Truth, goes an old proverb, is the daughter of time. Fifty years ago, G. G. Simpson (1944) brought paleontology into the Neodarwinian fold, arguing that evolutionary tempo can be documented in the geological record and used to inform debate about evolutionary mode. Today, increasingly sophisticated paleontological investigations of rate—be it diversification, extinction, migration, morphological change, or divergence in macromolecular sequence—require calibration of the geological time scale with a precision far greater than Simpson could have anticipated. Expanding research on the relationships between environmental history and evolution also requires unprecedented resolution in correlation and geochronometry.

The use of clade-shape statistics, particularly center of gravity, on paraphyletic groups has been questioned since the introduction of these descriptive statistics. In addition, previous studies have found that early-arising groups of organisms are bottom-heavy in center of gravity relative to later-arising groups, leading to macroevolutionary hypotheses about the nature of diversification. Paraphyletic groups have been asserted to be inherently bottom-heavy because of preconceived ideas as to how paraphyletic group formation affects center of gravity. In turn, early-arising groups of organisms have been asserted to be bottom-heavy because they also tend to be paraphyletic, thus calling into question the biological significance of the bottom-heaviness of early-arising groups.

In this study, both computer simulations and the evolutionary history of families of mammals show that paraphyletic groups are inherently top-heavy. Simulated monophyletic clades and monophyletic families of mammals have centers of gravity near their expected positions at the midpoint of clade duration, while paraphyletic groups are significantly top-heavy.

Early-arising families of mammals are found to be inherently top-heavy, rather than bottom-heavy as found by earlier studies. This new result is likely to be due to the use of updated stratigraphic range data and different taxonomic assignments rather than to bias due to inclusion of paraphyletic groups or bias due to unequal time-unit lengths in the Cenozoic time scale.

Hierarchies in natural science are ranked and nested structures such that units at each rank include parts that are units at lower ranks. Hierarchies are able to render complexity tractable, by homogenizing units into collectives and by ordering collectives in ranks of increasing inclusiveness. Hierarchies contrast with positional structures, such as phylogenetic trees, for in trees all positions are occupied by the same sort of entity—there are no ranked collectives—and positions are specified by the order of appearance or precedence of the entities. In hierarchies, interactions within ranks are most important; in trees, sequences of events along branches are of primary concern. As a result hierarchies do, and trees do not, display emergent properties.

The value of the hierarchical structure can be lost when ranks are misspecified. A common error is the use of only a fraction of entities that actually occur in a rank, as when genes are considered as a rank below cells, disregarding the remaining cell contents and rendering the nature of cellular organization moot. Misspecification is also common when attributes or processes are used in ranks without indications of the physical entities to which they refer, thus losing track of the proper composition and ranking of the collectives.

In this study I take advantage of an unusual system of fossil lakes in eastern North America to estimate the time for speciation of endemic semionotid fishes. Twenty-one species are all found in sedimentary cycle P4, the deposits of a single Early Jurassic lake, in the Towaco Formation of the Newark Basin in New Jersey. To determine the degree of endemism in the fauna from this fossil lake and estimate time for speciation, I surveyed more than 2000 museum specimens from 45 named localities in the Newark Basin and related basins of the Late Triassic to Early Jurassic Newark Supergroup. Six species not found in deposits equal in age to P4 or older are considered to be endemics, eight species occurring in older deposits presumably colonized Lake P4, and evidence for whether the remaining seven species were endemics or colonists is equivocal. The time for the formation, decline, and evaporation of Lake P4, in which P4 sediments were deposited, has been estimated at 21,000-24,000 years. Because all endemic Semionotus first occur in the first third of lake history, the estimated time for speciation of endemics is six species in 5000-8000 years. This rate is remarkably similar to that estimated for the five cichlids in Lake Nabugabo that diverged from Lake Victoria cichlids in about 4000 years.

Ptychopariid trilobites from the Marjumiid biomere of Laurentia underwent a statistically significant morphological diversification that is concordant with proposed adaptive radiations of trilobites in each of the Cambrian biomeres. An analysis of a subset consisting of the biomere's most characteristic taxa, the Asaphiscacea, Raymondinacea, and Marjumiacea, also illustrates this morphological diversification. In detail, the total data set and subset show a limited range of morphologies near the base of the biomere and a large increase in range in the upper portion of the biomere.

Regional assemblages from the Appalachians, Great Basin, and Texas were also studied to determine if they too show the larger-scale macroevolutionary patterns of trilobites from Laurentia as a whole. The regional assemblages illustrate similar, but not identical, morphological diversifications, which are also similar to the overall Laurentian pattern. Subsets of the characteristic taxa also show this diversification. These results suggest that regional assemblages can be used to investigate these larger-scale macroevolutionary patterns.

Causal mechanisms for the diversification patterns are not clear. Potential mechanisms include: (1) endemic evolution of new morphologies in Laurentia; (2) migration of new morphologies, including intra- and inter-continental migrations; and (3) environmental controls over the distribution of morphologies. Likely causes for the morphological diversification and its similarity among regions probably include aspects of all three mechanisms.

