How reliable are human phylogenetic hypotheses?

Form function of sulcus acusticus of the sagittal otolith in seven Sciaenidae (Acanthuriformes) species using geometric morphometrics (southwestern Atlantic)

The morphology of otoliths determines the function they perform, and it is influenced by genetic and environmental factors. Knowing those relationships is necessary to understand the role of hearing in fish. The objectives of this work were: exploring the shape of the sulcus of the sagittal otolith in seven species of Sciaenidae, in relation to sound production, and analyzing whether the shape and size of the sulcus can be used as a phylogenetic character. For this purpose, geometric morphometry analysis was carried out using landmarks data. It was found that there is an influence of size on the shape of the sulcus, and significant differences were found between the shapes of the sulcus (permutational multivariate analysis of variance). Three general shapes of the sulcus were identified (using principal component analysis, canonical variate analysis, and clustering): (1) in species that produce sounds at dominant frequencies <350 Hz, the deformation of the sulcus showed a tendency towards circularity of the ostium; (2) in those species that produce sounds at frequencies >350 Hz, the ostium showed a flattened ovoid shape, and the cauda increased its length; (3) the species that do not produce sounds, did not show any modifications, relative to the form of consensus. Despite finding sister species that presented similar sulcus shapes in the phylogeny, the results did not confirm that this can be used as a phylogenetic character. This work discusses whether the combined effects of phylogenetic legacy and natural functional selection have led to convergent evolution for the sulcus form. The differences presented by the sulcus of species that occupy the same clade, could indicate that there is a displacement of characters. The sagittal otolith and the sensory macula associated with the sulcus acusticus are highly plastic structures that are subject to strong evolutionary pressure in relation to environmental and behavioral factors, resulting in great variability in shapes that can be associated with a specific character. The variation in the shape of the sulcus would allow the analysed species to coexist in the same coastal soundscapes, without losing their particular hearing needs, even in case of overlapping their spatial and temporal distribution areas.

Implications of outgroup selection in the phylogenetic inference of hominoids and fossil hominins

Understanding the phylogenetic relationships among hominins and other hominoid species is critical to the study of human origins. However, phylogenetic inferences are dependent on both the character data and taxon sampling used. Previous studies of hominin phylogenetics have used Papio and Colobus as outgroups in their analyses; however, these extant monkeys possess many derived traits that may confound the polarities of morphological changes among living apes and hominins. Here, we consider Victoriapithecus and Ekembo as more suitable outgroups. Both Victoriapithecus and Ekembo are anatomically well known and are widely accepted as morphologically primitive stem cercopithecoid and hominoid taxa, respectively, making them more appropriate for inferring polarity for later-occurring hominoid- and hominin-focused analyses. Craniodental characters for both taxa were scored and then added to a previously published matrix of fossil hominin and extant hominoid taxa, replacing outgroups Papio and Colobus over a series of iterative analyses using both parsimony and Bayesian inference methods. Neither the addition nor replacement of outgroup taxa changed tree topology in any analysis. Importantly, however, bootstrap support values and posterior probabilities for nodes supporting their relationships generally increased compared to previous analyses. These increases were the highest at extant hominoid and basal hominin nodes, recovering the molecular ape phylogeny with considerably higher support and strengthening the inferred relationships among basal hominins. Interestingly, however, the inclusion of both extant and fossil outgroups reduced support for the crown hominid node. Our findings suggest that, in addition to improving character polarity estimation, including fossil outgroups generally strengthens confidence in relationships among extant hominoid and basal hominins.

A new approach to exploratory data analysis in hominin phylogenetic reconstruction

The phylogenetic relationships between fossil hominin taxa have been a contentious topic for decades. Recent discoveries of new taxa, rather than resolving the issue, have only further confused it. Compounding this problem are the limitations of some of the tools frequently used by paleoanthropologists to analyze these relationships. Most commonly, phylogenetic questions are investigated using analytical methods such as maximum parsimony and Bayesian analysis. While these are useful analytical tools, these tree-building methods can have limitations when investigating taxa that may have complex evolutionary histories. Exploratory data analysis can provide information about patterns in a dataset that are obscured by tree-based methods. These patterns include phylogenetic signal conflict, which is not depicted in tree-based methods. Signal conflict can have a number of sources, including methodological issues with character choice, taxonomic issues, homoplasy, and gene flow between taxa. In this study, an exploratory data analysis of fossil hominin morphological data is conducted using the tree-based analytical method neighbor-joining and the network-based analytical method neighbor-net with the goal of visualizing phylogenetic signal conflict within a hominin morphological data set. The data set is divided into cranial regions, and each cranial region is analyzed individually to investigate which regions of the skull contain the highest levels of signal conflict. Results of this analysis show that conflicting phylogenetic signals are present in the hominin fossil record during the relatively speciose period between 3 and 1 Ma, and they also indicate that levels of signal conflict vary by cranial region. Possible sources of these conflicting signals are then explored. Exploratory data analyses such as this can be a useful tool in generating phylogenetic hypotheses and in refining character choice. This study also highlights the value network-based approaches can bring to the hominin phylogenetic analysis toolkit.

