From teeth to pad: tooth loss and development of keratinous structures in sirenians.

Sirenians are a well-known example of morphological adaptation to a shallow-water grazing diet characterized by a modified feeding apparatus and orofacial morphology. Such adaptations were accompanied by an anterior tooth reduction associated with the development of keratinized pads, the evolution of which remains elusive. Among sirenians, the recently extinct Steller's sea cow represents a special case for being completely toothless. Here, we used µ-CT scans of sirenian crania to understand how motor-sensor systems associated with tooth innervation responded to innovations such as keratinized pads and continuous dental replacement. In addition, we surveyed nine genes associated with dental reduction for signatures of loss of function. Our results reveal how patterns of innervation changed with modifications of the dental formula, especially continuous replacement in manatees. Both our morphological and genomic data show that dental development was not completely lost in the edentulous Steller's sea cows. By tracing the phylogenetic history of tooth innervation, we illustrate the role of development in promoting the innervation of keratinized pads, similar to the secondary use of dental canals for innervating neomorphic keratinized structures in other tetrapod groups.

The developmental basis for scaling of mammalian tooth size.

When evolution leads to differences in body size, organs generally scale along. A well-known example of the tight relationship between organ and body size is the scaling of mammalian molar teeth. To investigate how teeth scale during development and evolution, we compared molar development from initiation through final size in the mouse and the rat. Whereas the linear dimensions of the rat molars are twice that of the mouse molars, their shapes are largely the same. Here, we focus on the first lower molars that are considered the most reliable dental proxy for size-related patterns due to their low within-species variability. We found that scaling of the molars starts early, and that the rat molar is patterned equally as fast but in a larger size than the mouse molar. Using transcriptomics, we discovered that a known regulator of body size, insulin-like growth factor 1 (Igf1), is more highly expressed in the rat molars compared to the mouse molars. Ex vivo and in vivo mouse models demonstrated that modulation of the IGF pathway reproduces several aspects of the observed scaling process. Furthermore, analysis of IGF1-treated mouse molars and computational modeling indicate that IGF signaling scales teeth by simultaneously enhancing growth and by inhibiting the cusp-patterning program, thereby providing a relatively simple mechanism for scaling teeth during development and evolution. Finally, comparative data from shrews to elephants suggest that this scaling mechanism regulates the minimum tooth size possible, as well as the patterning potential of large teeth.

A species-level timeline of mammal evolution integrating phylogenomic data.

High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies1-3. However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the growing number of available genomes4. In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties5,6, and thus the timescale of placental mammal evolution remains contentious7-10. Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show that increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Palaeogene8 and show that crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Palaeocene/Eocene. Our Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. This approach can be used to address other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets.

Phylogenetic Signal and Bias in Paleontology.

An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure the phylogenetic value of data typically used in paleontology (bones and teeth) from six data sets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological data sets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA data sets usually increases congruence of resulting topologies to the well-corroborated tree, but this varies among morphological data sets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artifacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation. [Concatenation; fossilization; morphology; parsimony; systematics; taphonomy; total-evidence.].

Developmental origins and homologies of the hyracoid dentition.

Understanding the origins of morphological specializations in mammals is a key goal in evolutionary biology. It can be accomplished by studying dental homology, which is at the core of most evolutionary and developmental studies. Here, we focused on the evolution and development of the specialized dentition of hyraxes for which dental homologies have long been debated, and could have implications on early placental evolution. Specifically, we analysed dental mineralization sequences of the three living genera of hyraxes and 17 fossil species using X-ray computed microtomography. Our results point out the labile position of vestigial upper teeth on jaw bones in extant species, associated with the frequently unusual premolar shape of deciduous canines over 50 Ma of hyracoid evolution. We proposed two evolutionary and developmental hypotheses to explain these original hyracoid dental characteristics. (a) The presence of a vestigial teeth on the maxilla in front of a complex deciduous canine could be interpreted as extra-teeth reminiscent of early placental evolution or sirenians, an order phylogenetically close to hyracoids and showing five premolars. (b) These vestigial teeth could also correspond to third incisors with a position unusually shifted on the maxilla, which could be explained by the dual developmental origin of these most posterior incisors and their degenerated condition. This integrative study allows discussion on the current evolutionary and developmental paradigms associated with the mammalian dentition. It also highlights the importance of nonmodel species to understand dental homologies.

