Simultaneous integration and modularity underlie the exceptional body shape diversification of characiform fishes

Evolutionary biology has long striven to understand why some lineages diversify exceptionally while others do not. Most studies have focused on how extrinsic factors can promote differences in diversification dynamics, but a clade's intrinsic modularity and integration can also catalyze or restrict its evolution. Here, we integrate geometric morphometrics, phylogenetic comparative methods and visualizations of covariance to infer the presence of distinct modules in the body plan of Characiformes, an ecomorphologically diverse fish radiation. Strong covariances reveal a cranial module, and more subtle patterns support a statistically significant subdivision of the postcranium into anterior (precaudal) and posterior (caudal) modules. We uncover substantial covariation among cranial and postcranial landmarks, indicating body-wide evolutionary integration as lineages transition between compressiform and fusiform body shapes. A novel method of matrix subdivision reveals that within- and among-module covariation contributes substantially to the overall eigenstructure of characiform morphospace, and that both phenomena led to biologically important divergence among characiform lineages. Functional integration between the cranium and post-cranial skeleton appears to have allowed lineages to optimize the aspect ratio of their bodies for locomotion, while the capacity for independent change in the head, body and tail likely eased adaptation to diverse dietary and hydrological regimes. These results reinforce a growing consensus that modularity and integration synergize to promote diversification.

Consilience of methods for phylogenetic analysis of variance

Simulation-based and permutation-based inferential methods are commonplace in phylogenetic comparative methods, especially as evolutionary data have become more complex and parametric methods more limited for their analysis. Both approaches simulate many random outcomes from a null model to empirically generate sampling distributions of statistics. Although simulation-based and permutation-based methods seem commensurate in purpose, results from analysis of variance (ANOVA) based on the distributions of random F-statistics produced by these methods can be quite different in practice. Differences could be from either the null-model process that generates variation across many simulations or random permutations of the data, or different estimation methods for linear model coefficients and statistics. Unfortunately, because the null-model process and coefficient estimation are intrinsically linked in phylogenetic ANOVA methods, the precise reason for methodological differences has not been fully considered. Here we show that the null-model processes of phylogenetic simulation and randomizing residuals in a permutation procedure are indeed commensurate, and that both also produce results consistent with parametric ANOVA, for cases where parametric ANOVA is possible. We also provide results that caution against using ordinary least-squares estimation along with phylogenetic simulation; a typical phylogenetic ANOVA implementation.

Divergent processes drive parallel evolution in marine and freshwater fishes

Evolutionary comparisons between major environmental divides, such as between marine and freshwater systems, can reveal the fundamental processes governing diversification dynamics. Although processes may differ due to the different scales of their biogeographic barriers, freshwater and marine environments nevertheless offer similar opportunities for diversification in benthic, demersal, and pelagic habitats. Here, we compare the evolutionary patterns and processes shaping teleost diversity both in each of these three habitats and between marine and freshwater systems. Using specimens from the National Museum of Natural History, we developed a dataset of linear measurements capturing body shape in 2,266 freshwater and 3,344 marine teleost species. With a novel comparative approach, we contrast the primary axis of morphological diversification in each habitat with the major axis defined by phylogenetic signal. By comparing angles between these axes, we find that fish in corresponding habitats have more similar primary axes of morphological diversity than would be expected by chance, but that different historical processes underlie these parallel patterns in freshwater and marine environments. Marine diversification is more strongly aligned with phylogenetic signal and shows a trend toward lineages occupying separate regions of morphospace. In contrast, ecological signal appears to be a strong driver of diversification in freshwater lineages through repeated morphological evolution in densely packed regions of morphospace. In spite of these divergent histories, our findings reveal that habitat has driven convergent patterns of evolutionary diversification on a global scale.

Decreased Mitochondrial Dynamics Is Associated with Insulin Resistance, Metabolic Rate, and Fitness in African Americans

CONTEXT

African American women (AAW) have a higher incidence of insulin resistance and are at a greater risk for the development of obesity and type 2 diabetes than Caucasian women (CW). Although several factors have been proposed to mediate these racial disparities, the mechanisms remain poorly defined. We previously demonstrated that sedentary lean AAW have lower peripheral insulin sensitivity, reduced maximal aerobic fitness (VO2max), and lower resting metabolic rate (RMR) than CW. We have also demonstrated that skeletal muscle mitochondrial respiration is lower in AAW and appears to play a role in these racial differences.

OBJECTIVE

The goal of this study was to assess mitochondrial pathways and dynamics to examine the potential mechanisms of lower insulin sensitivity, RMR, VO2max, and mitochondrial capacity in AAW.

