Evolution of Cranial Shape in Caecilians (Amphibia: Gymnophiona)

Insights into morphological diversification can be obtained from the ways the species of a clade occupy morphospace. Projecting a phylogeny into morphospace provides estimates of evolutionary trajectories as lineages diversified information that can be used to infer the dynamics of evolutionary processes that produced patterns of morphospace occupation. We present here a large-scale investigation into evolution of morphological variation in the skull of caecilian amphibians, a major clade of vertebrates. Because caecilians are limbless, predominantly fossorial animals, diversification of their skull has occurred within a framework imposed by the functional demands of head-first burrowing. We examined cranial shape in 141 species, over half of known species, using X-ray computed tomography and geometric morphometrics. Mapping an existing phylogeny into the cranial morphospace to estimate the history of morphological change (phylomorphospace), we find a striking pattern: most species occupy distinct clusters in cranial morphospace that closely correspond to the main caecilian clades, and each cluster is separated by unoccupied morphospace. The empty spaces in shape space are unlikely to be caused entirely by extinction or incomplete sampling. The main caecilian clades have different amounts of morphological disparity, but neither clade age nor number of species account for this variation. Cranial shape variation is clearly linked to phyletic divergence, but there is also homoplasy, which is attributed to extrinsic factors associated with head-first digging: features of caecilian crania that have been previously argued to correlate with differential microhabitat use and burrowing ability, such as subterminal and terminal mouths, degree of temporal fenestration (stegokrotaphy/zygokrotaphy), and eyes covered by bone, have evolved and many combinations occur in modern species. We find evidence of morphological convergence in cranial shape, among species that have eyes covered by bone, resulting in a narrow bullet-shaped head. These results reveal a complex history, including early expansion of morphospace and both divergent and convergent evolution resulting in the diversity we observe today.     

GEOMETRIC MORPHOMETRICS OF THE SKULL ROOF OF STEREOSPONDYLS (AMPHIBIA: TEMNOSPONDYLI)

Abstract:  Geometric morphometric analysis using relative warps is applied to the skull roof of 62 species of stereospondyls and their closest outgroups (i.e. basal archegosauriforms) from among temnospondyl amphibians. Twenty-one landmarks and five taxonomic groups are used for comparisons. Their skull evolution is quantified in a morphospace defined by two relative warps axes. The majority of groups show poor concordance between morphological and phylogenetic distances. The only exception is represented by Yates and Warren's study of stereospondyl relationships, in which concordance is high. Only basal archegosauriforms and rhinesuchids show significant overlap in morphospace, although this might be due to low sample sizes. Regression of estimated mean disparity against taxon sample size shows that species within both the trematosauroid and the rhytidostean groups are more widely dispersed in morphospace than species belonging to any of the remaining stereospondyl groups. Stereospondyl skull evolution was characterized by divergence between major clades and convergence within those clades. Changes in patterns of morphospace occupation through time agree with the hypothesis of an 'explosive' radiation in the early Early Triassic, after the extinction of basal archegosauriforms at the end of the Permian.     

From near extinction to recovery: Late Triassic to Middle Jurassic ammonoid shell geometry

The Triassic–Jurassic extinction resulted in the near demise of the ammonoids. Based on a survey of ammonoid expansion rates, coiling geometry and whorl shape, we use the Raup accretionary growth model to outline a universal morphospace for planispiral shell geometry. We explore the occupation of that planispiral morphospace in terms of both breadth and density of occupation in addition to separately reviewing the occurrence of heteromorphs. Four intervals are recognized: pre‐extinction (Carnian to Rhaetian); aftermath (Hettangian); post‐extinction (Sinemurian to Aalenian) and recovery (Bajocian to Callovian). The pre‐extinction and recovery intervals show maximum disparity. The aftermath is marked by the disappearance of heteromorphs and a dramatic reduction in the range of planispiral morphologies to a core area of the morphospace. It is also characterized by an expansion into an evolute, slowly expanding part of the morphospace that was not occupied prior to the extinction and is soon abandoned during the post‐extinction interval. Aftermath and post‐extinction ammonoid data show a persistent negative correlation whereby rapid expansion rates are associated with narrow umbilical widths and often compressed whorls. The permanently occupied core area of planispiral morphospace represents generalist demersals whose shells were probably optimizing both hydrodynamic efficiency and shell stability. All other parts of the planispiral morphospace, and the pelagic modes of life the shells probably exploited, were gradually reoccupied during the post‐extinction interval. Planispiral adaptation was by diffusion away from the morphospace core rather than by radical jumps. Recovery of disparity was not achieved until some 30 Myr after the extinction event.     

