P. David Polly

PHYLOGENETIC AND ENVIRONMENTAL COMPONENTS OF MORPHOLOGICAL VARIATION: SKULL, MANDIBLE, AND MOLAR SHAPE IN MARMOTS (MARMOTA, RODENTIA)

Abstract The phenotype is a product of its phylogenetic history and its recent adaptation to local environments, but the relative importance of the two factors is controversial. We assessed the effects of diet, habitat, elevation, tem‐perature, precipitation, body size, and mtDNA genetic divergence on shape variation in skulls, mandibles, and molars, structures that differ in their genetic and functional control. We asked whether these structures have adapted to environment to the same extent and whether they retain the same amount of phylogenetic signal. We studied these traits in intra‐ and interspecific populations of Eurasian marmots whose last common ancestor lived 2–5 million years ago. Path Analysis revealed that body size explained 10% of variation in skulls, 7% in mandibles, and 15% in molars. Local vegetation explained 7% of variation in skulls, 11% in mandibles, and 12% in molars. Dietary category explained 25% of variation in skulls, 11% in mandibles, and 9% in molars. Cyt b mtDNA divergence (phylogeny) explained 15% of variation in skulls, 7% in mandibles, and 5% in molars. Despite the percentages of phylogenetic variance, maximum‐likelihood trees based on molar and skull shape recovered most phylogenetic groupings correctly, but mandible shape did not. The good performance of molars and skulls was probably due to different factors. Skulls are genetically and functionally more complicated than teeth, and they had more mathematically independent components of variation (5‐6‐in skulls compared to 3‐in molars). The high proportion of diet‐related variance was not enough to mask the phylogenetic signal. Molars had fewer independent components, but they also have less ecophenotypic variation and evolve more slowly, giving each component a proportionally stronger phylogenetic signal. Molars require larger samples for each operational taxonomic unit than the other structures because the proportion of within‐taxon to between‐taxon variation was higher. Good phylogenetic signal in quantitative skeletal morphology is likely to be found only when the taxa have a common ancestry no older than hundreds of thousands or millions of years (1% to 10% mtDNA divergence)—under these conditions skulls and molars provide stronger signal than mandibles.

Paleontology and the Comparative Method: Ancestral Node Reconstructions versus Observed Node Values

Comparative methods are used to reconstruct ancestral node values for continuously varying traits. The confidence intervals (CIs) around such estimates may be wider than the range of tip data from which they are calculated. Without historical data with which to compare estimates, it is not clear whether such broad CIs reflect evolutionary lability or methodological imprecision. In this study, a fully resolved phylogeny of fossil carnivorans, in which observed samples are found not only at the tree tips but also along branches and at nodes, is used to compare observed ancestral node values with node estimates based on a Brownian motion model of evolution. As in previous studies, the CIs surrounding node estimates were wider than the range of tree tip values, but observed values fell well within them, reasonably close to the values predicted by comparative methods. Confidence intervals calculated using paleontological rate estimates were comparable to those calculated using only terminal taxa. This implies that evolution of at least some traits is conservative enough for node reconstruction techniques to be useful, despite their large standard errors. The Brownian motion model of evolutionary change was a good predictor of node values.

Variability, selection, and constraints; development and evolution in viverravid (Carnivora, Mammalia) molar morphology

Developmental constraints presumably operate by influencing patterns of variability: when development causes some features to vary more than others and when the level of variability is correlated with evolutionary change, then development can be said to constrain evolution. This idea was tested by examining the relationship between tooth variation and three other factors: developmental processes, tooth function, and evolutionary change. Data came from two lineages of viverravid carnivorans (Viverravidae, Carnivora) from the Paleogene of North America. Variability in cusp position was significantly correlated with position in the developmental cascade, with the amount of intercusp growth (when growth is relatively greater in some cusps than others), and with amount of evolutionary change. This indicates that tooth development exerts a local constraint on phenotypic variability and on the evolutionary response to functional selection, but comparative data suggest that the developmental constraint itself may evolve. Intense directional or stabilizing selection may modify the developmental cascade so that the constraint is either removed or modified to permit new evolutionary patterns. Thus development does not constrain evolution in an absolute sense, but rather introduces modifiable patterns of covariance among crown features. Both development and function seem to play important, intertwined roles in coordinating evolutionary change in mammalian molars.

