Does soil color affect fish evolution? Differences in color change rate between lineages of the sailfin tetra

ABSTRACT Several organisms match their skin color to the prevalent background color, granting crypsis against predators. The rate at which body color changes occur varies among organisms as a result of physiological constraints and adaptation to variation in contrasts between objects and the environmental background. Faster darkening of body color is favored in environments that show higher amounts of contrast between common objects and the prevailing background. Soil types in Amazon forest streams (igarapés) create distinct environments with respect to the amount of contrast, a result of the amount of sand and clay, which offers different contrasts against dead leaves. Here, we investigated differences in the rates of color change among populations of the sailfin tetra (Crenuchus spilurus) that represent lineages that live in regions of different soil types. Populations inserted into blackwaters (sandy soil) showed higher rates of color darkening in response to exposure to a dark environment composed by dead leaves. We propose that natural selection stemming from predation can favor faster color change rate in environments where there is higher variability of contrasts between leaf litter and soil, which is common in most blackwater streams.

IFN Signaling in Inflammation and Viral Infections: New Insights from Fish Models

The overarching structure of the type I interferon (IFN) system is conserved across vertebrates. However, the variable numbers of whole genome duplication events during fish evolution offer opportunities for the expansion, diversification, and new functionalization of the genes that are involved in antiviral immunity. In this review, we examine how fish models provide new insights about the implication of virus-driven inflammation in immunity and hematopoiesis. Mechanisms that have been discovered in fish, such as the strong adjuvant effect of type I IFN that is used with DNA vaccination, constitute good models to understand how virus-induced inflammatory mechanisms can interfere with adaptive responses. We also comment on new discoveries regarding the role of pathogen-induced inflammation in the development and guidance of hematopoietic stem cells in zebrafish. These findings raise issues about the potential interferences of viral infections with the establishment of the immune system. Finally, the recent development of genome editing provides new opportunities to dissect the roles of the key players involved in the antiviral response in fish, hence enhancing the power of comparative approaches.

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.