The macroevolutionary consequences of phenotypic integration: from development to deep time

Morphological variation and covariation in mandibular molars of platyrrhine primates

Molars are highly integrated biological structures that have been used for inferring evolutionary relationships among taxa. However, parallel and convergent morphological traits can be affected by developmental and functional constraints. Here, we analyze molar shapes of platyrrhines in order to explore if platyrrhine molar diversity reflects homogeneous patterns of molar variation and covariation. We digitized 30 landmarks on mandibular first and second molars of 418 extant and 11 fossil platyrrhine specimens to determine the degree of integration of both molars when treated as a single module. We combined morphological and phylogenetic data to investigate the phylogenetic signal and to visualize the history of molar shape changes. All platyrrhine taxa show a common shape pattern suggesting that a relatively low degree of phenotypic variation is caused by convergent evolution, although molar shape carries significant phylogenetic signal. Atelidae and Pitheciidae show high levels of integration with low variation between the two molars, whereas the Cebinae/Saimiriinae, and especially Callitrichinae, show greater variation between molars and trend toward a modular organization. We hypothesize that biomechanical constraints of the masticatory apparatus, and the dietary profile of each taxon are the main factors that determine high covariation in molars. In contrast, low molar shape covariation may result from the fact that each molar exhibits a distinct ecological signal, as molars can be exposed to distinct occlusal loadings during food processing, suggesting that different selective pressures on molars can reduce overall molar integration.

Adaptation and constraint in the evolution of the mammalian backbone

BACKGROUND

The axial skeleton consists of repeating units (vertebrae) that are integrated through their development and evolution. Unlike most tetrapods, vertebrae in the mammalian trunk are subdivided into distinct thoracic and lumbar modules, resulting in a system that is constrained in terms of count but highly variable in morphology. This study asks how thoracolumbar regionalization has impacted adaptation and evolvability across mammals. Using geometric morphometrics, we examine evolutionary patterns in five vertebral positions from diverse mammal species encompassing a broad range of locomotor ecologies. We quantitatively compare the effects of phylogenetic and allometric constraints, and ecological adaptation between regions, and examine their impact on evolvability (disparity and evolutionary rate) of serially-homologous vertebrae.

RESULTS

Although phylogenetic signal and allometry are evident throughout the trunk, the effect of locomotor ecology is partitioned between vertebral positions. Lumbar vertebral shape correlates most strongly with ecology, differentiating taxa based on their use of asymmetric gaits. Similarly, disparity and evolutionary rates are also elevated posteriorly, indicating a link between the lumbar region, locomotor adaptation, and evolvability.

CONCLUSION

Vertebral regionalization in mammals has facilitated rapid evolution of the posterior trunk in response to selection for locomotion and static body support.

Early bursts of disparity and the reorganization of character integration

'Early bursts' of morphological disparity (i.e. diversity of anatomical types) are common in the fossil record. We typically model such bursts as elevated early rates of independent character change. Developmental theory predicts that modules of linked characters can change together, which would mimic the effects of elevated independent rates on disparity. However, correlated change introducing suboptimal states should encourage breakup (parcellation) of character suites allowing new (or primitive) states to evolve until new suites arise (relinkage). Thus, correlated change-breakup-relinkage presents mechanisms for early bursts followed by constrained evolution. Here, I analyse disparity in 257 published character matrices of fossil taxa. For each clade, I use inverse-modelling to infer most probably rates of independent change given both time-homogeneous and separate 'early versus late' rates. These rates are used to estimate expected disparity given both independent change models. The correlated change-breakup-relinkage model also predicts elevated frequencies of compatible character state-pairs appearing out of order in the fossil record (e.g. 01 appearing after 00 and 11; = low stratigraphic compatibility), as one solution to suboptimal states induced by correlated change is a return to states held before that change. As predicted by the correlated change-breakup-relinkage model, early disparity in the majority of clades both exceeds the expectations of either independent change model and excess early disparity correlates with low stratigraphic compatibility among character-pairs. Although it is possible that other mechanisms for linking characters contribute to these patterns, these results corroborate the idea that reorganization of developmental linkages is often associated with the origin of groups that biologists recognize as new higher taxa and that such reorganization offers a source of new disparity throughout the Phanerozoic.

