Trait-based diversification shifts reflect differential extinction among fossil taxa.

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

The Implications of Stratigraphic Compatibility for Character Integration among Fossil Taxa.

Two characters are stratigraphically compatible if some phylogenies indicate that their combinations (state-pairs) evolved without homoplasy and in an order consistent with the fossil record. Simulations assuming independent character change indicate that we expect approximately 95% of compatible character pairs to also be stratigraphically compatible over a wide range of sampling regimes and general evolutionary models. However, two general models of rate heterogeneity elevate expected stratigraphic incompatibility: "early burst" models, where rates of change are higher among early members of a clade than among later members of that clade, and "integration" models, where the evolution of characters is correlated in some manner. Both models have important theoretical and methodological implications. Therefore, we examine 259 metazoan clades for deviations from expected stratigraphic compatibility. We do so first assuming independent change with equal rates of character change through time. We then repeat the analysis assuming independent change with separate "early" and "late" rates (with "early" = the first third of taxa in a clade), with the early and late rates chosen to maximize the probability of the observed compatibility among the early taxa and then the whole clade. We single out Cambrian trilobites as a possible "control" group because morphometric studies suggest that integration patterns are not conserved among closely related species. Even allowing for early bursts, we see excess stratigraphic incompatibility (i.e., negative deviations) in significantly more clades than expected at 0.50, 0.25, and 0.05 [Formula: see text] values. This pattern is particularly strong in chordates, echinoderms, and arthropods. However, stratigraphic compatibility among Cambrian trilobites matches the expectations of integration studies, as they (unlike post-Cambrian trilobites) do not deviate from the expectations of independent change with no early bursts. Thus, these results suggest that processes such as integration strongly affect the data that paleontologists use to study phylogeny, disparity, and rates.

Estimation of age-at-death for adult males using the acetabulum, applied to four Western European populations.

Methods to estimate adult age from observations of skeletal elements are not very accurate and motivate the development of better methods. In this article, we test recently published method based on the acetabulum and Bayesian inference, developed using Coimbra collection (Portugal). In this study, to evaluate its utility in other populations, this methodology was applied to 394 specimens from four different documented Western European collections. Four strategies of analysis to estimate age were outlined: (a) each series separately; (b) on Lisbon collection, taken as a reference Coimbra collection; (c) on Barcelona collection, taken as a reference both Portuguese collections; and (d) on London collection taken as reference the three Iberian collections combined. Results indicate that estimates are accurate (83-100%). As might be expected, the least accurate estimates were obtained when the most distant collection was used as a reference. Observations of the fused acetabulum can be used to make accurate estimates of age for adults of any age, with less accurate estimates when a more distant reference collection is used.

Using the acetabulum to estimate age at death of adult males.

The acetabular region is often present and adequately preserved in adult human skeletal remains. Close morphological examination of the 242 left male os coxae from the identified collection of Coimbra (Portugal) has enabled the recognition of seven variables that can be used to estimate age at death. This paper describes these variables and argues their appropriateness by analyzing the correlation between these criteria and the age, the intra- and interobserver consistence, and the accuracy in age prediction using Bayesian inference to estimate age of identified specimens. Results show significant close correlation between the acetabular criteria and age, nonsignificant differences in intra- and interobserver test, and 89% accuracy in Bayes prediction. Obtained estimated age of the specimens had similar accuracy in all ages. These results indicate that these seven variables, based on the acetabular area, are potentially useful to estimate age at death for adult specimens.

Native Americans' choice of species for medicinal use is dependent on plant family: confirmation with meta-significance analysis.

We test the hypothesis that the choice by traditional people of species of plants for medicinal use does or does not depend on the families to which those species belong. Our geographic context is continental North America north of the Rio Grande River. Our plant context is flowering plants. Our ethnological context is Native American traditions. Our null hypothesis is that the probability of any species being medicinal is the fraction of all species that are medicinal, no matter the family to which that species may belong. Classical statistical techniques and the experience of ethnobiologists had already made it clear that among very large plant families, most have either very many or very few medicinal species. Here we use intense computation to simulate thousands of data sets to create predictions to compare with the observed data for medium and small families. Our results clearly show that a surprising number of medium and small families also have very many or very few medicinal species. Recent molecular, fossil and cytological studies have confirmed the evolutionary naturalness of most plant families. This suggests that species in the same family may have inherited from common ancestors similar ecological adaptations, such as ways to protect themselves from herbivores, pathogens or decomposers. Some of these adaptations affect the physiology of the attacking organisms, suggesting an explanation for the clear preferences of Native American traditions to choose medicinal species from some families much more than from others, regardless of the size of those families.

The deepest divergences in land plants inferred from phylogenomic evidence.

Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.