What limits the morphological disparity of clades?

Angiosperm flowers reached their highest morphological diversity early in their evolutionary history

Flowers are the complex and highly diverse reproductive structures of angiosperms. Because of their role in sexual reproduction, the evolution of flowers is tightly linked to angiosperm speciation and diversification. Accordingly, the quantification of floral morphological diversity (disparity) among angiosperm subgroups and through time may give important insights into the evolutionary history of angiosperms as a whole. Based on a comprehensive dataset focusing on 30 characters describing floral structure across angiosperms, we used 1201 extant and 121 fossil flowers to measure floral disparity and explore patterns of floral evolution through time and across lineages. We found that angiosperms reached their highest floral disparity in the Early Cretaceous. However, decreasing disparity toward the present likely has not precluded the innovation of other complex traits at other morphological levels, which likely played a key role in the outstanding angiosperm species richness. Angiosperms occupy specific regions of the theoretical morphospace, indicating that only a portion of the possible floral trait combinations is observed in nature. The ANA grade, the magnoliids, and the early-eudicot grade occupy large areas of the morphospace (higher disparity), whereas nested groups occupy narrower regions (lower disparity).

Evolvability and Macroevolution: Overview and Synthesis

Evolvability is best addressed from a multi-level, macroevolutionary perspective through a comparative approach that tests for among-clade differences in phenotypic diversification in response to an opportunity, such as encountered after a mass extinction, entering a new adaptive zone, or entering a new geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers to recognize intrinsic differences in evolvability, aiming for a macroevolutionary analog of a common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining differences among extant populations that can be hypothesized to generate large-scale, long-term contrasts in evolvability among clades; or observing large-scale differences among clade histories that can by hypothesized to reflect contrasts in genetics and development observed directly in extant populations. However, many comparative analyses can be informative on their own, as explored in this overview. Differences in clade-level evolvability can be visualized in diversity-disparity plots, which can quantify positive and negative departures of phenotypic productivity from stochastic expectations scaled to taxonomic diversification. Factors that evidently can promote evolvability include modularity—when selection aligns with modular structure or with morphological integration patterns; pronounced ontogenetic changes in morphology, as in allometry or multiphase life cycles; genome size; and a variety of evolutionary novelties, which can also be evaluated using macroevolutionary lags between the acquisition of a trait and phenotypic diversification, and dead-clade-walking patterns that may signal a loss of evolvability when extrinsic factors can be excluded. High speciation rates may indirectly foster phenotypic evolvability, and vice versa. Mechanisms are controversial, but clade evolvability may be higher in the Cambrian, and possibly early in the history of clades at other times; in the tropics; and, for marine organisms, in shallow-water disturbed habitats.

Molecular phylogenies map to biogeography better than morphological ones

Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has rarely been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographic distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees we show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts and that biogeographic congruence increases over research time. We find no significant differences in stratigraphic congruence between morphological and molecular trees. These results have implications for understanding the distribution of homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses and the implications of analysing fossil groups for which molecular data are unavailable.

Using biogeographical and phylogenetic data, it is shown that molecular trees fit species geographical data better than trees inferred from morphology, and that these differences are not simply due to better tree resolution.

Why does pollen morphology vary? Evolutionary dynamics and morphospace occupation in the largest angiosperm order (Asterales)

Morphological diversity (disparity) is a key component of biodiversity and increasingly a focus of botanical research. Despite the wide range of morphologies represented by pollen grains, to date there are few studies focused on the controls on pollen disparity and morphospace occupation, and fewer still considering these parameters in a phylogenetic framework. Here, we analyse morphospace occupation, disparity and rates of morphological evolution in Asterales pollen, in a phylogenetic context. We use a dataset comprising 113 taxa from across the Asterales phylogeny, with pollen morphology described using 28 discrete characters. The Asterales pollen morphospace is phylogenetically structured around groups of related taxa, consistent with punctuated bursts of morphological evolution at key points in the Asterales phylogeny. There is no substantial difference in disparity among these groups of taxa, despite large differences in species richness and biogeographic range. There is also mixed evidence for whole-genome duplication as a driver of Asterales pollen morphological evolution. Our results highlight the importance of evolutionary history for structuring pollen morphospace. Our study is consistent with others that have shown a decoupling of biodiversity parameters, and reinforces the need to focus on disparity as a key botanical metric in its own right.