A fly in a tube: Macroevolutionary expectations for integrated phenotypes

Phenotypic integration and modularity are ubiquitous features of complex organisms, describing the magnitude and pattern of relationships among biological traits. A key prediction is that these relationships, reflecting genetic, developmental, and functional interactions, shape evolutionary processes by governing evolvability and constraint. Over the last 60 years, a rich literature of research has quantified patterns of integration and modularity across a variety of clades and systems. Only recently has it become possible to contextualize these findings in a phylogenetic framework to understand how trait integration interacts with evolutionary tempo and mode. Here, we review the state of macroevolutionary studies of integration and modularity, synthesizing empirical and theoretical work into a conceptual framework for predicting the effects of integration on evolutionary rate and disparity: a fly in a tube. While magnitude of integration is expected to influence the potential for phenotypic variation to be produced and maintained, thus defining the shape and size of a tube in morphospace, evolutionary rate, or the speed at which a fly moves around the tube, is not necessarily controlled by trait interactions. Finally, we demonstrate this reduced disparity relative to the Brownian expectation for a given rate of evolution with an empirical example: the avian cranium.

Avian predation intensity as a driver of clinal variation in colour morph frequency

Phenotypic variation provides the framework for natural selection to work upon, enabling adaptive evolution. One of the most discernible manifestations of phenotypic variability is colour variation. When this variation is discrete, genetically based colour pattern morphs occur simultaneously within a population. Why and how colour polymorphisms are maintained is an evolutionary puzzle. Several evolutionary drivers have been hypothesized as influencing clinal patterns of morph frequency, with spatial variation in climate and predation being considered especially important. Despite this, no study has examined both of their roles simultaneously. The aims of this study were to: (a) examine the covariation of physiology, environmental variables and colouration at a local scale; and (b) determine if these factors and their interplay explain broad clinal variation in morph frequency. We used the lizard Liopholis whitii as a model system, as this species displays a discrete, heritable polymorphism for colour pattern (plain-backed, patterned morphs) whose morph frequency varies latitudinally. We measured reflectance, field activity temperatures and microhabitat structure to test for differences in crypsis, thermal biology and microhabitat selection of patterned and plain-backed morphs within a single population where colour morphs occur sympatrically. We then used data from the literature to perform a broad-scale analysis to identify whether these factors also explained the latitudinal variation of morph frequency in this species. At the local scale, plain-backed morphs were found to be less cryptic than patterned morphs while no other differences were detected in terms of thermal biology, dorsal reflectance and microhabitat use. At a broader scale, predation was the most influential factor mediating morph frequency across latitudes. However, the observed pattern of morph frequency is opposite to what the modelling results suggest in that the incidence of the least cryptic morph is highest where predation pressure is most severe. Clinal variation in the level of background matching between morphs or the potential reproductive advantage by the plain-backed morph may, instead, be driving the observed morph frequency. Together, these results provide key insights into the evolution of local adaptation as well as the ecological forces involved in driving the dynamics of colour polymorphism.

Evolution of skeletal and muscular morphology within the functionally integrated lower jaw adduction system of sculpins and relatives (Cottoidei)

Vertebrate lever mechanics are defined by the morphology of skeletal elements and the properties of their muscular actuators; these metrics characterize functional diversity. The components of lever systems work in coordination ("functional integration") and may show strong covariation across evolutionary history ("evolutionary integration"), both of which have been hypothesized to constrain phenotypic diversity. We quantified evolutionary integration in a functionally integrated system - the lower jaw of sculpins and relatives (Actinopterygii: Cottoidei). Sculpins primarily rely on suction feeding for prey capture, but there is considerable variation in evasiveness of their prey, resulting in variation in anatomy of the lower jaw-closing mechanism. We used functionally-relevant linear measurements to characterize skeletal and muscular components of this system among 25 cottoid species and two outgroup Hexagrammoidei (greenling) species. We quantified evolutionary covariation and correlation of jaw-closing mechanical advantage (i.e., skeletal leverage) and muscle architecture (i.e., gearing) by correlating phylogenetically independent contrasts and fitting phylogenetically corrected generalized least squares models. We found no evidence of evolutionary covariation in muscle architecture and skeletal leverage. While we found a positive evolutionary correlation between out-lever length and adductor muscle fiber length, there was no significant evolutionary correlation between in-lever length and adductor muscle fiber length. We also found a positive evolutionary correlation between in- and out-lever lengths. These results suggest that skeletal morphology and muscle morphology contribute independently to biomechanical diversity among closely related species, indicating the importance of considering both skeletal and muscular variation in studies of ecomorphological diversification.

