Virtual reconstruction of the Canis arnensis type (Canidae, Mammalia) from the Upper Valdarno Basin (Italy, Early Pleistocene)

Taphonomic deformation, whether it be brittle or plastic, is possibly the most influential process hindering the correct understanding of fossil species morphology. This is especially true if the deformation affects type specimens or applies to or obscures taxonomically diagnostic or functionally significant traits. Target Deformation, a recently developed virtual manipulation protocol, was implemented to address this issue by applying landmark-guided restoration of the original, deformed fossils, using undeformed specimens (or parts thereof) of the same species as a reference. The enigmatic Early Pleistocene canid Canis arnensis provides a typical example of a fossil species in dire need of virtual restoration. Its lectotype specimen is heavily deformed and none of the few known skulls are well preserved, obscuring the recognition of its systematic and phylogenetic position. Our results indicate that the algorithm effectively countered the lectotype skull's laterolateral compression and its concomitant rostrocaudal elongation. Morphometrically, comparison of the retrodeformed cranium (IGF 867_W) with other specimens of the same species, and to other fossil and extant canid material, confirms IGF 867_W consistently clusters within C. arnensis variability. Overall, the evidence presented here confirms that Target Deformation provides a powerful tool to better characterize complex taxa like C. arnensis, whose knowledge is severely affected by the state of preservation of its fossil material.

The largest freshwater odontocete: A South Asian river dolphin relative from the proto-Amazonia

Several dolphin lineages have independently invaded freshwater systems. Among these, the evolution of the South Asian river dolphin Platanista and its relatives (Platanistidae) remains virtually unknown as fossils are scarce. Here, we describe Pebanista yacuruna gen. et sp. nov., a dolphin from the Miocene proto-Amazonia of Peru, recovered in phylogenies as the closest relative of Platanista. Morphological characters such as an elongated rostrum and large supraorbital crests, along with ecological interpretations, indicate that this odontocete was fully adapted to fresh waters. Pebanista constitutes the largest freshwater odontocete known, with an estimated body length of 3 meters, highlighting the ample resource availability and biotic diversity in the region, during the Early to Middle Miocene. The finding of Pebanista in proto-Amazonian layers attests that platanistids ventured into freshwater ecosystems not only in South Asia but also in South America, before the modern Amazon River dolphin, during a crucial moment for the Amazonian evolution.

A switch in jaw form-function coupling during the evolution of mammals

The evolutionary shift from a single-element ear, multi-element jaw to a multi-element ear, single-element jaw during the transition to crown mammals marks one of the most dramatic structural transformations in vertebrates. Research on this transformation has focused on mammalian middle-ear evolution, but a mandible comprising only the dentary is equally emblematic of this evolutionary radiation. Here, we show that the remarkably diverse jaw shapes of crown mammals are coupled with surprisingly stereotyped jaw stiffness. This strength-based morphofunctional regime has a genetic basis and allowed mammalian jaws to effectively resist deformation as they radiated into highly disparate forms with markedly distinct diets. The main functional consequences for the mandible of decoupling hearing and mastication were a trade-off between higher jaw stiffness versus decreased mechanical efficiency and speed compared with non-mammals. This fundamental and consequential shift in jaw form-function underpins the ecological and taxonomic diversification of crown mammals. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Dental topographic proxies for ecological characteristics in carnivoran mammals

Form-function relationships in mammalian feeding systems are active topics of research in evolutionary biology. This is due principally to their fundamental importance for understanding dietary adaptations in extinct taxa and macro-evolutionary patterns of morphological transformations through changing environments. We hypothesize that three-dimensional dental topographic metrics represent stronger predictors for dietary and other ecological variables than do linear measurements. To test this hypothesis, we measured three dental topographic metrics: Relief Index (RFI), Dirichlet Normal Energy (DNE), and Orientation Patch Count Rotated (OPCR) in 57 extant carnivoran species. Premolar and molar dental topographic indices were regressed against activity, diet breadth, habitat breadth, terrestriality, and trophic level variables within a phylogenetic framework. The results of this study showed significant correlations between RFI and the ecological variables diet breadth and trophic level. Weaker correlations are documented between OPCR and activity and between DNE and trophic level. Our results suggest that cusp height is strongly reflective of dietary ecology in carnivorans as a whole, and represents a proxy mainly for different degrees of hypercarnivory observed within this group of predatory mammals.

