Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans.

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.

Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting.

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 impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach.

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.

Long-term trends in housefly (Musca domestica L.) insecticide resistance in China.

Controlling housefly populations relies on the use of insecticides, which inevitably leads to the development of resistance. A better and more comprehensive understanding of the spatial and temporal distribution of resistance could guide the control of houseflies. However, most studies on housefly resistance in China are scattered and poorly coordinated. We collected resistance data from houseflies in the published literature and from the vector biomonitoring system of the Chinese Center for Disease Control and Prevention. A 5- or 10-year resolution was used to study the temporal dynamics of resistance to five commonly used insecticides: deltamethrin, permethrin, beta-cypermethrin, dichlorvos, and propoxur. ArcGIS was used to visualize their spatial distributions. The correlation between year and resistance coefficient was determined using SPSS 26.0 and RStudio to explore the changes in resistance over the years. A total of 2128 data were included in this study, ranging from 1982 to 2022, based on which we found significant increases in resistance over the past forty years for the five studied insecticides. Among them, pyrethroids had the most strikingly elevated resistance level and were mainly distributed in the northern and southeastern coastal areas. Dichlorvos and propoxur had intermediate increases in resistance, and most of these increases were identified in North China and the Yangtze River. Housefly resistance to commonly used insecticides in China is increasing and spatially heterogeneous. This finding also highlights the necessity of continuous routine surveillance of housefly resistance, which could guide future housefly control operations and slow the development of resistance.

Climate factors and the East Asian summer monsoon may drive large outbreaks of dengue in China.

OBJECTIVE: To investigate the relationship between climate variables, East Asian summer monsoon (EASM) and large outbreaks of dengue in China. METHODS: We constructed ecological niche models (ENMs) to analyse the influence of climate factors on dengue occurrence and predict dengue outbreak areas in China. Furthermore, we formulated a generalised additive model (GAM) to quantify the impact of the EASM on dengue occurrence in mainland China from 1980 to 2016. RESULTS: Mean Temperature of Coldest Quarter had a 62.6% contribution to dengue outbreaks. Southern China including Guangdong, Guangxi, Fujian and Yunnan provinces are more vulnerable to dengue emergence and resurgence. In addition, we found population density had a 68.7% contribution to dengue widely distribution in China using ENMs. Statistical analysis indicated a dome-shaped association between EASM and dengue outbreak using GAM, with the greatest impact in the South-East of China. Besides, there was a positive nonlinear association between monthly average temperature and dengue occurrence. CONCLUSION: We demonstrated the influence of climate factors and East Asian summer monsoon on dengue outbreaks, providing a framework for future studies on the association between climate change and vector-borne diseases.

Morphology and shape control of porous silica nanostructures with dual-templating approaches.

There has been great interest in the synthesis of porous silica nanostructures because of their potential applications in catalysis, adsorption, molecular separation, and biomedical engineering. In this paper, we report the synthesis of porous silica nanostructures with varied morphologies and shapes from two-phase systems by using lithocholic acid (LCA) and cetyltrimethylammmonium bromide (CATB) or LCA and Pluronic F127 in the lower ammonia aqueous phase as dual directing agents and tetraethylsiloxane (TEOS) in the upper oil phase as a silica precursor. Porous silica spheres are formed by using LCA/CTAB as a dual directing agent, while silica fibers with pits are synthesized by using LCA/F127 as a dual directing agent. The straight-to-helical shape transition of silica fibers with pits can be achieved by increasing the ammonia concentration in the low aqueous phase.

The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia.

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.

Transcriptome analysis of Kunming mice responses to the bite of Xenopsylla cheopis.

