What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda.

Developmental pathways encompass transcription factors and cis-regulatory elements that interact as transcription factor-regulatory element (TF-RE) units. Independent origins of similar phenotypes likely involve changes in different parts of these units, a hypothesis promisingly tested addressing the evolution of the rib-associated lumbar (RAL) morphotype that characterizes emblematic animals such as snakes and elephants. Previous investigation in these lineages identified a polymorphism in the Homology region 1 [H1] enhancer of the Myogenic factor-5 [Myf5], which interacts with HOX10 proteins to modulate rib development. Here we address the evolution of TF-RE units focusing on independent origins of RAL morphotypes. We compiled an extensive database for H1-Myf5 and HOX10 sequences with two goals: (i) evaluate if the enhancer polymorphism is present in amphibians exhibiting the RAL morphotype and (ii) test a hypothesis of enhanced evolutionary flexibility mediated by TF-RE units, according to which independent origins of the RAL morphotype might involve changes in either component of the interaction unit. We identified the H1-Myf5 polymorphism in lineages that diverged around 340 Ma, including Lissamphibia. Independent origins of the RAL morphotype in Tetrapoda involved sequence variation in either component of the TF-RE unit, confirming that different changes may similarly affect the phenotypic outcome of a given developmental pathway.

A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.

BACKGROUND: High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. FINDINGS: We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. CONCLUSIONS: These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

Peculiar relationships among morphology, burrowing performance and sand type in two fossorial microteiid lizards.

Associations among ecology, morphology and locomotor performance have been intensively investigated in several vertebrate lineages. Knowledge on how phenotypes evolve in natural environments likely benefits from identification of circumstances that might expand current ecomorphological equations. In this study, we used two species of Calyptommatus lizards from Brazilian Caatingas to evaluate if specific soil properties favor burrowing performance. As a derived prediction, we expected that functional associations would be easily detectable at the sand condition that favors low-resistance burrowing. We collected two endemic lizards and soil samples in their respective localities, obtained morphological data and recorded performance of both species in different sand types. As a result, the two species burrowed faster at the fine and homogeneous sand, the only condition where we detected functional associations between morphology and locomotion. In this sand type, lizards from both Calyptommatus species that have higher trunks and more concave heads were the ones that burrowed faster, and these phenotypic traits did not morphologically discriminate the two Calyptommatus populations studied. We discuss that integrative approaches comprising manipulation of environmental conditions clearly contribute to elucidate processes underlying phenotypic evolution in fossorial lineages.

Somitogenesis and Axial Development in Reptiles.

Among amniote vertebrates, reptiles display the greatest variation in axial skeleton morphology. Only recently have they been used in gene expression studies of somitogenesis , challenging previous assumptions about the segmentation clock and axial patterning. An increasing number of reptile genomes and transcriptomes are becoming available as next-generation sequencing becomes more affordable. Information regarding gene sequence and structure can be used to design and synthesize labeled riboprobes by in vitro transcription for gene expression analysis by in situ hybridization, thus, enabling the characterization of spatial and temporal expression patterns of genes involved in somitogenesis, a topic of great interest within evolutionary developmental studies of vertebrates.

Evolutionary Developmental Biology (Evo-Devo) Research in Latin America.

Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community.

Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles.

Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription factors with multiple functions. Some motifs mediating protein-protein interactions may be exclusive to particular developmental roles, but it is also possible that motifs are mostly shared among different processes. Here we focus on HoxA13, a protein essential for limb development. We asked whether the HoxA13 amino acid sequence evolved similarly in three limbless clades: Gymnophiona, Amphisbaenia and Serpentes. We explored variation in ω (dN/dS) using a maximum-likelihood framework and HoxA13sequences from 47 species. Comparisons of evolutionary models provided low ω global values and no evidence that HoxA13 experienced relaxed selection in limbless clades. Branch-site models failed to detect evidence for positive selection acting on any site along branches of Amphisbaena and Gymnophiona, while three sites were identified in Serpentes. Examination of alignments did not reveal consistent sequence differences between limbed and limbless species. We conclude that HoxA13 has no modules exclusive to limb development, which may be explained by its involvement in multiple developmental processes.

Musculoskeletal anatomical changes that accompany limb reduction in lizards.

Muscles, bones, and tendons in the adult tetrapod limb are intimately integrated, both spatially and functionally. However, muscle and bone evolution do not always occur hand in hand. We asked, how does the loss of limb bones affect limb muscle anatomy, and do these effects vary among different lineages? To answer these questions, we compared limb muscular and skeletal anatomy among gymnophthalmid lizards, which exhibit a remarkable variation in limb morphology and different grades of digit and limb reduction. We mapped the characters onto a phylogeny of the group to assess the likelihood that they were acquired independently. Our results reveal patterns of reduction of muscle and bone elements that did not always coincide and examples of both, convergent and lineage-specific non-pentadactyl musculoskeletal morphologies. Among lineages in which non-pentadactyly evolved independently, the degree of convergence seems to depend on the number of digits still present. Most tetradactyl and tridactyl limbs exhibited profound differences in pattern and degree of muscle loss/reduction, and recognizable morphological convergence occurred only in extremely reduced morphologies (e.g., spike-like appendix). We also found examples of muscles that persisted although the bones to which they plesiomorphically attach had been lost, and examples of muscles that had been lost although their normal bony attachments persisted. Our results demonstrate that muscle anatomy in reduced limbs cannot be predicted from bone anatomy alone, meaning that filling the gap between osteological and myological data is an important step toward understanding this recurrent phenomenon in the evolution of tetrapods.

Evolution of body elongation in gymnophthalmid lizards: relationships with climate.

The evolution of elongated body shapes in vertebrates has intrigued biologists for decades and is particularly recurrent among squamates. Several aspects might explain how the environment influences the evolution of body elongation, but climate needs to be incorporated in this scenario to evaluate how it contributes to morphological evolution. Climatic parameters include temperature and precipitation, two variables that likely influence environmental characteristics, including soil texture and substrate coverage, which may define the selective pressures acting during the evolution of morphology. Due to development of geographic information system (GIS) techniques, these variables can now be included in evolutionary biology studies and were used in the present study to test for associations between variation in body shape and climate in the tropical lizard family Gymnophthalmidae. We first investigated how the morphological traits that define body shape are correlated in these lizards and then tested for associations between a descriptor of body elongation and climate. Our analyses revealed that the evolution of body elongation in Gymnophthalmidae involved concomitant changes in different morphological traits: trunk elongation was coupled with limb shortening and a reduction in body diameter, and the gradual variation along this axis was illustrated by less-elongated morphologies exhibiting shorter trunks and longer limbs. The variation identified in Gymnophthalmidae body shape was associated with climate, with the species from more arid environments usually being more elongated. Aridity is associated with high temperatures and low precipitation, which affect additional environmental features, including the habitat structure. This feature may influence the evolution of body shape because contrasting environments likely impose distinct demands for organismal performance in several activities, such as locomotion and thermoregulation. The present study establishes a connection between morphology and a broader natural component, climate, and introduces new questions about the spatial distribution of morphological variation among squamates.