ORCID Profile
0000-0003-0550-9511
Current Organisation
The University of Edinburgh
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Publisher: Elsevier BV
Date: 04-2020
Publisher: Wiley
Date: 19-07-2021
DOI: 10.1111/EVO.14309
Abstract: 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.
Publisher: Elsevier BV
Date: 12-2018
DOI: 10.1016/J.IJID.2018.09.003
Abstract: To identify the high risk spatiotemporal clusters of dengue cases and explore the associated risk factors. Monthly indigenous dengue cases in 2005-2017 were aggregated at county level. Spatiotemporal cluster analysis was used to explore dengue distribution features using SaTScan9.4.4 and Arcgis10.3.0. In addition, the influential factors and potential high risk areas of dengue outbreaks were analyzed using ecological niche models in Maxent 3.3.1 software. We found a heterogeneous spatial and temporal distribution pattern of dengue cases. The identified high risk region in the primary cluster covered 13 counties in Guangdong Province and in the secondary clusters included 14 counties in Yunnan Province. Additionally, there was a nonlinear association between meteorological and environmental factors and dengue outbreaks, with 8.5%-57.1%, 6.7%-38.3% and 3.2%-40.4% contribution from annual average minimum temperature, land cover and annual average precipitation, respectively. The high risk areas of dengue outbreaks mainly are located in Guangdong and Yunnan Provinces, which are significantly shaped by environmental and meteorological factors, such as temperature, precipitation and land cover.
Publisher: University of Queensland Library
Date: 2021
DOI: 10.14264/44531A2
Publisher: Cold Spring Harbor Laboratory
Date: 04-2022
DOI: 10.1101/2022.03.31.486660
Abstract: Understanding the extent to which microevolutionary adaptation relies on novel beneficial mutations, as opposed to previously neutral standing genetic variation, is an important goal of evolutionary genetics. Progress towards this goal has been enhanced during the genomic era through the study of selective sweeps. Selective sweeps fall into two categories: hard sweeps via new mutations and soft sweeps via pre-existing mutations. However, data are currently lacking on the relative frequency of these two types of selective sweep. In this study, we examined 110 whole genome sequences from Drosophila serrata s led from eastern Australia and searched for hard and soft sweeps using a deep learning algorithm (diploS/HIC). Analyses revealed that approximately 15% of the D. serrata genome was directly impacted by soft sweeps, and that 46% of the genome was indirectly influenced via linkage to these soft sweeps. In contrast, hard sweep signatures were very rare, only accounting for 0.1% of the scanned genome. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under frequent selection due to evolutionary arms races (e.g. immunity and sperm competition) were detected. Within soft sweep regions and those flanking them, there was an over-representation of SNPs with predicted deleterious effects, suggesting positive selection drags deleterious variants to higher frequency due to their linkage with beneficial loci. This study provides insight into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.
Publisher: Oxford University Press (OUP)
Date: 22-04-2016
DOI: 10.1093/JME/TJW026
Abstract: The cat flea, Ctenocephalides felis felis (Bouché), feeds on different host species, causing annoyance or transmitting disease agents. In this study, the influence of the host of the cat flea on blood feeding, egg production, and sex ratio of the offspring was investigated. Two strains of C. felis were domesticated on either rats or mice for >10 yr in the laboratory, and in this study, these fleas were placed in the following groups and fed on rats or mice continuously: Group A (rat-domesticated C. felis with rats as host) Group B (rat-domesticated C. felis with mice as host) Group C (mouse-domesticated C. felis with rats as host) and Group D (mouse-domesticated C. felis with mice as host). In total, 240 adult fleas were in each group at a sex ratio of female:male = 1.7:1. The mean egg production per flea of Groups A, B, C, and D was 55.0, 19.2, 62.5, and 13.2, respectively. A significant correlation between egg production and the volume of blood consumed was detected for Groups A, B, C, and D. The sex ratio (F:M) of the offspring in Groups A and C was 2.07 and 2.11, respectively, whereas in Groups B and D, the ratio was 1.04 and 1.03, respectively. In conclusion, the C. felis with rats as host consumed more blood, produced more eggs, and had higher sex ratios of the offspring than those with mice as the host.
Publisher: Cold Spring Harbor Laboratory
Date: 04-2023
Abstract: The rates of mutation, recombination, and transposition are core parameters in models of evolution. They impact genetic ersity, 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 in iduals, 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.
