Isolation of microsatellite loci in the pollinating fig wasp of Ficus hispida, Ceratosolen solmsi

Microsatellite loci were isolated for Ceratosolen solmsi , pollinator of the dioecious Ficus hispida. We developed nine polymorphic microsatellite loci based on the method of polymerase chain reaction isolation of microsatellite arrays (PIMA). Enrichment of genomic libraries was performed by random amplified polymorphic DNA (RAPD). A subset of 38 positive clones was sequenced; 15 clones showed microsatellite loci. We tested 15 designed primer pairs and nine of them produced polymorphic amplification in 48 individual wasps collected from different fruits of the dioecious host fig Ficus hispida in China. Among the 48 individuals, 49 alleles were obtained at the nine loci. The observed heterozygosity ranged between 0.357 and 0.634.     

Pollinating fig wasp Ceratosolen solmsi adjusts the offspring sex ratio to other foundresses

Abstract Local mate competition theory predicts that offspring sex ratio in pollinating fig wasps is female‐biased when there is only one foundress, and increased foundress density results in increased offspring sex ratio. Information of other foundresses and clutch size have been suggested to be the main proximate explanations for sex ratio adjustment under local mate competition. Our focus was to show the mechanism of sex ratio adjustment in a pollinating fig wasp, Ceratosolen solmsi Mayr, an obligate pollinator of the functionally dioecious fig, Ficus hispida Linn., with controlled experiments in the field. First, we obtained offspring from one pollinator and offspring at different oviposition sequences, and found that offspring sex ratio decreased with clutch size, and pollinators produced most of their male offspring at the start of bouts, followed by mostly females. Second, we found that offspring sex ratio increased with foundress density, and pollinators did adjust their offspring sex ratio to other females in the oviposition patches. We suggest that when oviposition sites are not limited, pollinators will mainly adjust their offspring sex ratio to other foundresses independent of clutch size changes, whereas adjusting clutch size may be used to adjust sex ratio when oviposition sites are limited.     

Disturbance effects on community structure of Ficus tinctoria fig wasps in Xishuangbanna, China: Implications for the fig/fig wasp mutualism

Abstract  Fig trees are important components of tropical forests, because their fruits are eaten by so many vertebrates, but they depend on pollinating fig wasps to produce mature fruits. Disturbance to habitat structure can have a major impact on insect diversity and composition, potentially reducing fruit yields. We investigated the impact of habitat disturbance on the fig wasp community associated with male figs of Ficus tinctoria in Xishuangbanna, China. The community comprised one pollinator species Liporrhopalum gibbosae and six non-pollinating wasp species: Sycoscapter sp.1, Philotrypesis ravii , Philotrypesis sp.1, Neosycophila omeomorpha , Sycophila sp.1, and Walkerella sp.1. More disturbed areas were characterized by higher temperatures, less shade, and more vehicle noise. The response of the fig wasp community was complex, with no simple relationship between intensity of disturbance and pollinator abundance. However, the sex ratios (proportion of male progeny) of pollinators increased significantly in more disturbed areas. We conclude that potential changes in fig wasp community composition brought about by disturbance, are unpredictable, with unclear consequences for tropical rainforest biodiversity.     

垂叶榕榕小蜂群落及种间互作网络季节动态

群落中的物种相互作用构成了复杂的生态网络。有关物种的数量和组成的季节性动态变化已有较多的研究, 但是对于生态网络的动态变化知之甚少。揭示生态网络的动态变化对于理解群落的稳定性以及群落的动态变化过程和机理具有重要意义。本研究以垂叶榕(Ficus benjamina)榕小蜂群落为研究对象, 分别在西双版纳的干季和雨季采集了榕小蜂的种类和数量信息。比较了两个季节榕小蜂群落的动态变化以及共存网络的参数(例如网路直径、连接数、嵌套性和群落矩阵温度)变化。结果显示: 雨季榕果内传粉榕小蜂Eupristina koningsbergeri所占比例高于干季, 传粉榕小蜂的种群数量也高于干季, 而在干季非传粉榕小蜂的种类增加(干季15种小蜂, 雨季14种)。从榕树-传粉榕小蜂互利共生系统的适合度来看, 干季非传粉小蜂的增加对传粉榕小蜂和榕树的适合度是不利的。在干季, 共存网络物种间的连接数(干季0.95, 雨季0.47)多于雨季, 群落矩阵温度(干季23.24, 雨季2.64)也显著高于雨季。表明干季榕小蜂群落组成及种间关系较雨季更为复杂而多样, 高的矩阵温度暗示群落受到的干扰更大。     

