Nicolas Navarro

MDA: a MATLAB-based program for morphospace-disparity analysis

A MATLAB® program that examines patterns of state-space occupation is described. Four subroutines are available with which to visualize morphospace patterns: (i) in terms of their features such as dispersion, aggregation and location, thereby allowing users to extract complementary quantitative information about how the state-space is structured, and (ii) in terms of changes in those patterns that can be compared with other biotic (e.g., extinction, origination rates) or abiotic (e.g., environmental proxy) information. The program incorporates many of the latest and most widely used statistical parameters for describing multivariate spaces. The parameters are estimated on the basis of bootstrap resampling or bootstrap rarefaction procedures. Applications based on stochastic simulation of the evolution of monophyletic clade (using m-file contained in the help folder of the MDA program) are presented so as to illustrate the programs various options. The versatility of MDA allows the most interesting patterns to be extracted rapidly from data and the program to be applied readily to a wide range of state-space problems.

Developmental stability: a major role for cyclin G in Drosophila melanogaster

Morphological consistency in metazoans is remarkable given the pervasive occurrence of genetic variation, environmental effects, and developmental noise. Developmental stability, the ability to reduce developmental noise, is a fundamental property of multicellular organisms, yet its genetic bases remains elusive. Imperfect bilateral symmetry, or fluctuating asymmetry, is commonly used to estimate developmental stability. We observed that Drosophila melanogaster overexpressing Cyclin G (CycG) exhibit wing asymmetry clearly detectable by sight. Quantification of wing size and shape using geometric morphometrics reveals that this asymmetry is a genuine—but extreme—fluctuating asymmetry. Overexpression of CycG indeed leads to a 40-fold increase of wing fluctuating asymmetry, which is an unprecedented effect, for any organ and in any animal model, either in wild populations or mutants. This asymmetry effect is not restricted to wings, since femur length is affected as well. Inactivating CycG by RNAi also induces fluctuating asymmetry but to a lesser extent. Investigating the cellular bases of the phenotypic effects of CycG deregulation, we found that misregulation of cell size is predominant in asymmetric flies. In particular, the tight negative correlation between cell size and cell number observed in wild-type flies is impaired when CycG is upregulated. Our results highlight the role of CycG in the control of developmental stability in D. melanogaster. Furthermore, they show that wing developmental stability is normally ensured via compensatory processes between cell growth and cell proliferation. We discuss the possible role of CycG as a hub in a genetic network that controls developmental stability.

Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies

Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have undergone an adaptive radiation for wing-pattern mimicry and are influenced by distinct selection regimes. Using crosses between natural wing-pattern variants, we used genome-wide restriction site-associated DNA (RAD) genotyping, traditional linkage mapping and multivariate image analysis to study the evolution of the architecture of adaptive variation in two closely related species: Heliconius hecale and H. ismenius. We implemented a new morphometric procedure for the analysis of whole-wing pattern variation, which allows visualising spatial heatmaps of genotype-to-phenotype association for each quantitative trait locus separately. We used the H. melpomene reference genome to fine-map variation for each major wing-patterning region uncovered, evaluated the role of candidate genes and compared genetic architectures across the genus. Our results show that, although the loci responding to mimicry selection are highly conserved between species, their effect size and phenotypic action vary throughout the clade. Multilocus architecture is ancestral and maintained across species under directional selection, whereas the single-locus (supergene) inheritance controlling polymorphism in H. numata appears to have evolved only once. Nevertheless, the conservatism in the wing-patterning toolkit found throughout the genus does not appear to constrain phenotypic evolution towards local adaptive optima.

Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico

We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl) and 30 QTL responsible for the skull shape (SSH.qtl). Size, sex, and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315 MB and contained 2476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest.

Morphology and genetics reveal an intriguing pattern of differentiation at a very small geographic scale in a bird species, the forest thrush Turdus lherminieri

Mobile organisms are expected to show population differentiation only over fairly large geographical distances. However, there is growing evidence of discrepancy between dispersal potential and realized gene flow. Here we report an intriguing pattern of differentiation at a very small spatial scale in the forest thrush (Turdus lherminieri), a bird species endemic to the Lesser Antilles. Analysis of 331 individuals from 17 sampling sites distributed over three islands revealed a clear morphological and genetic differentiation between these islands isolated by 40–50 km. More surprisingly, we found that the phenotypic divergence between the two geographic zones of the island of Guadeloupe was associated with a very strong genetic differentiation (Fst from 0.073–0.153), making this pattern a remarkable case in birds given the very small spatial scale considered. Molecular data (mitochondrial control region sequences and microsatellite genotypes) suggest that this strong differentiation could have occurred in situ, although alternative hypotheses cannot be fully discarded. This study suggests that the ongoing habitat fragmentation, especially in tropical forests, may have a deeper impact than previously thought on avian populations.

