Exploring the functional meaning of head shape disparity in aquatic snakes

Phenotypic diversity, or disparity, can be explained by simple genetic drift or, if functional constraints are strong, by selection for ecologically relevant phenotypes. We here studied phenotypic disparity in head shape in aquatic snakes. We investigated whether conflicting selective pressures related to different functions have driven shape diversity and explore whether similar phenotypes may give rise to the same functional output (i.e., many‐to‐one mapping of form to function). We focused on the head shape of aquatically foraging snakes as they fulfill several fitness‐relevant functions and show a large amount of morphological variability. We used 3D surface scanning and 3D geometric morphometrics to compare the head shape of 62 species in a phylogenetic context. We first tested whether diet specialization and size are drivers of head shape diversification. Next, we tested for many‐to‐one mapping by comparing the hydrodynamic efficiency of head shape characteristic of the main axes of variation in the dataset. We 3D printed these shapes and measured the forces at play during a frontal strike. Our results show that diet and size explain only a small amount of shape variation. Shapes did not fully functionally converge as more specialized aquatic species evolved a more efficient head shape than others. The shape disparity observed could thus reflect a process of niche specialization.     

Feeding ecology has a stronger evolutionary influence on functional morphology than on body mass in mammals

Ecological specialization is a central driver of adaptive evolution. However, selective pressures may uniquely affect different ecomorphological traits (e.g., size and shape), complicating efforts to investigate the role of ecology in generating phenotypic diversity. Comparative studies can help remedy this issue by identifying specific relationships between ecologies and morphologies, thus elucidating functionally relevant traits. Jaw shape is a dietary correlate that offers considerable insight on mammalian evolution, but few studies have examined the influence of diet on jaw morphology across mammals. To this end, I apply phylogenetic comparative methods to mandibular measurements and dietary data for a diverse sample of mammals. Especially powerful predictors of diet are metrics that capture either the size of the angular process, which increases with greater herbivory, or the length of the posterior portion of the jaw, which decreases with greater herbivory. The size of the angular process likely reflects sizes of attached muscles that produce jaw movements needed to grind plant material. Further, I examine the impact of feeding ecology on body mass, an oft-used ecological surrogate in macroevolutionary studies. Although body mass commonly increases with evolutionary shifts to herbivory, it is outperformed by functional jaw morphology as a predictor of diet. Body mass is influenced by numerous factors beyond diet, and it may be evolutionarily labile relative to functional morphologies. This suggests that ecological diversification events may initially facilitate body mass diversification at smaller taxonomic and temporal scales, but sustained selective pressures will subsequently drive greater trait partitioning in functional morphologies.     

Making pore choices: repeated regime shifts in stomatal ratio

Ecologically important traits do not evolve without limits. Instead, evolution is constrained by the set of available and viable phenotypes. In particular, natural selection may only favour a narrow range of adaptive optima constrained within selective regimes. Here, I integrate data with theory to test whether selection explains phenotypic constraint. A global database of 599 plant species from 94 families shows that stomatal ratio, a trait affecting photosynthesis and defence against pathogens, is highly constrained. Most plants have their stomata on the lower leaf surface (hypostomy), but species with half their stomata on each surface (amphistomy) form a distinct mode in the trait distribution. A model based on a trade-off between maximizing photosynthesis and a fitness cost of upper stomata predicts a limited number of adaptive solutions, leading to a multimodal trait distribution. Phylogenetic comparisons show that amphistomy is the most common among fast-growing species, supporting the view that CO₂ diffusion is under strong selection. These results indicate that selective optima stay within a relatively stable set of selective regimes over macroevolutionary time.     

A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates

Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account nonindependence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty, but approaches accounting for all of them are less common. Here, we show how Bayesian statistics facilitates this task while relaxing the homogeneous rate assumption of the well-known phylogenetic generalized least squares (PGLS) framework. This Bayesian formulation allows uncertainty about phylogeny, evolutionary regimes, or other statistical parameters to be taken into account for studies as simple as testing for coevolution in two traits or as complex as testing whether bursts of phenotypic change are associated with evolutionary shifts in intertrait correlations. A mixture of validation approaches indicates that the approach has good inferential properties and predictive performance. We provide suggestions for implementation and show its usefulness by exploring the coevolution of ankle posture and forefoot proportions in Carnivora.     