Brawn before brains in placental mammals after the end-Cretaceous extinction

Mammals are the most encephalized vertebrates, with the largest brains relative to body size. Placental mammals have particularly enlarged brains, with expanded neocortices for sensory integration, the origins of which are unclear. We used computed tomography scans of newly discovered Paleocene fossils to show that contrary to the convention that mammal brains have steadily enlarged over time, early placentals initially decreased their relative brain sizes because body mass increased at a faster rate. Later in the Eocene, multiple crown lineages independently acquired highly encephalized brains through marked growth in sensory regions. We argue that the placental radiation initially emphasized increases in body size as extinction survivors filled vacant niches. Brains eventually became larger as ecosystems saturated and competition intensified.

Isotope data from amino acids indicate Darwin's ground sloth was not an herbivore

Fossil sloths are regarded as obligate herbivores for reasons including peculiarities of their craniodental morphology and that all living sloths feed exclusively on plants. We challenge this view based on isotopic analyses of nitrogen of specific amino acids, which show that Darwin's ground sloth Mylodon darwinii was an opportunistic omnivore. This direct evidence of omnivory in an ancient sloth requires reevaluation of the ecological structure of South American Cenozoic mammalian communities, as sloths represented a major component of these ecosystems across the past 34 Myr. Furthermore, by analyzing modern mammals with known diets, we provide a basis for reliable interpretation of nitrogen isotopes of amino acids of fossils. We argue that a widely used equation to determine trophic position is unnecessary, and that the relative isotopic values of the amino acids glutamate and phenylalanine alone permit reliable reconstructions of trophic positions of extant and extinct mammals.

The Earliest Ursine Bear Demonstrates the Origin of Plant-Dominated Omnivory in Carnivora

In Carnivora, increases in body size often lead to dietary specialization toward hypercarnivory. Ursine bears (Tremarctos and Ursus), however, are the only omnivorous Carnivora that evolved large body sizes (i.e., >50 kg). Traits contributing to their gigantism, and how those traits evolved, have never been studied. Here we propose that special dental characters of Ursinae (parallel buccal and lingual ridges) permit a sagittally oriented mastication associated with increasing emphasis on plant foods. This pattern can be traced back to a new early diverging bear of plant-dominated omnivorous diet, Aurorarctos tirawa gen. et sp. nov. from the late Middle Miocene of North America, which was supported as the earliest known ursine bear by phylogenetic analysis. The anatomical transition to increased masticatory efficiency, probably together with the ability to hibernate, helped bears break prior ecological limitations on body size and led to the evolution of a distinctive lineage of herbivorous-omnivorous, large-bodied Carnivora.

Cranial endocast of a stem platyrrhine primate and ancestral brain conditions in anthropoids

Understanding of ancestral conditions for anthropoids has been hampered by the paucity of well-preserved early fossils. Here, we provide an unprecedented view of the cerebral morphology of the 20-million-year-old Chilecebus carrascoensis, the best-preserved early diverging platyrrhine known, obtained via high-resolution CT scanning and 3D digital reconstruction. These analyses are crucial for reconstructing ancestral brain conditions in platyrrhines and anthropoids given the early diverging position of Chilecebus. Although small, the brain of Chilecebus is not lissencephalic and presents at least seven pairs of sulci on its endocast. Comparisons of Chilecebus and other basal anthropoids indicate that the major brain subdivisions of these early anthropoids exhibit no consistent scaling pattern relative to the overall brain size. Many gross cerebral features appear to have transformed in a mosaic fashion and probably have originated in platyrrhine and catarrhine anthropoids independently, involving multiple, independent instances of size increase, as well as some secondary decreases.