Morphological variation under domestication: how variable are chickens?

The process of domestication has long fascinated evolutionary biologists, yielding insights into the rapidity with which selection can alter behaviour and morphology. Previous studies on dogs, cattle and pigeons have demonstrated that domesticated forms show greater magnitudes of morphological variation than their wild ancestors. Here, we quantify variation in skull morphology, modularity and integration in chickens and compare those to the wild fowl using three-dimensional geometric morphometrics and multivariate statistics. Similar to other domesticated species, chickens exhibit a greater magnitude of variation in shape compared with their ancestors. The most variable part of the chicken skull is the cranial vault, being formed by dermal and neural crest-derived bones, its form possibly related to brain shape variation in chickens, especially in crested breeds. Neural crest-derived portions of the skull exhibit a higher amount of variation. Further, we find that the chicken skull is strongly integrated, confirming previous studies in birds, in contrast to the presence of modularity and decreased integration in mammals.

Contrasting patterns of RUNX2 repeat variations are associated with palate shape in phyllostomid bats and New World primates

Establishing the genetic basis that underlies craniofacial variability in natural populations is one of the main topics of evolutionary and developmental studies. One of the genes associated with mammal craniofacial variability is RUNX2, and in the present study we investigated the association between craniofacial length and width and RUNX2 across New World bats (Phyllostomidae) and primates (Catarrhini and Platyrrhini). Our results showed contrasting patterns of association between the glutamate/alanine ratios (Q/A ratio) and palate shape in these highly diverse groups. In phyllostomid bats, we found an association between shorter/broader faces and increase of the Q/A ratio. In New World monkeys (NWM) there was a positive correlation of increasing Q/A ratios to more elongated faces. Our findings reinforced the role of the Q/A ratio as a flexible genetic mechanism that would rapidly change the time of skull ossification throughout development. However, we propose a scenario in which the influence of this genetic adjustment system is indirect. The Q/A ratio would not lead to a specific phenotype, but throughout the history of a lineage, would act along with evolutionary constraints, as well as other genes, as a facilitator for adaptive morphological changes.

Morphological integration in the appendicular skeleton of two domestic taxa: the horse and donkey

Organisms are organized into suites of anatomical structures that typically covary when developmentally or functionally related, and this morphological integration plays a determinant role in evolutionary processes. Artificial selection on domestic species causes strong morphological changes over short time spans, frequently resulting in a wide and exaggerated phenotypic diversity. This raises the question of whether integration constrains the morphological diversification of domestic species and how natural and artificial selection may impact integration patterns. Here, we study the morphological integration in the appendicular skeleton of domestic horses and donkeys, using three-dimensional geometric morphometrics on 75 skeletons. Our results indicate that a strong integration is inherited from developmental mechanisms which interact with functional factors. This strong integration reveals a specialization in the locomotion of domestic equids, partly for running abilities. We show that the integration is stronger in horses than in donkeys, probably because of a greater degree of specialization and predictability of their locomotion. Thus, the constraints imposed by integration are weak enough to allow important morphological changes and the phenotypic diversification of domestic species.

Modularity promotes morphological divergence in ray-finned fishes

Modularity is considered a prerequisite for the evolvability of biological systems. This is because in theory, individual modules can follow quasi-independent evolutionary trajectories or evolve at different rates compared to other aspects of the organism. This may influence the potential of some modules to diverge, leading to differences in disparity. Here, we investigated this relationship between modularity, rates of morphological evolution and disparity using a phylogenetically diverse sample of ray-finned fishes. We compared the support for multiple hypotheses of evolutionary modularity and asked if the partitions delimited by the best-fitting models were also characterized by the highest evolutionary rate differentials. We found that an evolutionary module incorporating the dorsal, anal and paired fins was well supported by the data, and that this module evolves more rapidly and consequently generates more disparity than other modules. This suggests that modularity may indeed promote morphological disparity through differences in evolutionary rates across modules.

Shape variation and modularity of skull and teeth in domesticated horses and wild equids

BACKGROUND

In horses, the morphological changes induced by the process of domestication are reportedly less pronounced than in other species, such as dogs or pigs - although the horses' disparity has rarely been empirically tested. We investigated shape differences and modularity of domesticated horses, Przewalski's horses, donkeys and zebras. Mandibular and tooth shape have been shown to be valuable features for differentiating wild and domesticated forms in some mammals.

