Parallel habitat acclimatization is realized by the expression of different genes in two closely related salamander species (genus Salamandra)

Abstract

The utilization of similar habitats by different species provides an ideal opportunity to identify genes underlying adaptation and acclimatization. Here, we analysed the gene expression of two closely related salamander species: Salamandra salamandra in Central Europe and Salamandra infraimmaculata in the Near East. These species inhabit similar habitat types: 'temporary ponds' and 'permanent streams' during larval development. We developed two species-specific gene expression microarrays, each targeting over 12 000 transcripts, including an overlapping subset of 8331 orthologues. Gene expression was examined for systematic differences between temporary ponds and permanent streams in larvae from both salamander species to establish gene sets and functions associated with these two habitat types. Only 20 orthologues were associated with a habitat in both species, but these orthologues did not show parallel expression patterns across species more than expected by chance. Functional annotation of a set of 106 genes with the highest effect size for a habitat suggested four putative gene function categories associated with a habitat in both species: cell proliferation, neural development, oxygen responses and muscle capacity. Among these high effect size genes was a single orthologue (14-3-3 protein zeta/YWHAZ) that was downregulated in temporary ponds in both species. The emergence of four gene function categories combined with a lack of parallel expression of orthologues (except 14-3-3 protein zeta) suggests that parallel habitat adaptation or acclimatization by larvae from S. salamandra and S. infraimmaculata to temporary ponds and permanent streams is mainly realized by different genes with a converging functionality.

Plasticity and evolutionary divergence in gene expression associated with alternative habitat use in larvae of the European Fire Salamander

“…Samples and transcriptome data are identical to a subset of samples (specifically those from the Kottenforst) already analysed in Goedbloed et al. (). Freshly deposited larvae (with a visible ventral yolk patch) or large larvae with morphological signs of metamorphosis (appearing yellow knee patches, degeneration of gills) were not included in the sampling.…”

“…We used a species‐specific custom microarray described in detail in Goedbloed et al. . This microarray (Agilent Design ID 069636) probed 12,710 genes.…”

“…A recent ecological transcriptomics study compared the European Fire salamander S. salamandra (including populations from Kottenforst) with the Near Eastern Fire salamander S. infraimmaculata (Goedbloed et al. ). The analysis provided evidence that habitat‐specific transcriptome patterns are common among larvae at the species and population level.…”

Morphological and transcriptomic analyses reveal three discrete primary stages of postembryonic development in the common fire salamander, Salamandra salamandra

“…Total RNA from the tail‐clips of 23 individuals was extracted using Trizol, and subsequently hybridized to a gene expression microarray specifically developed for S. salamandra (Goedbloed et al., ) using the Agilent Low Input Quick Amp Labelling kit for “One‐Color Microarray‐Based Gene Expression Analysis.” The fluorescence signal intensities were quantified in an Agilent DNA Microarray Scanner type C. A normalization between arrays and a filtering of non‐expressed genes or genes expressed below the detection limit were performed using a customized R code (Czypionka et al., ). From the gene expression data, we performed an a priori hierarchical clustering from a distance matrix based on Pearson's correlation coefficient in R. Probes, for which at least one sample had missing data were excluded from the analysis of differential gene expression.…”

“…Total RNA from the tail-clips of 23 individuals was extracted using Trizol, and subsequently hybridized to a gene expression microarray specifically developed for S. salamandra (Goedbloed et al, 2017) using the Agilent Low Input Quick Amp Labelling kit for "One-Color Microarray-Based Gene Expression Analysis." The fluorescence signal intensities were quantified in an Agilent DNA Microarray Scanner type C. A normalization between arrays and a filtering of non-expressed genes or genes expressed below the detection limit were performed using a customized R code (Czypionka et al, 2015).…”