Mammaliaform extinctions as a driver of the morphological radiation of Cenozoic mammals

Adaptive radiations are hypothesized as a generating mechanism for much of the morphological diversity of extant species.^1-7 The Cenozoic radiation of placental mammals, the foundational example of this concept,^8,9 gave rise to much of the morphological disparity of extant mammals, and is generally attributed to relaxed evolutionary constraints following the extinction of non-avian dinosaurs.^10-13 However, study of this and other radiations has focused on variation in evolutionary rates,^4,5,7,14 leaving the extent to which relaxation of constraints enabled the origin of novel phenotypes less well characterized.^15-17 We evaluate constraints on morphological evolution among mammaliaforms (mammals and their closest relatives) using a new method that quantifies the capacity of evolutionary change to generate phenotypic novelty. We find that Mesozoic crown-group therians, which include the ancestors of placental mammals, were significantly more constrained than other mammaliaforms. Relaxation of these constraints occurred in the mid-Paleocene, post-dating the extinction of non-avian dinosaurs at the K/Pg boundary, instead coinciding with important environmental shifts and with declining ecomorphological diversity in non-theriimorph mammaliaforms. This relaxation occurred even in small-bodied Cenozoic mammals weighing <100 g, which are unlikely to have competed with dinosaurs. Instead, our findings support a more complex model whereby Mesozoic crown therian evolution was in part constrained by co-occurrence with disparate mammaliaforms, as well as by the presence of dinosaurs, within-lineage incumbency effects, and environmental factors. Our results demonstrate that variation in evolutionary constraints can occur independently of variation in evolutionary rate, and that both make important contributions to the understanding of adaptive radiations.

Functional assessment of morphological homoplasy in stem-gnathostomes

Osteostraci and Galeaspida are stem-gnathostomes, occupying a key phylogenetic position for resolving the nature of the jawless ancestor from which jawed vertebrates evolved more than 400 million years ago. Both groups are characterized by the presence of rigid headshields that share a number of common morphological traits, in some cases hindering the resolution of their interrelationships and the exact nature of their affinities with jawed vertebrates. Here, we explore the morphological and functional diversity of osteostracan and galeaspid headshields using geometric morphometrics and computational fluid dynamics to constrain the factors that promoted the evolution of their similar morphologies and informing on the ecological scenario under which jawed vertebrates emerged. Phylomorphospace, Mantel analysis and Stayton metrics demonstrate a high degree of homoplasy. Computational fluid dynamics reveals similar hydrodynamic performance among morphologically convergent species, indicating the independent acquisition of the same morphofunctional traits and, potentially, equivalent lifestyles. These results confirm that a number of the characters typically used to infer the evolutionary relationships among galeaspids, osteostracans and jawed vertebrates are convergent in nature, potentially obscuring understanding of the assembly of the gnathostome bodyplan. Ultimately, our results reveal that while the jawless relatives of the earliest jawed vertebrates were ecologically diverse, widespread convergence on the same hydrodynamic adaptations suggests they had reached the limits of their potential ecological diversity-overcome by jawed vertebrates and their later innovations.

Ecomorphological divergence and trophic resource partitioning in 15 syntopic Indo-Pacific parrotfishes (Labridae: Scarini)

Adaptive diversification is a product of both phylogenetic constraint and ecological opportunity. The species-rich parrotfish genera Scarus and Chlorurus display considerable variation in trophic cranial morphology, but these parrotfishes are often described as generalist herbivores. Recent work has suggested that parrotfish partition trophic resources at very fine spatial scales, raising the question of whether interspecific differences in cranial morphology reflect trophic partitioning. We tested this hypothesis by comparing targeted feeding substrata with a previously published dataset of nine cranial morphological traits. We sampled feeding substrata of 15 parrotfish species at Lizard Island, Great Barrier Reef, Australia, by following individuals until focused biting was observed, then extracting a bite core 22 mm in diameter. Three indices were parameterized for each bite core: substratum taphonomy, maximum turf height and cover of crustose coralline algae. Parrotfish species were spread along a single axis of variation in feeding substrata: successional status of the substratum taphonomy and epilithic and endolithic biota. This axis of trophic variation was significantly correlated with cranial morphology, indicating that morphological disparity within this clade is associated with interspecific partitioning of feeding substrata. Phylogenetic signal and phylomorphospace analyses revealed that the evolution of this clade involved a hitherto-unrecognized level of trophic diversification.

