Improving preservation state assessment of carbonate microfossils in paleontological research using label-free stimulated Raman imaging.

In micropaleontological and paleoclimatological studies based on microfossil morphology and geochemistry, assessing the preservation state of fossils is of the highest importance, as diagenetic alteration invalidates textural features and compromises the correct interpretation of stable isotope and trace elemental analysis. In this paper, we present a novel non-invasive and label-free tomographic approach to reconstruct the three-dimensional architecture of microfossils with submicron resolution based on stimulated Raman scattering (SRS). Furthermore, this technique allows deciphering the three-dimensional (3D) distribution of the minerals within these fossils in a chemically sensitive manner. Our method, therefore, allows to identify microfossils, to chemically map their internal structure and eventually to determine their preservation state. We demonstrate the effectiveness of this method by analyzing several benthic and planktonic foraminifera, obtaining full 3D distributions of carbonate, iron oxide and porosity for each specimen. Subsequently, the preservation state of each microfossil can be assessed using these 3D compositional maps. The technique is highly sensitive, non-destructive, time-efficient and avoids the need for sample pretreatment. Therefore, its predestined application is the final check of the state of microfossils before applying subsequent geochemical analyses.

Adding fossil occupancy trajectories to the assessment of modern extinction risk.

Besides helping to identify species traits that are commonly linked to extinction risk, the fossil record may also be directly relevant for assessing the extinction risk of extant species. Standing geographical distribution or occupancy is a strong predictor of both recent and past extinction risk, but the role of changes in occupancy is less widely assessed. Here we demonstrate, based on the Cenozoic fossil record of marine species, that both occupancy and its temporal trajectory are significant determinants of risk. Based on extinct species we develop a model on the additive and interacting effects of occupancy and its temporal changes on extinction risk. We use this model to predict extinction risk of extant species. The predictions suggest a moderate risk for marine species on average. However, some species seem to be on a long-term decline and potentially at a latent extinction risk, which is not considered in current risk assessments.

Settlement-Size Scaling among Prehistoric Hunter-Gatherer Settlement Systems in the New World.

Settlement size predicts extreme variation in the rates and magnitudes of many social and ecological processes in human societies. Yet, the factors that drive human settlement-size variation remain poorly understood. Size variation among economically integrated settlements tends to be heavy tailed such that the smallest settlements are extremely common and the largest settlements extremely large and rare. The upper tail of this size distribution is often formalized mathematically as a power-law function. Explanations for this scaling structure in human settlement systems tend to emphasize complex socioeconomic processes including agriculture, manufacturing, and warfare-behaviors that tend to differentially nucleate and disperse populations hierarchically among settlements. But, the degree to which heavy-tailed settlement-size variation requires such complex behaviors remains unclear. By examining the settlement patterns of eight prehistoric New World hunter-gatherer settlement systems spanning three distinct environmental contexts, this analysis explores the degree to which heavy-tailed settlement-size scaling depends on the aforementioned socioeconomic complexities. Surprisingly, the analysis finds that power-law models offer plausible and parsimonious statistical descriptions of prehistoric hunter-gatherer settlement-size variation. This finding reveals that incipient forms of hierarchical settlement structure may have preceded socioeconomic complexity in human societies and points to a need for additional research to explicate how mobile foragers came to exhibit settlement patterns that are more commonly associated with hierarchical organization. We propose that hunter-gatherer mobility with preferential attachment to previously occupied locations may account for the observed structure in site-size variation.

Contemporaneous trace and body fossils from a late Pleistocene Lakebed in Victoria, Australia, allow assessment of bias in the fossil record.

The co-occurrence of vertebrate trace and body fossils within a single geological formation is rare and the probability of these parallel records being contemporaneous (i.e. on or near the same bedding plane) is extremely low. We report here a late Pleistocene locality from the Victorian Volcanic Plains in south-eastern Australia in which demonstrably contemporaneous, but independently accumulated vertebrate trace and body fossils occur. Bite marks from a variety of taxa are also present on the bones. This site provides a unique opportunity to examine the biases of these divergent fossil records (skeletal, footprints and bite marks) that sampled a single fauna. The skeletal record produced the most complete fauna, with the footprint record indicating a markedly different faunal composition with less diversity and the feeding traces suggesting the presence, amongst others, of a predator not represented by either the skeletal or footprint records. We found that the large extinct marsupial predator Thylacoleo was the only taxon apparently represented by all three records, suggesting that the behavioral characteristics of large carnivores may increase the likelihood of their presence being detected within a fossil fauna. In contrast, Diprotodon (the largest-ever marsupial) was represented only by trace fossils at this site and was absent from the site's skeletal record, despite its being a common and easily detected presence in late Pleistocene skeletal fossil faunas elsewhere in Australia. Small mammals absent from the footprint record for the site were represented by skeletal fossils and bite marks on bones.

The generalized time variable reconstructed birth-death process.

