Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics.

The methods of geometric morphometrics are commonly used to quantify morphology in a broad range of biological sciences. The application of these methods to large datasets is constrained by manual landmark placement limiting the number of landmarks and introducing observer bias. To move the field forward, we need to automate morphological phenotyping in ways that capture comprehensive representations of morphological variation with minimal observer bias. Here, we present Morphological Variation Quantifier (morphVQ), a shape analysis pipeline for quantifying, analyzing, and exploring shape variation in the functional domain. morphVQ uses descriptor learning to estimate the functional correspondence between whole triangular meshes in lieu of landmark configurations. With functional maps between pairs of specimens in a dataset we can analyze and explore shape variation. morphVQ uses Consistent ZoomOut refinement to improve these functional maps and produce a new representation of shape variation, area-based and conformal (angular) latent shape space differences (LSSDs). We compare this new representation of shape variation to shape variables obtained via manual digitization and auto3DGM, an existing approach to automated morphological phenotyping. We find that LSSDs compare favorably to modern 3DGM and auto3DGM while being more computationally efficient. By characterizing whole surfaces, our method incorporates more morphological detail in shape analysis. We can classify known biological groupings, such as Genus affiliation with comparable accuracy. The shape spaces produced by our method are similar to those produced by modern 3DGM and to auto3DGM, and distinctiveness functions derived from LSSDs show us how shape variation differs between groups. morphVQ can capture shape in an automated fashion while avoiding the limitations of manually digitized landmarks, and thus represents a novel and computationally efficient addition to the geometric morphometrics toolkit.

Snapshots of human anatomy, locomotion, and behavior from Late Pleistocene footprints at Engare Sero, Tanzania.

Fossil hominin footprints preserve data on a remarkably short time scale compared to most other fossil evidence, offering snapshots of organisms in their immediate ecological and behavioral contexts. Here, we report on our excavations and analyses of more than 400 Late Pleistocene human footprints from Engare Sero, Tanzania. The site represents the largest assemblage of footprints currently known from the human fossil record in Africa. Speed estimates show that the trackways reflect both walking and running behaviors. Estimates of group composition suggest that these footprints were made by a mixed-sex and mixed-age group, but one that consisted of mostly adult females. One group of similarly-oriented trackways was attributed to 14 adult females who walked together at the same pace, with only two adult males and one juvenile accompanying them. In the context of modern ethnographic data, we suggest that these trackways may capture a unique snapshot of cooperative and sexually divided foraging behavior in Late Pleistocene humans.

Scythes, sickles and other blades: defining the diversity of pectoral fin morphotypes in Pachycormiformes.

The traditional terminology of 'scythe' or 'sickle' shaped is observed to be flawed as an effective descriptor for pectoral fin shape in pachycormids. The diversity of pachycormid pectoral fin shapes is assessed across the 14 recognised genera that preserve complete pectoral fins, and improved terms are defined to more effectively describe their form, supported by anatomical observation and aspect ratio analysis of individual fins, and corroborated by landmark analysis. Three clear and distinct pectoral fin structural morphotypes emerge (falceform, gladiform, falcataform), reflecting a diversity of pachycormid lifestyles throughout the Mesozoic, from agile pursuit predator to slow-cruising suspension feeder.

Hip extensor mechanics and the evolution of walking and climbing capabilities in humans, apes, and fossil hominins.

The evolutionary emergence of humans' remarkably economical walking gait remains a focus of research and debate, but experimentally validated approaches linking locomotor capability to postcranial anatomy are limited. In this study, we integrated 3D morphometrics of hominoid pelvic shape with experimental measurements of hip kinematics and kinetics during walking and climbing, hamstring activity, and passive range of hip extension in humans, apes, and other primates to assess arboreal-terrestrial trade-offs in ischium morphology among living taxa. We show that hamstring-powered hip extension during habitual walking and climbing in living apes and humans is strongly predicted, and likely constrained, by the relative length and orientation of the ischium. Ape pelves permit greater extensor moments at the hip, enhancing climbing capability, but limit their range of hip extension, resulting in a crouched gait. Human pelves reduce hip extensor moments but permit a greater degree of hip extension, which greatly improves walking economy (i.e., distance traveled/energy consumed). Applying these results to fossil pelves suggests that early hominins differed from both humans and extant apes in having an economical walking gait without sacrificing climbing capability. Ardipithecus was capable of nearly human-like hip extension during bipedal walking, but retained the capacity for powerful, ape-like hip extension during vertical climbing. Hip extension capability was essentially human-like in Australopithecus afarensis and Australopithecus africanus, suggesting an economical walking gait but reduced mechanical advantage for powered hip extension during climbing.

Dental microwear profilometry of African non-cercopithecoid catarrhines of the Early Miocene.

