply Bayesian inference, using phylogenetic and morphological clock methods, to 64 sloth genera. Thus, we investigate the evolution of the group in terms of the timing of divergence of different lineages and their diversity, morphological disparity and biogeographical history. The phylogeny obtained supports the existence of the commonly recognized clades for the group. Our results provide divergence time estimates for the major clades within Folivora that could not be dated with molecular methods. Lineage diversity shows an early increase, reaching a peak in the Early Miocene followed by a major drop at the end of the Santacrucian (Early Miocene). A second peak in the Late Miocene was also followed by a major drop at the end of the Huayquerian (Late Miocene). Both events show differential impact at the family level. After that, a slight Plio-Pleistocene decline was observed before the marked drop with the extinction at the end of the Pleistocene. Phenotypic evolutionary rates were high during the early history of the clade, mainly associated with Mylodontidae, but rapidly decreased to lower values around 25 Ma, whereas Megalonychidae had lower rates at the beginning followed by a steady increase, peaking during the Late Miocene and the Pliocene. Morphological disparity showed a similar trend, with an early increase, followed by a slowly increasing phase through the Late Oligocene and Early Miocene, and ending with another increase beginning at the middle of the Miocene. Biogeographic analysis showed southern South America as the most probable area of origin of the clade and the main region in which the early diversification events took place. Both Megatheriinae and Nothrotheriinae basal nodes were strongly correlated with Andean uplift events, whereas the early history of Mylodontidae is closely associated with southern South America and also shows an early occupation of the northern regions. Within Megalonychidae, our results show Choloepus as a descendant of an island dispersing ancestor and a probable re-ingression to South America by a clade that originated in Central or North America.

A new method for testing evolutionary rate variation and shifts in phenotypic evolution

Abstract Quantifying phenotypic evolutionary rates and their variation across phylogenetic trees is a major issue in evolutionary biology. A number of phylogenetic comparative methods (PCMs) currently perform such task. However, available PCMs can locate rate shifts pertaining to entire portions of the phylogeny, but not those expected to occur at the level of individual species and lineages, such as with the idea that body size changes more rapidly in insular vertebrates. Still, most PCMs cannot deal with fossil phylogenies, albeit fossils provide highly desirable information when it comes to understand trait variation and evolution. We developed a PCM based on phylogenetic ridge regression, which we named RRphylo, which assigns an evolutionary rate to each branch of the phylogeny, and is designed to locate rate shifts relating to entire clades, as well as to unrelated tree tips. We tested RRphylo on simulated trees and data to assess its performance under different conditions. Then, we repeated its application with two real case scenarios, the evolution of flight in ornithodirans and mammals and body size evolution in insular mammals, which are usually subsumed to evolve under different range regimes than terrestrial and continental species respectively. RRphylo performs well across all different conditions. The simulation experiments demonstrated it has low Type I and Type II error rate. We found significant evidence that flight accelerates the rate of body size evolution in vertebrates, and that the acquisition of very large body size slows down the rate. Still, insular mammals body size evolution is not faster than in continental species. RRphylo is a new PCM ideal to estimate variation and shift in the rate of phenotypic evolution with fossil data. In addition to testing evolutionary rate variation, it is open to a variety of further questions, such as the evolution of rates in time, the estimation of ancestral states and the estimation of phenotypic trends over time.

Long and attenuated: comparative trends in the domestication of tree fruits

This paper asks whether we can identify a recurrent domestication syndrome for tree crops (fruits, nuts) and track archaeologically the evolution of domestication of fruits from woody perennials. While archaeobotany has made major contributions to documenting the domestication process in cereals and other annual grains, long-lived perennials have received less comparative attention. Drawing on examples from across Eurasia, comparisons suggest a tendency for the larger domesticated fruits to contain seeds that are proportionally longer, thinner and with more pointed (acute to attenuated) apices. Therefore, although changes in flavour, such as increased sweetness, are not recoverable, seed metrics and shape provide an archaeological basis for tracking domestication episodes in fruits from woody perennials. Where available, metrical data suggest length increases, as well as size diversification over time, with examples drawn from the Jomon of Japan (Castanea crenata), Neolithic China (Prunus persica) and the later Neolithic of the Near East (Olea europaea, Phoenix dactylifera) to estimate rates of change. More limited data allow us to also compare Mesoamerica avocado (Persea americana) and western Pacific Canarium sp. nuts and Spondias sp. fruits. Data from modern Indian jujube (Ziziphus mauritiana) are also considered in relation to seed length:width trends in relation to fruit contents (flesh proportion, sugar content). Despite the long generation time in tree fruits, rates of change in their seeds are generally comparable to rates of phenotypic evolution in annual grain crops, suggesting that gradual evolution via unconscious selection played a key role in initial processes of tree domestication, and that this had begun in the later Neolithic once annual crops had been domesticated, in both west and east Asia.

