Sequence analyses of the distal-less homeobox gene family in East African cichlid fishes reveal signatures of positive selection

Evidence of positive selection on six spider developmental genes

Spiders constitute more than 49,000 described species distributed all over the world, and all ecological environments. Their order, Araneae, is defined by a set of characteristics with no parallel among their arachnid counterparts (e.g., spinnerets, silk glands, chelicerae that inoculate venom, among others). Changes in developmental pathways often underlie the evolution of morphological synapomorphies, and as such spiders are a promising model to study the role of developmental genes in the origin of evolutionary novelties. With that in mind, we investigated changes in the evolutionary regime of a set of six developmental genes, using spiders as our model. The genes were mainly chosen for their roles in spinneret ontogeny, yet they are pleiotropic, and it is likely that the origins of other unique morphological phenotypes are also linked to changes in their sequences. Our results indicate no great differences in the selective pressures on those genes when comparing spiders to other arachnids, but a few site-specific positive selection evidence were found in the Araneae lineage. These findings lead us to new insights on spider evolution that are to be further tested.

Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika

With more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3-9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.

Characterization of the distal-less homologue gene, PfDlx, involved in regulating the expression of Pif in the pearl oyster, Pinctada fucata

Distal-less (Dlx) homeobox transcription factors play an important role in regulating various aspects of vertebrate biology. In vertebrates and invertebrates, distal-less is a highly conserved and well-studied transcription factor. In pearl oyster, we have identified a homologue of this gene, Dlx, and cloned the full-length cDNA. Genomic structure analysis revealed that PfDlx genomic DNA contained three exons and two introns. Their deduced amino acid sequences all showed the highest identity with homologues in Crassostrea gigas. Analyses of PfDlx mRNA in tissues and developmental stages showed high expressions in gonad, polar body stage, 2-4 cells and 32 cells. After shell notching, the changes in expression of Dlx shows that it reached a maximum at 24h. In co-transfection experiments, PfDlx significantly activates reporter constructs containing a Pif promoter. Through using RNAi techniques, we demonstrated that down-regulation of Dlx in P. fucata did not significantly disrupt the development of the nacreous layer in scanning electron microscopy, but it significantly down-regulated the expression of Pif gene. Thus, our work suggests that PfDlx might participate in regulating the expression of the Pif gene in the pearl oyster.

Refuting the hypothesis that the acquisition of germ plasm accelerates animal evolution

Primordial germ cells (PGCs) give rise to the germ line in animals. PGCs are specified during embryogenesis either by an ancestral mechanism of cell-cell signalling (induction) or by a derived mechanism of maternally provided germ plasm (preformation). Recently, a hypothesis was set forth purporting that germ plasm liberates selective constraint and accelerates an organism's protein sequence evolution, especially for genes from early developmental stages, thereby leading to animal species radiations; empirical validation has been claimed in vertebrates. Here we present findings from global rates of protein evolution in vertebrates and invertebrates refuting this hypothesis. Contrary to assertions of the hypothesis, we find no effect of preformation on protein sequence evolution, the evolutionary rates of early-stage developmental genes, or on species diversification. We conclude that the hypothesis is mechanistically implausible, and our multi-faceted analysis shows no empirical support for any of its predictions.

Applications in the search for genomic selection signatures in fish

Selection signatures are genomic regions harboring DNA sequences functionally involved in the genetic variation of traits subject to selection. Selection signatures have been intensively studied in recent years because of their relevance to evolutionary biology and their potential association with genes that control phenotypes of interest in wild and domestic populations. Selection signature research in fish has been confined to a smaller scale, due in part to the relatively recent domestication of fish species and limited genomic resources such as molecular markers, genetic mapping, DNA sequences, and reference genomes. However, recent genomic technology advances are paving the way for more studies that may contribute to the knowledge of genomic regions underlying phenotypes of biological and productive interest in fish.

Immune-related functions of the Hivep gene family in East African cichlid fishes

Immune-related genes are often characterized by adaptive protein evolution. Selection on immune genes can be particularly strong when hosts encounter novel parasites, for instance, after the colonization of a new habitat or upon the exploitation of vacant ecological niches in an adaptive radiation. We examined a set of new candidate immune genes in East African cichlid fishes. More specifically, we studied the signatures of selection in five paralogs of the human immunodeficiency virus type I enhancer-binding protein (Hivep) gene family, tested their involvement in the immune defense, and related our results to explosive speciation and adaptive radiation events in cichlids. We found signatures of long-term positive selection in four Hivep paralogs and lineage-specific positive selection in Hivep3b in two radiating cichlid lineages. Exposure of the cichlid Astatotilapia burtoni to a vaccination with Vibrio anguillarum bacteria resulted in a positive correlation between immune response parameters and expression levels of three Hivep loci. This work provides the first evidence for a role of Hivep paralogs in teleost immune defense and links the signatures of positive selection to host-pathogen interactions within an adaptive radiation.