Ecometrics (functional trait macroecology) by P. David Polly
Globoal Ecology and Biogeography, 2022
Aim: Factors that make species resilient to climate change can be difficult to study with empiric... more Aim: Factors that make species resilient to climate change can be difficult to study with empirical data because conditions cannot be experimentally controlled. We used trait-based evolutionary ecological agent-based modelling to understand how dispersal, selection, extirpation, and other factors contribute to resilience under three climate change scenarios to test the extent to which high dispersal rate contributes to persistence of species and the extent to which they occupy large geographic ranges on an evolutionary timescale involving speciation, dispersal, gene flow, and extinction.
Geodiversitas, 2020
Cats possess some of the highest ankle gear ratios of any extant carnivorans, a feature that faci... more Cats possess some of the highest ankle gear ratios of any extant carnivorans, a feature that facili- tates leaping and sprinting involved in ambush predation and scansorial lifestyles. In today’s North American carnivoran communities, the high gear ratio of cats contributes to an overall high ecometric average for this trait and contributes strongly to measures of ecometric disparity at the community level. But cats were late additions to North American communities, arriving from Eurasia about 17 Ma at the end of the “cat gap”. This paper uses ecometric analysis to document changes in hindlimb functional diversity in North American carnivoran communities over the last 19 million years in order to better understand the roles of trait evolution, clade turnover, and environmental change in community assembly. To accomplish this, I look at the phylogenetic history of ankle gear ratios of cats and other carnivorans, and the history of their occupation of high gear ratio niches in North American communities. The primary focus is on the Great Plains, which experienced profound changes in vegetation and climate through this period. Across all Carnivoramorpha, including a variety of extinct clades, it was found that gear ratios range from 1.08 (with extant ursids and viver- rids and extinct miacids and barbourofelids, one of the three cat groups considered in this paper, having the lowest values) to 1.46 (with extant felids, herpestids, and canids having the highest val- ues). Using the fossil record combined with phylogenetic ancestor reconstruction, it is shown that stem carnivorans and early felids had gear ratios about halfway between these extremes, consistent with a semidigitigrade or mildly digitigrade stance that was not overly specialized for either leaping or sprinting. Barbourofelids and some machairodontines evolved lower gear ratios that emphasized mechanical efficiency over advantage. When cats first entered North American communities in the Miocene they did not occupy high gear ratio niches and, in fact, occupied some of the lowest gear ratio niches during the Barstovian, Clarendonian, and Hemphillian. A major restructuring of gear ratio distributions in North American carnivoran communities occurred during the Blancan that appears to have resulted from clade sorting processes involving the selective loss of low gear ratio groups, as well as the evolution of increased gear ratios in felids and canids.
Methods in Paleoecology: Reconstructing Cenozoic Terrestrial Environments and Ecological Communities, 2018
Ecometrics is a trait-based approach to study ecosystem variability through time. An ecometric va... more Ecometrics is a trait-based approach to study ecosystem variability through time. An ecometric value is derived from describing the distribution of functional traits at the community level, which may arise by environmental filtering, extinction, or convergence. An ecometric relationship describes the correspondence between spatially explicit ecometric values and corresponding environmental variation. Transfer functions and maximum likelihood approaches have been developed with modern trait-environment relationships to reconstruct paleotemperature, paleoprecipitation, and paleovegetation cover given the distribution of functional traits within a community. Because the focus for this approach is on the traits and not on species, it is transferable through space and time and can be used to compare novel communities. In this paper we review the concepts and history of ecometric analysis and then describe practical methods for implementing an ecometric study.
Ecometrics is a trait-based approach to study ecosystem variability through time. An ecometric va... more Ecometrics is a trait-based approach to study ecosystem variability through time. An ecometric value is derived from describing the distribution of functional traits at the community level, which may arise by environmental filtering, extinction, or convergence. An ecometric relationship describes the correspondence between spatially explicit ecometric values and corresponding environmental variation. Transfer functions and maximum likelihood approaches have been developed with modern trait-environment relationships to reconstruct paleotemperature, paleoprecipitation, and paleovegetation cover given the distribution of functional traits within a community. Because the focus for this approach is on the traits and not on species, it is transferable through space and time and can be used to compare novel communities. In this paper we review the concepts and history of ecometric analysis and then describe practical methods for implementing an ecometric study.