Adaptation,punctuation and information: a rate-distortion approach to non-cognitive 'learning plateaus' in evolutionary process

We extend recent information-theoretic phase transition approaches to evolutionary and cognitive process via the Rate Distortion and Joint Asymptotic Equipartition Theorems, in the circumstance of interaction with a highly structured environment. This suggests that learning plateaus in cognitive systems and punctuated equilibria in evolutionary process are formally analogous, even though evolution is not cognitive. Extending arguments by Adami et al. (2000), we argue that 'adaptation' is the process by which a distorted genetic image of a coherently structured environment is imposed upon a species.     

Factors contributing to the accumulation of reproductive isolation: A mixed model approach

The analysis of large datasets describing reproductive isolation between species has been extremely influential in the study of speciation. However, the statistical methods currently used for these data limit the ability to make direct inferences about the factors predicting the evolution of reproductive isolation. As a result, our understanding of iconic patterns and rules of speciation rely on indirect analyses that have clear statistical limitations. Phylogenetic mixed models are commonly used in ecology and evolution, but have not been applied to studies of reproductive isolation. Here I describe a flexible framework using phylogenetic mixed models to analyze data collected at different evolutionary scales, to test both categorical and continuous predictor variables, and to test the effect of multiple predictors on rates and patterns of reproductive isolation simultaneously. I demonstrate the utility of this framework by re‐analyzing four classic datasets, from both animals and plants, and evaluating several hypotheses that could not be tested in the original studies: In the Drosophila and Bufonidae datasets, I found support for more rapid accumulation of reproductive isolation in sympatric species pairs compared to allopatric species pairs. Using Silene and Nolana, I found no evidence supporting the hypothesis that floral differentiation elevates postzygotic reproductive isolation. The faster accumulation of postzygotic isolation in sympatry is likely the result of species coexistence determined by the level of postzygotic isolation between species. In addition, floral trait divergence does not appear to translate into pleiotropic effects on postzygotic reproductive isolation. Overall, these methods can allow researchers to test new hypotheses using a single statistical method, while remedying the statistical limitations of several previous methods.     

Abundance, distribution and life histories of grassland plants: a comparative study of 81 species

1 This study examines the abundance and distribution of grassland plant species in particular relation to features affecting colonization. Seed production (inversely related to seed size) and recruitment success (positively related) affect colonization ability, suggesting that seed size can be used as a key trait.
2 Data on seed size, dispersal mode, life form, geographical range size and abundance were gathered for 81 grassland plant species in a field study area in Sweden. Seed production and plant size were estimated for 69 of these species. Analyses were performed both across species, with species treated as independent data points, and for 43 'phylogenetically independent contrasts'.
3 The cross-species analyses suggested that local abundance was related to life forms but not dispersal or plant size. Perennials were generally most abundant, as were clonal species. If abundance reflects colonization we predicted that species with intermediately sized seeds (or intermediate seed production) would be most abundant, and this was supported by the phylogenetic contrast but not by cross-species analyses. In the former analysis, a high abundance of species was significantly associated with a small seed size deviation (and seed number deviation) from the median values of these traits in the community.
4 Local abundance, seed production and seed size deviation from the community median value were positively related to geographical range size in the cross-species analysis, but no relationships were seen in the phylogenetic contrast analysis.
5 We conclude that colonization processes do have a significant influence on abundance patterns in grasslands. Seed size is a key trait for colonizing ability, and the effects of the trade-off of seed size vs. seed number must be considered. No single mechanism can be identified that influences both abundance and geographical distribution range.     

