Almost at the end of his chapter on Mutation, G. G. Simpson in 1953 in The Major Features of Evolution noted that “There is also increasing evidence that mutation rate is itself, to some degree, a genetically controlled character.” If for mutation one uses the broad definition of the origin of new hereditary types, then the glimmerings to which Simpson referred now have become a documented fact at the molecular level.

The evolution of different spore size classes, or heterospory, is a fundamental reproductive innovation in land plants. The appearance of heterospory is particularly notable during the Devonian, when most known origins of the trait occur. Here we provide a perspective on the evolution of heterospory during this time interval, particularly from the late Early Devonian through the Middle Devonian (Emsian to Givetian Stages; 408–383 Ma), which shows an unusually high concentration of heterospory origins. We use theoretical considerations and compilations of fossil and extant spore sizes to suggest that the basic features of most heterosporous lineages, large spores and gametophytes that mature within the spore wall, are difficult to evolve in combination, because large spores disperse poorly but small spores cannot support a functional gametophyte developing within their walls; evolving spores between 100 and 200 microns in diameter appears to represent a particularly important barrier for the evolution of heterospory. We then discuss why this barrier may have been lower in the Devonian, noting that the appearance and spread of heterospory is coincident with the emergence of peat-accumulating wetland habitats. We suggest that more widespread wetland habitats would have generally lowered barriers to the evolution of heterospory by reducing dispersal limitation in larger spores. Ultimately, we suggest that the initial evolution of heterospory may be explained by major changes in sedimentology, thought to have been driven by plant evolution itself, that increased the diversity of terrestrial depositional environments and led to a greater number of habitats where large spores could be successful.

Heterochrony describes acceleration, displacement, and/or retardation of descendants’ development events compared with ancestral states and has often been cited as an important process to bring about morphological novelty. It was coined one-and-a-half centuries ago and has been discussed by both paleobiologists and biologists frequently ever since. Many types of fossil organisms preserve aspects of their development histories in their bones or shells that have been used for heterochrony analyses, with body size being used as a developmental age indicator, despite questions being raised regarding this practice. For organisms whose hard structures consist of multiple chambers, or that contain growth lines, age information suggested by these structures independently can facilitate ontogenetic modeling. In this way, relations among size, shape, and age can be established to document patterns of morphological development.

Morphological analysis of pseudoschwagerine fusulinids, a fossil foraminifera group that developed a morphologically novel spherical shell, along with their presumptive triticitid ancestors illustrates this approach to heterochrony analysis. Ontogenetic trajectory comparisons of four major pseudoschwagerine genera, as well as those of triticitids, document relations between their shapes, sizes, and developmental ages. A complex of heterochronic patterns, including peramorphic predisplacement, hypermorphosis, and acceleration, characterize pseudoschwagerine development and appear to be responsible for the novel appearance of large, inflated fusiform and spherical tests in these late Paleozoic benthic foraminifera. The morphometric approach employed in this investigation could be applied widely in the quantitative morphological studies of development histories in a variety of other fossil groups.

The first size reduction (FSR) in the Reticulofenestra-Gephyrocapsa-Emiliania (RGE) lineage (order Isochrysidales), which occurred in the early Oligocene (~32 Ma), is of great significance for understanding the Lilliput effect that has affected coccolithophore communities from the late Eocene to this day. We conducted a morphologic analysis on the coccoliths of Reticulofenestra species that lived during the late middle Eocene to early Oligocene (~40–31 Ma), using marine sediments from the South Atlantic Ocean. Our data show increasing size and decreasing abundance of the large species during the late Eocene, leading to their disappearance at the FSR, and a concurrent decrease in the size variability of the small- to medium-sized coccoliths whose central opening diameter had become very reduced. Although the cosmopolitan late Paleogene through Neogene size decrease in coccolithophores has been linked to the concomitant long-term decline in global pCO2, we suggest here that the FSR was the result of environmental destabilization caused by the expansion of eutrophic environments following the late Eocene establishment of overturning circulation associated with ice buildup on Antarctica. This study also leads us to propose a hypothetical model that links coccolith morphology of species of the RGE lineage and trophic resources in the upper ocean: the small- to medium-sized, r-selected coccolithophores with smaller coccolith central openings live in nutrient-rich waters where they rely mostly on photosynthesis and little on mixotrophy, whereas the larger, K-selected species with larger coccolith central openings live in oligotrophic waters where they are more dependent on mixotrophy.