高榕隐头果内小蜂群落的动态变化

高榕隐头果内的小蜂群落是我国目前所知榕小蜂群落中最为丰富多样的群落。通过600个果内78063号小蜂标本的分类、统计,在高榕果内共有25种榕小蜂,隶属于7科、14属,其中两种为传粉小蜂,23种为非传传粉小蜂。在榕小蜂群落中,传粉小蜂优势度较为明显,除1月份为18.42%外,其余月份均达51.62%以上,有时甚至达100%。在单个榕果内,小蜂的种类和数量呈现较大变幅,有1~8种,普遍寄生2~4种;榕小蜂数量从1~561只/果不等,寄生100~200只/果较多。1年中不同小蜂出现的相对频度差异也较大,E up ristina sp.和Sy coscap ter sp.2每月都出现,有的非传粉小蜂仅于特定月份出现,并且数量极少。榕小蜂的丰富度随着月份而变化,变幅3~19种,并于1月、4月和8月出现3个高峰。自然群落中,传粉小蜂与非传粉小蜂的数量变化呈显著负相关;多样性指数与传粉小蜂比例呈显著负相关,与非传粉小蜂比例呈显著正相关,而且都具较高的拟合优度。通过3个不同生境样地的多样性指数、丰富度和均匀度比较,结果表明:在人为干扰较严重的样地内,3项指标都较低,除均匀度指标未达显著外,多样性指数和丰富度均达显著水平。但生境对传粉小蜂和非传粉小蜂的影响却不相同,非传粉小蜂会随生境的恶化而迅速消亡,而传粉小蜂的种群则急速膨大,占领全部生境。反之,随着生境的改善,传粉小蜂的种群数量将有所下降,而非传粉小蜂的种类和数量将增加。     

Analysis of fungal community structure in the soil of Zoige Alpine Wetland

To understand the soil fungal community diversity in different zones of the Zoige Alpine Wetland, BIOLOG analysis and traditional culture method were employed in our research. Three sample sites namely the Conservatory Station up-hill slope (CSUS), the Flower Lake side (FLS) and the Conservatory Station down slope (CSDS) with increasing by water content were investigated. The results of BIOLOG showed that fungal catabolic richness index (S) and Shannon diversity index (H) increasingly rose with water content augmented from CSUS to CSDS, while different from the former tendency, the fungal catabolic activity was highest at CSDS and lowest at FLS. Principal component analysis (PCA) results demonstrated the functional diversity of fungal community varied among the three sample sites, showing us more similarity between CSDS and FLS, and considerable difference between CSUS and the former two sites. The outcome of traditional culture method illustrated the number of soil fungi increased from CSUS to CSDS, while the sort of fungal species that could be cultured did not show much difference among the three sample sites.     

Analysis of fungal community structure in the soil of Zoige Alpine Wetland

To understand the soil fungal community diversity in different zones of the Zoige Alpine Wetland, BIOLOG analysis and traditional culture method were employed in our research. Three sample sites namely the Conservatory Station up-hill slope (CSUS), the Flower Lake side (FLS) and the Conservatory Station down slope (CSDS) with increasing by water content were investigated. The results of BIOLOG showed that fungal catabolic richness index (S) and Shannon diversity index (H) increasingly rose with water content augmented from CSUS to CSDS, while different from the former tendency, the fungal catabolic activity was highest at CSDS and lowest at FLS. Principal component analysis (PCA) results demonstrated the functional diversity of fungal community varied among the three sample sites, showing us more similarity between CSDS and FLS, and considerable difference between CSUS and the former two sites. The outcome of traditional culture method illustrated the number of soil fungi increased from CSUS to CSDS, while the sort of fungal species that could be cultured did not show much difference among the three sample sites.     

The ecology and evolution of the New World non-pollinating fig wasp communities

Abstract. We present data on several previously undescribed species from six genera of New World non-pollinating fig wasps. We show that many of these species have a negative effect on the reproductive success of both the pollinator wasps and the host figs. Our results suggest that the two most abundant genera of non-pollinating wasps, the Idarnes and the Critogaster , compete for the same pool of female flowers as the pollinating wasps in the Urostigma and Pharmacosycea figs, respectively. Wasps from the genus Aepocerus induce and develop within large galls, in the Urostigma figs. By draining resources from the fruit these wasps may have a detrimental effect on the production of pollinator wasps and viable seeds. Some of the species investigated are parasitoids of other non-pollinating species. We examine the importance of the various forms of spatial heterogeneity in the parasitism rate that can act to stabilise the host-parasitoid interaction. Finally, we discuss the factors underlying the large variation in the abundance and diversity of the non-pollinating wasps both among and within fruit crops.     

