Different evolutionary pathways underlie the morphology of wrist bones in hominoids

Behavioral and phylogenetic correlates of limb length proportions in extant apes and monkeys: Implications for interpreting hominin fossils

The body proportions of extant animals help inform inferences about the behaviors of their extinct relatives, but relationships between body proportions, behavior, and phylogeny in extant primates remain unclear. Advances in behavioral data, molecular phylogenies, and multivariate analytical tools make it an opportune time to perform comprehensive comparative analyses of primate traditional limb length proportions (e.g., intermembral, humerofemoral, brachial, and crural indices), body size-adjusted long bone proportions, and principal components. In this study we used a mix of newly-collected and published data to investigate whether and how the limb length proportions of a diverse sample of primates, including monkeys, apes, and modern humans, are influenced by behavior and phylogeny. We reconfirm that the intermembral index, followed by the first principal component of traditional limb length proportions, is the single most effective variable distinguishing hominoids and other anthropoids. Combined limb length proportions and positional behaviors are strongly correlated in extant anthropoid groups, but phylogeny is a better predictor of limb length proportion variation than of behavior. We confirm convergences between members of the Atelidae and extant apes (especially Pan), members of the Hylobatidae and Pongo, and a potential divergence of Presbytis limb proportions from some other cercopithecoids, which correlate with adaptations for forelimb-dominated behaviors in some colobines. Collectively, these results substantiate hypotheses indicating that extinct hominins and other hominoid taxa can be distinguished by analyzing combinations of their limb length proportions at different taxonomic levels. From these results, we hypothesize that fossil skeletons characterized by notably disparate limb length proportions are unlikely to have exhibited similar behavioral patterns.

Cortical bone architecture of hominid intermediate phalanges reveals functional signals of locomotion and manipulation

OBJECTIVES

Reconstruction of fossil hominin manual behaviors often relies on comparative analyses of extant hominid hands to understand the relationship between hand use and skeletal morphology. In this context, the intermediate phalanges remain understudied. Thus, here we investigate cortical bone morphology of the intermediate phalanges of extant hominids and compare it to the cortical structure of the proximal phalanges, to investigate the relationship between cortical bone structure and inferred loading during manual behaviors.

MATERIALS AND METHODS

Using micro-CT data, we analyze cortical bone structure of the intermediate phalangeal shaft of digits 2-5 in Pongo pygmaeus (n = 6 individuals), Gorilla gorilla (n = 22), Pan spp. (n = 23), and Homo sapiens (n = 23). The R package morphomap is used to study cortical bone distribution, cortical thickness and cross-sectional properties within and across taxa.

RESULTS

Non-human great apes generally have thick cortical bone on the palmar shaft, with Pongo only having thick cortex on the peaks of the flexor sheath ridges, while African apes have thick cortex along the entire flexor sheath ridge and proximal to the trochlea. Humans are distinct in having thicker dorsal shaft cortex as well as thick cortex at the disto-palmar region of the shaft.

DISCUSSION

Variation in cortical bone distribution and properties of the intermediate phalanges is consistent with differences in locomotor and manipulative behaviors in extant great apes. Comparisons between the intermediate and proximal phalanges reveals similar patterns of cortical bone distribution within each taxon but with potentially greater load experienced by the proximal phalanges, even in knuckle-walking African apes. This study provides a comparative context for the reconstruction of habitual hand use in fossil hominins and hominids.

A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape

Shape measurements are crucial for evolutionary and developmental biology; however, they present difficulties in the objective and automatic quantification of arbitrary shapes. Conventional approaches are based on anatomically prominent landmarks, which require manual annotations by experts. Here, we develop a machine-learning approach by presenting morphological regulated variational AutoEncoder (Morpho-VAE), an image-based deep learning framework, to conduct landmark-free shape analysis. The proposed architecture combines the unsupervised and supervised learning models to reduce dimensionality by focusing on morphological features that distinguish data with different labels. We applied the method to primate mandible image data. The extracted morphological features reflected the characteristics of the families to which the organisms belonged, despite the absence of correlation between the extracted morphological features and phylogenetic distance. Furthermore, we demonstrated the reconstruction of missing segments from incomplete images. The proposed method provides a flexible and promising tool for analyzing a wide variety of image data of biological shapes even those with missing segments.