The Early Miocene of Kenya has yielded the remains of many important stem catarrhine species that provide a glimpse of the East African primate radiation at a time of major faunal turnover. These taxa have been subject to innumerable studies, yet there is still no consensus on their dietary niches. Here we report results of an analysis of dental microwear textures of non-cercopithecoid catarrhines from the Early Miocene of Kenya. Scanning confocal profilometry of all available molar specimens with undamaged occlusal surfaces revealed 82 individuals with unobscured antemortem microwear, representing Dendropithecus, Micropithecus, Limnopithecus, Proconsul, and Rangwapithecus. Scale-sensitive fractal analysis was used to generate microwear texture attributes for each individual, and the fossil taxa were compared with each other using conservative non-parametric statistical tests. This study revealed no discernible variation in microwear texture among the fossil taxa, which is consistent with results from a previous feature-based microwear study using smaller samples. Our results suggest that, despite their morphological differences, these taxa likely often consumed foods with similar abrasive and fracture properties. However, statistical analyses of microwear texture data indicate differences between the Miocene fossil sample and several extant anthropoid primate genera. This suggests that the African non-cercopithecoid catarrhines included in our study, despite variations in tooth form, had generalist diets that were not yet specialized to the degree of many modern taxa.

Remnants of an ancient forest provide ecological context for Early Miocene fossil apes.

The lineage of apes and humans (Hominoidea) evolved and radiated across Afro-Arabia in the early Neogene during a time of global climatic changes and ongoing tectonic processes that formed the East African Rift. These changes probably created highly variable environments and introduced selective pressures influencing the diversification of early apes. However, interpreting the connection between environmental dynamics and adaptive evolution is hampered by difficulties in locating taxa within specific ecological contexts: time-averaged or reworked deposits may not faithfully represent individual palaeohabitats. Here we present multiproxy evidence from Early Miocene deposits on Rusinga Island, Kenya, which directly ties the early ape Proconsul to a widespread, dense, multistoried, closed-canopy tropical seasonal forest set in a warm and relatively wet, local climate. These results underscore the importance of forested environments in the evolution of early apes.

Laetoli footprints preserve earliest direct evidence of human-like bipedal biomechanics.

BACKGROUND: Debates over the evolution of hominin bipedalism, a defining human characteristic, revolve around whether early bipeds walked more like humans, with energetically efficient extended hind limbs, or more like apes with flexed hind limbs. The 3.6 million year old hominin footprints at Laetoli, Tanzania represent the earliest direct evidence of hominin bipedalism. Determining the kinematics of Laetoli hominins will allow us to understand whether selection acted to decrease energy costs of bipedalism by 3.6 Ma. METHODOLOGY/PRINCIPAL FINDINGS: Using an experimental design, we show that the Laetoli hominins walked with weight transfer most similar to the economical extended limb bipedalism of humans. Humans walked through a sand trackway using both extended limb bipedalism, and more flexed limb bipedalism. Footprint morphology from extended limb trials matches weight distribution patterns found in the Laetoli footprints. CONCLUSIONS: These results provide us with the earliest direct evidence of kinematically human-like bipedalism currently known, and show that extended limb bipedalism evolved long before the appearance of the genus Homo. Since extended-limb bipedalism is more energetically economical than ape-like bipedalism, energy expenditure was likely an important selection pressure on hominin bipeds by 3.6 Ma.

Stratigraphic interpretation of the Kulu Formation (Early Miocene, Rusinga Island, Kenya) and its implications for primate evolution.

Early Miocene fossils from Rusinga Island, Kenya, provide some of the best evidence for catarrhine evolution and diversification, and, together with more than eighty-five other mammalian species, form an important comparative reference for understanding faunal succession in East Africa. While there is consensus over the stratigraphic position of most of Rusinga's volcaniclastic deposits, the lacustrine Kulu Formation has been placed in various parts of the geological sequence by different researchers. To resolve this discrepancy, we conducted detailed geological analyses which indicate that the Kulu Formation was formed in the Early Miocene during a period of volcanic inactivity and subsidence following the early, mainly explosive hyper-alkaline phase of the Kisingiri complex and prior to the final eruptions of nephelinitic lavas. The underlying Hiwegi and older formations were locally deformed and deeply eroded before sedimentation began in the Kulu basin, so that the Kulu sediments may be significantly younger than the 17.8 Ma Hiwegi Formation and not much older than the overlying Kiangata Agglomerata-Lunene Lava series, loosely dated to ca. 15 Ma. The overall similarities between Kulu and Hiwegi faunas imply long-term ecological stability in this region. Our stratigraphic interpretation suggests that the Kulu fauna is contemporaneous with faunas from West Turkana, implying that differences between these assemblages-particularly in the primate communities--reflect paleobiogeographic and/or paleocological differences. Finally, the position of the Kulu Formation restricts the time frame during which the substantial faunal turnover seen in the differences between the primate and mammalian communities of Rusinga and Maboko Islands could have occurred.