Reconstructing the Diet of an Extinct Hominin Taxon: The Role of Extant Primate Models

Modern humans represent the only surviving species of an otherwise extinct clade of primates, the hominins. As the closest living relatives to extinct hominins, extant primates are an important source of comparative information for the reconstruction of the diets of extinct hominins. Methods such as comparative and functional morphology, finite element analysis, dental wear, dental topographic analysis, and stable isotope biogeochemistry must be validated and tested within extant populations before they can be applied to extinct taxa. Here we review how these methods have and might be used to reconstruct the diet of a particular extinct hominin, Paranthropus boisei, which has no extant analogue for its highly derived masticatory morphology. Our review emphasizes the potential and limitations of using extant primates as models for the reconstruction of extinct hominin diets. We encourage paleoanthropologists and those who study the feeding behaviors of extant primates to work together to investigate and validate methods for interpreting the diets of all extinct primates, including hominins.     

Back-casting sociality in extinct species: new perspectives using mass death assemblages and sex ratios

Despite 150 years of interest in the ecology of dinosaurs, mammoths, proto-hominids and other extinct vertebrates, a general framework to recreate patterns of sociality has been elusive. Based on our recent discovery of a contemporary heterospecific mass death assemblage in the Gobi Desert (Mongolia), we fit predictions about gender-specific associations and group living in extant ungulates to extinct ones. We relied on comparative data on sex-ratio variation and body-size dimorphism, basing analyses on 38 additional mass mortality sites from Asia, Africa, Europe and North America that span 50 million years. Both extant and extinct species died in aggregations with biased adult sex ratios, but the skew (from 1:1) was greater for extinct dimorphic taxa, suggesting that sociality in these extinct species can be predicted from spatial and demographic traits of extant ones. However, extinct rhinos, horses and zebras were inconsistent with predictions about adult sex ratios, which underscores the inherent difficulty in backcasting historic patterns to some monomorphic taxa. These findings shed light not only on the sociality of extinct species but provide a sound, although limited, footing for interpretation of modern death assemblages within the context of the emerging science of taphonomy and palaeobehaviour.     

Preliminary Analysis of Osteocyte Lacunar Density in Long Bones of Tetrapods: All Measures Are Bigger in Sauropod Dinosaurs

Osteocytes harbour much potential for paleobiological studies. Synchrotron radiation and spectroscopic analyses are providing fascinating data on osteocyte density, size and orientation in fossil taxa. However, such studies may be costly and time consuming. Here we describe an uncomplicated and inexpensive method to measure osteocyte lacunar densities in bone thin sections. We report on cell lacunar densities in the long bones of various extant and extinct tetrapods, with a focus on sauropodomorph dinosaurs, and how lacunar densities can help us understand bone formation rates in the iconic sauropod dinosaurs. Ordinary least square and phylogenetic generalized least square regressions suggest that sauropodomorphs have lacunar densities higher than scaled up or comparably sized mammals. We also found normal mammalian-like osteocyte densities for the extinct bovid Myotragus, questioning its crocodilian-like physiology. When accounting for body mass effects and phylogeny, growth rates are a main factor determining the density of the lacunocanalicular network. However, functional aspects most likely play an important role as well. Observed differences in cell strategies between mammals and dinosaurs likely illustrate the convergent nature of fast growing bone tissues in these groups.     

Uncovering cryptic evolutionary diversity in extant and extinct populations of the southern Australian arid zone Western and Thick-billed Grasswrens (Passeriformes: Maluridae: Amytornis)

The Western and Thick-billed Grasswrens (Aves: Passeriformes: Maluridae: Amytornis textilis and Amytornis modestus, respectively) exemplify issues surrounding the evolution, biogeography and conservation of Australia’s arid and semi-arid zone fauna. The two species together have historically occurred across much of southern Australia. They showed high intraspecific taxonomic diversity and short range endemism but suffered high rates of recent anthropogenic extinction. Of 11 named and 1 un-named subspecies, 5 are extinct and 3 are vulnerable or critically endangered. To clarify taxonomic issues, and to understand their pre-extinction phylogeography and identify extant populations and taxa of conservation value, we sequenced ~1,000 bp of the mtDNA ND2 gene from all extant populations and all but one extinct population. We confirmed reciprocal monophyly of A. modestus and A. textilis and identified strong phylogeographic structure associated with morphological divergence within each species. Populations of A. t. myall at the western edge of their range in South Australia may preserve “ghost” lineages of extinct subspecies from Western Australia as a result of ancient gene flow. Our results support recent taxonomic revisions, and highlight the critical importance of including samples of extirpated populations and extinct species to fully understand and interpret extant diversity. Conservation and management plans should recognise and seek to preserve the unique evolutionary diversity present in surviving populations.     

