Erik Otárola-Castillo

geomorph: an r package for the collection and analysis of geometric morphometric shape data

Summary 1. Many ecological and evolutionary studies seek to explain patterns of shape variation and its covariation with other variables. Geometric morphometrics is often used for this purpose, where a set of shape variables are obtained from landmark coordinates following a Procrustes superimposition. 2. We introduce geomorph: a software package for performing geometric morphometric shape analysis in the R statistical computing environment. 3. Geomorph provides routines for all stages of landmark-based geometric morphometric analyses in two and three-dimensions. It is an open source package to read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform statistical analyses of shape variation and covariation, and to provide graphical depictions of shapes and patterns of shape variation. An important contribution of geomorph is the ability to perform Procrustes superimposition on landmark points, as well as semilandmarks from curves and surfaces. 4. A wide range of statistical methods germane to testing ecological and evolutionary hypotheses of shape variation are provided. These include standard multivariate methods such as principal components analysis, and approaches for multivariate regression and group comparison. Methods for more specialized analyses, such as for assessing shape allometry, comparing shape trajectories, examining morphological integration, and for assessing phylogenetic signal, are also included. 5. Several functions are provided to graphically visualize results, including routines for examining variation in shape space, visualizing allometric trajectories, comparing specific shapes to one another and for plotting phylogenetic changes in morphospace. 6. Finally, geomorph participates to make available advanced geometric morphometric analyses through the R statistical computing platform.

Effects of mammalian herbivore declines on plant communities: observations and experiments in an African savanna

1. Herbivores influence the structure and composition of terrestrial plant communities. However, responses of plant communities to herbivory are variable and depend on environmental conditions, herbivore identity and herbivore abundance. As anthropogenic impacts continue to drive large declines in wild herbivores, understanding the context dependence of herbivore impacts on plant communities becomes increasingly important. 2. Exclosure experiments are frequently used to assess how ecosystems reorganize in the face of large wild herbivore defaunation. Yet in many landscapes, declines in large wildlife are often accompanied by other anthropogenic activities, especially land conversion to livestock production. In such cases, exclosure experiments may not reflect typical outcomes of human-driven extirpations of wild herbivores. 3. Here, we examine how plant community responses to changes in the identity and abundance of large herbivores interact with abiotic factors (rainfall and soil properties). We also explore how effects of wild herbivores on plant communities differ between large-scale herbivore exclosures and landscape sites where anthropogenic activity has caused wildlife declines, often accompanied by livestock increases. 4. Abiotic context modulated the responses of plant communities to herbivore declines with stronger effect sizes in lower-productivity environments. Also, shifts in plant community structure, composition and species richness following wildlife declines differed considerably between exclosure experiments and landscape sites in which wild herbivores had declined and were often replaced by livestock. Plant communities in low wildlife landscape sites were distinct in both composition and physical structure from both exclosure and control sites in experiments. The power of environmental (soil and rainfall) gradients in influencing plant response to herbivores was also greatly dampened or absent in the landscape sites. One likely explanation for these observed differences is the compensatory effect of livestock associated with the depression or extirpation of wildlife. 5. Synthesis. Our results emphasize the importance of abiotic environmental heterogeneity in modulating the effects of mammalian herbivory on plant communities and the importance of such covariation in understanding effects of wild herbivore declines. They also suggest caution when extrapolating results from exclosure experiments to predict the consequences of defaunation as it proceeds in the Anthropocene.

Evidence for Patterns of Selective Urban Migration in the Greater Indus Valley (2600- 1900 BC): A Lead and Strontium Isotope Mortuary Analysis

Just as modern nation-states struggle to manage the cultural and economic impacts of migration, ancient civilizations dealt with similar external pressures and set policies to regulate people’s movements. In one of the earliest urban societies, the Indus Civilization, mechanisms linking city populations to hinterland groups remain enigmatic in the absence of written documents. However, isotopic data from human tooth enamel associated with Harappa Phase (2600-1900 BC) cemetery burials at Harappa (Pakistan) and Farmana (India) provide individual biogeochemical life histories of migration. Strontium and lead isotope ratios allow us to reinterpret the Indus tradition of cemetery inhumation as part of a specific and highly regulated institution of migration. Intra-individual isotopic shifts are consistent with immigration from resource-rich hinterlands during childhood. Furthermore, mortuary populations formed over hundreds of years and composed almost entirely of first-generation immigrants suggest that inhumation was the final step in a process linking certain urban Indus communities to diverse hinterland groups. Additional multi disciplinary analyses are warranted to confirm inferred patterns of Indus mobility, but the available isotopic data suggest that efforts to classify and regulate human movement in the ancient Indus region likely helped structure socioeconomic integration across an ethnically diverse landscape.

