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opencc-by-4.0Mar 2020View details →

WiDiv_PAM_Clustering_Integrated_Phenotypes

Root phenotype and performance data for the Wisconsin Diversity Panel collected from the field under well-watered and water stress conditions in Willcox, AZ, in 2016. Images of root architecture and anatomy were analyzed for each genotype, two replicates per treatment. Architectural data was collected using DIRT. Anatomical data was collected with RootScan2 and MIPAR. Also included is the R script to conduct a PAM clustering analysis to identify clusters of root phenotypes related to performance.

opencc-zeroDec 2020View details →

Phenotypic integration in feliform carnivores: covariation patterns and disparity in hypercarnivores versus generalists

The skeleton is a complex arrangement of anatomical structures that covary to various degrees depending on both intrinsic and extrinsic factors. Among the Feliformia, many species are characterized by predator lifestyles providing a unique opportunity to investigate the impact of highly specialised hypercarnivorous diet on phenotypic integration and shape diversity. To do so, we compared the shape of the skull, mandible, humerus, and femur of species in relation to their feeding strategies (hypercarnivorous versus generalist species) and prey preference (predators of small versus large prey) using three-dimensional geometric morphometric techniques. Our results highlight different degrees of morphological integration in the Feliformia depending on the functional implication of the anatomical structure, with an overall higher covariation of structures in hypercarnivorous species. The skull and the forelimb are not integrated in generalist species whereas they are in hypercarnivores. These results can potentially be explained by the different feeding strategies of these species. Contrary to our expectations, hypercarnivores display a higher disparity for the skull than generalist species. This is probably due to the fact that a specialisation toward high-meat diet could be achieved through various phenotypes. Finally, humeri and femora display shape variations depending on relative prey size preference. Large species feeding on large prey tend to have robust long bones due to higher biomechanical constraints.

opencc-zeroDec 2018View details →

Data from: Integration of anatomy ontologies and evo-devo using structured Markov models suggests a new framework for modeling discrete phenotypic traits

Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes – hierarchical and hidden – which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of structured Markov models with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of gene regulatory networks and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing "tail color problem," in which the trait is scored for species with tails of different colors or no tails. It also presents a previously unknown issue called the "two-scientist paradox," in which the nature of coding the trait and the hidden processes driving the trait's evolution are confounded; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This paper gives practical examples of using the new framework for phylogenetic inference and comparative analysis.

opencc-zeroDec 2016View details →

Data from: Ontogenetic changes in the phenotypic integration and modularity of leaf functional traits

1.Changes in resource availability, functional demands, hormonal regulation and developmental constraints can promote differences in the expression of leaf traits during plant development and foster changes in the targets of natural selection. As a consequence, the pattern and magnitude of covariation among traits, and therefore their phenotypic integration and modularity are equally expected to change throughout ontogeny. However, these changes have not been described yet. 2.We measured leaf economic, defensive and morphological traits in plants of Turnera velutina and estimated the magnitude and pattern of foliar integration and modularity for juvenile and reproductive individuals. In addition, we assessed the relationship between plant biomass and foliar integration within and among ontogenetic stages. 3.Both the pattern and magnitude of foliar integration changed across plant ontogeny. Foliar integration was lower in juvenile than in reproductive plants, and the pattern of phenotypic integration and modularity was different between ontogenetic stages: whereas leaves from juvenile plants showed two functional modules related to plant defence and leaf economy, traits from reproductive plants had greater interconnectivity and hence lower modularity. 4.The relationship between plant biomass and foliar integration was negative within each ontogenetic stage but positive between ontogenetic stages, suggesting that processes intrinsic to plant development influenced the magnitude of foliar integration to a greater extent than plant size. 5.Our findings indicate that plants can change the patterns of covariation among leaf traits during their development. Whereas a lower foliar integration in juvenile plants could allow for greater lability to explore a multi-trait phenotypic space, canalization of leaf attributes along ontogeny should promote greater phenotypic integration, constraining the number of multi-trait combinations that plants can express. Hence, we suggest that ontogenetic changes in foliar integration allow plants to deal with changing selective dynamics and physiological priorities along their development.

opencc-zeroDec 2015View details →

Data from: Disintegrating the fly: a mutational perspective on phenotypic integration and covariation

The structure of environmentally induced phenotypic covariation can influence the effective strength and magnitude of natural selection. Yet our understanding of the factors that contribute to and influence the evolutionary lability of such covariation is poor. Most studies have either examined environmental variation without accounting for covariation, or examined phenotypic and genetic covariation without distinguishing the environmental component. In this study we examined the effect of mutational perturbations on different properties of environmental covariation, as well as mean shape. We use strains of Drosophila melanogaster bearing well-characterized mutations known to influence wing shape, as well as naturally-derived strains, all reared under carefully-controlled conditions and with the same genetic background. We find that mean shape changes more freely than the covariance structure, and that different properties of the covariance matrix change independently from each other. The perturbations affect matrix orientation more than they affect matrix eccentricity or total variance. Yet, mutational effects on matrix orientation do not cluster according to the developmental pathway that they target. These results suggest that it might be useful to consider a more general concept of 'decanalization', involving all aspects of variation and covariation.

opencc-zeroDec 2009View details →

Data from: Colour, design, and reward: phenotypic integration of fleshy fruit displays

The functional or structural linkage among traits (phenotypic integration; PI) within complex structures can constrain the evolutionary response of individual traits. To analyse whether frugivores with distinct sensory ecology have shaped the patterns of fruit diversification differently, we compared PI values of fleshy fruits that are consumed by birds and mammals. We used phylogenetic comparative analyses of PI among 13 morphological, nutritional and visual fruit traits from 111 Mediterranean plant species. Results showed that morphological traits had higher PI values than nutritional and colour traits. Visual and nutritional traits show positive phylogenetic covariance, while negative covariation occurs between fruits size and nutrients. Importantly, fruits consumed by birds were relatively more integrated than fruits consumed partly or solely by mammals. Hence we show that major groups of mutualistic frugivores can shape the covariance among some fruit traits differently and thereby influence fruit diversification.

opencc-zeroDec 2014View details →

Data from: Phenotypic integration in the feeding system of the eastern diamondback rattlesnake (Crotalus adamanteus)

Selection can vary geographically across environments and temporally over the lifetime of an individual. Unlike geographic contexts, where different selective regimes can act on different alleles, age-specific selection is constrained to act on the same genome by altering age-specific expression. Snake venoms are exceptional traits for studying ontogeny because toxin expression variation directly changes the phenotype; relative amounts of venom components determine, in part, venom efficacy. Phenotypic integration is the dependent relationship between different traits that collectively produce a complex phenotype and, in venomous snakes, may include traits as diverse as venom, head shape and fang length. We examined the feeding system of the eastern diamondback rattlesnake (Crotalus adamanteus) across environments and over the lifetime of individuals and used a genotype–phenotype map approach, protein expression data and morphological data to demonstrate that: (i) ontogenetic effects explained more of the variation in toxin expression variation than geographic effects, (ii) both juveniles and adults varied geographically, (iii) toxin expression variation was a result of directional selection and (iv) different venom phenotypes covaried with morphological traits also associated with feeding in temporal (ontogenetic) and geographic (functional) contexts. These data are the first to demonstrate, to our knowledge, phenotypic integration between multiple morphological characters and a biochemical phenotype across populations and age classes. We identified copy number variation as the mechanism driving the difference in the venom phenotype associated with these morphological differences, and the parallel mitochondrial, venom and morphological divergence between northern and southern clades suggests that each clade may warrant classification as a separate evolutionarily significant unit.

opennotspecifiedDec 2017View details →

FIGURE 1 in Speciation in Indo-Pacific swiftlets (Aves: Apodidae): integrating molecular and phenotypic data for a new provisional taxonomy of the Collocalia esculenta complex

FIGURE 1. Distribution of the white-bellied swiftlet (Collocalia esculenta) complex across the Indo-Pacific region, with Stresemann's Line separating eastern and western taxa.

opennotspecifiedDec 2017View details →

FIGURE 2 in Speciation in Indo-Pacific swiftlets (Aves: Apodidae): integrating molecular and phenotypic data for a new provisional taxonomy of the Collocalia esculenta complex

FIGURE 2. Phylogenetic tree topology based on Bayesian analysis of cyt b sequence data. Taxon names and localities are given for each population. High branch support is given in Maximum Parsimony bootstrap, Maximum Likelihood bootstrap and Bayesian posterior probability (multiplied by 100 for ease of reference) in the same order with a cut-off of Ż85 for bootstrap and Ż99 for posterior probability.

