Pattern and process in hominin brain size evolution are scale-dependent.

A large brain is a defining feature of modern humans, yet there is no consensus regarding the patterns, rates and processes involved in hominin brain size evolution. We use a reliable proxy for brain size in fossils, endocranial volume (ECV), to better understand how brain size evolved at both clade- and lineage-level scales. For the hominin clade overall, the dominant signal is consistent with a gradual increase in brain size. This gradual trend appears to have been generated primarily by processes operating within hypothesized lineages-64% or 88% depending on whether one uses a more or less speciose taxonomy, respectively. These processes were supplemented by the appearance in the fossil record of larger-brained Homo species and the subsequent disappearance of smaller-brained Australopithecus and Paranthropus taxa. When the estimated rate of within-lineage ECV increase is compared to an exponential model that operationalizes generation-scale evolutionary processes, it suggests that the observed data were the result of episodes of directional selection interspersed with periods of stasis and/or drift; all of this occurs on too fine a timescale to be resolved by the current human fossil record, thus producing apparent gradual trends within lineages. Our findings provide a quantitative basis for developing and testing scale-explicit hypotheses about the factors that led brain size to increase during hominin evolution.

Simple versus complex models of trait evolution and stasis as a response to environmental change.

Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor-descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies, we find that stasis is common in the fossil record, as is a strict version of stasis that entails no real evolutionary changes. Incidence of directional evolution is relatively low (13%), but higher than in previous studies because our analytical approach can more sensitively detect noisy trends. Complex evolutionary models are often favored, overwhelmingly so for sequences comprising many samples. This finding is consistent with evolutionary dynamics that are, in reality, more complex than any of the models we consider. Furthermore, the timing of shifts in evolutionary dynamics varies among traits measured from the same series. Finally, we use our empirical collection of evolutionary sequences and a long and highly resolved proxy for global climate to inform simulations in which traits adaptively track temperature changes over time. When realistically calibrated, we find that this simple model can reproduce important aspects of our paleontological results. We conclude that observed paleontological patterns, including the prevalence of stasis, need not be inconsistent with adaptive evolution, even in the face of unstable physical environments.

Taxonomy and Phylogeny Can Yield Comparable Results in Comparative Paleontological Analyses.

Many extinct taxa with extensive fossil records and mature taxonomic classifications have not yet been the subject of formal phylogenetic analysis. Here, we test whether the taxonomies available for such groups represent useful (i.e., non-misleading) substitutes for trees derived from matrix-based phylogenetic analyses. We collected data for 52 animal clades that included fossil representatives, and for which a recent cladogram and pre-cladistic taxonomy were available. We quantified the difference between the time-scaled phylogenies implied by taxonomies and cladograms using the matching cluster distance metric. We simulated phenotypic trait values and used them to estimate a series of commonly used, phylogenetically explicit measures (phylogenetic signal [Blomberg's [Formula: see text]], phylogenetic generalized least squares [PGLS], mode of evolution [Brownian vs. Ornstein-Uhlenbeck], and phylogenetic clustering of extinction [Fritz and Purvis' [Formula: see text]]) in order to determine the degree to which they co-varied on taxonomic and cladistic trees. With respect to topology taxonomies are good approximations of the underlying evolutionary relationships as recorded in inferred cladograms. Detection of phylogenetic clustering of extinction could not be properly assessed. For all other evolutionary analyses, results from taxonomy-based phylogenies (TBPs) co-varied with those from cladogram-based phylogenies (CBPs), but individual comparisons could be misleading. The relative length of terminal branches (influenced by stratigraphy and sampling rate) is a key control on the shared information between, and therefore the relative performance of, TBP and CBP. Collectively these results suggest that under particular circumstances and after careful consideration some taxonomies, or composite trees that incorporate taxonomic information, could be used in place of a formal analytical solution, but workers must be cautious. This opens certain parts of a previously inaccessible section of the fossil record to interrogation within an explicit comparative framework, which will help to test many classical macroevolutionary hypotheses formulated for groups that currently lack formal phylogenetic estimates.