抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Genetics and analysis of quantitative traits

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract The housefly ( Musca domestica ) is a wide-ranging insect, often associated with decaying matter from livestock and humans. The septic environments in which houseflies live are believed to be a rich source for microbial acquisition. Although the housefly can harbor a wide range of microorganisms, it is not yet well known which microbes are always recurrent, which are dispensable and which environmentally dependent. In the present study, we aim at identifying which microbes are recurrently associated with the housefly gut throughout the species’ life cycle and whether their acquisition relies on the fly’s living environment. We surveyed three housefly strains—two of them kept under standard laboratory conditions for a long time and one wild-caught. To track any shifts happening throughout the lifecycle of the housefly and to test the consistency of the revealed microbial communities, we sampled houseflies at five developmental stages over the course of four consecutive generations. Both the bacterial and fungal microbiota of five developmental stages were studied for all samples, using amplicon sequencing for the 16S and ITS1 rRNA gene, respectively. Results revealed diverse microbial communities yet consistent for each of the two distinct sampling environments. The wild-caught population showed a more diverse and more distinct gut microbiota than the two laboratory strains, even though the strain was phylogenetically similar and shared geographic origin with one of them. Two bacterial genera, Myroides and Providencia , and two yeasts, Trichosporon and Candida tropicalis, were present in all sampled larvae and pupae, regardless of the strain. Analysis of the provided diet revealed that the flies acquired the yeasts through feeding. Our main findings show that houseflies might lose microbial diversity when reared in controlled environments, however they can maintain a consistent set of bacteria. We conclude that although the environment can facilitate certain microbial transmission routes for the housefly, and despite the fungal microbiota being largely acquired through diet, the larval bacterial gut microbiome remains relatively consistent within the same developmental stage. 

/pdf/houseflies-harbor-less-diverse-microbiota-under-laboratory-21u4jx2h.pdf

Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria

Insects as Natural Enemies

Transitions among sex-determination systems

The quantitative genetics of sex determination

Insects are the new livestock. They are increasingly being used for food, feed, and pest control. Humans have been breeding cattle and poultry to increase their size or egg and milk production for centuries. Methods to improve the performance of livestock can be roughly divided as genetics-based or environment-induced. For example, artificial selection is a geneticmethod that has been extensively used by livestock breeders to increase yields, such as meat production. It refers to selecting only those individuals to breed the next generation that show a certain desired trait. Nutrient fortification of diet is an example of an environmental factor that can improve livestock performance. In contrast to the enormous efforts and successes in improving methodology for breeding traditional livestock, such approaches have hardly been successful to increase the efficiency of insects in pest control. But articles in this special issue on pest control reveal that times are finally changing. More types of organisms are being used for pest control, such as mites, fungi, and bacteria, but insects have a long tradition of being exploited for biological control, going back to 304 AD (Huang & Yang, 1987). Most articles in this issue deal with parasitoid wasps, themain insect group used to control pests. However, this issue also contains articles about herbivorous thrips that are being applied to fight invasive weeds. Also featured in this issue is a field closely related to biological control, the sterile insect technique (SIT). SIT controls pest infestations through mass release of sterilisedmales that outcompete natural males of a pest species. Like biocontrol, it requires knowledge of the genetics, physiology and behaviour of the insect. The two practices also both involve mass rearing and field performancemonitoring. All insects carry a diversity of microorganisms in their body, collectively referred to as their microbiome. There is an increasing realisation that the microbiome affects many important life-history characteristics of their insect carriers. Thismeans that there is enormous potential in exploiting and manipulating the insect microbiome for improving biological control agents. With reference to the opening sentence of this introduction, insects can therefore be considered as the new mini livestock and their microbiome as the new micro livestock. The 14 papers in this issue present a variety of novel approaches for exploiting genetic and environmental factors to improve insect control agents. Lommen et al. (2017) begin this issue with a minireview on how genetic variation within species may be exploited by selecting for genotypes that potentially improve traits of interest for pest control. It requires knowledge of the genetic basis and heritability of insect life-history traits that affect their rearing and performance. Recent advances in genome science and genome-editing techniques make it possible to link genes to traits, and thus identify what we might call ‘biological control genes’. These are genes that code for traits significant to biological control, such as host specificity and desiccation resistance. Cui et al. (2017) review the application of the CRISPR gene-editing technique in insect functional genomics studies. Although still in its infancy and not without ethical issues, this technique is currently revolutionising medical science and will undoubtedly also find its application in the biological control industry. S anchez-Rosario et al. (2017) apply artificial selection to increase mating competitiveness of Anastrepha ludens (Loew) (Diptera: Tephritidae) for SIT application. They find that selection for improved mating success may trade off with fecundity and survival, calling for careful management and balancing of traits when practising such strategies. Clarke et al. (2017) highlight the importance of paying closer attention to the variability within host species. They find strong differences in the parasitism success of the parasitoid Aphidius ervi Haliday (Hymenoptera: Braconidae) on genetically distinct clonal lines of the potato aphid Macrosiphum euphorbiae Thomas (Hemiptera: Aphididae). Additionally, in contrast to previous studies that found endosymbiont-induced resistance, the Hamiltonella and Regiella of their Macrosiphum lines appear to provide little protection against parasitism. *Correspondence: E-mail: l.w.beukeboom@rug.nl

https://onlinelibrary.wiley.com/doi/pdf/10.1111/eea.12543

Leo W. Beukeboom

Papers

Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria

Insects as Natural Enemies

Transitions among sex-determination systems

The quantitative genetics of sex determination

Improving pest control: Mass rearing and field performance - an introduction