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.

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.

Taxonomic attribution of the KNM-ER 1500 partial skeleton from the Burgi Member of the Koobi Fora Formation, Kenya.

Paranthropus boisei is well represented in the eastern African fossil record by craniodental remains, but very few postcranial fossils can be securely attributed to this taxon. For this reason, KNM-ER 1500 from East Turkana, Kenya, is especially important. KNM-ER 1500 is a badly weathered and fragmented postcranial skeleton associated with a small piece of mandibular corpus. It derives from the Burgi Member, which has yielded diagnostic craniodental fossils attributable to P. boisei, Homo habilis, Homo rudolfensis and Homo erectus. Although it has been proposed that KNM-ER 1500 may be attributable to P. boisei based on the small mandibular fragment, this hypothesis remained challenging to test. Here we re-examine the preserved portions of KNM-ER 1500 and reassess support for its taxonomic attribution. There are compelling features of the mandible, proximal femur, and especially the proximal radius that support attribution of KNM-ER 1500 to P. boisei. These features include the absolute width of the mandible and its lack of a lateral intertoral sulcus, an anteroposteriorly compressed femoral neck with a distinctive posteroinferior marginal ridge, the rim of the radial head that is proximodistally uniform in thickness around its circumference, and a long radial neck that is elliptical in cross section. No feature serves to align KNM-ER 1500 with Homo to the exclusion of Paranthropus. KNM-ER 1500 was a small-bodied individual and attributing this specimen to P. boisei confirms that significant postcranial-size dimorphism was present in this species.

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.

The effect of data provenance on estimates of gestation length in African and Asian colobines.

OBJECTIVES: It seems to be commonly accepted that gestation length within the subfamily Colobinae lasts several weeks longer in the African tribe (Colobini) than in the Asian tribe (Presbytini) even though closely related taxa of similar body mass should have similar life histories. Suspecting problems with data provenance to cause the difference, we revisited the published records expecting similar gestation lengths in both tribes if based on vetted, accurate data. MATERIALS AND METHODS: We compiled published gestation length data for Colobini and Presbytini, labeling them as "unspecified" (n = 16) if the primary reference could not be located, methods were not described, and/or conceptions, the beginning of gestation, were determined based on sporadic observations of mating. If conceptions were determined based on changing hormone levels or patterns of daily mating records, we labeled the data as "accurate" (n = 12). We analyzed the ln transformed data in a phylogenetic framework in relation to adult female body mass. RESULTS: In the unspecified dataset, gestation length in the two tribes overlapped extensively and did not differ significantly. However, in the accurate dataset, gestation length was significantly shorter in Colobini (not longer, as previously assumed). DISCUSSION: Data provenance had a strong impact on the comparison, reversing the relationship in gestation length in the two sister tribes. It remains to be determined why gestation lengths differ, whether, relative to the other primates, Colobini have a shortened gestation or Presbytini a lengthened gestation, and whether similar differences exist in other closely related taxa. Addressing these questions will require additional, broader, comparative analyses.

Evolution and function of the hominin forefoot.

The primate foot functions as a grasping organ. As such, its bones, soft tissues, and joints evolved to maximize power and stability in a variety of grasping configurations. Humans are the obvious exception to this primate pattern, with feet that evolved to support the unique biomechanical demands of bipedal locomotion. Of key functional importance to bipedalism is the morphology of the joints at the forefoot, known as the metatarsophalangeal joints (MTPJs), but a comprehensive analysis of hominin MTPJ morphology is currently lacking. Here we present the results of a multivariate shape and Bayesian phylogenetic comparative analyses of metatarsals (MTs) from a broad selection of anthropoid primates (including fossil apes and stem catarrhines) and most of the early hominin pedal fossil record, including the oldest hominin for which good pedal remains exist, Ardipithecus ramidus Results corroborate the importance of specific bony morphologies such as dorsal MT head expansion and "doming" to the evolution of terrestrial bipedalism in hominins. Further, our evolutionary models reveal that the MT1 of Ar. ramidus shifts away from the reconstructed optimum of our last common ancestor with apes, but not necessarily in the direction of modern humans. However, the lateral rays of Ar. ramidus are transformed in a more human-like direction, suggesting that they were the digits first recruited by hominins into the primary role of terrestrial propulsion. This pattern of evolutionary change is seen consistently throughout the evolution of the foot, highlighting the mosaic nature of pedal evolution and the emergence of a derived, modern hallux relatively late in human evolution.