A comparative probabilistic analysis of human and chimpanzee rotator cuff functional capacity

Computational musculoskeletal modeling represents a valuable approach to examining biological systems in physical anthropology. Probabilistic modeling builds on computational musculoskeletal models by associating mathematical distributions of specific musculoskeletal features within known ranges of biological variability with functional outcomes. The purpose of this study was to determine if overlap in rotator cuff muscle force predictions would occur between species during the performance of an evolutionarily relevant horizontal bimanual arm suspension task. This necessitated creating novel probabilistic models of the human and chimpanzee glenohumeral joint through augmentation of previously published deterministic models. Glenohumeral musculoskeletal features of anthropological interest were probabilistically modeled to produce distributions of predicted human and chimpanzee rotator cuff muscle force that were representative of the specific anatomical manipulations. Musculoskeletal features modeled probabilistically included rotator cuff origins and deltoid insertion, glenoid inclination, and joint stability. Predicted human rotator cuff muscle force distributions were mostly limited to alternating between infraspinatus and teres minor, with both 100% and 0% muscle force predicted for both muscles. The chimpanzee model predicted low-to-moderate muscle force across all rotator cuff muscles. Rotator cuff muscle force predictions were most sensitive to changes of muscle origins and insertions. Results indicate that functional rotator cuff overlap is unlikely between chimpanzees and humans without greater modifications of the glenohumeral musculoskeletal phenotypes. The results also highlight the low efficacy of the human upper extremity in overhead, weight-bearing tasks, and propensity for rotator cuff injury.

The endocast from Dana Aoule North (DAN5/P1): A 1.5 million year-old human braincase from Gona, Afar, Ethiopia

The nearly complete cranium DAN5/P1 was found at Gona (Afar, Ethiopia), dated to 1.5-1.6 Ma, and assigned to the species Homo erectus. Its size is, nonetheless, particularly small for the known range of variation of this taxon, and the cranial capacity has been estimated as 598 cc. In this study, we analyzed a reconstruction of its endocranial cast, to investigate its paleoneurological features. The main anatomical traits of the endocast were described, and its morphology was compared with other fossil and modern human samples. The endocast shows most of the traits associated with less encephalized human taxa, like narrow frontal lobes and a simple meningeal vascular network with posterior parietal branches. The parietal region is relatively tall and rounded, although not especially large. Based on our set of measures, the general endocranial proportions are within the range of fossils included in the species Homo habilis or in the genus Australopithecus. Similarities with the genus Homo include a more posterior position of the frontal lobe relative to the cranial bones, and the general endocranial length and width when size is taken into account. This new specimen extends the known brain size variability of Homo ergaster/erectus, while suggesting that differences in gross brain proportions among early human species, or even between early humans and australopiths, were absent or subtle.

An updated analysis of hominin phylogeny with an emphasis on re-evaluating the phylogenetic relationships of Australopithecus sediba

The discovery and description of Australopithecus sediba has reignited the debate over the evolutionary history of the australopiths and the genus Homo. It has been suggested that A. sediba may be an ancestor of Homo because it possesses a mosaic of derived Homo-like and primitive australopith-like traits. However, an alternative hypothesis proposes that the majority of the purported Homo-like craniodental characters can be attributed to the juvenile status of the type specimen, MH1. We conducted an independent character assessment of the craniodental morphology of A. sediba, with particular emphasis on evaluating whether the ontogenetic status of MH1 may have affected its purported Homo-like characteristics. In doing so, we have also expanded fossil hypodigms to incorporate the new Australopithecus anamensis cranium from Woranso-Mille (MRD-VP-1/1), as well as recently described Paranthropus robustus cranial remains from Drimolen (DNH 7, DNH 155). Morphological character data were analyzed using both standard parsimony and Bayesian techniques. In addition, we conducted a series of Bayesian analyses constrained to evaluate the hypothesis that Australopithecus africanus and A. sediba are sister taxa. Based on the results of the parsimony and Bayesian analyses, we could not reject the hypothesis that A. sediba shares its closest phylogenetic affinities with the genus Homo. Therefore, based on currently available craniodental evidence, we conclude that A. sediba is plausibly the terminal end of a lineage that shared a common ancestor with the earliest representatives of Homo. We caution, however, that the discovery of new A. sediba fossils preserving adult cranial morphology or the inclusion of postcranial characters may ultimately necessitate a re-evaluation of this hypothesis.

The taxonomic attribution of African hominin postcrania from the Miocene through the Pleistocene: Associations and assumptions

Postcranial bones may provide valuable information about fossil taxa relating to their locomotor habits, manipulative abilities and body sizes. Distinctive features of the postcranial skeleton are sometimes noted in species diagnoses. Although numerous isolated postcranial fossils have become accepted by many workers as belonging to a particular species, it is worthwhile revisiting the evidence for each attribution before including them in comparative samples in relation to the descriptions of new fossils, functional analyses in relation to particular taxa, or in evolutionary contexts. Although some workers eschew the taxonomic attribution of postcranial fossils as being less important (or interesting) than interpreting their functional morphology, it is impossible to consider the evolution of functional anatomy in a taxonomic and phylogenetic vacuum. There are 21 widely recognized hominin taxa that have been described from sites in Africa dated from the Late Miocene to the Middle Pleistocene; postcranial elements have been attributed to 17 of these. The bones that have been thus assigned range from many parts of a skeleton to isolated elements. However, the extent to which postcranial material can be reliably attributed to a specific taxon varies considerably from site to site and species to species, and is often the subject of considerable debate. Here, we review the postcranial remains attributed to African hominin taxa from the Late Miocene to the Middle and Late Pleistocene and place these assignations into categories of reliability. The catalog of attributions presented here may serve as a guide for making taxonomic decisions in the future.