RESULTS

Both mandible and teeth, show a pattern of shape space occupation analogous to that of the cranium, with domesticated horses occupying a similar extension in shape space to that of wild equids. Only cranial shape data exhibit a tendency to separate domesticated horses and Przewalski's horses from donkeys and zebras. Maximum likelihood model-based tests confirm the horse cranium is composed of six developmental modules, as reported for placental mammals in general. The magnitude of integration in domesticated horse skull was lower than in wild equids across all six cranial modules, and lower values of integration were associated with higher disparity values across all modules.

CONCLUSION

This is the first study that combines different skeletal features for the description and comparison of shape changes in all living equid groups using geometric morphometrics. We support Darwin's hypothesis that the shape variation in the skull of domesticated horses is similar to the shape variation of all wild equid species existing today. Lower magnitudes of module integration are recovered in domesticated horses compared to their wild relatives.

Multimethod Approach to the Early Postnatal Growth of the Mandible in Mice from a Zone of Robertsonian Polymorphism

The western European house mouse (Mus musculus domesticus) shows high karyotypic diversity owing to Robertsonian translocations. Morphometric studies conducted with adult mice suggest that karyotype evolution due to these chromosomal reorganizations entails variation in the form and the patterns of morphological covariation of the mandible. However, information is much scarcer regarding the effect of these rearrangements on the growth pattern of the mouse mandible over early postnatal ontogeny. Here we compare mandible growth from the second to the eighth week of postnatal life between two ontogenetic series of mice from wild populations, with the standard karyotype and with Robertsonian translocations respectively, reared under the same conditions. A multi-method approach is used, including bone histology analyses of mandible surfaces and cross-sections, as well as geometric morphometric analyses of mandible form. The mandibles of both standard and Robertsonian mice display growth acceleration around weaning, anteroposterior direction of bone maturation, a predominance of bone deposition fields over ontogeny, and relatively greater expansion of the posterior mandible region correlated with the ontogenetic increase in mandible size. Nevertheless, differences exist between the two mouse groups regarding the timing of histological maturation of the mandible, the localization of certain bone remodeling fields, the temporospatial patterns of morphological variation, and the organization into two main modules. The dissimilarities in the process of mandible growth between the two groups of mice become more evident around sexual maturity, and could arise from alterations that Robertsonian translocations may exert on genes involved in the bone remodeling mechanism. Anat Rec, 2018. © 2018 Wiley Periodicals, Inc.

The impact of artificial selection on morphological integration in the appendicular skeleton of domestic horses

The relationships between the different component parts of organisms, such as the sharing of common development or function, produce a coordinated variation between the different traits. This morphological integration contributes to drive or constrain morphological variation and thus impacts phenotypic diversification. Artificial selection is known to contribute significantly to phenotypic diversification of domestic species. However, little attention has been paid to its potential impact on integration patterns. This study explores the patterns of integration in the limb bones of different horse breeds, using 3D geometric morphometrics. The domestic horse is known to have been strongly impacted by artificial selection, and was often selected for functional traits. Our results confirm that morphological integration among bones within the same limb is strong and apparently partly produced by functional factors. Most importantly, they reveal that artificial selection, which led to the diversification of domestic horses, impacts covariation patterns. The influence of selection on the patterns of covariation varies along the limbs and modulates bone shape, likely due to a differential ligament or muscle development. These results highlight that, in addition to not being constrained by a strong morphological integration, artificial selection has modulated the covariation patterns according to the locomotor specificities of the breeds. More broadly, it illustrates the interest in studying how micro-evolutionary processes impact covariation patterns and consequently contribute to morphological diversification of domestic species.

Study of morphological variation of northern Neotropical Ariidae reveals conservatism despite macrohabitat transitions

BACKGROUND

Morphological convergence triggered by trophic adaptations is a common pattern in adaptive radiations. The study of shape variation in an evolutionary context is usually restricted to well-studied fish models. We take advantage of the recently revised systematics of New World Ariidae and investigate skull shape evolution in six genera of northern Neotropical Ariidae. They constitute a lineage that diversified in the marine habitat but repeatedly adapted to freshwater habitats. 3D geometric morphometrics was applied for the first time in catfish skulls and phylogenetically informed statistical analyses were performed to test for the impact of habitat on skull diversification after habitat transition in this lineage.