Congruence, fossils and the evolutionary tree of rodents and lagomorphs.

Given an evolutionary process, we expect distinct categories of heritable data, sampled in ever larger amounts, to converge on a single tree of historical relationships. We tested this assertion by undertaking phylogenetic analyses of a new morphology-DNA dataset for mammals, focusing on Glires and including the oldest known skeletons of geomyoid and Ischyromys rodents. Our results support geomyoids in the mouse-related clade (Myomorpha) and a ricochetal locomotor pattern for the common ancestor of geomyoid rodents. They also support Ischyromys in the squirrel-related clade (Sciuromorpha) and the evolution of sciurids and Aplodontia from extinct, 'protrogomorph'-grade rodents. Moreover, ever larger samples of characters from our dataset increased congruence with an independent, well-corroborated tree. Addition of morphology from fossils increased congruence to a greater extent than addition of morphology from extant taxa, consistent with fossils' temporal proximity to the common ancestors of living species, reflecting the historical, phylogenetic signal present in our data, particularly in morphological characters from fossils. Our results support the widely held but poorly tested intuition that fossils resemble the common ancestors shared by living species, and that fossilizable hard tissues (i.e. bones and teeth) help to reconstruct the evolutionary tree of life.

Open data and digital morphology.

Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.

Inner ear development in cetaceans.

Cetaceans face the challenge of maintaining equilibrium underwater and obtaining sensory input within a dense, low-visibility medium. The cetacean ear represents a key innovation that marked their evolution from terrestrial artiodactyls to among the most fully aquatic mammals in existence. Using micro-CT and histological data, we document shape and size changes in the cetacean inner ear during ontogeny, and demonstrate that, as a proportion of gestation time, the cetacean inner ear is precocial in its growth compared with that of suid artiodactyls. Cetacean inner ears begin ossifying and reach near-adult shape as early as at 32% of the gestation period, and near-adult dimensions as early as at 27% newborn total length. Our earliest embryos with measurable inner ears (13% newborn length) exhibit a flattened cochlea (i.e. smaller distance from cochlear apex to round window) compared with later and adult stages. Inner ears of Sus scrofa have neither begun ossifying nor reached near-adult dimensions at 55% of the gestation period, but have an adult-like ratio of cochlear diameters to each other, suggesting an adult-like shape. The precocial development of the cetacean inner ear complements previous work demonstrating precocial development of other cetacean anatomical features such as the locomotor muscles to facilitate swimming at the moment of birth.

The hidden teeth of sloths: evolutionary vestiges and the development of a simplified dentition.

Xenarthrans are unique among mammals in retaining simplified teeth that are rootless and homodont, which makes it difficult to determine dental homologies. We apply computerized tomography to prenatal developmental series of extant sloths, Bradypus and Choloepus, to further elucidate the patterns of morphological variation in their dentition. We also propose new criteria based on sequences of dental mineralization, and the presence of vestigial teeth, to distinguish between caniniforms and postcaniniforms. We report for the first time the presence of vestigial incisors in Bradypus. We also show the presence of a vestigial tooth in front of the lower caniniform in both extant sloth genera and the existence of two generations for the upper caniniform in Choloepus. The study of their sequence of mineralization indicates that the lower and upper caniniform teeth are not homologous in sloths, and suggests that upper caniniforms are not homologous between the two extant sloth genera. Our results show that assessing the developmental processes and functional constraints remains crucial to understand the dental variations observed in sloths, and more generally, tooth class homology issues in mammals. Applied to the tooth row of all extinct sloths, these developmental data illuminate a potentially ancestral dental formula for sloths.

Jaw anatomy of Potamogale velox (Tenrecidae, Afrotheria) with a focus on cranial arteries and the coronoid canal in mammals.