Human manual distal phalanges from the Middle Stone Age deposits of Klasies River Main Site, Western Cape Province, South Africa.

Two new distal manual phalanges from the Middle Stone Age deposits of Klasies River Main Site are described. One (SAM-AP 6387) likely derives from ray II or ray III, whereas the other (SAM-AP 6388) is from the thumb. Both derive from a late adolescent or fully adult individual. They were recovered by H. Deacon from the same stratigraphic unit (submember W or possibly submember R) of the Shell and Sand Member of Cave 1, which places them between 100 and 90 ka. Both are comparatively small elements, and the possibility that they came from the same hand cannot be discounted at this time. These bones add to the meager and all too fragmentary postcranial human fossil sample from the Late Pleistocene of South Africa. These two specimens provide some additional evidence pertaining to the morphological attributes of the distal phalanges of the Middle Stone Age inhabitants of South Africa. Together with the distal pollical phalanx from Die Kelders (SAM-AP 6402), they are relatively small in comparison with homologs from recent human samples as well as Late Pleistocene specimens from Eurasia. Given their small sizes, the distal pollical phalanges from Klasies and Die Kelders are not dissimilar to Holocene Khoesan homologs. As expected, the Klasies elements differ noticeably from Neandertal homologs, especially in the narrowness of their shafts and distal tuberosities.

Secular trends in cranial size and shape among black South Africans over the late 19th and 20th centuries.

BACKGROUND: Previous studies of secular change in cranial size among black South Africans have produced conflicting results. AIM: We re-examined cranial size change in this population during the 19th and 20th century by evaluating its relationship with individual year-of-birth, and the significance of trends among eight decennial cohorts. SUBJECTS AND METHODS: This study is based on 102 male and 89 female adults born between 1865 and 1959. Linear regressions were employed to evaluate possible relationships between year-of-birth and cranial dimensions; ANOVAs were used to evaluate the significance of long-term trends among decennial cohorts. RESULTS: No analysis revealed a secular change in cranial length in either sex; however, the ANOVA for cranial length in the combined sex sample was significant. There is no secular trend in female cranial breadth, but males display a negative trend in this dimension. This results in a secular trend for increased male dolichocephaly. CONCLUSIONS: The factors that underlie the negative secular trend in male cranial breadth and the absence of a secular trend in overall cranial size in this population are unclear. Nevertheless, these observations accord with findings related to stature and long bone strength in this population and are consistent with observations for other sub-Saharan African populations.

Expanded character sampling underscores phylogenetic stability of Ardipithecus ramidus as a basal hominin.

Phylogenetic relationships among hominins provide a necessary framework for assessing their evolution. Reconstructing these relationships hinges on the strength of the character data analyzed. The phylogenetic position of Ardipithecus ramidus is critical to understanding early hominin evolution, and while many accept that it is most likely the sister taxon to all later hominins, others have argued that Ar. ramidus was ancestral to Pan. Although the study by Strait and Grine (2004) suggested the former, available evidence permitted only 26% of characters in their matrix to be assessed for Ar. ramidus. Fossils described subsequently by Suwa, White and colleagues in 2009 have enabled the number of characters that can be coded for this species to be expanded to 78% of the matrix. Here, we incorporate these new character data to evaluate their impact on the phylogenetic relationships of Ar. ramidus. Moreover, we have further revised the Strait and Grine (2004) matrix as necessitated by additions to the hypodigms of other fossil taxa. This updated matrix was analyzed using both parsimony and Bayesian techniques in a sequence of four iterative steps to independently evaluate the impact of matrix and expanded character revisions on tree topology. Despite the new data and matrix revisions, tree topology has remained remarkably stable. The addition of new craniodental material has served to markedly strengthen the support for the placement of Ar. ramidus as being derived relative to Sahelanthropus, and as the sister taxon of all later hominins. These findings support the phylogenetic hypothesis originally proposed by White and colleagues in 1994. This updated matrix provides a basis for the assessment of additional extinct species.

