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The interaction of evolutionary processes to determine quantitative genetic variation has implications for contemporary and future phenotypic evolution, as well as for our ability to detect causal genetic variants. While theoretical studies have provided robust predictions to discriminate among competing models, empirical assessment of these has been limited. In particular, theory highlights the importance of pleiotropy in resolving observations of selection and mutation, but empirical investigations have typically been limited to few traits. Here, we applied high-dimensional Bayesian Sparse Factor Genetic modeling to gene expression datasets in 2 species, Drosophila melanogaster and Drosophila serrata, to explore the distributions of genetic variance across high-dimensional phenotypic space. Surprisingly, most of the heritable trait covariation was due to few lines (genotypes) with extreme [>3 interquartile ranges (IQR) from the median] values. Intriguingly, while genotypes extreme for a multivariate factor also tended to have a higher proportion of individual traits that were extreme, we also observed genotypes that were extreme for multivariate factors but not for any individual trait. We observed other consistent differences between heritable multivariate factors with outlier lines vs those factors without extreme values, including differences in gene functions. We use these observations to identify further data required to advance our understanding of the evolutionary dynamics and nature of standing genetic variation for quantitative traits.

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. [ABSTRACT FROM AUTHOR]

What conditions favor the evolution of elaborate sexual ornaments? In freshwater killifishes, Sowersby et al. found that larger sexual ornaments were negatively associated with locomotive performance. Although selection clearly favored large ornamental fins in environments with fewer predators, there was no clear association between large ornamental fins and differences in life‐history strategy. This finding illustrates that habitat differences in predation risk have the potential to influence the evolution of secondary sexual traits such as ornaments through natural selection. [ABSTRACT FROM AUTHOR]

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, betacypermethrin, 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. [ABSTRACT FROM AUTHOR]

What conditions favor the evolution of elaborate sexual ornaments? In freshwater killifishes, Sowersby et al. found that larger sexual ornaments were negatively associated with locomotive performance. Although selection clearly favored large ornamental fins in environments with fewer predators, there was no clear association between large ornamental fins and differences in life‐history strategy. This finding illustrates that habitat differences in predation risk have the potential to influence the evolution of secondary sexual traits such as ornaments through natural selection. [ABSTRACT FROM AUTHOR]

The classification of severe fever with thrombocytopenia syndrome virus (SFTSV) lacked consistency due to limited virus sequences used across previous studies, and the origin and transmission dynamics of the SFTSV remains not fully understood. In this study, we analyzed the diversity and phylodynamics of SFTSV using the most comprehensive and largest dataset publicly available for a better understanding of SFTSV classification and transmission. A total of 1267 L segments, 1289 M segments, and 1438 S segments collected from China, South Korea, and Japan were included in this study. Maximum likelihood trees were reconstructed to classify the lineages. Discrete phylogeographic analysis was conducted to infer the phylodynamics of SFTSV. We found that the L, M, and S segments were highly conserved, with mean pairwise nucleotide distances of 2.80, 3.36, and 3.35% and could be separated into 16, 13, and 15 lineages, respectively. The evolutionary rate for L, M, and the S segment was 0.61 × 10 -4 (95% HPD: 0.48-0.73 × 10 -4 ), 1.31 × 10 -4 (95% HPD: 0.77-1.77 × 10 -4 ) and 1.27 × 10 -4 (95% HPD: 0.65-1.85 × 10 -4 ) subs/site/year. The SFTSV most likely originated from South Korea around the year of 1617.6 (95% HPD: 1513.1-1724.3), 1700.4 (95% HPD: 1493.7-1814.0), and 1790.1 (95% HPD: 1605.4-1887.2) for L, M, and S segments, respectively. Hubei Province in China played a critical role in the geographical expansion of the SFTSV. The effective population size of SFTSV peaked around 2010 to 2013. We also identified several codons under positive selection in the RdRp, Gn-Gc, and NS genes. By leveraging the largest dataset of SFTSV, our analysis could provide new insights into the evolution and dispersal of SFTSV, which may be beneficial for the control and prevention of severe fever with thrombocytopenia syndrome., Competing Interests: None declared.None declared., (© The Author(s) 2024. Published by Oxford University Press.)

The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern animal biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in the animal tree of life has proven to be a major challenge, hindering understanding of early animal evolution and the fossil record. This is particularly true in the species-rich and highly varied Mollusca where dramatic inconsistency among paleontological, morphological, and molecular evidence has led to a long-standing debate about the group's phylogeny and the nature of dozens of enigmatic fossil taxa. A critical step needed to overcome this issue is to supplement available genomic data, which is plentiful for well-studied lineages, with genomes from rare but key lineages, such as Scaphopoda. Here, by presenting chromosome-level genomes from both extant scaphopod orders and leveraging complete genomes spanning Mollusca, we provide strong support for Scaphopoda as the sister taxon of Bivalvia, revitalizing the morphology-based Diasoma hypothesis originally proposed 50 years ago. Our molecular clock analysis confidently dates the split between Bivalvia and Scaphopoda at ~520 Ma, prompting a reinterpretation of controversial laterally compressed Early Cambrian fossils, including Anabarella , Watsonella, and Mellopegma, as stem diasomes. Moreover, we show that incongruence in the phylogenetic placement of Scaphopoda in previous phylogenomic studies was due to ancient incomplete lineage sorting (ILS) that occurred during the rapid radiation of Conchifera. Our findings highlight the need to consider ILS as a potential source of error in deep phylogeny reconstruction, especially in the context of the unique nature of the Cambrian Explosion.

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 Drosophila 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 element (TE) insertions. Compared to the European D. melanogaster , we find the West African population has a lower mutation rate (1.67 × 10 -9 site -1 gen -1 vs. 4.86 × 10 -9 site -1 gen -1 ) and a lower transposition rate (8.99 × 10 -5 copy -1 gen -1 vs. 23.36 × 10 -5 copy -1 gen -1 ), but a higher recombination rate (3.44 cM/Mb 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 estimates of these parameters in D. melanogaster and D. simulans will benefit future studies in population and evolutionary genetics., (© 2023 Wang et al.; Published by Cold Spring Harbor Laboratory Press.)

What conditions favor the evolution of elaborate sexual ornaments? In freshwater killifishes, Sowersby et al. found that larger sexual ornaments were negatively associated with locomotive performance. Although selection clearly favored large ornamental fins in environments with fewer predators, there was no clear association between large ornamental fins and differences in life-history strategy. This finding illustrates that habitat differences in predation risk have the potential to influence the evolution of secondary sexual traits such as ornaments through natural selection., (© 2021 The Authors. Evolution © 2021 The Society for the Study of Evolution.)