草地贪夜蛾核型多角体病毒对我国草地贪夜蛾不同地理种群毒力的比较分析

草地贪夜蛾Spodoptera frugiperda（J. E. Smith）入侵我国多个地区,逐渐形成地理种群。在草地贪夜蛾核型多角体病毒Spodoptera frugiperda multiple nucleopolyhedrovirus（SfMNPV）生物农药的生产过程中发现,不同地理来源的宿主对SfMNPV的敏感性和产量存在明显差异,显著影响了SfMNPV的生产效率。为解析其敏感性差异及其产生的原因,本研究首先对云南德宏、广东广州、广西钦州、西藏林芝4个地区草地贪夜蛾种群基因型进行了鉴定,采用生物测定法测试SfMNPV对4龄幼虫的口服毒力,然后,通过向幼虫体内注射草地贪夜蛾核多角体病毒出芽型病毒粒子（budded virions,BVs）的方式,越过口服感染中肠的过程,分析敏感性差异发生的阶段。最后比较了高敏感和低敏感种群中肠肠液pH,并基于16S rDNA测序测定了肠道菌群组成。结果表明,广西种群属于纯合玉米型,其余种群为带有水稻型COI标记的杂合玉米型。广西种群对SfMNPV的口服敏感性最低,西藏种群的敏感性最高,但两者注射BV后死亡率差异无统计学意义,暗示病毒敏感性差异发生在口服感染阶段。广西种群中肠pH略低于西藏种群,并且较于西藏种群,广西种群相肠道乳杆菌Lactobacillus丰度高。本文结果表明,肠道微环境的差异可能是不同地理种群草地贪夜蛾对SfMNPV口服敏感性产生差异的原因。     

Environment changes epistasis to alter trade‐offs along alternative evolutionary paths

The fitness effect of a mutation can depend on both its genetic background, known as epistasis, and the prevailing external environment. Many examples of these dependencies are known, but few studies consider both aspects in combination, especially as they affect mutations that have been selected together. We examine interactions between five coevolved mutations in eight diverse environments. We find that mutations are, on average, beneficial across environments, but that there is high variation in their fitness effects, including many examples of mutations conferring a cost in some, but not other, genetic background‐environment combinations. Indeed, even when global interaction trends are accounted for, specific local mutation interactions are common and differed across environments. One consequence of this dependence is that the range of trade‐offs in genotype fitness across selected and alternative environments are contingent on the particular evolutionary path followed over the mutation landscape. Finally, although specific interactions were common, there was a consistent pattern of diminishing returns epistasis whereby mutation effects were less beneficial when added to genotypes of higher fitness. Our results underline that specific mutation effects are highly dependent on the combination of genetic and external environments, and support a general relationship between a genotype's current fitness and its potential to increase in fitness.     

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed “consensus calling,” to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.     

Genetic variation in gorillas

This review summarizes what is currently known concerning genetic variation in gorillas, on both inter- and intraspecific levels. Compared to the human species, gorillas, along with the other great apes, possess greater genetic variation as a consequence of a demographic history of rather constant population size. Data and hence conclusions from analysis of mitochondrial DNA (mtDNA), the usual means of describing intraspecific patterns of genetic diversity, are limited at this time. An important task for future studies is to determine the degree of confidence with which gorilla mtDNA can be analyzed, in view of the risk that one will inadvertently analyze artifactual rather than genuine sequences. The limited information available from sequences of nuclear genomic segments does not distinguish western from eastern gorillas, and, in comparison with results from the two chimpanzee species, suggests a relatively recent common ancestry for all gorillas. In the near future, the greatest insights are likely to come from studies aimed at genetic characterization of all individual members of social groups. Such studies, addressing topics such as behavior of individuals with kin and non-kin, and the actual success of male reproductive strategies, will provide a link between behavioral and genetic studies of gorillas.     

Genotypic Differences of Candida albicans and C. dubliniensis Isolates Related to Ethnic/Racial Differences within the Same Geographic Area

Candida albicans and C. dubliniensis genotype differences among Israeli ethnic groups were assessed. Isolates from Jews (51), Arabs (35) and Druze (25) were genotyped. The distributions among ethnic groups were not different, however they differed (p = 0.002) from global populations. Therefore, C. albicans and C. dubliniensis genotype distribution differences in Israel are related to changes in all ethnic groups.     

