Insects Population and Evolutionary Genetics
1. Germline mutation rates across eukaryotics
In this meta-analysis, we make a comprehensive search of the literature for mutation rate estimates in eukaryotes, identifying 140 mutation accumulation (MA) and parent–offspring (PO) sequencing studies covering 134 species. Based on these data, we revisit differences in the single-nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide diversity—while accounting for phylogenetic nonindependence. We do not find a significant difference between MA and PO in estimated mutation rates, but we confirm that mammal and plant lineages have higher mutation rates than arthropods and that unicellular eukaryotes have the lowest mutation rates. We find that mutation rates are higher in species with longer generation times and larger genome sizes, even when accounting for phylogenetic relationships. Moreover, although nucleotide diversity is positively correlated with mutation rate, the gradient of the relationship is significantly less than one (on a logarithmic scale), consistent with higher mutation rates in populations with smaller effective size. For the 29 species for which data are available, we find that indel mutation rates are positively correlated with nucleotide mutation rates and that short deletions are generally more common than short insertions. Nevertheless, despite recent progress, no estimates of either SNM or indel mutation rates are available for the majority of deeply branching eukaryotic lineages—or even for most animal phyla. Even among charismatic megafauna, experimental mutation rate estimates remain unknown for amphibia and scarce for reptiles and fish.
2. Mutation rate, recombination rate and transposon rate in Drosophila
The rates of mutation, recombination, and transposition are core parameters in models of evolution. They impact genetic diversity, responses to ongoing selection, and levels of genetic load. However, even for key evolutionary model species such as Drosophila melanogaster and D. simulans, few estimates of these parameters are available, and we have little idea of how rates vary between individuals, sexes, or populations. Knowledge of this variation is fundamental for parameterizing models of genome evolution. Here, we provide direct estimates of mutation, recombination, and transposition rates and their variation in a West African and a European population of D. melanogaster and a European population of D. simulans Across 89 flies, we observe 58 single nucleotide mutations, 286 crossovers, and 89 transposable elements (TE) insertions. Compared to the European D. melanogaster, we find the West African population has a lower mutation rate (1.67 vs. 4.86 × 10-9 site-1 gen-1) and a lower transposition rate (8.99 vs. 23.36 × 10-5 copy-1 gen-1), but a higher recombination rate (3.44 vs. 2.06 cM/Mb). The European D. simulans population has a similar mutation rate to European D. melanogaster, but a significantly higher recombination rate and a lower, but not significantly different, transposition rate. Overall, we find paternal-derived mutations are more frequent than maternal ones in both species. Our study quantifies the variation in rates of mutation, recombination, and transposition among different populations and sexes, and our direct estimate of these parameters in D. melanogaster and D. simulans will benefit future studies in population and evolutionary genetics
3. Selective sweeps in Drosophila serrata
This study explores the impact of positive selection on the genetic composition of a Drosophila serrata population in eastern Australia through a comprehensive analysis of 110 whole genome sequences. Utilizing an advanced deep learning algorithm (partialS/HIC) and a range of inferred demographic histories, we identified that approximately 14% of the genome is directly affected by sweeps, with soft sweeps being more prevalent (10.6%) than hard sweeps (2.1%), and partial sweeps being uncommon (1.3%). The algorithm demonstrated robustness to demographic assumptions in classifying complete sweeps but faced challenges in distinguishing neutral regions from partial sweeps and linked regions under demographic misspecification. The findings reveal the indirect influence of sweeps on nearly two-thirds of the genome through linkage, with an over-representation of putatively deleterious variants suggesting that positive selection drags deleterious variants to higher frequency due to hitchhiking with beneficial loci. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under positive selection due to evolutionary arms races (e.g. immunity) were detected in hard sweeps. This study provides valuable insights into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.
4. Insecticide resistance in mosquitoes
A dengue fever outbreak in Guangzhou, Guangdong Province, China, in 2014 resulted in ∼37,000 cases and five deaths. Insecticides were sprayed to control the vector of this outbreak, Aedes albopictus (Skuse), a species of mosquito. Aedes albopictus specimens collected from Huadu District (HD), Huangpu District (HP), Luogang District (LG), and Nansha District (NS) in Guangzhou were evaluated using WHO-recommended bioassays for both larvae and adult mosquitoes to determine population resistance to deltamethrin, beta-cypermethrin, cypermethrin, permethrin, dichlorvos, temephos, propoxur, and DDT. Compared with a susceptible laboratory strain of Ae. albopictus (S-lab), all populations showed decreased sensitivities to the eight insecticides, with resistance ratios (RRs) ranging from 2.2 to 275. The RRs were 6.8-275 for pyrethroids, 2.2-4.4 for organophosphates, 5.7-9.0 for carbamates, and 5.3-94.3 for organochlorines. For adult mosquitoes, all populations were sensitive to dichlorvos with 100% mortalities. Mosquitoes from HP, LG, and NS were also sensitive to propoxur. But for other tested insecticides, different degrees of resistance (mortality rate ranging from 11.7% to 94.7%) were observed. Among the four field populations, the resistance levels are presented as follows in descending order: HP > HD > NS > LG. The levels among insecticides classes were pyrethroids > organochlorines > carbamates > organophosphates.