Carpal allometry of African apes among mammals

OBJECTIVES

Morphological variation in African ape carpals has been used to support the idea that Pan and Gorilla evolved knuckle-walking independently. Little work, however, has focused on the effect of body mass on carpal morphology. Here, we compare carpal allometry in Pan and Gorilla to that of other quadrupedal mammals with similar body mass differences. If allometric trends in Pan and Gorilla carpals mirror those of other mammals with similar body mass variation, then body mass differences may provide a more parsimonious explanation for African ape carpal variation than the independent evolution of knuckle-walking.

MATERIALS AND METHODS

Three linear measurements were collected on the capitate, hamate, lunate, and scaphoid (or scapholunate) of 39 quadrupedal species from six mammalian families/subfamilies. Relationships between linear measurements and estimated body mass were analyzed using reduced major axis regression. Slopes were compared to 0.33 for isometry.

RESULTS

Within Hominidae, higher body mass taxa (Gorilla) have relatively anteroposteriorly wider, mediolaterally wider, and/or proximodistally shorter capitates, hamates, and scaphoids than low body mass taxa (Pan). These allometric relationships are mirrored in most, but not all, mammalian families/subfamilies included in the analysis.

CONCLUSIONS

Within most mammalian families/subfamilies, carpals of high body mass taxa are proximodistally shorter, anteroposteriorly wider, and mediolaterally wider than those of low body mass taxa. These distinctions may be caused by the need to accommodate relatively higher forelimb loading associated with greater body mass. Because these trends occur within multiple mammalian families/subfamilies, some carpal variation in Pan and Gorilla is consistent with body mass differences.

3D geometric morphometric analysis of the distal radius insertion sites of the palmar radiocarpal ligaments indicates a relationship between wrist anatomy and unique locomotor behavior in hylobatids

OBJECTIVES

The objective of this study is to explore the anatomical differences in the insertion sites of the palmar radiocarpal ligaments between hylobatids and other hominoids that may be related to their different locomotor behaviors.

MATERIALS AND METHODS

The morphology of the insertion sites of the palmar radiocarpal ligaments was analyzed with three-dimensional geometric morphometrics (3D GM) in the distal radial epiphysis of 44 hylobatids, 25 Pan, 31 Gorilla and 15 Pongo.

RESULTS

Relative to other hominoids, hylobatid insertion sites of the palmar radiocarpal ligaments were relatively larger and the insertion site of the short radiolunate ligament had a palmar orientation.

DISCUSSION

Larger palmar radiocarpal ligaments in hylobatids can help stabilize the wrist during the radial and ulnar displacement that occurs in ricochetal brachiation, the characteristic locomotor behavior of hylobatids, and compensate for the large traction loads on the wrist during extended-elbow vertical climbing.

Functional signals and covariation in triquetrum and hamate shape of extant primates using 3D geometric morphometrics

In this study, we want to investigate the covariation in the shape of two carpal bones, the triquetrum and hamate, and the possible association with locomotor behavior in a broad range of primate taxa. We applied 3D Geometric Morphometrics on a large data set comprising 309 anthropoid primates of 12 different genera. Principal component analyses were performed on the covariance matrix of 18 (triquetrum) and 23 (hamate) Procrustes-aligned surface landmarks. A two-block partial least square analysis was done to test the covariance between triquetrum and hamate shape, without relying on the predictive models implicit in regression analyses. The results show that the carpal shape of quadrupedal anthropoids, which mainly use their wrist under compressive conditions, differs from that of suspensory primates as their wrist is possibly subjected to tensile and torsional forces. Within the hominids, differences in shape also distinguish more terrestrial from more arboreal species. Even within the great apes, we are able to capture shape differences between species of the same genus. In combination with behavioral and biomechanical studies, the results of this research can be used to establish form-function relationships of the primate hand which will aid the functional interpretation of primate fossil remains.

Osteological characters of birds and reptiles are more congruent with molecular phylogenies than soft characters are

Despite increased use of genomic data in phylogenetics, morphological information remains vital for resolving evolutionary relationships, particularly for fossil taxa. The properties and models of evolution of molecular sequence data are well characterized and mature, relative to those of morphological data. Furthermore, heterogeneity, integration and relative homoplasy of empirical morphological data could prove problematic for phylogenetic reconstruction. Here we compare osteological and non-osteological characters of 28 morphological datasets of extant saurians in terms of their homoplasy relative to molecular trees. Analysis of individual avian datasets finds osteological characters to be significantly more consistent with molecular data than soft characters are. Significant differences between morphological partitions were also observed in the age at which characters resolved on molecular trees. Osteological character changes occur relatively earlier in deep branches, whilst soft-tissue character transitions are more recent in shallow branches. The combined results demonstrate differences in evolutionary dynamics between morphological partitions. This may reflect evolutionary constraints acting on osteological characters, compared with the relative lability of soft characters. Furthermore, it provides some support to phylogenetic interpretations of fossil data, including dinosaurs, which are predominately osteological. Recent advances in amphibian and mammal phylogenetics may make these patterns possible to test for all tetrapods.

