The morphological interdependence of traits, or their integration, is commonly thought to influence their evolution. As such, study of morphological integration and the factors responsible for its generation form an important branch of the field of morphological evolution. However, most research to date on post-cranial morphological integration has focused on adult patterns of integration. This study investigates patterns of correlation (i.e., morphological integration) among skeletal elements of the fore- and hind limbs of developing marsupial and placental mammals. The goals of this study are to establish how patterns of limb integration vary over development in marsupials and placentals, and identify factors that are likely responsible for their generation. Our results indicate that although the overall pattern of correlation among limb elements is consistent with adult integration throughout mammalian development, correlations vary at the level of the individual element and stage. As a result, the relative integration among fore- and hind limb elements varies dynamically between stages during development in both marsupial and placental mammals. Therefore, adult integration studies of the limbs may not be indicative of developmental integration. Results are also consistent with integration during early limb development being more heavily influenced by genetic and developmental factors, and later by function. Additionally, results are generally consistent with a constraint on marsupial forelimb evolution caused by the functional requirements of the crawl to the teat that operates by limiting morphological variation before and at the time of birth, and not after.

The decline of species richness from equator to pole, or latitudinal diversity gradient (LDG), is nearly universal among clades of living organisms, yet whether it was such a pervasive pattern in the geologic past remains uncertain. Here, we calculate the strength of the LDG for terrestrial mammals in North America over the past 65 My, using 27,903 fossil occurrences of Cenozoic terrestrial mammals from western North America downloaded from the Paleobiology Database. Accounting for temporal and spatial variation in sampling, the LDG was substantially weaker than it is today for most of the Cenozoic and the robust modern LDG of North American mammals evolved only over the last 4 My. The strength of the LDG correlates negatively with global temperature, suggesting a role of global climate patterns in the establishment and maintenance of the LDG for North American mammals.

Variation among individuals is a prerequisite of evolution by natural selection. As such, identifying the origins of variation is a fundamental goal of biology. We investigated the link between gene interactions and variation in gene expression among individuals and species using the mammalian limb as a model system. We first built interaction networks for key genes regulating early (outgrowth; E9.5-11) and late (expansion and elongation; E11-13) limb development in mouse. This resulted in an Early (ESN) and Late (LSN) Stage Network. Computational perturbations of these networks suggest that the ESN is more robust. We then quantified levels of the same key genes among mouse individuals and found that they vary less at earlier limb stages and that variation in gene expression is heritable. Finally, we quantified variation in gene expression levels among four mammals with divergent limbs (bat, opossum, mouse and pig) and found that levels vary less among species at earlier limb stages. We also found that variation in gene expression levels among individuals and species are correlated for earlier and later limb development. In conclusion, results are consistent with the robustness of the ESN buffering among-individual variation in gene expression levels early in mammalian limb development, and constraining the evolution of early limb development among mammalian species.

Coleoptera (beetles) is the most species-rich metazoan order, with approximately 380 000 species. To understand how they came to be such a diverse group, we compile a database of global fossil beetle occurrences to study their macroevolutionary history. Our database includes 5553 beetle occurrences from 221 fossil localities. Amber and lacustrine deposits preserve most of the beetle diversity and abundance. All four extant suborders are found in the fossil record, with 69% of all beetle families and 63% of extant beetle families preserved. Considerable focus has been placed on beetle diversification overall, however, for much of their evolutionary history it is the clade Polyphaga that is most responsible for their taxonomic richness. Polyphaga had an increase in diversification rate in the Early Cretaceous, but instead of being due to the radiation of the angiosperms, this was probably due to the first occurrences of beetle-bearing amber deposits in the record. Perhaps, most significant is that polyphagan beetles had a family-level extinction rate of zero for most of their evolutionary history, including across the Cretaceous–Palaeogene boundary. Therefore, focusing on the factors that have inhibited beetle extinction, as opposed to solely studying mechanisms that may promote speciation, should be examined as important determinants of their great diversity today.