牛科(哺乳纲:偶蹄目)动物与生境利用有关的适应形态模式

对广义牛科动物颅后骨骼的多元变量分析揭示了牛科生境利用和体型之间的骨学特征。利用逐步分辨分析方法和一个基于机器学习的决策树方法鉴别了每种生境中牛科动物颅后解剖结构的形态特征。从110个广义牛科动物测量了43个指标进行了这项分析。利用所有主要肢骨测量值和以单根肢骨测量为主的测量值获得的分辨函数和决策树可以完美地区分适应开阔生境、森林和山地的牛科动物(在所有分析中得到了100 %正确的再分类)。由于调整的函数仅涉及到很小的颅后骨骼测量集,这些函数可以应用于研究考古学和古生物学发掘物中保存的不完整标本。这些表征生境利用的生态适应函数与那些用颅齿部性状建立、用于推测牛科动物食物选择的函数结合,具有刻画已灭绝的分类类群的古个体生态学和重建古环境的潜力。我们还分析了多元回归是否较单一因子回归表现出较高的预测能力,并提出了从每一种单根主要肢骨测量的颅后形态变量得到的最好代数函数     

Big cat,small cat: reconstructing body size evolution in living and extinct Felidae

The evolution of body mass is a fundamental topic in evolutionary biology, because it is closely linked to manifold life history and ecological traits and is readily estimable for many extinct taxa. In this study, we examine patterns of body mass evolution in Felidae (Placentalia, Carnivora) to assess the effects of phylogeny, mode of evolution, and the relationship between body mass and prey choice in this charismatic mammalian clade. Our data set includes 39 extant and 26 extinct taxa, with published body mass data supplemented by estimates based on condylobasal length. These data were run through ‘SURFACE’ and ‘bayou’ to test for patterns of body mass evolution and convergence between taxa. Body masses of felids are significantly different among prey choice groupings (small, mixed and large). We find that body mass evolution in cats is strongly influenced by phylogeny, but different patterns emerged depending on inclusion of extinct taxa and assumptions about branch lengths. A single Ornstein–Uhlenbeck optimum best explains the distribution of body masses when first‐occurrence data were used for the fossil taxa. However, when mean occurrence dates or last known occurrence dates were used, two selective optima for felid body mass were recovered in most analyses: a small optimum around 5 kg and a large one around 100 kg. Across living and extinct cats, we infer repeated evolutionary convergences towards both of these optima, but, likely due to biased extinction of large taxa, our results shift to supporting a Brownian motion model when only extant taxa are included in analyses.     

Sauropod dinosaurs evolved moderately sized genomes unrelated to body size

Sauropodomorph dinosaurs include the largest land animals to have ever lived, some reaching up to 10 times the mass of an African elephant. Despite their status defining the upper range for body size in land animals, it remains unknown whether sauropodomorphs evolved larger-sized genomes than non-avian theropods, their sister taxon, or whether a relationship exists between genome size and body size in dinosaurs, two questions critical for understanding broad patterns of genome evolution in dinosaurs. Here we report inferences of genome size for 10 sauropodomorph taxa. The estimates are derived from a Bayesian phylogenetic generalized least squares approach that generates posterior distributions of regression models relating genome size to osteocyte lacunae volume in extant tetrapods. We estimate that the average genome size of sauropodomorphs was 2.02 pg (range of species means: 1.77–2.21 pg), a value in the upper range of extant birds (mean = 1.42 pg, range: 0.97–2.16 pg) and near the average for extant non-avian reptiles (mean = 2.24 pg, range: 1.05–5.44 pg). The results suggest that the variation in size and architecture of genomes in extinct dinosaurs was lower than the variation found in mammals. A substantial difference in genome size separates the two major clades within dinosaurs, Ornithischia (large genomes) and Saurischia (moderate to small genomes). We find no relationship between body size and estimated genome size in extinct dinosaurs, which suggests that neutral forces did not dominate the evolution of genome size in this group.     