Body mass predicts isotope enrichment in herbivorous mammals

Carbon isotopic signatures recorded in vertebrate tissues derive from ingested food and thus reflect ecologies and ecosystems. For almost two decades, most carbon isotope-based ecological interpretations of extant and extinct herbivorous mammals have used a single diet–bioapatite enrichment value (14‰). Assuming this single value applies to all herbivorous mammals, from tiny monkeys to giant elephants, it overlooks potential effects of distinct physiological and metabolic processes on carbon fractionation. By analysing a never before assessed herbivorous group spanning a broad range of body masses—sloths—we discovered considerable variation in diet–bioapatite δ¹³C enrichment among mammals. Statistical tests (ordinary least squares, quantile, robust regressions, Akaike information criterion model tests) document independence from phylogeny, and a previously unrecognized strong and significant correlation of δ¹³C enrichment with body mass for all mammalian herbivores. A single-factor body mass model outperforms all other single-factor or more complex combinatorial models evaluated, including for physiological variables (metabolic rate and body temperature proxies), and indicates that body mass alone predicts δ¹³C enrichment. These analyses, spanning more than 5 orders of magnitude of body sizes, yield a size-dependent prediction of isotopic enrichment across Mammalia and for distinct digestive physiologies, permitting reconstruction of foregut versus hindgut fermentation for fossils and refined mean annual palaeoprecipitation estimates based on δ¹³C of mammalian bioapatite.

Structure-function covariation with nonfeeding ecological variables influences evolution of feeding specialization in Carnivora

Skull shape convergence is pervasive among vertebrates. Although this is frequently inferred to indicate similar functional underpinnings, neither the specific structure-function linkages nor the selective environments in which the supposed functional adaptations arose are commonly identified and tested. We demonstrate that nonfeeding factors relating to sexual maturity and precipitation-related arboreality also can generate structure-function relationships in the skulls of carnivorans (dogs, cats, seals, and relatives) through covariation with masticatory performance. We estimated measures of masticatory performance related to ecological variables that covary with cranial shape in the mammalian order Carnivora, integrating geometric morphometrics and finite element analyses. Even after accounting for phylogenetic autocorrelation, cranial shapes are significantly correlated to both feeding and nonfeeding ecological variables, and covariation with both variable types generated significant masticatory performance gradients. This suggests that mechanisms of obligate shape covariation with nonfeeding variables can produce performance changes resembling those arising from feeding adaptations in Carnivora.

A unique feeding strategy of the extinct marine mammal Kolponomos: convergence on sabretooths and sea otters

Mammalian molluscivores feed mainly by shell-crushing or suction-feeding. The extinct marine arctoid, Kolponomos, has been interpreted as an otter-like shell-crusher based on similar dentitions. However, neither the masticatory biomechanics of the shell-crushing adaptation nor the way Kolponomos may have captured hard-shelled prey have been tested. Based on mandibular symphyseal morphology shared by Kolponomos and sabre-toothed carnivores, we hypothesize a sabretooth-like mechanism for Kolponomos prey-capture, whereby the mandible functioned as an anchor. Torque generated from jaw closure and head flexion was used to dislodge prey by prying, with prey then crushed using cheek teeth. We test this hypothesized feeding sequence using phylogenetically informed biomechanical simulations and shape analyses, and find a strongly supported, shared high mandibular stiffness in simulated prey-capture bites and mandibular shape in Kolponomos and the sabre-toothed cat Smilodon. These two distantly related taxa converged on using mandibles to anchor cranial torqueing forces when prying substrate-bound prey in the former and sabre-driving forces during prey-killing in the latter. Simulated prey-crushing bites indicate that Kolponomos and sea otters exhibit alternative structural stiffness-bite efficiency combinations in mandibular biomechanical adaptation for shell-crushing. This unique feeding system of Kolponomos exemplifies a mosaic of form-function convergence relative to other Carnivora.

A New 13 Million Year Old Gavialoid Crocodylian from Proto-Amazonian Mega-Wetlands Reveals Parallel Evolutionary Trends in Skull Shape Linked to Longirostry

Gavialoid crocodylians are the archetypal longirostrine archosaurs and, as such, understanding their patterns of evolution is fundamental to recognizing cranial rearrangements and reconstructing adaptive pathways associated with elongation of the rostrum (longirostry). The living Indian gharial Gavialis gangeticus is the sole survivor of the group, thus providing unique evidence on the distinctive biology of its fossil kin. Yet phylogenetic relationships and evolutionary ecology spanning ~70 million-years of longirostrine crocodylian diversification remain unclear. Analysis of cranial anatomy of a new proto-Amazonian gavialoid, Gryposuchus pachakamue sp. nov., from the Miocene lakes and swamps of the Pebas Mega-Wetland System reveals that acquisition of both widely separated and protruding eyes (telescoped orbits) and riverine ecology within South American and Indian gavialoids is the result of parallel evolution. Phylogenetic and morphometric analyses show that, in association with longirostry, circumorbital bone configuration can evolve rapidly for coping with trends in environmental conditions and may reflect shifts in feeding strategy. Our results support a long-term radiation of the South American forms, with taxa occupying either extreme of the gavialoid morphospace showing preferences for coastal marine versus fluvial environments. The early biogeographic history of South American gavialoids was strongly linked to the northward drainage system connecting proto-Amazonian wetlands to the Caribbean region.