Context-dependent effects of large-wildlife declines on small-mammal communities in central Kenya.

Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large-wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife declines on other animals in a community, we examined the effects of three common forms of large-wildlife loss (removal without replacement [using fences], removal followed by replacement with domestic stock, and removal accompanied by crop agricultural use) on small-mammal abundance, diversity, and community composition, in landscapes that varied in several abiotic attributes (rainfall, soil fertility, land-use intensity) in central Kenya. We found that small-mammal communities were indeed heavily impacted by all forms of large-wildlife decline, showing, on average: (1) higher densities, (2) lower species richness per site, and (3) different species assemblages in sites from which large wildlife were removed. However, the nature and magnitude of these effects were strongly context dependent. Rainfall, type of land-use change, and the interaction of these two factors were key predictors of both the magnitude and type of responses of small mammals. The strongest effects, particularly abundance responses, tended to be observed in low-rainfall areas. Whereas isolated wildlife removal primarily led to increased small-mammal abundance, wildlife removal associated with secondary uses (agriculture, domestic stock) had much more variable effects on abundance and stronger impacts on diversity and composition. Collectively, these results (1) highlight the importance of context in determining the impacts of large-wildlife decline on small-mammal communities, (2) emphasize the challenges in extrapolating results from controlled experimental studies to predict the effects of wildlife declines that are accompanied by secondary land-uses, and (3) suggest that, because of the context-dependent nature of the responses to large-wildlife decline, large-wildlife status alone cannot be reliably used to predict small-mammal community changes.

A 3-D geometric morphometric study of intraspecific variation in the ontogeny of the temporal bone in modern Homo sapiens

This study addresses how the human temporal bone develops the population-specific pattern of morphology observed among adults and at what point in ontogeny those patterns arise. Three-dimensional temporal bone shape was captured using 15 landmarks on ontogenetic series of specimens from seven modern human populations. Discriminant function analysis revealed that population-specific temporal bone morphology is evident early in ontogeny, with significant shape differences among many human populations apparent prior to the eruption of the first molar. As early as five years of age, temporal bone shape reflects population history and can be used to reliably sort populations, although those in closer geographic proximity and molecular affinity are more likely to be misclassified. The deviation of cold-adapted populations from this general pattern of congruence between temporal bone morphology and genetic distances, identified in previous work, was confirmed here in adult and subadult specimens, and was revealed to occur earlier in ontogeny than previously recognized. Significant differences exist between the ontogenetic trajectories of some pairs of populations, but not among others, and the angles of these trajectories do not reflect genetic relationships or final adult temporal bone size. Significant intrapopulation differences are evident early in ontogeny, with differences becoming amplified by divergent trajectories in some groups. These findings elucidate how the congruence between adult human temporal bone morphology and population history develops, and reveal that this pattern corresponds closely to that described previously for facial ontogeny.

A partial hominoid innominate from the Miocene of Pakistan: Description and preliminary analyses

Significance The living apes share a number of important morphological similarities of torso and limbs; torsos are broad and shallow, lumbar regions short, and forelimbs adapted to mobility. For more than a century it was assumed that most of these similarities are homologous, reflecting descent from a common ancestor with these features. As the ape fossil record slowly expands, the story becomes more complicated, particularly in the case of the south Asian Miocene ape Sivapithecus. Sivapithecus has facial features resembling specifically the living orangutan, but no postcranial features resembling orangutans. This newly described hipbone differs from that of all living apes. Either postcranial similarities of apes are not fully homologous or the facial similarities of Sivapithecus and orangutans cannot be homologous. We describe a partial innominate, YGSP 41216, from a 12.3 Ma locality in the Siwalik Group of the Potwar Plateau in Pakistan, assigned to the Middle Miocene ape species Sivapithecus indicus. We investigate the implications of its morphology for reconstructing positional behavior of this ape. Postcranial anatomy of extant catarrhines falls into two distinct groups, particularly for torso shape. To an extent this reflects different although variable and overlapping positional repertoires: pronograde quadrupedalism for cercopithecoids and orthogrady for hominoids. The YGSP innominate (hipbone) is from a primate with a narrow torso, resembling most extant monkeys and differing from the broader torsos of extant apes. Other postcranial material of S. indicus and its younger and similar congener Sivapithecus sivalensis also supports reconstruction of a hominoid with a positional repertoire more similar to the pronograde quadrupedal patterns of most monkeys than to the orthograde patterns of apes. However, Sivapithecus postcranial morphology differs in many details from any extant species. We reconstruct a slow-moving, deliberate, arboreal animal, primarily traveling above supports but also frequently engaging in antipronograde behaviors. There are no obvious synapomorphic postcranial features shared exclusively with any extant crown hominid, including Pongo.

