Modeling body size evolution in Felidae under alternative phylogenetic hypotheses

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that "good" phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies.     

The origin of the turtle body plan: evidence from fossils and embryos

The origin of the unique body plan of turtles has long been one of the most intriguing mysteries in evolutionary morphology. Discoveries of several new stem-turtles, together with insights from recent studies on the development of the shell in extant turtles, have provided crucial new information concerning this subject. It is now possible to develop a comprehensive scenario for the sequence of evolutionary changes leading to the formation of the turtle body plan within a phylogenetic framework and evaluate it in light of the ontogenetic development of the shell in extant turtles. The fossil record demonstrates that the evolution of the turtle shell took place over millions of years and involved a number of steps.     

Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns

Although studies describing molecular‐based phylogenies within tardigrades are now frequently being published, this is not the case for studies combining molecular and morphological characters. Tardigrade phylogeny is still based, from a morphological point of view, almost exclusively on chitinous structures and little attention has been given to detecting and using novel morphological data. Consequently, we analysed the musculature of seven tardigrade species belonging to the main phyletic lines by confocal laser scanning microscopy and compared these morphological results with new molecular analyses (18S+28S rRNA genes). Finally, we analysed all the data with a total evidence approach. A consilience in the phylogenetic relationships among orders and superfamilies of tardigrades was obtained among the evolutionary trees obtained from morphological, molecular and total evidence approaches. Comparative analysis on the musculature allowed the identification of serial homologies and repeated metameric patterns along the longitudinal animal body axis. A phenomenon of mosaic evolution was detected in musculature anatomy, as dorsal musculature was found to be highly modified with respect to the other body muscle groups, probably related to the evolution of dorsal cuticular plates. An understanding of tardigrade musculature anatomy will give fundamental information to understand the evolution of segmental pattern within Panarthropoda. © 2013 The Linnean Society of London     

No substitute for real data: A cautionary note on the use of phylogenies from birth–death polytomy resolvers for downstream comparative analyses

The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth–death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (unsampled) taxa onto phylogenetic trees, using taxonomic information alone. Recent studies of birds and mammals have used this approach to generate pseudoposterior distributions of phylogenetic trees that are complete at the species level, even in the absence of genetic data for many species. Many researchers have used these distributions of phylogenies for downstream evolutionary analyses that involve inferences on phenotypic evolution, geography, and community assembly. I demonstrate that the use of phylogenies constructed in this fashion is inappropriate for many questions involving traits. Because species are placed on trees at random with respect to trait values, the birth–death polytomy resolver breaks down natural patterns of trait phylogenetic structure. Inferences based on these trees are predictably and often drastically biased in a direction that depends on the underlying (true) pattern of phylogenetic structure in traits. I illustrate the severity of the phenomenon for both continuous and discrete traits using examples from a global bird phylogeny.     

The evolution of myiasis in humans and other animals in the Old and New Worlds (part I): phylogenetic analyses

Myiasis, the infestation of live vertebrates with dipterous larvae, seems to take two distinct forms that, it has been suggested, evolved from two distinct phylogenetic roots: saprophagous and sanguinivorous. However, the convergent evolution of morphological and life-history traits seems to have had a major role in simplifying this overall assessment of the evolutionary routes by which myiasis arose. Moreover, this somewhat simplistic division is further complicated by the existence of both ectoparasitic and endoparasitic species of myiasis-causing Diptera, the evolutionary affinities of which remain to be resolved. To understand how different forms of parasitism arose, the evolution of the various groups of myiasis-causing flies must be separated from the evolution of the myiasis habit per se. Until recently, evolutionary studies of myiasis-causing flies were little more than discussions of morphology-based taxonomy. Since the mid-1990s, however, several formal phylogenies - based on both morphological and, increasingly, molecular data - have been published, enabling reassessment of the hypotheses concerning myiasis evolution. In part I of this review, we focus on some recent landmark studies in this often-neglected branch of parasitology and draw together phylogenetic studies based on molecular and morphological data to provide a framework for the subsequent analysis of biochemical, immunological, behavioural, biogeographical and fossil evidence relating to the evolution of myiasis.     

Annelid phylogeny and the status of Sipuncula and Echiura

Background  

Annelida comprises an ancient and ecologically important animal phylum with over 16,500 described species and members are the dominant macrofauna of the deep sea. Traditionally, two major groups are distinguished: Clitellata (including earthworms, leeches) and "Polychaeta" (mostly marine worms). Recent analyses of molecular data suggest that Annelida may include other taxa once considered separate phyla (i.e., Echiura, and Sipuncula) and that Clitellata are derived annelids, thus rendering "Polychaeta" paraphyletic; however, this contradicts classification schemes of annelids developed from recent analyses of morphological characters. Given that deep-level evolutionary relationships of Annelida are poorly understood, we have analyzed comprehensive datasets based on nuclear and mitochondrial genes, and have applied rigorous testing of alternative hypotheses so that we can move towards the robust reconstruction of annelid history needed to interpret animal body plan evolution.     