Developmental integration in a functional unit: deciphering processes from adult dental morphology

The evolution of mammalian dentition is constrained by functional necessity and by the non‐independence of morphological structures. Efficient chewing implies coherent tooth coordination from development to motion, involving covariation patterns (integration) within dental parts. Using geometric morphometrics, we investigate the modular organization of the highly derived vole dentition. Integration patterns between and within the upper and lower molar rows are analyzed to identify potential modules and their origins (functional and developmental). Results support an integrated adult dentition pattern for both developmental and functional aspects. The integration patterns between opposing molar pairs suggest a transient role for the second upper and lower molars during the chewing motion. Upper and lower molar rows form coherent units but the relative integration of molar pairs is in contradiction with existing developmental models. Emphasis on the first three cusps to grow leads to a very different integration pattern, which would be congruent with developmental models. The early developmental architecture of traits is masked by later stages of growth, but may still be deciphered from the adult phenotype, if careful attention is paid to relevant features.

When less means more: evolutionary and developmental hypotheses in rodent molars

Tooth number in rodents is an example of reduction in evolution. All rodents have a toothless diastema lacking canine and most premolars present in most other mammals. Whereas some rodent lineages retained one premolar (p4), many others lost it during evolution. Recently, an ‘inhibitory cascade’ developmental model (IC) has been used to predict how the first molar (m1) influences the number and relative sizes of the following distal molars (m2 and m3). The model does not, however, consider the presence of premolars, and here we examine whether the premolar could influence and constrain molar proportions during development and evolution. By investigating a large data set of both extinct and extant rodent families over more than 40 million years, we show that the basal phenotype is characterized by the presence of premolars together with equally sized molars. More recent rodent families, with and without premolar, show more unequal molar sizes. Analysing molar areas, we demonstrated that (i) rodents harbour almost all the molar proportions known in mammals, and the IC model can explain about 80% of taxa in our data set; (ii) proportions of molars are influenced by the presence or absence of p4; and (iii) the most variable teeth in the dental row are m1 and m3, whether p4 is present or not. Moreover, m1 can represent up to half of the total molar area when p4 is absent. We hypothesize that p4 loss during evolution released the constraint on m1 development, resulting in a more variable size of m1 and thereby having an indirect effect on the evolution of the whole molar row.

Does 3D Phenotyping Yield Substantial Insights in the Genetics of the Mouse Mandible Shape

We describe the application of high-resolution 3D microcomputed tomography, together with 3D landmarks and geometric morphometrics, to validate and further improve previous quantitative genetic studies that reported QTL responsible for variation in the mandible shape of laboratory mice using a new backcross between C57BL/6J and A/J inbred strains. Despite the increasing availability of 3D imaging techniques, artificial flattening of the mandible by 2D imaging techniques seems at first an acceptable compromise for large-scale phenotyping protocols, thanks to an abundance of low-cost digital imaging systems such as microscopes or digital cameras. We evaluated the gain of information from considering explicitly this additional third dimension, and also from capturing variation on the bone surface where no precise anatomical landmark can be marked. Multivariate QTL mapping conducted with different landmark configurations (2D vs. 3D; manual vs. semilandmarks) broadly agreed with the findings of previous studies. Significantly more QTL (23) were identified and more precisely mapped when the mandible shape was captured with a large set of semilandmarks coupled with manual landmarks. It appears that finer phenotypic characterization of the mandibular shape with 3D landmarks, along with higher density genotyping, yields better insights into the genetic architecture of mandibular development. Most of the main variation is, nonetheless, preferentially embedded in the natural 2D plane of the hemi-mandible, reinforcing the results of earlier influential investigations.

Perturbation vectors to evaluate air quality using lichens and bromeliads: a Brazilian case study

Samples of one lichen species, Parmotrema crinitum, and one bromeliad species, Tillandsia usneoides, were collected in the state of Rio de Janeiro, Brazil, at four sites differently affected by anthropogenic pollution. The concentrations of aluminum, cadmium, copper, iron, lanthanum, lead, sulfur, titanium, zinc, and zirconium were determined by inductively coupled plasma–atomic emission spectroscopy. The environmental diagnosis was established by examining compositional changes via perturbation vectors, an underused family of methods designed to circumvent the problem of closure in any compositional dataset. The perturbation vectors between the reference site and the other three sites were similar for both species, although body concentration levels were different. At each site, perturbation vectors between lichens and bromeliads were approximately the same, whatever the local pollution level. It should thus be possible to combine these organisms, though physiologically different, for air quality surveys, after making all results comparable with appropriate correction. The use of perturbation vectors seems particularly suitable for assessing pollution level by biomonitoring, and for many frequently met situations in environmental geochemistry, where elemental ratios are more relevant than absolute concentrations.