Complete permanent mandibular dentition of early Homo from the upper Burgi Member of the Koobi Fora Formation, Ileret, Kenya.

The KNM-ER 64060 dentition derives from a horizon that most likely dates to between 2.02 and 2.03 Ma. A proximate series of postcranial bones (designated KNM-ER 64061) derives from the same siltstone unit and may be associated with the dentition, but their separation on the surface of the site leaves some room for doubt. KNM-ER 64060 is one of fewer than ten hominin specimens from the Early Pleistocene of East Africa that comprises a full or nearly complete mandibular dentition. Its taxonomic attribution is potentially significant, especially if the postcranial elements are related. At least three, and probably four hominin species, including Paranthropus boisei and Homo erectus (= H. ergaster), are known at about this time in East Africa. Other penecontemporaneous fossils have been referred to a single, highly variable species, H. habilis, or two taxa, namely H. habilis and H. rudolfensis. Although the weight of evidence supports the attribution of these specimens to two species, there is notable lack of agreement over the assignation of individual fossils. We take a conservative approach and group all such specimens under the designation "early Homo sp." for comparative purposes. KNM-ER 64060 is clearly attributable to Homo rather than Paranthropus. The preponderance of the evidence suggests that the affinities of KNM-ER 64060 are with fossils assigned to the early Homo sp. category rather than with H. erectus. This is indicated by the overall sizes of the KNM-ER 64060 canine, premolar and molar crowns, the size relationships of the P3 to P4, the relative narrowness of its premolar crowns, the cusp proportions of the M1 and especially those of the M2 and M3, and seemingly the possession of a two-rooted P4. Some of these comparisons suggest further that among the fossils comprising the early Homo sp. sample, the KNM-ER 64060 dentition exhibits greater overall similarity to specimens such as OH 7 and OH 16 that represent Homo habilis sensu stricto.

Cross-sectional structural variation relative to midshaft along hominine diaphyses. I. The forelimb.

OBJECTIVES: Analyses of hominine forelimb diaphyseal structure typically employ sections located at midshaft. This study addresses three questions. First, how accurately must midshaft be defined to yield comparable data? Second, does variation in midshaft location due to alternative definitions fall within error ranges such that data gathered using different length measurements are comparable? Third, do error ranges and length metric effects differ between elements or taxa such that certain bones or species are more prone to issues of comparability? MATERIALS AND METHODS: Humeri, radii, and ulnae of Homo, Pan, and Gorilla were CT-scanned at full length and error ranges for three structural parameters (CSA, J, Imax /Imin ) were calculated around midshafts. RESULTS: Distances proximally and distally from midshaft where structural values become significantly different from midshaft values vary between elements, taxa, and structural parameters. Error ranges are largest for the humerus and smallest for the ulna. Among taxa, error ranges for gorillas are largest and those for humans are smallest. Among structural parameters, error ranges depend on element and taxon such that no parameter consistently exhibits larger or smaller error ranges across all bones or species. Variation in midshaft locations originating from different length definitions is small and falls within error ranges defined by maximum length across all elements and taxa. DISCUSSION: Including fragmentary specimens for which midshaft location is uncertain in comparisons of forelimb diaphyseal structure requires evaluation on a case-by-case basis, with consideration to element, taxon, and structural traits of interest. However, midshaft data for all three structural parameters considered here that are recorded using different length measurements can be reasonably compared.

Cross-sectional structural variation relative to midshaft along hominine diaphyses. II. The hind limb.

OBJECTIVES: In comparative analyses of hominine hind limb diaphyseal structure, homologous cross sections are located according to half bone length (midshaft). Here, we address three questions. First, how accurately must midshaft be defined to yield comparable data? Second, does variation in midshaft location due to different ways of measuring length fall within error ranges such that data gathered using different metrics are comparable? Third, do error ranges and length metric effects differ between elements or taxa such that certain bones or species are more prone to issues of comparability? MATERIALS AND METHODS: Femora and tibiae of Homo, Pan, and Gorilla were CT-scanned longitudinally and error ranges for multiple structural parameters (CSA, J, Imax /Imin ) were calculated around midshafts. RESULTS: Distances proximally and distally from midshaft where structural values differ significantly from midshaft values vary between bones, species, and structural traits. Femoral error ranges are typically larger than tibial ranges. In the femur, error ranges are generally largest for chimpanzees and smallest for gorillas. A similar taxonomic pattern is not evident in the tibia. No structural trait consistently displays larger or smaller error ranges across both elements and all species. Variation in midshaft locations stemming from different length definitions is small and falls within observed error ranges defined by any one metric. DISCUSSION: Incorporating fragmentary specimens (e.g., fossils) for which midshaft location is unknown in comparisons of diaphyseal structure necessitates evaluation on a case-by-case basis, with thought to element, taxon, and structural traits of interest. Midshaft data recorded from distinct length measurements are generally comparable.

Variation, sexual dimorphism, and enlargement of the frontal sinus with age in adult South Africans.

OBJECTIVES: To document frontal sinus volume (FSV) in a sample of sub-Saharan Africans with a view to evaluating claims that such populations exhibit comparatively small sinuses. This study also addresses questions related to sexual dimorphism, incidence of sinus aplasia, and the possibility that FSV continues to increase through adulthood. MATERIALS AND METHODS: FSV was measured from CT scans of adult crania from the Dart Collection. Sex and age were known for each individual. Linear cranial dimensions were used to compute a geometric mean from which a scaled FSV was computed for each cranium. RESULTS: FSV does not differ significantly between sexes, but females exhibit a higher incidence of aplasia. There is considerable variation in FSV in this sample, with the average ranking among the higher means reported for other population samples. The incidence of FS aplasia falls within the range of values recorded for other population samples. Although our study is cross-sectional rather than longitudinal, there is strong evidence that FSV continues to increase with age throughout adulthood. DISCUSSION: The FSV mean of our sample contradicts the notion that sub-Saharan Africans possess small sinuses. In a global context, geography (climate and altitude) does not appear to be related to FSV. The absence of sexual dimorphism in our sample is unexpected, as significant dimorphism has been reported for most other population samples. Our results support other indications that the frontal sinus continues to expand throughout adulthood, especially in females, and that it is likely due to bone resorption.

Metopism in adult South Africans and its relationship to frontal sinus size.

This study documents the incidences of complete and partial metopism and their possible relationship to frontal sinus volume (FSV) in a sample of modern adult black South Africans with a view to evaluating the hypothesis that metopism affects frontal sinus hypoplasia. FSV was measured from CT scans and the incidence of metopism was recorded from direct observations of dried cadaveric crania. The sex of each individual was known. Four linear cranial dimensions were used to compute a geometric mean by which to scale FSV. The incidence of partial metopism (38%) is comparable to that reported for other population samples, although there is considerable variation among these global sample frequencies. It is significantly more common in male than female South Africans. FSV in individuals with complete metopism is smaller than average but not inordinately so. On the other hand, FSV is significantly larger in individuals with partial metopism than in those that do not present with this sutural remnant. The data on FSV in individuals with and without partial metopism contradict the hypothesis that there is a relationship between partial metopism and frontal sinus hypoplasia. As such, the metopic remnant evinced by the Late Pleistocene cranium from Hofmeyr, South Africa is unlikely to be related to its very small FSV.

Hypercementosis in Late Pleistocene Homo sapiens fossils from Klasies River Main Site, South Africa.

OBJECTIVE: To examine early Homo sapiens fossils from the Late Pleistocene site of Klasies River Main Site, South Africa for evidence of hypercementosis. The specimens represent seven adult individuals dated to between 119,000 and 58,000 years ago. These observations are contextualized in relation to the incidences of hypercementosis among recent human populations and fossil human samples and the potential etiologies of hypercementosis. DESIGN: The fossils were investigated utilizing micro-CT and nano-CT scanning to visualize and measure cementum apposition on permanent incisor, premolar and molar roots. Cementum thickness was measured at mid-root level, and the volume of the cementum sleeve was calculated for the two fossil specimens that display marked hypercementosis. RESULTS: Two of the fossils display no evidence of cementum hypertrophy. Three exhibit moderate cementum thickening, barely attaining the quantitative threshold for hypercementosis. Two evince marked hypercementosis. One of the Klasies specimens with marked hypercementosis is judged to be an older individual with periapical abscessing. The second specimen is a younger adult, and seemingly similar in age to other Klasies fossils that exhibit only minimal cementum apposition. However, this second specimen exhibits dento-alveolar ankylosis of the premolar and molars. CONCLUSIONS: These two fossils from Klasies River Main Site provide the earliest manifestation of hypercementosis in Homo sapiens.

Rules of teeth development align microevolution with macroevolution in extant and extinct primates.

Macroevolutionary biologists have classically rejected the notion that higher-level patterns of divergence arise through microevolutionary processes acting within populations. For morphology, this consensus partly derives from the inability of quantitative genetics models to correctly predict the behaviour of evolutionary processes at the scale of millions of years. Developmental studies (evo-devo) have been proposed to reconcile micro- and macroevolution. However, there has been little progress in establishing a formal framework to apply evo-devo models of phenotypic diversification. Here we reframe this issue by asking whether using evo-devo models to quantify biological variation can improve the explanatory power of comparative models, thus helping us bridge the gap between micro- and macroevolution. We test this prediction by evaluating the evolution of primate lower molars in a comprehensive dataset densely sampled across living and extinct taxa. Our results suggest that biologically informed morphospaces alongside quantitative genetics models allow a seamless transition between the micro- and macroscales, whereas biologically uninformed spaces do not. We show that the adaptive landscape for primate teeth is corridor like, with changes in morphology within the corridor being nearly neutral. Overall, our framework provides a basis for integrating evo-devo into the modern synthesis, allowing an operational way to evaluate the ultimate causes of macroevolution.

A common mechanism drives the alignment between the micro- and macroevolution of primate molars.

A central challenge for biology is to reveal how different levels of biological variation interact and shape diversity. However, recent experimental studies have indicated that prevailing models of evolution cannot readily explain the link between micro- and macroevolution at deep timescales. Here, we suggest that this paradox could be the result of a common mechanism driving a correlated pattern of evolution. We examine the proportionality between genetic variance and patterns of trait evolution in a system whose developmental processes are well understood to gain insight into how such alignment between morphological divergence and genetic variation might be maintained over macroevolutionary time. Primate molars present a model system by which to link developmental processes to evolutionary dynamics because of the biased pattern of variation that results from the developmental architecture regulating their formation. We consider how this biased variation is expressed at the population level, and how it manifests through evolution across primates. There is a strong correspondence between the macroevolutionary rates of primate molar divergence and their genetic variation. This suggests a model of evolution in which selection is closely aligned with the direction of genetic variance, phenotypic variance, and the underlying developmental architecture of anatomical traits.