From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida,driven by the Devonian biotic crisis

Mass extinctions have altered the trajectory of evolution a number of times over the Phanerozoic. During these periods of biotic upheaval a different selective regime appears to operate, although it is still unclear whether consistent survivorship rules apply across different extinction events. We compare variations in diversity and disparity across the evolutionary history of a major Paleozoic arthropod group, the Eurypterida. Using these data, we explore the group's transition from a successful, dynamic clade to a stagnant persistent lineage, pinpointing the Devonian as the period during which this evolutionary regime shift occurred. The late Devonian biotic crisis is potentially unique among the “Big Five” mass extinctions in exhibiting a drop in speciation rates rather than an increase in extinction. Our study reveals eurypterids show depressed speciation rates throughout the Devonian but no abnormal peaks in extinction. Loss of morphospace occupation is random across all Paleozoic extinction events; however, differential origination during the Devonian results in a migration and subsequent stagnation of occupied morphospace. This shift appears linked to an ecological transition from euryhaline taxa to freshwater species with low morphological diversity alongside a decrease in endemism. These results demonstrate the importance of the Devonian biotic crisis in reshaping Paleozoic ecosystems.     

Morphological evolution of the lizard skull: a geometric morphometrics survey

Patterns of diversity among lizard skulls were studied from a morphological, phylogenetic, and functional perspective. A sample of 1,030 lizard skulls from 441 species in 17 families was used to create a lizard skull morphospace. This morphospace was combined with a phylogeny of lizard families to summarize general trends in the evolution of the lizard skull. A basal morphological split between the Iguania and Scleroglossa was observed. Iguanians are characterized by a short, high skull, with large areas of attachment for the external adductor musculature, relative to their sister group. The families of the Iguania appear to possess more intrafamilial morphological diversity than families of the Scleroglossa, but rarefaction of the data reveals this to be an artifact caused by the greater number of species represented in Iguanian families. Iguanian families also appear more dissimilar to one another than families of the Scleroglossa. Permutation tests indicate that this pattern is real and not due to the smaller number of families in the Iguanidae. Parallel and convergent evolution is observed among lizards with similar diets: ant and termite specialists, carnivores, and herbivores. However, these patterns are superimposed over the more general phylogenetic pattern of lizard skull diversity. This study has three central conclusions. Different clades of lizards show different patterns of disparity and divergence in patterns of morphospace occupation. Phylogeny imposes a primary signal upon which a secondary ecological signal is imprinted. Evolutionary patterns in skull metrics, taken with functional landmarks, allow testing of trends and the development of new hypotheses concerning both shape and biomechanics.     

Morphospace occupation in thalattosuchian crocodylomorphs: skull shape variation, species delineation and temporal patterns

Abstract: Skull shape variation in thalattosuchians is examined using geometric morphometric techniques in order to delineate species, especially with respect to the classification of Callovian species, and to explore patterns of disparity during their evolutionary history. The pattern of morphological diversity in thalattosuchian skulls was found to be very similar to modern crocodilians: the main sources of variation are the length and the width of the snout, but these broad changes are correlated with size of supratemporal fenestra and frontal bone, length of the nasal bone, size of the orbit and premaxilla and position of the narial opening. Patterns of shape variation, in combination with discrete‐state morphology and stratigraphic and geographic range data were used to distinguish nine species of teleosaurid and 14 species of metriorhynchid, with the four currently recognized Callovian species being split into eight. Metriorhynchids were found to be more disparate from the average shape of morphospace than teleosaurids. However, short‐snouted metriorhynchids and long‐snouted teleosaurids showed the greatest amount of disparity with respect to snout morphotypes, indicating that each group tended to explore opposite areas of morphospace. Phylogeny was found to have a moderate influence on the pattern of morphospace occupation in metriorhynchids, but little effect in teleosaurids suggesting that other factors or constraints control the pattern of skull shape variation in thalattosuchians. A comparison of thalattosuchians with dyrosaur/pholidosaurids shows that thalattosuchians have a unique skull morphology, implying that there are multiple ways to construct a ‘long snout’. Moreover, the skull geometry of the problematic species Pelagosaurus typus was found to converge on the teleosaurid area of morphospace. Finally, the temporal distribution of thalattosuchian species and morphotypes demonstrate a clear and highly correlated relationship with sea level curves and mass extinction events through the Jurassic and the Early Cretaceous.     