Protocol combining tree-based Maximum Parsimony and web-like Phylogenetic Networks analyses to investigate reticulate human evolution

Our protocol combines Maximum Parsimony and Phylogenetic Networks approaches to understand the phylogenetic relationships and evolutionary processes of hominin species that might have shared inheritance from multiple ancestors. By addressing the questions of pattern and process in human phylogeny, the protocol can be used to clarify the taxonomic definition(s) of diverse hominin groups and ascertain whether or not the mode of evolution of genus Homo is reticulate. Using high quality and informative phenotypic data sets is necessary to yield meaningful results.

For complete details on the use and execution of this protocol, please refer to Caparros and Prat (2021).

•

Combine Maximum Parsimony and Phylogenetic Networks in human phylogenetic research

•

Maximum Parsimony (MP) is used to clarify taxonomic definitions of hominin groups

•

MP results are validated by comparing them with alternative statistical analysis

•

Phylogenetic Networks approach used to make inferences about modes of evolution

Facial asymmetry tracks genetic diversity among Gorilla subspecies

Mountain gorillas are particularly inbred compared to other gorillas and even the most inbred human populations. As mountain gorilla skeletal material accumulated during the 1970s, researchers noted their pronounced facial asymmetry and hypothesized that it reflects a population-wide chewing side preference. However, asymmetry has also been linked to environmental and genetic stress in experimental models. Here, we examine facial asymmetry in 114 crania from three Gorilla subspecies using 3D geometric morphometrics. We measure fluctuating asymmetry (FA), defined as random deviations from perfect symmetry, and population-specific patterns of directional asymmetry (DA). Mountain gorillas, with a current population size of about 1000 individuals, have the highest degree of facial FA (explaining 17% of total facial shape variation), followed by Grauer gorillas (9%) and western lowland gorillas (6%), despite the latter experiencing the greatest ecological and dietary variability. DA, while significant in all three taxa, explains relatively less shape variation than FA does. Facial asymmetry correlates neither with tooth wear asymmetry nor increases with age in a mountain gorilla subsample, undermining the hypothesis that facial asymmetry is driven by chewing side preference. An examination of temporal trends shows that stress-induced developmental instability has increased over the last 100 years in these endangered apes.

Relative tooth size, Bayesian inference, and Homo naledi

OBJECTIVES

Size-corrected tooth crown measurements were used to estimate phenetic affinities among Homo naledi (~335-236 ka) and 11 other Plio-Pleistocene and recent species. To assess further their efficacy, and identify dental evolutionary trends, the data were then quantitatively coded for phylogenetic analyses. Results from both methods contribute additional characterization of H. naledi relative to other hominins.

MATERIALS AND METHODS

After division by their geometric mean, scaled mesiodistal and buccolingual dimensions were used in tooth size apportionment analysis to compare H. naledi with Australopithecus africanus, A. afarensis, Paranthropus robustus, P. boisei, H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, H. sapiens, and Pan troglodytes. These data produce equivalently scaled samples unaffected by interspecific size differences. The data were then gap-weighted for Bayesian inference.

RESULTS

Congruence in interspecific relationships is evident between methods, and with many inferred from earlier systematic studies. However, the present results place H. naledi as a sister taxon to H. habilis, based on a symplesiomorphic pattern of relative tooth size. In the preferred Bayesian phylogram, H. naledi is nested within a clade comprising all Homo species, but it shares some characteristics with australopiths and, particularly, early Homo.

DISCUSSION

Phylogenetic analyses of relative tooth size yield information about evolutionary dental trends not previously reported in H. naledi and the other hominins. Moreover, with an appropriate model these data recovered plausible evolutionary relationships. Together, the findings support recent study suggesting H. naledi originated long before the geological date of the Dinaledi Chamber, from which the specimens under study were recovered.

Detecting Phylogenetic Signal and Adaptation in Papionin Cranial Shape by Decomposing Variation at Different Spatial Scales

Phylogenetic reconstruction based on morphometric data is hampered by homoplasies. For example, many similarities in cranial form between primate taxa more strongly reflect ecological similarities rather than phylogenetic relatedness. However, the way in which the different cranial bones constitute cranial form is, if at all, of less functional relevance and thus largely hidden from selection. We propose that these “constructional details” are better indicators of phylogenetic history than any large-scale shape feature or raw form variable. Within a geometric morphometric context, we show how to analyze the relative extent of bones independently of differences in overall shape. We also show how to decompose total shape variation into small-scale and large-scale shape variation. We apply both methods to the midsagittal cranial morphology of papionin monkeys, which are well known for the discrepancy between morphological similarities and phylogenetic relationships. We study phylogenetic signal and functional adaptation using a molecular phylogeny and contextual data on feeding ecology and locomotor behavior. As expected, total cranial shape, bone outline shape, and large-scale shape features were only weakly associated with phylogenetic distance. But the relative bone contributions and small-scale shape features were both highly correlated with phylogenetic distances. By contrast, the association with ecological and behavioral variables was strongest for the outline shape and large-scale shape features. Studies of morphological adaptation and phylogenetic history thus profit from a decomposition of shape variation into different spatial scales. [Adaptation; canalization; cranial shape; geometric morphometrics; papionini; partial warps; phylogeny.]