Correlated evolution in fig pollination

This is the first comparative study of correlated evolution between figs (Ficus species, Moraceae) and their pollinators (Hymenoptera: Agaoninae) based on molecular phylogenies of both lineages. Fig relationships based on the internal transcribed spacer region (ITS) of nuclear ribosomal DNA and pollinator relationships inferred from mitochondrial cytochrome oxidase I (COI) sequences enabled the study of correlated evolution based on molecular phylogenies for the largest set of interacting species ever compared. Comparative methods have been applied to tests of adaptation, but the application of these methods in tests of coadaptation, defined as reciprocal evolutionary change in interacting lineages, has received less attention. I have extended tests of correlated evolution between two traits along a phylogeny to the case of interacting lineages, where two traits may or may not share a common phylogenetic history. Independent contrasts and phylogenetic autocorrelation rejected the null hypothesis that trait correlations within lineages are stronger than trait correlations between interacting lineages. Fig style lengths and pollinator ovipositor lengths, for example, were more highly correlated than were pollinator body size and ovipositor length. Mutualistic interactions between figs and their pollinators illustrate the novel ways in which phylogenies and comparative methods can detect patterns of correlated evolution. The most outstanding evidence of correlated evolution between these obligate mutualists is that interacting trait correlations are stronger than within-lineage allometric relationships.     

The closest unicellular relatives of animals

Molecular phylogenies support a common ancestry between animals (Metazoa) and Fungi, but the evolutionary descent of the Metazoa from single-celled eukaryotes (protists) and the nature and taxonomic affiliation of these ancestral protists remain elusive. We addressed this question by sequencing complete mitochondrial genomes from taxonomically diverse protists to generate a large body of molecular data for phylogenetic analyses. Trees inferred from multiple concatenated mitochondrial protein sequences demonstrate that animals are specifically affiliated with two morphologically dissimilar unicellular protist taxa: Monosiga brevicollis (Choanoflagellata), a flagellate, and Amoebidium parasiticum (Ichthyosporea), a fungus-like organism. Statistical evaluation of competing evolutionary hypotheses confirms beyond a doubt that Choanoflagellata and multicellular animals share a close sister group relationship, originally proposed more than a century ago on morphological grounds. For the first time, our trees convincingly resolve the currently controversial phylogenetic position of the Ichthyosporea, which the trees place basal to Choanoflagellata and Metazoa but after the divergence of Fungi. Considering these results, we propose the new taxonomic group Holozoa, comprising Ichthyosporea, Choanoflagellata, and Metazoa. Our findings provide insight into the nature of the animal ancestor and have broad implications for our understanding of the evolutionary transition from unicellular protists to multicellular animals.     

Phylogenetic estimates of diversification rate are affected by molecular rate variation

Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric‐based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies.     

Evolution of gene regulatory networks controlling body plan development

Evolutionary change in animal morphology results from alteration of the functional organization of the gene regulatory networks (GRNs) that control development of the body plan. A major mechanism of evolutionary change in GRN structure is alteration of cis-regulatory modules that determine regulatory gene expression. Here we consider the causes and consequences of GRN evolution. Although some GRN subcircuits are of great antiquity, other aspects are highly flexible and thus in any given genome more recent. This mosaic view of the evolution of GRN structure explains major aspects of evolutionary process, such as hierarchical phylogeny and discontinuities of paleontological change.     

Hybrid origin of the Pliocene ancestor of wild goats

Recent theories on speciation suggest that interspecific hybridization is an important mechanism for explaining adaptive radiation. According to this view, hybridization can promote the rapid transfer of adaptations between different species; the hybrid population thus invades new habitats and diversifies into a variety of new species. Although hybridization is well accepted as a fairly common mechanism for diversification in plants, its role in the evolution of animals is more controversial, because reduced fitness would typically condemn animal hybrids to an evolutionary dead-end. Here, we examine DNA sequences of four mitochondrial and four nuclear genes selected for resolving phylogenetic relationships between goats, sheep, and their allies. Our analyses provide evidence of strong discordance for the position of Capra between mitochondrial and nuclear phylogenies. We suggest that the common ancestor of wild goats arose from interspecific hybridization, and that the mitochondrial genome of a species better adapted to life at high altitudes was transferred via this route into the common ancestor of Capra. We propose that the acquisition of more efficient mitochondria has conferred a selective advantage on goats, allowing their rapid adaptive radiation during the Plio-Pleistocene epoch. Our study therefore agrees with theories that predict an important role for interspecific hybridization in the evolution and diversification of animal species.     