Variation in Foot Strike Patterns among Habitually Barefoot and Shod Runners in Kenya

Runners are often categorized as forefoot, midfoot or rearfoot strikers, but how much and why do individuals vary in foot strike patterns when running on level terrain? This study used general linear mixed-effects models to explore both intra- and inter-individual variations in foot strike pattern among 48 Kalenjin-speaking participants from Kenya who varied in age, sex, body mass, height, running history, and habitual use of footwear. High speed video was used to measure lower extremity kinematics at ground contact in the sagittal plane while participants ran down 13 meter-long tracks with three variables independently controlled: speed, track stiffness, and step frequency. 72% of the habitually barefoot and 32% of the habitually shod participants used multiple strike types, with significantly higher levels of foot strike variation among individuals who ran less frequently and who used lower step frequencies. There was no effect of sex, age, height or weight on foot strike angle, but individuals were more likely to midfoot or forefoot strike when they ran on a stiff surface, had a high preferred stride frequency, were habitually barefoot, and had more experience running. It is hypothesized that strike type variation during running, including a more frequent use of forefoot and midfoot strikes, used to be greater before the introduction of cushioned shoes and paved surfaces.

Sexual selection targets cetacean pelvic bones.

Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land‐dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis that seems to serve no other function except to anchor muscles that maneuver the penis. Here, we create a novel morphometric pipeline to analyze the size and shape evolution of pelvic bones from 130 individuals (29 species) in the context of inferred mating system. We present two main findings: (1) males from species with relatively intense sexual selection (inferred by relative testes size) tend to evolve larger penises and pelvic bones compared to their body length, and (2) pelvic bone shape has diverged more in species pairs that have diverged in inferred mating system. Neither pattern was observed in the anterior‐most pair of vertebral ribs, which served as a negative control. This study provides evidence that sexual selection can affect internal anatomy that controls male genitalia. These important functions may explain why cetacean pelvic bones have not been lost through evolutionary time.

A model of hunter-gatherer skeletal element transport: the effect of prey body size, carriers, and distance.

Zooarchaeologists frequently use the relative abundance of skeletal elements in faunal assemblages in conjunction with foraging theory models to infer subsistence decisions made by prehistoric hunter-gatherers. However, foraging models applied to ethnoarchaeological cases have had variable success linking skeletal transport decisions with foraging predictions. Here, we approach this issue with the well-known Hadza data to statistically model the skeletal element transport decisions in response to distance from the residential hub and the number of carriers available for carcass transport. We compare our modeling approach to the traditional skeletal element utility curves from Binfords work with the Nunamiut, and to the more recently proposed Shannon evenness measure. Our approach, based on standard yet powerful statistical modeling techniques, can help researchers gain increased insight into the prey part transport responses of hunter-gatherers. Our analyses treat individual prey skeletal elements by body size as the response variable. The results of this analysis suggest that utility curves, and the Shannon evenness approach as a proxy for utility curves, are problematic for making statements about prehistoric foraging from zooarchaeological data. Transport distance does not explain a significant portion of small prey (size class 2) skeletal element transport variation. However, distance explains a great deal of transport variation in large prey (size classes 4 and 5). Inferences from skeletal element profiles should be made relative to prey body size and the discard probability of individual elements. Understanding the influence of these variables allows construction of a framework for testing archaeological element profiles against ethnographically derived transport models.

When mothers need others: The impact of hominin life history evolution on cooperative breeding

The evolution of cooperative breeding is particularly complex in humans because many other traits that directly affect parental care (shorter birth intervals, increased offspring survivorship, juvenile dependence, and older ages at dispersal) also emerge during the Pleistocene. If human cooperative breeding is ancient, it likely evolved in a hominin lacking a fully modern life history. However, the impact that changing life history traits has on parental care and cooperative breeding has not been analytically investigated. We develop an exploratory model to simulate an economic problem that would have arisen over the course of hominin life history evolution to identify those transitions that produced the strongest pressures for cooperative childrearing. The model generates two central predictions. First, help within maternal-offspring groups can support early changes in juvenile dependence, dispersal age, birth intervals, and fertility. If so, maternal-juvenile cooperation may be an important but understudied step in the evolution of human cooperative breeding. Second, pressure to recruit adult cooperation is most pronounced under more derived conditions of late dispersal and later ages of juvenile dependence, with a strong interaction at short birth intervals. Our findings indicate that changes in life history traits that affect parental care are critical in considering background selective forces that shaped the evolution of cooperative breeding.