Effects of Captivity on the Morphology of the Insertion Sites of the Palmar Radiocarpal Ligaments in Hominoid Primates

Simple Summary

In this manuscript, we report the results of our 3D geometric morphometric analyses of the distal radial epiphysis in wild and captive gorillas, chimpanzees, and orangutans. We have identified significant differences in the insertion sites of the palmar radiocarpal ligaments between the wild and captive specimens of each species that are likely related to the locomotor behaviors developed in captivity. We believe that our study deals with a subject of great social impact in today’s world: the well-being of animals living in captivity, especially hominoid primates. Our findings provide novel information on the effect of captivity on the anatomy and locomotor behavior of hominoid primates. We trust that this information can be a basis for improving the artificial spaces where these captive primates live by increasing their available space and providing structures that more closely simulate their natural environment.

Abstract

The environmental conditions of captive hominoid primates can lead to modifications in several aspects of their behavior, including locomotion, which can then alter the morphological characteristics of certain anatomical regions, such as the knee or wrist. We have performed tridimensional geometric morphometrics (3D GM) analyses of the distal radial epiphysis in wild and captive gorillas, chimpanzees, and orangutans. Our objective was to study the morphology of the insertion sites of the palmar radiocarpal ligaments, since the anatomical characteristics of these insertion sites are closely related to the different types of locomotion of these hominoid primates. We have identified significant differences between the wild and captive specimens that are likely related to their different types of locomotion. Our results indicate that the habitat conditions of captive hominoid primates may cause them to modify their locomotor behavior, leading to a greater use of certain movements in captivity than in the wild and resulting in the anatomical changes we have observed. We suggest that creating more natural environments in zoological facilities could reduce the impact of these differences and also increase the well-being of primates raised in captive environments.

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10$\times $ in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.].

The biomechanics of knuckle-walking: 3-D kinematics of the chimpanzee and macaque wrist, hand and fingers

The origin and evolution of knuckle-walking has long been a key focus in understanding African ape, including human, origins. Yet, despite numerous studies documenting morphological characteristics potentially associated with knuckle-walking, little quantitative three-dimensional (3-D) data exist of forelimb motion during knuckle-walking. Nor do any comparative 3-D data exist for hand postures used during quadrupedalism in monkeys. This lack of data has limited the testability of proposed adaptations for knuckle-walking in African apes. This study presents the first 3-D kinematic data of the wrist, hand and metacarpophalangeal joints during knuckle-walking in chimpanzees and in macaques using digitigrade and palmigrade hand postures. These results clarify the unique characteristics of, and commonalities between, knuckle-walking and digitigrady/palmigrady in multiple planes of motion. Notably, chimpanzees utilized more wrist ulnar deviation than any macaque hand posture. Maximum extension of the chimpanzee wrist was slight (5-20 deg) and generally overlapped with macaque digitigrady. Metacarpophalangeal joint motion displayed distinct differences between digits in both species, likely related to the timing of force application. These data also reveal that maximum metacarpophalangeal extension angles during knuckle-walking (26-59 deg) were generally higher than previously considered. In macaques, maximum metacarpophalangeal extension during digitigrady and palmigrady overlapped for most digits, highlighting additional complexity in the interpretation of skeletal features that may be related to limiting metacarpophalangeal motion. Most importantly, however, these new 3-D data serve as a fundamental dataset with which evaluation of proposed musculoskeletal adaptations for knuckle-walking can be tested.

Three-dimensional geometric morphometric analysis of the distal radius insertion sites of the palmar radiocarpal ligaments in hominoid primates

OBJECTIVES

To identify anatomic differences in the insertion sites of the palmar radiocarpal ligaments in different species of hominoid primates that may be related to their different types of locomotion.