Background: Ecometric patterning is the sorting of mean values of functional traits in communitie... more Background: Ecometric patterning is the sorting of mean values of functional traits in communities in space through time at continental scales. Ecometric patterns can emerge from intraspecific population-level processes (selection along an environmental gradient), species-level processes (geographic sorting of species based on functional trait differences), or clade-level processes (geographic sorting based on phylogenetically shared traits). We analysed a hind limb ratio related to locomotion in carnivores (Mammalia, Carnivora) to determine (1) whether its ecometric patterning involves intraspecific population-level evolutionary processes; (2) whether ecometric patterning is produced by clade sorting processes; and (3) how ecometric patterns are altered by species turnover during glacial–interglacial cycles. Data: We analysed (1) intraspecific variation in hind limb ratio in five species to evaluate the importance of population-level processes in ecometric patterning; (2) the distributions of ratios within and among communities to evaluate the importance of clade sorting; and (3) the distributions of ratios of seven glacial fossil assemblages to evaluate temporal dynamics in ecometric patterns. We also analysed three-dimensional calcaneum shape to assess the strength of phylogenetic and functional components of hind limb variation. Analytical methods: Geometric morphometrics, phylogenetic comparative methods, and phylogenetic community assembly methods were used to evaluate trait-based clade sorting; RLQ analysis was used to measure the correlation between vegetation openness, spatial scale, species occurrences, phylogeny, and hind limb traits; and trait space was used to analyse turnover between glacial and extant carnivore communities. Results: Population-level selection is either too weak or ineffective to produce hind limb trait gradients within carnivore species; however, clade-level trait-based sorting has a strong impact on community-level trait distributions. RLQ analysis demonstrates that clade membership interacts with hind limb ratios and vegetation openness in carnivore community assembly. Glacial–interglacial cycles produced turnover in faunas and hind limb trait distributions regardless of location or biome.
BACKGROUND: The pace and magnitude of human-caused global change has accelerated dramatically ove... more BACKGROUND: The pace and magnitude of human-caused global change has accelerated dramatically over the past 50 years, overwhelming the capacity of many ecosystems and species to maintain themselves as they have under the more stable conditions that prevailed for at least 11,000 years. The next few decades threaten even more rapid transformations because by 2050, the human population is projected to grow by 3 billion while simultaneously increasing per capita consumption. Thus, to avoid losing many species and the crucial aspects of ecosystems that we need—for both our physical and emotional well-being—new conservation paradigms and integration of information from conservation biology, paleobiology, and the Earth sciences are required.
The Paleontological Society Papers, 21, 2015
Ecometrics is the quantitative study of functional traits at the community level, and the environ... more Ecometrics is the quantitative study of functional traits at the community level, and the environmental sorting of those traits at regional and continental scales. Functional traits are properties of
organisms that have a direct physical or physiological relationship to an underlying quality of the environment, which in turn has indirect links to broader environmental factors such as temperature, precipitation, elevation, atmospheric composition, or sea level. When the same environmental factor affects the performance of many taxa, ecometric sorting is the result. Ecometric patterns in trait distributions across space and through time are therefore a product of biogeographic sorting, evolution, and extinction driven by changes in Earth systems. We review concepts associated with ecometrics, with examples that illustrate how trait-based approaches differ from taxon-based methods, how ecometrics can be used to study Earth-life transitions in the fossil record, and how ecometrics can be used to compare Earth-life transitions that differ in temporal or geographic scale. This paper focuses on the climatic and biome changes of the Great Plains of North America during the Miocene, when grasslands came to be the dominant vegetation type, and of the Anthropocene of the American Midwest, which saw extensive landscape changes in the nineteenth century.