Development of a comparative chimpanzee musculoskeletal glenohumeral model: implications for human function

Modern human shoulder function is affected by the evolutionary adaptations that have occurred to ensure survival and prosperity of the species. Robust examination of behavioral shoulder performance and injury risk can be holistically improved through an interdisciplinary approach that integrates anthropology and biomechanics. Coordination of these fields can allow different perspectives to contribute to a more complete interpretation of biomechanics of the modern human shoulder. The purpose of this study was to develop a novel biomechanical and comparative chimpanzee glenohumeral model, designed to parallel an existing human glenohumeral model, and compare predicted musculoskeletal outputs between the two models. The chimpanzee glenohumeral model consists of three modules - an external torque module, a musculoskeletal geometric module and an internal muscle force prediction module. Together, these modules use postural kinematics, subject-specific anthropometrics, a novel shoulder rhythm, glenohumeral stability ratios, hand forces, musculoskeletal geometry and an optimization routine to estimate joint reaction forces and moments, subacromial space dimensions, and muscle and tissue forces. Using static postural data of a horizontal bimanual suspension task, predicted muscle forces and subacromial space were compared between chimpanzees and humans. Compared with chimpanzees, the human model predicted a 2 mm narrower subacromial space, deltoid muscle forces that were often double those of chimpanzees and a strong reliance on infraspinatus and teres minor (60-100% maximal force) over other rotator cuff muscles. These results agree with previous work on inter-species differences that inform basic human rotator cuff function and pathology.

Additive genetic variation in the craniofacial skeleton of baboons (genus Papio) and its relationship to body and cranial size

OBJECTIVES

Determining the genetic architecture of quantitative traits and genetic correlations among them is important for understanding morphological evolution patterns. We address two questions regarding papionin evolution: (1) what effect do body and cranial size, age, and sex have on phenotypic (V_P ) and additive genetic (V_A ) variation in baboon crania, and (2) how might additive genetic correlations between craniofacial traits and body mass affect morphological evolution?

MATERIALS AND METHODS

We use a large captive pedigreed baboon sample to estimate quantitative genetic parameters for craniofacial dimensions (EIDs). Our models include nested combinations of the covariates listed above. We also simulate the correlated response of a given EID due to selection on body mass alone.

RESULTS

Covariates account for 1.2-91% of craniofacial V_P . EID V_A decreases across models as more covariates are included. The median genetic correlation estimate between each EID and body mass is 0.33. Analysis of the multivariate response to selection reveals that observed patterns of craniofacial variation in extant baboons cannot be attributed solely to correlated response to selection on body mass, particularly in males.

DISCUSSION

Because a relatively large proportion of EID V_A is shared with body mass variation, different methods of correcting for allometry by statistically controlling for size can alter residual V_P patterns. This may conflate direct selection effects on craniofacial variation with those resulting from a correlated response to body mass selection. This shared genetic variation may partially explain how selection for increased body mass in two different papionin lineages produced remarkably similar craniofacial phenotypes.

Late Australopiths and the Emergence of Homo

New fossil discoveries and new analyses increasingly blur the lines between Australopithecus and Homo, changing scientific ideas about the transition between the two genera. The concept of the genus itself remains an unsettled issue, though recent fossil discoveries and theoretical advances, alongside developments in phylogenetic reconstruction and hypothesis testing, are helping us approach a resolution. A review of the latest discoveries and research reveals that (a) despite the recent recovery of key fossil specimens, the antiquity of the genus Homo remains uncertain; (b) although there exist several australopith candidate ancestors for the genus Homo, there is little consensus about which of these, if any, represents the actual ancestor; and (c) potential convergent evolution (homoplasy) in adaptively significant features in late australopiths and basal members of the Homo clade, combined with probable reticulate evolution, makes it currently impossible to identify the direct ancestor of Homo erectus.

Early Homo, plasticity and the extended evolutionary synthesis

The Modern Synthesis led to fundamental advances in understandings of human evolution. For human palaeontology, a science that works from ancestral phenotypes (i.e. the fossil record), particularly important have been perspectives used to help understand the heritable aspects of phenotypes and how fossil individuals might then be aggregated into species, and relationships among these groups understood. This focus, coupled with the fragmentary nature of the fossil record, however, means that individual phenotypic variation is often treated as unimportant 'noise', rather than as a source of insight into population adaptation and evolutionary process. The emphasis of the extended evolutionary synthesis on plasticity as a source of phenotypic novelty, and the related question of the role of such variation in long-term evolutionary trends, focuses welcome attention on non-genetic means by which novel phenotypes are generated and in so doing provides alternative approaches to interpreting the fossil record. We review evidence from contemporary human populations regarding some of the aspects of adult phenotypes preserved in the fossil record that might be most responsive to non-genetic drivers, and we consider how these perspectives lead to alternate hypotheses for interpreting the fossil record of early genus Homo. We conclude by arguing that paying closer attention to the causes and consequences of intraspecific phenotypic variation in its own right, as opposed to as noise around a species mean, may inspire a new generation of hypotheses regarding species diversity in the Early Pleistocene and the foundations for dispersal and regional diversification in Homo erectus and its descendants.