The complex effects of mass extinctions on morphological disparity

Studies of biodiversity through deep time have been a staple for biologists and paleontologists for over 60 years. Investigations of species richness (diversity) revealed that at least five mass extinctions punctuated the last half billion years, each seeing the rapid demise of a large proportion of contemporary taxa. In contrast to diversity, the response of morphological diversity (disparity) to mass extinctions is unclear. Generally, diversity and disparity are decoupled, such that diversity may decline as morphological disparity increases, and vice versa. Here, we develop simulations to model disparity changes across mass extinctions using continuous traits and birth-death trees. We find no simple null for disparity change following a mass extinction but do observe general patterns. The range of trait values decreases following either random or trait-selective mass extinctions, whereas variance and the density of morphospace occupation only decline following trait-selective events. General trends may differentiate random and trait-selective mass extinctions, but methods struggle to identify trait selectivity. Long-term effects of mass extinction trait selectivity change support for phylogenetic comparative methods away from the simulated Brownian motion toward Ornstein-Uhlenbeck and Early Burst models. We find that morphological change over mass extinction is best studied by quantifying multiple aspects of morphospace occupation.

Craniodental and Postcranial Characters of Non-Avian Dinosauria Often Imply Different Trees

Despite the increasing importance of molecular sequence data, morphology still makes an important contribution to resolving the phylogeny of many groups, and is the only source of data for most fossils. Most systematists sample morphological characters as broadly as possible on the principle of total evidence. However, it is not uncommon for sampling to be focused on particular aspects of anatomy, either because characters therein are believed to be more informative, or because preservation biases restrict what is available. Empirically, the optimal trees from partitions of morphological data sets often represent significantly different hypotheses of relationships. Previous work on hard-part versus soft-part characters across animal phyla revealed significant differences in about a half of sampled studies. Similarly, studies of the craniodental versus postcranial characters of vertebrates revealed significantly different trees in about one-third of cases, with the highest rates observed in non-avian dinosaurs. We test whether this is a generality here with a much larger sample of 81 published data matrices across all major dinosaur groups. Using the incongruence length difference test and two variants of the incongruence relationship difference test, we found significant incongruence in about 50% of cases. Incongruence is not uniformly distributed across major dinosaur clades, being highest (63%) in Theropoda and lowest (25%) in Thyreophora. As in previous studies, our partition tests show some sensitivity to matrix dimensions and the amount and distribution of missing entries. Levels of homoplasy and retained synapomorphy are similar between partitions, such that incongruence must partly reflect differences in patterns of homoplasy between partitions, which may itself be a function of modularity and mosaic evolution. Finally, we implement new tests to determine which partition yields trees most similar to those from the entire matrix. Despite no bias across dinosaurs overall, there are striking differences between major groups. The craniodental characters of Ornithischia and the postcranial characters of Saurischia yield trees most similar to the "total evidence" trees derived from the entire matrix. Trees from these same character partitions also tend to be most stratigraphically congruent: a mutual consilience suggesting that those partitions yield more accurate trees. [Dinosauria; homoplasy; partition homogeneity.].

Misunderstanding graphs: The confusion of biological clade diversity diagrams and archaeological frequency seriation diagrams

Graph perception involves the accurate decipherment of (often quantitative) data displayed in visual form. Because graph style may reflect discipline-specific tradition, similar graph styles in distinct disciplines can be subject to misinterpretation. Both archaeologist James A. Ford and paleobiologist Stephen Jay Gould confused spindle diagrams representing archaeological frequency seriation and paleontological clade diversity analysis as displaying the same kinds of data and representing the same processes. Similarities between the two kinds of analysis are, however, limited to the use of the same graph style-spindle diagrams-to illustrate the history of frequencies of things. The kinds of frequencies differ in two ways between the two disciplines; frequencies are of low-level Linnaean taxa within a clade representing a higher taxon in paleobiology, and are frequencies of artifact specimens within each of several types in archaeology. Further, frequencies are absolute in clade diversity and relative in frequency seriation. Clade diversity analysis, as practiced by Gould and colleagues, is a time-series analysis that requires knowing the age of taxa prior to analysis of the shape of the spindle diagram. Frequency seriation in archaeology involves ordering multiple collections of artifacts that share at least some types; ordering is based on similar frequencies and a presumed unimodal frequency distribution, and the order is inferred to be a chronology. Different analytical assumptions and goals result in discipline specific rules of graph decipherment, though each of the two kinds of analyses can be performed in each of the two disciplines.