Ecometric patterning is community-level sorting of functional traits along environmental gradient... more Ecometric patterning is community-level sorting of functional traits along environmental gradients that arises historically by geographic sorting, trait evolution, and extinction. We developed a stochastic model to explore how ecometric patterns and clade dynamics emerge from microevolutionary processes. Strong selection, high probability of extirpation, and high heritability led to strong ecometric patterning, but high rates of dispersal and weak selection do not. Phylogenetic structuring arose only when selection intensity, dispersal, and extirpation are all high. Ancestry and environmental geography produced historical effects on patterns of trait evolution and local diversity of species, but ecometric patterns appeared to be largely deterministic. Phylogenetic trait correlations and clade sorting appear to arise more easily in changing environments than static ones. Microevolutionary parameters and historical factors both affect ecometric lag time and thus balance between extinction, adaptation, and geographic reorganization as responses to climate change.
Climate change research is increasingly focusing on the dynamics among species, ecosystems and cl... more Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by differences in their temporal and geographical scales. One productive way to unite data across scales is the study of functional morphological traits, which can form a common denominator for studying interactions between species and climate across taxa, across ecosystems, across space and through time—an approach we call ‘ecometrics’. The sampling methods that have become established in palaeontology to standardize over different scales can be synthesized with tools from community ecology and climate change biology to improve our understanding of the dynamics among species, ecosystems, climates and earth systems over time. Developing these approaches into an integrative climate change biology will help enrich our understanding of the changes our modern world is undergoing.
That ankle posture in Carnivora is linked to substrate is well known. Large species from open se... more That ankle posture in Carnivora is linked to substrate is well known. Large species from open settings like grasslands are often cursorial with digitigrade stance, whereas smaller species from closed woodlands are often arboreal with plantigrade or semidigitigrade stance. Digitigrade species typically have feet that are proportionally longer than plantigrade species. It is less well known that the proportional length of the foot varies within mammalian species according to substrate, as demonstrated by previous authors. Taken together, these two observations suggest that a simple index of digitigrady calculated either for a single species or an entire fauna across a broad geographic range could reveal variation in palaeocommunity types.
Here, 135 terrestrial carnivoran species were studied to determine whether three index ratios were associated with locomotor habit and posture: (1) the femur/metatarsal III; (2) the in-lever to the out-lever of the calcaneum; and (3) the position of the sustentacular facet (measured from the proximal end of the calcaneum) to the total length of the calcaneum. All three indices were correlated with posture, all but the second were correlated with locomotor habit, and all were correlated with taxonomic family. The third index was associated with posture and is easily measured in fossil speciemens and so was chosen as an ecomorphological “gear ratio” index.
The calcaneal gear ratio was measured in 45 out of 49 North American carnivoran species and used to estimate the mean gear ratio at points spaced 50 km apart across the whole continent. Mean gear ratio in carnivorans was highly correlated with ecological province (the latter explained 70% of the geographic variance in mean gear ratio), mean annual temperature (which explained 48% of variance), and vegetation cover (49% of variance). Mean calcaneal gear ratio was not correlated with number of carnivoran species (which explained 5% of variance), elevation (7% of variance), or mean annual precipitation (1% of variance). The potential for mean gear ratio in carnivorans to be a proxy for ecological province, vegetation cover, or palaeotemperature is strong.
Morphological traits that have a functional relationship with the environment can be used to stud... more Morphological traits that have a functional relationship with the environment can be used to study relationships between organisms and environments through time and across space. Dynamics of the trait-environment complex can be studied with ecometrics in individuals, in populations, and in communities. We
explored how closely correlated three skeletal traits are with substrate use, and thus macrohabitat, among communities of snakes with the goal of better understanding how climate and macrovegetation might affect snake assemblages. Substrate use
explained a large part of the variance in mean length-to-width ratio of vertebrae (R2 ¼ 0.66), PC1 of vertebral shape of a mid trunk vertebra (R2 ¼ 0.46), and relative tail length (R2 ¼ 0.71). Furthermore, mean relative tail length in snake
assemblages across North America is strongly associated with ecoregions and vegetation cover (R2 ¼ 0.65 and 0.47, respectively). The close relationship with macrovegetation makes relative tail length a useful tool for predicting how snake assemblages will change as climates and biomes change across space or through
time. This “ecometric” approach provides a medium-scale link between data collected from ecological studies over decades to data assembled from the fossil record over thousands, tens of thousands, or even millions of years. We show how historical vegetation changes between the early twentieth and twenty-first centuries at five preserves in North America resulted in ecometric changes that parallel the geographic distribution of relative tail length in snake communities across North America.