An integrative method for testing form-function linkages and reconstructed evolutionary pathways of masticatory specialization

Morphology serves as a ubiquitous proxy in macroevolutionary studies to identify potential adaptive processes and patterns. Inferences of functional significance of phenotypes or their evolution are overwhelmingly based on data from living taxa. Yet, correspondence between form and function has been tested in only a few model species, and those linkages are highly complex. The lack of explicit methodologies to integrate form and function analyses within a deep-time and phylogenetic context weakens inferences of adaptive morphological evolution, by invoking but not testing form-function linkages. Here, we provide a novel approach to test mechanical properties at reconstructed ancestral nodes/taxa and the strength and direction of evolutionary pathways in feeding biomechanics, in a case study of carnivorous mammals. Using biomechanical profile comparisons that provide functional signals for the separation of feeding morphologies, we demonstrate, using experimental optimization criteria on estimation of strength and direction of functional changes on a phylogeny, that convergence in mechanical properties and degree of evolutionary optimization can be decoupled. This integrative approach is broadly applicable to other clades, by using quantitative data and model-based tests to evaluate interpretations of function from morphology and functional explanations for observed macroevolutionary pathways.

Bony labyrinth shape variation in extant Carnivora: a case study of Musteloidea

The bony labyrinth provides a proxy for the morphology of the inner ear, a primary cognitive organ involved in hearing, body perception in space, and balance in vertebrates. Bony labyrinth shape variations often are attributed to phylogenetic and ecological factors. Here we use three-dimensional (3D) geometric morphometrics to examine the phylogenetic and ecological patterns of variation in the bony labyrinth morphology of the most species-rich and ecologically diversified traditionally recognized superfamily of Carnivora, the Musteloidea (e.g. weasels, otters, badgers, red panda, skunks, raccoons, coatis). We scanned the basicrania of specimens belonging to 31 species using high-resolution X-ray computed micro-tomography (μCT) to virtually reconstruct 3D models of the bony labyrinths. Labyrinth morphology is captured by a set of six fixed landmarks on the vestibular and cochlear systems, and 120 sliding semilandmarks, slid at the center of the semicircular canals and the cochlea. We found that the morphology of this sensory structure is not significantly influenced by bony labyrinth size, in comparisons across all musteloids or in any of the individual traditionally recognized families (Mephitidae, Procyonidae, Mustelidae). PCA (principal components analysis) of shape data revealed that bony labyrinth morphology is clearly distinguishable between musteloid families, and permutation tests of the Kmult statistic confirmed that the bony labyrinth shows a phylogenetic signal in musteloids and in most mustelids. Both the vestibular and cochlear regions display morphological differences among the musteloids sampled, associated with the size and curvature of the semicircular canals, angles between canals, presence or absence of a secondary common crus, degree of lateral compression of the vestibule, orientation of the cochlea relative to the semicircular canals, proportions of the cochlea, and degree of curvature of its turns. We detected a significant ecological signal in the bony labyrinth shape of musteloids, differentiating semi-aquatic taxa from non-aquatic ones (the taxa assigned to terrestrial, arboreal, semi-arboreal, and semi-fossorial categories), and a significant signal for mustelids, differentiating the bony labyrinths of terrestrial, semi-arboreal, arboreal, semi-fossorial and semi-aquatic species from each other. Otters and minks are distinguished from non-aquatic musteloids by an oval rather than circular anterior canal, sinuous rather than straight lateral canal, and acute rather than straight angle between the posterior and lateral semicircular canals - each of these morphological characters has been related previously to animal sensitivity for detecting head motion in space.