EXTINCTION SPACE—A METHOD FOR THE QUANTIFICATION AND CLASSIFICATION OF CHANGES IN MORPHOSPACE ACROSS EXTINCTION BOUNDARIES

Three main modes of extinction are responsible for reductions in morphological disparity: (1) random (caused by a nonselective extinction event); (2) marginal (a symmetric, selective extinction event trimming the margin of morphospace); and (3) lateral (an asymmetric, selective extinction event eliminating one side of the morphospace). These three types of extinction event can be distinguished from one another by comparing changes in three measures of morphospace occupation: (1) the sum of range along the main axes; (2) the sum of variance; and (3) the position of the centroid. Computer simulations of various extinction events demonstrate that the pre‐extinction distribution of taxa (random or normal) in the morphospace has little influence on the quantification of disparity changes, whereas the modes of the extinction events play the major role. Together, the three disparity metrics define an “extinction‐space” in which different extinction events can be directly compared with one another. Application of this method to selected extinction events (Frasnian‐Famennian, Devonian‐Carboniferous, and Permian‐Triassic) of the Ammonoidea demonstrate the similarity of the Devonian events (selective extinctions) but the striking difference from the end‐Permian event (nonselective extinction). These events differ in their mode of extinction despite decreases in taxonomic diversity of similar magnitude.     

Body size trends in a Holocene island bird assemblage

Despite the robust observation in macroecology that there are many small-bodied species, recent comparative studies have found little evidence for elevated net rates of diversification among small-bodied species within taxa. Here we examine the relationship between body size and species richness using the New Zealand land bird fauna, a well resolved palaeoecological Holocene assemblage. We test whether there is any evidence that net cladogenesis depended on body size in an assemblage prior to the impact of human-induced extinction. We also test whether net cladogenesis depends on the level at which taxa are endemic to New Zealand, to see whether there is evidence for bursts of cladogenesis following taxon establishment, and examine how the body sizes of New Zealand land birds relate to those in Australia, the most likely source pool for colonising taxa. Most New Zealand land bird species are small-bodied. We find no evidence, however, that this is due to higher net cladogenesis in small-bodied taxa. The body mass distributions of endemic and recent colonist species do not differ statistically, but recent colonists tend to be smaller-bodied than their closest endemic relative. This tendency is more marked for small-bodied than large-bodied taxa. More endemic taxa do not tend to be more species rich in New Zealand, although there is a positive relationship between level of endemism and species richness for forest taxa. The body mass distribution of New Zealand birds is very similar to that for Australia. Body mass does not dictate the likelihood that a family has colonised New Zealand from Australia, but the number of species in the family does: it is the species rich Australian families that have successfully colonised. We discuss the implications of these results for the evolution of body size distributions, and for the "island rule" of body size evolution on islands.     

Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?

MOTIVATION: The distributions of many genome-associated quantities, including the membership of paralogous gene families can be approximated with power laws. We are interested in developing mathematical models of genome evolution that adequately account for the shape of these distributions and describe the evolutionary dynamics of their formation. RESULTS: We show that simple stochastic models of genome evolution lead to power-law asymptotics of protein domain family size distribution. These models, called Birth, Death and Innovation Models (BDIM), represent a special class of balanced birth-and-death processes, in which domain duplication and deletion rates are asymptotically equal up to the second order. The simplest, linear BDIM shows an excellent fit to the observed distributions of domain family size in diverse prokaryotic and eukaryotic genomes. However, the stochastic version of the linear BDIM explored here predicts that the actual size of large paralogous families is reached on an unrealistically long timescale. We show that introduction of non-linearity, which might be interpreted as interaction of a particular order between individual family members, allows the model to achieve genome evolution rates that are much better compatible with the current estimates of the rates of individual duplication/loss events.     