Development and phenotypic correlations: the evolution of tooth shape in Sorex araneus

Summary Do morphogenetic processes cause common patterns of phenotypic covariation, and do those patterns evolve over microevolutionary timescales? Evolution of molar shape variance–covariance (P) matrixes was studied in five populations of the common shrew, Sorex araneus. P matrix evolution was assessed using matrix correlation, matrix disparity, and common principal component analysis (CPCA). Significant changes in covariance structure were found among the populations, but the differences were small. A computer model was used to estimate the theoretical covariance introduced into the phenotype by developmental interactions. Molar developmental processes explained some of the covariance in the shrew samples, especially as measured by matrix correlation, but the proportion was relatively small. Developmental principal components (PCs) were only infrequently associable with common principal components. The results suggest that molar shape P matrixes can evolve quickly in a manner only loosely constrained by development, and that their shared covariance is probably dominated by factors more proximate than development. Rarefaction showed that sample size severely affected P comparisons when n < 15 for matrix correlation and disparity, and when n < 30 for CPCA. Among CPCA evaluation criteria, Akaike Information Criterion performed better than jump‐up at n < 30, but worse at n > 30.

Selection in a cycling population : Differential response among skeletal traits

Abstract Population density cycles influence phenotypic evolution through both density‐dependent selection during periods of high density and through enhanced genetic drift during periods of low density. We investigated the response of different phenotypic traits to the same density cycles in a population of the yellow‐necked mouse, Apodemus flavicollis, from Białowieza National Park in Poland. We examined nonmetric skull traits, skull and mandible size, skull and mandible shape, and transferrin allele frequencies. We found that all of the traits changed significantly over the seven‐year study period. The greatest changes in nonmetric traits and mandible size occurred during periods of increasing density, and the magnitude of changes in skull and mandible shape was correlated with the magnitude of density changes. Frequencies of transferrin alleles changed the most when population density was in decline. Changes among the five phenotypic traits were generally uncorrelated with one another, except for skull and mandible shape. Nonmetric traits were selectively neutral when assessed with QST/FST analysis, whereas mandible size, mandible shape, and skull shape showed evidence of fairly strong selection. Selection on skull size was weak or nonexistent. We discuss how different assumptions about the genetic components of variance affect QST estimates when phenotypic variances are substituted for genetic ones. We also found that change in mandible size, mandible shape, skull size, and skull shape were greater than expected under a neutral model given reasonable assumptions about heritability and effective population size.

On the Occlusal Fit of Tribosphenic Molars: Are We Underestimating Species Diversity in the Mesozoic?

The complex occlusal fits between tribosphenic teeth are a rich source of information for taxonomic, phylogenetic, and evolutionary analysis. The degree of fit between upper and lower cheek teeth has been used to refer specimens to species-level taxa, but statistical data on occlusal fit in relation to taxonomic identity have been lacking. We used landmarks on upper and lower first molars of 20 bat populations representing 16 species to assess the degree of occlusal fit (1) between teeth from the same individual; (2) between teeth from different individuals belonging to the same populations; and (3) between teeth belonging to different populations. We found that the fit of teeth belonging to different populations was significantly worse than between those of the same population and that the degree of misfit increased linearly with time since common ancestry, albeit with substantial variance. We used our comparisons to assess the species-level diversity within Batodon, the smallest known placental mammal from the Cretaceous. Our data suggest, with caveats, that instead of belonging to a single species, the specimens assigned to Batodon represent at least two species as different as those belonging to different genera or families of living bats.

The Evolution of Enamel Microstructure: How Important Is Amelogenin?

The shape, size, and orientation of enamel prisms have heretofore been thought to be controlled solely by the shape of the Tomes process. It is known, however, that amelogenin proteins play an important role in enamel deposition and maturation and it is possible that they contribute independently to enamel structure. Using a phylogenetic framework, we clarify the role of amelogenin proteins in the formation of enamel microstructure. We found a negative association between evolutionary changes in amelogenin protein sequences and enamel complexity: amelogenin evolution slows as enamel complexity increases. This is probably because selective constraints on amelogenin increase as enamel complexity increases. Monotremes, which have lost their adult dentition, have particularly high rates of amelogenin evolution while rodents, which have very complex enamel, have very low rates. There is a positive correlation between the number of different amelogenin proteins in a given species and the complexity of its enamel microstructure. An increased number of amelogenins may be necessary for the formation of multiple enamel types in the same tooth. Alternative splicing of amelogenin exons, which allows multiple protein products to be produced from the same gene, may be a key innovation in the diversification of enamel microstructure.

