Ecological and phylogenetic dimensions of cranial shape diversification in South American caviomorph rodents (Rodentia: Hystricomorpha)

Caviomorph rodents represent an excellent model to explore morphological diversification on a macroevolutionary scale, as they are ecologically and morphologically diverse. We analysed cranial shape variation using geometric morphometrics and phylogenetic comparative methods. Most variation involved the shape of the rostrum, basicranium, and cranial vault, and clearly matched the phylogenetic structure. At the same time, a strong allometric pattern was associated with the length of the rostrum and cranial vault, size of the auditory bulla, and depth of the zygomatic arch. After accounting for size influence, and taking phylogenetic structure into account, shape variation was significantly associated with habitat. Our results highlight the presence of complex relationships between morphological, phylogenetic, and ecological dimensions in the diversification of the caviomorph cranium. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 898–913.     

Ecological and phylogenetic influence on mandible shape variation of South American caviomorph rodents (Rodentia: Hystricomorpha)

We analyzed mandible shape variation of 17 genera belonging to three superfamilies (Cavioidea, Chinchilloidea, and Octodontoidea) of South American caviomorph rodents using geometric morphometrics. The relative influence of phylogeny and ecology on this variation was assessed using phylogenetic comparative methods. Most morphological variation was concentrated in condylar, coronoid, and angular processes, as well as the diastema. Features potentially advantageous for digging (i.e. high coronoid and condylar processes, relatively short angular process, and diastema) were present only in octodontoids; cavioids showed opposing trends, which could represent a structural constraint for fossorial habits. Chinchilloids showed intermediate features. Genera were distributed in the morphospace according to their classification into superfamilial clades. The phylogenetic signal for shape components was significant along phylogeny, whereas the relationship between mandibular shape and ecology was nonsignificant when phylogenetic structure was taken into account. An early evolutionary divergence in the mandible shape among major caviomorph clades would explain the observed strong phylogenetic influence on the variation of this structure. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 828–837.     

Macroevolution of arboreality in salamanders

Evolutionary theory predicts that selection in distinct microhabitats generates correlations between morphological and ecological traits, and may increase both phenotypic and taxonomic diversity. However, some microhabitats exert unique selective pressures that act as a restraining force on macroevolutionary patterns of diversification. In this study, we use phylogenetic comparative methods to investigate the evolutionary outcomes of inhabiting the arboreal microhabitat in salamanders. We find that arboreality has independently evolved at least five times in Caudata and has arisen primarily from terrestrial ancestors. However, the rate of transition from arboreality back to terrestriality is 24 times higher than the converse. This suggests that macroevolutionary trends in microhabitat use tend toward terrestriality over arboreality, which influences the extent to which use of the arboreal microhabitat proliferates. Morphologically, we find no evidence for an arboreal phenotype in overall body proportions or in foot shape, as variation in both traits overlaps broadly with species that utilize different microhabitats. However, both body shape and foot shape display reduced rates of phenotypic evolution in arboreal taxa, and evidence of morphological convergence among arboreal lineages is observed. Taken together, these patterns suggest that arboreality has played a unique role in the evolution of this family, providing neither an evolutionary opportunity, nor an evolutionary dead end.     

Ecological and evolutionary factors in the morphological diversification of South American spiny rats

Understanding the processes underlying morphological diversification is a central goal in ecology and evolutionary biology and requires the integration of information about phylogenetic divergence and ecological niche diversity. In the present study, we use geometric morphometrics and comparative methods to investigate morphological diversification in Neotropical spiny rats of the family Echimyidae. Morphological diversification is studied as shape variation in the skull, comprising a structure composed of four distinct units: vault, base, orognathofacial complex, and mandible. We demonstrate association among patterns of variation in shape in different cranial units, levels of phylogenetic divergence, and ecological niche diversification. At the lower level of phylogenetic divergence, there is significant and positive concordance between patterns of phylogenetic divergence and cranial shape variation in all cranial units. This concordance may be attributable to the phylogenetic and shape distances being calculated between species that occupy the same niche. At higher phylogenetic levels of divergence and with ecological niche diversity, there is significant concordance between shape variation in all four cranial units and the ecological niches. In particular, the orognathofacial complex revealed the most significant association between shape variation and ecological niche diversity. This association may be explained by the great functional importance of the orognathofacial complex.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 646–660.     