Paleecological data allow not only the study of trends along deep-time chronological transects but can also be used to reconstruct ecological gradients through time, which can help identify causal factors that may be strongly correlated in modern ecosystems. We have applied such an analysis to Bergmann’s rule, which posits a causal relationship between temperature and body size in mammals. Bergmann’s rule predicts that latitudinal gradients should exist during any interval of time, with larger taxa toward the poles and smaller taxa toward the equator. It also predicts that the strength of these gradients should vary with time, becoming weaker during warmer periods and stronger during colder conditions. We tested these predictions by reconstructing body-mass trends within canid and equid genera at different intervals of the Oligo-Miocene along the West Coast of North America. To allow for comparisons with modern taxa, body mass was reconstructed along the same transect for modern Canis and Odocoileus. Of the 17 fossil genera analyzed, only two showed the expected positive relationship with latitude, nor was there consistent evidence for a relationship between paleotemperature and body mass. Likewise, the strength of body-size gradients does not change predictably with climate through time. The evidence for clear gradients is ambiguous even in the modern genera analyzed. These results suggest that, counter to Bergmann’s rule, temperature alone is not a primary driver of body size and underscore the importance of regional-scale paleoecological analyses in identifying such drivers.

In earlier and simpler times in North American geology, there was an extraordinarily large amount of unexplored ground per available geologist to study it. State and territorial geological surveys, which undertook the first comprehensive mapping programs in the nineteenth century, were at first able to make only the grossest descriptions of outcrops in order to complete their assignments to map an area. In these pioneer surveys, black shales stood out as very easily identifiable strata; characteristically colored, fine grained, with distinctive lamination, and well known to lack fossils found so commonly in adjacent strata. “Black shale, undivided” is a very familiar legend in older outcrop descriptions; the lack of comparability of black shales to other strata effectively prevented their division, for both conceptual and technical reasons. This is one of the many paradoxes we can recognize in relation to black shales; they are as difficult to interpret as they are easy to recognize.

The Signor-Lipps effect states that even a sudden mass extinction will invariably appear gradual in the fossil record, due to incomplete fossil preservation. Most previous work on the Signor–Lipps effect has focused on testing whether taxa in a mass extinction went extinct simultaneously or gradually. However, many authors have proposed scenarios in which taxa went extinct in distinct pulses. Little methodology has been developed for quantifying characteristics of such pulsed extinction events. Here we introduce a method for estimating the number of pulses in a mass extinction, based on the positions of fossil occurrences in a stratigraphic section. Rather than using a hypothesis test and assuming simultaneous extinction as the default, we reframe the question by asking what number of pulses best explains the observed fossil record.

Using a two-step algorithm, we are able to estimate not just the number of extinction pulses but also a confidence level or posterior probability for each possible number of pulses. In the first step, we find the maximum likelihood estimate for each possible number of pulses. In the second step, we calculate the Akaike information criterion and Bayesian information criterion weights for each possible number of pulses, and then apply a k-nearest neighbor classifier to these weights. This method gives us a vector of confidence levels for the number of extinction pulses—for instance, we might be 80% confident that there was a single extinction pulse, 15% confident that there were two pulses, and 5% confident that there were three pulses. Equivalently, we can state that we are 95% confident that the number of extinction pulses is one or two. Using simulation studies, we show that the method performs well in a variety of situations, although it has difficulty in the case of decreasing fossil recovery potential, and it is most effective for small numbers of pulses unless the sample size is large. We demonstrate the method using a data set of Late Cretaceous ammonites.