MATERIALS AND METHODS

We have used three-dimensional geometric morphometrics (3D GM) to analyze the distal radius ligament insertion sites in 31 Homo sapiens, 25 Pan troglodytes, 31 Gorilla gorilla, and 15 Pongo pygmaeus. We have also dissected the radioscaphocapitate (RSC), long radiolunate (LRL) and short radiolunate (SRL) ligaments in six H. sapiens and five P. troglodytes to obtain quantitative values that were then compared with the results of the 3D GM analysis.

RESULTS

H. sapiens had a relatively larger insertion site of the RSC + LRL ligament than the other hominoid primates. P. pygmaeus and P. troglodytes had a relatively large SRL ligament insertion site with a palmar orientation. In G. gorilla, the two ligament insertion sites were relatively smaller and the SRL insertion site had an ulnopalmar orientation.

DISCUSSION

The morphological differences observed can be related to the types of locomotion used by the different species and to quantitative data obtained from the dissection of ligaments in H. sapiens and P. troglodytes. 3D GM analysis of ligament insertion sites can help in interpreting the types of locomotion used by extinct hominoid primates through the analysis of preserved fossilized fragments of the distal radius.

Functional Morphology and Behavioral Correlates to Postcranial Musculature

In this the second issue of a two-volume set of the Anatomical Record on the relationship between muscle functional morphology and behavior, the focus is on the postcranial musculature. Traditionally, when talking of the postcranium we think of the skeletal parts that primarily provide the lever system necessary for body movements. However, without the force produced by muscle, the postcranial skeleton could not perform these or most other tasks. In this special issue, our colleagues present ten papers that focus on postcranial muscle morphology and function from different perspectives. They include papers on forelimb and hindlimb muscle functional morphology of vertebrates, including lizards, bats, primates, a carnivoran and a rodent, and involved in different substrate use (arboreal, terrestrial, and flying) and locomotion behavior (quadrupedal, leaper, and suspensory) along with a historical overview to help bookend the contextualization of the issues. The picture that these papers provide is one of great liveliness in the field of muscle functional morphology where both young students and affirmed professors continue to contribute with both traditional approaches and new techniques to further our knowledge of muscle morphology and its relationship with animal behavior. Anat Rec, 301:419-423, 2018. © 2018 Wiley Periodicals, Inc.

Trabecular bone patterning across the human hand

Hand bone morphology is regularly used to link particular hominin species with behaviors relevant to cognitive/technological progress. Debates about the functional significance of differing hominin hand bone morphologies tend to rely on establishing phylogenetic relationships and/or inferring behavior from epigenetic variation arising from mechanical loading and adaptive bone modeling. Most research focuses on variation in cortical bone structure, but additional information about hand function may be provided through the analysis of internal trabecular structure. While primate hand bone trabecular structure is known to vary in ways that are consistent with expected joint loading differences during manipulation and locomotion, no study exists that has documented this variation across the numerous bones of the hand. We quantify the trabecular structure in 22 bones of the human hand (early/extant modern Homo sapiens) and compare structural variation between two groups associated with post-agricultural/industrial (post-Neolithic) and foraging/hunter-gatherer (forager) subsistence strategies. We (1) establish trabecular bone volume fraction (BV/TV), modulus (E), degree of anisotropy (DA), mean trabecular thickness (Tb.Th) and spacing (Tb.Sp); (2) visualize the average distribution of site-specific BV/TV for each bone; and (3) examine if the variation in trabecular structure is consistent with expected joint loading differences among the regions of the hand and between the groups. Results indicate similar distributions of trabecular bone in both groups, with those of the forager sample presenting higher BV/TV, E, and lower DA, suggesting greater and more variable loading during manipulation. We find indications of higher loading along the ulnar side of the forager sample hand, with high site-specific BV/TV distributions among the carpals that are suggestive of high loading while the wrist moves through the 'dart-thrower's' motion. These results support the use of trabecular structure to infer behavior and have direct implications for refining our understanding of human hand evolution and fossil hominin hand use.