DESIGN

To achieve this goal, we assessed several mitochondrial pathways in skeletal muscle using gene array technology and semiquantitative protein analysis.

RESULTS

We report alterations in mitochondrial pathways associated with inner membrane small molecule transport genes, fusion-fission, and autophagy in lean AAW. These differences were associated with lower insulin sensitivity, RMR, and VO2max.

CONCLUSIONS

Together these data suggest that the metabolic racial disparity of insulin resistance, RMR, VO2max, and mitochondrial capacity may be mediated by perturbations in mitochondrial pathways associated with membrane transport, fission-fusion, and autophagy. The mechanisms contributing to these differences remain unknown.

Comparing the strength of modular signal, and evaluating alternative modular hypotheses, using covariance ratio effect sizes with morphometric data

The study of modularity is paramount for understanding trends of phenotypic evolution, and for determining the extent to which covariation patterns are conserved across taxa and levels of biological organization. However, biologists currently lack quantitative methods for statistically comparing the strength of modular signal across datasets, and a robust approach for evaluating alternative modular hypotheses for the same dataset. As a solution to these challenges, we propose an effect size measure ( Z CR ) derived from the covariance ratio, and develop hypothesis-testing procedures for their comparison. Computer simulations demonstrate that Z CR displays appropriate statistical properties and low levels of mis-specification, implying that it correctly identifies modular signal, when present. By contrast, alternative methods based on likelihood (EMMLi) and goodness of fit (MINT) suffer from high false positive rates and high model mis-specification rates. An empirical example in sigmodontine rodent mandibles is provided to illustrate the utility of Z CR for comparing modular hypotheses. Overall, we find that covariance ratio effect sizes are useful for comparing patterns of modular signal across datasets or for evaluating alternative modular hypotheses for the same dataset. Finally, the statistical philosophy for pairwise model comparisons using effect sizes should accommodate any future analytical developments for characterizing modular signal.

Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in multivariate phenotypes are derived from distances and directions between species in a multivariate phenotype space. For these patterns to be interpretable, phenotypes should be characterized by traits in commensurate units and scale. Visualizing such trends, as is achieved with phylomorphospaces, should continue to play a prominent role in macroevolutionary analyses. Evaluating phylogenetic generalized least squares (PGLS) models (e.g., phylogenetic analysis of variance and regression) is valuable, but using parametric procedures is limited to only a few phenotypic variables. In contrast, nonparametric, permutation-based PGLS methods provide a flexible alternative and are thus preferred for high-dimensional multivariate phenotypes. Permutation-based methods for evaluating covariation within multivariate phenotypes are also well established and can test evolutionary trends in phenotypic integration. However, comparing evolutionary rates and modes in multivariate phenotypes remains an important area of future development.

Multivariate Phylogenetic Comparative Methods: Evaluations, Comparisons, and Recommendations

Recent years have seen increased interest in phylogenetic comparative analyses of multivariate data sets, but to date the varied proposed approaches have not been extensively examined. Here we review the mathematical properties required of any multivariate method, and specifically evaluate existing multivariate phylogenetic comparative methods in this context. Phylogenetic comparative methods based on the full multivariate likelihood are robust to levels of covariation among trait dimensions and are insensitive to the orientation of the data set, but display increasing model misspecification as the number of trait dimensions increases. This is because the expected evolutionary covariance matrix (V) used in the likelihood calculations becomes more ill-conditioned as trait dimensionality increases, and as evolutionary models become more complex. Thus, these approaches are only appropriate for data sets with few traits and many species. Methods that summarize patterns across trait dimensions treated separately (e.g., SURFACE) incorrectly assume independence among trait dimensions, resulting in nearly a 100% model misspecification rate. Methods using pairwise composite likelihood are highly sensitive to levels of trait covariation, the orientation of the data set, and the number of trait dimensions. The consequences of these debilitating deficiencies are that a user can arrive at differing statistical conclusions, and therefore biological inferences, simply from a dataspace rotation, like principal component analysis. By contrast, algebraic generalizations of the standard phylogenetic comparative toolkit that use the trace of covariance matrices are insensitive to levels of trait covariation, the number of trait dimensions, and the orientation of the data set. Further, when appropriate permutation tests are used, these approaches display acceptable Type I error and statistical power. We conclude that methods summarizing information across trait dimensions, as well as pairwise composite likelihood methods should be avoided, whereas algebraic generalizations of the phylogenetic comparative toolkit provide a useful means of assessing macroevolutionary patterns in multivariate data. Finally, we discuss areas in which multivariate phylogenetic comparative methods are still in need of future development; namely highly multivariate Ornstein-Uhlenbeck models and approaches for multivariate evolutionary model comparisons.