Another Look at Ethnicity as a Biological Concept: Moving Anthropology Beyond the Race Concept

Montagu referred to race as ‘man’s most dangerous myth’, while Lévi-Strauss called it ‘the original sin of anthropology’. Although persuasive arguments against the concept of race were made throughout the 20th century, race remains a particular problem for anthropologists who deal in the classification of human populations. Racial terminology has been perpetuated within anthropology largely owing to the fact that, historically, race formed the very core of anthropological study. Despite the conceptual inadequacy of race, the anthropological enterprise has yet to move beyond it as an explanatory tool for understanding human biological variation because of the lack of a conceptual and/or methodological replacement. This article re-analyses historical anthropological literature on ethnicity and biocultural interaction as a replacement for the race concept, and recasts it in the context of modern philosophical and psychological perspectives on population variation.

The relative correspondence of cranial and genetic distances in papionin taxa and the impact of allometric adjustments

The reconstruction of phylogenetic relationships in the primate fossil record is dependent upon a thorough understanding of the phylogenetic utility of craniodental characters. Here, we test three previously proposed hypotheses for the propensity of primate craniomandibular data to exhibit homoplasy, using a study design based on the relative congruence between cranial distance matrices and a consensus genetic distance matrix ("genetic congruence") for papionin taxa: 1) matrices based on cranial regions subjected to less masticatory strain are more genetically congruent than high-strain cranial matrices; 2) matrices based on cranial regions developing earlier in ontogeny are more genetically congruent than matrices based on regions that develop later; and 3) matrices based on cranial regions with greater anatomical/functional complexity are more genetically congruent than matrices based on anatomically simpler regions. Morphological distance matrices based on the shape of 15 different cranial regions, delineated on the basis of previous catarrhine studies, were statistically compared to a matrix of known genetic distances in papionins. Since sexual dimorphism and allometry are known to characterize this clade, several analytical iterations were conducted: 1) mixed-sex, male-only, and female-only analyses and 2) with and without an allometric scaling adjustment. Across all datasets, the chondrocranium matrix was the most consistently correlated with genetic distances, which is also consistent with previous studies of cercopithecoid taxa; however, there was no support for the internal predictions of the three hypotheses tested. Allometric scaling corrections had the largest impact on the genetic congruence of facial shape matrices, a result consistent with previous studies that have described facial homoplasy in papionin taxa. These findings differ from patterns described for hominoid taxa, suggesting that no single predictive criterion can explain phylogenetic utility of cranial datasets across catarrhine primate taxa. Many of the differences in morphological-genetic matrix correlations could result from different levels of phenotypic integration and evolvability in cercopithecoids and hominoids, suggesting that further study of these phenomena in extant primates is warranted.

Contextualising primate origins--an ecomorphological framework

Ecomorphology - the characterisation of the adaptive relationship between an organism's morphology and its ecological role - has long been central to theories of the origin and early evolution of the primate order. This is exemplified by two of the most influential theories of primate origins: Matt Cartmill's Visual Predation Hypothesis, and Bob Sussman's Angiosperm Co-Evolution Hypothesis. However, the study of primate origins is constrained by the absence of data directly documenting the events under investigation, and has to rely instead on a fragmentary fossil record and the methodological assumptions inherent in phylogenetic comparative analyses of extant species. These constraints introduce particular challenges for inferring the ecomorphology of primate origins, as morphology and environmental context must first be inferred before the relationship between the two can be considered. Fossils can be integrated in comparative analyses and observations of extant model species and laboratory experiments of form-function relationships are critical for the functional interpretation of the morphology of extinct species. Recent developments have led to important advancements, including phylogenetic comparative methods based on more realistic models of evolution, and improved methods for the inference of clade divergence times, as well as an improved fossil record. This contribution will review current perspectives on the origin and early evolution of primates, paying particular attention to their phylogenetic (including cladistic relationships and character evolution) and environmental (including chronology, geography, and physical environments) contextualisation, before attempting an up-to-date ecomorphological synthesis of primate origins.

