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

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Evolution of Protein Molecules

Evolutionary biologists have adopted simplelikelihood models for purposes of estimating ancestral states and evaluating character independence on specieed phylogenies; however, for pur- poses of estimating phylogenies byusing discrete morphological data, maximum parsimony remains the only option. This paper explores the possibility of using standard, well-behaved Markov models for estimating morphological phylogenies (including branch lengths) under the likelihood criterion. AnimportantmodiecationofstandardMarkovmodelsinvolvesmakingthelikelihoodconditionalon characters being variable, because constant characters are absent in morphological data sets. Without this modiecation, branch lengths are often overestimated, resulting in potentially serious biases in tree topology selection. Several new avenues of research are opened by an explicitly model-based approach to phylogenetic analysis of discrete morphological data, including combined-data likeli- hood analyses (morphologyCsequence data), likelihood ratio tests, and Bayesian analyses. (Discrete morphological character; Markov model; maximum likelihood; phylogeny.) The increased availability of nucleotide and protein sequences from a diversity of both organisms and genes has stimu- lated the development of stochastic models describing evolutionary change in molecu- lar sequences over time. Such models are not only useful for estimating molecular evolutionary parameters of interest but also important as the basis for phylogenetic inference using the method of maximum likelihood (ML) and Bayesian inference. ML provides a very general framework for esti- mation and has been extensively applied in diverse eelds of science (Casella and Berger, 1990); however, the popularity of ML in phylogenetic inference has lagged behind thatofotheroptimality criteria(suchas max- imum parsimony), primarily because of its much greater computational cost for evalu- ating any givencandidate tree.Recent devel- opments on the algorithmic aspects of ML inference as applied to phylogeny recon- struction (Olsen et al., 1994; Lewis, 1998; Salter and Pearl, 2001; Swofford, 2001) have succeeded in reducing this computational cost substantially, and ML phylogeny esti- mates involving hundreds of terminal taxa are now entering the realm of feasibility. Bayesian methods (based on a likelihood foundation) offer the prospect of obtaining meaningful nodal support measures with- out the unreasonable computational burden imposed by existing methods such as boot- strapping (Rannala and Yang, 1996; Yang and Rannala, 1997; Larget and Simon, 1999;

http://l.academicdirect.org/Horticulture/GAs/Refs/Lewis_2001.pdf

A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data

We redescribe the only previously known species of Myrsidea from bulbuls, M. pycnonoti Eichler. Sixteen new species are described; they and their type hosts are: M. phillipsi ex Pycnonotus goiavier goiavier (Scopoli), M. gieferi ex P. goiavier suluensis Mearns, M. kulpai ex P. flavescens Blyth, M. finlaysoni ex P. finlaysoni Strickland, M. kathleenae ex P. cafer (L.), M. warwicki ex Ixos philippinus (J. R. Forster), M. mcclurei ex Microscelis amaurotis (Temminck), M. zeylanici ex P. zeylanicus (Gmelin), M. plumosi ex P. plumosus Blyth, M. eutiloti ex P. eutilotus (Jardine and Selby), M. adamsae ex P. urostictus (Salvadori), M. ochracei ex Criniger ochraceus F. Moore, M. borbonici ex Hypsipetes borbonicus (J. R. Forster), M. johnsoni ex P. atriceps (Temminck), M. palmai ex C. ochraceus, and M. claytoni ex P. eutilotus. A key is provided for the identification of these 17 species.