Kinetic basis of spontaneous mutation. Misinsertion frequencies, proofreading specificities and cost of proofreading by DNA polymerases of Escherichia coli

Repeating members of multiple-copy sequence families display high levels of sequence homogeneity. In order to examine the rates at which this is achieved, and to compare the rates with those assessed for the ribosomal DNA and histone gene families (Coen et al., 1982, accompanying paper), we have examined the patterns of variation in the Drosophila melanogaster species subgroup for the “complex” noncoding families of high copy-number. Our analysis reveals that the evolution of some of the families has involved the gradual replacement of ancestral repeats by variant repeats, independently within each species. Hybridizations between genomes at different levels of stringency indicate the presence of two basic ancestral families (the “500” and “360” families) within the subgroup. The majority of repeats representative of these families can be characterized by restriction sites and patterns of organization that are uniquely diagnostic for each species, excepting the two most closely related species. Drosophila mauritiana and Drosophila simulans. Another family (the “180” family) is confined to the one species. Drosophila orena, with features suggestive of a more rapid origin. The wide karyotypic distribution of some members of the 500 and 180 families, revealed by hybridization in situ, shows that chromosomes are evolving in concert with respect to gradual and rapidly evolving families. The distribution of sequence and pattern variation within the subgroup shows that the time required for gradual fixation (concerted evolution) of variants within large families, distributed throughout the karyotype, is longer than that required for the smaller and chromosomally restricted families of rDNA and histone genes (Coen et al., 1982). We discuss the forces that might either accelerate or retard the fixation of variants in karyotypically dispersed families.     

LINEAGES THAT CHEAT DEATH: SURVIVING THE SQUEEZE ON RANGE SIZE

Evolutionary lineages differ greatly in their net diversification rates, implying differences in rates of extinction and speciation. Lineages with a large average range size are commonly thought to have reduced extinction risk (although linking low extinction to high diversification has proved elusive). However, climate change cycles can dramatically reduce the geographic range size of even widespread species, and so most species may be periodically reduced to a few populations in small, isolated remnants of their range. This implies a high and synchronous extinction risk for the remaining populations, and so for the species as a whole. Species will only survive through these periods if their individual populations are “threat tolerant,” somehow able to persist in spite of the high extinction risk. Threat tolerance is conceptually different from classic extinction resistance, and could theoretically have a stronger relationship with diversification rates than classic resistance. I demonstrate that relationship using primates as a model. I also show that narrowly distributed species have higher threat tolerance than widespread ones, confirming that tolerance is an unusual form of resistance. Extinction resistance may therefore operate by different rules during periods of adverse global environmental change than in more benign periods.     

CALIBRATED DIVERSITY,TREE TOPOLOGY AND THE MOTHER OF MASS EXTINCTIONS: THE LESSON OF TEMNOSPONDYLS

Abstract: Three family‐level cladistic analyses of temnospondyl amphibians are used to evaluate the impact of taxonomic rank, tree topology, and sample size on diversity profiles, origination and extinction rates, and faunal turnover. Temnospondyls are used as a case study for investigating replacement of families across the Permo‐Triassic boundary and modality of recovery in the aftermath of the end‐Permian mass extinction. Both observed and inferred (i.e. tree topology‐dependent) values of family diversity have a negligible effect on the shape of the diversity curve. However, inferred values produce both a flattening of the curve throughout the Cisuralian and a less pronounced increase in family diversity from Tatarian through to Induan than do observed values. Diversity curves based upon counts of genera and species display a clearer distinction between peaks and troughs. We use rarefaction techniques (specifically, rarefaction of the number of genera and species within families) to evaluate the effect of sampling size on the curve of estimated family‐level diversity during five time bins (Carboniferous; Cisuralian; Guadalupian–Lopingian; Early Triassic; Middle Triassic–Cretaceous). After applying rarefaction, we note that Cisuralian and Early Triassic diversity values are closer to one another than they are when the observed number of families is used; both values are also slightly higher than the Carboniferous estimated diversity. The Guadalupian–Lopingian value is lower than raw data indicate, reflecting in part the depauperate land vertebrate diversity from the late Cisuralian to the middle Guadalupian (Olson’s gap). The time‐calibrated origination and extinction rate trajectories plot out close to one another and show a peak in the Induan, regardless of the tree used to construct them. Origination and extinction trajectories are disjunct in at least some Palaeozoic intervals, and background extinctions exert a significant role in shaping temnospondyl diversity in the lowermost Triassic. Finally, species‐, genus‐, and family trajectories consistently reveal a rapid increase in temnospondyl diversity from latest Permian to earliest Triassic as well as a decline near the end of the Cisuralian. However, during the rest of the Cisuralian family diversity increases slightly and there is no evidence for a steady decline, contrary to previous reports.     