The record of the taxonomic evolution of North American ungulates is critical to our understanding of mammalian evolution and environmental change throughout the Cenozoic. The distribution of sampling in the, ungulate fossil record over time and geographic space and the degree to which this biases the observed patterns of taxonomic evolution is poorly understood. To address these issues, I placed fossil collections and occurrences drawn from the Paleobiology Database into 2-Myr time intervals between 55 and 1 Ma. I determined the variation in numbers of fossil collections and occurrences, using three metrics to measure geographic variation: first, the area of the convex hull containing all collections in an interval, to determine the areal coverage of sampling; second, the mean pairwise geographic distance among collections as a measurement of the dispersion of collections within that area; and third, the interval-to-interval migration of the geographic centroid of all collections, to calculate changes in the geographic location of sampling. Each of these showed considerable variation over the Cenozoic, and both the area of the convex hull (ACH) encompassing all collections in an interval, and mean pairwise distance (MPWD) among them showed increasing trends over time.To minimize the effect of variation in numbers of fossil samples over time, I used standard sample-standardization procedures. To minimize the effect of geographic variation in sampling over time, I standardized the area of sampling among intervals. I also employed both standardizations sequentially. Each standardization procedure had surprisingly little effect on observed patterns of taxonomic richness and rates. This indicates that, for North American ungulates, neither variation in number nor geographic distribution of fossil samples exerts an overwhelming influence on perceived macroevolutionary patterns. These results confirm the ungulate fossil record as a critical and faithful record for our understanding of Cenozoic environmental change and the mammalian evolutionary response.

Summary Observed patterns in the fossil record reflect not just macroevolutionary dynamics, but preservation patterns. Sampling rates themselves vary not simply over time or among major taxonomic groups, but within time intervals over geography and environment, and among species within clades. Large databases of presences of taxa in fossil‐bearing collections allow us to quantify variation in per‐collection sampling rates among species within a clade. We do this separately not just for different time/stratigraphic intervals, but also for different geographic or ecologic units within time/stratigraphic intervals. We then re‐assess per‐million‐year sampling rates given the distributions of per‐collection sampling rates We use simple distribution models (geometric and lognormal) to assess general models of per‐locality sampling rate distributions given occurrences among appropriate fossiliferous localities. We break these down not simply by time period, but by general biogeographic units in order to accommodate variation over space as well as among species. We apply these methods to occurrence data for Meso‐Cenozoic mammals drawn from the Paleobiology Database and the New and Old Worlds fossil mammal database. We find that all models of distributed rates do vastly better than the best uniform sampling rates and that the lognormal in particular does an excellent job of summarizing sampling rates. We also show that the lognormal distributions vary fairly substantially among biogeographic units of the same age. As an example of the utility of these rates, we assess the most likely divergence times for basal (Eocene–Oligocene) carnivoramorphan mammals from North America and Eurasia using both stratigraphic and morphological data. The results allow for unsampled taxa or unsampled portions of sampled lineages to be in either continent and also allow for the variation in sampling rates among species. We contrast five models using stratigraphic likelihoods in different ways to summarize how they might affect macroevolutionary inferences.

Tetrapod limb development has been studied extensively for decades, yet the strength and role of developmental constraints in this process remains unresolved. Mammals exhibit a particularly wide array of limb morphologies associated with various locomotion modes and behaviors, providing a useful system for identifying periods of developmental constraint and conserved developmental mechanisms or morphologies. In this study, landmark-based geometric morphometrics are used to investigate levels and patterns of morphological diversity (disparity) among the developing forelimbs of four mammals with diverse limb morphologies: mice, opossums, horses, and pigs. Results indicate that disparity among the forelimbs of these species slightly decreases or stays the same from the appearance of the limb ridge to the bud stage, and increases dramatically from the paddle through tissue regression stages. Heterochrony exhibited by the precocial opossum limb was not found to drive these patterns of morphological disparity, suggesting that the low disparity of the middle stages of limb development (e.g., paddle stage) is driven by processes operating within the limb and is likely not a result of embryo-wide constraint.