New Neandertal wrist bones from El Sidrón, Spain (1994-2009)

Twenty-nine carpal bones of Homo neanderthalensis have been recovered from the site of El Sidrón (Asturias, Spain) during excavations between 1994 and 2009, alongside ∼2500 other Neandertal skeletal elements dated to ∼49,000 years ago. All bones of the wrist are represented, including adult scaphoids (n = 6), lunates (n = 2), triquetra (n = 4), pisiforms (n = 2), trapezia (n = 2), trapezoids (n = 5), capitates (n = 5), and hamates (n = 2), as well as one fragmentary and possibly juvenile scaphoid. Several of these carpals appear to belong to the complete right wrist of a single individual. Here we provide qualitative and quantitative morphological descriptions of these carpals, within a comparative context of other European and Near Eastern Neandertals, early and recent Homo sapiens, and other fossil hominins, including Homo antecessor, Homo naledi, and australopiths. Overall, the El Sidrón carpals show characteristics that typically distinguish Neandertals from H. sapiens, such as a relatively flat first metacarpal facet on the trapezium and a more laterally oriented second metacarpal facet on the capitate. However, there are some distinctive features of the El Sidrón carpals compared with most other Neandertals. For example, the tubercle of the trapezium is small with limited projection, while the scaphoid tubercle and hamate hamulus are among the largest seen in other Neandertals. Furthermore, three of the six adult scaphoids show a distinctive os-centrale portion, while another is a bipartite scaphoid with a truncated tubercle. The high frequency of rare carpal morphologies supports other evidence of a close genetic relationship among the Neandertals found at El Sidrón.

Forearm pronation efficiency in A.L. 288-1 (Australopithecus afarensis) and MH2 (Australopithecus sediba): Insights into their locomotor and manipulative habits

OBJECTIVES

The locomotor and manipulative abilities of australopithecines are highly debated in the paleoanthropological context. Australopithecus afarensis and Australopithecus sediba likely engaged in arboreal locomotion and, especially the latter, in certain activities implying manipulation. Nevertheless, their degree of arboreality and the relevance of their manipulative skills remain unclear. Here we calculate the pronation efficiency of the forearm (E_rot ) in these taxa to explore their arboreal and manipulative capabilities using a biomechanical approach.

MATERIALS AND METHODS

Three-dimensional humeral images and upper limb measurements of A.L. 288-1 (Au. afarensis) and MH2 (Au. sediba) were used to calculate E_rot using a previously described biomechanical model.

RESULTS

Maximal E_rot in elbow flexion occurs in a rather supinated position of the forearm in Au. afarensis, similarly to Pan troglodytes. In elbow extension, maximal E_rot in this fossil taxon occurs in the same forearm position as in Pongo spp. In Au. sediba the forearm positions where E_rot is maximal are largely coincident with those for Hylobatidae.

CONCLUSIONS

The pattern in Au. afarensis suggests relevant arboreal capabilities, which would include vertical climbing, although it is suggestive of poorer manipulative skills than in modern humans. The similarity between Au. sediba and Hylobatidae is difficult to interpret, but the differences between Au. sediba and Au. afarensis suggest that the capacity to rotate the forearm followed different evolutionary processes in these australopithecine species. Although functional inferences from the upper limb are complex, the observed differences between both taxa point to the existence of two distinct anatomical models.

Lower Ilium Evolution in Apes and Hominins

Elucidating the pelvic morphology of the Pan-Homo last common ancestor (LCA) is crucial for understanding ape and human evolution. The pelvis of Ardipithecus ramidus has been the basis of controversial interpretations of the LCA pelvis. In particular, it was proposed that the lower ilium became elongate independently in the orangutan and chimpanzee clades, making these taxa poor analogues for the pelvis of the LCA. This study examines the variation in relative lower ilium height between and within living and fossil hominoid species (and other anthropoids), and models its evolution using available fossil hominoids as calibration points. We find nuanced differences in relative lower ilium height among living hominoids, particularly in regards to gorillas, which do not have elongate lower ilia (because they are likely to represent the plesiomorphic hominoid condition for this trait). We also show that differences in relative lower ilium height among hominoid taxa are not readily explained by differences in size between species. Our maximum likelihood ancestral state reconstructions support inferences that chimpanzees (Pan troglodytes in particular) and orangutans evolved their elongate lower ilia independently. We also find that the predicted lower ilium height of the Pan-Homo LCA is shorter than all great apes except gorillas. This study adds to a growing body of evidence that finds different regions of the body show different evolutionary histories in different hominoids, and underscores that the unique combinations of morphologies of each modern and fossil hominoid species should be considered when reconstructing the mosaic nature of the Pan-Homo LCA. Anat Rec, 300:828-844, 2017. © 2017 Wiley Periodicals, Inc.

Evolution of the hominoid scapula and its implications for earliest hominid locomotion

OBJECTIVES

The higher primate scapula has been subject to many explanations of the putative "adaptive value" of its individual traits. However, the shift from the bone's position in above branch quadrupeds to its more posterolateral position in recent hominoids obviously required fundamental changes to its general form. We hypothesize that most features argued to be individually adaptive are more likely secondary consequences of changes in its fundamental bauplan, a view more consistent with modern developmental biology.