The 'temporal effect' in hominids: Reinvestigating the nature of support for a chimp-human clade in bone morphology

In 2004, an analysis by Lockwood and colleagues of hard-tissue morphology, using geometric morphometrics on the temporal bone, succeeded in recovering the correct phylogeny of living hominids without resorting to potentially problematic methods for transforming continuous shape variables into meristic characters. That work has increased hope that by using modern analytical methods and phylogenetically informative anatomical data we might one day be able to accurately infer the relationships of hominins, including the closest extinct relatives of modern humans. In the present study, using 3D virtually generated models of the hominid temporal bone and a larger suite of geometric morphometric and comparative techniques, we have re-examined the evidence for a Pan-Homo clade. Despite differences in samples, as well as the type of raw data, the effect of measurement error (and especially landmark digitization by a different operator), but also a broader perspective brought in by our diverse set of approaches, our reanalysis largely supports Lockwood and colleagues' original results. However, by focusing not only mainly on shape (as in the original 2004 analysis) but also on size and 'size-corrected' (non-allometric) shape, we demonstrate that the strong phylogenetic signal in the temporal bone is largely related to similarities in size. Thus, with this study, we are not suggesting the use of a single 'character', such as size, for phylogenetic inference, but we do challenge the common view that shape, with its highly complex and multivariate nature, is necessarily more phylogenetically informative than size and that actually size and size-related shape variation (i.e., allometry) confound phylogenetic inference based on morphology. This perspective may in fact be less generalizable than often believed. Thus, while we confirm the original findings by Lockwood et al., we provide a deep reinterpretation of their nature and potential implications for hominid phylogenetics and we show how crucial it is not to overlook size in geometric morphometric analyses.

Heritability of the Human Craniofacial Complex

Quantifying normal variation and the genetic underpinnings of anatomical structures is one of the main goals of modern morphological studies. However, the extent of genetic contributions to normal variation in craniofacial morphology in humans is still unclear. The current study addresses this gap by investigating the genetic underpinnings of normal craniofacial morphology. The sample under investigation consists of 75 linear and angular measurements spanning the entire craniofacial complex, recorded from lateral cephalographs of 1,379 participants in the Fels Longitudinal Study. Heritabilities for each trait were estimated using SOLAR, a maximum-likelihood variance components approach utilizing all pedigree information for parameter estimation. Trait means and mean effects of the covariates age, sex, age(2) , sex × age, and sex × age(2) were simultaneously estimated in the analytic models. All traits of the craniofacial complex were significantly heritable. Heritability estimates ranged from 0.10 to 0.60, with the majority being moderate. It is important to note that we found similar ranges of heritability occurring across the different functional/developmental components of the craniofacial complex, the splanchnocranium, the basicranium, and the neurocranium. This suggests that traits from different regions of the craniofacial complex are of comparable utility for the purposes of population history and phylogeny reconstruction. At the same time, this genetic influence on craniofacial morphology signals a caution to researchers of nongenetic studies to consider the implications of this finding when selecting samples for study given their project design and goals.

A comparison of catarrhine genetic distances with pelvic and cranial morphology: implications for determining hominin phylogeny

Inferring the evolutionary history of the hominins is necessarily reliant on comparative analyses of fossilized skeletal anatomy. However, the reliability of different primate skeletal regions for recovering phylogenetic relationships is currently poorly understood. Historically, postcranial variation has largely been conceived of as reflecting locomotory and postural adaptation. The shape of the os coxae is central to such discussions given the divergent morphology displayed by the bipedal hominin pelvis relative to other primate taxa. While previous cladistic studies have suggested that postcranial and cranial datasets do not differ in terms of their propensity for homoplasy, methodological issues such as the numbers of characters and their quantification make it difficult to evaluate these findings. Here, we circumvent these problems by constructing morphological distance matrices based on cranial, mandibular and os coxae three-dimensional shape. Statistical comparisons of these morphological distance matrices against a single genetic distance matrix for 11 catarrhine taxa show that cranial and os coxae shape reflect genetic relationships better than the mandible when humans are included, and that the cranium and os coxae do not differ statistically in terms of their genetic correlations. When humans were excluded from the analyses, all three anatomical regions were equally strongly correlated with genetic distance. Moreover, a second analysis focusing solely on os coxae variation of 16 taxa demonstrated that os coxae shape correctly recovers catarrhine taxonomic relationships at the sub-family level, even when humans are included. Taken together, our results suggest that there is no a priori reason to favor cranial shape data over os coxae morphology when inferring the genetic relationships of extant or extinct primate taxa. Morphological similarities between humans and other primates differ depending on the skeletal element, suggesting that combining skeletal elements into a single analysis may provide more accurate reconstructions of genetic relationships.

Phenotypic variation in infants, not adults, reflects genotypic variation among chimpanzees and bonobos

Studies comparing phenotypic variation with neutral genetic variation in modern humans have shown that genetic drift is a main factor of evolutionary diversification among populations. The genetic population history of our closest living relatives, the chimpanzees and bonobos, is now equally well documented, but phenotypic variation among these taxa remains relatively unexplored, and phenotype-genotype correlations are not yet documented. Also, while the adult phenotype is typically used as a reference, it remains to be investigated how phenotype-genotye correlations change during development. Here we address these questions by analyzing phenotypic evolutionary and developmental diversification in the species and subspecies of the genus Pan. Our analyses focus on the morphology of the femoral diaphysis, which represents a functionally constrained element of the locomotor system. Results show that during infancy phenotypic distances between taxa are largely congruent with non-coding (neutral) genotypic distances. Later during ontogeny, however, phenotypic distances deviate from genotypic distances, mainly as an effect of heterochronic shifts between taxon-specific developmental programs. Early phenotypic differences between Pan taxa are thus likely brought about by genetic drift while late differences reflect taxon-specific adaptations.