Ecometrics is the study of the relationship between organismal traits and environments. This stud... more Ecometrics is the study of the relationship between organismal traits and environments. This study used Monte Carlo methods to assess the effects of extinction, extirpation, and exotic species on ecometric correlations at the continental scale. These potentially confounding processes arise from anthropogenic activities, taphonomic biases in fossil assemblages, and selective mass extinctions. Random, independent local extinctions introduced a predictable downward bias in ecometric correlations, which can be corrected by rarefaction if correlations are being estimated from fossil assemblages. Random global extinctions on species have a less predictable effect on ecometric correlations and introduce pronounced effects if more than 25% of the continental fauna is affected; however, global extinctions do not bias the estimation of R2 even though they increase its uncertainty. Selective extinction and introduction of exotic species had little impact on ecometric correlations, though caution is urged in generalizing this result.
We outline here an approach for understanding the biology of climate change, one that integrates ... more We outline here an approach for understanding the biology of climate change, one that integrates data at multiple spatial and temporal scales. Taxon-free trait analysis, or " ecometrics, " is based on the idea that the distribution in a community of ecomorphological traits such as tooth structure, limb proportions, body mass, leaf shape, incubation temperature, claw shape, any aspect of anatomy or physiology can be measured across some subset of the organisms in a community. Regardless of temporal or spatial scale, traits are the means by which organisms interact with their environment, biotic and abiotic. Ecometrics measures these interactions by focusing on traits which are easily measurable, whose structure is closely related to their function, and whose function interacts directly with local environment. Ecometric trait distributions are thus a comparatively universal metric for exploring systems dynamics at all scales. The main challenge now is to move beyond investigating how future climate change will affect the distribution of organisms and how it will impact ecosystem services and to shift the perspective to ask how biotic systems interact with changing climate in general, and how climate change affects the interactions within and between the components of the whole biotic-physical system. We believe that it is possible to provide believable, quantitative answers to these questions. Because of this we have initiated an IUBS program iCCB (integrative Climate Change Biology).
Fossil discoveries over the past 30 years have radically transformed traditional views of Mesozoi... more Fossil discoveries over the past 30 years have radically transformed traditional views of Mesozoic mammal evolution. In addition, recent research provides a more detailed account of the Cretaceous diversification of flowering plants. Here, we examine patterns of morphological disparity and functional morphology associated with diet in early mammals. Two analyses were performed: (i) an examination of diversity based on functional dental type rather than higher-level taxonomy, and (ii) a morphometric analysis of jaws, which made use of modern analogues, to assess changes in mammalian morphological and dietary disparity. Results demonstrate a decline in diversity of molar types during the mid-Cretaceous as abundances of triconodonts, symmetrodonts, docodonts and eupantotherians diminished. Multituberculates experience a turnover in functional molar types during the mid-Cretaceous and a shift towards plant-dominated diets during the late Late Cretaceous. Although therians undergo a taxonomic expansion coinciding with the angiosperm radiation, they display small body sizes and a low level of morphological disparity, suggesting an evolutionary shift favouring small insectivores. It is concluded that during the mid-Cretaceous, the period of rapid angiosperm radiation, mammals experienced both a decrease in morphological disparity and a functional shift in dietary morphology that were probably related to changing ecosystems.
Evolutionary Process by P. David Polly
Palaeontology, 2019
Evolution is a fundamentally population level process in which variation, drift and selection pro... more Evolution is a fundamentally population level process in which variation, drift and selection produce both temporal and spatial patterns of change. Statistical model fitting is now commonly used to estimate which kind of evolutionary process best explains patterns of change through time using models like Brownian motion, stabilizing selection (Ornstein-Uhlenbeck) and directional selection on traits measured from stratigraphic sequences or on phylogenetic trees. But these models assume that the traits possessed by a species are homogeneous. Spatial processes such as dispersal, gene flow and geographical range changes can produce patterns of trait evolution that do not fit the expectations of standard models, even when evolution at the local-population level is governed by drift or a typical OU model of selection. The basic properties of population level processes (variation, drift, selection and population size) are reviewed and the relationship between their spatial and temporal dynamics is discussed. Typical evolutionary models used in palaeontology incorporate the temporal component of these dynamics, but not the spatial. Range expansions and contractions introduce rate variability into drift processes, range expansion under a drift model can drive directional change in trait evolution, and spatial selection gradients can create spatial variation in traits that can produce long-term directional trends and punctuation events depending on the balance between selection strength, gene flow, extirpation probability and model of speciation. Using computational modelling that spatial processes can create evolutionary outcomes that depart from basic population-level notions from these standard macroevolutionary models.