Evolutionary constraints on disparity of ericaceous pollen grains

BACKGROUND AND AIMS

Flowering plants show a high diversity of pollen morphology, assumed to reflect not only variations in the underlying design, but also stress imposed by ecological conditions related to pollen survival and germination. Both components are expected to constrain the accumulation of pollen disparity. However, this assumption has rarely been tested using empirical data.

METHODS

This study is designed to test this hypothesis by inferring the accumulation of pollen disparity in Ericaceae, a large eudicot family with recent, ongoing radiations, with focus on three functionally significant pollen characters using a dated phylogeny.

KEY RESULTS

Multiple lines of evidence supported the hypothesis that pollen disparity in Ericaceae did not evolve steadily but rather pulsed over time, clearly decoupling from the relative constant rate pattern of species diversification inferred. In a 3-D pollen morphospace, most major clades appear to occupy distinct neighbouring regions, whereas the subfamily Epacridoideae overlaps extensively with other subfamilies. No evidence for correlations was found between dimension of pollen disparity and species diversity at either the subfamily or generic level. Furthermore, the distribution of species in present pollen morphospace showed a strong central tendency, with the core compartment containing a large number of species from species-rich genera.

CONCLUSIONS

The recovered evidence fits well with the expectations of limitations on available pollen morphological disparity, and suggests that innovation of pollen germination traits may have little effect on species diversification.

Phylogenetic incongruence and homoplasy in the appendages and bodies of arthropods: why broad character sampling is best

Notwithstanding the rapidly increasing sampling density of molecular sequence data, morphological characters still make an important contribution to our understanding of the evolutionary relationships of arthropod groups. In many clades, characters relating to the number and morphological specialization of appendages are ascribed particular phylogenetic significance and may be preferentially sampled. However, previous studies have shown that partitions of morphological character matrices often imply significantly different phylogenies. Here, we ask whether a similar incongruence is observed in the appendage and non-appendage characters of arthropods. We apply tree length (incongruence length difference, ILD) and tree distance (incongruence relationship difference, IRD) tests to these partitions in an empirical sample of 53 published neontological datasets for arthropods. We find significant incongruence about one time in five: more often than expected, but markedly less often than in previous partition studies. We also find similar levels of homoplasy in limb and non-limb characters, both in terms of internal consistency and consistency relative to molecular trees. Taken together, these findings imply that sampled limb and non-limb characters are of similar phylogenetic utility and quality, and that a total evidence approach to their analysis is preferable.

Shifts in cranial integration associated with ecological specialization in pinnipeds (Mammalia, Carnivora)

Patterns of trait integration reflect the underlying genetic and developmental architecture of morphology and significantly influence the direction of evolution. Nevertheless, the relationship between integration and disparity is complex and unlikely to be uniform across large phylogenetic and ecological scales. To date, there are little data comparing patterns of integration across major ecological transitions, limiting understanding of the processes driving changes in trait integration and their consequences. Here, we investigated patterns of cranial integration and disparity across pinnipeds, three closely related carnivoran families that have undergone a secondary adaptation to the aquatic niche with varying levels of ecological differentiation. With a three-dimensional geometric morphometric dataset of 677 specimens spanning 15 species, we compared five models of trait integration, and examined the effects of sexual dimorphism and allometry on model support. Pinnipeds varied greatly in patterns of cranial integration compared to terrestrial carnivorans. Interestingly, this variation is concentrated in phocids, which may reflect the broader range of ecological and life-history specializations across phocid species, and greater independence from the terrestrial habitat observed in that group, relative to otariids. Overall, these results indicate that major ecological transitions, and presumably large changes in selection pressures, may drive changes in phenotypic trait integration.

Approaches to Macroevolution: 2. Sorting of Variation, Some Overarching Issues, and General Conclusions