Afrotheria is a strongly supported clade within placental mammals, but morphological synapomorphies for the entire group have only recently come to light. Soft tissue characters represent an underutilized source of data for phylogenetic analysis, but nonetheless provide features shared by some or all members of Afrotheria. Here, we investigate the developmental anatomy of Potamogale velox (Tenrecidae) with histological and computerized tomographic data at different ontogenetic ages, combined with osteological data from other mammals, to investigate patterns of cranial arterial supply and the distribution of the coronoid canal. Potamogale is atypical among placental mammals in exhibiting a small superior stapedial artery, a primary supply of the posterior auricular by the posterior stapedial artery, and the development of vascular plexuses (possibly with relevance for heat exchange) in the posterior and dorsal regions of its neck. In addition, the posterior aspect of Meckel's cartilage increases its medial deflection in larger embryonic specimens as the mandibular condyle extends mediolaterally during embryogenesis. We also map the distribution of the coronoid canal across mammals, and discuss potential confusion of this feature with alveoli of the posterior teeth. The widespread distribution of the coronoid canal among living and fossil proboscideans, sirenians, and hyracoids supports previous interpretations that a patent coronoid canal is a synapomorphy of paenungulates, but not afrotherians as a whole.

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.

Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157-170 Ma, crown Placentalia diverged 86-100 Ma, and crown Atlantogenata diverged 84-97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.

Convergence vs. Specialization in the ear region of moles (Mammalia).

We investigated if and how the inner ear region undergoes similar adaptations in small, fossorial, insectivoran-grade mammals, and found a variety of inner ear phenotypes. In our sample, afrotherian moles (Chrysochloridae) and the marsupial Notoryctes differ from most other burrowing mammals in their relatively short radii of semicircular canal curvature; chrysochlorids and fossorial talpids share a relatively long interampullar width. Chrysochlorids are unique in showing a highly coiled cochlea with nearly four turns. Extensive cochlear coiling may reflect their greater ecological dependence on low frequency auditory cues compared to talpids, tenrecids, and the marsupial Notoryctes. Correspondingly, the lack of such extensive coiling in the inner ear of other fossorial species may indicate a greater reliance on other senses to enable their fossorial lifestyle, such as tactile sensation from vibrissae and Eimer's organs. The reliance of chrysochlorids on sound is evident in the high degree of coiling and in the diversity of its mallear types, and may help explain the lack of any semiaquatic members of that group. The simplest mallear types among chrysochlorids are not present in the basal-most members of that clade, but all extant chrysochlorids investigated to date exhibit extensive cochlear coiling. The chrysochlorid ear region thus exhibits mosaic evolution; our data suggest that extensive coiling evolved in chrysochlorids prior to and independently of diversification in middle ear ossicle size and shape.

Phylogeny, paleontology, and primates: do incomplete fossils bias the tree of life?

Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here, we apply a heuristic means to assess how a fossil's incompleteness detracts from inferring its phylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated the extinction of living species by deleting an extant taxon's molecular data and keeping only those morphological characters present in actual fossils. The choice of characters present in a given living taxon (the subject) was defined by those present in a given fossil (the template). By measuring congruence between a well-corroborated phylogeny to those incorporating artificial fossils, and by comparing real vs. random character distributions and states, we tested the information content of paleontological datasets and determined if extinction of a living species leads to bias in phylogeny reconstruction. We found a positive correlation between fossil completeness and topological congruence. Real fossil templates sampled for 36 or more of the 360 available morphological characters (including dental) performed significantly better than similarly complete templates with random states. Templates dominated by only one partition performed worse than templates with randomly sampled characters across partitions. The template based on the Eocene primate Darwinius masillae performs better than most other templates with a similar number of sampled characters, likely due to preservation of data across multiple partitions. Our results support the interpretation that Darwinius is strepsirhine, not haplorhine, and suggest that paleontological datasets are reliable in primate phylogeny reconstruction.

Organized labor and the origins of the Occupational Safety and Health Act.