Publisher: Informa UK Limited
Date: 09-2012
DOI: 10.1080/00222895.2012.721406
Abstract: Parkinson's disease (PD) is a common neurodegenerative disease, the risk factors of which are gaining more attentions. Among all these risk factors, catechol-o-methyltransferase (COMT) has been widely studied, and believed to be associated with PD. However, the relationship between COMT polymorphism and PD has not been confirmed hitherto. Therefore, a meta-analysis was performed to evaluate the effect of COMT polymorphism on PD patients. A total of 24 study subjects comprising 3,807 patients with PD and 3,942 unrelated healthy controls were recruited in this meta-analysis. Heterogeneity testing and sensitivity analysis were conducted with Review Manager 5.0 software (The Nordic Cochrane Centre, The Cochrane Collaboration, Copenhagen, Denmark) and Stata software (StataCorp, College Station, TX), together with publication bias by funnel plot method and modified Egger's linear regression test. No evidences of publication bias and heterogeneity were detected. In the 24 studies, the estimated odds ratios (OR) in PD patients are 0.98 for the Met allele (95% confidence interval [0.92, 1.05]) under a fixed-effects model. The authors also conducted a stratified analysis according to geographic region among Europe, Asia, and North America, the ORs for the Met allele are 0.92, 1.02, and 1.10, respectively. According to the results of the meta-analysis, a conclusion could be drawn that polymorphism of Val108/158Met are not associated with the risk of PD. However, more convincing studies are warranted to have a solid conclusion supported.
Publisher: Cold Spring Harbor Laboratory
Date: 14-09-2022
DOI: 10.1101/2022.09.12.507595
Abstract: Mutation, recombination, and transposition occurring during meiosis provide the variation on which natural selection can act and the rates at which they occur are important parameters in models of evolution. The de novo mutation rate determines levels of genetic ersity, responses to ongoing selection, and levels of genetic load. Recombination breaks up haplotypes and reduces the effects of linkage, helping to spread beneficial alleles and purge deleterious ones. Transposable elements (TE) selfishly replicate themselves through the genome, imposing fitness costs on the host and introducing complex mutations that can affect gene expression and give rise to new genes. However, even for key evolutionary models such as Drosophila melanogaster and D. simulans few estimates of these parameters are available, and we have little idea of how rates vary between in iduals, sexes, populations, or species. 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 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 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. De novo mutation rates are 1.67 × 10 −9 site −1 gen −1 (95% HPD CI: 0.54 – 3.14 × 10 −9 ), 4.86 × 10 −9 site −1 gen −1 (2.11 – 8.02 × 10 −9 ), and 4.51 × 10 −9 site −1 gen −1 (1.94 – 7.75 × 10 −9 ) for the West African D. melanogaster , the European D. melanogaster and the European D. simulans population, respectively. In females, recombination rates in the absence of large genomic inversions are 3.44 cM/Mb (2.72 – 4.18), 2.06 cM/Mb (1.57 - 2.57), and 3.04 cM/Mb (2.45 - 3.73) for the three populations, respectively. There was no strong evidence of recombination observed in males. Mutations (SNMs and indels) are male-biased. The West African D. melanogaster population has a lower TE activity than the other populations and CMC-Transib is the dominant active TE. The European D. melanogaster population has multiple active TEs: Gypsy, CMC-Transib, Pao, Jockey and hAT-hobo while in European D. simulans , they are Gypsy, CMC-Transib, Pao, hAT-hobo, Copia and TcMar-Mariner .
Publisher: Springer Science and Business Media LLC
Date: 20-12-2019
DOI: 10.1038/S41598-019-56112-8
Abstract: In China, the knowledge of the underlying causes of heterogeneous distribution pattern of dengue fever in different high-risk areas is limited. A comparative study will help us understand the influencing factors of dengue in different high-risk areas. In the study, we compared the effects of climate, mosquito density and imported cases on dengue fever in two high-risk areas using Generalized Additive Model (GAM), random forests and Structural Equation Model (SEM). GAM analysis identified a similar positive correlation between imported cases, density of Aedes larvae, climate variables and dengue fever occurrence in the studied high-risk areas of both Guangdong and Yunnan provinces. Random forests showed that the most important factors affecting dengue fever occurrence were the number of imported cases, BI and the monthly average minimum temperature in Guangdong province whereas the imported cases, the monthly average temperature and monthly relative humidity in Yunnan province. We found the rainfall had the indirect effect on dengue fever occurrence in both areas mediated by mosquito density while the direct effect in high-risk areas of Guangdong was dominated by temperature and no obvious effect in Yunnan province by SEM. In total, climate factors and mosquito density are the key drivers on dengue fever incidence in different high-risk areas of China. These findings could provide scientific evidence for early warning and the scientific control of dengue fever in high-risk areas.
Publisher: Proceedings of the National Academy of Sciences
Date: 22-09-2023
Publisher: Oxford University Press (OUP)
Date: 12-08-2022
Abstract: 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 [& interquartile ranges (IQR) from the median] values. Intriguingly, while genotypes extreme for a multivariate factor also tended to have a higher proportion of in idual traits that were extreme, we also observed genotypes that were extreme for multivariate factors but not for any in idual 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.
Publisher: Oxford University Press (OUP)
Date: 23-12-2016
DOI: 10.1093/JEE/TOW254
Abstract: 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.
Publisher: Springer Science and Business Media LLC
Date: 12-2019
DOI: 10.1186/S13071-019-3829-5
Abstract: Mutation of the voltage-gated sodium channel (VGSC) gene, or knockdown resistance ( kdr ) gene, is an important resistance mechanism against DDT and pyrethroids for dengue vector Aedes albopictus . A phenylalanine to serine (F1534S), leucine (F1534L) and cysteine (F1534C) substitution were detected in many Ae. albopictus populations around the world, and the mutant allele frequencies have been increasing in recent years. Therefore, it is essential to establish a simple, time-saving and cost-effective procedure to monitor the alleles in large-scale studies. Based on the mutation genotypes of the 1534 locus in the kdr gene, F/F, F/S, F/C, F/L, S/S, C/C, L/L and S/C, we designed specific forward and reverse primers and optimized the reaction conditions for establishing of the allele-specific PCR(AS-PCR) detection technique. DNA sequencing in this study was taken as the gold standard, and used to determine the accuracy of AS-PCR. The designed AS-PCR technique showed high specificity for distinguishing the mutations at the 1534 locus, as the accuracy for F/F, F/S, F/C, F/L, S/S, C/C and S/C were 100%, 95.35%, 100%, 100%, 100%, 100% and 100%, respectively. The designed AS-PCR technique effectively distinguished in idual genotypes for the mutations at the 1534 locus in the kdr gene, which could facilitate the knockdown resistance surveillance in Ae. albopictus in large-scale studies.
Publisher: Wiley
Date: 05-07-2021
DOI: 10.1111/EVO.14294
Abstract: 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.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 12-2013
DOI: 10.1161/HYPERTENSIONAHA.113.01965
Abstract: Published literature reports controversial results about the association of physical activity (PA) with risk of hypertension. A meta-analysis of prospective cohort studies was performed to investigate the effect of PA on hypertension risk. PubMed and Embase databases were searched to identify all related prospective cohort studies. The Q test and I 2 statistic were used to examine between-study heterogeneity. Fixed or random effects models were selected based on study heterogeneity. A funnel plot and modified Egger linear regression test were used to estimate publication bias. Thirteen prospective cohort studies were identified, including 136 846 persons who were initially free of hypertension, and 15 607 persons developed hypertension during follow-up. The pooled relative risk (RR) of main results from these studies suggests that both high and moderate levels of recreational PA were associated with decreased risk of hypertension (high versus low: RR, 0.81 95% confidence interval, 0.76–0.85 and moderate versus low: RR, 0.89 95% confidence interval, 0.85–0.94). The association of high or moderate occupational PA with decreased hypertension risk was not significant (high versus low: RR, 0.93 95% confidence interval, 0.81–1.08 and moderate versus low: RR, 0.96 95% confidence interval, 0.87–1.06). No publication bias was observed. The results of this meta-analysis suggested that there was an inverse dose–response association between levels of recreational PA and risk of hypertension, whereas there was no significant association between occupational PA and hypertension.
Publisher: Cold Spring Harbor Laboratory
Date: 25-01-2023
DOI: 10.1101/2023.01.24.525323
Abstract: Mutation is the ultimate source of all genetic variation, and over the last ten 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 single nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide ersity—while accounting for phylogenetic non-independence. 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 ersity 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 hibia and scarce for reptiles and fish. Over the past decade, the sequencing revolution has led to an ever-increasing number of mutation-rate estimates from mutation accumulation or parent-offspring sequencing studies in eukaryotes. However, studies rarely quantify to what extent the mutation rate varies among these species. Also, despite strong predictions as to how mutation rate should vary with (e.g.) generation time, there have been few recent or wide-ranging analyses of such predictors while accounting for the inherent similarity between closely-related species. Of particular note, there has been surprisingly little effort to robustly test the ‘drift barrier’ hypothesis that mutation rates should decrease with increasing effective population size. In this study, we used a comprehensive literature search to identify all the available experimental estimates of mutation rate in eukaryotes and subject them to phylogenetic mixed-model analyses. We find that per-nucleotide per-generation mutation rates differ by orders of magnitude among species: plants and mammals tend to have higher mutation rates than arthropods, and unicellular organisms have the lowest mutation rates. Our analysis also shows that mutation rates increase significantly with increasing generation time and genome size, and nucleotide ersity increases with mutation rate with a gradient less than one—as predicted by the drift-barrier hypothesis.
Publisher: Cold Spring Harbor Laboratory
Date: 21-04-2022
DOI: 10.1101/2022.04.21.488876
Abstract: 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 modelling to 3,385 gene expression traits from Drosophila melanogaster and from D. serrata to explore how genetic variance is distributed across high-dimensional phenotypic space. Surprisingly, most of the heritable trait covariation was due to few lines (genotypes) with extreme ( IQR from the median) values. This observation, in the two independently s led species, suggests that the House of Cards (HoC) model might apply not only to in idual expression traits, but also to emergent co-expression phenotypes. Intriguingly, while genotypes extreme for a multivariate factor also tended to have a higher proportion of in idual traits that were extreme, we also observed genotypes that were outliers for multivariate factors but not for any in idual traits. We observed other consistent differences between heritable multivariate factors with outlier lines versus those factors that conformed to a Gaussian distribution of genetic effects, 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.
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Yiguan Wang.