BACKGROUND: Flea bites could trigger a series of complex molecular responses in the host. However, our understanding of the responses at the molecular level is still relatively limited. This study quantifies the changes in gene expression in mice after flea bites by RNA sequencing (RNA-seq) from their spleens, revealing the potential biological effects of host response to flea bites. METHODS: RNA-seq was used for transcriptome analysis to screen for differentially expressed genes (DEGs) between the control mice group and the flea bite mice group. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed on DEGs. Protein-protein interaction (PPI) network analysis on DEGs related to immune processes was performed. Finally, we randomly selected several genes from the screened DEGs to validate the results from the transcriptome data by real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR). RESULTS: A total of 521 DEGs were identified, including 277 upregulated and 244 downregulated. There were 258 GO terms significantly enriched by upregulated DEGs and 419 GO terms significantly enriched by downregulated DEGs. Among the upregulated DEGs, 22 GO terms were associated with immune cells (e.g., B cells and T cells) and immune regulatory processes, while among the downregulated DEGs, 58 GO terms were associated with immune cells and immune regulatory processes. Through PPI analysis, we found that CD40 molecules with significantly downregulated expression levels after flea bites may play an important role in host immune regulation. Through KEGG pathway enrichment analysis, a total of 26 significantly enriched KEGG pathways were identified. The RT-qPCR analysis results indicated that the transcriptome sequencing results were reliable. CONCLUSIONS: Through in-depth analysis of transcriptome changes in mice caused by flea bites, we revealed that flea bites could stimulate a series of biological and immunological responses in mice. These findings not only provided a deeper understanding of the impact of flea bites on the host but also provided a basis for further research on the interaction between ectoparasites and the host. We believe that digging deeper into the significance of these transcriptome changes will help reveal more about the adaptive response of the host to ectoparasites.

Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis.

Mutation is the ultimate source of all genetic variation, and over the last 10 years the ready availability of whole-genome sequencing has permitted direct estimation of mutation rate for many non-model species across the tree of life. 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.

The epidemiology and evolutionary dynamics of massive dengue outbreak in China, 2019.

Introduction: In 2019, China experienced massive dengue outbreaks with high incidence and expanded outbreak areas. The study aims to depict dengue's epidemiology and evolutionary dynamics in China and explore the possible origin of these outbreaks. Methods: Records of confirmed dengue cases in 2019 were obtained from the China Notifiable Disease Surveillance System. The sequences of complete envelope gene detected from the outbreak provinces in China in 2019 were retrieved from GenBank. Maximum Likelihood trees were constructed to genotype the viruses. The median-joining network was used to visualize fine-scale genetic relationships. Four methods were used to estimate the selective pressure. Results: A total of 22,688 dengue cases were reported, 71.4% of which were indigenous cases and 28.6% were imported cases (including from abroad and from other domestic provinces). The abroad cases were predominantly imported from Southeast Asia countries (94.6%), with Cambodia (3,234 cases, 58.9%), and Myanmar (1,097 cases, 20.0%) ranked as the top two. A total of 11 provinces with dengue outbreaks were identified in the central-south of China, of which Yunnan and Guangdong provinces had the highest number of imported and indigenous cases. The primary source of imported cases in Yunnan was from Myanmar, while in the other ten provinces, the majority of imported cases were from Cambodia. Guangdong, Yunnan and Guangxi provinces were China's primary sources of domestically imported cases. Phylogenetic analysis of the viruses in outbreak provinces revealed three genotypes: (I, IV, and V) in DENV 1, Cosmopolitan and Asian I genotypes in DENV 2, and two genotypes (I and III) in DENV 3. Some genotypes concurrently circulated in different outbreak provinces. Most of the viruses were clustered with those from Southeast Asia. Haplotype network analysis showed that Southeast Asia, possibly Cambodia and Thailand, was the respective origin of the viruses in clade 1 and 4 for DENV 1. Positive selection was detected at codon 386 in clade 1. Conclusion: Dengue importation from abroad, especially from Southeast Asia, resulted in the dengue epidemic in China in 2019. Domestic transmission between provinces and positive selection on virus evolution may contribute to the massive dengue outbreaks.

Clinical relevance and distribution of Helicobacter pylori virulence factors in isolates from Chinese patients.

Background: At present, the relationship between virulence factors of Helicobacter pylori (H. pylori) and gastrointestinal diseases is still under discussion. This study investigated the association between distinct virulence factors in H. pylori and different gastrointestinal diseases. Methods: Gastric biopsy specimens were obtained from 160 patients with different gastrointestinal diseases in China, including 77 patients with chronic gastritis (CG), 36 with peptic ulcer disease (PUD), and 38 with gastric carcinoma (GC). The presence of certain virulence genes was determined by polymerase chain reaction (PCR), and the results were analyzed using chi-squared tests. Results: A total of 160 H. pylori strains were successfully isolated from gastric biopsy specimens. Overall, all strains of H. pylori were cagA, cagE positive, and the most common vacA genotypes were s1 (98.8%) and m2 (68.1%). The positive rates of the jhp0562, jhp0563, homA, homB, hopQI, and hopQII genes were 99.4%, 32.5%, 33.1%, 71.3%, 100%, and 6.9%, respectively. There was no significant association between these genes and different disease types. The dominant hpyIIIR-positive genotype was detected in 83.1% of the strains, making it significantly more prevalent than the hrgA-positive genotype (P<0.001). Surprisingly, the mixed genotype of hrgA and hpyIIIR was common and accounted for 41.3%. The hrgA-positive strains were more common in GC patients (71.1%) compared to CG patients (50.7%, P<0.05). The mixed genotype was prevalent and accounted for 55.3% and 31.2% of strains from GC and CG patients, respectively. Multivariate analysis showed that the hrgA gene exhibited a positive correlation with GC and increased the risk of GC [odds ratio (OR) =3.606, P<0.05]. In contrast, the presence of hrgA exhibited a negative correlation with CG (OR =0.499, P<0.05). Conclusions: These results suggested that the universal presence of cagA, cagE, vacA s1, jhp0562, homB, and hopQI made it impossible to examine disease-specific associations with any of these virulence factors. In addition, they may synergistically contribute to more virulent strains and severe diseases in China. Furthermore, there was a strong association between the hrgA gene and progression to GC, indicating the potential application of other virulence factors in clinical detection.

