Diffusive coevolution and mutualism maintenance mechanisms in a fig-fig wasp system

In reciprocal mutualism systems, the exploitation events by exploiters might disrupt the reciprocal mutualism, wherein one exploiter species might even exclude other coexisting exploiter species over an evolutionary time frame. What remains unclear is how such a community is maintained. Niche partitioning, or spatial heterogeneity among the mutualists and exploiters, is generally believed to enable stability within a mutualistic system. However, our examination of a reciprocal mutualism between a fig species (Ficus racemosa) and its pollinator wasp (Ceratosolen fusciceps) shows that spatial niche partitioning does not sufficiently prevent exploiters from overexploiting the common resource (i.e., the female flowers), because of the considerable niche overlap between the mutualists and exploiters. In response to an exploiter, our experiment shows that the fig can (1) abort syconia-containing flowers that have been galled by the exploiter, Apocryptophagus testacea, which oviposits before the pollinators do; and (2) retain syconia-containing flowers galled by Apocryptophagus mayri, which oviposit later than pollinators. However, as a result of (2), there is decreased development of adult non-pollinators or pollinator species in syconia that have not been sufficiently pollinated, but not aborted. Such discriminative abortion of figs or reduction in offspring development of exploiters while rewarding cooperative individuals with higher offspring development by the fig will increase the fitness of cooperative pollinating wasps, but decrease the fitness of exploiters. The fig fig wasp interactions are diffusively coevolved, a case in which fig wasps diversify their genotype, phenotype, or behavior as a result of competition between wasps, while figs diverge their strategies to facilitate the evolution of cooperative fig waps or lessen the detrimental behavior by associated fig wasps. In habitats or syconia that suffer overexploitation, discriminative abortion of figs or reduction in the offspring development of exploiters in syconia that are not or not sufficiently pollinated will decrease exploiter fitness and perhaps even drive the population of exploiters to local extinction, enabling the evolution and maintenance of cooperative pollinators through the movement between habitats or syconia (i.e., the metapopulations).

Molecular systematics of Xenocyprinae (Teleostei : Cyprinidae): Taxonomy, biogeography, and coevolution of a special group restricted in east Asia

We surveyed mitochondrial DNA (mtDNA) sequence variation in the subfamily Xenocyprinae from China and used these data to estimate intraspecific, interspecific, and intergeneric phylogeny and assess biogeographic scenarios underlying the geographic structu

Episodic evolution of prolactin receptor gene in mammals: coevolution with its ligand

Divergence of proteins in signaling pathways requires ligand and receptor coevolution to maintain or improve binding affinity and/or specificity. In this paper we show a clear case of coevolution between the prolactin (PRL) gene and its receptor (prolactin receptor, PRLR) in mammals. First we observed episodic evolution of the extracellular and intracellular domains of the PRLR, which is closely consistent with that seen in PRL. Correlated evolution was demonstrated both between PRL and its receptor and between the two domains of the PRLR using Pearson's correlation coefficient. On comparing the ratio of the nonsynonymous substitution rate to synonymous substitution rate (omega=d(N)/d(S)) for each branch of the star phylogeny of mammalian PRLRs, separately for the extracellular domain (ECD) and the transmembrane domain/intracellular domain (TMD/ICD), we observed a lower omega ratio for ECD than TMD/ICD along those branches leading to pig, dog and rabbit but a higher ratio for ECD than TMD/ICD on the branches leading to primates, rodents and ruminants, on which bursts of rapid evolution were observed. These observations can be best explained by coevolution between PRL and its receptor and between the two domains of the PRLR.

A paradigm for virus-host coevolution: Sequential counter-adaptations between endogenous and exogenous retroviruses

Endogenous retroviruses ( ERVs) are remnants of ancient retroviral infections of the host germline transmitted vertically from generation to generation. It is hypothesized that some ERVs are used by the host as restriction factors to block the infection o

Molecular systematics of Xenocyprinae (Teleostei : Cyprinidae): Taxonomy, biogeography, and coevolution of a special group restricted in east Asia