Morphological integration and adaptation in the snake feeding system: a comparative phylogenetic study

A long-standing hypothesis for the adaptive radiation of macrostomatan snakes is that their enlarged gape--compared to both lizards and basal snakes--enables them to consume "large" prey. At first glance, this hypothesis seems plausible, or even likely, given the wealth of studies showing a tight match between maximum consumed prey mass and head size in snakes. However, this hypothesis has never been tested within a comparative framework. We address this issue here by testing this hypothesis in 12 monophyletic clades of macrostomatan snakes using recently published phylogenies, published maximum consumed prey mass data and morphological measurements taken from a large sample of museum specimens. Our nonphylogenetically corrected analysis shows that head width--independent of body size--is significantly related to mean maximum consumed prey mass among these clades, and this relationship becomes even more significant when phylogeny is taken into account. Therefore, these data do support the hypothesis that head shape is adapted to prey size in snakes. Additionally, we calculated a phylogenetically corrected morphological variance-covariance matrix to examine the role of morphological integration during head shape evolution in snakes. This matrix shows that head width strongly covaries with both jaw length and out-lever length of the lower jaw. As a result, selection on head width will likely be associated with concomitant changes in jaw length and lower jaw out-lever length in snakes.     

The narrow-leaf syndrome: a functional and evolutionary approach to the form of fog-harvesting rosette plants

Plants that use fog as an important water-source frequently have a rosette growth habit. The performance of this morphology in relation to fog interception has not been studied. Some first-principles from physics predict that narrow leaves, together with other ancillary traits (large number and high flexibility of leaves, caudices, and/or epiphytism) which constitute the “narrow-leaf syndrome” should increase fog-interception efficiency. This was tested using aluminum models of rosettes that differed in leaf length, width and number and were exposed to artificial fog. The results were validated using seven species of Tillandsia and four species of xerophytic rosettes. The total amount of fog intercepted in rosette plants increased with total leaf area, while narrow leaves maximized interception efficiency (measured as interception per unit area). The number of leaves in the rosettes is physically constrained because wide-leafed plants can only have a few blades. At the limits of this constraint, net fog interception was independent of leaf form, but interception efficiency was maximized by large numbers of narrow leaves. Atmospheric Tillandsia species show the narrow-leaf syndrome. Their fog interception efficiencies were correlated to the ones predicted from aluminum-model data. In the larger xerophytic rosette species, the interception efficiency was greatest in plants showing the narrow-leaf syndrome. The adaptation to fog-harvesting in several narrow-leaved rosettes was tested for evolutionary convergence in 30 xerophytic rosette species using a comparative method. There was a significant evolutionary tendency towards the development of the narrow-leaf syndrome the closer the species grew to areas where fog is frequently available. This study establishes convergence in a very wide group of plants encompassing genera as contrasting as Tillandsia and Agave as a result of their dependence on fog. Electronic Supplementary Material The online version of this article () contains supplementary material, which is available to authorized users.     

Disentangling determinants of egg size in the Geometridae (Lepidoptera) using an advanced phylogenetic comparative method

We present a phylogenetic comparative study assessing the evolutionary determinants of egg size in the moth family Geometridae. These moths were found to show a strong negative allometric relationship between egg size and maternal body size. Using recently developed comparative methods based on an Ornstein-Uhlenbeck process, we show that maternal body size explains over half the variation in egg size. However, other determinants are less clear: ecological factors, previously hypothesized to affect egg size, were not found to have a considerable influence in the Geometridae. The limited role of such third factors suggests a direct causal link between egg size and body size rather than an indirect correlation mediated by some ecological factors. Notably, no large geometrid species lay small eggs. This pattern suggests that maternal body size poses a physical constraint on egg size, but within these limits, there appears to be a rather invariable selection for larger eggs.     

Wing shape and migration in shorebirds: a comparative study

Migration is an energetically expensive and hazardous stage of the annual cycle of non‐resident avian species, and requires certain morphological adaptations. Wing shape is one of the morphological traits that is expected to be evolutionarily shaped by migration. Aerodynamic theory predicts that long‐distance migrants should have more pointed wings with distal primaries relatively longer than proximal primaries, an arrangement that minimizes induced drag and wing inertia, but this prediction has mostly been tested in passerine species. We applied the comparative method of phylogenetically independent contrasts to assess convergent evolution between wing shape and migration within shorebirds. We confirmed the assumption that long‐distance migrants have less rounded wings than species migrating shorter distances. Furthermore, wing roundedness negatively correlates with fat load and mean distance of migratory flights, the basic components of migration strategies. After controlling for interspecific differences in body size, we found no support for a link between wing length and migration, indicating that wing shape is a more important predictor of shorebird migratory behaviour than wing length. The results suggest that total migration distance and migratory strategy may simultaneously act on the evolution of wing shape in shorebirds, and possibly in other avian species.     

