Data from: Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies

1. 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 2. 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. 3. 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. 4. 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

Data from: The fossil record and macroevolutionary history of the beetles

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

Data from: Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies

1. 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 2. 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. 3. 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. 4. 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

SmithMarcot_BeetleOccurrence

Database of fossil beetle occurrences reported in the international paleontological and entomological literature. Fossils are from localities that range in age from the Permian through the Pliocene

SmithMarcot_BeetleCollections

Database of fossil beetle collections reported in the international paleontological and entomological literature. Localities range in age from the Permian through the Pliocene

Data from: Late Cenozoic onset of the latitudinal diversity gradient of North American mammals

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

Data from: The development of integration in marsupial and placental limbs

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

Length_data

Length calculations from landmarks for all specimens

Data from: The development of integration in marsupial and placental limbs

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

Stable Isotope Data from Zachos et al. 2001

These include the stable isotope data and dates used to calculate correlation between d18O and fossil slopes. All data are from Zachos J, Pagani M, Sloan L, Thomas E, Billups K (2001) Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292(5517):686–693