Implications of Diet for the Extinction of Saber-Toothed Cats and American Lions

The saber-toothed cat, Smilodon fatalis, and American lion, Panthera atrox, were among the largest terrestrial carnivores that lived during the Pleistocene, going extinct along with other megafauna ∼12,000 years ago. Previous work suggests that times were difficult at La Brea (California) during the late Pleistocene, as nearly all carnivores have greater incidences of tooth breakage (used to infer greater carcass utilization) compared to today. As Dental Microwear Texture Analysis (DMTA) can differentiate between levels of bone consumption in extant carnivores, we use DMTA to clarify the dietary niches of extinct carnivorans from La Brea. Specifically, we test the hypothesis that times were tough at La Brea with carnivorous taxa utilizing more of the carcasses. Our results show no evidence of bone crushing by P. atrox, with DMTA attributes most similar to the extant cheetah, Acinonyx jubatus, which actively avoids bone. In contrast, S. fatalis has DMTA attributes most similar to the African lion Panthera leo, implying that S. fatalis did not avoid bone to the extent previously suggested by SEM microwear data. DMTA characters most indicative of bone consumption (i.e., complexity and textural fill volume) suggest that carcass utilization by the extinct carnivorans was not necessarily more complete during the Pleistocene at La Brea; thus, times may not have been “tougher” than the present. Additionally, minor to no significant differences in DMTA attributes from older (∼30–35 Ka) to younger (∼11.5 Ka) deposits offer little evidence that declining prey resources were a primary cause of extinction for these large cats.     

POTENTIAL PITFALLS OF RECONSTRUCTING DEEP TIME EVOLUTIONARY HISTORY WITH ONLY EXTANT DATA,A CASE STUDY USING THE CANIDAE (MAMMALIA,CARNIVORA)

Reconstructing evolutionary patterns and their underlying processes is a central goal in biology. Yet many analyses of deep evolutionary histories assume that data from the fossil record is too incomplete to include, and rely solely on databases of extant taxa. Excluding fossil taxa assumes that character state distributions across living taxa are faithful representations of a clade's entire evolutionary history. Many factors can make this assumption problematic. Fossil taxa do not simply lead‐up to extant taxa; they represent now‐extinct lineages that can substantially impact interpretations of character evolution for extant groups. Here, we analyze body mass data for extant and fossil canids (dogs, foxes, and relatives) for changes in mean and variance through time. AIC‐based model selection recovered distinct models for each of eight canid subgroups. We compared model fit of parameter estimates for (1) extant data alone and (2) extant and fossil data, demonstrating that the latter performs significantly better. Moreover, extant‐only analyses result in unrealistically low estimates of ancestral mass. Although fossil data are not always available, reconstructions of deep‐time organismal evolution in the absence of deep‐time data can be highly inaccurate, and we argue that every effort should be made to include fossil data in macroevolutionary studies.     

Evolution of Sirenian Pachyosteosclerosis,a Model-case for the Study of Bone Structure in Aquatic Tetrapods

Osteosclerosis, or inner bone compaction, and pachyostosis, or outer hyperplasy of bone cortices (swollen bones), are typical features of tetrapods secondarily adapted to life in water. These peculiarities are spectacularly exemplified by the ribs of extant and extinct Sirenia. Sea cows are thus the best model for studying this kind of bone structural specializations. In order to document how these features differentiated during sirenian evolution, the ribs of 15 species, from the most basal form (Pezosiren portelli) up to extant taxa, were studied, and compared to those of other mammalian species from both morphometric and histological points of view. Pachyostosis was the first of these two specializations to occur, by the middle of the Eocene, and is a basal feature of the Sirenia. However, it subsequently regressed in some taxa that do not exhibit hyperplasic rib cortices. Osteosclerosis was only incipient in P. portelli. Its full development occurred later, by the end of the Eocene. These two structural specializations of bone are variably pronounced in extinct and extant sirenians, and relatively independent from each other, although frequently associated. They are possibly due to similar heterochronic mechanisms bearing on the timing of osteoblast activity. These results are discussed with respect to the functional constraints of locomotion in water.     