The developmental gene expression, morphogenesis, and population variation in mammalian molar tee... more The developmental gene expression, morphogenesis, and population variation in mammalian molar teeth has become increasingly well understood, providing a model system for synthesizing evolution and developmental genetics. In this study, we estimated additive genetic covariances in molar shape (G) using parent-offspring regression in Cryptotis parva, the Least Shrew. We found that crown shape had an overall h 2 value of 0.34 (±0.08), with higher heritabilities in molar cusps than notches. We compared the genetic covariances to phenotypic (P) and environmental (E) covariances, and to the covariances in crown features expected from the enamel knot developmental cascade (D). We found that G and D were not strongly correlated and that major axes of G (evolutionary lines of least resistance) are better predictors of evolutionary divergences in soricines than is D. We conclude that the enamel knot cascade does impose constraints on the evolution of molar shape, but that it is so permissive that the divergences among soricines (whose last common ancestor lived about 14 million years ago) do not fully explore its confines. Over tens of millions of years, G will be a better predictor of the major axes of evolution in molar shape than D.
Background: Efficient gene expression involves a trade-off between (i) premature termination of p... more Background: Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results: In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences.
Modern morphometrics, especially geometric morphometrics, is a powerful tool for modeling the evo... more Modern morphometrics, especially geometric morphometrics, is a powerful tool for modeling the evolution and development of the phenotype. Complicated morphological transformations can be simulated by using standard evolutionary genetic equations for processes such as selection and drift in the same morphospaces that are used for empirical morphometric studies. Such applications appear to be consistent with the theory of quantitative evolution of the phenotype. Nevertheless, concerns exist whether simulations of phenotypic changes directly in morphospaces is realistic because trajectories traced in such spaces describe continuous gradations in the phenotype and because the gain and loss of structures is often impossible because morphospaces are necessarily constructed from variables shared in common by all the phenotypes being considered. Competing models of phenotypic change emphasize morphological discontinuity and novelty. Recently developed models of phenotypic evolution that introduce a “phenotypic landscape” between evolutionary genetic constructs like the adaptive landscape and morphospace may correct this shortcoming.
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Ecometrics (functional trait macroecology) by P. David Polly
organisms that have a direct physical or physiological relationship to an underlying quality of the environment, which in turn has indirect links to broader environmental factors such as temperature, precipitation, elevation, atmospheric composition, or sea level. When the same environmental factor affects the performance of many taxa, ecometric sorting is the result. Ecometric patterns in trait distributions across space and through time are therefore a product of biogeographic sorting, evolution, and extinction driven by changes in Earth systems. We review concepts associated with ecometrics, with examples that illustrate how trait-based approaches differ from taxon-based methods, how ecometrics can be used to study Earth-life transitions in the fossil record, and how ecometrics can be used to compare Earth-life transitions that differ in temporal or geographic scale. This paper focuses on the climatic and biome changes of the Great Plains of North America during the Miocene, when grasslands came to be the dominant vegetation type, and of the Anthropocene of the American Midwest, which saw extensive landscape changes in the nineteenth century.
Here, 135 terrestrial carnivoran species were studied to determine whether three index ratios were associated with locomotor habit and posture: (1) the femur/metatarsal III; (2) the in-lever to the out-lever of the calcaneum; and (3) the position of the sustentacular facet (measured from the proximal end of the calcaneum) to the total length of the calcaneum. All three indices were correlated with posture, all but the second were correlated with locomotor habit, and all were correlated with taxonomic family. The third index was associated with posture and is easily measured in fossil speciemens and so was chosen as an ecomorphological “gear ratio” index.
