Fine Mapping without Phenotyping: Identification of Selection Targets in Secondary Evolve and Resequence Experiments

Signatures of selection in Mulinia lateralis underpinning its rapid adaptation to laboratory conditions

The dwarf surf clam, Mulinia lateralis, is considered as a model species for bivalves because of its rapid growth and short generation time. Recently, successful breeding of this species for multiple generations in our laboratory revealed its acquisition of adaptive advantages during artificial breeding. In this study, 310 individuals from five different generations were genotyped with 22,196 single nucleotide polymorphisms (SNPs) with the aim of uncovering the genetic basis of their adaptation to laboratory conditions. Results revealed that M. lateralis consistently maintained high genetic diversity across generations, characterized by high observed heterozygosity (H o: 0.2733-0.2934) and low levels of inbreeding (F is: -0.0244-0.0261). Population analysis indicated low levels of genetic differentiation among generations of M. lateralis during artificial breeding (F st <0.05). In total, 316 genomic regions exhibited divergent selection, with 168 regions under positive selection. Furthermore, 227 candidate genes were identified in the positive selection regions, which have functions including growth, stress resistance, and reproduction. Notably, certain selection signatures with significantly higher F st value were detected in genes associated with male reproduction, such as GAL3ST1, IFT88, and TSSK2, which were significantly upregulated during artificial breeding. This suggests a potential role of sperm-associated genes in the rapid evolutionary response of M. lateralis to selection in laboratory conditions. Overall, our findings highlight the phenotypic and genetic changes, as well as selection signatures, in M. lateralis during artificial breeding. This contributes to understanding their adaptation to laboratory conditions and underscores the potential for using this species to explore the adaptive evolution of bivalves.

Highly Parallel Genomic Selection Response in Replicated Drosophila melanogaster Populations with Reduced Genetic Variation

Many adaptive traits are polygenic and frequently more loci contributing to the phenotype are segregating than needed to express the phenotypic optimum. Experimental evolution with replicated populations adapting to a new controlled environment provides a powerful approach to study polygenic adaptation. Because genetic redundancy often results in nonparallel selection responses among replicates, we propose a modified evolve and resequence (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29 °C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Because two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.