Phylogenetic patterns of trilobite clades were used to deduce biogeographic patterns during the Middle Devonian, a time of active plate collision between North America (Laurentia) and other plates, coincident with several major episodes of sea-level rise and fall. The mapping of biogeographic states onto phylogenies for asteropyginid and proetid trilobites indicated that during their history these trilobite clades often shifted the areas they occupied, and also underwent vicariant differentiation, followed by range expansion, followed by subsequent vicariance. Biogeographic patterns in these individual phylogenies were evaluated and synthesized using a modified version of Brooks Parsimony Analysis, which is discussed. This method makes it possible using cladistic methods to distinguish between episodes of vicariance and episodes of dispersal. Two types of dispersal are recognized herein: (1) the individualistic responses of certain taxa in a single clade that cannot be generalized, i.e., traditional ad hoc dispersal, and (2) those patterns of congruent range expansion that are replicated across several clades. The latter are not treated as true dispersal, expansion of a taxon's range over a barrier accompanied by diversification, but rather as a result of the temporary removal of barriers to marine taxa, due either to relative sea-level rise or to the collision of formerly disjunct plates. These are interpreted as changes in the structure of areas, and this type of dispersal is referred to as geo-dispersal. Geo-dispersal was found to have occurred in the Middle Devonian trilobite fauna of Eastern North America.

Biogeographic analysis indicated that Eastern North America is a strongly supported area, with the Appalachian and Michigan Basins as sister areas. Armorica and the Canadian Arctic are also sister areas. Congruence was found between area cladograms produced by vicariance and dispersal analyses for Middle Devonian trilobites, suggesting that in some cases the geological processes governing vicariance, such as sea-level changes, were the same as those that caused dispersal.

We compare the preservation (taphonomic grade) and age of Chione (bivalve) and foraminifera from modern siliciclastic tidal flat sediments of Bahia la Choya, Sonora, Mexico (northern Gulf of California). Disarticulated shells of Chione collected from the sediment-water interface of Choya Bay exhibit a substantial range in taphonomic grade and age, several hundred years to ∼80–125 ka based on Accelerator Mass Spectrometer 14C dates and D-Alloisoleucine/L-Isoleucine values. There is not, however, a one-to-one correspondence between age and taphonomic alteration of Chione: old (or young) valves may be highly altered or they may be relatively pristine. In contrast to Chione, most foraminiferal tests at Choya Bay are quite pristine, which suggests a quite young age, but tests are surprisingly old (up to ∼2,000 calendar years based on Accelerator Mass Spectrometer 14C dates).

We suggest that following seasonal pulses in reproduction, some foraminiferal tests are rapidly incorporated into a subsurface shell layer by “Conveyor Belt” deposit feeders and preserved there, while the rest of the reproductive pulse rapidly dissolves. Ultimately, some of these buried tests, along with Chione, are transported back to the surface by biological activity and storms. The much greater range of taphonomic grades and ages among Chione shells suggests that they, unlike foraminifera, are sufficiently large and preservable (low surface/volume ratio and chemical reactivity) to undergo many cycles of degradation, burial, and exhumation before complete destruction. The age of foraminiferal tests indicates that time-averaging of microfossil assemblages at Choya Bay is much more insidious than would be expected considering the relatively pristine state of the tests alone.

Based on our studies, the lower limit of temporal resolution of shallow shelf microfossil assemblages appears to be ∼1000 years. We caution, however, that each depositional setting (taphofacies) should be evaluated on a case-by-case basis before gross generalizations are made. Indeed, the discrepancy between age and taphonomic grade of fossil assemblages at Choya Bay suggests that neither hardpart size or taphonomic grade are infallible indicators of test preservability or likely temporal resolution of the host assemblage, and that the dynamics of hardpart input and loss must also be evaluated.

I examine the late Pleistocene megafaunal extinctions by testing the only extinction model with strong a priori predictions, the blitzkrieg model (Martin 1973; Mosimann and Martin 1975). I first test an assumption of the blitzkrieg and other extinction models that the megafaunal extinctions occurred in the terminal Wisconsin (12-10 Ka). This assumption has been disputed by Grayson (1989, 1991), but I find that both a reanalysis of Grayson's data and an analysis of new reliable data support a terminal Wisconsin extinction.

The blitzkrieg model predicts that the ranges of megafauna in North America were constricted as the semicircular front of hunters moved southeastward; hence the extinctions should be time-transgressive from northwest to southeast. I test this prediction in three separate analyses that examine (1) the location of terminal sites for each taxon relative to all their other late Wisconsin fossil sites, (2) the location of terminal sites for each taxon relative to all their other reliably dated late Wisconsin fossil sites, and (3) the spatio-temporal pattern of all the reliably dated terminal Wisconsin sites without regard to taxonomy. The geographic distribution of the megafaunal remains does not support the blitzkrieg hypothesis in any of the three analyses. Moreover, all of the patterns in the data are in a direction opposite to that predicted by the blitzkrieg hypothesis. I examine how these conclusions affect both climatic and predation models, particularly in relation to the testability of other extinction hypotheses.

It has been suggested that a sudden event at the end of the Cretaceous period caused a major extinction that was felt disproportionately by creatures in the water column. It also has been argued that benthic deposit feeders, being relatively independent of abundance of organic particles in the water column, should have survived the crisis more readily than suspension feeders, which depended more upon feeding upon phytoplankton. I argue that the hypothesis of relative immunity of deposit feeders is insufficient, because deposit feeders by and large depend upon a supply of organic matter from the water column and would have succumbed to food shortage nearly as rapidly as suspension feeders, possibly within a maximum of three to six months. This near simultaneity of extinction would have been especially true of continental shelf environments. Even in some parts of the deep sea, it is likely that a dependence upon the water column above might have caused deep-sea deposit feeders to succumb rapidly. Therefore, deposit feeders would not necessarily have outsurvived suspension feeders during a crisis of depleted water-column phytoplankton, increased shading by inert particles, or poisoning of the water column and killing of phytoplankton. The relatively lower rate of extinction of nuculoid bivalves may relate instead to their presence in deeper-water refuge habitats, their apparent relative ability to diversify in higher latitudes, or their resistance to factors other than food shortage.