The calcaneal gear ratio was measured in 45 out of 49 North American carnivoran species and used to estimate the mean gear ratio at points spaced 50 km apart across the whole continent. Mean gear ratio in carnivorans was highly correlated with ecological province (the latter explained 70% of the geographic variance in mean gear ratio), mean annual temperature (which explained 48% of variance), and vegetation cover (49% of variance). Mean calcaneal gear ratio was not correlated with number of carnivoran species (which explained 5% of variance), elevation (7% of variance), or mean annual precipitation (1% of variance). The potential for mean gear ratio in carnivorans to be a proxy for ecological province, vegetation cover, or palaeotemperature is strong.
explored how closely correlated three skeletal traits are with substrate use, and thus macrohabitat, among communities of snakes with the goal of better understanding how climate and macrovegetation might affect snake assemblages. Substrate use
explained a large part of the variance in mean length-to-width ratio of vertebrae (R2 ¼ 0.66), PC1 of vertebral shape of a mid trunk vertebra (R2 ¼ 0.46), and relative tail length (R2 ¼ 0.71). Furthermore, mean relative tail length in snake
assemblages across North America is strongly associated with ecoregions and vegetation cover (R2 ¼ 0.65 and 0.47, respectively). The close relationship with macrovegetation makes relative tail length a useful tool for predicting how snake assemblages will change as climates and biomes change across space or through
time. This “ecometric” approach provides a medium-scale link between data collected from ecological studies over decades to data assembled from the fossil record over thousands, tens of thousands, or even millions of years. We show how historical vegetation changes between the early twentieth and twenty-first centuries at five preserves in North America resulted in ecometric changes that parallel the geographic distribution of relative tail length in snake communities across North America.
Evolutionary Process by P. David Polly
organisms that have a direct physical or physiological relationship to an underlying quality of the environment, which in turn has indirect links to broader environmental factors such as temperature, precipitation, elevation, atmospheric composition, or sea level. When the same environmental factor affects the performance of many taxa, ecometric sorting is the result. Ecometric patterns in trait distributions across space and through time are therefore a product of biogeographic sorting, evolution, and extinction driven by changes in Earth systems. We review concepts associated with ecometrics, with examples that illustrate how trait-based approaches differ from taxon-based methods, how ecometrics can be used to study Earth-life transitions in the fossil record, and how ecometrics can be used to compare Earth-life transitions that differ in temporal or geographic scale. This paper focuses on the climatic and biome changes of the Great Plains of North America during the Miocene, when grasslands came to be the dominant vegetation type, and of the Anthropocene of the American Midwest, which saw extensive landscape changes in the nineteenth century.
Here, 135 terrestrial carnivoran species were studied to determine whether three index ratios were associated with locomotor habit and posture: (1) the femur/metatarsal III; (2) the in-lever to the out-lever of the calcaneum; and (3) the position of the sustentacular facet (measured from the proximal end of the calcaneum) to the total length of the calcaneum. All three indices were correlated with posture, all but the second were correlated with locomotor habit, and all were correlated with taxonomic family. The third index was associated with posture and is easily measured in fossil speciemens and so was chosen as an ecomorphological “gear ratio” index.
The calcaneal gear ratio was measured in 45 out of 49 North American carnivoran species and used to estimate the mean gear ratio at points spaced 50 km apart across the whole continent. Mean gear ratio in carnivorans was highly correlated with ecological province (the latter explained 70% of the geographic variance in mean gear ratio), mean annual temperature (which explained 48% of variance), and vegetation cover (49% of variance). Mean calcaneal gear ratio was not correlated with number of carnivoran species (which explained 5% of variance), elevation (7% of variance), or mean annual precipitation (1% of variance). The potential for mean gear ratio in carnivorans to be a proxy for ecological province, vegetation cover, or palaeotemperature is strong.