Macrostratigraphy uses packages of continuous sedimentation that are bound by hiatuses of non-deposition, erosion, or alternations between environments/lithologies to characterize spatiotemporal patterns of sedimentation. Previous work has linked the macrostratigraphy of marine shelf environments to many different macroevolutionary patterns in the marine animal fossil record. Here we use an improved macrostratigraphic database for North America, combined with fossil occurrence data in the Paleobiology Database, to show that macroevolutionary and macrostratigraphic patterns are correlated more strongly in marine environments than in non-marine environments. We also test the hypothesis that the temporal distribution of lithological diversity (measured as evenness, similar to ecological evenness based on the number of lithostratigraphic units with a given lithologic type within each time interval) has a relationship to genus-level taxonomic diversity in both the marine and non-marine realms. Uneven sampling of lithologies and their corresponding depositional environments can bias our perception of taxonomic diversity by causing taxa from poorly sampled environments to be underrepresented in the fossil record. Our results show a negative correlation between lithologic evenness and marine vertebrate generic richness — less even sampling of lithologies corresponds to a higher observed taxonomic richness, and no correlation with lithologic evenness and non-marine diversity measures. This suggests a difference in the relationship between biologic and sedimentary processes at work in the marine and non-marine realms, and possibly differences in the magnitude of the bias imposed by the rock record on the underlying biologic patterns.

Mammal faunas from western North America exhibit no significant change in species richness with latitude during the Torrejonian (ca. 63–60 Ma) and Tiffanian (ca. 60–58 Ma) North American Land Mammal Ages, in contrast to a strong richness gradient in modern mammalian faunas of the same region today. The latitudinal gradient in oxygen isotope composition of mammalian bioapatite from the Paleocene faunas is similar to that of modern meteoric and surface waters, suggesting that the temperature gradient in the Paleocene was similar to the modern one. The flat richness gradient in the middle Paleocene indicates either different responses to climatic gradients of faunas dominated by extinct clades of placental mammals or distinct ecological processes during the Paleocene diversification of mammals following the end-Cretaceous mass extinction.

Quantitative phylogenetic inference estimates the probability of observed character distributions given trees and rates. Most available programs for doing this assume (tacitly or explicitly) that the sampled taxa are contemporaneous. However, paleontologists usually sample taxa over a clade's history. Thus, we must estimate the probability of observed character-state distributions over time given trees and rates. When we include information about sampling intensity, then we really are estimating the probability of the observed record given trees and rates. Some additional problems thatshouldbe issues for neontologists, but which are much more obvious concerns for paleontologists include: 1) ancestor-descendant relationships; 2) punctuated versus continuous morphological change; and, 3) the effects of extinction and speciation rates on prior probabilities of trees. Future goals of paleosystematists include incorporating these and other “nuisance” parameters so that, ultimately, our tests of phylogeny are really tests of evolutionary histories.

At least two predominating modes of evolution have been proposed for the Early Tithonian oppeliid ammonite genus Semiformiceras, including phyletic transformation of a single lineage (S. darwini-S. semiforme-S. fallauxi) and, most recently, a bifurcating or cladogenetic model of speciation. We discuss methodological obstacles in past studies that have focused on specific modes of evolution, and offer a reanalysis of the morphological data first presented by Cecca and Rouget [Palaeontology, 49, 1069-1080] using the stratocladistic software StrataPhy. The present analysis utilizes 11 ammonite taxa and 15 characters (14 morphological and one stratigraphic) and assesses all previous phylogenetic hypotheses, including those that recruit OTUs in ancestral or 'nodal' positions, without excluding evolutionary modes. The results cast doubt on the monophyly of S. darwini, S. semiforme and S. fallauxi, but do not follow completely the direct anagenetic progression proposed by stratophenetic hypotheses. We conclude that stratocladistics is a helpful tool for elucidating the extent of anagenesis and cladogenesis in extinct lineages owing to its capacity to reconstruct phylograms in their temporal framework, and to assess the distinctness and monophyly, not just of clades but of the OTUs themselves. Ultimately, this study addresses the novel utility of computer-assisted stratocladistic analysis in assessing evolutionary modes beyond the reach of traditional cladistic-based methodologies.