Rates of morphological evolution, asymmetry and morphological integration of shell shape in scallops

BackgroundRates of morphological evolution vary across different taxonomic groups, and this has been proposed as one of the main drivers for the great diversity of organisms on Earth. Of the extrinsic factors pertaining to this variation, ecological hypotheses feature prominently in observed differences in phenotypic evolutionary rates across lineages. But complex organisms are inherently modular, comprising distinct body parts that can be differentially affected by external selective pressures. Thus, the evolution of trait covariation and integration in modular systems may also play a prominent role in shaping patterns of phenotypic diversity. Here we investigate the role ecological diversity plays in morphological integration, and the tempo of shell shape evolution and of directional asymmetry in bivalved scallops.ResultsOverall, the shape of both valves and the magnitude of asymmetry of the whole shell (difference in shape between valves) are traits that are evolving fast in ecomorphs under strong selective pressures (gliders, recessers and nestling), compared to low rates observed in other ecomorphs (byssal-attaching, free-living and cementing). Given that different parts of an organism can be under different selective pressures from the environment, we also examined the degree of evolutionary integration between the valves as it relates to ecological shifts. We find that evolutionary morphological integration is consistent and surprisingly high across species, indicating that while the left and right valves of a scallop shell are diversifying in accordance with ecomorphology, they are doing so in a concerted fashion.ConclusionsOur study on scallops adds another strong piece of evidence that ecological shifts play an important role in the tempo and mode of morphological evolution. Strong selective pressures from the environment, inferred from the repeated evolution of distinct ecomorphs, have influenced the rate of morphological evolution in valve shape and the magnitude of asymmetry between valves. Our observation that morphological integration of the valves making up the shell is consistently strong suggests tight developmental pathways are responsible for the concerted evolution of these structures while environmental pressures are driving whole shell shape. Finally, our study shows that directional asymmetry in shell shape among species is an important aspect of scallop macroevolution.

Lineage Diversity and Size Disparity in Musteloidea: Testing Patterns of Adaptive Radiation Using Molecular and Fossil-Based Methods.

Adaptive radiation is hypothesized to be a primary mechanism that drives the remarkable species diversity and morphological disparity across the Tree of Life. Tests for adaptive radiation in extant taxa are traditionally estimated from calibrated molecular phylogenies with little input from extinct taxa. With 85 putative species in 33 genera and over 400 described extinct species, the carnivoran superfamily Musteloidea is a prime candidate to investigate patterns of adaptive radiation using both extant- and fossil-based macroevolutionary methods. The species diversity and equally impressive ecological and phenotypic diversity found across Musteloidea is often attributed to two adaptive radiations coinciding with two major climate events, the Eocene-Oligocene transition and the Mid-Miocene Climate Transition. Here, we compiled a novel time-scaled phylogeny for 88% of extant musteloids and used it as a framework for testing the predictions of adaptive radiation hypotheses with respect to rates of lineage diversification and phenotypic evolution. Contrary to expectations, we found no evidence for rapid bursts of lineage diversification at the origin of Musteloidea, and further analyses of lineage diversification rates using molecular and fossil-based methods did not find associations between rates of lineage diversification and the Eocene-Oligocene transition or Mid-Miocene Climate Transition as previously hypothesized. Rather, we found support for decoupled diversification dynamics driven by increased clade carrying capacity in the branches leading to a subclade of elongate mustelids. Supporting decoupled diversification dynamics between the subclade of elongate mustelids and the ancestral musteloid regime is our finding of increased rates of body length evolution, but not body mass evolution, within the decoupled mustelid subclade. The lack of correspondence in rates of body mass and length evolution suggest that phenotypic evolutionary rates under a single morphological metric, even one as influential as mass, may not capture the evolution of diversity in clades that exhibit elongate body shapes. The discordance in evolutionary rates between body length and body mass along with evidence of decoupled diversification dynamics suggests that body elongation might be an innovation for the exploitation of novel Mid-Miocene resources, resulting in the radiation of some musteloids.

Natural History Constrains the Macroevolution of Foot Morphology in European Plethodontid Salamanders.

The natural history of organisms can have major effects on the tempo and mode of evolution, but few examples show how unique natural histories affect rates of evolution at macroevolutionary scales. European plethodontid salamanders (Plethodontidae: Hydromantes) display a particular natural history relative to other members of the family. Hydromantes commonly occupy caves and small crevices, where they cling to the walls and ceilings. On the basis of this unique and strongly selected behavior, we test the prediction that rates of phenotypic evolution will be lower in traits associated with climbing. We find that, within Hydromantes, foot morphological traits evolve at significantly lower rates than do other phenotypic traits. Additionally, Hydromantes displays a lower rate of foot morphology evolution than does a nonclimbing genus, Plethodon. Our findings suggest that macroevolutionary trends of phenotypic diversification can be mediated by the unique behavioral responses in taxa related to particular attributes of their natural history.

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes.

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson’s hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits.

Song evolution, speciation, and vocal learning in passerine birds.

Phenotypic divergence can promote reproductive isolation and speciation, suggesting a possible link between rates of phenotypic evolution and the tempo of speciation at multiple evolutionary scales. To date, most macroevolutionary studies of diversification have focused on morphological traits, whereas behavioral traits─including vocal signals─are rarely considered. Thus, although behavioral traits often mediate mate choice and gene flow, we have a limited understanding of how behavioral evolution contributes to diversification. Furthermore, the developmental mode by which behavioral traits are acquired may affect rates of behavioral evolution, although this hypothesis is seldom tested in a phylogenetic framework. Here, we examine evidence for rate shifts in vocal evolution and speciation across two major radiations of codistributed passerines: one oscine clade with learned songs (Thraupidae) and one suboscine clade with innate songs (Furnariidae). We find that evolutionary bursts in rates of speciation and song evolution are coincident in both thraupids and furnariids. Further, overall rates of vocal evolution are higher among taxa with learned rather than innate songs. Taken together, these findings suggest an association between macroevolutionary bursts in speciation and vocal evolution, and that the tempo of behavioral evolution can be influenced by variation in developmental modes among lineages.