explored how closely correlated three skeletal traits are with substrate use, and thus macrohabitat, among communities of snakes with the goal of better understanding how climate and macrovegetation might affect snake assemblages. Substrate use
explained a large part of the variance in mean length-to-width ratio of vertebrae (R2 ¼ 0.66), PC1 of vertebral shape of a mid trunk vertebra (R2 ¼ 0.46), and relative tail length (R2 ¼ 0.71). Furthermore, mean relative tail length in snake
assemblages across North America is strongly associated with ecoregions and vegetation cover (R2 ¼ 0.65 and 0.47, respectively). The close relationship with macrovegetation makes relative tail length a useful tool for predicting how snake assemblages will change as climates and biomes change across space or through
time. This “ecometric” approach provides a medium-scale link between data collected from ecological studies over decades to data assembled from the fossil record over thousands, tens of thousands, or even millions of years. We show how historical vegetation changes between the early twentieth and twenty-first centuries at five preserves in North America resulted in ecometric changes that parallel the geographic distribution of relative tail length in snake communities across North America.
The evolution of molar tooth morphology in shrews is simulated under four different evolutionary modes: (1) randomly fluctuating selection; (2) directional selection; (3) stabilizing selection; and (4) genetic drift. Each of these modes leaves a distinctive imprint on the distribution of morphological distances that can be used to reconstruct the mode from real comparative data. A comparison of the results with real data on shrew molar diversity suggests that teeth have evolved predominantly by randomly fluctuating selection. The rate of divergence in shrew molars is greater than expected under drift, but it is neither linear nor static as expected with directional or stabilizing selection.
The evolution of morphology with randomly fluctuating selection is also simulated on a phylogenetic tree. Daughter species share derived morphologies and positions within the principal components spaces within which the simulation is run. This result suggests that phylogeny can be successfully reconstructed from multivariate morphometric data when they have evolved under any mode except strong stabilizing selection.
A redefined adaptive zone concept was used to explain the relative effects of ecological adaptation and common ancestry in phylogeny reconstruction from quantitative morphological data. As used here, an adaptive zone is a bounded range of phenotypes linked to specific functional roles, a definition that emphasizes morphology rather than environment or fitness. The following criteria were proposed for testing for the existence of an adaptive zone: (1) the zone must be occupied by real taxa; (2) their phenotypes must lie within a limited morphospace whose major axes are associated with functional factors; (3) the zone’s occupants must have diversified throughout the zone without crossing its boundaries except through a major change in lifestyle, and (4) phenotypes that lie outside the zone must be functionally incompatible with the functions associated with the zone axes. Criterion 3 requires that the phylogeny of the group be independently known, at least in part.
The shape of the calcaneum and astragalus were analyzed using a new technique for 3D surfaces. Bone surfaces were represented as a quadrilateral grids of points applied to the surface of the scanned object. The technique for placing the grid was modified from Eigenshape outline analysis. The point grids were superimposed using Procrustes ordination and analyzed using the standard statistical procedures used in analysis of Cartesian landmarks. The new method allows results to be illustrated as shaded three-dimensional bones rather than constellations of landmarks or numeric data tables.
Variation in tarsal morphology was found to be associated with stance, number of digits, and locomotor type. The long held opinion that intertarsal mobility is enhanced by disparity in size and curvature of occluding facets was not supported. Ancestral morphotypes of the calcaneum and astragalus were reconstructed using GLM algorithms. The reconstruction at the base of the carnivoran tree had a morphology compatible with five digit, digitigrade or semidigitigrade terrestrial locomotion, a hypothesis consistent with the earliest carnivoran fossil taxa. Fissiped tarsals fell within an adaptive zone whose major phenotypic axes were associated with intertarsal mobility, stance, and locomotor type. During their phylogenetic history, fissiped clades crossed the adaptive zone space many times as different clades convergently evolved locomotor specializations. The only lineage to pass through the boundaries of the adaptive zone morphospace was that leading to the pinniped Phoca. Pinnipeds acquired their derived morphology by colonizing new regions of shape space, but not by evolving more quickly than fissiped clades. Evolution within the adaptive zone is an example of an Ornstein-Uhlenbeck process, which erases deep phylogenetic history. Consequently, phylogenetic patterns are unlikely to be accurately reconstructed from quantitative representations of tarsal shape for species whose last common ancestor is older than 5 to 15 million years.
common ancestor of Neanderthals and modern humans ([N-MH]
LCA). Recently developed analytical techniques now allow this
problem to be addressed using a probabilistic morphological framework.