Deconstructing a Species-Complex: Geometric Morphometric and Molecular Analyses Define Species in the Western Rattlesnake (Crotalus viridis)

Morphological data are a conduit for the recognition and description of species, and their acquisition has recently been broadened by geometric morphometric (GM) approaches that co-join the collection of digital data with exploratory 'big data' analytics. We employed this approach to dissect the Western Rattlesnake (Crotalus viridis) species-complex in North America, currently partitioned by mitochondrial (mt)DNA analyses into eastern and western lineages (two and seven subspecies, respectively). The GM data (i.e., 33 dorsal and 50 lateral head landmarks) were gleaned from 2,824 individuals located in 10 museum collections. We also downloaded and concatenated sequences for six mtDNA genes from the NCBI GenBank database. GM analyses revealed significant head shape differences attributable to size and subspecies-designation (but not their interactions). Pairwise shape distances among subspecies were significantly greater than those derived from ancestral character states via squared-change parsimony, with the greatest differences separating those most closely related. This, in turn, suggests the potential for historic character displacement as a diversifying force in the complex. All subspecies, save one, were significantly differentiated in a Bayesian discriminant function analysis (DFA), regardless of whether our priors were uniform or informative (i.e., mtDNA data). Finally, shape differences among sister-clades were significantly greater than expected by chance alone under a Brownian model of evolution, promoting the hypothesis that selection rather than drift was the driving force in the evolution of the complex. Lastly, we combine head shape and mtDNA data so as to derived an integrative taxonomy that produced robust boundaries for six OTUs (operational taxonomic units) of the C. viridis complex. We suggest these boundaries are concomitant with species-status and subsequently provide a relevant nomenclature for its recognition and representation.

Contemporary evolutionary divergence for a protected species following assisted colonization

Background

Contemporary evolution following assisted colonization may increase the probability of persistence for refuge populations established as a bet-hedge for protected species. Such refuge populations are considered “genetic replicates” that might be used for future re-colonization in the event of a catastrophe in the native site. Although maladaptive evolutionary divergence of captive populations is well recognized, evolutionary divergence of wild refuge populations may also occur on contemporary time scales. Thus, refuge populations may lose their “value” as true genetic replicates of the native population. Here, we show contemporary evolutionary divergence in body shape in an approximately 30-year old refuge population of the protected White Sands pupfish (Cyprinodon tularosa) resulting in a body-shape mismatch with its native environment.

Methodology/Principal Findings

Geometric morphometic data were collected from C. tularosa cultures raised in experimental mesocosms. Cultures were initiated with fish from the two native populations, plus hybrids, in high or low salinity treatments representing the salinities of the two native habitats. We found that body shape was heritable and that shape variation due to phenotypic plasticity was small compared to shape variation due to population source. C. tularosa from the high salinity population retained slender body shapes and fish from the low salinity population retained deep body shapes, irrespective of mesocosm salinity. These data suggest that the observed divergence of a recently established pupfish population was not explained by plasticity. An analysis of microsatellite variation indicated that no significant genetic drift occurred in the refuge population, further supporting the adaptive nature of changes in body shape. These lines of evidence suggest that body shape divergence of the refuge population reflects a case of contemporary evolution (over a 30-year period).

Conclusions/Significance

These results suggest assisted colonization can introduce novel, and/or relaxed selection, and lead to unintended evolutionary divergence.

PHENOTYPIC PLASTICITY OF NATIVE VS. INVASIVE PURPLE LOOSESTRIFE: A TWO-STATE MULTIVARIATE APPROACH

The differences in phenotypic plasticity between invasive (North American) and native (German) provenances of the invasive plant Lythrum salicaria (purple loosestrife) were examined using a multivariate reaction norm approach testing two important attributes of reaction norms described by multivariate vectors of phenotypic change: the magnitude and direction of mean trait differences between environments. Data were collected for six life history traits from native and invasive plants using a split-plot design with experimentally manipulated water and nutrient levels. We found significant differences between native and invasive plants in multivariate phenotypic plasticity for comparisons between low and high water treatments within low nutrient levels, between low and high nutrient levels within high water treatments, and for comparisons that included both a water and nutrient level change. The significant genotype x environment (G x E) effects support the argument that invasiveness of purple loosestrife is closely associated with the interaction of high levels of soil nutrient and flooding water regime. Our results indicate that native and invasive plants take different strategies for growth and reproduction; native plants flowered earlier and allocated more to flower production, while invasive plants exhibited an extended period of vegetative growth before flowering to increase height and allocation to clonal reproduction, which may contribute to increased fitness and invasiveness in subsequent years.