The contribution of the facultative feeding period to echinoid larval development and size at metamorphosis: a comparative approach

Planktotrophic invertebrate larvae have two dissociable stages during development, a facultative feeding period, whose length is determined by the amount of maternal provisioning in the egg, and an obligate feeding period, whose length is determined by the quantity of exogenous energy needed to reach metamorphic competence. Here we set out to experimentally test the impact of feeding during the facultative feeding period at two food concentrations (limiting and nonlimiting) on larval development time and juvenile quality. We used two closely related subtropical sand dollar species that differ in the quantity of maternal investment for these comparisons: Leodia sexiesperforata (large egg, long facultative feeding period) and Mellita tenuis (small egg, short facultative feeding period). We found that feeding during the facultative period accelerates development to metamorphosis only in M. tenuis and only at the high food ration. Feeding during the facultative feeding period had no effect on development time for M. tenuis at a food limiting concentration and for L. sexiesperforata at either food concentration. Furthermore, we found feeding during the facultative period to significantly increase quantity of carbohydrates and lipids at metamorphosis only for M. tenuis in nonlimiting food concentration. Thus, our data reveal a two-fold benefit of the facultative feeding period for a poorly provisioned species under high food conditions but little effect on a well-provisioned species. We discuss our results in reference to McEdward's [McEdward, L.R., 1997. Reproductive strategies of marine benthic invertebrates revisited: facultative feeding by planktotrophic larvae. Am. Nat. 150, 48-72] facultative feeding model.     

Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework

We examine the evolution of mesic forest ecosystems in the Pacific Northwest of North America using a statistical phylogeography approach in four animal and two plant lineages. Three a priori hypotheses, which explain the disjunction in the mesic forest ecosystem with either recent dispersal or ancient vicariance, are tested with phylogenetic and coalescent methods. We find strong support in three amphibian lineages (Ascaphus spp., and Dicampton spp., and Plethodon vandykei and P. idahoensis) for deep divergence between coastal and inland populations, as predicted by the ancient vicariance hypothesis. Unlike the amphibians, the disjunction in other Pacific Northwest lineages is likely due to recent dispersal along a northern route. Topological and population divergence tests support the northern dispersal hypothesis in the water vole (Microtus richardsoni) and northern dispersal has some support in both the dusky willow (Salix melanopsis) and whitebark pine (Pinus albicaulis). These analyses demonstrate that genetic data sampled from across an ecosystem can provide insight into the evolution of ecological communities and suggest that the advantages of a statistical phylogeographic approach are most pronounced in comparisons across multiple taxa in a particular ecosystem. Genetic patterns in organisms as diverse as willows and salamanders can be used to test general regional hypotheses, providing a consistent metric for comparison among members of an ecosystem with disparate life-history traits.     

Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling

A major bottleneck in comparative protein structure modeling is the quality of input alignment between the target sequence and the template structure. A number of alignment methods are available, but none of these techniques produce consistently good solutions for all cases. Alignments produced by alternative methods may be superior in certain segments but inferior in others when compared to each other; therefore, an accurate solution often requires an optimal combination of them. To address this problem, we have developed a new approach, Multiple Mapping Method (MMM). The algorithm first identifies the alternatively aligned regions from a set of input alignments. These alternatively aligned segments are scored using a composite scoring function, which determines their fitness within the structural environment of the template. The best scoring regions from a set of alternative segments are combined with the core part of the alignments to produce the final MMM alignment. The algorithm was tested on a dataset of 1400 protein pairs using 11 combinations of two to four alignment methods. In all cases MMM showed statistically significant improvement by reducing alignment errors in the range of 3 to 17%. MMM also compared favorably over two alignment meta-servers. The algorithm is computationally efficient; therefore, it is a suitable tool for genome scale modeling studies.