When assessing the timing of branching events in a phylogeny, the most important tools currently recognized are a reliable molecular phylogeny and a continuous, relatively complete fossil record. Coralline algae (Rhodophyta, Corallinales, and Sporolithales) constitute an ideal group for this endeavor because of their excellent fossil record and their consistent phylogenetic reconstructions. We present the evolutionary history of the corallines following a novel, combined approach using their fossil record, molecular phylogeny (based on the 18S rDNA gene sequences of 39 coralline species), and molecular clocks. The order of appearance of the major monophyletic taxa of corallines in the fossil record perfectly matches the sequence of branching events in the phylogeny. We were able to demonstrate the robustness of the node ages in the phylogeny based on molecular clocks by performing an analysis of confidence intervals and maximum temporal ranges of three monophyletic groups of corallines (the families Sporolithaceae and Hapalidiaceae, as well as the subfamily Lithophylloideae). The results demonstrate that their first occurrences are close to their observed appearances, a clear indicator of a very complete stratigraphic record. These chronological data are used to confidently constrain the ages of the remaining branching events in the phylogeny using molecular clocks.

The Corbulidae are one of a handful of a primarily marine bivalve clades that exhibit a remarkable radiation, marked by increased species richness and divergent morphologies, within a long-lived lake. For corbulids, this diversification occurred within the lower to middle Miocene Pebas Formation of western Amazonia. Only one taxon associated with this radiation (Anticorbula) remains extant. We conducted a series of phylogenetic analyses to characterize diversification of Corbulidae within the Pebas Formation and relate that diversification to geologically older freshwater corbulids from the Paleocene Fort Union Formation of the northern Great Plains (United States). We used these results, as well as a quantitative examination of morphospace occupation, to infer whether Pebasian corbulids represent a true species flock, and whether the lacustrine system represented by the Pebas Formation represents a cradle of, or reservoir for, freshwater corbulid diversity. We conducted two sets of phylogenetic analyses using shell morphology characters. A genus-level data set incorporated type species of freshwater corbulid genera, any Paleocene representatives of these genera, and selected brackish and marine corbulid genera. A species-level analysis added all described freshwater corbulid taxa to the genus-level matrix. Our results were highly resolved (few most-parsimonious trees), but not particularly robust (low branch support). For the genus-level matrix, we used a taxon jackknife procedure to explore the effects of taxon sampling on tree stability and topology. Jackknife results recover a subclade of freshwater taxa (including both Anticorbula and Pachydon species and the Paleocene Ostomya sp.) in 92.4% of trees, although placement of this subclade across the ingroup varies, as do the topologic positions of other freshwater species. Freshwater and marine corbulids also are morphologically distinct from each other, a factor that likely reduced the robustness of our phylogenetic results. By combining these results with paleoecologic, stratigraphic, and morphologic data, we infer that freshwater corbulids arose once within the family, prior to the Cenozoic, with three distinct freshwater lineages present at their first appearance in the late Paleocene of North America. Within the Miocene Pebas system of South America, we reconstruct supralimital morphologic evolution within three lineages as freshwater taxa became variously adapted to the fluid, dysoxic muds characterizing lake-bottom facies representative of the Pebas lacustrine system. In addition, corbulids apparently successfully coped with high predation pressures from co-occurring shell-crushing predators. Finally, we consider that freshwater Corbulidae were primarily fluvial taxa throughout their geologic history, with a relatively ephemeral radiation within the Pebasian lake system, thus making the Pebasian system a cradle of diversity for several corbulid lineages.

Variations in the orientation and cross-sectional shape of filamentous microfossils provide quantitative measures for characterizing them and probing their native mechanical structure. Here, we determine the tangent correlation length, which is the characteristic length scale for the variation in direction of a sinuous curve, for both a suite of Precambrian filamentous microfossils and six strains of modern filamentous cyanobacteria, all with diameters of a few microns. Among 1.9–2-Ga microfossils, Gunflintia grandis, Gunflintia minuta and Eomycetopsis filiformis possess, respectively, correlation lengths of 360 ± 40 µm, 670 ± 40 µm and 700 ± 100 µm in two dimensions. Hundreds of times larger than the filament diameters, these values lie in the same range as the cyanobacteria Geitlerinema and Pseudanabaena, but are smaller than several strains of Oscillatoria. In contrast, the 2-Ga microfossil trichome Halythrix, is found to have a short correlation length of 29 ± 4 µm in two dimensions. Micron-wide pyritic replacement filaments observed in 3.23-Ga volcanogenic deposits also display a modest correlation length of 100 ± 15 µm in two dimensions. Sequences of species in two genera of our modern cyanobacteria possess tangent correlation lengths that rise as a power of the filament diameter D—D^{3.3 ± 1} for Oscillatoria and D^{5.1 ± 1} for Geitlerinema. These results can be compared with power-law scaling of D³ for hollow tubes and D⁴ for solid cylinders that is expected from continuum mechanics. Extrapolating the observed scaling behavior to smaller filament diameters, the measured correlation length of the pyrite filaments is consistent with modern Geitlerinema whereas that of Halythrix lies not far from modern Oscillatoria, suggesting that there may be structural similarities among these genera.