The Osteichtyes,from the Paleozoic to the extant time,through histology and palaeohistology of bony tissues

The aim of this short review is to emphasize the richness of the comparative histological studies on both fossil and extant Osteichthyes. Some selected examples in both Sarcopterygii (excluding tetrapods) and Actinopterygii show how it is possible to improve our knowledge on bone biology of extinct species but also to obtain new data on their palaeobiology or on their paleobiogeography. After a brief survey of the organization of bony tissues in osteichthyes, we review some examples of skeletal peculiarities in the following extinct and extant taxa: the histological structure of polypterid scales that suggests a hypothesis on the possible age and the biogeographical history of this basal actinopterygian taxon; the ossified lung of the fossil coelacanthids, with a discussion on its potential function; the histological organization of the sarcopterygian derived elasmoid scales (of Eusthenopteron sp., Latimeria sp. and Neoceratodus sp.). These comparative palaeohistological and histological data provide the basis of a general discussion of the evolutionary trends of bony tissues and their derivatives in Osteichthyes.     

Relationships between dental microwear and diet in Carnivora (Mammalia) — Implications for the reconstruction of the diet of extinct taxa

Food consumption causes distinct microwear patterns on teeth, especially in mammals that actively masticate food. Here we perform a microwear analysis to assess the relationships between diet and microwear features of diverse Carnivora. Our database includes approximately 230 individuals of 17 extant species having different diets. We analyse both slicing and grinding facets of M1 and m1. The proposed method is reproducible and allows the differentiation, especially on slicing facets, of microwear poles that are significantly distinct from one another. In carnivorans, the microwear features mainly result from their foraging behavior and the proportion of certain food items consumed. We applied our method to extinct taxa such as the amphicyonid Amphicyon major. The results on the m1 slicing facet indicate dietary similarities between this large Miocene predator and the extant red fox; results from the m1 grinding facet do not have equivalent in extant taxa, however.     

ESTIMATING SPECIATION AND EXTINCTION RATES FROM DIVERSITY DATA AND THE FOSSIL RECORD

Understanding the processes that underlie biodiversity requires insight into the evolutionary history of the taxa involved. Accurate estimation of speciation, extinction, and diversification rates is a prerequisite for gaining this insight. Here, we develop a stochastic birth–death model of speciation and extinction that predicts the probability distribution of both extinct and extant numbers of species in a clade. We present two estimation methods based on this model given data on the number of extinct species (from the fossil record) and extant species (from diversity assessments): a multivariate method of moments approach and a maximum-likelihood approach. We show that, except for some special cases, the two estimation methods produce very similar estimates. This is convenient, because the usually preferred maximum-likelihood approach is much more computationally demanding, so the method of moments can serve as a proxy. Furthermore, we introduce a correction for possible bias that can arise by the mere fact that we will normally only consider extant clades. We find that in some cases the bias correction affects the estimates profoundly. Finally, we show how our model can be extended to incorporate incomplete preservation. Preservation rates can, however, not be reliably estimated on the basis of numbers of extant and extinct species alone.     

Bite club: comparative bite force in big biting mammals and the prediction of predatory behaviour in fossil taxa

We provide the first predictions of bite force (BS) in a wide sample of living and fossil mammalian predators. To compare between taxa, we calculated an estimated bite force quotient (BFQ) as the residual of BS regressed on body mass. Estimated BS adjusted for body mass was higher for marsupials than placentals and the Tasmanian devil (Sarcophilus harrisii) had the highest relative BS among extant taxa. The highest overall BS was in two extinct marsupial lions. BFQ in hyaenas were similar to those of related, non-osteophagous taxa challenging the common assumption that osteophagy necessitates extreme jaw muscle forces. High BFQ in living carnivores was associated with greater maximal prey size and hypercarnivory. For fossil taxa anatomically similar to living relatives, BFQ can be directly compared, and high values in the dire wolf (Canis dirus) and thylacine (Thylacinus cynocephalus) suggest that they took relatively large prey. Direct inference may not be appropriate where morphologies depart widely from biomechanical models evident in living predators and must be considered together with evidence from other morphological indicators. Relatively low BFQ values in two extinct carnivores with morphologies not represented among extant species, the sabrecat, Smilodon fatalis, and marsupial sabretooth, Thylacosmilus atrox, support arguments that their killing techniques also differed from extant species and are consistent with 'canine-shear bite' and 'stabbing' models, respectively. Extremely high BFQ in the marsupial lion, Thylacoleo carnifex, indicates that it filled a large-prey hunting niche.     