Is specialization an evolutionary dead end? Testing for differences in speciation,extinction and trait transition rates across diverse phylogenies of specialists and generalists

Specialization has often been claimed to be an evolutionary dead end, with specialist lineages having a reduced capacity to persist or diversify. In a phylogenetic comparative framework, an evolutionary dead end may be detectable from the phylogenetic distribution of specialists, if specialists rarely give rise to large, diverse clades. Previous phylogenetic studies of the influence of specialization on macroevolutionary processes have demonstrated a range of patterns, including examples where specialists have both higher and lower diversification rates than generalists, as well as examples where the rates of evolutionary transitions from generalists to specialists are higher, lower or equal to transitions from specialists to generalists. Here, we wish to ask whether these varied answers are due to the differences in macroevolutionary processes in different clades, or partly due to differences in methodology. We analysed ten phylogenies containing multiple independent origins of specialization and quantified the phylogenetic distribution of specialists by applying a common set of metrics to all datasets. We compared the tip branch lengths of specialists to generalists, the size of specialist clades arising from each evolutionary origin of a specialized trait and whether specialists tend to be clustered or scattered on phylogenies. For each of these measures, we compared the observed values to expectations under null models of trait evolution and expected outcomes under alternative macroevolutionary scenarios. We found that specialization is sometimes an evolutionary dead end: in two of the ten case studies (pollinator‐specific plants and host‐specific flies), specialization is associated with a reduced rate of diversification or trait persistence. However, in the majority of studies, we could not distinguish the observed phylogenetic distribution of specialists from null models in which specialization has no effect on diversification or trait persistence.     

Size as a line of least evolutionary resistance: diet and adaptive morphological radiation in New World monkeys

New World monkeys (NWM) display substantial variation (two orders of magnitude) in body size. Despite this, variation in skull size and associated shape show a conserved allometric relationship, both within and between genera. Maximum likelihood estimates of quantitative ancestral states were used to compare the direction of morphological differentiation with the phenotypic (p(max)) and genetic (g(max)) lines of least evolutionary resistance (LLER). Diversification in NWM skulls occurred principally along the LLER defined by size variation. We also obtained measures of morphological amount and pace of change using our skull data together with published genetic distances to test whether the LLER influenced the amount and pace of diversification. Moreover, data on an ecological factor (diet) was obtained from the literature and used to test the association of this niche-related measure with the morphological diversification. Two strategies were used to test the association of LLER with the morphological and dietary amount and pace of change, one focusing on both contemporary genera and maximum likelihood reconstructed ancestors and the other using only the 16 contemporary genera in a phylogenetic comparative analysis. Our results suggest that the LLER influenced the path, amount, and pace of morphological change. Evolution also occurred away from the LLER in some taxa but this occurred at a slower pace and resulted in a relatively low amount of morphological change. We found that longer branch lengths (time) are associated with larger differences in p(max) orientation. However, on a macroevolutionary scale there is no such trend. Diet is consistently associated with both absolute size differences and morphological integration patterns, and we suggest that this ecological factor might be driving adaptive radiation in NWM. Invasion of diet-based adaptive zones involves changes in absolute size, due to metabolic and foraging constraints, resulting in simple allometric skull diversification along the LLER. While it is clear that evolutionary change occurred along the LLER, it is not clear whether this macroevolutionary pattern results from a conservation of within-population genetic covariance patterns or long-term adaptation along a size dimension or whether both constraints and selection were inextricably involved.     

Early evolutionary differentiation of morphological variation in the mandible of South American caviomorph rodents (Rodentia, Caviomorpha)

Caviomorphs are a clade of South American rodents recorded at least since the early Oligocene (> 31.5 Ma) that exhibit ample eco-morphological variation. It has been proposed that phylogenetic structure is more important than ecological factors for understanding mandibular shape variation in this clade. This was interpreted as a result of the long-standing evolutionary history of caviomorphs and the early divergence of major lineages. In this work, we test this hypothesis through the analysis of morphological variation in the mandible of living and extinct species and compare this information with that obtained through comparative phylogenetic analyses. Our results support the hypothesis of early origin of mandibular variation; moreover, they suggest the conservation of early differentiated morphologies, which could indicate the existence of constrained evolutionary diversification.     