FIGURE 2 in Integrating voice and phenotype in a revision of the brush cuckoo Cacomantis variolosus (Aves: Cuculidae) complex

FIGURE 2. The seven element shapes found in the Cacomantis variolosus complex. Taxon names given represent the following geographic song types (see Results): sepulcralis—Sundaland and Philippines, virescens—Sulawesi and Sula, aeruginosus—resident Moluccas, variolosus—Australasia, blandus—Admiralty Islands, addendus—Solomon Islands.

FIGURE 4 in Integrating voice and phenotype in a revision of the brush cuckoo Cacomantis variolosus (Aves: Cuculidae) complex

FIGURE 4. Boxplots of vocal measurements. Explanation of variables: pacing—elements per second; element duration in seconds; changes in center frequency in Hertz. For further explanation of vocal parameters, see Methods.

FIGURE 3 in Integrating voice and phenotype in a revision of the brush cuckoo Cacomantis variolosus (Aves: Cuculidae) complex

FIGURE 3. Principal component analysis plot based on the four vocal parameters measured. The first principal component (PC1) chiefly differentiates addendus and virescens, while the second PC splits the sepulcralis group and variolosus group. The inferred Australian migrant variolosus individual (ML 168559) found on Flores, Nusa Tenggara, Indonesia, is denoted by an arrow.

FIGURE 1 in Integrating voice and phenotype in a revision of the brush cuckoo Cacomantis variolosus (Aves: Cuculidae) complex

FIGURE 1. Distribution of the Cacomantis variolosus complex across the Indo-Pacific region: (a) showing the ranges of taxa listed in Table 1; (b) showing all species and subspecies recognized as a result of this study, with species encircled.

opencc-zeroDec 2014View details →

Data from: Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize

The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet's crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research.

opencc-zeroJul 2021View details →

Condition-dependence of phenotypic integration and the evolvability of genitalic traits in a neriid fly

The spectacular diversity of insect male genitalia, and their relative insensitivity to the environment, have long puzzled evolutionary biologists and taxonomists. We asked whether the unusual evolvability of male genitalia could be associated with low morphological integration of genitalic traits, by comparison with male somatic traits and female traits. We also asked whether this pattern was robust to variation in resource availability during development, which affects adult condition. To address these questions, we manipulated larval diet quality in a split-brood design and compared levels of integration of male and female genitalic and somatic traits in the neriid fly, Telostylinus angusticollis. We found that male genitalic traits were substantially less integrated than male somatic traits, and less integrated than female genitalic traits. Female genitalic traits were also less integrated than female somatic traits, but the difference was less pronounced than in males. However, integration of male genitalic traits was negatively condition-dependent, with high-condition males exhibiting lower trait integration than low-condition males. Finally, genitalic traits exhibited lower larval diet family interactions than somatic traits. These results could help explain the unusually high evolvability of male genitalic traits in insects.

Fig. 3 in An integrated approach for the characterization of wild Crocus species adopting phenotypical and phytochemical traits

Fig. 3. Biplot from Principal Component Analysis for the phytochemical components (flavonols and crocins) for fifteen wild Crocus samples and saffron. All components were used for the analysis, but only the ones with the longest vectors were represented in the graph. See Table 1 for the coding of populations (S = saffron) and Tables 4 and 5 for the coding of phytochemicals.

Fig. 4 in An integrated approach for the characterization of wild Crocus species adopting phenotypical and phytochemical traits

Fig. 4. Wild Crocus taxa collected in Southern Italy: Crocus biflorus; C. longiflorus; C. siculus; C. thomasii; C. neapolitanus.

Fig. 1 in An integrated approach for the characterization of wild Crocus species adopting phenotypical and phytochemical traits

Fig. 1. Biplot from Principal Component Analysis for the floral traits in the sixteen Crocus populations. Lops and Lips: outer and inner perigone segments; Lsb: length of style-branches; Lpt: Length of perigone tube; Lanth: length of anther of the 16 Crocus samples. See Table 1 for the coding of populations.

Fig. 2 in An integrated approach for the characterization of wild Crocus species adopting phenotypical and phytochemical traits

Fig. 2. General molecular structures of flavonoids (flavonols) and apocarotenoids (crocins) characterised in the stigmas of wild Crocus samples and saffron.