A Miocene hyperdiverse crocodylian community reveals peculiar trophic dynamics in proto-Amazonian mega-wetlands

Amazonia contains one of the world's richest biotas, but origins of this diversity remain obscure. Onset of the Amazon River drainage at approximately 10.5 Ma represented a major shift in Neotropical ecosystems, and proto-Amazonian biotas just prior to this pivotal episode are integral to understanding origins of Amazonian biodiversity, yet vertebrate fossil evidence is extraordinarily rare. Two new species-rich bonebeds from late Middle Miocene proto-Amazonian deposits of northeastern Peru document the same hyperdiverse assemblage of seven co-occurring crocodylian species. Besides the large-bodied Purussaurus and Mourasuchus, all other crocodylians are new taxa, including a stem caiman-Gnatusuchus pebasensis-bearing a massive shovel-shaped mandible, procumbent anterior and globular posterior teeth, and a mammal-like diastema. This unusual species is an extreme exemplar of a radiation of small caimans with crushing dentitions recording peculiar feeding strategies correlated with a peak in proto-Amazonian molluscan diversity and abundance. These faunas evolved within dysoxic marshes and swamps of the long-lived Pebas Mega-Wetland System and declined with inception of the transcontinental Amazon drainage, favouring diversification of longirostrine crocodylians and more modern generalist-feeding caimans. The rise and demise of distinctive, highly productive aquatic ecosystems substantially influenced evolution of Amazonian biodiversity hotspots of crocodylians and other organisms throughout the Neogene.

The genus Macroteleia Westwood in Middle Miocene amber from Peru (Hymenoptera, Platygastridae s.l., Scelioninae)

A new species of the scelionine genus Macroteleia Westwood (Platygastridae s.l., Scelioninae) is described and figured from a female beautifully preserved in Middle Miocene amber from Peru. Macroteleia yaguarum Perrichot & Engel, sp. n., shows a unique combination of characters otherwise seen independently within its congeners. It is most similar to the modern M. surfacei Brues, but differs from it by the non-foveolate notauli, the contiguous punctures of the vertex, and the continuous propodeum. The new species is the first New World fossil of the genus, suggesting a Cretaceous origin for the group and a relatively old age of the South American, tropical African, and Australian faunas, and a younger age of the modern Holarctic faunas.

Comparative study of notoungulate (Placentalia, Mammalia) bony labyrinths and new phylogenetically informative inner ear characters

The phylogenetic relationships of notoungulates, an extinct group of predominantly South American herbivores, remain poorly resolved with respect to both other placental mammals and among one another. Most previous phylogenetic analyses of notoungulates have not included characters of the internal cranium, not least because few such features, including the bony labyrinth, have been described for members of the group. Here we describe the inner ears of the notoungulates Altitypotherium chucalensis (Mesotheriidae), Pachyrukhos moyani (Hegetotheriidae) and Cochilius sp. (Interatheriidae) based on reconstructions of bony labyrinths obtained from computed tomography imagery. Comparisons of the bony labyrinths of these taxa with the basally diverging notoungulate Notostylops murinus (Notostylopidae), an isolated petrosal from Itaboraí, Brazil, referred to Notoungulata, and six therian outgroups, yielded an inner ear character matrix of 25 potentially phylogenetically informative characters, 14 of them novel to this study. Two equivocally optimized character states potentially support a pairing of Mesotheriidae and Hegetotheriidae, whereas four others may be diagnostic of Notoungulata. Three additional characters are potentially informative for diagnosing more inclusive clades: one for crown Placentalia; another for a clade containing Kulbeckia, Zalambdalestes, and Placentalia; and a third for Eutheria (crown Placentalia plus stem taxa). Several other characters are apomorphic for at least one notoungulate in our study and are of potential interest for broader taxonomic sampling within Notoungulata to clarify currently enigmatic interrelationships. Measures of the semicircular canals were used to infer agility (e.g. capable of quick movements vs. lethargic movements) of these taxa. Agility scores calculated from these data generally corroborate interpretations based on postcranial remains of these or closely related species. We provide estimates of the low-frequency hearing limits in notoungulates based on the ratio of radii of the apical and basal turns of the cochlea. These limits range from 15 Hz in Notostylops to 149 Hz in Pachyrukhos, values comparable to the Asian elephant (Elephas maximus) and the California sea lion (Zalophus californianus) when hearing in air, respectively.