Taxonomic and evolutionary pattern revisions resulting from geometric morphometric analysis of Pennsylvanian Neognathodus conodonts, Illinois Basin

Abstract. n Conodont fossils are highly valuable for Paleozoic biostratigraphy and for interpreting evolutionary change, but identifying and describing conodont morphologies, and characterizing gradual shape variation remain challenging. We used geometric morphometric (GM) analysis to conduct the first landmark-based morphometric analysis of the biostratigraphically useful conodont genus Neognathodus. Our objective is to assess whether previously defined morphotype groups are reliably distinct from one another. As such, we reevaluate patterns of morphologic change in Neognathodus P1elements, perform maximum-likelihood tests of evolutionary modes, and construct novel, GM-based biozonations through a Desmoinesian (Middle Pennsylvanian) section in the Illinois Basin. Our GM results record the entire spectrum of shape variability among Neognathodus morphotypes, thus alleviating the problem of documenting and classifying gradualmorphologic transitions betweenmorphotypes. Statistically distinct GM groups support previously established classifications of N. bassleri, N. bothrops, and N. roundyi. Statistically indistinct pairs of GM groups do not support literature designations of N. medadultimus and N. medexultimus, and N. dilatus and N. metanodosus, and we synonymize each pair. Maximum-likelihood tests of evolutionary modes provide the first statistical assessment of Neognathodus evolutionary models in the Desmoinesian. The most likely evolutionary models are an unbiased random walk or a general random walk. We name four distinct biozones through the Desmoinesian using GM results, and these align with previous biozonation structure based on the Neognathodus Index (NI), illustrating that Neognathodus-based biostratigraphic correlations would not change between GM or NI methods. The structural similarity between both biozonations showcases that determining GM-based biozones is not redundant, as this comparison validates using landmark-based GM work to construct viable biozonations for subsequent stratigraphic correlations.Although this study is limited to the Illinois Basin, our quantitativemethodology can be applied broadly to test taxonomic designations of additional genera, interpret statistically robust evolutionary patterns, and construct valid biozones for this significant chordate group.

Introduction: Paleomammalogy In Honor of Professor Emeritus William Alvin Clemens, Jr.

We paleontologists usually earn our keep by examining events of the ancient past. Decades—or even centuries—tend to be so inconsequential in our minds that we rarely give them a passing glance. Thus, on very special occasions such as this, it is good for our souls to examine just how far our own scientific discipline has come within recent history. To gain a little perspective, we arbitrarily focus on the past century and a half and examine how much influence a single individual can have upon a discipline through a span of less than 50 years. Our principal area of interest is paleomammalogy, and the primary person of interest is our former mentor, Professor Emeritus William A. Clemens. Bill’s first scientific contribution was an abstract that appeared in 1959, and his first regular publications appeared the following year. The year 1960, therefore, provides a convenient point of departure for our little exercise. Paleomammalogy already was an unmanageably large subject by 1960. More than 50,000 papers on fossil mammals had been published through the preceding century,3 with the topics reflecting new discoveries, changing theoretical priorities, and vacillations in global political agendas. In 1860, for example, the dominant theme had been the antiquity of humans. Studies of Neanderthal fossils, remnants of continental glacial ice, and successions of stone-tool industries engaged the educated. These elite scholars already were assimilating the antiquity of Earth, the extinction of species, and the transmutation of species through time by evolution. All those ideas were fresh then—and no older than Kimura’s neutral theory of evolution is today. Darwin’s Origin was only a year old. The debates between Thomas Henry Huxley and Archbishop Wilberforce took place in 1860, placing human origins prominently in the public eye. But stone tools and fossil men were not the only reports on fossil mammals appearing in 1860. Lightly interspersed were papers on Miocene fossils from Pikermi (French and English troops had been stationed there during the Crimean war of the preceding decade); ancient whales from southern Russia (industrial whaling was then heading to its climax,