Differential local genetic adaptation to pesticide use in organic and conventional agriculture in an aquatic non-target species

Pesticide application is an important stressor to non-target species and can profoundly affect ecosystem functioning. Debates continue on the choice of agricultural practices regarding their environmental impact, and organic farming is considered less detrimental compared to conventional practices. Nevertheless, comparative studies on the impacts of both agricultural approaches on the genetic adaptation of non-target species are lacking. We assessed to what extent organic and conventional agriculture elicit local genetic adaptation of populations of a non-target aquatic species, Daphnia magna . We tested for genetic differences in sensitivity of different D. magna populations ( n = 7), originating from ponds surrounded by conventional and organic agriculture as well as nature reserves, to pesticides used either in conventional (chlorpyrifos) or organic agriculture (deltamethrin and copper sulfate). The results indicate that D. magna populations differentially adapt to local pesticide use. Populations show increased resistance to chlorpyrifos as the percentage of conventional agriculture in the surrounding landscape increases, whereas populations from organic agriculture sites are more resistant to deltamethrin. While organic agriculture is considered less harmful for non-target species than conventional, both types of agriculture shape the evolution of pesticide resistance in non-target species in a specific manner, reflecting the differences in selection pressure.

Culture is Reducing Genetic Heritability and Superseding Genetic Adaptation

Uchiyama, Spicer, and Muthukrishna reveal how group-structured cultural variation influences measurements of trait heritability. We argue that understanding culture’s influence on phenotypic heritability can clarify the impact of culture on genetic inheritance, which has implications for long-term gene-culture coevolution. Their analysis may provide guidance for testing our hypothesis that cultural adaptation is superseding genetic adaptation in the long term.

Detecting Cd adaptation footprint in C. riparius with a multi-genomic approach

Evolutionary processes and acquired tolerance to toxicants are important factors governing how animals respond to chemical exposure. Evidence for increased tolerance to cadmium (Cd), a widely distributed toxic metal in aquatic environments, in Chironomus riparius is conflicting and still questioned if it happens through phenotypic plasticity or genetic adaptation. The present study considered the relevance of directional environmental changes by increasing contaminant concentration in a multigenerational selection experiment. Evaluation of measurable life-cycle traits, transcriptomic responses and quantitative genetics from an evolve and resequencing (E&R) experiment were integrated to assess the potential of C. riparius to adapt to Cd. Survival tests revealed some adaptation to Cd exposure. Genomic analyses showed a strong, genome-wide selective response in all replicates, emphasizing that even control laboratory conditions continually exert selective pressure. The integration of transcriptomic and genomic data could isolate the genes related to Cd acquired resistance. Those genes could be linked to an efflux of metals. Therefore, it is possible to conclude that C. riparius can endure long-term Cd exposure also through genetic adaptation.

The Escherichia coli SOS Response: Much More than DNA Damage Repair

The Escherichia coli SOS response is an inducible DNA damage repair pathway controlled by two key regulators, LexA, a repressor and RecA, an inducer. Upon DNA damage RecA is activated and stimulates self cleavage of LexA, leading to, in E. coli, derepresion of approximately 50 SOS genes. The response is triggered by exogenous and endogenous signals that bacteria encounter at a number of sites within the host. Nevertheless, besides regulating DNA damage repair the SOS response plays a much broader role. Thus, SOS error prone polymerases promote elevated mutation rates significant for genetic adaptation and diversity, including antibiotic resistance. Here we review the E. coli SOS response in relation to recalcitrance to antimicrobials, including persister and biofilm formation, horizontal gene tranfer, gene mobility, bacterial pathogenicity, as well SOS induced bacteriocins that drive diversification. Phenotypic heterogeneity in expression of the SOS regulator genes, recA and lexA as well as colicin activity genes is also discussed.

Recruitments of Sherpa highlanders and non-Sherpa lowlanders v1

In order to carry out the research project of genetic adaptation to high-altitude hypoxia in Sherpa highlanders, we recruited Sherpa highlanders in Namche Bazaar village at a high altitude of 3,440 meters (m) above sea level and non-Sherpa lowlanders in Kathmandu city at 1,300 m in Nepal. Venous blood was sampled to obtain plasma and extract DNA in each subject. The concentrations of factors in plasma were measured. The single-nucleotide polymorphisms (SNPs) in the hypoxia-associated genes were genotyped.

Genetic and climatic factors in the dispersal of Anatomically Modern Humans Out of Africa

The evolutionarily recent dispersal of Anatomically Modern Humans (AMH) out of Africa and across Eurasia provides an opportunity to study rapid genetic adaptation to multiple new environments. Genomic analyses of modern human populations have detected limited signals of strong selection such as hard sweeps, but genetic admixture between populations is capable of obscuring these patterns and is well known in recent human history, such as during the Bronze Age4. Here we show that ancient human genomic datasets contain multiple genetic signatures of strong selection including 57 hard sweeps, many with strong associations with cold adaptation. Similar genetic signatures of adaptation are also observed in adaptively-introgressed archaic hominin loci, as well as modern Arctic human groups. Consistent targets include the regulation of fat storage, skin physiology, cilia function and neural development; with multiple associations to modern western diseases. The spatiotemporal patterns of the hard sweeps allow reconstruction of early AMH population dispersals, and reveal a prolonged period of genetic adaptation (~80-50,000 years) following their initial out of Africa movement, before a rapid spread across Eurasia reaching as far as Australia.

Achromobacter spp. genetic adaptation in cystic fibrosis

Achromobacter spp. are emerging pathogens in patients with cystic fibrosis (CF) and Achromobacter spp. caused infections are associated with more severe disease outcomes and high intrinsic antibiotic resistance. While conventional CF pathogens are studied extensively, little is known about the genetic determinants leading to antibiotic resistance and the genetic adaptation in Achromobacter spp. infections. Here, we analysed 101 Achromobacter spp. genomes from 51 patients with CF isolated during the course of up to 20 years of infection to identify within-host adaptation, mutational signatures and genetic variation associated with increased antibiotic resistance. We found that the same regulatory and inorganic ion transport genes were frequently mutated in persisting clone types within and between Achromobacter species, indicating convergent genetic adaptation. Genome-wide association study of six antibiotic resistance phenotypes revealed the enrichment of associated genes involved in inorganic ion transport, transcription gene enrichment in β-lactams, and energy production and translation gene enrichment in the trimethoprim/sulfonamide group. Overall, we provide insights into the pathogenomics of Achromobacter spp. infections in patients with CF airways. Since emerging pathogens are increasingly recognized as an important healthcare issue, our findings on evolution of antibiotic resistance and genetic adaptation can facilitate better understanding of disease progression and how mutational changes have implications for patients with CF.