Response to comment on "The placental mammal ancestor and the post-K-Pg radiation of placentals"

Tree-building with diverse data maximizes explanatory power. Application of molecular clock models to ancient speciation events risks a bias against detection of fast radiations subsequent to the Cretaceous-Paleogene (K-Pg) event. Contrary to Springer et al., post-K-Pg placental diversification does not require "virus-like" substitution rates. Even constraining clade ages to their model, the explosive model best explains placental evolution.

The oldest known primate skeleton and early haplorhine evolution

Reconstructing the earliest phases of primate evolution has been impeded by gaps in the fossil record, so that disagreements persist regarding the palaeobiology and phylogenetic relationships of the earliest primates. Here we report the discovery of a nearly complete and partly articulated skeleton of a primitive haplorhine primate from the early Eocene of China, about 55 million years ago, the oldest fossil primate of this quality ever recovered. Coupled with detailed morphological examination using propagation phase contrast X-ray synchrotron microtomography, our phylogenetic analysis based on total available evidence indicates that this fossil is the most basal known member of the tarsiiform clade. In addition to providing further support for an early dichotomy between the strepsirrhine and haplorhine clades, this new primate further constrains the age of divergence between tarsiiforms and anthropoids. It also strengthens the hypothesis that the earliest primates were probably diurnal, arboreal and primarily insectivorous mammals the size of modern pygmy mouse lemurs.

The placental mammal ancestor and the post-K-Pg radiation of placentals

To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species. Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest members of Afrotheria.

Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification

Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

Inner ear of a notoungulate placental mammal: anatomical description and examination of potentially phylogenetically informative characters

We provide the first detailed description of the inner ear of a notoungulate, an extinct group of endemic South American placental mammals, based on a three-dimensional reconstruction extracted from CT imagery of a skull of Notostylops murinus. This description provides new anatomical data that should prove to be phylogenetically informative, an especially significant aspect of this research given that both the interrelationships of notoungulates and the position of Notoungulata within Placentalia are still unresolved. We also assess the locomotor agility of Notostylops based on measurements of the semicircular canals. This is the best available data on the locomotion of a notostylopid because significant postcranial remains for this group have not been described. The cochlea of Notostylops has 2.25 turns, and the stapedial ratio is 1.6. The stapedial ratio is one of the lowest recorded for a eutherian, which typically have ratios greater than 1.8. The fenestra cochleae is located posterior to the fenestra vestibuli, a condition previously only reported for some stem primates. The separation of the saccule and utricule of the vestibule is visible on the digital endocast of the bony labyrinth. The posterior arm of the LSC and the inferior arm of the PSC are confluent, but these do not form a secondary crus commune, and the phylogenetic or functional significance of this confluence is unclear at this time. Locomotor agility scores for Notostylops suggest a medium or 'average' degree of agility of motion compared to extant mammals. In terms of its locomotion, we tentatively predict that Notostylops was a generalized terrestrial mammal, with cursorial tendencies, based on its agility scores and the range of locomotor patterns inferred from postcranial analyses of other notoungulates.

The correlated evolution of Runx2 tandem repeats, transcriptional activity, and facial length in carnivora

To assess the ability of protein-coding mutations to contribute to subtle, inter-specific morphologic evolution, here, we test the hypothesis that mutations within the protein-coding region of runt-related transcription factor 2 (Runx2) have played a role in facial evolution in 30 species from a naturally evolving group, the mammalian order Carnivora. Consistent with this hypothesis, we find significant correlations between changes in Runx2 glutamine-alanine tandem-repeat ratio, and both Runx2 transcriptional activity and carnivoran facial length. Furthermore, we identify a potential evolutionary mechanism for the correlation between Runx2 tandem repeat ratio and facial length. Specifically, our results are consistent with the Runx2 tandem repeat system providing a flexible genetic mechanism to rapidly change the timing of ossification. These heterochronic changes, in turn, potentially act on existing allometric variation in carnivoran facial length to generate the disparity in adult facial lengths observed among carnivoran species. Our results suggest that despite potentially great pleiotropic effects, changes to the protein-coding regions of genes such as Runx2 do occur and have the potential to affect subtle morphologic evolution across a diverse array of species in naturally evolving lineages.