Patterns of morphological variation in enamel-dentin junction and outer enamel surface of human molars

Tooth crown patterning is governed by the growth and folding of the inner enamel epithelium (IEE) and the following enamel deposition forms outer enamel surface (OES). We hypothesized that overall dental crown shape and covariation structure are determined by processes that configurate shape at the enamel-dentine junction (EDJ), the developmental vestige of IEE. This this hypothesis was tested by comparing patterns of morphological variation between EDJ and OES in human permanent maxillary first molar (UM1) and deciduous second molar (um2). Using geometric morphometric methods, we described morphological variation and covariation between EDJ and OES, and evaluated the strength of two components of phenotypic variability, canalization and morphological integration, in addition to the relevant evolutionary flexibility, i.e. the ability to respond to selective pressure. The strength of covariation between EDJ and OES was greater in um2 than in UM1, and the way that multiple traits covary between EDJ and OES was different between these teeth. The variability analyses showed that EDJ had less shape variation and a higher level of morphological integration than OES, which indicated that canalization and morphological integration acted as developmental constraints. These tendencies were greater in UM1 than in um2. On the other hand, EDJ and OES had a comparable level of evolvability in these teeth. Amelogenesis could play a significant role in tooth shape and covariation structure, and its influence was not constant among teeth, which may be responsible for the differences in the rate and/or period of enamel formation.

Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa. Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium. I sample 16 extant taxa (one from each platyrrhine genus) and 20 extinct taxa of platyrrhines. The tree structure is constrained with a "molecular scaffold" of extant species as implemented in maximum parsimony using PAUP with the molecular-based 'backbone' approach. The data set encompasses most of the known extinct species of platyrrhines, ranging in age from latest Oligocene (∼26 Ma) to the Recent. The tree is rooted with extant catarrhines, and Late Eocene and Early Oligocene African anthropoids. Among the more interesting patterns to emerge are: (1) known early platyrrhines from the Late Oligocene through Early Miocene (26-16.5Ma) represent only stem platyrrhine taxa; (2) representatives of the three living platyrrhine families first occur between 15.7 Ma and 13.5 Ma; and (3) recently extinct primates from the Greater Antilles (Cuba, Jamaica, Hispaniola) are sister to the clade of extant platyrrhines and may have diverged in the Early Miocene. It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates. The following biogeographic scenario is consistent with the phylogenetic findings and climatic and geologic evidence: Tropical South America has been a center for platyrrhine diversification since platyrrhines arrived on the continent in the middle Cenozoic. Platyrrhines dispersed from tropical South America to Patagonia at ∼25-24 Ma via a "Paraná Portal" through eastern South America across a retreating Paranense Sea. Phylogenetic bracketing suggests Antillean primates arrived via a sweepstakes route or island chain from northern South America in the Early Miocene, not via a proposed land bridge or island chain (GAARlandia) in the Early Oligocene (∼34 Ma). Patagonian and Antillean platyrrhines went extinct without leaving living descendants, the former at the end of the Early Miocene and the latter within the past six thousand years. Molecular evidence suggests crown platyrrhines arrived in Central America by crossing an intermittent connection through the Isthmus of Panama at or after 3.5Ma. Any more ancient Central American primates, should they be discovered, are unlikely to have given rise to the extant Central American taxa in situ.

Molecular phylogenetic analysis of the Papionina using concatenation and species tree methods

The Papionina is a geographically widespread subtribe of African cercopithecid monkeys whose evolutionary history is of particular interest to anthropologists. The phylogenetic relationships among arboreal mangabeys (Lophocebus), baboons (Papio), and geladas (Theropithecus) remain unresolved. Molecular phylogenetic analyses have revealed marked gene tree incongruence for these taxa, and several recent concatenated phylogenetic analyses of multilocus datasets have supported different phylogenetic hypotheses. To address this issue, we investigated the phylogeny of the Lophocebus + Papio + Theropithecus group using concatenation methods, as well as alternative methods that incorporate gene tree heterogeneity to estimate a 'species tree.' Our compiled DNA sequence dataset was ∼56 kb pairs long and included 57 independent partitions. All analyses of concatenated alignments strongly supported a Lophocebus + Papio clade and a basal position for Theropithecus. The Bayesian concordance analysis supported the same phylogeny. A coalescent-based Bayesian method resulted in a very poorly resolved species tree. The topological agreement between concatenation and the Bayesian concordance analysis offers considerable support for a Lophocebus + Papio clade as the dominant relationship across the genome. However, the results of the Bayesian concordance analysis indicate that almost half the genome has an alternative history. As such, our results offer a well-supported phylogenetic hypothesis for the Papio/Lophocebus/Theropithecus trichotomy, while at the same time providing evidence for a complex evolutionary history that likely includes hybridization among lineages.

