Graham J Slater

Smithsonian Institution · Department of Paleobiology

The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most...

Macroevolutionary trends exhibited by retroviruses are complex and not entirely understood. The sloth endogenized foamy-like retrovirus (SloEFV), which demonstrates incongruence in virus-host evolution among extant sloths (Order Folivora), has not been investigated heretofore in any extinct sloth lineages and its premodern history within folivorans...

Significance Many of the most diverse lineages of animals and plants are hypothesized to have arisen via the process of adaptive radiation. Most modern definitions of adaptive radiation focus on the role of ecological opportunity in regulating rates of morphological diversification. Using the rich fossil record of North American canids (wolves, fox...

In Wonderful Life, Stephen Jay Gould attempted to explain how the bizarre animal fossils from the 500 million-y-old Burgess Shale fauna teach a valuable lesson about the nature of morphological evolution (1). Finding such a remarkable diversity of body plans so early in the history of metazoan life should not be surprising, he argued, for this is a...

In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, mole...

Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutio...

Alignment of Neomonachus tropicalis cytb with extant monk seal cytb sequences.

Fifty percent majority-rule consensus tree based on 1000 bootstrap pseudoreplicates generated using the maximum parsimony phylogenetic optimality criterion.

Amplicons covering cytb in this study.

Alignment of three Neomonachus tropicalis D-loop hypervariable region sequences (from USNM 100358, 102527, and 102534).

Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data has increased dramatically in the last few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger...

In a recent paper (Slater 2013), I described and implemented two “mode shift” models, where a continuous trait evolves under an Ornstein-Uhlenbeck (OU) process over the basal portion of a phylogenetic tree and shifts to an unconstrained Brownian Motion (BM) process, with or without a novel variance parameter, at a user specified time before the pre...

Pantherine felids ('big cats') include the largest living cats, apex predators in their respective ecosystems. They are also the earliest diverging living cat lineage, and thus are important for understanding the evolution of all subsequent felid groups. Although the oldest pantherine fossils occur in Africa, molecular phylogenies point to Asia as...

A central prediction of much theory on adaptive radiations is that traits should evolve rapidly during the early stages of a clade's history and subsequently slowdown in rate as niches become saturated - a so-called "Early Burst". Although a common pattern in the fossil record, evidence for early bursts of trait evolution in phylogenetic comparativ...

The aim of macroevolutionary research is to understand pattern and process in phenotypic evolution and lineage diversification at and above the species level. Historically, this kind of research has been tackled separately by palaeontologists, using the fossil record, and by evolutionary biologists, using phylogenetic comparative methods. Although...

Phylogenetic comparative methods provide a powerful way of addressing classic questions about tempo and mode of phenotypic evolution in the fossil record, such as whether mammals increased in body size diversity after the C retaceous‐ P alaeogene ( K ‐ P g) extinction. Most often, these kinds of questions are addressed in the context of variation i...

The ability to grasp and manipulate is often considered a hallmark of hominins and associated with the evolution of their bipedal locomotion and tool use. Yet, many other mammals use their forelimbs to grasp and manipulate objects. Previous investigations have suggested that grasping may be derived from digging behaviour, arboreal locomotion or hun...

Abstract Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on the planet, but our understanding of their mode of diversification remains limited. Here we test whether the diversity of the damselfishes (Pomacentridae), one of the most species-rich families of reef-associated fishes, was produced by a single...

Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models to phylogenetic comparative data consisting of a molecular phylogeny with branch lengths and trait measurements from extant taxa. These kinds of approaches ignore historical evidence for evolutionary pattern and proc...

Relationship between clade age and log-transformed species richness for 327 subfamilies of beetles, using phylogeny from Hunt et al. [26]. There is no significant relationship between age and richness for this dataset (PGLS β = −0.002, t = −0.54, p = 0.59). (EPS)

Relationship between the mean age-diversity correlation predicted by MEDUSA model of rate variation and the (log-transformed) number of clades in each dataset. The 12 datapoints correspond to the taxonomic subsets (e.g., coleopterans, angiosperms, amphibians) presented in Figure 3. (EPS)

Relationship between stem clade age and species richness for subsets of the data containing young clades only. The full dataset was pruned to contain only those clades younger than a given “truncation age,” and the full PGLS analysis was repeated on each subset. Thus, the analysis for “truncation age = 50” corresponds to the subset of clades younge...

Conditioned birth-death expectation for the relationship between clade age and species richness under four relative extinction rates, defined as the ratio of the extinction rate (μ) to the speciation rate (λ). (A) and (B) display identical information, but species richness in (A) has been log-transformed. Black line, pure-birth process with μ/λ = 0...

Test of the relationship between clade age and species richness for all possible subtrees with 10 or more descendant clades (352 total). (A) Across the full timetree, a total of 22 subtrees (defined by red circles on nodes) are characterized by significant age-richness relationships. For comparison, subtrees defining sets of clades with significant...