MODULARITY AND RATES OF EVOLUTIONARY CHANGE IN A POWER‐AMPLIFIED PREY CAPTURE SYSTEM

The dynamic interplay among structure, function, and phylogeny form a classic triad of influences on the patterns and processes of biological diversification. Although these dynamics are widely recognized as important, quantitative analyses of their interactions have infrequently been applied to biomechanical systems. Here we analyze these factors using a fundamental biomechanical mechanism: power amplification. Power‐amplified systems use springs and latches to generate extremely fast and powerful movements. This study focuses specifically on the power amplification mechanism in the fast raptorial appendages of mantis shrimp (Crustacea: Stomatopoda). Using geometric morphometric and phylogenetic comparative analyses, we measured evolutionary modularity and rates of morphological evolution of the raptorial appendage's biomechanical components. We found that “smashers” (hammer‐shaped raptorial appendages) exhibit lower modularity and 10‐fold slower rates of morphological change when compared to non‐smashers (spear‐shaped or undifferentiated appendages). The morphological and biomechanical integration of this system at a macroevolutionary scale and the presence of variable rates of evolution reveal a balance between structural constraints, functional variation, and the “roles of development and genetics” in evolutionary diversification.     

Ecomorphological variation in male and female wall lizards and the macroevolution of sexual dimorphism in relation to habitat use

Understanding how phenotypic diversity evolves is a major interest of evolutionary biology. Habitat use is an important factor in the evolution of phenotypic diversity of many animal species. Interestingly, male and female phenotypes have been frequently shown to respond differently to environmental variation. At the macroevolutionary level, this difference between the sexes is frequently analysed using phylogenetic comparative tools to assess variation in sexual dimorphism (SD) across taxa in relation to habitat. A shortcoming of such analyses is that they evaluate the degree of dimorphism itself and therefore they do not provide access to the evolutionary trajectories of each sex. As such, the relative contribution of male and female phenotypes on macroevolutionary patterns of sexual dimorphism cannot be directly assessed. Here, we investigate how habitat use shapes phenotypic diversity in wall lizards using phylogenetic comparative tools to simultaneously assess the tempo and mode of evolution in males, females and the degree of sexual dimorphism. We find that both sexes have globally diversified under similar, but not identical, processes, where habitat use seems to drive macroevolutionary variation in head shape, but not in body size or relative limb length. However, we also observe small differences in the evolutionary dynamics of male and female phenotypes that have a marked impact on macroevolutionary patterns of SD, with important implications for our interpretation of what drives phenotypic diversification within and between the sexes.     

ADAPTIVE RADIATIONS,ECOLOGICAL SPECIALIZATION,AND THE EVOLUTIONARY INTEGRATION OF COMPLEX MORPHOLOGICAL STRUCTURES

The evolutionary integration of complex morphological structures is a macroevolutionary pattern in which morphogenetic components evolve in a coordinated fashion, which can result from the interplay among processes of developmental, genetic integration, and different types of selection. We tested hypotheses of ecological versus developmental factors underlying patterns of within‐species and evolutionary integration in the mandible of phyllostomid bats, during the most impressive ecological and morphological radiation among mammals. Shape variation of mandibular morphogenetic components was associated with diet, and the transition of integration patterns from developmental to within‐species to evolutionary was examined. Within‐species (as a proxy to genetic) integration in different lineages resembled developmental integration regardless of diet specialization, however, evolutionary integration patterns reflected selection in different mandibular components. For dietary specializations requiring extensive functional changes in mastication patterns or biting, such as frugivores and sanguivores, the evolutionary integration pattern was not associated with expected within‐species or developmental integration. On the other hand, specializations with lower mastication demands or without major functional reorganization (such as nectarivores and carnivores), presented evolutionary integration patterns similar to the expected developmental pattern. These results show that evolutionary integration patterns are largely a result of independent selection on specific components regardless of developmental modules.     

Patterns of cranial shape diversification during the phylogenetic branching process of New World monkeys (Primates: Platyrrhini)

One of the central topics in evolutionary biology is understanding the processes responsible for phenotypic diversification related to ecological factors. New World monkeys are an excellent reference system to investigate processes of diversification at macroevolutionary scales. Here, we investigate the cranial shape diversification related to body size and ecology during the phylogenetic branching process of platyrrhines. To investigate this diversification, we used geometric morphometric techniques, a molecular phylogenetic tree, ecological data and phylogenetic comparative methods. Our statistical analyses demonstrated that the phylogenetic branching process is the most important dimension to understand cranial shape variation among extant platyrrhines and suggested that the main shape divergence among the four principal platyrrhine clades probably occurred during the initial branching process. The phylogenetic conservatism, which is the retention of ancestral traits over time within the four principal platyrrhine clades, could be the most important characteristic of platyrrhine cranial shape diversification. Different factors might have driven early shape divergence and posterior relative conservatism, including genetic drift, stabilizing selection, genetic constraints owing to pleiotropy, developmental or functional constraint, lack of genetic variation, among others. Understanding the processes driving the diversification among platyrrhines will probably require further palaeontological, phylogenetic and comparative studies.     