THE EVOLUTION OF ENCEPHALIZATION IN CANIFORM CARNIVORANS

A weighted-average model, which reliably estimates endocranial volume from three external measurements of the neurocranium of extant taxa in the mammalian order Carnivora, was tested for its applicability to fossil taxa by comparing model-estimated endocranial volumes to known endocast volumes. The model accurately reproduces endocast volumes for a wide array of fossil taxa across the crown radiation of the Carnivora, three stem carnivoramorphan taxa, and Pleistocene fossils of two extant species. Applying this model to fossil taxa without known endocast volumes expanded the sample of fossil taxa with estimated brain volumes in the carnivoran suborder Caniformia from 11 to 60 taxa. This then allowed a comprehensive assessment of the evolution of relative brain size across this clade. An allometry of brain volume to body mass was calculated on phylogenetically independent contrasts for the set of extant taxa, and from this, log-transformed encephalization quotients (logEQs) were calculated for all taxa, extant, and fossil. A series of Mann-Whitney tests demonstrated that the distributions of logEQs for taxa early in caniform evolutionary history possessed significantly lower median logEQs than extant taxa. Median logEQ showed a pronounced shift around the Miocene-Pliocene transition. Support tests, based on likelihood ratios, demonstrated that the variances of these distributions also were significantly lower than among modern taxa, but logEQ variance increased gradually through the history of the clade, not abruptly. Reconstructions of ancestral logEQs using weighted squared-change parsimony demonstrate that increased encephalization is observed across all major caniform clades (with the possible exception of skunks) and that these increases were achieved in parallel, although an "ancestor-descendant differencing" method could not rule out drift as a hypothesis. Peculiarities in the estimated logEQs for the extinct caniform family Amphicyonidae were also investigated; these unusual patterns are likely due to a unique allometry in scaling brain to body size in this single clade.

Amber from western Amazonia reveals Neotropical diversity during the middle Miocene

Tertiary insects and arachnids have been virtually unknown from the vast western Amazonian basin. We report here the discovery of amber from this region containing a diverse fossil arthropod fauna (13 hexapod families and 3 arachnid species) and abundant microfossil inclusions (pollen, spores, algae, and cyanophyceae). This unique fossil assemblage, recovered from middle Miocene deposits of northeastern Peru, greatly increases the known diversity of Cenozoic tropical-equatorial arthropods and microorganisms and provides insights into the biogeography and evolutionary history of modern Neotropical biota. It also strengthens evidence for the presence of more modern, high-diversity tropical rainforest ecosystems during the middle Miocene in western Amazonia.

Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record

A recent molecular phylogeny of the mammalian order Carnivora implied large body size as the ancestral condition for the caniform subclade Arctoidea using the distribution of species mean body sizes among living taxa. "Extant taxa-only" approaches such as these discount character state observations for fossil members of living clades and completely ignore data from extinct lineages. To more rigorously reconstruct body sizes of ancestral forms within the Caniformia, body size and first appearance data were collected for 149 extant and 367 extinct taxa. Body sizes were reconstructed for four ancestral nodes using weighted squared-change parsimony on log-transformed body mass data. Reconstructions based on extant taxa alone favored large body sizes (on the order of 10 to 50 kg) for the last common ancestors of both the Caniformia and Arctoidea. In contrast, reconstructions incorporating fossil data support small body sizes (< 5 kg) for the ancestors of those clades. When the temporal information associated with fossil data was discarded, body size reconstructions became ambiguous, demonstrating that incorporating both character state and temporal information from fossil taxa unambiguously supports a small ancestral body size, thereby falsifying hypotheses derived from extant taxa alone. Body size reconstructions for Caniformia, Arctoidea, and Musteloidea were not sensitive to potential errors introduced by uncertainty in the position of extinct lineages relative to the molecular topology, or to missing body size data for extinct members of an entire major clade (the aquatic Pinnipedia). Incorporating character state observations and temporal information from the fossil record into hypothesis testing has a significant impact on the ability to reconstruct ancestral characters and constrains the range of potential hypotheses of character evolution. Fossil data here provide the evidence to reliably document trends of both increasing and decreasing body size in several caniform clades. More generally, including fossils in such analyses incorporates evidence of directional trends, thereby yielding more reliable ancestral character state reconstructions.