Effect of error in the estimation of clade age on a true positive relationship between clade age and species richness. We took the observed set of angiosperm clade ages as fixed (N = 330 clades) and simulated species richness on that set of ages assuming a constant-rate birth death process for the entire angiosperm radiation. Then, holding these ri...

Analysis of relationship between clade age and species richness from non-phylogenetic model (ordinary least-squares regression) when richness values are generated under a model with phylogenetic signal in clade size (see Materials and Methods). Although no relationship between age and richness was input into the simulation model, many simulations y...

Richness values for clades represented in the timetree and their associated sources. (DOC)

Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fun...

Shape variation in the vertebrate skull is often studied by considering this bony structure as a single discrete unit, but it can also be interpreted exploring covariation among functionally and developmentally distinct regions, or modules. In this paper, we explore the evolution of skull shape in extant and fossil carnivoran cats by looking at cov...

In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree-based method cal...

Extant chelonians (turtles and tortoises) span almost four orders of magnitude of body size, including the startling examples of gigantism seen in the tortoises of the Galapagos and Seychelles islands. However, the evolutionary determinants of size diversity in chelonians are poorly understood. We present a comparative analysis of body size evoluti...

Inside the mammalian nose lies a labyrinth of bony plates covered in epithelium collectively known as turbinates. Respiratory turbinates lie anteriorly and aid in heat and water conservation, while more posterior olfactory turbinates function in olfaction. Previous observations on a few carnivorans revealed that aquatic species have relatively larg...

The polar bear is the only living ursid with a fully carnivorous diet. Despite a number of well-documented craniodental adaptations for a diet of seal flesh and blubber, molecular and paleontological data indicate that this morphologically distinct species evolved less than a million years ago from the omnivorous brown bear. To better understand th...

Modern whales are frequently described as an adaptive radiation spurred by either the evolution of various key innovations (such as baleen or echolocation) or ecological opportunity following the demise of archaic whales. Recent analyses of diversification rate shifts on molecular phylogenies raise doubts about this interpretation since they find n...

Patterns of skull shape in Carnivora provide examples of parallel and convergent evolution for similar ecomorphological adaptations. However, although most researchers report on skull homoplasies among hypercarnivorous taxa, evolutionary trends towards herbivory remain largely unexplored. In this study, we analyse the skull of the living herbivorou...

After visiting the Falkland Islands during the voyage of the Beagle, Charles Darwin remarked on the surprising presence of a wolf-like canid unique to the islands [1 • Darwin C. The zoology of the voyage of H.M.S. Beagle, under the command of Captain Fitzroy, R.N., during the years 1832 to 1836. Smith, Elder and Co, London, London1838 • Google Sc...

Allometric patterns of skull-shape variation can have significant impacts on cranial mechanics and feeding performance, but have received little attention in previous studies. Here, we examine the impacts of allometric skull-shape variation on feeding capabilities in the cat family (Felidae) with linear morphometrics and finite element analysis. Ou...

The shape of the cranium varies widely among members of the order Carnivora, but the factors that drive the evolution of differences in shape remain unclear. Selection for increased bite force, bite speed or skull strength may all affect cranial morphology. We investigated the relationship between cranial form and function in the trophically divers...

The shape of the cranium varies widely among members of the order Carnivora, but the factors that drive the evolution of differences in shape remain unclear. Selection for increased bite force, bite speed or skull strength may all affect cranial morphology. We investigated the relationship between cranial form and function in the trophically divers...

The widespread availability of three-dimensional imaging and computational power has fostered a rapid increase in the number of biologists using finite element analysis (FEA) to investigate the mechanical function of living and extinct organisms. The inevitable rise of studies that compare finite element models brings to the fore two critical quest...

Sabertooths exhibit one of the most extreme feeding adaptations seen in mammals. The functional consequences of accommodating extremely elongate upper canine teeth are severe, resulting in a well-documented suite of cranial modifications. We used geometric morphometric methods to study the evolution of overall shape in the skulls of extant and exti...

The prior probability distributions and posterior probability distributions for eight calibration points employed in dating analyses using the program BEAST [141]. The posterior probability distributions for eight calibration points derived from MCMC analyses without data were run to assess the choice of the joint priors on the posterior estimates...

Sample origin. The species, common name and sample origin for taxa sampled.

Genbank accession numbers. Genbank accession numbers.

Leaf stability analysis results. Three measures of leaf stability (maximum, difference, and entropy) based on MP bootstrap analyses of the 46 taxa data set.

Likelihood values for the reconstruction of ancestral areas. Proportional likelihood values for the reconstruction of ancestral areas in the two-state and four-state analyses (shown in Figures 3 and 4, respectively).

Nuclear gene primer information. Gene symbol and name, primer sequences and description of the 21 nuclear gene segments used in the study.

Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is a central concept in evolutionary biology and characterizes the evolutionary histories of many groups of organisms. One such group is the Mustelidae, the most species-rich family within the mammalian order Carnivora, encompassing 59 species classifie...