Much recent research has investigated the effect that different time variable birth-death processes have on the distribution of branching times in phylogenies of extant taxa. Previous work has shown how to calculate the distributions of number of lineages and branching times for a reconstructed constant rate birth-death process that started with one or two reconstructed lineages at some time in the past or ended with some number of lineages in the present. Here I expand that work to include any time variable birth-death process that starts with any number of reconstructed lineages and/or ends with any number of reconstructed lineages at any time, and I calculate a number of distributions under that process. I also explore the discrete time birth-death process which operates as an efficient and accurate numerical solution to any time-variable birth-death process and allows for the analytical incorporation of sampling and mass extinctions. I describe how these distributions can be used to compare different time variable models using maximum likelihood analysis, and I show how to simulate random trees under any of these models. I also introduce two visual methods for evaluating different time variable birth-death processes; these methods illustrate the shape of distributions for the number of lineages and waiting times by plotting them over time.

A critical framework for the assessment of biological palaeoproxies: predicting past climate and levels of atmospheric CO(2) from fossil leaves.

This review uses proxies of past temperature and atmospheric CO(2) composition based on fossil leaves to illustrate the uncertainties in biologically based proxies of past environments. Most leaf-based proxies are geographically local or genetically restricted and therefore can be confounded by evolution, extinction, changes in local environment or immigration of species. Stomatal frequency proxies illustrate how genetically restricted proxies can be particularly vulnerable to evolutionary change. High predictive power in the modern world resulting from the use of a very narrow calibration cannot be confidently extrapolated into the past (the Ginkgo paradox). Many foliar physiognomic proxies of climate are geographically local and use traits that are more or less fixed for individual species. Such proxies can therefore be confounded by floristic turnover and biome shifts in the region of calibration. Uncertainty in proxies tends to be greater for more ancient fossils. I present a set of questions that should be considered before using a proxy. Good proxies should be relatively protected from environmental and genetic change, particularly through having high information content and being founded on biomechanical or biochemical principles. Some current and potential developments are discussed, including those that involve more mechanistically sound proxies and better use of multivariate approaches.

Dating primate divergences through an integrated analysis of palaeontological and molecular data.

Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times. This is done by using a stochastic forwards-modeling approach where speciation and fossil preservation and discovery are simulated forward in time. We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth-death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes. To perform the inference, a new approximate Bayesian computation (ABC) algorithm is introduced, where the structure of the model can be exploited in an ABC-within-Gibbs algorithm to provide a more efficient analysis.

Some problems with assessing Cope's Rule.

Cope's Rule states that the size of species tends to increase along an evolutionary lineage. A basic statistical framework is elucidated for testing Cope's Rule and some surprising complications are pointed out. If Cope's Rule is formulated in terms of mean size, then it is not invariant to the way in which size is measured. If Cope's Rule is formulated in terms of median size, then it is not invariant to the degree of separation between ancestral and descendant species. Some practical problems in assessing Cope's Rule are also described. These results have implications for the empirical assessment of Cope's Rule.

Seriation in paleontological data using markov chain Monte Carlo methods.

Given a collection of fossil sites with data about the taxa that occur in each site, the task in biochronology is to find good estimates for the ages or ordering of sites. We describe a full probabilistic model for fossil data. The parameters of the model are natural: the ordering of the sites, the origination and extinction times for each taxon, and the probabilities of different types of errors. We show that the posterior distributions of these parameters can be estimated reliably by using Markov chain Monte Carlo techniques. The posterior distributions of the model parameters can be used to answer many different questions about the data, including seriation (finding the best ordering of the sites) and outlier detection. We demonstrate the usefulness of the model and estimation method on synthetic data and on real data on large late Cenozoic mammals. As an example, for the sites with large number of occurrences of common genera, our methods give orderings, whose correlation with geochronologic ages is 0.95.

Do homoiologies impede phylogenetic analyses of the fossil hominids? An assessment based on extant papionin craniodental morphology.

Homoiologies are phylogenetically misleading resemblances among taxa that can be attributed to phenotypic plasticity. Recently, it has been claimed that homoiologies are widespread in the hominid skull, especially in those regions affected by mastication-related strain, and that their prevalence is a major reason why researchers have so far been unable to obtain a reliable estimate of hominid phylogeny. To evaluate this "homoiology hypothesis", we carried out analyses of a group of extant primates for which a robust molecular phylogeny is available-the papionins. We compiled a craniometric dataset from measurements that differ in their susceptibility to mastication-related strain according to developmental considerations and experimental evidence. We used the coefficient of variation and analysis of variance with post hoc least significant difference comparisons in order to evaluate the variability of the measurements. The prediction from the homoiology hypothesis was that dental measurements, which do not remodel in response to strain, should be less variable than low-to-moderate-strain measurements, and that the latter should be less variable than high-strain measurements. We then performed phylogenetic analyses using characters derived from the measurements and compared the resulting phylogenetic hypotheses to the group's consensus molecular phylogeny. The prediction was that, if the homoiology hypothesis is correct, the agreement between the craniometric and molecular phylogenies would be best in the analyses of dental characters, intermediate in the analyses of low-to-moderate-strain characters, and least in the analyses of high-strain characters. The results of this study support the suggestion that mastication-related mechanical loading can result in variation in hominid cranial characters. However, they do not support the hypothesis that homoiology is a major reason why phylogenetic analyses of hominid crania have so far yielded conflicting and weakly supported hypotheses of relationship. These findings are consistent with a recent test of the homoiology hypothesis using craniodental data from extant hominoids, and cast doubt on the validity of the homoiology hypothesis, as originally formulated.