RESULTS

We found that skull shape is conserved throughout phylogeny. A morphospace analysis revealed that freshwater and marine species occupy extreme ends of the first principal component axis and that they exhibit similar Procrustes variances. Yet freshwater species occupy the smallest shape space compared to marine and brackish species (based on partial disparity), and marine and freshwater species have the largest Procrustes distance to each other. We observed a single case of shape convergence as derived from 'C-metrics', which cannot be explained by the occupation of the same habitat.

CONCLUSIONS

Although Ariidae occupy such a broad spectrum of different habitats from sea to freshwater, the morphospace analysis and analyses of shape and co-variation with habitat in a phylogenetic context shows that conservatism dominates skull shape evolution among ariid genera.

Structure-function covariation with nonfeeding ecological variables influences evolution of feeding specialization in Carnivora

Skull shape convergence is pervasive among vertebrates. Although this is frequently inferred to indicate similar functional underpinnings, neither the specific structure-function linkages nor the selective environments in which the supposed functional adaptations arose are commonly identified and tested. We demonstrate that nonfeeding factors relating to sexual maturity and precipitation-related arboreality also can generate structure-function relationships in the skulls of carnivorans (dogs, cats, seals, and relatives) through covariation with masticatory performance. We estimated measures of masticatory performance related to ecological variables that covary with cranial shape in the mammalian order Carnivora, integrating geometric morphometrics and finite element analyses. Even after accounting for phylogenetic autocorrelation, cranial shapes are significantly correlated to both feeding and nonfeeding ecological variables, and covariation with both variable types generated significant masticatory performance gradients. This suggests that mechanisms of obligate shape covariation with nonfeeding variables can produce performance changes resembling those arising from feeding adaptations in Carnivora.

Shape Covariation (or the Lack Thereof) Between Vertebrae and Other Skeletal Traits in Felids: The Whole is Not Always Greater than the Sum of Parts

Within carnivorans, cats show comparatively little disparity in overall morphology, with species differing mainly in body size. However, detailed shape analyses of individual osteological structures, such as limbs or skulls, have shown that felids display significant morphological differences that correlate with their observed ecological and behavioural ranges. Recently, these shape analyses have been extended to the felid axial skeleton. Results demonstrate a functionally-partitioned vertebral column, with regions varying greatly in level of correlation between shape and ecology. Moreover, a clear distinction is evident between a phylogenetically-constrained neck region and a selection-responsive posterior spine. Here, we test whether this regionalisation of function reflected in vertebral column shape is also translated into varying levels of phenotypic integration between this structure and most other skeletal elements. We accomplish this comparison by performing pairwise tests of integration between vertebral and other osteological units, quantified with 3D geometric morphometric data and analysed both with and without phylogenetic correction. To our knowledge, this is the first study to test for integration across a comprehensive sample of whole-skeleton elements. Our results show that, prior to corrections, strong covariation is present between vertebrae across the vertebral column and all other elements, with the exception of the femur. However, most of these significant correlations disappear after correcting for phylogeny, which is a significant influence on cranial and limb morphology of felids and other carnivorans. Our results thus suggest that the vertebral column of cats displays relative independence from other skeletal elements and may represent several distinct evolutionary morphological modules.

Developmental origins of mosaic evolution in the avian cranium

Studies reconstructing morphological evolution have long relied on simple representations of organismal form or on limited sampling of species, hindering a comprehensive understanding of the factors shaping biological diversity. Here, we combine high-resolution 3D quantification of skull shape with dense taxonomic sampling across a major vertebrate clade, birds, to demonstrate that the avian skull is formed of multiple semi-independent regions that epitomize mosaic evolution, with cranial regions and major lineages evolving with distinct rates and modes. We further show that the evolvability of different cranial regions reflects their disparate embryonic origins. Finally, we present a hypothetical reconstruction of the ancestral bird skull using this high-resolution shape data to generate a detailed estimate of extinct forms in the absence of well-preserved three-dimensional fossils.