Morphometric variation in the hominoid orbital aperture: a case study with implications for the use of variable characters in Miocene catarrhine systematics

Variable characters are ubiquitous in hominoid systematics and present a number of unique problems for phylogenetic analyses that include extinct taxa. As yet, however, few studies have quantified ranges of variation in complex morphometric characters within extant taxa and then used those data to assess the consistency with which discrete character states can be applied to poorly represented fossil species. In this study, ranges of intrageneric morphometric variation in the shape of the hominoid orbital aperture are estimated using exact randomization of average pairwise taxonomic distances (ATDs) derived from size-adjusted centroid, height-width, and elliptic Fourier (EF) variables. Using both centroid and height-width variables, 19 of the 21 possible ATDs between individuals representing seven extinct catarrhine taxa (Aegyptopithecus, Afropithecus, Ankarapithecus, Ouranopithecus, Paranthropus, Sivapithecus and Turkanapithecus) can be observed within a single extant hominoid subspecies, although generally with low probabilities. A resampling study is employed as a means for gauging the effect that this intrataxonomic variation may have on the consistency with which discrete orbital shape character states can be delimited given the small sample sizes available for most Miocene catarrhine taxa preserving this feature (i.e., n=1). For each type of morphometric variable, 100 cluster (UPGMA) analyses of pairwise ATDs are performed in which a single individual is randomly selected from each hominoid genus and analyzed alongside known extinct taxa; consensus trees are computed in order to obtain the frequencies with which different shape clusters appeared in each of the three analyses. The two major clusters appearing most frequently in all three consensus trees are found in only 57% (centroid variables), 49% (height-width variables), and 36% (EF variables) of these trees. If ranges of variation within represented extinct taxa could also be estimated, these frequencies would certainly be far lower. Hominoids clearly exhibit considerable intrageneric, intraspecific, and even intrasubspecific variation in orbit shape, and substantial morphometric overlap exists between taxa; consequently, discrete character states delimiting these patterns of continuous variation are likely to be highly unreliable in phylogenetic analyses of living and extinct species, particularly as the number of terminal taxa increases. Morphological phylogenetic studies of extant catarrhines that assess the effect of different methods (e.g., use of objective a priori weighting or frequency coding of variable characters, inclusion vs. exclusion of variable characters, use of specific vs. supraspecific terminal taxa) on phylogenetic accuracy may help to improve the techniques that systematists employ to make phylogenetic inferences about extinct taxa.     

A Pelican Tarsometatarsus (Aves: Pelecanidae) from the Latest Pliocene Siwaliks of India

We report a new fossil specimen of a pelican from the Tatrot Formation of the Siwalik Hills, India. It likely represents Pelecanus sivalensis Davies, 1880, the smaller of the two previously published species from the Siwalik Group stratigraphic sequence. This complete tarsometatarsus is the first fossil bone of a pelican collected in India for over 100 years. It is from the latest Pliocene (∼2.6 Ma), and is the youngest pelican fossil from the region. The new specimen exhibits a derived distoplantar ‘slant’ to the plantar margin of the medial crest of the hypotarsus, and a combination of features related to the morphology of the hypotarsus, the distal foramen, trochleae, and overall size that allow further differentiation from known tarsometatarsi of fossil and extant pelicans, including the three species of extant pelicans that occur in India (Pelecanus crispus, P. onocrotalus, and P. philippensis). It is of appropriate size for Pelecanus sivalensis, which to date has been known only by fragments of other skeletal elements of the wing, leg, and shoulder girdle. Thus, the observation that this tarsometatarsus is morphologically distinct from those of known pelicans provides further support for the distinctiveness of at least one extinct species of pelican from the Siwalik Group sediments. While the morphology of the tarsometatarsus allows for separation from other taxa known from tarsometatarsi, we found no clear shared derived states to place this taxon with any confidence in a phylogenetic context relative to any other pelican species, or even determine if it is part of the crown group of Pelecanidae. However, published molecular data are consistent with an origin of the crown clade prior to the Pleistocene, suggesting (along with one morphological character) the possibility that this species belongs to the Old World clade of pelican species.     