MATERIALS AND METHODS

We tested this hypothesis with scapular metrics and angles from a broad anthropoid sample.

RESULTS

Our results support our hypothesis. Contrary to earlier predictions, vertebral border length differs little relative to body size in anthropoids, inferior angle position primarily reflects mediolateral scapular breadth, and supraspinous and infraspinous fossa sizes largely reflect scapular spine orientation. Suspensory taxa have cranially oriented glenoids, whereas slow clamberers and humans do not. Australopithecus most closely resembles the latter.

DISCUSSION

Most scapular features can be explained by only two primary changes: (1) reduction in mediolateral breadth and (2) change in the glenoid position relative to the vertebral border with increased reliance on suspension, which led to a more cranially angled scapular spine. Virtually all other scapular traits appear to be byproducts of these two changes. Based on fossil morphology, hominids¹ were derived from a last common ancestor primarily adapted for clambering and not for suspension. Scapular form in early hominids such as Australopithecus is therefore primitive and largely reflects the genus's general clambering heritage.

Sampling diverse characters improves phylogenies: Craniodental and postcranial characters of vertebrates often imply different trees

Morphological cladograms of vertebrates are often inferred from greater numbers of characters describing the skull and teeth than from postcranial characters. This is either because the skull is believed to yield characters with a stronger phylogenetic signal (i.e., contain less homoplasy), because morphological variation therein is more readily atomized, or because craniodental material is more widely available (particularly in the palaeontological case). An analysis of 85 vertebrate datasets published between 2000 and 2013 confirms that craniodental characters are significantly more numerous than postcranial characters, but finds no evidence that levels of homoplasy differ in the two partitions. However, a new partition test, based on tree-to-tree distances (as measured by the Robinson Foulds metric) rather than tree length, reveals that relationships inferred from the partitions are significantly different about one time in three, much more often than expected. Such differences may reflect divergent selective pressures in different body regions, resulting in different localized patterns of homoplasy. Most systematists attempt to sample characters broadly across body regions, but this is not always possible. We conclude that trees inferred largely from either craniodental or postcranial characters in isolation may differ significantly from those that would result from a more holistic approach. We urge the latter.

The Independent Evolution Method Is Not a Viable Phylogenetic Comparative Method

Phylogenetic comparative methods (PCMs) use data on species traits and phylogenetic relationships to shed light on evolutionary questions. Recently, Smaers and Vinicius suggested a new PCM, Independent Evolution (IE), which purportedly employs a novel model of evolution based on Felsenstein’s Adaptive Peak Model. The authors found that IE improves upon previous PCMs by producing more accurate estimates of ancestral states, as well as separate estimates of evolutionary rates for each branch of a phylogenetic tree. Here, we document substantial theoretical and computational issues with IE. When data are simulated under a simple Brownian motion model of evolution, IE produces severely biased estimates of ancestral states and changes along individual branches. We show that these branch-specific changes are essentially ancestor-descendant or “directional” contrasts, and draw parallels between IE and previous PCMs such as “minimum evolution”. Additionally, while comparisons of branch-specific changes between variables have been interpreted as reflecting the relative strength of selection on those traits, we demonstrate through simulations that regressing IE estimated branch-specific changes against one another gives a biased estimate of the scaling relationship between these variables, and provides no advantages or insights beyond established PCMs such as phylogenetically independent contrasts. In light of our findings, we discuss the results of previous papers that employed IE. We conclude that Independent Evolution is not a viable PCM, and should not be used in comparative analyses.

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

Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. Phenotypic integration and modularity have been hypothesized to shape morphological evolution, and we extended simulations to confirm that trait integration can influence both the trajectory and magnitude of response to selection. We further demonstrate that phenotypic integration can produce both more and less disparate organisms than would be expected under random walk models by repartitioning variance in preferred directions. This effect can also be expected to favour homoplasy and convergent evolution. New empirical analyses of the carnivoran cranium show that rates of evolution, in contrast, are not strongly influenced by phenotypic integration and show little relationship to morphological disparity, suggesting that phenotypic integration may shape the direction of evolutionary change, but not necessarily the speed of it. Nonetheless, phenotypic integration is problematic for morphological clocks and should be incorporated more widely into models that seek to accurately reconstruct both trait and organismal evolution.