This study provides a quantitative reconstruction of the
expected dental morphology of the [N-MH]LCA and an assessment
of whether known fossil species are compatible with this ancestral
position. We show that no known fossil species is a suitable candidate
for being the [N-MH]LCA and that all late Early and Middle
Pleistocene taxa from Europe have Neanderthal dental affinities,
pointing to the existence of a European clade originated around
1 Ma. These results are incongruent with younger molecular divergence
estimates and suggest at least one of the following must be
true: (i) European fossils and the [N-MH]LCA selectively retained
primitive dental traits; (ii) molecular estimates of the divergence
between Neanderthals and modern humans are underestimated;
or (iii) phenotypic divergence and speciation between both species
were decoupled such that phenotypic differentiation, at least in
dental morphology, predated speciation.
The functional diversity of mammal limbs is facilitated by sometimes subtle structural differences. A small discrepancy in the proportion of one limb segment and its distal neighbor can translate into significant disparity in running speed. The position of a muscle insertion along a long bone shaft can make the difference between a mammal that can tear its way through thick turf and one that cannot. The fusion of two bones in the forearm or wrist may mean that one animal cannot turn its palm to grasp a limb as it tries to climb, while another species can easily wrap its forelimbs around a tree trunk and scamper to safety. A large part of a mammal's lifestyle can, therefore, be read in the structure of its limbs.
This chapter first reviews the anatomical structure of the mammalian limb. Some brief mention of comparative differences is made in relation to structure, but those are reserved for the most striking ones in which the number of elements differs or the structure of homologous elements is particularly diverse. Special emphasis is given to the structures that are most obviously related to function. The chapter then reviews the functional diversity of the mammalian limb from the perspective of gross ecomorphological categories, groups that are primarily locomotory in nature. The chapter then reviews aspects of variation, genetics, and development of the mammalian limb. Finally, the early evolution of the mammalian limb is reviewed.
Stratocladistics offers some solutions to these problems because it operates in the universe of phylogenetic trees rather than cladograms—the monophyly and paraphyly of taxa are determined as a result of analysis rather than included as assumptions. This is possible because the basic units of analysis are lineage segments rather then lineages and because Fisher’s total parsimony debt allows the evaluation of hypotheses that alternatively place a taxon in a terminal position or as part of a continuous lineage.
This, in turn, allows species definitions such as Simpson’s evolutionary species to be operationalized in a cladistic framework. The definition of a species-level taxon can be separated from its morphological diagnosis using a formula like the following: a species is the set of ancestor-descendant populations that occurred between speciation (cladogenic) events. Typological problems associated with many morphological species definitions, including those relying on autapomorphies, are thus avoided.
This method is applied to a revision of Clarkforkian and Wasatchian viverravid carnivorans from the Bighorn and Clarks Fork basins, Wyoming. It is concluded that seven species, one new, were present: Viverravus laytoni, V. acutus, V. rosei (sp. nov.), V. politus, Didymictis proteus, D. leptomylus, and D. protenus. The species Protictis laytoni is referred to the genus Viverravus and synonymized with V. bowni. Furthermore, P. dellensis is found to be conspecific with D. proteus and the two are synonymized under the latter name. For the same reason, P. schaffi is synonymized with V. politus. The taxon Didymictida is rejected. The species V. acutus is concluded to be sexually dimorphic with high variability in linear measurements of its dentition.
paleontology. Every published paper, master’s thesis, and doctoral dissertation relies on these data to document patterns
and processes in evolution, ecology, taphonomy, geography, geologic time, and functional morphology, to name just a few. In
turn, the vertebrate paleontology community relies on published data in order to reproduce and verify others’ work, as well
as to expand upon published analyses in new ways without having to reconstitute data sets that have been used by earlier
authors and to accurately preserve data for future generations of researchers. Here, we review several databases that are of
interest to vertebrate paleontologists and strongly advocate for more deposition of basic research data in publicly accessible
databases by vertebrate paleontologists.
sequence of the Jebel Qatrani Formation and of the upper part of the Qasr el Sagha Formation is consistent with recent paleomagnetic dating that suggests that these rocks differ in age by only one to two million years.