PASOS: a method for the phylogenetic analysis of shape ontogenies

Patterns of allometric and heterochronic changes in the early ontogeny of species of Physalaemus (Anura: Leptodactylidae)

We studied the relationship between shape, size, and developmental time in the embryonic ontogeny of 15 species of the frog genus Physalaemus. As in other anuran exotrophic embryos, shape changes are correlated with size increase and mainly concern tail elongation, decrease in body height, and increase in fin height. Size ranges and developmental times vary interspecifically. Embryos of the P. signifer Clade and the P. gracilis Group are among the largest, are slightly peramorphic, and develop fast regarding congeneric species. Embryos of P. cicada combine the smallest sizes with fast development and the most peramorphic shapes. The paedomorphic shapes of embryos of P. biligonigerus and P. henselii groups are correlated with fast vs. slow developmental times respectively. Trajectories in the P. cuvieri Group are diverse and in general differ in size and developmental time. The embryos of P. cristinae and from the Argentinean lineage of P. cuvieri stand out with the longest development. Sequences of developmental events are overall conserved in the genus, and main differences concern mouthpart ontogeny. This study constitutes the first attempt to evaluate morphological, allometric, and heterochronic parameters of the early ontogeny of anurans and how these can vary and contribute to diversification in taxonomic groups.

A three-dimensional geometric morphometric analysis of the morphological transformation of Caiman lower jaw during post-hatching ontogeny

Shape ontogenetic changes of the lower jaw in crocodylians are poorly understood. In order to answer some questions related to the inter- and intraspecific morphological variation of the mandible of two extant Caiman species, we performed a three-dimensional geometric morphometric approach. For this purpose, we used landmarks and semilandmarks on two ontogenetic mandibular series of 48 and 15 post-hatching specimens of C. yacare and C. latirostris, respectively. We have also examined the relationship between these anatomical transformations and ontogenetic shifts in diet. We performed a principal component analysis (PCA) for the two species, and regression and partial least squares (PLS) analyses for each species, separately. As a result, species were segregated along the PC1 with specimens of C. yacare showing more gracile mandibles, and specimens of C. latirostris more robust ones. The PC2 and regression analyses showed an age gradient and represented ontogenetic shape changes. Adult caiman mandibles are higher and wider than juvenile ones, and shape changes are more conspicuous in C. latirostris. The PLS analyses showed a significant relationship between shape and diet. Morphological changes of the PLS1 of block-1 match with those of the regression analysis for both species. We have detected morphological transformations in areas where the musculature in charge of mandibular movements is attached. Common morphological changes occurring during ontogeny seem to reflect the same mechanical properties required for crushing and killing in both species, driven by an ontogenetic shift in the diet from invertebrates to vertebrates. Additionally, interspecific differences were also found to be correlated to ontogenetic changes in diet and could be related to dissimilar feeding mechanical requirements (e.g., stiffness and toughness of the item consumed), and to different habitat preferences. Robust mandibles would be more suitable for shallow and fully vegetated environments, as it can be seen in C. latirostris, whereas slender jaws seem to be more suitable for more aquatic species such as C. yacare.

SPASOS 1.1: a program for the inference of ancestral shape ontogenies

We recently published a method to infer ancestral landmark-based shape ontogenies that takes into account the possible existence of changes in developmental timing. Here we describe SPASOS, a software to perform that analysis. SPASOS is an open-source Windows program written in C. Input data include landmark coordinates for each specimen -with the corresponding information about developmental timing- and a phylogenetic tree showing the relationships among the species sampled. As output, the program produces image files for an easy visualization of the results and data files useful for post-processing. The program incorporates an interpolating function, based on weighting moving averages, which allows analysis of data with scarce information along the ontogenetic trajectory. An empirical evaluation of this function showed its suitability to fill in incomplete ontogenetic trajectories. Finally, we present the results of a reanalysis in SPASOS of a published dataset, where changes in developmental timing were originally inferred by considering PCA scores as shape variables. Both approaches retrieved the same four largest changes in developmental timing, but differed in the ancestral shapes inferred.

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10$\times $ in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.].