The role of changing childhood diets in the prehistoric evolution of food production: An isotopic assessment.

Earlier weaning has often been suggested as a cause for population growth after the evolution of food production. However, evidence for weaning-time reduction is largely circumstantial. Collagen stable nitrogen- and carbon-isotope ratios from juvenile and adult burials from four sites in eastern North America were measured to estimate weaning onsets and durations before and after the appearance of intensive food production. Two preagricultural Late Archaic sites (Indian Knoll and Carlston Annis) are compared with two highly agricultural Middle Mississippian sites (Angel and Tinsley Hill). Isotopic data and paleodemographic measures of birth rates provide no evidence for changes in weaning behavior or fertility with the development of food production in the prehistoric Lower Ohio Valley. Birth rates and weaning behavior appear to have been roughly the same at all four sites. These results indicate that models attributing population growth after the appearance of food production to earlier weaning are not universally applicable.

Stride lengths, speed and energy costs in walking of Australopithecus afarensis: using evolutionary robotics to predict locomotion of early human ancestors.

This paper uses techniques from evolutionary robotics to predict the most energy-efficient upright walking gait for the early human relative Australopithecus afarensis, based on the proportions of the 3.2 million year old AL 288-1 'Lucy' skeleton, and matches predictions against the nearly contemporaneous (3.5-3.6 million year old) Laetoli fossil footprint trails. The technique creates gaits de novo and uses genetic algorithm optimization to search for the most efficient patterns of simulated muscular contraction at a variety of speeds. The model was first verified by predicting gaits for living human subjects, and comparing costs, stride lengths and speeds to experimentally determined values for the same subjects. Subsequent simulations for A. afarensis yield estimates of the range of walking speeds from 0.6 to 1.3 m s-1 at a cost of 7.0 J kg-1 m-1 for the lowest speeds, falling to 5.8 J kg-1 m-1 at 1.0 m s-1, and rising to 6.2 J kg-1 m-1 at the maximum speed achieved. Speeds previously estimated for the makers of the Laetoli footprint trails (0.56 or 0.64 m s-1 for Trail 1, 0.72 or 0.75 m s-1 for Trail 2/3) may have been underestimated, substantially so for Trail 2/3, with true values in excess of 0.7 and 1.0 m s-1, respectively. The predictions conflict with suggestions that A. afarensis used a 'shuffling' gait, indicating rather that the species was a fully competent biped.

The calcaneus: sex assessment of prehistoric New Zealand Polynesian skeletal remains.

The increasing pace of urbanisation has meant that prehistoric Polynesian skeletal remains are frequently being recovered in New Zealand. Since such material must often be reinterred quickly, it is important that the sex of individuals be determined from the remains in a relatively short time. For this purpose, discriminant function analysis was utilised for sex determination of prehistoric adult New Zealand Polynesian calcanei (26 male and 22 female). Five measurements were taken and subjected to Statistical Package for the Social Sciences (SPSS) discriminant function analysis. For the discriminant functions derived, accuracy of sex determination ranged from 88.4 to 93.5%. Reduction in error over random assignment by sex ranged from 77 to 87%.

An empirical assessment of taxic paleobiology.

The analysis of major changes in faunal diversity through time is a central theme of analytical paleobiology. The most important sources of data are literature-based compilations of stratigraphic ranges of fossil taxa. The levels of error in these compilations and the possible effects of such error have often been discussed but never directly assessed. We compared our comprehensive database of trilobites to the equivalent portion of J. J. Sepkoski Jr.'s widely used global genus database. More than 70% of entries in the global database are inaccurate; however, as predicted, the error is randomly distributed and does not introduce bias.

Testing for multiple species in fossil samples: an evaluation and comparison of tests for equal relative variation.

Tests for equal relative variation are valuable and frequently used tools for evaluating hypotheses about taxonomic heterogeneity in fossil hominids. In this study, Monte Carlo methods and simulated data are used to evaluate and compare 11 tests for equal relative variation. The tests evaluated include CV-based parametric bootstrap tests, modifications of Levene's test, and modified weighted scores tests. The results of these simulations show that a modified version of the weighted scores test developed by Fligner and Killeen ([1976] J. Am. Stat. Assoc. 71:210-213) is the only test that maintains an acceptable balance of type I and type II errors, even under conditions where all other tests have extraordinarily high type I error rates or little power.

A kill curve for Phanerozoic marine species.

A kill curve for Phanerozoic species is developed from an analysis of the stratigraphic ranges of 17,621 genera, as compiled by Sepkoski. The kill curve shows that a typical species' risk of extinction varies greatly, with most time intervals being characterized by very low risk. The mean extinction rate of 0.25/m.y. is thus a mixture of long periods of negligible extinction and occasional pulses of much higher rate. Because the kill curve is merely a description of the fossil record, it does not speak directly to the causes of extinction. The kill curve may be useful, however, to li¿mit choices of extinction mechanisms.