Establishing laboratory cultures and performing ecological and evolutionary experiments with the emerging model species <i>Chironomus riparius</i>

Foucault

2020

Molecular Ecology

Self Cite

Evolve and Resquence (E&R) studies are a useful tool to study genomic processes during rapid adaptation, e.g., in the framework of adaptive responses to global climate change. We applied different thermal regimes to a natural Chironomus riparius (Diptera) population in an E&R framework to infer its evolutionary potential for rapid thermal adaptation. We exposed two replicates to three temperatures each (14°C, 20°C and 26°C) for more than two years, the experiment thus lasting 22, 44 or 65 generations, respectively. The two higher temperatures presented a priori moderate, respectively strong selection pressures. Life‐cycle fitness tests revealed no appreciable adaptation to thermal regimes but a common adaptation of all six replicates probably due to the rearing conditions, presumably increased larval density and water quality. Genomic analyses showed a strong, genome‐wide selective response in all replicates (mean s of selected SNPs = 0.305). This genomic response was significantly similar at all genomic levels among all replicates (SNPs, 10 kb windows, genes, exons, regions of elevated allele frequency change [REA]). The intersections among the replicates exposed to the same temperature were either insignificant or underrepresented. This confirmed a selective response to identical selection pressure(s), however, not to thermal regime. Genes closest to the SNP with the highest selection coefficient per REA were enriched for GO terms related to ion transport, regulation of transcription and signal transduction, which supported the presumed acting selection pressures. Our study showed the evolutionary potential for rapid adaptation by genome‐wide and probably polygenic selection on standing genetic variation in C. riparius. However, because of the impossibility to accurately predict the acting selective regime in evolutionary experiments, we discuss the sobering perspectives for inferring the evolutionary potential of natural populations with this approach.

Section: Methodsmentioning

confidence: 99%

Genomic processes underlying rapid adaptation of a natural Chironomus riparius population to unintendedly applied experimental selection pressures

Foucault

2020

Molecular Ecology

Self Cite

“…The experimental procedure in producing short-term accumulation lines is mostly straightforward (Foucault et al, 2019). One important issue is the necessity to start with an excess of MA lines (1.5-2 times the intended number), since it is not uncommon that single lines fail to reproduce at some point during the process.…”

Section: Discussionmentioning

confidence: 99%

“…Conductivity was maintained between 550 - 650 μS/cm and pH around 8. All the lines were fed as described elsewhere (Foucault et al, 2019; Oppold and Pfenninger, 2017).…”

Section: Methodsmentioning

confidence: 99%

Measuring mutagenicity in ecotoxicology: A case study of Cd exposure inChironomus riparius

Doria

Waldvogel

2020

Preprint

Self Cite

Existing mutagenicity tests for metazoans lack the direct observation of enhanced germline mutation rates after exposure to anthropogenic substances, therefore being inefficient. Cadmium (Cd) is a metal described as a mutagen in mammalian cells and listed as a group 1 carcinogenic and mutagenic substance. But Cd mutagenesis mechanism is not yet clear. Therefore, in the present study, we propose a method coupling short-term mutation accumulation (MA) lines with subsequent whole genome sequencing (WGS) and a dedicated data analysis pipeline to investigate if chronic Cd exposure on Chironomus riparius can alter the rate at which de novo point mutations appear. Results show that Cd exposure did not affect the basal germline mutation rate nor the mutational spectrum in C. riparius, thereby arguing that exposed organisms might experience a range of other toxic effects before any mutagenic effect may occur. We show that it is possible to establish a practical and easily implemented pipeline to rapidly detect germ cell mutagens in a metazoan test organism. Furthermore, our data implicate that it is questionable to transfer mutagenicity assessments based on in vitro methods to complex metazoans.

“…To provide a fine-scale resolution of the relation between temperature and µ, we report here directly estimated spontaneous single nucleotide mutation rates in the non-biting midge Chironomus riparius under different temperature regimes. C. riparius is a fully developed system for multigeneration experiments 25 with comprehensive genomic resources 26 . A haploid spontaneous single nucleotide µ of 2.1 × 10 -9 has been previously reported 27 .…”

mentioning

confidence: 99%

Temperature-dependence of spontaneous mutation rates

Waldvogel

2020

Preprint

Self Cite

Mutation is the source of genetic variation and the fundament of evolution. At the inter-phase of ecology and evolution, temperature has long been suggested to have a direct impact on realised spontaneous mutation rates. The question is whether mutation rates can be a species-specific constant under variable environmental conditions, such as variation of the ambient temperature. By combining mutation accumulation with whole genome sequencing in a multicellular organism, we provide empirical support to reject this null hypothesis. Instead mutation rates depend on temperature in a U-shaped manner with increasing rates towards both temperature extremes. This relation has important implications for mutation dependent processes in molecular evolution, processes shaping the evolution of mutation rates and even the evolution of biodiversity as such.