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.     

Predicting functional divergence in protein evolution by site-specific rate shifts

Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.     

Bird communities and wind farms: a phylogenetic and morphological approach

The undeniable environmental benefits of wind energy are undermined by the negative effects of wind farms on bird populations through mortality by collision with the energy-generating structures. Studies have documented morphological, ecological, and behavioral traits associated with vulnerability to wind turbines. However, practically all studies have concentrated on the effects on particular populations, and community-level analyses are lacking. Here we assess the susceptibility of species on the basis of their morphology, and examine the effect of selective mortality on the topology and dispersion of phylogenies, and on the structure and volume of the ecological morphospace of bird assemblages. Using an extensive database of bird occurrences and fatalities in a wind farm located in southern Mexico, and performing null models to establish statistical significance, we compared sets of affected and unaffected species in terms of their wing morphology and position in a phylogeny. We found that birds more likely to fly in the risk zone tend to be smaller, with longer wings, and with heavier wing loadings. Within this group, species more likely to collide with blades and die are smaller, with short wings, and supporting lighter wing loadings. These patterns determine that the set of species less affected distribute in morphospace leaving noticeable holes (morphologies not represented). Birds flying in the risk zone tend to be related to each other, but species that actually collide with turbines belong to several separate clades. These differential effects on morphology and phylogenetic diversity pose important and complex challenges to the conservation of birds in areas where wind farms are being established.     

The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina

Background  

Previous studies in Ascomycetes have shown that the function of gene families of which the size is considerably larger in extant pathogens than in non-pathogens could be related to pathogenicity traits. However, by only comparing gene inventories in extant species, no insights can be gained into the evolutionary process that gave rise to these larger family sizes in pathogens. Moreover, most studies which consider gene families in extant species only tend to explain observed differences in gene family sizes by gains rather than by losses, hereby largely underestimating the impact of gene loss during genome evolution.     

Ecological variation in South American geophagine cichlids arose during an early burst of adaptive morphological and functional evolution

Diversity and disparity are unequally distributed both phylogenetically and geographically. This uneven distribution may be owing to differences in diversification rates between clades resulting from processes such as adaptive radiation. We examined the rate and distribution of evolution in feeding biomechanics in the extremely diverse and continentally distributed South American geophagine cichlids. Evolutionary patterns in multivariate functional morphospace were examined using a phylomorphospace approach, disparity-through-time analyses and by comparing Brownian motion (BM) and adaptive peak evolutionary models using maximum likelihood. The most species-rich and functionally disparate clade (CAS) expanded more efficiently in morphospace and evolved more rapidly compared with both BM expectations and its sister clade (GGD). Members of the CAS clade also exhibited an early burst in functional evolution that corresponds to the development of modern ecological roles and may have been related to the colonization of a novel adaptive peak characterized by fast oral jaw mechanics. Furthermore, reduced ecological opportunity following this early burst may have restricted functional evolution in the GGD clade, which is less species-rich and more ecologically specialized. Patterns of evolution in ecologically important functional traits are consistent with a pattern of adaptive radiation within the most diverse clade of Geophagini.     

Global diversity of mayflies (Ephemeroptera, Insecta) in freshwater

The extant global Ephemeroptera fauna is represented by over 3,000 described species in 42 families and more than 400 genera. The highest generic diversity occurs in the Neotropics, with a correspondingly high species diversity, while the Palaearctic has the lowest generic diversity, but a high species diversity. Such distribution patterns may relate to how long evolutionary processes have been carrying on in isolation in a bioregion. Over an extended period, there may be extinction of species, but evolution of more genera. Dramatic extinction events such as the K-T mass extinction have affected current mayfly diversity and distribution. Climatic history plays an important role in the rate of speciation in an area, with regions which have been climatically stable over long periods having fewer species per genus, when compared to regions subjected to climatic stresses, such as glaciation. A total of 13 families are endemic to specific bioregions, with eight among them being monospecific. Most of these have restricted distributions which may be the result of them being the relict of a previously more diverse, but presently almost completely extinct family, or may be the consequence of vicariance events, resulting from evolution due to long-term isolation. Guest editors: E. V. Balian, C. Lévêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment