Great apes and humans evolved from a long-backed ancestor.

There is current debate whether the Homo/Pan last common ancestor (LCA) had a short, stiff lumbar column like great apes or a longer, flexible column observed in generalized Miocene hominoids. Beyond having only four segments, three additional features contribute to lumbar stiffening: the position of the transitional vertebra (TV), orientation of the lumbar spinous processes, and entrapment of lumbar vertebrae between the iliac blades. For great apes, these features would be homologous if inherited from a short-backed LCA but likely functionally convergent through dissimilar phenotypes if evolved from a long-backed LCA. We quantitatively and qualitatively analyzed human, ape, and monkey thoracic and lumbar vertebrae using 3D surface scanning and osteological measurements to compare spinous process morphology and sacral depth. We also used a large sample of hominoid vertebral counts to assess variation in the position of the TV and lumbosacral boundary. All extant hominoids modally place the TV at the ultimate thoracic. However, humans and orangutans place the TV at the 19th postcranial vertebral segment, whereas other apes place the TV at the 20th. Furthermore, chimpanzees, gorillas, and orangutans each have distinct patterns of spinous process angulation and morphology associated with lumbar stiffening, while human spinous process morphology is similar to that of longer backed gibbons, monkeys, and Miocene hominoids Morotopithecus and Pierolapithecus. Finally, chimpanzees are unique compared with other hominoids with a greater sacral depth facilitating lumbar entrapment, and there are differences among African apes with respect to the mechanisms governing variation in the lumbosacral boundary. These differences suggest that lumbar stiffening is convergent among great apes and that human bipedalism evolved from a more generalized long-backed ancestor. Such a model is more consistent with evidence of TV placement in Australopithecus.

Human-specific loss of regulatory DNA and the evolution of human-specific traits.

Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage. Another deletion removes a forebrain subventricular zone enhancer near the tumour suppressor gene growth arrest and DNA-damage-inducible, gamma (GADD45G), a loss correlated with expansion of specific brain regions in humans. Deletions of tissue-specific enhancers may thus accompany both loss and gain traits in the human lineage, and provide specific examples of the kinds of regulatory alterations and inactivation events long proposed to have an important role in human evolutionary divergence.

The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary.

The mesopodium forms at the boundary between the zeugopod and autopod and is composed of short nodular bones that typically lack growth plates. Hoxa11 and Hoxa13 are expressed in mutually exclusive proximal-distal domains that demarcate the zeugopod/autopod boundary. Similarly, Hoxd genes are deployed in two distinct phases during limb development. The early phase corresponds to proximal segments including the zeugopod, and a late phase occurs in the digits. This arrangement produces a gap of low Hoxd expression that is traditionally viewed to correspond to the mesopodium. In contrast to the other mesopodials, the mammalian pisiform and calcaneus form true growth plates. We show that these bones, along with other proximal mesopodials, develop within the Hoxa11 and Hoxd11 expression domains. We also observe that the pisiform growth plate becomes disorganized with Hoxa11 or Hoxd11 loss of function, indicating a direct role for Hox11 in its development. Hoxa13 loss of function has minimal effect on the pisiform and proximal calcaneus as these bones still form secondary centers and undergo longitudinal growth. Consideration of the phenotypes resulting from hypodactyly (Hd) and synpolydactyly homolog (spdh) mutations, which result from altered HOXA13 and HOXD13 proteins, respectively, confirms that Hox13 plays a limited role in the development of the pisiform and calcaneus and suggests that they lie within the early phase of Hox expression. Therefore, with respect to patterns of ossification and gene expression, these bones share much more in common with the zeugopod than the autopod. Such an interpretation fits with the timing of autopod origins during tetrapod evolution.

Developmental identity versus typology: Lucy has only four sacral segments.

OBJECTIVES: Both interspecific and intraspecific variation in vertebral counts reflect the action of patterning control mechanisms such as Hox. The preserved A.L. 288-1 ("Lucy") sacrum contains five fused elements. However, the transverse processes of the most caudal element do not contact those of the segment immediately craniad to it, leaving incomplete sacral foramina on both sides. This conforms to the traditional definition of four-segmented sacra, which are very rare in humans and African apes. It was recently suggested that fossilization damage precludes interpretation of this specimen and that additional sacral-like features of its last segment (e.g., the extent of the sacral hiatus) suggest a general Australopithecus pattern of five sacral vertebrae. METHODS: We provide updated descriptions of the original Lucy sacrum. We evaluate sacral/coccygeal variation in a large sample of extant hominoids and place it within the context of developmental variation in the mammalian vertebral column. RESULTS: We report that fossilization damage did not shorten the transverse processes of the fifth segment of Lucy's sacrum. In addition, we find that the extent of the sacral hiatus is too variable in apes and hominids to provide meaningful information on segment identity. Most importantly, a combination of sacral and coccygeal features is to be expected in vertebrae at regional boundaries. DISCUSSION: The sacral/caudal boundary appears to be displaced cranially in early hominids relative to extant African apes and humans, a condition consistent with the likely ancestral condition for Miocene hominoids. While not definitive in itself, a four-segmented sacrum accords well with the "long-back" model for the Pan/Homo last common ancestor. Am J Phys Anthropol 160:729-739, 2016. © 2016 Wiley Periodicals, Inc.

The pisiform growth plate is lost in humans and supports a role for Hox in growth plate formation.

The human pisiform is a small, nodular, although functionally significant, bone of the wrist. In most other mammals, including apes and Australopithecus afarensis, pisiforms are elongate. An underappreciated fact is that the typical mammalian pisiform forms from two ossification centers. We hypothesize that: (i) the presence of a secondary ossification center in mammalian pisiforms indicates the existence of a growth plate; and (ii) human pisiform reduction results from growth plate loss. To address these hypotheses, we surveyed African ape pisiform ossification and confirmed the presence of a late-forming secondary ossification center in chimpanzees and gorillas. Identification of the initial ossification center occurs substantially earlier in apes relative to humans, raising questions concerning the homology of the human pisiform and the two mammalian ossification centers. Second, we conducted histological and immunohistochemical analyses of pisiform ossification in mice. We confirm the presence of two ossification centers separated by organized columnar and hypertrophic chondrocyte zones. Flattened chondrocytes were highly mitotic, indicating the presence of a growth plate. Hox genes have been proposed to play a fundamental role in growth plate patterning. The existence of a pisiform growth plate presents an interesting test case for the association between Hox expression and growth plate formation, and could explain the severe effects on the pisiform observed in Hoxa11 and Hoxd11 knockout mice. Consistent with this hypothesis, we show that Hoxd11 is expressed adjacent to the pisiform in late-stage embryonic mouse limbs supporting a role for Hox genes in growth plate specification. This raises questions concerning the mechanisms regulating Hox expression in the developing carpus.

Genetic and developmental basis for parallel evolution and its significance for hominoid evolution.

Greater understanding of ape comparative anatomy and evolutionary history has brought a general appreciation that the hominoid radiation is characterized by substantial homoplasy.(1-4) However, little consensus has been reached regarding which features result from repeated evolution. This has important implications for reconstructing ancestral states throughout hominoid evolution, including the nature of the Pan-Homo last common ancestor (LCA). Advances from evolutionary developmental biology (evo-devo) have expanded the diversity of model organisms available for uncovering the morphogenetic mechanisms underlying instances of repeated phenotypic change. Of particular relevance to hominoids are data from adaptive radiations of birds, fish, and even flies demonstrating that parallel phenotypic changes often use similar genetic and developmental mechanisms. The frequent reuse of a limited set of genes and pathways underlying phenotypic homoplasy suggests that the conserved nature of the genetic and developmental architecture of animals can influence evolutionary outcomes. Such biases are particularly likely to be shared by closely related taxa that reside in similar ecological niches and face common selective pressures. Consideration of these developmental and ecological factors provides a strong theoretical justification for the substantial homoplasy observed in the evolution of complex characters and the remarkable parallel similarities that can occur in closely related taxa. Thus, as in other branches of the hominoid radiation, repeated phenotypic evolution within African apes is also a distinct possibility. If so, the availability of complete genomes for each of the hominoid genera makes them another model to explore the genetic basis of repeated evolution.

Metapodial or phalanx? An evolutionary and developmental perspective on the homology of the first ray's proximal segment.

The first mammalian metapodial (MP1) has periodically been argued to actually be a phalanx, because the first ray has one less element than the four posterior rays, and because the MP1 growth plate is proximal like those of all phalanges, rather than distal as in metapodials 2-5. However, growth plates are formed at both ends in non-therian tetrapod metapodials, and phylogenetic analysis demonstrates that growth plate loss is a therian synapomorphy that postdates the establishment of the mammalian phalangeal formula. These data, along with results of developmental and morphological studies, suggest that the MP1 is not a phalanx. The singular, proximal growth plates in MPs 2-5 are likely to be an adaptation to dynamic erect quadrupedal gait which was characterized by conversion of the posterior metapodials into rigid struts with the carpus/tarsus. While the adaptive significance of the reversed ossification of MP1 is less clear, we present three functional/developmental hypotheses.

Modified Periodic Acid-Schiff (PAS) Is an Alternative to Safranin O for Discriminating Bone-Cartilage Interfaces.

Cartilage histomorphometry is often performed on decalcified, paraffin-embedded bone sections, which provide versatility in staining applications from basic morphology to immunohistochemistry. Safranin O is a cationic dye that binds to proteoglycans in cartilage and is routinely used to assess growth plate dynamics and/or fracture repair at bone-cartilage interfaces. When used with a counterstain such as fast green, safranin O can offer exquisite differentiation of cartilage from surrounding bone. However, various decalcification and processing methods can deplete proteoglycans, rendering inconsistent, weak, or absent safranin O staining with indiscriminate bone-cartilage boundaries. We sought to develop an alternative staining methodology that preserves the contrast of bone and cartilage in cases of proteoglycan depletion that can be applied when other cartilage stains are unsuccessful. Here, we describe and validate a modified periodic acid-Schiff (PAS) protocol that we developed using Weigert's iron hematoxylin and light green stains as an alternative to safranin O for discriminating bone-cartilage interfaces of skeletal tissues. This method provides a practical solution for differentiating bone and cartilage when safranin O staining is not detected after decalcification and paraffin processing. The modified PAS protocol can be useful for studies in which identification of the bone-cartilage interface is essential but may not be preserved with standard staining approaches. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

Ossification pattern of the unusual pisiform in two-toed (Choloepus) and three-toed sloths (Bradypus).

Two-toed (Choloepus sp.) and three-toed (Bradypus sp.) sloths possess short, rounded pisiforms that are rare among mammals and differ from other members of Xenarthra like the giant anteater (Myrmecophaga tridactyla) which retain elongated, rod-like pisiforms in common with most mammals. Using photographs, radiographs, and µCT, we assessed ossification patterns in the pisiform and the paralogous tarsal, the calcaneus, for two-toed sloths, three-toed sloths, and giant anteaters to determine the process by which pisiform reduction occurs in sloths and compare it to other previously studied examples of pisiform reduction in humans and orangutans. Both extant sloth genera achieve pisiform reduction through the loss of a secondary ossification center and the likely disruption of the associated growth plate based on an unusually porous subchondral surface. This represents a third unique mechanism of pisiform reduction among mammals, along with primary ossification center loss in humans and retention of two ossification centers with likely reduced growth periods in orangutans. Given the remarkable similarities between two-toed and three-toed sloth pisiform ossification patterns and the presence of pisiform reduction in fossil sloths, extant sloth pisiform morphology does not appear to represent a recent convergent adaptation to suspensory locomotion, but instead is likely to be an ancestral trait of Folivora that emerged early in the radiation of extant and fossil sloths.

Identifying the homology of the short human pisiform and its lost ossification center.

BACKGROUND: The pisiform and calcaneus are paralogous bones of the wrist and ankle and are the only carpal and tarsal, respectively, to develop from two ossification centers with an associated growth plate in mammals. Human pisiforms and calcanei have undergone drastic evolutionary changes since our last common ancestor with chimpanzees and bonobos. The human pisiform is truncated and has lost an ossification center with the associated growth plate, while the human calcaneus has expanded and retained two ossification centers and a growth plate. Mammalian pisiforms represent a wide range of morphologies but extremely short pisiforms are rare and ossification center loss is even rarer. This raises the question of whether the sole human pisiform ossification center is homologous to the primary center or the secondary center of other species. We performed an ontogenetic study of pisiform and calcaneus ossification patterns and timing in macaques, apes, and humans (n = 907) from museum skeletal collections to address this question. RESULTS: Human pisiforms ossify irregularly and lack characteristic features of other primates while they develop. Pisiform primary and secondary center ossification timing typically matches that of the calcaneus of non-human primates, while the human pisiform corresponds with calcaneal secondary center ossification. Finally, human pisiforms ossify at the same dental stages as pisiform and calcaneal secondary centers in other hominoids. CONCLUSIONS: These data indicate that the human pisiform is homologous to the pisiform epiphysis of other species, and that humans have lost a primary ossification center and associated growth plate while retaining ossification timing of the secondary center. This represents an exceptional evolutionary event and demonstrates a profound developmental change in the human wrist that is unusual not only among primates, but among mammals.

Patterns of correlation and covariation of anthropoid distal forelimb segments correspond to Hoxd expression territories.

Anthropoids in general and hominoids in particular exhibit differential adaptations in forearm and digital skeletal proportions to a diverse array of locomotor modes. Hox genes act as selector genes with spatially regulated expression patterns during development. Their expression in the forelimb appears to define modules that specify differential skeletal growth. Here we explore forelimb skeletal proportions in a large sample of anthropoids from a background provided by Hoxd expression patterns in late-stage murine embryonic forelimbs. Interspecific correlation and principal components analyses of primate forelimb data indicate that morphological variation in anthropoids reflects well-defined developmental modules downstream of Hoxd expression. The phalanges of digit one appear to represent a single growth module, whereas the metacarpals and manual phalanges of the posterior digits correspond to a second, independent, expression territory that extends proximally into the distal zeugopod. In particular, hominoids show very high correlations among the posterior digits and the independence of digit one. In addition, the distal radius is generally highly correlated with the posterior digits and not digit one. Relying on established functional differences among Hox paralogs, we present a model that parsimoniously explains hominoid forearm and digital proportions as a consequence of downstream effects of Hox. We, therefore, suggest that Hox-defined developmental modules have served as evolutionary modules during manual evolution in anthropoids.

Ossification of the mouse metatarsal: differentiation and proliferation in the presence/absence of a defined growth plate.

There is significant diversity in growth plate behavior among sites within an individual skeleton and between skeletons of different species. This variation within wild-type animals is an underutilized resource for studying skeletal development. One bone that potentially exhibits the most diverse behavior is the metatarsal. While one end forms a growth plate with an epiphyseal secondary center of ossification as in other long bones, the opposite end undergoes direct ossification in a manner more similar to short bones. Although descriptions of human metatarsal/metacarpal ossification are available, a detailed comparative analysis has yet to be conducted in an animal model amenable to biomolecular analysis. Here we report an analysis of proximal and distal ossification in an age series of mouse metatarsals. Safranin O staining was used for qualitative and quantitative histology, and chondrocyte differentiation and proliferation were analyzed using immunohistochemistry for type X collagen and proliferative cell nuclear antigen expression. We establish that, as in the human, both growth plate formation and direct ossification occur in the mouse metatarsal, with chondrocyte populations showing distinct differentiation patterns at opposite ends of the bone. In addition, growth plate formation is characterized by a peak of proliferation in reserve zone chondrocytes that distinguishes it from both established growth plates and direct ossification. Our analysis demonstrates that the mouse metatarsal is a productive model for investigating natural variation in ossification that can further understanding of vertebrate skeletal development and evolution.

First steps of bipedality in hominids: evidence from the atelid and proconsulid pelvis.

Upright walking absent a bent-hip-bent-knee gait requires lumbar lordosis, a ubiquitous feature in all hominids for which it can be observed. Its first appearance is therefore a central problem in human evolution. Atelids, which use the tail during suspension, exhibit demonstrable lordosis and can achieve full extension of their hind limbs during terrestrial upright stance. Although obviously homoplastic with hominids, the pelvic mechanisms facilitating lordosis appear largely similar in both taxa with respect to abbreviation of upper iliac height coupled with broad sacral alae. Both provide spatial separation of the most caudal lumbar(s) from the iliac blades. A broad sacrum is therefore a likely facet of earliest hominid bipedality. All tailed monkeys have broad alae. By contrast all extant apes have very narrow sacra, which promote "trapping" of their most caudal lumbars to achieve lower trunk rigidity during suspension. The alae in the tailless proconsul Ekembo nyanzae appear to have been quite broad, a character state that may have been primitive in Miocene hominoids not yet adapted to suspension and, by extension, exaptive for earliest bipedality in the hominid/panid last common ancestor. This hypothesis receives strong support from other anatomical systems preserved in Ardipithecus ramidus.

From Lucy to Kadanuumuu: balanced analyses of Australopithecus afarensis assemblages confirm only moderate skeletal dimorphism.

Sexual dimorphism in body size is often used as a correlate of social and reproductive behavior in Australopithecus afarensis. In addition to a number of isolated specimens, the sample for this species includes two small associated skeletons (A.L. 288-1 or "Lucy" and A.L. 128/129) and a geologically contemporaneous death assemblage of several larger individuals (A.L. 333). These have driven both perceptions and quantitative analyses concluding that Au. afarensis was markedly dimorphic. The Template Method enables simultaneous evaluation of multiple skeletal sites, thereby greatly expanding sample size, and reveals that A. afarensis dimorphism was similar to that of modern humans. A new very large partial skeleton (KSD-VP-1/1 or "Kadanuumuu") can now also be used, like Lucy, as a template specimen. In addition, the recently developed Geometric Mean Method has been used to argue that Au. afarensis was equally or even more dimorphic than gorillas. However, in its previous application Lucy and A.L. 128/129 accounted for 10 of 11 estimates of female size. Here we directly compare the two methods and demonstrate that including multiple measurements from the same partial skeleton that falls at the margin of the species size range dramatically inflates dimorphism estimates. Prevention of the dominance of a single specimen's contribution to calculations of multiple dimorphism estimates confirms that Au. afarensis was only moderately dimorphic.

A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae.

Previous studies show that humans have a large genomic deletion downstream of the Androgen Receptor gene that eliminates an ancestral mammalian regulatory enhancer that drives expression in developing penile spines and sensory vibrissae. Here we use a combination of large-scale sequence analysis and PCR amplification to demonstrate that the penile spine/vibrissa enhancer is missing in all humans surveyed and in the Neandertal and Denisovan genomes, but is present in DNA samples of chimpanzees and bonobos, as well as in multiple other great apes and primates that maintain some form of penile integumentary appendage and facial vibrissae. These results further strengthen the association between the presence of the penile spine/vibrissa enhancer and the presence of penile spines and macro- or micro- vibrissae in non-human primates as well as show that loss of the enhancer is both a distinctive and characteristic feature of the human lineage.

An enlarged postcranial sample confirms Australopithecus afarensis dimorphism was similar to modern humans.