What can DNA Tell us About the Cambrian Explosion?

Molecular data is ideal for exploring deep evolutionary historybecause of its universality, stochasticity and abundance. Thesefeatures provide a means of exploring the evolutionary historyof all organisms (including those that do not tend to leavefossils), independently of morphological evolution, and withina statistical framework that allows testing of evolutionaryhypotheses. In particular, molecular data have an importantrole to play in examining hypotheses concerning the tempo andmode of evolution of animal body plans. Examples are given wheremolecular phylogenies have led to a re-examination of some fundamentalassumptions in metazoan evolution, such as the immutabilityof early developmental characters, and the evolvability of bauplancharacters. Molecular data is also providing a new and controversialtimescale for the evolution of animal phyla, pushing the majordivisions of the animal kingdom deep into the Precambrian. Therehave been many reasons to question the accuracy and precisionof molecular date estimates, such as the failure to accountfor lineage-specific rate variation and unreliable estimationof rates of molecular evolution. While these criticisms havebeen largely countered by recent studies, one problem has remaineda challenge: could temporal variation in the rate of molecularevolution, perhaps associated with "explosive" adaptive radiations,cause overestimation of diversification dates? Empirical evidencefor an effect of speciation rate, morphological evolution orecological diversification on rates of molecular evolution isexamined, and the potential for rate-variable methods for moleculardating are discussed.     

EVOLUTIONARY CHARACTER ANALYSIS: TRACING CHARACTER CHANGE ON A CLADOGRAM

Abstract— There has been little formal discussion concerning character analysis in cladistics, even though characters and their character state trees are central to phylogenetic analyses. We refer to this field as Evolutionary Character Analysis. This paper defines the components of evolutionary character analysis: character state trees, transmodal characters, cladogram characters, attribute and character phylogenies; and the use of these components in phylogenetic inference and evolutionary studies. Character state trees and their effect on cladogram construction are discussed. A new method for numerically coding complex character state trees is described that further reduces the number of variables required to describe them. This method, ordinal coding, reduces the size of data matrices, and facilitates retrieval of state codes. This paper advocates the use of both biological evidence and evidence internal to the cladogram itself to construct character state trees (CSTs). We discuss general models of character evolution (morphocline analysis, Fitch minimum mutation model, etc.) and their role in forming CSTs. Character state trees formed with theories of character evolution are referred to as transmodal characters. These transmodal characters are contrasted with cladogram characters (Mickevich, 1982), and the place of each in a phylogenetic analysis is discussed. The method for determining cladogram characters is detailed with more complicated examples than found in previous publications. We advocate testing transmodal characters by comparing them with the resultant cladogram characters. This comparison involves transformation series analysis (TSA; Mickevich, 1982) which is viewed as an extension of reciprocal illumination. The TSA procedure and its place in hypothesis testing are reviewed. Tracing the evolution of characters interests both systematists and non-systematists alike. When character state trees (transmodal characters) are optimized on pre-existing phylogenies, character phylogenies and attribute phylogenies result. Attributes are defined as a feature that may or may not be homologous (i.e., ecological categories, plant hosts, etc.). We provide two illustrations of this approach, one involving the evolution of the anuran ear and another involving the coevolution of the butterfly Heliconius and its hostplants. Finally, the components of phylogenetic character analysis can be used to test more general evolutionary theories such as the biogenetic law and vicariance biogeography.     

Towards resolving the complete fern tree of life

In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a 'supermatrix' approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.     

Mosaic evolution,preadaptation, and the evolution of evolvability in apes

A major goal in postsynthesis evolutionary biology has been to better understand how complex interactions between traits drive movement along and facilitate the formation of distinct evolutionary pathways. I present analyses of a character matrix sampled across the haplorrhine skeleton that revealed several modules of characters displaying distinct patterns in macroevolutionary disparity. Comparison of these patterns to those in neurological development showed that early ape evolution was characterized by an intense regime of evolutionary and developmental flexibility. Shifting and reduced constraint in apes was met with episodic bursts in phenotypic innovation that built a wide array of functional diversity over a foundation of shared developmental and anatomical structure. Shifts in modularity drove dramatic evolutionary changes across the ape body plan in two distinct ways: (1) an episode of relaxed integration early in hominoid evolution coincided with bursts in evolutionary rate across multiple character suites; (2) the formation of two new trait modules along the branch leading to chimps and humans preceded rapid and dramatic evolutionary shifts in the carpus and pelvis. Changes to the structure of evolutionary mosaicism may correspond to enhanced evolvability that has a “preadaptive” effect by catalyzing later episodes of dramatic morphological remodeling.     