We surveyed mitochondrial DNA (mtDNA) sequence variation in the subfamily Xenocyprinae from China and used these data to estimate intraspecific, interspecific, and intergeneric phylogeny and assess biogeographic scenarios underlying the geographic structure of lineages. We sequenced 1140 bp of cytochrome b from 30 individuals of Xenocyprinae and one putative outgroup (Myxocypris asiaticus) and also sequenced 297 bp of ND4L, 1380 bp of ND4, 68 bp of tRNA(His), and 69 bp of tRNA(Ser) from 17 individuals of Xenocyprinae and the outgroup (M. asiaticus). We detected high levels of nucleotide variation among populations, species, and genera. The phylogenetic analysis suggested that Distoechodon hupeinensis might be transferred to the genus Xenocypris, the taxonomic status of the genus Plagiognathops might be preserved, and species of Xenocypris and Plagiognathops form a monophyletic group that is sister to the genus Distoechodon and Pseudobrama. The introgressive hybridization might occur among the populations of X. argentea and X. davidi, causing the two species to not be separated by mtDNA patterns according to their species identification, and the process and direction of hybridization are discussed. The spatial distributions of mtDNA lineages among populations of Xenocypris were compatible with the major geographic region, which indicated that the relationship between Hubei + Hunan and Fujian is closer than that between Hubei + Hunan and Sichuan, From a perspective of parasite investigation, our data suggested that the fauna of Hexamita in Xenocyprinae could be used to infer the phylogeny of their hosts. (C) 2001 Academic Press.

Fast evolution of growth hormone receptor in primates and ruminants

Pituitary growth hormone (GH) evolves very slowly in most of mammals, but the evolutionary rates appear to have increased markedly on two occasions during the evolution of primates and ruminants. To investigate the evolutionary pattern of growth hormone receptor (GHR), we sequenced the extracellular domain of GHR genes from four primate species. Our results suggested that GHR in mammal also shows an episodic evolutionary pattern, which is consistent with that observed in pituitary growth hormone. Further analysis suggested that this pattern of rapid evolution observed in primates and ruminants is likely the result of coevolution between pituitary growth hormone and its receptor.

A possible evolutionary lag in the relationship between freshwater mussels and European bitterling

The coevolutionary dynamics between European bitterling Rhodeus amarus and freshwater unionid mussels, which the former parasitize by laying eggs on their gills, were tested. In a series of experiments fish preferences and mussel responses were compared in parasites and hosts of recent (Europe) and ancient (Asia) sympatry. Rhodeus amarus readily oviposited on the gills of all mussel species tested. Fish that laid their eggs on the gills of Asian Anodonta woodiana, however, suffered a dramatic reduction in reproductive success compared to fish that oviposited on the gills of European mussels: Unio pictorum, Unio tumidus, Anodonta anatina and Anodonta cygnea. This difference was the result of egg ejection behaviour by mussels rather than the unsuitability of the internal gill environment for European bitterling embryo development. The ejection response of mussels with a long sympatry with European bitterling was considerably more pronounced than that of mussels with a substantially shorter sympatry. The data support a coevolutionary arms race between bitterling and mussels and point to an evolutionary lag in the relationship between R. amarus and its European mussel hosts. (c) 2007 The Authors. Journal compilation (c) 2007 The Fisheries Society of the British Isles.

Evidence of host specificity and congruence between phylogenies of bitterling and freshwater mussels

Evidence of host specificity and congruence between phylogenies of bitterling and freshwater mussels. Zoological Studies 45(3): 428-434. Bitterling (Cyprinidae: Acheilognathinae) are freshwater fishes with a unique spawning relationship with freshwater mussels on whose gills they lay their eggs. During the breeding season of bitterling fishes, we collected 843 mussels belonging to 16 species from Lake Qinglan, central China and examined their gill chambers for the presence of bitterling larvae. Three species of bitterling larvae were identified; Acheilognathus tonkinensis, Ach. cf. meridianus, and Ach. barbatulus, in 3 species of mussel: Unio douglasiae, Lamprotula caveata, and L. tortuosa, suggesting host specialization. Using our own and other published data, we compared the respective phylogenies of bitterling and mussels, but failed to show clear congruence. However, broad specializations are evident, with Acheilognathus and Tanakia showing preferences for mussels with a relatively simple gill structure (Ableminae), and Rhodeus spp. showing preferences for mussels of the Anodontinae and Unioninae, which have more-complex gill structures.

The costs and benefits in an unusual symbiosis: experimental evidence that bitterling fish (Rhodeus sericeus) are parasites of unionid mussels in Europe

Interspecific symbiotic relationships involve a complex network of interactions, and understanding their outcome requires quantification of the costs and benefits to both partners. We experimentally investigated the costs and benefits in the relationship between European bitterling fish (Rhodeus sericeus) and freshwater mussels that are used by R. sericeus for oviposition. This relationship has hitherto been thought mutualistic, on the premise that R. sericeus use mussels as foster parents of their embryos while mussels use R. sericeus as hosts for their larvae. We demonstrate that R. sericeus is a parasite of European mussels, because it (i) avoids the cost of infection by mussel larvae and (ii) imposes a direct cost on mussels. Our experiments also indicate a potential coevolutionary arms race between bitterling fishes and their mussel hosts; the outcome of this relationship may differ between Asia, the centre of distribution of bitterling fishes, and Europe where they have recently invaded.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

