Similarities and differences in the associations of biological entities among species can provide us with a better understanding of evolutionary relationships. Often the evolution of new phenotypes results from changes to interactions in pre-existing biological networks and comparing networks across species can identify evidence of conservation or adaptation. Gene co-expression networks (GCNs), constructed from high-throughput gene expression data, can be used to understand evolution and the rise of new phenotypes. The increasing abundance of gene expression data makes GCNs a valuable tool for the study of evolution in non-model organisms. In this paper, we cover motivations for why comparing these networks across species can be valuable for the study of evolution. We also review techniques for comparing GCNs in the context of evolution, including local and global methods of graph alignment. While some protein-protein interaction (PPI) bioinformatic methods can be used to compare co-expression networks, they often disregard highly relevant properties, including the existence of continuous and negative values for edge weights. Also, the lack of comparative datasets in non-model organisms has hindered the study of evolution using PPI networks. We also discuss limitations and challenges associated with cross-species comparison using GCNs, and provide suggestions for utilizing co-expression network alignments as an indispensable tool for evolutionary studies going forward.

The freshwater snail Physella acuta was selected to expand the perspective of comparative snail immunology. Analysis of Physella acuta, belonging to the Physidae, taxonomic sister family to Planorbidae, affords family-level comparison of immune features characterized from Biomphalaria glabrata, the model snail often used to interpret general gastropod immunity. To capture constitutive and induced immune sequences, transcriptomes of an individual Physella acuta snail, 12 h post injection with bacteria (Gram -/+) and one sham-exposed snail were recorded with 454 pyrosequencing. Assembly yielded a combined reference transcriptome containing 24,288 transcripts. Additionally, genomic Illumina reads were obtained (∼15-fold coverage). Recovery of transcripts for two macin-like antimicrobial peptides (AMPs), 12 aplysianins, four LBP/BPIs and three physalysins indicated that Physella acuta shares a similar organization of antimicrobial defenses with Biomphalaria glabrata, contrasting a modest AMP arsenal with a diverse set of antimicrobial proteins. The lack of predicted transmembrane domains in all seven Physella acuta PGRP transcripts supports the notion that gastropods do not employ cell-bound PGRP receptors, different from ecdysozoan invertebrates yet similar to mammals (vertebrate deuterostomes). The well-documented sequence diversification by Biomphalaria glabrata FREPs (immune lectins comprising immunoglobulin superfamily domains and fibrinogen domains), resulting from somatic mutations of a large FREP gene family is hypothesized to be unique to Planorbidae; Physella acuta revealed just two bonafide FREP genes and these were not diversified. Furthermore, the flatworm parasite Echinostoma paraensei, confirmed here to infect both snail species, did not evoke from Physella acuta the abundant expression of FREP proteins at 2, 4 and 8 days post exposure that was previously observed from Biomphalaria glabrata. The Physella acuta reference transcriptome also revealed 24 unique transcripts encoding proteins consisting of a single fibrinogen-related domain (FReDs), with a short N-terminal sequence encoding either a signal peptide, transmembrane domain or no predicted features. The Physella acuta FReDs are candidate immune genes based on implication of similar sequences in immunity of bivalve molluscs. Overall, comparative analysis of snails of sister families elucidated the potential for taxon-specific immune features and investigation of strategically selected species will provide a more comprehensive view of gastropod immunity.

In the past century, recently emerged infectious diseases have become major drivers of species decline and extinction. The fungal disease chytridiomycosis has devastated many amphibian populations and exacerbated the amphibian conservation crisis. Biologists are beginning to understand what host traits contribute to disease susceptibility, but more work is needed to determine why some species succumb to chytridiomycosis while others do not. We conducted an integrative laboratory experiment to examine how two toad species respond to infection with the pathogen Batrachochytrium dendrobatidis in a controlled environment. We selected two toad species thought to differ in susceptibility - Bufo marinus (an invasive and putatively resistant species) and Bufo boreas (an endangered and putatively susceptible species). We measured infection intensity, body weight, histological changes and genomewide gene expression using a custom assay developed from transcriptome sequencing. Our results confirmed that the two species differ in susceptibility with the more susceptible species, B. boreas, showing higher infection intensities, loss in body weight, more dramatic histological changes and larger perturbations in gene expression. We found key differences in skin expression responses in multiple pathways including upregulation of skin integrity-related genes in the resistant B. marinus. Together, our results show intrinsic differences in host response between related species, which are likely to be important in explaining variation in response to a deadly emerging pathogen in wild populations. Our study also underscores the importance of understanding differences among host species to better predict disease outcomes and reveal generalities about host response to emerging infectious diseases of wildlife.

Insects are the most diverse group of organisms on the planet. Variation in gene expression lies at the heart of this biodiversity and recent advances in sequencing technology have spawned a revolution in researchers\' ability to survey tissue-specific transcriptional complexity across a wide range of insect taxa. Increasingly, studies are using a comparative approach (across species, sexes and life stages) that examines the transcriptional basis of phenotypic diversity within an evolutionary context. In the present review, we summarize much of this research, focusing in particular on three critical aspects of insect biology: morphological development and plasticity; physiological response to the environment; and sexual dimorphism. A common feature that is emerging from these investigations concerns the dynamic nature of transcriptome evolution as indicated by rapid changes in the overall pattern of gene expression, the differential expression of numerous genes with unknown function, and the incorporation of novel, lineage-specific genes into the transcriptional profile.