Ecological ordination can reveal gradients in the species composition of fossil assemblages that can be correlated with paleoenvironmental gradients. Ordinations of simulated data sets suggest that nonmetric multidimensional scaling (NMDS) generally produces less distorted results than detrended correspondence analysis (DCA). We ordinated 113 brachiopod-dominated samples from the Frasnian (Late Devonian) Brallier, Scherr, and lower Foreknobs Formations of southwest Virginia, which represent a range of siliciclastic marine paleoenvironments. A clear environmental signal in the ordination results was obscured by (apparently) opportunistic species that occurred at high abundance in multiple environments; samples dominated by these species aggregated in ordination space regardless of paleoenvironmental provenance. After the opportunist-dominated samples were removed, NMDS revealed a gradient in species composition that was highly correlated with substrate (grain size); a second, orthogonal gradient likely reflects variation in disturbance intensity or frequency within grain-size regimes. Additional environmental or ecological factors, such as oxygenation, may also be related to the gradients. These two gradients, plus the environmental factors that controlled the occurrence of opportunistic species, explain much of the variation in assemblage composition in the fauna. In general, the composition of fossil assemblages is probably influenced by multiple paleoecological and paleoenvironmental factors, but many of these can be decomposed and analyzed.

Patterns preserved in the fossil record are of the highest importance in addressing questions about long-term evolutionary processes, yet both the description of pattern and its translation into process can be difficult. With respect to gradual phyletic change, we know that randomly generated sequences may exhibit characteristics of a “trend”; apparent patterns, therefore, must be interpreted with caution. Furthermore, even when the claim of a gradual trend can be statistically justified, interpretation of the underlying mechanisms may be challenging. Given that we can observe populations changing rapidly over tens or hundreds of years, it is now more difficult to explain instances of geologically gradual (as opposed to punctuated) change.

Here we describe morphologic change in two bivalve lineages from the late Miocene Lake Pannon. We evaluate change according to the model-based methods of Hunt. Both lineages exhibit size increases and shape changes over an interval of nearly 4 million years. Size and two shape variables in the conjungens lineage are best fit by a model of directional evolution; remaining shape variables mostly conform to unbiased random walks. Body-size evolution in the diprosopum lineage is also significantly directional but all shape variables are best fit by the unbiased random walk model; the small number of sampling intervals available for this lineage (n  =  6) makes determination of the actual pattern more difficult. Model-fitting results indicate that the parallel trajectories of increasing log shell height over time in the two lineages can be accounted for by an underlying trend shared by both lineages, suggesting that the size increases may be a shared response to the same cause. The pace of phenotypic change, measured as Lynch's Δ, is slower than the neutral expectation for all size and shape traits.

Our examples illustrate well the paradox of gradualism; the sequences exhibit significant directional morphological evolution, but rates of change as measured over the long-term are apparently too slow for directional selection or even drift to be the cause. Viewing long-term phenotypic evolution in terms of populations tracking peaks on adaptive landscapes is useful in this context. Such a view allows for intervals of directional selection (during times of peak movement—resulting in the overall trends we can detect) interspersed with intervals of stasis (during times of peak stability—resulting in overall changes that appear to proceed more slowly than the neutral expectation). The paradox of gradualism thus reduces to (1) peak movements and their drivers, which are not restricted in rate as are population-genetic drivers, and (2) the maintenance of stasis, on which no consensus exists.

We can identify no environmental parameter in the central European Neogene that exhibits consistent change across the interval of gradual morphologic change. It may be that in Lake Pannon the long-term persistence of generally ameliorating conditions (plentiful resources and habitat space, few predators or competitors) resulted in geologically slow but consistent peak shifts, which in turn facilitated size increase and shape change in these lineages.

All else being equal, species with short life spans are expected to be overrepresented in time-averaged death assemblages relative to their standing abundance in the living community, but the magnitude of the distortion of proportional abundance and assemblage evenness has received little attention. Here, information from 30 data sets on the living and dead abundances of marine bivalves in local habitats is combined with a global compilation of bivalve life spans to determine whether bias from mortality rate can explain observed differences in species proportional abundances. Although bivalve maximum life spans range from one to 75 years in these data sets, indicating annual mortality rates of 0.97 to 0.09, the “life span bias” (LB) of a species—the difference between its proportional abundance expected dead and that observed alive—is consistently small in magnitude (average change <2%, maximum about 20%) and random in sign relative to observed discordance (OD  =  difference between that species' proportional abundance observed dead and that observed alive). The aggregate result for 413 living species occurrences is a significantly positive but weak correlation of OD to LB, with only 10% of variation in OD explained. The model performs better among longer-lived species than among shorter-lived species, probably because longer-lived species conform better to the model assumption that species maintain a constant proportional abundance in the living assemblage over time. Among individual data sets, only seven exhibit significant positive correlations between OD and LB. The model also under-predicts the cases where a death assemblage is dominated by a species that is shorter lived than the dominant species in the living assemblage, indicating that some factor(s) other than or in addition to mortality rate is responsible for OD. We can find no evidence of preservational bias linked to life span, for example through body size. This negative outcome reflects a weak biological relationship between life span and living abundance among bivalves in local habitats, contrary to the terrestrial paradigm, and points toward a simpler model of time-averaged death assemblage formation where higher abundances reflect (undersampled) past populations. Contrary to long-held expectations, variation in population turnover among species is not a major source of taphonomic bias in time-averaged death assemblages among bivalves and perhaps among other marine groups: bias must arise largely from other factors.

