Siobhan Cooke | Johns Hopkins University School of Medicine (original) (raw)

Papers by Siobhan Cooke

Phylogeny, Molecular Population Genetics, 2016

The extant radiation of Neotropical primates, the platyrrhines, occupy a great variety of ecologi... more The extant radiation of Neotropical primates, the platyrrhines, occupy
a great variety of ecological niches in the tropical forests of Central and
South America. This diversity includes large-bodied suspensory ripe fruit
specialists such as Ateles, mid-canopy dwelling seed consuming pitheciids,
the predominantly folivorous genera Alouatta and Brachyteles, the very
small-bodied insect- and sap-consuming pygmy marmoset as well as the
only nocturnal anthropoid, Aotus or the Owl Monkey, among many others.
Though this radiation is incredibly diverse today, at the terminal
Pleistocene, there were several species unlike any extant forms; these
included the very large-bodied (20 kg) Brazilian atelids and several species
of endemic Caribbean primates with unique morphological adaptations. In
this chapter, we review the history of the discovery of the Brazilian and
Caribbean extinct primates, discuss their major morphological adaptations
including their unique cranial, postcranial, and dental morphologies, and
review possible extinction scenarios. Though the exact timing of their
extinction is unclear, these primates seem to have disappeared from their
respective environments after the arrival of human beings. Finally, we
discuss the ecological impact that these extinctions may have had and the
ways that paleontologists can contribute to understanding extinction
processes today.

The most advanced conditions of this canine morphology are found in the pitheciines, in which the... more The most advanced conditions of this canine morphology are found in the pitheciines, in which the lower canines are massive and everted. Functionally, the pitheciine canine is used to husk hard-shelled fruit, suggesting that the torus might serve to reinforce the tooth against bending stress and the position of the apex may minimize eccentric loading of the crown shaft via the tip.

Journal of Vertebrate Paleontology, 2018

Hispaniola once had a large and diverse endemic rodent community. Today, a single species, Plagio... more Hispaniola once had a large and diverse endemic rodent community. Today, a single species, Plagiodontia aedium, survives alongside invasive murids. Ecological adaptations and resource competition among species have not been previously studied. Here, we undertake the first investigation of the foraging ecology of the endemic taxa using estimated body mass and carbon and oxygen isotope values in incisor enamel. Our sample includes nine endemic taxa, eight of which are extinct, from two Holocene cave assemblage in southern Haiti. We also measured isotopic signatures for the invasive genus Rattus to explore potential niche overlap and competition between introduced and endemic fauna. We expected to detect isotopic evidence for niche partitioning among phylogenetically related rodents with similar morphological adaptations. We find clear differences in body mass and isotope values among rodent taxa. The combination of carbon and oxygen isotopes suggests that some taxa lived in the forest understory, whereas others likely frequented the canopy or open habitats. We may also be able to distinguish dietary preferences (e.g., folivory, frugivory, and potentially trophic omnivory). Small individuals attributed to an undescribed species of Isolobodon are isotopically distinct from their congeners, I. montanus and I. portoricensis, and appear to have relied to a modest degree on C4 foods. Rattus had a broad generalist niche, which coincided with several endemics, including extant P. aedium. Although preliminary, these data shed light on how a closely related community of island rodents partitions resources and provide context for understanding the ecological role that invasive species may play in extinction processes and future conservation efforts.

Recent paleontological collection in submerged caves in the eastern Dominican Republic has yielde... more Recent paleontological collection in submerged caves in the eastern Dominican Republic has yielded new specimens of Antillothrix bernensis. Here we describe a complete cranium of an adult individual (MHD 20) and provide phenetic comparisons to other endemic Caribbean taxa and extant mainland platyrrhines using three-dimensional geometric morphometric methods (3DGM). Qualitative and quantitative comparisons support conclusions based on other recently described fossil material: Antillothrix has a dentition lacking clear dietary specialization, an elongated brain case with strong temporal lines, and a vertically oriented nuchal plane. MHD 20 shares a combination of traits with a previously published subadult specimen (MHD 01) including a deep depression at glabella, dorsoventrally elongated orbits, and a relatively large face. This shared morphology reinforces the taxonomic affinity of the two specimens , with differences between the two likely reflecting the younger ontogenetic age of MHD 01. Comparisons to the extant platyrrhines paint a complicated picture as the results of between-group principal components analyses (bgPCA) indicate that Antillothrix does not share a suite of morphological features exclusively with any one genus. Depending on which bgPC axes are visualized, and which subset of landmarks is included (i.e., only those describing the shape of the face/palate for inclusion of Xenothrix), MHD 20 is most similar in shape to the atelids, Alouatta, Lagothrix, and Brachyteles, or an otherwise "empty" region of shape space. It groups neither with Cebus nor Callicebus, two taxa that Antillothrix has been associated with in previous studies based on much less complete material. The Antillothrix cranium does not exhibit any of the derived characters classically used to diagnose or define any single clade; rather its morphology shares features with multiple platyrrhine groups. This is consistent with the interpretation that Antillothrix preserves a primitive morphology, which accords with the hypothesis positing an early arrival of platyrrhines in the Caribbean.

