Nesomyinae (Rodentia,Mammalia) protocoles for skull form evolution study
Here we aim to define how skull morphology of an endemic and monophyletic clade of rodents (sub-family Nesomyinae), that show considerable morphological variation, has evolved and how its disparity is characterized in this particular geographical and ecological context. We performed a two-dimensional geometric morphometric analysis on 371 dorsal and 400 ventral skull images of 19 species (comprising all nine extant endemic genera) from various Museums voucher specimens (FMNH,MNHN,UADBA, NHM) and tested the influence of three ecological parameters (climate, locomotor habitat and nychthemeral cycle) in a phylogenetic context on size and shape. We addressed the following question: What shaped the morphological diversity observed in extant Nesomyinae rodents in the particular context of Madagascar? To what extent does the skull shape of Nesomyinae reflect their phylogenetic history? Did environmental parameters significantly influenced the shape of the skull and if so, how? To answer those questions, we performed shape analysis of Nesomyinae skulls in dorsal and ventral views, using geometric morphometrics methods. Then, we assessed the significance of phylogenetic signal and tested the influence of ecology on the skull shape and size. We expect that the skulls of different nesomyines, and especially size, to display adaptations to local environments, as insular context is known to favor rapid character displacement towards local optima, but, Madagascar being a particular case with several geographical and ecological continental characteristics more at a continental level, typical insular evolutionary trends might not be observed. In addition, skull morphology can also show low evolutionary lability because of the strong phylogenetic signal in teeth, that are morphologically conserved. In this case, because of the strength of phylogenetic signal, we would expect Nesomyinae skull to be less influenced by ecological variability. As main results of our study: Skull shape appears to importantly reflect phylogeny, whereas skull size does not carry a significant phylogenetic signal. Skull shape also revealed to be significantly influenced by climate while, conversely to what is expected in insular context, skull size is not impacted by any of the ecological factors tested.
Steps to reproduce
The original TPS data and nexus file for the phylogenetic tree have been stored in OSF site: https://osf.io/a8eth/?view_only=abd1896945ee4bbd83cbbbead4c736ea Nesomyinae skull photographs were taken with a macro-photographic CANON EOS including 371 dorsal and 400 ventral images. The images were collected in a standardized way to prevent any bias due to the effect of parallax . The frontal part of the skull was horizontally oriented (parallel to the photographic plane), and in ventral view molar rows were oriented as to be parallel to the photographic plane. We did not included juveniles and very old specimens in our sample. To minimize any potential bias due to sexual dimorphism we have included for each species as many specimens as possible and of both sexes. We defined 27 anatomical landmarks in dorsal and 42 in ventral view digitized using the software tpsDig2. Ventral and dorsal data sets were analyzed separately. First, we performed a Generalized Procrustes Analysis (GPA) using the gpagen function of the geomorph library under the free software R (R Core Team 2016). Asymmetric component was explored using MorphoJ and was removed using bilat.symmetry from geomorph. Principal component analyses (PCA) were performed on shape using gm.prcomp function of the geomorph library. We tested the sexual dimorphism on shape and size with Procrustes ANOVA. We also tested the interspecific allometries with procD.lm from geomorph against centroid size. The phylogenetic signal was the tested on a tree pruned to keep only species of interest using the function keep.tip of the library ape. To quantify phylogenetic signal in size we used the K-statistic methods on size and shape. Phylogeny was then projected on PCA on mean shape per species using using phylomorphospace from the phytools library. Based on recognized ecological characteristics of Nesomyinae , we assigned categories to characterize the three main ecological parameters tested here : locomotion, nychthemeral cycle and climate. Specimens have been assigned to climatic areas based on the locality of their collection.To quantify the influence of ecological factors on size, we performed ANOVA , on shape MANOVA analyses. When morphological descriptors found to carry significant phylogenetic signals we used phylogenetics MANOVA (MANOVAphy). Fit of generalized least square linear model was performed using penalized likelihood method and prior four evolutionary models were tested and compared with the Generalized Information Criterion (GIC). When no significant phylogenetic signal was found in morphological descriptors, the influence of ecological factors was determined using the function aov of the Stats library.