Recent progresses in our knowledge of mouse odontogenesis have enhanced rodent tooth morphology as a model for Evo-Devo studies. Deciphering the connection between macroevolution and microevolution, however, especially in the case of mammalian teeth, requires examples to illustrate how morphological differences among species, or higher taxa, can stem from population-level processes. In this paper we use paleontological material to study intraspecific variation of tooth morphology in the late Miocene species Progonomys clauzoni, over a short span of geological time in a restricted area. Progonomys is of particular interest as a stem genus of all murine rodents (Old World rats and mice). We use morphometrical and statistical methods to illustrate how change in the amplitude in variation at the population level through geological time is associated with the emergence of new characters. Some of these new characters, including functional ones, become fixed in parallel in distinct murine lineages. Nine million years ago, Progonomys clauzoni displayed variational properties of the developmental system shared by the Murinae, which can also explain some singular tooth characteristics that now are scattered among the diverse lineages. Further morphometric studies, however, are necessary to explain how the variety of cusp patterns observed in Progonomys clauzoni can be explained by developmental properties.

Constrained seriation of a species-locality matrix of the Australian Cenozoic mammal record resolves a preliminary sixfold succession of land mammal ages apparently spanning the late Oligocene to the present. The applied conditions of local chronostratigraphic succession and inferences of relative stage-of-evolution biochronology lead to the expression of a continental geological timescale consisting of, from the base, the Etadunnan, Wipajirian, Camfieldian, Waitean, Tirarian, and Naracoortean land mammal ages. Approximately 99% of the 360 fossil assemblages analyzed are classifiable using this method. Each is characterized by a diagnostic suite of species. An interval of age magnitude may eventually be shown to lie between the Camfieldian and Waitean, but is currently insufficiently represented by fossils to diagnose. Development of a land mammal age framework marks a progressive step in Australian vertebrate biochronology, previously expressed only in terms of local faunas. Overall, however, the record remains poorly calibrated to the Standard Chronostratigraphic Scale. Codifying the empirical record as a land mammal age sequence provides an objective basis for expressing faunal succession without resort to standard chronostratigraphic terms with the attendant (and hitherto commonly taken) risks of miscorrelating poorly dated Australian events to well-dated global events.

Paleoecological analyses that test for spatial or temporal variation in diversity must consider not only sampling and preservation bias, but also the effects of temporal scale (i.e., time-averaging). The species-time relationship (STR) describes how species diversity increases with the elapsed time of observation, but its consequences for assessing the effects of time-averaging on diversity of fossil assemblages remain poorly explored. Here, we use a neutral, dispersal-limited model of metacommunity dynamics, with parameters estimated from living assemblages of 31 molluscan data sets, to model the effects of within-habitat time-averaging on the mean composition and multivariate dispersion of assemblages, on diversity at point (single station) and habitat scales (pooled multiple stations), and on beta diversity. We hold sample size constant in STRs to isolate the effects of time-averaging from sampling effects. With increasing within-habitat time-averaging, stochastic switching in the identity of species in living (dispersal-limited) assemblages (1) decreases the proportional abundance of abundant species, reducing the steepness of the rank-abundance distribution, and (2) increases the proportional richness of rare, temporally short-lived species that immigrate from the neutral metacommunity with many rare species. These two effects together (1) can shift the mean composition away from the non-averaged (dispersal-limited) assemblages toward averaged assemblages that are less limited by dispersal, resembling that of the metacommunity; (2) allow the point and habitat diversity to increase toward metacommunity diversity under a given sample size (i.e., the diversity in averaged assemblages is inflated relative to non-averaged assemblages); and (3) reduce beta diversity because species unique to individual stations become shared by other stations when limited by a larger but static species pool. Surprisingly, these scale-dependent changes occur at fixed sample sizes and can become significant after only a few decades or centuries of time-averaging, and are accomplished without invoking ecological succession, environmental changes, or selective postmortem preservation. Time-averaging results in less inflation of diversity at habitat than at point scales; paleoecological studies should thus analyze data at multiple spatial scales, including that of the habitat where multiple bulk samples have been pooled in order to minimize time-averaging effects. The diversity of assemblages that have accumulated over 1000 years at point and habitat scales is expected to be inflated by an average of 2.1 and 1.6, respectively. This degree of inflation is slightly higher than that observed in molluscan death assemblages at these same spatial scales (1.8 and 1.3). Thus, neutral metacommunity models provide useful quantitative constraints on directional but predictable effects of time-averaging. They provide minimal estimates for the rate of increase in diversity with time-averaging because they assume no change in environmental conditions and in the composition of the metacommunity within the window of averaging.