ANALYSIS OF CHARACTER DIVERGENCE ALONG ENVIRONMENTAL GRADIENTS AND OTHER COVARIATES

Character displacement is typically identified by comparing phenotypic differences in sympatry and allopatry. Recently, however, Goldberg and Lande (2006) pointed out that when phenotypic characters vary along an environmental gradient, the standard approach may fail to identify sympatric character divergence. Here we present a general analytical procedure for identifying sympatric character divergence while accounting for phenotypic changes that covary with environmental variables. Our approach uses residual randomization from a generalized linear model, and allows the statistical comparison of sympatric phenotypic divergence to allopatric phenotypic divergence while accounting for phenotypic variation along a gradient. Through simulation we demonstrate that our approach correctly identifies patterns of sympatric character divergence when they are present, and does not identify such patterns when they are not. Our analytical approach complements and extends the suggestions of Goldberg and Lande (2006), by allowing a full statistical assessment of the varied patterns of character displacement along environmental gradients, or while accounting for other covariates and sources of variation.

ANALYSIS OF TWO-STATE MULTIVARIATE PHENOTYPIC CHANGE IN ECOLOGICAL STUDIES

Analyses of two-state phenotypic change are common in ecological research. Some examples include phenotypic changes due to phenotypic plasticity between two environments, changes due to predator/non-predator character shifts, character displacement via competitive interactions, and patterns of sexual dimorphism. However, methods for analyzing phenotypic change for multivariate data have not been rigorously developed. Here we outline a method for testing vectors of phenotypic change in terms of two important attributes: the magnitude of change (vector length) and the direction of change described by trait covariation (angular difference between vectors). We describe a permutation procedure for testing these attributes, which allows non-targeted sources of variation to be held constant. We provide examples that illustrate the importance of considering vector attributes of phenotypic change in biological studies, and we demonstrate how greater inference can be made than by evaluating variance components with MANOVA alone. Finally, we consider how our method may be extended to more complex data.

Location-specific sympatric morphological divergence as a possible response to species interactions in West Virginia Plethodon salamander communities

1. The competitive interactions of closely related species have long been considered important determinants of community composition and a major cause of phenotypic diversification. However, while patterns such as character displacement are well documented, less is known about how local adaptation influences diversifying selection from interspecific competition. 2. We examined body size and head shape variation among allopatric and sympatric populations of two salamander species, the widespread Plethodon cinereus and the geographically restricted P. nettingi. We quantified morphology from 724 individuals from 20 geographical localities throughout the range of P. nettingi. 3. Plethodon nettingi was more robust in cranial morphology relative to P. cinereus, and sympatric localities were more robust relative to allopatric localities. Additionally, there was significantly greater sympatric head shape divergence between species relative to allopatric communities, and sympatric localities of P. cinereus exhibited greater morphological variation than sympatric P. nettingi. 4. The sympatric morphological divergence and increase in cranial robustness of one species (P. nettingi) were similar to observations in other Plethodon communities, and were consistent with the hypothesis of interspecific competition. These findings suggest that interspecific competition in Plethodon may play an important role in phenotypic diversification in this group. 5. The increase in among-population variance in sympatric P. cinereus suggests a species-specific response to divergent natural selection that is influenced in part by other factors. We hypothesize that enhanced morphological flexibility and ecological tolerance allow P. cinereus to more rapidly adapt to local environmental conditions, and initial differences among populations have allowed the evolutionary response of P. cinereus to vary across replicate sympatric locations, resulting in distinct evolutionary trajectories of morphological change.

Phenotypic plasticity in two marine snails: constraints superseding life history

In organisms encountering predictable environments, fixed development is expected, whereas in organisms that cannot predict their future environment, phenotypic plasticity would be optimal to increase local adaptation. To test this prediction we experimentally compared phenotypic plasticity in two rocky-shore snail species; Littorina saxatilis releasing miniature snails on the shore, and Littorina littorea releasing drifting larvae settling on various shores, expecting L. littorea to show more phenotypic plasticity than L. saxatilis. We compared magnitude and direction of vectors of phenotypic difference in juvenile shell traits after 3 months exposure to different stimuli simulating sheltered and crab-rich shores, or wave-exposed and crab-free shores. Both species showed similar direction and magnitude of vectors of phenotypic difference with minor differences only between ecotypes of the nondispersing species, indicating that plasticity is an evolving trait in L. saxatilis. The lack of a strong plastic response in L. littorea might be explained by limits rather than costs to plasticity.