Nicolas Navarro

Nicolas Navarro
Ecole Pratique des Hautes Etudes | EPHE · UMR Biogéosciences, CNRS, Université Bourgogne Franche-Comté

PhD

About

89
Publications
21,004
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,109
Citations
Additional affiliations
December 2011 - present
Ecole Pratique des Hautes Etudes
Position
  • Professor (Associate)
June 2009 - January 2011
University of Geneva
Position
  • PostDoc Position
September 2007 - May 2009
Autonomous University of Barcelona
Position
  • PostDoc Position

Publications

Publications (89)
Article
Full-text available
We describe the application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to validate and further improve previous quantitative genetic studies that reported QTLs responsible for variation in mandible shape of laboratory mice using a new backcross between C57BL/6J and A/J inbred strains. De...
Article
Full-text available
Molar size in Mammals shows considerable disparity and exhibits variation similar to that predicted by the Inhibitory Cascade model. The importance of such developmental systems in favoring evolutionary trajectories is also underlined by the fact that this model can predict macroevolutionary patterns. Using backcross mice, we mapped QTL for molar s...
Article
Full-text available
Fluctuating asymmetry is a classic concept linked to organismal development. It has traditionally been used as a measure of developmental instability, which is the inability of an organism to buffer environmental fluctuations during development. Developmental stability has a genetic component that influences the final phenotype of the organism and...
Article
Full-text available
The genetic architecture of skull shape has been extensively studied in mice and the results suggest a highly polygenic and additive basis. In contrast few studies have explored the genetic basis of the skull variability. Canalization and developmental stability are the two components of phenotypic robustness. They have been proposed to be emergent...
Article
In mammals, significant changes take place during postnatal growth, linked to changes in diet (from sucking to gnawing). During this period, mandible development is highly interconnected with muscle growth and the epigenetic interactions between muscle and bone control the spatialization of bone formation and remodeling in response to biomechanical...
Article
Full-text available
Facial morphology—a conspicuous feature of human appearance—is highly heritable. Previous studies on the genetic basis of facial morphology were performed mainly in European-ancestry cohorts (EUR). Applying a data-driven phenotyping and multivariate genome-wide scanning protocol to a large collection of three-dimensional facial images of individual...
Article
Full-text available
Background Obstructive sleep apnea (OSA) remains massively underdiagnosed, due to limited access to polysomnography (PSG), the highly complex gold standard for diagnosis. Performance scores in predicting OSA are evaluated for machine learning (ML) analysis applied to 3D maxillofacial shapes. Methods The 3D maxillofacial shapes were scanned on 280...
Preprint
We report a genome-wide association study for facial features in > 6,000 Latin Americans. We placed 106 landmarks on 2D frontal photographs using the cloud service platform Face++. After Procrustes superposition, genome-wide association testing was performed for 301 inter-landmark distances. We detected nominally significant association (P-value <...
Article
In Sumba Island – Indonesia, the implantation of vernacular houses, inside and outside traditional villages, is considered to be an efficient proxy for the on-going complex cultural transformations resulting from globalization. This study presents an easily reproducible workflow allowing buildings to be automatically detected from satellite imagery...
Article
Full-text available
The Mediterranean Region is a biodiversity/endemism hotspot whose freshwater fauna remains largely unexplored. Our integrative study challenges the taxonomic status of two freshwater palaemonid shrimps, Palaemon antennarius and Palaemon minos. Three molecular operational taxonomic units (MOTUs) were defined based on 352 cytochrome oxidase subunit I...
Preprint
Full-text available
Facial morphology, the most conspicuous feature of human appearance, is highly heritable. Previous studies on the genetic basis of facial morphology were mainly performed in European populations. Applying a proven data-driven phenotyping and multivariate genome-wide scanning protocol to the largest collection of 3D facial images of an East Asian po...
Article
Full-text available
Archaeologists working with pottery spend a considerable amount of time on a fundamental task – providing precise descriptions of pottery fragments. This study presents a survey of existing computational solutions to identify the best matches for a given fragment, based on its shape. Four methods (ICP, DCT, RDP, and RTC) are compared, using a potte...
Article
Revealing carved parts in rock art is of primary importance and remains a major challenge for archaeological documentation. Computational geometry applied to 3D imaging provides a unique opportunity to document rock art. This study evaluates five algorithms and derivatives used to compute ambient occlusion and sky visibility on 3D models of Mongoli...
Article
Full-text available
To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits...
Article
Significant environmental changes have already been documented in the Southern Ocean (e.g. sea water temperature increase and salinity drop) but its marine life is still incompletely known given the heterogeneous nature of biogeographic data. However, to establish sustainable conservation areas, understanding species and communities distribution pa...