Rates of morphological evolution are correlated with species richness in salamanders

The tempo and mode of species diversification and phenotypic evolution vary widely across the tree of life, yet the relationship between these processes is poorly known. Previous tests of the relationship between rates of phenotypic evolution and rates of species diversification have assumed that species richness increases continuously through time. If this assumption is violated, simple phylogenetic estimates of net diversification rate may bear no relationship to processes that influence the distribution of species richness among clades. Here, we demonstrate that the variation in species richness among plethodontid salamander clades is unlikely to have resulted from simple time-dependent processes, leading to fundamentally different conclusions about the relationship between rates of phenotypic evolution and species diversification. Morphological evolutionary rates of both size and shape evolution are correlated with clade species richness, but are uncorrelated with simple estimators of net diversification that assume constancy of rates through time. This coupling between species diversification and phenotypic evolution is consistent with the hypothesis that clades with high rates of morphological trait evolution may diversify more than clades with low rates. Our results indicate that assumptions about underlying processes of diversity regulation have important consequences for interpreting macroevolutionary patterns.     

Convergent evolution across the Australian continent: ecotype diversification drives morphological convergence in two distantly related clades of Australian frogs

Animals from different clades but subject to similar environments often evolve similar body shapes and physiological adaptations due to convergent evolution, but this has been rarely tested at the transcontinental level and across entire classes of animal. Australia's biome diversity, isolation and aridification history provide excellent opportunities for comparative analyses on broad‐scale macroevolutionary patterns. We collected morphological and environmental data on eighty‐four (98%) Australian hylid frog species and categorized them into ecotypes. Using a phylogenetic framework, we tested the hypothesis that frogs from the same ecotype display similar body shape patterns: (i) across all the Australian hylids, and (ii) through comparison with a similar previous study on 127 (97%) Australian myobatrachid species. Body size and shape variation did not follow a strong phylogenetic pattern and was not tightly correlated with environment, but there was a stronger association between morphotype and ecotype. Both arboreal and aquatic frogs had long limbs, whereas limbs of fossorial species were shorter. Other terrestrial species were convergent on the more typical frog body shape. We quantified the strength of morphological convergence at two levels: (i) between fossorial myobatrachid and hylid frogs, and (ii) in each ecomorph within the hylids. We found strong convergence within ecotypes, especially in fossorial species. Ecotypes were also reflected in physiological adaptations: both arboreal and cocooned fossorial frogs tend to have higher rates of evaporative water loss. Our results illustrate how adaptation to different ecological niches plays a crucial role in morphological evolution, boosting phenotypic diversity within a clade. Despite phylogenetic conservatism, morphological adaptation to repeatedly emerging new environments can erase the signature of ancestral morphotypes, resulting in phenotypic diversification and convergence both within and between diverse clades.     

Phylogenetic signal,function and integration in the subunits of the carnivoran mandible

Complex phenotypes could be interpreted as the result of functional integration between identifiable subunits. Common developmental or ecological factors may favour macroevolutionary morphological integration so that functional subunits also covary above the species level. We investigate shape variation and functional integration in two subunits of the mammalian mandible: the corpus and the ramus in a subset of extant terrestrial Carnivora using geometric morphometric and comparative methods. More specifically, we test if corpus and ramus shape exhibit similar degree of homoplasy and if these traits covary above species level. Additionally, broad functional categorisations (predaceous and non predaceous) are investigated to test if differences in morphological variation and integration at macroevolutionary scale occur. Principal components of shape data show a significant phylogenetic signal in both mandibular subunits, with the ramus exhibiting a higher degree of homoplasy than the corpus. Functional groups (predators and non-predators) are significantly distinct in corpus shape, while in the ramus significance emerges only after removing the phylogenetic signal. Partial Least Square shows that mandibular corpus and ramus region covaries above species level even if this trend is not supported when employing comparative methods. Only in a subset of predaceous species covariation still hold. We conclude that mandibular subunits of Carnivora differ considerably in shape among predaceous and non-predaceous species because of the adaptive selection pressure imposed by catching and hold of live prey. This selective process also favoured macroevolutionary integration in predaceous carnivorans.     