工业有机污染对小型水体沉积物真菌群落的影响分析

【背景】有机污染对水体沉积物中的微生物多样性影响极大,而目前有关污染水体沉积物中真菌多样性的研究较少。【目的】研究不同程度有机污染下水体沉积物中真菌种群的多样性特征,探究工业有机污染对真菌群落的影响。【方法】应用化学分析方法和高通量测序技术进行研究,并分析水质、沉积物成分等环境因子与沉积物真菌多样性的相关性。【结果】随着污染程度的降低,水体沉积物中真菌序列数、OTU数和Shannon多样性指数均呈上升趋势。未分类真菌、子囊菌门和担子菌门是沉积物真菌群落中的主要优势种类,主要优势属为Zopfiella、Westerdykella、Clypeosphaeria、Ilyonectria、Paracremonium、Aspergillus。真菌Shannon指数与水体溶解氧(dissolvedoxygen,DO)极显著正相关,与沉积物有机质和总磷含量显著负相关,Simpson指数与水体总氮(total nitrogen,TN)、氨氮(NH3-N)、总磷(total phosphorus,TP)显著相关。【结论】有机污染导致水体溶解氧下降和沉积物有机质增加,从而导致污染区真菌多样性显著下降。Zopfiella、Penicillium、Emericellopsis、Westerdykella、Jugulospora、Chromelosporium可能参与曝气处理区域沉积物兼氧条件下污染物的去除,Ilyonectria、Mortierella、Epicoccum可能主要参与水生生物残体分解、污染物的吸附沉降等过程。     

Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata: insights into the evolutionary dynamics of bracoviruses

Bracoviruses represent the most complex endogenous viral elements (EVEs) described to date. Nudiviral genes have been hosted within parasitoid wasp genomes since approximately 100 Ma. They play a crucial role in the wasp life cycle as they produce bracovirus particles, which are injected into parasitized lepidopteran hosts during wasp oviposition. Bracovirus particles encapsidate multiple dsDNA circles encoding virulence genes. Their expression in parasitized caterpillars is essential for wasp parasitism success. Here, we report on the genomic organization of the proviral segments (i.e. master sequences used to produce the encapsidated dsDNA circles) present in the Cotesia congregata parasitoid wasp genome. The provirus is composed of a macrolocus, comprising two-thirds of the proviral segments and of seven dispersed loci, each containing one to three segments. Comparative genomic analyses with closely related species gave insights into the evolutionary dynamics of bracovirus genomes. Conserved synteny in the different wasp genomes showed the orthology of the proviral macrolocus across different species. The nudiviral gene odv-e66-like1 is conserved within the macrolocus, suggesting an ancient co-localization of the nudiviral genome and bracovirus proviral segments. By contrast, the evolution of proviral segments within the macrolocus has involved a series of lineage-specific duplications.     

Low‐coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

Population divergence and gene flow are key processes in evolution and ecology. Model‐based analysis of genome‐wide data sets allows discrimination between alternative scenarios for these processes even in nonmodel taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum [bSFS], the second on the pairwise sequentially Markovian coalescent [PSMC]) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia and are separated into The Northern population is to the north of the Southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of postdivergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196 kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57 kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome‐level data for small population samples of tiny, nonmodel organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.     

Delving into the dark ecology: A continent-wide assessment of patterns of composition in soil fungal communities from Australian tussock grasslands

Soil fungi play essential roles in many terrestrial processes, but our knowledge of the forces governing fungal distribution and community composition along broad-scale environmental gradients is still limited. In this study, we explored biogeographic distribution and composition of soil fungal communities associated with 62 tussock grasslands across different regions of Australia. Climatic parameters had only a limited correlation with fungal community structure, while edaphic variables and spatial distance were significantly associated with changes in fungal community composition. We also observed high variations in composition among fungal assemblages from different ecological regions, suggesting some regional endemism in these communities. The discrete distribution of fungi in soil was further confirmed by indicator analysis, which identified distinct indicator operational taxonomic units associated with grasslands from different climatic regions. Finally, fungi with flexible trophic interactions had a central role in the network architecture of both arid and temperate communities. Taken together, the results from our study confirm the prominent role of soil physico-chemical status and geographic location in determining fungal biogeographic patterns over large scales in Australia.     