Approaches to macroevolution require integration of its two fundamental components, within a hierarchical framework. Following a companion paper on the origin of variation, I here discuss sorting within an evolutionary hierarchy. Species sorting-sometimes termed species selection in the broad sense, meaning differential origination and extinction owing to intrinsic biological properties-can be split into strict-sense species selection, in which rate differentials are governed by emergent, species-level traits such as geographic range size, and effect macroevolution, in which rates are governed by organism-level traits such as body size; both processes can create hitchhiking effects, indirectly causing the proliferation or decline of other traits. Several methods can operationalize the concept of emergence, so that rigorous separation of these processes is increasingly feasible. A macroevolutionary tradeoff, underlain by the intrinsic traits that influence evolutionary dynamics, causes speciation and extinction rates to covary in many clades, resulting in evolutionary volatility of some clades and more subdued behavior of others; the few clades that break the tradeoff can achieve especially prolific diversification. In addition to intrinsic biological traits at multiple levels, extrinsic events can drive the waxing and waning of clades, and the interaction of traits and events are difficult but important to disentangle. Evolutionary trends can arise in many ways, and at any hierarchical level; descriptive models can be fitted to clade trajectories in phenotypic or functional spaces, but they may not be diagnostic regarding processes, and close attention must be paid to both leading and trailing edges of apparent trends. Biotic interactions can have negative or positive effects on taxonomic diversity within a clade, but cannot be readily extrapolated from the nature of such interactions at the organismic level. The relationships among macroevolutionary currencies through time (taxonomic richness, morphologic disparity, functional variety) are crucial for understanding the nature of evolutionary diversification. A novel approach to diversity-disparity analysis shows that taxonomic diversifications can lag behind, occur in concert with, or precede, increases in disparity. Some overarching issues relating to both the origin and sorting of clades and phenotypes include the macroevolutionary role of mass extinctions, the potential differences between plant and animal macroevolution, whether macroevolutionary processes have changed through geologic time, and the growing human impact on present-day macroevolution. Many challenges remain, but progress is being made on two of the key ones: (a) the integration of variation-generating mechanisms and the multilevel sorting processes that act on that variation, and (b) the integration of paleontological and neontological approaches to historical biology.

Multiple phase transitions in an agent-based evolutionary model with neutral fitness

Null models are crucial for understanding evolutionary processes such as speciation and adaptive radiation. We analyse an agent-based null model, considering a case without selection-neutral evolution-in which organisms are defined only by phenotype. Universal dynamics has previously been demonstrated in a related model on a neutral fitness landscape, showing that this system belongs to the directed percolation (DP) universality class. The traditional null condition of neutral fitness (where fitness is defined as the number of offspring each organism produces) is extended here to include equal probability of death among organisms. We identify two types of phase transition: (i) a non-equilibrium DP transition through generational time (i.e. survival), and (ii) an equilibrium ordinary percolation transition through the phenotype space (based on links between mating organisms). Owing to the dynamical rules of the DP reaction-diffusion process, organisms can only sparsely fill the phenotype space, resulting in significant phenotypic diversity within a cluster of mating organisms. This highlights the necessity of understanding hierarchical evolutionary relationships, rather than merely developing taxonomies based on phenotypic similarity, in order to develop models that can explain phylogenetic patterns found in the fossil record or to make hypotheses for the incomplete fossil record of deep time.

The significance of developmental robustness for species diversity

BACKGROUND

The origin of new species and of new forms is one of the fundamental characteristics of evolution. However, the mechanisms that govern the diversity and disparity of lineages remain poorly understood. Particularly unclear are the reasons why some taxa are vastly more species-rich than others and the manner in which species diversity and morphological disparity are interrelated.

SCOPE AND CONCLUSIONS

Evolutionary innovations and ecological opportunities are usually cited as among the major factors promoting the evolution of species diversity. In many cases it is likely that these factors are positively reinforcing, with evolutionary innovations creating ecological opportunities that in turn foster the origin of new innovations. However, we propose that a third factor, developmental robustness, is very often essential for this reinforcement to be effective. Evolutionary innovations need to be stably and robustly integrated into the developmental genetic programme of an organism to be a suitable substrate for selection to 'explore' ecological opportunities and morphological 'design' space (morphospace). In particular, we propose that developmental robustness of the bauplan is often a prerequisite for the exploration of morphospace and to enable the evolution of further novelties built upon this bauplan Thus, while robustness may reduce the morphological disparity at one level, it may be the basis for increased morphological disparity and for evolutionary innovations at another level, thus fostering species diversity.

Hunting Darwin's Snark: which maps shall we use?

The 11 contributions to this thematic volume touch on a large range of issues concerning the landscape of biological possibilities and the manner by which it may be traversed by evolving life forms. The contributors also consider how this landscape might be mapped by evolutionary biologists, with an emphasis on how one might identify the limits of such maps. While some agreements emerge on the question of limits on evolution, not surprisingly few contributors look towards the same horizons. Rather than providing a potted summary of the 11 papers, our aim in this introduction is to identify eight principal themes that might serve as common ground and, as importantly, to listen out for the sound of rushing subterranean waters that hint at caverns of concealed knowledge. By no means all of these themes are addressed by all authors, but in gathering the many strands of enquiry we hope that this will allow us to ask: What, if any, are the limits to evolution?