Molecular phylogeny of the carnivora (mammalia): assessing the impact of increased sampling on resolving enigmatic relationships

This study analyzed 76 species of Carnivora using a concatenated sequence of 6243 bp from six genes (nuclear TR-i-I, TBG, and IRBP; mitochondrial ND2, CYTB, and 12S rRNA), representing the most comprehensive sampling yet undertaken for reconstructing the phylogeny of this clade. Maximum parsimony and Bayesian methods were remarkably congruent in topologies observed and in nodal support measures. We recovered all of the higher level carnivoran clades that had been robustly supported in previous analyses (by analyses of morphological and molecular data), including the monophyly of Caniformia, Feliformia, Arctoidea, Pinnipedia, Musteloidea, Procyonidae + Mustelidae sensu stricto, and a clade of (Hyaenidae + (Herpestidae + Malagasy carnivorans)). All of the traditional "families," with the exception of Viverridae and Mustelidae, were robustly supported as monophyletic groups. We further have determined the relative positions of the major lineages within the Caniformia, which previous studies could not resolve, including the first robust support for the phylogenetic position of marine carnivorans (Pinnipedia) within the Arctoidea (as the sister-group to musteloids [sensu lato], with ursids as their sister group). Within the pinnipeds, Odobenidae (walrus) was more closely allied with otariids (sea lions/fur seals) than with phocids ("true" seals). In addition, we recovered a monophyletic clade of skunks and stink badgers (Mephitidae) and resolved the topology of musteloid interrelationships as: Ailurus (Mephitidae (Procyonidae, Mustelidae [sensu stricto])). This pattern of interrelationships of living caniforms suggests a novel inference that large body size may have been the primitive condition for Arctoidea, with secondary size reduction evolving later in some musteloids. Within Mustelidae, Bayesian analyses are unambiguous in supporting otter monophyly (Lutrinae), and in both MP and Bayesian analyses Martes is paraphyletic with respect to Gulo and Eira, as has been observed in some previous molecular studies. Within Feliformia, we have confirmed that Nandinia is the outgroup to all other extant feliforms, and that the Malagasy Carnivora are a monophyletic clade closely allied with the mongooses (Herpestidae [sensu stricto]). Although the monophyly of each of the three major feliform clades (Viverridae sensu stricto, Felidae, and the clade of Hyaenidae + (Herpestidae + Malagasy carnivorans)) is robust in all of our analyses, the relative phylogenetic positions of these three lineages is not resolvable at present. Our analyses document the monophyly of the "social mongooses," strengthening evidence for a single origin of eusociality within the Herpestidae. For a single caniform node, the position of pinnipeds relative to Ursidae and Musteloidea, parsimony analyses of data for the entire Carnivora did not replicate the robust support observed for both parsimony and Bayesian analyses of the caniform ingroup alone. More detailed analyses and these results demonstrate that outgroup choice can have a considerable effect on the strength of support for a particular topology. Therefore, the use of exemplar taxa as proxies for entire clades with diverse evolutionary histories should be approached with caution. The Bayesian analysis likelihood functions generally were better able to reconstruct phylogenetic relationships (increased resolution and more robust support for various nodes) than parsimony analyses when incompletely sampled taxa were included. Bayesian analyses were not immune, however, to the effects of missing data; lower resolution and support in those analyses likely arise from non-overlap of gene sequence data among less well-sampled taxa. These issues are a concern for similar studies, in which different gene sequences are concatenated in an effort to increase resolving power.

Single origin of Malagasy Carnivora from an African ancestor

The Carnivora are one of only four orders of terrestrial mammals living in Madagascar today. All four (carnivorans, primates, rodents and lipotyphlan insectivores) are placental mammals with limited means for dispersal, yet they occur on a large island that has been surrounded by a formidable oceanic barrier for at least 88 million years, predating the age of origin for any of these groups. Even so, as many as four colonizations of Madagascar have been proposed for the Carnivora alone. The mystery of the island's mammalian origins is confounded by its poor Tertiary fossil record, which leaves us with no direct means for estimating dates of initial diversification. Here we use a multi-gene phylogenetic analysis to show that Malagasy carnivorans are monophyletic and thus the product of a single colonization of Madagascar by an African ancestor. Furthermore, a bayesian analysis of divergence ages for Malagasy carnivorans and lemuriforms indicates that their respective colonizations were temporally separated by tens of millions of years. We therefore conclude that a single event, such as vicariance or common dispersal, cannot explain the presence of both groups in Madagascar.