A new species

/pdf/ants-standard-methods-for-measuring-and-monitoring-3zz2q4s25c.pdf

Ants : standard methods for measuring and monitoring biodiversity

Agriculture is a specialized form of symbiosis that is known to have evolved in only four animal groups: humans, bark beetles, termites, and ants. Here, we reconstruct the major evolutionary transitions that produced the five distinct agricultural systems of the fungus-growing ants, the most well studied of the nonhuman agriculturalists. We do so with reference to the first fossil-calibrated, multiple-gene, molecular phylogeny that incorporates the full range of taxonomic diversity within the fungus-growing ant tribe Attini. Our analyses indicate that the original form of ant agriculture, the cultivation of a diverse subset of fungal species in the tribe Leucocoprineae, evolved ≈50 million years ago in the Neotropics, coincident with the early Eocene climatic optimum. During the past 30 million years, three known ant agricultural systems, each involving a phylogenetically distinct set of derived fungal cultivars, have separately arisen from the original agricultural system. One of these derived systems subsequently gave rise to the fifth known system of agriculture, in which a single fungal species is cultivated by leaf-cutter ants. Leaf-cutter ants evolved remarkably recently (≈8–12 million years ago) to become the dominant herbivores of the New World tropics. Our analyses identify relict, extant attine ant species that occupy phylogenetic positions that are transitional between the agricultural systems. Intensive study of those species holds particular promise for clarifying the sequential accretion of ecological and behavioral characters that produced each of the major ant agricultural systems.

https://www.pnas.org/content/pnas/105/14/5435.full.pdf

Major evolutionary transitions in ant agriculture

Ants are the world's most diverse and ecologically dominant eusocial organisms. Resolving the phylogeny and timescale for major ant lineages is vital to understanding how they achieved this success. Morphological, molecular, and paleontological studies, however, have presented conflicting views on early ant evolution. To address these issues, we generated the largest ant molecular phylogenetic data set published to date, containing approximately 6 kb of DNA sequence from 162 species representing all 20 ant subfamilies and 10 aculeate outgroup families. When these data were analyzed with and without outgroups, which are all distantly related to ants and hence long-branched, we obtained conflicting ingroup topologies for some early ant lineages. This result casts strong doubt on the existence of a poneroid clade as currently defined. We compare alternate attachments of the outgroups to the ingroup tree by using likelihood tests, and find that several alternative rootings cannot be rejected by the data. These alternatives imply fundamentally different scenarios for the early evolution of ant morphology and behavior. Our data strongly support several notable relationships within the more derived formicoid ants, including placement of the enigmatic subfamily Aenictogitoninae as sister to Dorylus army ants. We use the molecular data to estimate divergence times, employing a strategy distinct from previous work by incorporating the extensive fossil record of other aculeate Hymenoptera as well as that of ants. Our age estimates for the most recent common ancestor of extant ants range from approximately 115 to 135 million years ago, indicating that a Jurassic origin is highly unlikely.

https://www.pnas.org/content/pnas/103/48/18172.full.pdf

Evaluating alternative hypotheses for the early evolution and diversification of ants.

▪ Abstract Agriculture has evolved independently in three insect orders: once in ants, once in termites, and seven times in ambrosia beetles. Although these insect farmers are in some ways quite different from each other, in many more ways they are remarkably similar, suggesting convergent evolution. All propagate their cultivars as clonal monocultures within their nests and, in most cases, clonally across many farmer generations as well. Long-term clonal monoculture presents special problems for disease control, but insect farmers have evolved a combination of strategies to manage crop diseases: They (a) sequester their gardens from the environment; (b) monitor gardens intensively, controlling pathogens early in disease outbreaks; (c) occasionally access population-level reservoirs of genetically variable cultivars, even while propagating clonal monocultures across many farmer generations; and (d) manage, in addition to the primary cultivars, an array of “auxiliary” microbes providing disease suppression...

The Evolution of Agriculture in Insects

Cultivation of fungi for food by fungus-growing ants (Attini: Formicidae) originated about 50 million years ago. The subsequent evolutionary history of this agricultural symbiosis was inferred from phylogenetic and population-genetic patterns of 553 cultivars isolated from gardens of "primitive" fungus-growing ants. These patterns indicate that fungus-growing ants succeeded at domesticating multiple cultivars, that the ants are capable of switching to novel cultivars, that single ant species farm a diversity of cultivars, and that cultivars are shared occasionally between distantly related ant species, probably by lateral transfer between ant colonies.

https://science.sciencemag.org/content/sci/281/5385/2034.full.pdf

Ted R. Schultz

Papers

Ants : standard methods for measuring and monitoring biodiversity

Major evolutionary transitions in ant agriculture

Evaluating alternative hypotheses for the early evolution and diversification of ants.

The Evolution of Agriculture in Insects

The Evolution of Agriculture in Ants