RFID系统优化模型与智能算法研究

射频识别技术（Radio Frequency Identification, RFID）作为采集与处理信息的高新技术和信息化标准的基础，被列为本世纪十大重要技术之一。但是，RFID技术的大规模实际应用仍处于探索阶段，RFID系统的应用基础技术还存在着大量尚未解决的关键问题，其中RFID系统优化是RFID技术研究和应用的重要课题。由于RFID系统本身的动态性和不确定性， RFID系统优化面对的一般是非线性、多目标、大规模的复杂优化问题，传统的数学优化算法在处理这些问题时，存在困难。为此，研究新的优化算法成为RFID技术实际应用和理论研究中必须解决的课题。 智能计算方法是求解复杂RFID系统优化问题的一种可供选择的算法。智能计算作为一个新兴领域，其发展已引起了多个学科领域研究人员的关注，目前已经成为人工智能、经济、社会、生物等交叉学科的研究热点和前沿领域。智能计算的各类算法已在传统NP问题求解及诸多实际应用领域中展现出其优异的性能和巨大的发展潜力。 本文旨在对RFID系统的各种优化问题进行深入研究和探讨，面向RFID技术的实际应用需求构建其优化模型，并基于智能计算思想设计能够有效求解这些复杂模型的新型智能优化算法。具体研究内容包括： 首先，进行了RFID读写器网络的调度问题研究。在深入分析RFID网络中读写器冲突类型和成因的基础上，考虑RFID网络中的读写器冲突约束，以最小化系统中的频道数量、时隙分配以及总处理时间建立了RFID读写器网络调度的数学优化模型。从生物学的角度出发提出基于生态捕食模型的改进PSO算法（Particle Swarm Optimizer based on Predator-prey Coevolution, PSOPC），在一定程度上解决了PSO算法在迭代后期随着多样性丧失而陷入局部最优的缺点。应用PSOPC设计了求解RFID读写器网络调度模型的智能求解算法，分别给出算法的求解框架、关键步骤的实现机制。通过在不同规模的RFID读写器网络上进行实例仿真，验证了算法的有效性和模型的正确性。 其次，进行了基于菌群自适应觅食算法RFID网络规划问题的研究。考虑RFID系统在不同应用环境下的系统需求，建立了RFID网络规化的数学模型，其目标函数分别为：RFID网络标签覆盖率的最大化目标函数、RFID读写器冲突的最小化目标函数、RFID网络运行的经济效益最大化目标函数、RFID网络运行的负载平衡目标函数以及同时考虑全局目标的混合目标函数。将自然界生物觅食所采用的自适应搜索策略与细菌的趋化行为和群体感应机制相集成，提出了适合求解复杂RFID网络规划问题的菌群自适应觅食算法（Adaptive Bacterial Foraging Optimization, ABFO）。通过仿真实验基于ABFO算法分别对RFID网络规划模型中的五个目标函数进行了实例求解和分析，测试结果与标准PSO算法和遗传算法进行了比较分析。 再次，进行了基于系统智能方法的RFID网络规划分布式决策模型研究。采用分布式决策的思想建立了RFID网络规划的层次模型，在一定程度上缓解、分散了RFID网络规划问题的复杂性，以解决具有混合变量（包括离散变量和连续变量）的多目标RFID网络规划问题。针对层次模型求解的复杂性，以复杂适应系统理论为指导思想设计了一种新型系统智能优化算法对RFID网络规划的层次模型进行求解。系统智能算法将群体智能中的单层群体系统概念扩展为多层涌现系统，仿真实验表明新提出的算法显著提高了智能计算方法的寻优能力，以及算法的适应性、鲁棒性和平衡性等性能。 最后，进行了RFID网络目标跟踪系统中的数据融合研究。以基于RFID技术的目标定位与跟踪系统为应用背景，提出了基于模糊聚类方法的多RFID读写器数据融合模型框架。通过深入分析蜜蜂采蜜的基本生物学规律，对蜜蜂的个体行为及群体行为进行模拟，提出了一类新型群体智能优化算法-蜂群优化算法（Bee Swarm Optimization, BSO），并将BSO算法嵌入RFID目标定位跟踪系统，作为其模糊聚类的基本算法。仿真研究表明，提出的融合模型能够有效的过滤读写器对跟踪目标的错误监测数据，显著提高目标定位与跟踪的精度。