Journeys through discrete‐character morphospace: synthesizing phylogeny,tempo, and disparity

Palaeontologists have long employed discrete categorical data to capture morphological variation in fossil species, using the resulting character–taxon matrices to measure evolutionary tempo, infer phylogenies and capture morphological disparity. However, to date these have been seen as separate approaches despite a common goal of understanding morphological evolution over deep time. Here I argue that there are clear advantages to considering these three lines of enquiry in a single space: the phylomorphospace. Conceptually these high‐dimensional spaces capture how a phylogenetic tree explores morphospace and allow us to consider important process questions around evolutionary rates, constraints, convergence and directional trends. Currently the literature contains fundamentally different approaches used to generate such spaces, with no direct comparison between them, despite the differing evolutionary histories they imply. Here I directly compare five different phylomorphospace approaches, three with direct literature equivalents and two that are novel. I use a single empirical case study of coelurosaurian theropod dinosaurs (152 taxa, 853 characters) to show that under many analyses the literature‐derived approaches tend to reflect introduced phylogenetic (rather than the intended morphological) signal. The two novel approaches, which produce limited ancestral state estimates prior to ordination, are able to minimize this phylogenetic signal and thus exhibit more realistic amounts of phylogenetic signal, rate heterogeneity, and convergent evolution.     

Investigating the timing of origin and evolutionary processes shaping regional species diversity: Insights from simulated data and neotropical butterfly diversification rates

Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta‐analyses of time‐calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta‐analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre‐Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode (“how” and “why” of speciation). By using simulated phylogenies under four diversification scenarios, constant‐rate, diversity‐dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta‐analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence.     

Challenging received wisdoms: Some contributions of the new microscopy to the new animal phylogeny

Inspired by the emerging new view of animal phylogeny, recentcomparative morphological studies have applied the range ofavailable new and established microscopical techniques to shednew light on many received wisdoms about animal evolution. HereI review some illustrative recent work of the participants inthe symposium "The New Microscopy: Toward a Phylogenetic Synthesis"held at the annual Society for Integrative and Comparative Biologymeeting in San Diego in January 2005. I will discuss 6 casestudies. Of these, 3 have generated new morphological insightsthat are significantly at odds with received wisdom about high-levelanimal phylogeny but congruent with emerging molecular phylogenies.These examples examine the value of characteristics of arthropodneurogenesis in supporting a controversial new hypothesis ofhigh-level arthropod phylogeny, the insights into annelid phylogenyprovided by studies on central nervous system development inclitellates, and how new data on the source of mesoderm in phoronidscorroborates their placement in the Lophotrochozoa. The remaining3 case studies shed new light particularly on the evolutionof important innovations that are at the base of successfulclades. The examples deal with the evolution of torsion as amajor synapomorphy of the gastropods, illustrate how the originof gastrulation could be studied in sponges, and show that trochophorelarvae may characterize a larger clade of spiralians than hithertosuspected.     

Comparative Genomics Sheds Light on the Convergent Evolution of Miniaturized Wasps

Miniaturization has occurred in many animal lineages, including insects and vertebrates, as a widespread trend during animal evolution. Among Hymenoptera, miniaturization has taken place in some parasitoid wasp lineages independently, and may have contributed to the diversity of species. However, the genomic basis of miniaturization is little understood. Diverged approximately 200 Ma, Telenomus wasps (Platygastroidea) and Trichogramma wasps (Chalcidoidea) have both evolved to a highly reduced body size independently, representing a paradigmatic example of convergent evolution. Here, we report a high-quality chromosomal genome of Telenomus remus, a promising candidate for controlling Spodoptera frugiperda, a notorious pest that has recently caused severe crop damage. The T. remus genome (129 Mb) is characterized by a low density of repetitive sequence and a reduction of intron length, resulting in the shrinkage of genome size. We show that hundreds of genes evolved faster in two miniaturized parasitoids Trichogramma pretiosum and T. remus. Among them, 38 genes exhibit extremely accelerated evolutionary rates in these miniaturized wasps, possessing diverse functions in eye and wing development as well as cell size control. These genes also highlight potential roles in body size regulation. In sum, our analyses uncover a set of genes with accelerated evolutionary rates in Tri. pretiosum and T. remus, which might be responsible for their convergent adaptations to miniaturization, and thus expand our understanding on the evolutionary basis of miniaturization. Additionally, the genome of T. remus represents the first genome resource of superfamily Platygastroidea, and will facilitate future studies of Hymenoptera evolution and pest control.