A novel strategy for screening mutations in the voltage-gated sodium channel gene of Aedes albopictus based on multiplex PCR-mass spectrometry minisequencing technology.

BACKGROUND: The current prevention and control strategy for Aedes albopictus heavily relies on comprehensive management, such as environmental management and chemical control. However, the wide application of pyrethroids has facilitated the development of insecticide resistance, primarily via mutations in the voltage-gated sodium channel (VGSC) gene. This study aims to develop a novel strategy for detecting mutations in the VGSC gene in Ae. albopictus using multiplex PCR-mass spectrometry (MPCR-MS) minisequencing technology. METHODS: We established a new strategy for detecting mutations in the VGSC gene in Ae. albopictus using MPCR-MS minisequencing technology. MPCR amplification and mass probe extension (MPE) were first used, followed by single nucleotide polymorphism (SNP) typing mass spectrometry, which allows the simultaneous detection of multiple mutation sites of the VGSC gene in 96 samples of Ae. albopictus. A total of 70 wild-collected Ae. albopictus were used to evaluate the performance of the method by comparing it with other methods. RESULTS: Three target sites (1016, 1532, 1534) in the VGSC gene can be detected simultaneously by double PCR amplification combined with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry, achieving a detection limit of 20 fg/µl. We applied this method to 70 wild-collected Ae. albopictus, and the obtained genotypes were consistent with the routine sequencing results, suggesting the accuracy of our method. CONCLUSIONS: MPCR-MS minisequencing technology provides a sensitive and high-throughput approach to Ae. albopictus VGSC gene mutation screening. Compared with conventional sequencing, this method is economical and time-saving. It is of great value for insecticide resistance surveillance in areas with a high risk of vector-borne disease.

Effects of the source of information and knowledge of dengue fever on the mosquito control behavior of residents of border areas of Yunnan, China.

BACKGROUND: Strengthening the mosquito control measures undertaken by residents of an area where dengue fever is present can significantly decrease the spread of this disease. The aim of this study was to explore the effects of the source of information and knowledge of dengue fever on the mosquito control behavior of residents of areas at high risk of this disease to determine effective ways of enhancing this behavior. METHODS: A survey was conducted via face-to-face interviews or questionnaires between March and May 2021 in three regions of the province of Yunnan, China. The survey included basic information about the respondents, the source(s) of their dengue fever information, the level of their dengue fever knowledge, and the measures they had implemented to control mosquitoes. Principal component analysis was used to extract the main components of the sources of information. Correlation analysis and structural equation analysis were used to explore the impact of the sources of information and residents' dengue fever knowledge on their mosquito control behavior. RESULTS: Publicity achieved through mass media, including official WeChat accounts, magazines/newspapers, poster leaflets, television/radio and the Internet, had a direct effect on dengue fever knowledge and mosquito control behavior, and indirectly affected mosquito control behavior through dengue fever knowledge. Organized publicity campaigns, including information provided by medical staff and through community publicity, had a direct effect on dengue fever knowledge and indirectly affected mosquito control behavior through dengue fever knowledge. The residents' level of dengue fever knowledge had a significant, positive, direct effect on their mosquito control behavior. CONCLUSIONS: Mosquito control is an important measure for the prevention and control of outbreaks of dengue fever. An effective source of information can improve the level of dengue fever knowledge among residents and thus enhance their mosquito control behavior.

Digest: More than just a pretty fin: The evolution of sexual ornaments in killifish.

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.