In this study, we assess the precision, accuracy, and repeatability of craniodental landmarks (Ty... more In this study, we assess the precision, accuracy, and repeatability of craniodental landmarks (Types I, II, and III, plus curves of semilandmarks) on a single macaque cranium digitally reconstructed with three different surface scanners and a microCT scanner. Nine researchers with varying degrees of osteological and geometric morphometric knowledge land-marked ten iterations of each scan (40 total) to test the effects of scan quality, researcher experience, and landmark type on levels of intra-and interobserver error. Two researchers additionally landmarked ten specimens from seven different macaque species using the same landmark protocol to test the effects of the previously listed variables relative to species level morphological differences (i.e., observer variance versus real biological variance). Error rates within and among researchers by scan type were calculated to determine whether or not data collected by different individuals or on different digitally rendered crania are consistent enough to be used in a single dataset. Results indicate that scan type does not impact rate of intra-or interobserver error. Interobserver error is far greater than intraob-server error among all individuals, and is similar in variance to that found among different macaque species. Additionally, experience with osteology and morphometrics both positively contribute to precision in multiple landmarking sessions, even where less experienced researchers have been trained in point acquisition. Individual training increases precision (although not necessarily accuracy), and is highly recommended in any situation where multiple researchers will be collecting data for a single project. PLOS ONE | https://doi.org/10.1371/journal.pone.

Body mass is an important component of any paleobiological reconstruction. Reliable skeletal dime... more Body mass is an important component of any paleobiological reconstruction. Reliable skeletal dimensions for making estimates are desirable but extant primate reference samples with known body masses are rare. We estimated body mass in a sample of extinct platyrrhines and Fayum anthropoids based on four measurements of the articular surfaces of the humerus and femur. Estimates were based on a large extant reference sample of wild-collected individuals with associated body masses, including previously published and new data from extant platyrrhines, cercopithecoids, and hominoids. In general, scaling of joint dimensions is positively allometric relative to expectations of geometric isometry, but negatively allometric relative to expectations of maintaining equivalent joint surface areas. Body mass prediction equations based on articular breadths are reasonably precise, with %SEEs of 17e25%. The breadth of the distal femoral articulation yields the most reliable estimates of body mass because it scales similarly in all major anthropoid taxa. Other joints scale differently in different taxa; therefore, locomotor style and phylogenetic affinity must be considered when calculating body mass estimates from the proximal femur, proximal humerus, and distal humerus. The body mass prediction equations were applied to 36 Old World and New World fossil anthropoid specimens representing 11 taxa, plus two Haitian specimens of uncertain taxonomic affinity. Among the extinct platyrrhines studied, only Cebu-pithecia is similar to large, extant platyrrhines in having large humeral (especially distal) joints. Our body mass estimates differ from each other and from published estimates based on teeth in ways that reflect known differences in relative sizes of the joints and teeth. We prefer body mass estimators that are biomechanically linked to weight-bearing, and especially those that are relatively insensitive to differences in locomotor style and phylogenetic history. Whenever possible, extant reference samples should be chosen to match target fossils in joint proportionality.

The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate ext... more The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread overlap between humans and now-extinct native mammals. Humans arrived in four waves (Lithic, Archaic, Ceramic, and European), each associated with increased environmental impact. Large-bodied mammals and several bats were extinct by the Archaic, following protracted extinction dynamics perhaps reflecting habitat loss. Most small-bodied rodents and lipotyphlan insectivores survived the Ceramic, but extensive landscape transformation and the introduction of invasive mammals following European colonization caused further extinctions, leaving a threatened remnant fauna. Both large-and small-bodied nonvolant mammals disappeared, reflecting complex relationships between body size, ecology, and anthropogenic change. Extinct bats were generally larger species, paralleling declines from natural catastrophes.