Article
The present study evaluates a methodological workflow that could identify dinosaur tracks and trackways more comprehensively at outcrop scale. The approach described here is based both on 3D modelling by photogrammetry at different resolutions, and on suitably processed digital elevation models (DEMs). The ichnosite of Anza, Morocco, was chosen to...
Article
The present study proposes a workflow to extract from orthomosaics the enormous amount of dry stones used by past societies to construct funeral complexes in the Mongolian steppes. Several different machine learning algorithms for binary pixel classification (i.e. stone vs non-stone) were evaluated. Input features were extracted from high-resolutio...
Article
Full-text available
The Southern Ocean (SO) is among the regions on Earth that are undergoing regionally the fastest environmental changes. The unique ecological features of its marine life make it particularly vulnerable to the multiple effects of climate change. A network of Marine Protected Areas (MPAs) has started to be implemented in the SO to protect marine ecos...
Article
Full-text available
Photospheres, or 360° photos, offer valuable opportunities for perceiving space, especially when viewed through head-mounted displays designed for virtual reality. Here, we propose to take advantage of this potential for archaeology and cultural heritage, and to extend it by augmenting the images with existing documentation, such as 2D maps or 3D m...
Article
Modularity and integration are variational properties expressed at various levels of the biological hierarchy. Mismatches among these levels, for example developmental modules that are integrated in a functional unit, could be informative of how evolutionary processes and trade‐offs have shaped organismal morphologies as well as clade diversificati...
Article
Full-text available
Archaeologists spend considerable time orienting and drawing ceramic fragments by hand for documentation, to infer their manufacture, the nature of the discovery site and its chronology, and to develop hypotheses about commercial and cultural exchanges, social organisation, resource exploitation, and taphonomic processes. This study presents a surv...
Article
Full-text available
Unravelling the genetic basis of adaptive traits is a major challenge in evolutionary biology. Doing so informs our understanding of evolution towards an adaptive optimum, the distribution of locus effect sizes, and the influence of genetic architecture on the evolvability of a trait. In the Müllerian co-mimics Heliconius melpomene and Heliconius e...
Article
Full-text available
Accurate species identification in fossil remains is a complex task but is a key component for developing good inferences on many, if not all, fundamental questions in macroecology and macroevolution. In the Quaternary, arvicolines are very abundant remains in archeological and paleontological sites in Western Europe and their identification is oft...
Article
Full-text available
Rock art studies are facing major technical challenges for extensive documentation. Nowadays, recording is essentially obtained from time-consuming tracing and rubbing, techniques that also require a high level of expertise. Recent advances in 3D modelling of natural objects and computational treatment of the modelled surfaces may provide an altern...
Chapter
Full-text available
Although directional and fluctuating asymmetry have been frequently assessed independently, they are indeed associated concepts both in theory and in practice. However, they can be difficult to disentangle in genome-wide association studies, where the appropriate shape statistics are not fully developed. Although the usage of Procrustes distances t...
Article
Full-text available
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 zirconiumwere determined by ind...
Article
Full-text available
Within the framework of landscape genetics, resistance surface modelling is particularly relevant to explicitly test competing hypotheses about landscape effects on gene flow. To investigate how fragmentation of tropical forest affects population connectivity in a forest-specialist bird species, we optimized resistance surfaces without a priori spe...
Poster
Full-text available
The DACORD functional system orients and draws archaeological pottery, based on 3D model geometry, using modern mathematical, graphical, optimization methods. The orientation workflow combines existing approaches (normal vectors, horizontal/vertical sections, etc.) with new methods, to segment fragments (external and internal surfaces), and to eras...
Conference Paper
Parmi les productions métalliques connues de l'âge du Bronze en Europe, certaines sont considérées comme des productions en série et sont nommées comme telles. Il s'agit en particulier des lames de haches à talon du Bronze moyen au milieu du deuxième millénaire avant notre ère, produites et utilisées massivement en Europe occidentale. Ces objets so...
Data
Full-text available
Data
Full-text available
Data
Full-text available
Article
Full-text available
In the Arctic, food limitation is one of the driving factors behind small mammal population fluctuations. Active throughout the year, voles and lemmings (arvicoline rodents) are central prey in arctic food webs. Snow cover, however, makes the estimation of their winter diet challenging. We analyzed the isotopic composition of ever-growing incisors...
Article
The classification of Western European flanged axes dating to the Middle Bronze Age (1650–1350 BC) is very complex. Many types of axe have been identified, some of which have numerous variant forms. In the current French terminology, all axes are divided into two generic groups: namely " Atlantic " (Atlantique) and " Eastern " (Orientale). Each of...
Article
Full-text available
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 e...
Article
Full-text available
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 re...
Article
Full-text available
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...
Article
Full-text available
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 organizatio...
Article
Full-text available
The characteristics of dissolved organic matter (DOM) in soils are often determined through laboratory experiments. Many different protocols can be used to extract organic matter from soil. In this study, we used five air-dried soils to compare three extraction methods for water-extractable organic matter (WEOM) as follows: (i) pressurised hot-wate...
Article
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...
Chapter
Full-text available
Our understanding of evolutionary processes has changed tremendously in the last few decades, most notably by advances in genetics and developmental biology that have transformed the approaches of evolutionary biologists (Amundson, 2005; Klingenberg, 2010). Among other changes, the use of model systems has become more widespread in evolutionary bio...
Book
Full-text available
http://www.cambridge.org/gb/knowledge/isbn/item6687735/Evolution-of-the-House-Mouse/?site_locale=en_GB
Data
Superimposition of wings. In each case, photos of the two wings of the same individual were superimposed: in red the left wing and in green the right wing. A, B and C: Individuals overexpressing CycG ubiquitously under control of the da::Gal4 driver using different RCG lines (RCG23.3, RCG69) or CG line (CG2.1). D and E: Individuals overexpressing C...
Data
Effects of CycG deregulation in a yw67c23 background. A, B, and C: CycG overexpression; D, E and F: CycG inactivation. A and D: Discriminant analysis of the wing shape data. Each dot represents an individual fly (wing shape averaged over the right and left sides). GOF flies and LOF flies are completely discriminated from control flies, respectively...
Data
Overexpression and downregulation of CycG. Total RNA was extracted from third instar larvae using the RNeasy kit (Qiagen). Real-time PCR was performed in triplicate using Taqman® Gene Expression Assays (Dm02151951_m1 CycG, Applied Biosystems) on a ABI prism 7700 detection system. Results were normalized against Gapdh1 (Dm01843827_s1, Applied Biosys...
Data
Comparison of patterns of shape FA (females). Correlation of PC1s of FA matrices for all genotypes as measured by the angles among PCs. In brackets are the associated P-values. Top: H0 = the null hypothesis is that the angles between FA PCs are not different from those between pairs of random vectors (10000 random 26 dimensional vectors). A signifi...
Data
Effects on mean cell size and cell number. Mean wing cell size and cell number and standard deviations (Sd) are provided. Note that cell size is in arbitrary unit, being computed as one divided by the number of cells counted in the standardized area (see Figure 3C′). Cell number strongly underestimate the real cell number in the wing: only one side...
Data
Impact of allometry on mean wing shape discrimination (yw67c2 background). A: Discriminant analysis applied to the shape variables (i.e. non null PC scores; grouping factor: genotype*sex). B: Discriminant analysis applied to the residuals of a multivariate regression of size on shape variables. Grey: +/+ females; black: +/+ males; light green: GOF...
Data
Wing shape FA. Results of the Procrustes ANOVAs (individual and side as main effects). MS and FA10 values are multiplied by 107. Df = degrees of freedom; MS = mean squares; F = Fisher's F value. (DOC)
Data
Effects on cell size and cell number FA. FA values for each genotype and sex is provided, as well as the statistical tests of comparison with the controls (F tests). The correlation between cell size and cell number FA with wing size FA were computed. Both Pearson parametric correlation coefficient and Spearman non parametric correlation were compu...
Data
Effects of CycG deregulation on mean wing size and shape. Mean centroid size values and standard deviations (Sd) are provided. Results of the ANOVAs on centroid size and MANOVAs on the PC scores (genotype and sex as fixed factors). GOF = gain of function; LOF = loss of function; +/+ = controls; f = females; m = males. Sd = standard deviation; Df =...
Data
Wing size FA. Results of the two-way mixed model ANOVAs on centroid size (individual = random; side = fixed). The tests are presented for the three control genotypes in the GOF experiments using da as driver (see Material and Methods). FA10 and FA4 are two FA indices (see Material and Methods). FA effect refers to the ratio of the GOF or LOF FA val...
Data
Femur length FA. Results of the two-way mixed model ANOVAs on femur length (individual = random; side = fixed). Df = degrees of freedom; MS = mean squares; F = Fisher's F value. (DOC)
Data
Covariation between cell size and cell number. Top: Pearson 's correlation coefficients (r) were computed for each genotypes. They were then compared statistically after applying a Fisher r to Z transformation. Bottom: Analysis of the residuals of regressions of cell size over cell number for each genotype and sex. Statistical significance of varia...
Article
Full-text available
Models in QTL mapping can be improved by considering all potential variables, i.e. we can use remaining traits other than the trait under study as potential predictors. QTL mapping is often conducted by correcting for a few fixed effects or covariates (e.g. sex, age), although many traits with potential causal relationships between them are recorde...