Unexpectedly many extinct hominins

Recent studies indicate that Neanderthal and Denisova hominins may have been separate species, while debate continues on the status of Homo floresiensis. The decade-long debate between "splitters," who recognize over 20 hominin species, and "lumpers," who maintain that all these fossils belong to just a few lineages, illustrates that we do not know how many extinct hominin species to expect. Here, we present probability distributions for the number of speciation events and the number of contemporary species along a branch of a phylogeny. With estimates of hominin speciation and extincton rates, we then show that the expected total number of extinct hominin species is 8, but may be as high as 27. We also show that it is highly unlikely that three very recent species disappeared due to natural, background extinction. This may indicate that human-like remains are too easily considered distinct species. Otherwise, the evidence suggesting that Neanderthal and the Denisova hominin represent distinct species implies a recent wave of extinctions, ostensibly driven by the only survivor, H. sapiens.

The relative congruence of cranial and genetic estimates of hominoid taxon relationships: implications for the reconstruction of hominin phylogeny

Previous analyses of extant catarrhine craniodental morphology have often failed to recover their molecular relationships, casting doubt on the accuracy of hominin phylogenies based on anatomical data. However, on the basis of genetic, morphometric and environmental affinity patterns, a growing body of literature has demonstrated that particular aspects of cranial morphology are remarkably reliable proxies for neutral modern human population history. Hence, it is important to test whether these intra-specific patterns can be extrapolated to a broader primate taxon level such that inference rules for understanding the morphological evolution of the extinct hominins may be devised. Here, we use a matrix of molecular distances between 15 hominoid taxa to test the genetic congruence of 14 craniomandibular regions, defined and morphometrically delineated on the basis of previous modern human analyses. This methodology allowed us to test directly whether the cranial regions found to be reliable indicators of population history were also more reliable proxies for hominoid genetic relationships. Cranial regions were defined on the basis of three criteria: developmental-functional units, individual bones, and regions differentially affected by masticatory stress. The results found that all regions tested were significantly and strongly correlated with the molecular matrix. However, the modern human predictions regarding the relative congruence of particular regions did not hold true, as the face was statistically the most reliable indicator of hominoid genetic distances, as opposed to the vault or basicranium. Moreover, when modern humans were removed from the analysis, all cranial regions improved in their genetic congruence, suggesting that it is the inclusion of morphologically-derived humans that has the largest effect on incongruence between morphological and molecular estimates of hominoid relationships. Therefore, it may be necessary to focus on smaller intra-generic taxonomic levels to more fully understand the effects of neutral and selective evolutionary processes in generating morphological diversity patterns.

A priori assumptions about characters as a cause of incongruence between molecular and morphological hypotheses of primate interrelationships

When molecules and morphology produce incongruent hypotheses of primate interrelationships, the data are typically viewed as incompatible, and molecular hypotheses are often considered to be better indicators of phylogenetic history. However, it has been demonstrated that the choice of which taxa to include in cladistic analysis as well as assumptions about character weighting, character state transformation order, and outgroup choice all influence hypotheses of relationships and may positively influence tree topology, so that relationships between extant taxa are consistent with those found using molecular data. Thus, the source of incongruence between morphological and molecular trees may lie not in the morphological data themselves but in assumptions surrounding the ways characters evolve and their impact on cladistic analysis. In this study, we investigate the role that assumptions about character polarity and transformation order play in creating incongruence between primate phylogenies based on morphological data and those supported by multiple lines of molecular data. By releasing constraints imposed on published morphological analyses of primates from disparate clades and subjecting those data to parsimony analysis, we test the hypothesis that incongruence between morphology and molecules results from inherent flaws in morphological data. To quantify the difference between incongruent trees, we introduce a new method called branch slide distance (BSD). BSD mitigates many of the limitations attributed to other tree comparison methods, thus allowing for a more accurate measure of topological similarity. We find that releasing a priori constraints on character behavior often produces trees that are consistent with molecular trees. Case studies are presented that illustrate how congruence between molecules and unconstrained morphological data may provide insight into issues of polarity, transformation order, homology, and homoplasy.

Phylogenetic rate shifts in feeding time during the evolution of Homo

Unique among animals, humans eat a diet rich in cooked and nonthermally processed food. The ancestors of modern humans who invented food processing (including cooking) gained critical advantages in survival and fitness through increased caloric intake. However, the time and manner in which food processing became biologically significant are uncertain. Here, we assess the inferred evolutionary consequences of food processing in the human lineage by applying a Bayesian phylogenetic outlier test to a comparative dataset of feeding time in humans and nonhuman primates. We find that modern humans spend an order of magnitude less time feeding than predicted by phylogeny and body mass (4.7% vs. predicted 48% of daily activity). This result suggests that a substantial evolutionary rate change in feeding time occurred along the human branch after the human-chimpanzee split. Along this same branch, Homo erectus shows a marked reduction in molar size that is followed by a gradual, although erratic, decline in H. sapiens. We show that reduction in molar size in early Homo (H. habilis and H. rudolfensis) is explicable by phylogeny and body size alone. By contrast, the change in molar size to H. erectus, H. neanderthalensis, and H. sapiens cannot be explained by the rate of craniodental and body size evolution. Together, our results indicate that the behaviorally driven adaptations of food processing (reduced feeding time and molar size) originated after the evolution of Homo but before or concurrent with the evolution of H. erectus, which was around 1.9 Mya.