In a previous study, we introduced the template method as a means of enlarging the Australopithecus afarensis postcranial sample to more accurately estimate its skeletal dimorphism. Results indicated dimorphism to be largely comparable to that of Homo sapiens. Some have since argued that our results were biased by artificial homogeneity in our Au. afarensis sample. Here we report the results from inclusion of 12 additional, newly reported, specimens. The results are consistent with those of our original study and with the hypothesis that early hominid demographic success derived from a reproductive strategy involving male provisioning of pair-bonded females.

Variation in mammalian proximal femoral development: comparative analysis of two distinct ossification patterns.

The developmental anatomy of the proximal femur is complex. In some mammals, including humans, the femoral head and greater trochanter emerge as separate ossification centres within a common chondroepiphysis and remain separate throughout ontogeny. In other species, these secondary centres coalesce within the chondroepiphysis to form a single osseous epiphysis much like the proximal humerus. These differences in femoral ontogeny have not been previously addressed, yet are critical to an understanding of femoral mineralization and architecture across a wide range of mammals and may have key implications for understanding and treating hip abnormalities in humans. We evaluated femora from 70 mammalian species and categorized each according to the presence of a 'separate' or 'coalesced' proximal epiphysis based on visual assessment. We found that ossification type varies widely among mammals: taxa in the 'coalesced' group include marsupials, artiodactyls, perissodactyls, bats, carnivores and several primates, while the 'separate' group includes hominoids, many rodents, tree shrews and several marine species. There was no clear relationship to body size, phylogeny or locomotion, but qualitative and quantitative differences between the groups suggest that ossification type may be primarily an artefact of femoral shape and neck length. As some osseous abnormalities of the human hip appear to mimic the normal morphology of species with coalesced epiphyses, these results may provide insight into the aetiology and treatment of human hip disorders such as femoroacetabular impingement and early-onset osteoarthritis.

Growth plate formation and development in alligator and mouse metapodials: evolutionary and functional implications.

Mammalian metapodials (metacarpals and metatarsals), unlike most long bones, form a single growth plate, and undergo longitudinal growth at only one end. The growth dynamics of non-mammalian tetrapod metapodials have not been systematically examined in order to determine if unidirectional growth is unique to mammals. Here we compare murine metapodial ossification in growth stages that parallel those of embryonic, juvenile and subadult American alligators (Alligator mississippiensis). Safranin O staining was used for qualitative histology, and chondrocyte differentiation and proliferation were assessed via immunohistochemistry for type X collagen and proliferative cell nuclear antigen (PCNA). We establish that growth plates form at both ends of alligator metapodials and are maintained in the subadult. PCNA results show that alligators and mice share common patterns of chondrocyte proliferation during growth plate formation. In addition, while alligators and mice differ initially in the degree of organization and pace of chondrocyte differentiation, these parameters are largely similar in established growth plates. However, the replacement of cartilage by bone is highly irregular throughout growth in the alligator, in contrast to the more uniform process in the mouse. These results indicate that while alligators and mammals share common mechanisms of chondrocyte regulation, they differ substantially in their processes of ossification. Phylogenetic analysis indicates that the direct ossification of one epiphysis and reliance on a single growth plate is a derived character (synapomorphy) in therian mammals and likely indicates an adaptation for erect quadrupedal gait.

Sexual dimorphism in Australopithecus afarensis was similar to that of modern humans.

The substantial fossil record for Australopithecus afarensis includes both an adult partial skeleton [Afar Locality (A.L.) 288-1, "Lucy"] and a large simultaneous death assemblage (A.L. 333). Here we optimize data derived from both to more accurately estimate skeletal size dimorphism. Postcranial ratios derived from A.L. 288-1 enable a significant increase in sample size compared with previous studies. Extensive simulations using modern humans, chimpanzees, and gorillas confirm that this technique is accurate and that skeletal size dimorphism in A. afarensis was most similar to that of contemporary Homo sapiens. These data eliminate some apparent discrepancies between the canine and skeletal size dimorphism in hominoids, imply that the species was not characterized by substantial sexual bimaturation, and greatly increase the probability that the reproductive strategy of A. afarensis was principally monogamy.