The Jamaican primate, Xenothrix mcgregori, regarded variously as either a pitheciid or a stem pla... more The Jamaican primate, Xenothrix mcgregori, regarded variously as either a pitheciid or a stem platyrrhine, was the terminal branch of a clade that likely entered the West Indies at least as early as the Early Miocene, although its lineage is represented by fossils of Quaternary age only. We present a new direct radiocarbon-based date of 1,477 ± 34 calibrated years before present (cal BP) for the last documented appearance of this species in the fossil record. We employed the Gaussian-resampled, inverse-weighted McInerny et al. (GRIWM) method to estimate the extinction date of X. mcgregori, based on the data presented here as well as 6 other dates derived from X. mcgregori sites. On this basis, we estimated a last occurrence ~900 BP. The cause or causes of this extinction, as well as the many others that occurred in late Quaternary of the Greater Antilles, remain a matter of debate. The likeliest inference is that these losses were largely if not completely anthropogenically driven. Although many species and populations of primates are critically threatened today, the loss of X. mcgregori stands as the most recent species-level extinction within Anthropoidea corroborated by radiometric evidence. El primate de Jamaica Xenothrix mcgregori, considerado alternativamente como un Pitheciidae o como un Platyrrhini troncal, fue la rama terminal de un clado que probablemente ingresó a las Indias Occidentales al menos en el Mioceno Temprano, aunque su linaje está representado únicamente por fósiles del Cuaternario. Aquí presentamos una nueva datación radiocarbónica de ca. 1,477 ± 34 AP para la aparición más reciente documentada de esta especie en el registro fósil. También empleamos el método Gaussian-resampled inverse-weighted de McInerny et al. (GRIWM) para estimar el momento de extinción de X. mcgregori, basado tanto en datos presentados aquí, así como en otros seis fechados derivados de sitios con este primate. De otra forma, estimamos el último registro en ca. 900 AP. La causa o causas de esta extinción, así como las otras que ocurrieron en el Cuaternario tardío en las Antillas Mayores siguen siendo un tema de debate. La inferencia más probable es que estas pérdidas fueron en gran medida, si no completamente, impulsadas por la acción antrópica. Aunque muchas especies y poblaciones de primates están críticamente amenazadas hoy en día, la pérdida de X. mcgregori es la extinción más reciente a nivel específico dentro de Anthropoidea corroborada por evidencia radiométrica.

Much debate surrounds the phylogenetic affinities of the endemic Greater Antillean platyrrhines. ... more Much debate surrounds the phylogenetic affinities of the endemic Greater Antillean platyrrhines. Thus far, most phylogenetic analyses have been constructed and tested using craniodental characters. We add to this dialog by considering how features of the distal humerus support or refute existing hypotheses for the origins of fossil Caribbean primates, utilizing three-dimensional geometric morphometric data in combination with character based cladistic analyses. We also add to the sample of fossil platyrrhine humeri with the description of UF 114718, a new distal humerus from Haiti. We reconstruct UF 114718 to be a generalized, arboreal quadruped attributed to the species Insulacebus toussantiana. Our results from phylogenetic analyses lend some support to the idea that some Greater Antillean fossil taxa including Xenothrix mcgregori, Antillothrix bernensis, and Insulacebus toussaintiana could form a monophyletic clade that is sister to either extant Platyrrhini or basal pitheciids. Based on the distal humeral data, we reconstruct the earliest ancestral platyrrhine to be a generalized, arboreal quadruped that potentially emphasized pronated arm postures during locomotion and may have engaged in some limited climbing, most similar in shape to early anthropoids and some of the earliest Antillean forms. However, aspects of shape and standard qualitative characters relating to the distal humerus seem to be variable and prone to both homoplasy and reversals; thus these results must be interpreted cautiously and (where possible) within the context provided by other parts of the skeleton.

Journal of Human Evolution

Endemic New World monkeys are an important element of the extinct mammal faunas of the Caribbean'... more Endemic New World monkeys are an important element of the extinct mammal faunas of the Caribbean's Greater Antilles. Here we report the first geochronometric evidence that the primate Antillothrix bernensis existed in the Dominican Republic during the Pleistocene, based on the uranium-series age of carbonate speleothem that encased a tibia when it was collected in a flooded cave. Three-dimensional geometric morphometrics of laser-scanned living and extinct samples provide evidence to support the hypothesis that this specimen and other Dominican primate tibial remains belong to that same species. U–Th dating of the host cave carbonate returns ages consistently at the 600 ka upper limit of the technique. However, U–Pb, capable of resolving ages of greater antiquity, is more robust in this context, returning a secure age of 1.32 ± 0.11 Ma, which is the oldest chronometric age recorded for a Hispaniolan mammal. While its origins and manner and time of arrival are obscure, the morphometric studies are consistent with phylogenetic analyses that place A. bernensis within the pitheciid clade of the platyrrhines. The species apparently endured for over 1 million years during the climatic perturbations of the Pleistocene, as a frugivorous climbing quadruped, one of two known primate species occupying the hazard prone island of Hispaniola.