New Solutions is republishing this 1991 article by Robert Asher, which reviews the history of organized labor's efforts in the United States to secure health and safety protections for workers. The 1877 passage of the Massachusetts factory inspection law and the implementation of primitive industrial safety inspection systems in many states paralleled labor action for improved measures to protect workers' health and safety. In the early 1900s labor was focusing on workers' compensation laws. The New Deal expanded the federal government's role in worker protection, supported at least by the Congress of Industrial Organizations (CIO), but challenged by industry and many members of the U.S. Congress. The American Federation of Labor (AFL) and the CIO backed opposing legal and inspection strategies in the late 1940s and through the 1950s. Still, by the late 1960s, several unions were able to help craft the Occupational Safety and Health Act of 1970 and secure new federal protections for U.S. workers.

Ossification sequence and genetic patterning in the mouse axial skeleton.

We provide novel data on vertebral ontogeny in the mouse, the mammalian model-of-choice for developmental studies. Most previous studies on ossification sequences in mice have focused on pooled elements of the spine (cervicals, thoracics, lumbars, sacrals, and caudals). Here, we contribute data on ossification sequences in the neural arches and centra to provide a comparative basis upon which to evaluate mammalian diversity of the axial skeleton. In attempt to explain the ossification pattern observed, we compared our observations with the phenotype of Cdx over-expresser mice. We use high-resolution X-ray microtomography and clearing and staining techniques to quantify the precise sequential ossification pattern of the mouse spine. We show that micro-CT scans perform better in all cases whereas clearing and staining exhibit sensitivity to the presence of semi-opaque tissue. We observe that the centra of wild-type mice always ossify after neural arches and that the ossification of the neural arches proceeds from two loci. The ossification of the centra appears more complex, especially in the neck where ossification is delayed and does not just follow the order of the vertebrae along the anterior-posterior axis. Our findings also suggest that Cdx genes' expression levels may be involved in the delayed ossification in the neck centra.

Patterns of ossification in southern versus northern placental mammals.

Consensus on placental mammal phylogeny is fairly recent compared to that for vertebrates as a whole. A stable phylogenetic hypothesis enables investigation into the possibility that placental clades differ from one another in terms of their development. Here, we focus on the sequence of skeletal ossification as a possible source of developmental distinctiveness in "northern" (Laurasiatheria and Euarchontoglires) versus "southern" (Afrotheria and Xenarthra) placental clades. We contribute data on cranial and postcranial ossification events during growth in Afrotheria, including elephants, hyraxes, golden moles, tenrecs, sengis, and aardvarks. We use three different techniques to quantify sequence heterochrony: continuous method, sequence-ANOVA (analysis of variance) and event-paring/Parsimov. We show that afrotherians significantly differ from other placentals by an early ossification of the orbitosphenoid and caudal vertebrae. Our analysis also suggests that both southern placental groups show a greater degree of developmental variability; however, they rarely seem to vary in the same direction, especially regarding the shifts that differ statistically. The latter observation is inconsistent with the Atlantogenata hypothesis in which afrotherians are considered as the sister clade of xenarthrans. Interestingly, ancestral nodes for Laurasiatheria and Euarchontoglires show very similar trends and our results suggest that developmental homogeneity in some ossification sequences may be restricted to northern placental mammals (Boreoeutheria).

Development and embryonic staging in non-model organisms: the case of an afrotherian mammal.

Studies of evolutionary developmental biology commonly use 'model organisms' such as fruit flies or mice, and questions are often functional or epigenetic. Phylogenetic investigations, in contrast, typically use species that are less common and mostly deal with broad scale analyses in the tree of life. However, important evolutionary transformations have taken place at all taxonomic levels, resulting in such diverse forms as elephants and shrews. To understand the mechanisms underlying morphological diversification, broader sampling and comparative approaches are paramount. Using a simple, standardized protocol, we describe for the first time the development of soft tissues and some parts of the skeleton, using µCT-imaging of developmental series of Echinops telfairi and Tenrec ecaudatus, two tenrecid afrotherian mammals. The developmental timing of soft tissue and skeletal characters described for the tenrecids is briefly compared with that of other mammals, including mouse, echidna, and the opossum. We found relatively few heterochronic differences in development in the armadillo vs. tenrec, consistent with a close relationship of Xenarthra and Afrotheria. Ossification in T. ecaudatus continues well into the second half of overall gestation, resembling the pattern seen in other small mammals and differing markedly from the advanced state of ossification evident early in the gestation of elephants, sheep, and humans.