Correlates between calcaneal morphology and locomotion in extant and extinct carnivorous mammals

Locomotor mode is an important component of an animal's ecology, relating to both habitat and substrate choice (e.g., arboreal versus terrestrial) and in the case of carnivores, to mode of predation (e.g., ambush versus pursuit). Here, we examine how the morphology of the calcaneum, the ‘heel bone’ in the tarsus, correlates with locomotion in extant carnivores. Other studies have confirmed the correlation of calcaneal morphology with locomotion behaviour and habitat. The robust nature of the calcaneum means that it is frequently preserved in the fossil record. Here, we employ linear measurements and 2D‐geometric morphometrics on a sample of calcanea from eighty‐seven extant carnivorans and demonstrate a signal of correlation between calcaneal morphology and locomotor mode that overrides phylogeny. We used this correlation to determine the locomotor mode, and hence aspects of the palaeobiology of, 47 extinct carnivorous mammal taxa, including both Carnivora and Creodonta. We found ursids (bears), clustered together, separate from the other carnivorans. Our results support greater locomotor diversity for nimravids (the extinct ‘false sabertooths’, usually considered to be more arboreal), than previously expected. However, there are limitations to interpretation of extinct taxa because their robust morphology is not fully captured in the range of modern carnivoran morphology.     

Ancient DNA Provides New Insights into the Evolutionary History of New Zealand's Extinct Giant Eagle

Prior to human settlement 700 years ago New Zealand had no terrestrial mammals—apart from three species of bats—instead, approximately 250 avian species dominated the ecosystem. At the top of the food chain was the extinct Haast's eagle, Harpagornis moorei. H. moorei (10–15 kg; 2–3 m wingspan) was 30%–40% heavier than the largest extant eagle (the harpy eagle, Harpia harpyja), and hunted moa up to 15 times its weight. In a dramatic example of morphological plasticity and rapid size increase, we show that the H. moorei was very closely related to one of the world's smallest extant eagles, which is one-tenth its mass. This spectacular evolutionary change illustrates the potential speed of size alteration within lineages of vertebrates, especially in island ecosystems.     

Of teeth and trees: A fossil tip‐dating approach to infer divergence times of extinct and extant squaliform sharks

Fossil tip‐dating allows for the inclusion of morphological data in divergence time estimates based on both extant and extinct taxa. Neoselachii have a cartilaginous skeleton, which is less prone to fossilization compared to skeletons of Osteichthyans. Therefore, the majority of the neoselachian fossil record is comprised of single teeth, which fossilize more easily. Neoselachian teeth can be found in large numbers as they are continuously replaced. Tooth morphologies are of major importance on multiple taxonomic levels for identification of shark and ray taxa. Here, we review dental morphological characters of squalomorph sharks and test these for their phylogenetic signal. Subsequently, we combine DNA sequence data (concatenated exon sequences) with dental morphological characters from 85 fossil and extant taxa to simultaneously infer the phylogeny and re‐estimate divergence times using information of 61 fossil tip‐dates as well as eight node age calibrations of squalomorph sharks. Our findings show that the phylogenetic placement of fossil taxa is mostly in accordance with their previous taxonomic allocation. An exception is the phylogenetic placement of the extinct genus ?Protospinax , which remains unclear. We conclude that the high number of fossil taxa as well as the comprehensive DNA sequence data for extant taxa may compensate for the limited number of morphological characters identifiable on teeth, serving as a backbone for reliably estimating the phylogeny of both extinct and extant taxa. In general, tip‐dating mostly estimates older node ages compared to previous studies based on calibrated molecular clocks.