The correlation between diet and dental topography is of importance to paleontologists seeking to... more The correlation between diet and dental topography is of importance to paleontologists
seeking to diagnose ecological adaptations in extinct taxa. Although the subject is well represented
in the literature, few studies directly compare methods or evaluate dietary signals
conveyed by both upper and lower molars. Here, we address this gap in our knowledge by
comparing the efficacy of three measures of functional morphology for classifying an ecologically
diverse sample of thirteen medium- to large-bodied platyrrhines by diet category
(e.g., folivore, frugivore, hard object feeder). We used Shearing Quotient (SQ), an index derived
from linear measurements of molar cutting edges and two indices of crown surface topography,
Occlusal Relief (OR) and Relief Index (RFI). Using SQ, OR, and RFI, individuals
were then classified by dietary category using Discriminate Function Analysis. Both upper
and lower molar variables produce high classification rates in assigning individuals to diet
categories, but lower molars are consistently more successful. SQs yield the highest classification
rates. RFI and OR generally perform above chance. Upper molar RFI has a success
rate below the level of chance. Adding molar length enhances the discriminatory power for
all variables. We conclude that upper molar SQs are useful for dietary reconstruction, especially
when combined with body size information. Additionally, we find that among our sample
of platyrrhines, SQ remains the strongest predictor of diet, while RFI is less useful at
signaling dietary differences in absence of body size information. The study demonstrates
new ways for inferring the diets of extinct platyrrhine primates when both upper and lower
molars are available, or, for taxa known only from upper molars. The techniques are useful
in reconstructing diet in stem representatives of anthropoid clade, who share key aspects of
molar morphology with extant platyrrhines.

The howler monkey clade includes species of Alouatta and four extinct genera, Stirtonia , Paralou... more The howler monkey clade includes species of Alouatta and four extinct genera, Stirtonia , Paralouatta , Protopithecus , and probably Solimoea as well. Contrary to expectations, this radiation may have originated as a largely frugivorous group; advanced, Alouatta -like leaf-eating is a novelty well-developed in the Alouatta-Stirtonia sublineage only. Revised body mass estimates place Stirtonia and Paralouatta within the size range exhibited by the living forms and confi rm the * Since this chapter was written, additional study by Halenar and Rosenberger ( 2013 ) of the material discussed here as Protopithecus led to the conclusion that the two samples actually represent two different genera. The essentially complete Bahian skeleton, which forms the basis of the present discussion, is being assigned to a new genus and species, Cartelles coimbrafi lhoi , within subfamily Alouattinae. The original Lund material from Minas Gerais bears the original name Protopithecus , but its affi nities are more likely to be found among atelines than alouattines.

Geometric morphometrics (GM) has increasingly become an important tool in assessing and studying ... more Geometric morphometrics (GM) has increasingly become an important
tool in assessing and studying shape variation in a wide variety of
taxa. While the GM toolkit has unparalleled power to quantify shape, its
use in studies of functional morphology have been questioned. Here, we
assess the state of the field of GM and provide an overview of the techniques
available to assess shape, including aspects of visualization, statistical
analysis, phylogenetic control, and more. Additionally, we briefly
review the history of functional morphology and summarize the main
tools available to the functional morphologist. We explore the intersection
of geometric morphometrics and functional morphology and we suggest
ways that we may be able to move forward in profitably combining these
two research areas. Finally, this paper provides a brief introduction to the
papers in this special issue and highlights the ways in which the contributing
authors have approached the intersection of GM and functional
morphology.

Cranial and temporomandibular joint (TMJ) form has been shown to reflect masticatory forces and m... more Cranial and temporomandibular joint (TMJ) form has been shown to
reflect masticatory forces and mandibular range of motion, which vary in
relation to feeding strategy. Similarly, the dentition, as the portion of the
masticatory apparatus most directly involved in triturating food items,
strongly reflects dietary profile. Fine control over condylar and mandibular
movements guides the teeth into occlusion, while the topography and position
of the dental arcade mediate mandibular movements. We hypothesize
that masticatory, and particularly TMJ, morphology and dental form covary
in predictable ways with one another and with diet. We employed threedimensional
geometric morphometric techniques to examine inter-specific
variation in ten platyrrhine species. Landmarks were collected on six datasets
describing the upper and lower molars, cranium, glenoid fossa, mandible,
and mandibular condyle; two-block partial least squares analyses were
performed to assess covariation between cranial morphology, dentition, and
diet. Significant relationships were identified between the molars and the
cranium, mandible, and glenoid fossa. Some of these shape complexes reflect
feeding strategy; for example, higher crowned/cusped dentitions, as found in
primates consuming larger quantities of structural carbohydrates (e.g.,
Alouatta and Saimiri), correspond to anteroposterior longer and deeper glenoid
fossae. These results indicate strong covariance between dental and
TMJ form, aspects of which are related to feeding behavior. However, other
aspects of morphological variation display a strong phylogenetic signal; we
must therefore examine further ways in which to control for phylogeny when
examining covariation in interspecific masticatory form.