Predictive Validity of Discriminant Analysis for Genetic Data

We examined the predictive validity of the results using discriminant analysis to distinguish statistically among two or more populations with a large sample of random amplified polymorphic DNA (RAPD) loci, but a small sample of genotypes from each population. We compared and contrasted results from randomized data with results from real data of three studies by 100 randomized shuffling of genotypes into various populations. We generally obtained substantial differences between results from randomized data compared to those from the real data in several characteristics of discriminant analysis. We showed that a high level of correctly classified percentage is also obtainable in the analysis of randomized data, mainly with a low number of populations. However, the correctly classified percentage obtained from the real data was generally significantly higher than the percentage obtained from the randomized data. We suggested that the high level of real differences in allele frequencies of the RAPD polymorphic loci clearly distinguished the various populations and that the populations differ significantly in their RAPD contents in accordance with ecological heterogeneity. We obtained either no or a low level of difference between the correct classification rate obtained by the leaving-one-out procedure and that obtained from the original data, attributed to a low number of loci selected by the stepwise method. The results strengthen and support our conclusion and lead us to focus on the discriminant analysis by selecting only low numbers of discriminating variables.     

A technical note for using microsatellite DNA analyses in haploid male DNA pools of social Hymenoptera

Summary The analyses of haploid male DNA pooled (MDP) samples can increase the cost efficiency in population genetic studies for a variety of applications in fundamental and applied screening of social Hymenoptera populations. Depending on the research problem addressed it can reduce the number of genotyped samples per study by orders of magnitude. In this study we show the feasibility of MDPs for assessing population allele frequencies, mother queen genotypes and mutation rates for microsatellite loci in the honeybee (Apis mellifera). The main purpose of MDP genotyping is not to replace individual based analyses but to discard non-informative samples and monomorphic loci from further analyses.     

Multilocus enzyme electrophoresis analysis of Trypanosoma cruzi isolates from a geographically restricted endemic area for Chagas' disease in Argentina

A set of 65 Trypanosoma cruzi stocks from dogs, opossums, insect vectors and humans was isolated in a geographically restricted endemic area for Chagas' disease in Argentina and was analysed by multilocus enzyme electrophoresis for 15 loci. The results show that at least five multilocus genotypes (clonets) circulate in the study area, one belonging to T. cruzi IIe, one to T. cruzi IId and three clonets belonging to T. cruzi I; and they confirm the presence of these lineages in the country. The three clonets attributed to T. cruzi I were identical to each other for all loci except for Sod-2, where three different patterns were identified. These patterns suggest the presence of two homozygous genotypes and one heterozygous genotype. Our results also suggest association of clonet IIe with dogs, clonet IId with humans and the three T. cruzi I clonets with Didelphis albiventris. On the other hand, there was no significant association between Triatoma infestans and any particular clonet circulating in the area. These findings are consistent with the hypothesis of natural selection, from mixed populations of T. cruzi in vectors, toward more restricted populations in mammals. The epidemiological implications of the possible selection of different clonets by different mammal hosts and the significance of two homozygous genotypes and one heterozygous genotype for the Sod-2 locus are discussed.     

Apical membrane antigen-1 (AMA-1) gene sequences of re-emerging Plasmodium vivax in South Korea

Plasmodium vivax malaria re-emerged in South Korea in 1993, and epidemics continue since then. We examined genetic variation in the region encompassing the apical membrane antigen-1 (PvAMA-1) of the parasites by DNA sequencing of the 22 re-emerging P. vivax isolates. The genotype of the PvAMA-1, which was based on sequence data previously reported for the polymorphic regions, showed that two haplotypes were present at one polymorphic site. Compared with reported data, the two types, SKOR type I and type II, were similar to Chinese CH-10A and CH-05A isolates, respectively. Thus, the present study showed that two genotypes of AMA-1 genes coexist in the re-emerging Korean P. vivax.     

Cryptosporidium hominis n. sp. (Apicomplexa: Cryptosporidiidae) from Homo sapiens

The structure and infectivity of the oocysts of a new species of Cryptosporidium from the feces of humans are described. Oocysts are structurally indistinguishable from those of Cryptosporidium parvum. Oocysts of the new species are passed fully sporulated, lack sporocysts. and measure 4.4-5.4 microm (mean = 4.86) x 4.4-5.9 microm (mean = 5.2 microm) with a length to width ratio 1.0-1.09 (mean 1.07) (n = 100). Oocysts were not infectious for ARC Swiss mice, nude mice. Wistar rat pups, puppies, kittens or calves, but were infectious to neonatal gnotobiotic pigs. Pathogenicity studies in the gnotobiotic pig model revealed significant differences in parasite-associated lesion distribution (P = 0.005 to P = 0.02) and intensity of infection (P = 0.04) between C. parvum and this newly described species from humans. In vitro cultivation studies have also revealed growth differences between the two species. Multi-locus analysis of numerous unlinked loci, including a preliminary sequence scan of the entire genome demonstrated this species to be distinct from C. parvum and also demonstrated a lack of recombination, providing further support for its species status. Based on biological and molecular data, this Cryptosporidium infecting the intestine of humans is proposed to be a new species Cryptosporidium hominis n. sp.