High morphological variation of vestibular system accompanies slow and infrequent locomotion in three-toed sloths.

The semicircular canals (SCs), part of the vestibular apparatus of the inner ear, are directly involved in the detection of angular motion of the head for maintaining balance, and exhibit adaptive patterns for locomotor behaviour. Consequently, they are generally believed to show low levels of intraspecific morphological variation, but few studies have investigated this assumption. On the basis of high-resolution computed tomography, we present here, to our knowledge, the first comprehensive study of the pattern of variation of the inner ear with a focus on Xenarthra. Our study demonstrates that extant three-toed sloths show a high level of morphological variation of the bony labyrinth of the inner ear. Especially, the variation in shape, relative size and angles of their SCs greatly differ from those of other, faster-moving taxa within Xenarthra and Placentalia in general. The unique pattern of variation in three-toed sloths suggests that a release of selection and/or constraints on their organ of balance is associated with the observed wide range of phenotypes. This release is coincident with their slow and infrequent locomotion and may be related, among other possible factors, to a reduced functional demand for a precise sensitivity to movement.

RUNX2 tandem repeats and the evolution of facial length in placental mammals.

BACKGROUND: When simple sequence repeats are integrated into functional genes, they can potentially act as evolutionary 'tuning knobs', supplying abundant genetic variation with minimal risk of pleiotropic deleterious effects. The genetic basis of variation in facial shape and length represents a possible example of this phenomenon. Runt-related transcription factor 2 (RUNX2), which is involved in osteoblast differentiation, contains a functionally-important tandem repeat of glutamine and alanine amino acids. The ratio of glutamines to alanines (the QA ratio) in this protein seemingly influences the regulation of bone development. Notably, in domestic breeds of dog, and in carnivorans in general, the ratio of glutamines to alanines is strongly correlated with facial length. RESULTS: In this study we examine whether this correlation holds true across placental mammals, particularly those mammals for which facial length is highly variable and related to adaptive behavior and lifestyle (e.g., primates, afrotherians, xenarthrans). We obtained relative facial length measurements and RUNX2 sequences for 41 mammalian species representing 12 orders. Using both a phylogenetic generalized least squares model and a recently-developed Bayesian comparative method, we tested for a correlation between genetic and morphometric data while controlling for phylogeny, evolutionary rates, and divergence times. Non-carnivoran taxa generally had substantially lower glutamine-alanine ratios than carnivorans (primates and xenarthrans with means of 1.34 and 1.25, respectively, compared to a mean of 3.1 for carnivorans), and we found no correlation between RUNX2 sequence and face length across placental mammals. CONCLUSIONS: Results of our diverse comparative phylogenetic analyses indicate that QA ratio does not consistently correlate with face length across the 41 mammalian taxa considered. Thus, although RUNX2 might function as a 'tuning knob' modifying face length in carnivorans, this relationship is not conserved across mammals in general.

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny.

The fossil record suggests a rapid radiation of placental mammals following the Cretaceous-Paleogene (K-Pg) mass extinction 65 million years ago (Ma); nevertheless, molecular time estimates, while highly variable, are generally much older. Early molecular studies suffer from inadequate dating methods, reliance on the molecular clock, and simplistic and over-confident interpretations of the fossil record. More recent studies have used Bayesian dating methods that circumvent those issues, but the use of limited data has led to large estimation uncertainties, precluding a decisive conclusion on the timing of mammalian diversifications. Here we use a powerful Bayesian method to analyse 36 nuclear genomes and 274 mitochondrial genomes (20.6 million base pairs), combined with robust but flexible fossil calibrations. Our posterior time estimates suggest that marsupials diverged from eutherians 168-178 Ma, and crown Marsupialia diverged 64-84 Ma. Placentalia diverged 88-90 Ma, and present-day placental orders (except Primates and Xenarthra) originated in a ∼20 Myr window (45-65 Ma) after the K-Pg extinction. Therefore we reject a pre K-Pg model of placental ordinal diversification. We suggest other infamous instances of mismatch between molecular and palaeontological divergence time estimates will be resolved with this same approach.