Dental topographic analysis is the quantitative assessment of shape of three-dimensional models ... more Dental topographic analysis is the quantitative
assessment of shape of three-dimensional models
of tooth crowns and component features. Molar topographic
curvature, relief, and complexity correlate with
aspects of feeding behavior in certain living primates,
and have been employed to investigate dietary ecology in
extant and extinct primate species. This study investigates
whether dental topography correlates with diet
among a diverse sample of living platyrrhines, and compares
platyrrhine topography with that of prosimians. We
sampled 111 lower second molars of 11 platyrrhine genera
and 121 of 20 prosimian genera. For each tooth we calculated
Dirichlet normal energy (DNE), relief index (RFI),
and orientation patch count (OPCR), quantifying surface
curvature, relief, and complexity respectively. Shearing
ratios and quotients were also measured. Statistical analyses
partitioned effects of diet and taxon on topography
in platyrrhines alone and relative to prosimians. Discriminant
function analyses assessed predictive diet models.
Results indicate that platyrrhine dental topography correlates
to dietary preference, and platyrrhine-only predictive
models yield high rates of accuracy. The same is true
for prosimians. Topographic variance is broadly similar
among platyrrhines and prosimians. One exception is
that platyrrhines display higher average relief and lower
relief variance, possibly related to lower relative molar
size and functional links between relief and tooth longevity
distinct from curvature or complexity. Explicitly incorporating
phylogenetic distance matrices into statistical
analyses of the combined platyrrhine-prosimian sample
results in loss of significance of dietary effects for
OPCR and SQ, while greatly increasing dietary significance
of RFI.

Phylogeny, Molecular Population Genetics, 2016

Journal of Vertebrate Paleontology, 2018

Journal of Human Evolution

La Venta is a Colombian Middle Miocene paleontological site that has yielded fossils critical for... more La Venta is a Colombian Middle Miocene paleontological site that has yielded fossils critical for understanding the evolution of the platyrrhines and the endemic South American vertebrate fauna that existed prior to the Great American Interchange. Despite being highly fossiliferous, no systematic fossil collection has been conducted at La Venta since the late 1980s. During the summers of 2013-2014, our team began field expeditions to both previously known and unexplored areas of La Venta. Here we present our initial discoveries and analyses of both primate and broader vertebrate fauna with particular concentration on those collected from newly discovered localities.

In two field seasons, we have identified 25 new localities and collected over 1500 individual fossil specimens, including a new calcaneum of Neosaimiri from the Monkey Beds of the Villavieja formation. This layer and the layer below the Tatacoa Sandstone beds from t he La Victoria formation were the most diverse and the only layers to yield significant numbers of mammals. Fossil Crocodylia and Testudines were common throughout all fossiliferous layers, although other sauropsids were also discovered, notably snake vertebrae which augment a clade previously known from a single specimen. Osteichthyes are abundant in some layers, but are nearly absent in others. Fluctuations in faunal percentages may correspond with changes in the paleoecology of the proto-Magdalena River Basin through time. Our two expeditions to La Venta have yielded many fossils that demonstrate the diversity and importance of these formations and impel continuing field expeditions in future seasons.

This research was funded by Northeastern Illinois University’s Summer Research Stipend, Grand Valley State University’s CSCE Research Grant-in-Aid and Mini-Grant programs, and the NSF GRFP.

The origin and relationships of the endemic Caribbean primates are one of the least understood as... more The origin and relationships of the endemic Caribbean primates are one of the least understood aspects of platyrrhine evolution. This project addresses the paleobiology of Paralouatta varonai, a species found in Miocene to sub-recent deposits in Cuba ). Originally, this taxon was assigned to the Alouattini based on cranial synapomorphies (Rivera & Arredondo, 1991), but more primitive aspects of the skull and dentition caused some authors to place Paralouatta and other Caribbean platyrrhines in a sister clade to Callicebus (MacPhee et al., 1995 et seq.). New analyses of the cranium and dentition using three-dimensional geometric morphometrics support the original interpretation, but with caveats.