A PHYLOGENETIC TEST OF ECOMORPHOLOGICAL ADAPTATION IN CANCER CRABS

We used McPeek's (1995a) method of evolutionary contrasts, and phylogenetic trees derived from maximum-parsimony, neighbor-joining, and maximum-likelihood analyses of data from the cytochrome oxidase I (COI) gene to evaluate the hypothesis that macroevolutionary changes in habitat use have driven the morphological diversification of Cancer crabs. All of our analyses suggested that habitat shifts from structurally complex substrates (e.g., the rocky intertidal zone) to more homogeneous substrates (e.g., sand or mud) have occurred independently in three Cancer lineages. Evolutionary contrasts analyses indicated that these habitat shifts were accompanied by increased morphological change toward larger body sizes. These macroevolutionary patterns support the hypothesis that the morphological diversification of Cancer crabs is strongly related to size-dependent habitat use; ancillary evidence suggests that increased predation pressure in homogeneous habitats represents the main selective agent for increased body size.     

Assessing Trait Covariation and Morphological Integration on Phylogenies Using Evolutionary Covariance Matrices

Morphological integration describes the degree to which sets of organismal traits covary with one another. Morphological covariation may be evaluated at various levels of biological organization, but when characterizing such patterns across species at the macroevolutionary level, phylogeny must be taken into account. We outline an analytical procedure based on the evolutionary covariance matrix that allows species-level patterns of morphological integration among structures defined by sets of traits to be evaluated while accounting for the phylogenetic relationships among taxa, providing a flexible and robust complement to related phylogenetic independent contrasts based approaches. Using computer simulations under a Brownian motion model we show that statistical tests based on the approach display appropriate Type I error rates and high statistical power for detecting known levels of integration, and these trends remain consistent for simulations using different numbers of species, and for simulations that differ in the number of trait dimensions. Thus, our procedure provides a useful means of testing hypotheses of morphological integration in a phylogenetic context. We illustrate the utility of this approach by evaluating evolutionary patterns of morphological integration in head shape for a lineage of Plethodon salamanders, and find significant integration between cranial shape and mandible shape. Finally, computer code written in R for implementing the procedure is provided.     

Experimental approach to the hypotheses of heterochronic evolution in lower vertebrates

Heterochronies, temporal changes in ancestral ontogeny, are proposed to play the major role in microand macroevolutionary transformations of lower vertebrates. However, the evolutionary role of heterochronies often remains hypothetical, not verified experimentally. In the present paper, participation of heterochronies in (1) the origin of lacustrine fish species flocks, (2) the diversification of skeletal morphology in teleosts, and (3) the skull evolution in amphibians is experimentally verified. For this purpose, the temporal parameters of ontogeny were directly changed via artificial alterations of the thyroid hormones level in different representatives of lower vertebrates. The data obtained indicate that heterochronies are among the main mechanisms responsible for the current morphological diversity displayed by lower vertebrates at different phylogenetic levels.     

CONVERGENT EVOLUTION OF SEXUAL DIMORPHISM IN SKULL SHAPE USING DISTINCT DEVELOPMENTAL STRATEGIES

Studies integrating evolutionary and developmental analyses of morphological variation are of growing interest to biologists as they promise to shed fresh light on the mechanisms of morphological diversification. Sexually dimorphic traits tend to be incredibly divergent across taxa. Such diversification must arise through evolutionary modifications to sex differences during development. Nevertheless, few studies of dimorphism have attempted to synthesize evolutionary and developmental perspectives. Using geometric morphometric analysis of head shape for 50 Anolis species, we show that two clades have converged on extreme levels of sexual dimorphism through similar, male‐specific changes in facial morphology. In both clades, males have evolved highly elongate faces whereas females retain faces of more moderate proportion. This convergence is accomplished using distinct developmental mechanisms; one clade evolved extreme dimorphism through the exaggeration of a widely shared, potentially ancestral, developmental strategy whereas the other clade evolved a novel developmental strategy not observed elsewhere in the genus. Together, our analyses indicate that both shared and derived features of development contribute to macroevolutionary patterns of morphological diversity among Anolis lizards.