Mosaic evolution, which results from multiple influences shaping morphological traits and can lead to the presence of a mixture of ancestral and derived characteristics, has been frequently invoked in describing evolutionary patterns in birds. Mosaicism implies the hierarchical organization of organismal traits into semiautonomous subsets, or modules, which reflect differential genetic and developmental origins. Here, we analyze mosaic evolution in the avian skull using high-dimensional 3D surface morphometric data across a broad phylogenetic sample encompassing nearly all extant families. We find that the avian cranium is highly modular, consisting of seven independently evolving anatomical regions. The face and cranial vault evolve faster than other regions, showing several bursts of rapid evolution. Other modules evolve more slowly following an early burst. Both the evolutionary rate and disparity of skull modules are associated with their developmental origin, with regions derived from the anterior mandibular-stream cranial neural crest or from multiple embryonic cell populations evolving most quickly and into a greater variety of forms. Strong integration of traits is also associated with low evolutionary rate and low disparity. Individual clades are characterized by disparate evolutionary rates among cranial regions. For example, Psittaciformes (parrots) exhibit high evolutionary rates throughout the skull, but their close relatives, Falconiformes, exhibit rapid evolution in only the rostrum. Our dense sampling of cranial shape variation demonstrates that the bird skull has evolved in a mosaic fashion reflecting the developmental origins of cranial regions, with a semi-independent tempo and mode of evolution across phenotypic modules facilitating this hyperdiverse evolutionary radiation.

Musculoskeletal networks reveal topological disparity in mammalian neck evolution

BACKGROUND

The increase in locomotor and metabolic performance during mammalian evolution was accompanied by the limitation of the number of cervical vertebrae to only seven. In turn, nuchal muscles underwent a reorganization while forelimb muscles expanded into the neck region. As variation in the cervical spine is low, the variation in the arrangement of the neck muscles and their attachment sites (i.e., the variability of the neck's musculoskeletal organization) is thus proposed to be an important source of neck disparity across mammals. Anatomical network analysis provides a novel framework to study the organization of the anatomical arrangement, or connectivity pattern, of the bones and muscles that constitute the mammalian neck in an evolutionary context.

RESULTS

Neck organization in mammals is characterized by a combination of conserved and highly variable network properties. We uncovered a conserved regionalization of the musculoskeletal organization of the neck into upper, mid and lower cervical modules. In contrast, there is a varying degree of complexity or specialization and of the integration of the pectoral elements. The musculoskeletal organization of the monotreme neck is distinctively different from that of therian mammals.

CONCLUSIONS

Our findings reveal that the limited number of vertebrae in the mammalian neck does not result in a low musculoskeletal disparity when examined in an evolutionary context. However, this disparity evolved late in mammalian history in parallel with the radiation of certain lineages (e.g., cetartiodactyls, xenarthrans). Disparity is further facilitated by the enhanced incorporation of forelimb muscles into the neck and their variability in attachment sites.

Sexual dimorphism, phenotypic integration, and the evolution of head structure in casque-headed lizards

Sexes can differ in features associated with differential reproduction, which can be used during courtship or aggressive encounters. Some traits tend to evolve independently between sexes and emerge as sexually dimorphic within the organismal phenotype. We characterize such a relationship by estimating the phenotypic integration of the head morphology and modularity of the crest in the casque‐headed lizards (Corytophanidae). In this clade, some species show extreme sexual dimorphism (e.g., head crests in the genus Basiliscus) while in others, both sexes are monomorphic. To characterize these patterns, we define phenotypic integration at the interspecific level as a pattern or network of traits evidenced by phylogenetically adjusted correlations that persist among species. At this level, modularity is an increased connectedness (e.g., higher correlation) among sections of these networks that persist in a lineage during the evolution of complex phenotypes. To test both concepts, we used phylogenetic geomorphometrics to characterize the head structure of corytophanid lizards, based on a time‐calibrated phylogeny that includes candidate fossil ancestors. We found evidence of an older diversification of corytophanids than previously reported (~67 vs. ~23.5 MYA) and show that this clade includes two morphological head architectures: (1) Sexually dimorphic crests present in males that are evolving independently from the rest of the head structure, and (2) full integration of the head morphology in monomorphic species. We propose that both architectures are optimal evolutionary trajectories of the parietal crest bones in the head of these lizards. In sexually dimorphic species, these bones are elongated and thinner, and gave rise to the extended crest used in male courtship displays. In monomorphic species, the parietal crest grew thicker in both sexes to allow for a better insertion of muscles associated with a stronger bite.