Digest: Nature and nurture: Influences of parental care and rearing environment on phenotypic plasticity in Nicrophorus vespilloides.

What conditions favor niche expansion in nature? In the burying beetle Nicrophorus vespilloides, Schrader et al. found that larvae reared with parental care on larger carcasses were better equipped for resource use than individuals reared without parental care on smaller carcasses. This finding illustrates that developmental plasticity induced by parental care and carcass size has the potential to influence adaptive diversification.

Factors Associated With Severe Fever With Thrombocytopenia Syndrome in Endemic Areas of China.

Objective: To explore the influence of climatic, environmental and socioeconomic factors on SFTS occurrence in Shandong Province, China. Methods: We used generalized additive model to estimate the association between SFTS cases and climatic factors, environmental factors and socioeconomic factors, including annual average temperature, precipitation, land cover, normalized difference vegetation index, altitude, population density, meat production, milk production, and gross domestic product (GDP). Results: There were a total of 4,830 cases reported in 100 (70.9%) counties and districts in Shandong Province from 2010 to 2020. The results showed that the annual average temperature, precipitation, forest and grassland coverage rate, altitude and meat production (square root transform) had a reversed "V" relationship with SFTS occurrence, with the inflection points around 12.5-13.0°C in temperature, around 650 mm in precipitation, around 0.3 in forest and grassland coverage rate, around 300 m in altitude, and around 200-300 tons in meat production (square root transform), respectively. SFTS occurrence had a "V" relationship with milk production (square root transform) and GDP (square root transform), with the inflection points around 100-200 tons in milk production (square root transform), and around 150,000-200,000 yuan in GDP (square root transform), respectively. Conclusions: Climatic, environmental, and socioeconomic factors contributed to the heterogeneous distribution of SFTS in Shandong Province, and the influence of these factors on SFTS occurrence was nonlinear.

Epidemiological characteristics and temporal-spatial analysis of overseas imported dengue fever cases in outbreak provinces of China, 2005-2019.

BACKGROUND: Overseas imported dengue fever is an important factor in local outbreaks of this disease in the mainland of China. To better prevent and control such local outbreaks, the epidemiological characteristics and temporal-spatial distribution of overseas imported dengue fever cases in provincial-level administrative divisions (PLADs) where dengue fever is outbreak in the mainland of China were explored. METHODS: Using the Chinese National Notifiable Infectious Disease Reporting Information System (CNNDS), we identified overseas imported dengue fever cases in dengue fever outbreak areas in the mainland of China from 2005 to 2019 to draw the epidemic curve and population characteristic distribution of overseas imported cases in each PLAD. Based on spatial autocorrelation analysis of ArcGIS 10.5 and temporal-spatial scanning analysis of SaTScan 9.5, we analyzed the temporal-spatial distribution of overseas imported dengue fever in dengue fever outbreak areas in the mainland of China. RESULTS: A total of 11,407 imported cases, mainly from Southeast Asia, were recorded from 2005 to 2019 in these 13 PLADs. Of which 62.1% were imported into Yunnan and Guangdong Provinces. Among the imported cases, there were more males than females, mainly from the 21-50 age group. The hot spots were concentrated in parts of Yunnan, Guangdong and Fujian Provinces. We found the cluster of infected areas were expanding northward. CONCLUSIONS: Based on the analysis of overseas imported dengue cases in 13 PLADs of the mainland of China from 2005 to 2019, we obtained the epidemiological characteristics and spatial distribution of imported dengue cases. Border controls need to pay attention to key population sectors, such as 21-50 years old men and education of key populations on dengue prevention. There is a need to improve the awareness of the prevention and control of imported cases in border areas. At the same time, northern regions cannot relax their vigilance.

Maintenance of quantitative genetic variance in complex, multitrait phenotypes: the contribution of rare, large effect variants in 2 Drosophila species.

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.

Digest: Positive selection and recombination shape the genomic landscape in flycatchers.

Whether background selection is sufficient to explain observed genomic differentiation is a long-standing debate. Using four species of flycatcher, Chase et al. addressed this issue and found that the effect of background selection may not be as great as previously thought. Instead, both positive selection and recombination were shown to have a significant effect on genomic differentiation.

Digest: Does size matter? Condition-dependent sexual selection in Drosophila melanogaster.

What conditions favor competitive outcomes at different stages of the reproductive process? De Nardo et al. found that in Drosophila melanogaster, the evolution of male secondary sexual traits was influenced by sexual selection through mating success and competitive fertilization.