The determinants of the molecular substitution process in turtles

Neutral rates of molecular evolution vary across species, and this variation has been shown to be related to biological traits. One of the first patterns to be observed in vertebrates has been an inverse relationship between body mass (BM) and substitution rates. The effects of three major life-history traits (LHT) that covary with BM - metabolic rate, generation time and longevity (LON) - have been invoked to explain this relationship. However, most of the theoretical and empirical evidence supporting this relationship comes from endothermic vertebrates, that is, mammals and birds, in which the environmental conditions, especially temperature, do not have a direct impact on cellular and molecular biology. We analysed the variations in mitochondrial and nuclear rates of synonymous substitution across 224 turtle species and examined their correlation with two LHT (LON and BM) and two environmental variables [latitude (LAT) and habitat]. Our analyses indicate that in turtles, neutral rates of molecular evolution are hardly correlated with LON or BM. Rather, both the mitochondrial and nuclear substitution rates are significantly correlated with LAT - faster evolution in the tropics - and especially so for aquatic species. These results question the generality of the relationships reported in mammals and birds and suggest that environmental factors might be the strongest determinants of the mutation rate in ectotherms.

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true gene content is unclear, and from which SNP definition is uneasy. Here, the transcriptomes of five diverse non-model animal species (hare, turtle, ant, oyster and tunicate) were assembled from newly generated 454 and Illumina sequence reads. In two species for which a reference genome is available, a new procedure was introduced to annotate each predicted contig as either a full-length cDNA, fragment, chimera, allele, paralogue, genomic sequence or other, based on the number of, and overlap between, blast hits to the appropriate reference. Analyses showed that (i) the highest quality assemblies are obtained when 454 and Illumina data are combined, (ii) typical de novo assemblies include a majority of irrelevant cDNA predictions and (iii) assemblies can be appropriately cleaned by filtering contigs based on length and coverage. We conclude that robust, reference-free assembly of thousands of genes from transcriptomic NGS data is possible, opening promising perspectives for transcriptome-based population genomics in animals. A Galaxy pipeline implementing our best-performing assembling strategy is provided.

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true gene content is unclear, and from which SNP definition is uneasy. Here, the transcriptomes of five diverse non-model animal species (hare, turtle, ant, oyster and tunicate) were assembled from newly generated 454 and Illumina sequence reads. In two species for which a reference genome is available, a new procedure was introduced to annotate each predicted contig as either a full-length cDNA, fragment, chimera, allele, paralogue, genomic sequence or other, based on the number of, and overlap between, blast hits to the appropriate reference. Analyses showed that (i) the highest quality assemblies are obtained when 454 and Illumina data are combined, (ii) typical de novo assemblies include a majority of irrelevant cDNA predictions and (iii) assemblies can be appropriately cleaned by filtering contigs based on length and coverage. We conclude that robust, reference-free assembly of thousands of genes from transcriptomic NGS data is possible, opening promising perspectives for transcriptome-based population genomics in animals. A Galaxy pipeline implementing our best-performing assembling strategy is provided.

New evidence for parallel evolution of colour patterns in Malagasy poison frogs (Mantella)

Malagasy poison frogs of the genus Mantella are diurnal and toxic amphibians of highly variable and largely aposematic coloration. Previous studies provided evidence for several instances of homoplastic colour evolution in this genus but were unable to sufficiently resolve relationships among major species groups or to clarify the phylogenetic position of several crucial taxa. Here, we provide cytochrome b data for 143 individuals of three species in the Mantella madagascariensis group, including four newly discovered populations. Three of these new populations are characterized by highly variable coloration and patterns but showed no conspicuous increase of haplotype diversity which would be expected under a scenario of secondary hybridization or admixture of chromatically uniform populations. Several populations of these variable forms and of M. crocea were geographically interspersed between the distribution areas of Mantella aurantiaca and Mantella milotympanum. This provides further support for the hypothesis that the largely similar uniformly orange colour of the last two species evolved in parallel. Phylogenies based on over 2000 bp of two nuclear genes (Rag-1 and Rag-2) identified reliably a clade of the Mantella betsileo and Mantella laevigata groups as sister lineage to the M. madagascariensis group, but did not support species within the latter group as monophyletic. The evolutionary history of these frogs might have been characterized by fast and recurrent evolution of colour patterns, possibly triggered by strong selection pressures and mimicry effects, being too complex to be represented by simple bifurcating models of phylogenetic reconstruction.