Morphological modularity in the vertebral column of Felidae (Mammalia, Carnivora)

BACKGROUND

Previous studies have demonstrated that the clear morphological differences among vertebrae across the presacral column are accompanied by heterogeneous functional signals in vertebral shape. Further, several lines of evidence suggest that the mammalian axial skeleton is a highly modular structure. These include its composition of serial units, a trade-off between high shape variance and strong conservation of vertebral count, and direct association of regions with anterior expression sites of Hox genes. Here we investigate the modular organisation of the presacral vertebral column of modern cats (Felidae, Carnivora, Mammalia) with pairwise comparisons of vertebral shape covariation (i.e. integration) and evaluate our results against hypotheses of developmental and functional modularity. We used three-dimensional geometric morphometrics to quantify vertebral shape and then assessed integration between pairs of vertebrae with phylogenetic two-block partial least square analysis (PLS).

RESULTS

Six modules were identified in the pairwise analyses (vertebrae included are designated as 'C' for cervical, 'T' for thoracic, and 'L' for lumbar): an anterior module (C1 to T1); a transitional module situated between the last cervicals and first thoracics (C6 to T2); an anterior to middle thoracic set (T4 to T8); an anticlinal module (T10 and T11); a posterior set composed of the last two thoracics and lumbars (T12 to L7); and a module showing covariation between the cervicals and the posterior set (T12 to L7). These modules reflect shared developmental pathways, ossification timing, and observed ecological shape diversification in living species of felids.

CONCLUSIONS

We show here that patterns of shape integration reflect modular organisation of the vertebral column of felids. Whereas this pattern corresponds with hypotheses of developmental and functional regionalisation in the axial skeleton, it does not simply reflect major vertebral regions. This modularity may also have permitted vertebral partitions, specifically in the posterior vertebral column, to be more responsive to selection and achieve higher morphological disparity than other vertebral regions.

Approaches to Macroevolution: 1. General Concepts and Origin of Variation

Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities-i.e., an uneven density distribution-of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, "punctuated equilibrium" and "phyletic gradualism" simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions.

Out on a limb: bandicoot limb co-variation suggests complex impacts of development and adaptation on marsupial forelimb evolution

Marsupials display far less forelimb diversity than placentals, possibly because of the laborious forelimb-powered climb to the pouch performed by most marsupial neonates. This is thought to result in stronger morphological integration (i.e., higher co-variance) within the marsupial forelimb skeleton, and lower integration between marsupial fore- and hind limbs, compared to other mammals. Possible mechanisms for this constraint are a fundamental developmental change in marsupial limb patterning, or alternatively more immediate perinatal biomechanical and metabolic requirements. In the latter case, peramelid marsupials (bandicoots), which have neonates that climb very little, should show lower within-limb and higher between-limb integration, compared to other marsupials. We tested this in four peramelid species and the related bilby, using partial correlation analyses of between-landmark linear measurements of limb bones, and Procrustes-based two-block partial least-squares analysis (2B-PLS) of limb bone shapes using the same landmarks. We find extensive between-limb integration in partial correlation analyses of only bone lengths, consistent with a reduction of a short-term biomechanical/allocation constraint in peramelid forelimbs. However, partial correlations of bone proportions and 2B-PLS reveal extensive shape divergence between correlated bone pairs. This result contradicts expectations of developmental constraints or serial homology, instead suggesting a function-driven integration pattern. Comparing visualizations from cross-species principal components analysis and 2B-PLS, we tentatively identify selection for digging and half-bounding as the main driver of bandicoot limb integration patterning. This calls for further assessments of functional versus developmental limb integration in marsupials with a more strenuous neonatal climb to the pouch.

Exceptional Evolutionary Expansion of Prefrontal Cortex in Great Apes and Humans

One of the enduring questions that has driven neuroscientific enquiry in the last century has been the nature of differences in the prefrontal cortex of humans versus other animals [1]. The prefrontal cortex has drawn particular interest due to its role in a range of evolutionarily specialized cognitive capacities such as language [2], imagination [3], and complex decision making [4]. Both cytoarchitectonic [5] and comparative neuroimaging [6] studies have converged on the conclusion that the proportion of prefrontal cortex in the human brain is greatly increased relative to that of other primates. However, considering the tremendous overall expansion of the neocortex in human evolution, it has proven difficult to ascertain whether this extent of prefrontal enlargement follows general allometric growth patterns, or whether it is exceptional [1]. Species' adherence to a common allometric relationship suggests conservation through phenotypic integration, while species' deviations point toward the occurrence of shifts in genetic and/or developmental mechanisms. Here we investigate prefrontal cortex scaling across anthropoid primates and find that great ape and human prefrontal cortex expansion are non-allometrically derived features of cortical organization. This result aligns with evidence for a developmental heterochronic shift in human prefrontal growth [7, 8], suggesting an association between neurodevelopmental changes and cortical organization on a macroevolutionary scale. The evolutionary origin of non-allometric prefrontal enlargement is estimated to lie at the root of great apes (∼19-15 mya), indicating that selection for changes in executive cognitive functions characterized both great ape and human cortical organization.

How many more? Sample size determination in studies of morphological integration and evolvability

1. The variational properties of living organisms are an important component of current evolutionary theory. As a consequence, researchers working on the field of multivariate evolution have increasingly used integration and evolvability statistics as a way of capturing the potentially complex patterns of trait association and their effects over evolutionary trajectories. Little attention has been paid, however, to the cascading effects that inaccurate estimates of trait covariance have on these widely used evolutionary statistics. 2. Here, we analyze the relationship between sampling effort and inaccuracy in evolvability and integration statistics calculated from 10-trait matrices with varying patterns of covariation and magnitudes of integration. We then extrapolate our initial approach to different numbers of traits and different magnitudes of integration and estimate general equations relating the inaccuracy of the statistics of interest to sampling effort. We validate our equations using a dataset of cranial traits, and use them to make sample size recommendations. 3. Our results suggest that highly inaccurate estimates of evolvability and integration statistics resulting from small sample sizes are likely common in the literature, given the sampling effort necessary to properly estimate them. We also show that patterns of covariation have no effect on the sampling properties of these statistics, but overall magnitudes of integration interact with sample size and lead to varying degrees of bias, imprecision, and inaccuracy. 4. Finally, we provide R functions that can be used to calculate recommended sample sizes or to simply estimate the level of inaccuracy that should be expected in these statistics, given a sampling design.

Analyzing endocrine system conservation and evolution

Analyzing variation in rates of evolution can provide important insights into the factors that constrain trait evolution, as well as those that promote diversification. Metazoan endocrine systems exhibit apparent variation in evolutionary rates of their constituent components at multiple levels, yet relatively few studies have quantified these patterns and analyzed them in a phylogenetic context. This may be in part due to historical and current data limitations for many endocrine components and taxonomic groups. However, recent technological advancements such as high-throughput sequencing provide the opportunity to collect large-scale comparative data sets for even non-model species. Such ventures will produce a fertile data landscape for evolutionary analyses of nucleic acid and amino acid based endocrine components. Here I summarize evolutionary rate analyses that can be applied to categorical and continuous endocrine traits, and also those for nucleic acid and protein-based components. I emphasize analyses that could be used to test whether other variables (e.g., ecology, ontogenetic timing of expression, etc.) are related to patterns of rate variation and endocrine component diversification. The application of phylogenetic-based rate analyses to comparative endocrine data will greatly enhance our understanding of the factors that have shaped endocrine system evolution.

EMMLi: A maximum likelihood approach to the analysis of modularity

Identification of phenotypic modules, semiautonomous sets of highly correlated traits, can be accomplished through exploratory (e.g., cluster analysis) or confirmatory approaches (e.g., RV coefficient analysis). Although statistically more robust, confirmatory approaches are generally unable to compare across different model structures. For example, RV coefficient analysis finds support for both two- and six-module models for the therian mammalian skull. Here, we present a maximum likelihood approach that takes into account model parameterization. We compare model log-likelihoods of trait correlation matrices using the finite-sample corrected Akaike Information Criterion, allowing for comparison of hypotheses across different model structures. Simulations varying model complexity and within- and between-module contrast demonstrate that this method correctly identifies model structure and parameters across a wide range of conditions. We further analyzed a dataset of 3-D data, consisting of 61 landmarks from 181 macaque (Macaca fuscata) skulls, distributed among five age categories, testing 31 models, including no modularity among the landmarks and various partitions of two, three, six, and eight modules. Our results clearly support a complex six-module model, with separate within- and intermodule correlations. Furthermore, this model was selected for all five age categories, demonstrating that this complex pattern of integration in the macaque skull appears early and is highly conserved throughout postnatal ontogeny. Subsampling analyses demonstrate that this method is robust to relatively low sample sizes, as is commonly encountered in rare or extinct taxa. This new approach allows for the direct comparison of models with different parameterizations, providing an important tool for the analysis of modularity across diverse systems.