Fungal community associated with adults of the chestnut gall wasp Dryocosmus kuriphilus after emergence from galls: Taxonomy and functional ecology

The diversity of the fungal community associated with adults of Dryocosmus kuriphilus following emergence was examined using HTS analysis. Ascomycota dominated the fungal core-biome community. The functional guilds of the 90 taxa forming the core-biome were assessed, demonstrating three main groups: saprotrophs, plant pathogens and entomopathogens. Twenty-nine OTUs out of 90 were resolved to species level identifying 26 different fungal species. Among these species, many were cosmopolitan or previously recorded in Europe. Ten taxa were previously recorded on chestnut, including some recognized plant pathogens associated with foliage and green tissues such as Epicoccum nigrum, Gnomoniopsis castanea, Colletotrichum acutatum, Stromatoseptoria castaneicola, Ramularia endophylla. Beauveria bassiana; within the core microbiome, Fusarium larvarum represented the most abundant entomopathogenic species. Some of these species are known to impact directly or indirectly the vitality of the insects in the galls. The chestnut blight pathogen, Cryphonectria parasitica, was never found associated with D. kuriphilus. Based on the present study, an active role for D. kuriphilus as a vector of chestnut fungal endophyte/pathogens cannot be demonstrated but neither ruled out.     

New insights into the diversity dynamics of Triassic conodonts

In this paper, we examine the diversity trends and the evolutionary patterns of Triassic conodonts through a newly powered large-scale data-set compiled directly from the primary literature. Paleodiversity dynamics analyses have been undertaken by working at the species level and using a system of time units based on biozone subdivisions for a fine temporal level resolution. The role of heterogeneous duration of taxa in diversity estimates has been evaluated through the probabilistic profiles. Results reveal three different stages in the diversity behaviour of Triassic conodonts from standing metrics delimited by two inflections at the mid-Anisian and mid-Carnian. Survivorship analysis supports this pattern. Origination–extinction metrics report a diversification pattern characterised by important fluctuations during the Lopingian–Induan (earliest Triassic), the early-middle Olenekian (Early Triassic) and the Anisian–Ladinian transitions (Middle Triassic), as well as in the early Late Triassic. In addition, two clear diversification peaks are observed in the late Carnian and in the end-Norian. Reported patterns are interpreted in the context of deep extinction and environmental instability by documenting the biological signal of the main diversification and turnover patterns observed from such records. This study emphasises the singularity behaviour of diversity trends derived from the conodont record.     

New insights into the evolutionary history of Plasmodium falciparum from mitochondrial genome sequence analyses of Indian isolates

Estimating genetic diversity and inferring the evolutionary history of Plasmodium falciparum could be helpful in understanding origin and spread of virulent and drug‐resistant forms of the malaria pathogen and therefore contribute to malaria control programme. Genetic diversity of the whole mitochondrial (mt) genome of P. falciparum sampled across the major distribution ranges had been reported, but no Indian P. falciparum isolate had been analysed so far, even though India is highly endemic to P. falciparum malaria. We have sequenced the whole mt genome of 44 Indian field isolates and utilized published data set of 96 genome sequences to present global genetic diversity and to revisit the evolutionary history of P. falciparum. Indian P. falciparum presents high genetic diversity with several characteristics of ancestral populations and shares many of the genetic features with African and to some extent Papua New Guinean (PNG) isolates. Similar to African isolates, Indian P. falciparum populations have maintained high effective population size and undergone rapid expansion in the past with oldest time to the most recent common ancestor (TMRCA). Interestingly, one of the four single nucleotide polymorphisms (SNPs) that differentiates P. falciparum from P. falciparum‐like isolates (infecting non‐human primates in Africa) was found to be segregating in five Indian P. falciparum isolates. This SNP was in tight linkage with other two novel SNPs that were found exclusively in these five Indian isolates. The results on the mt genome sequence analyses of Indian isolates on the whole add to the current understanding on the evolutionary history of P. falciparum.     

New insights into the patterns and drivers of avian altitudinal migration from a growing crowdsourcing data source

Altitudinal migration is a common and important but understudied behavior in birds. Difficulty in characterizing avian altitudinal migration has prevented a comprehensive understanding of this behavior. To address this, we investigated the altitudinal migration patterns and explored potential drivers for a major proportion (~70%) of the entire resident bird community along an almost 4000 m elevational gradient on the main island of Taiwan. Based on the occurrence records collected by citizen scientists, we examined the seasonal shifts in the center and the upper and lower boundaries of elevational distributions for 104 individual species. We then built phylogeny‐controlled regression models to investigate the associations between the birds’ seasonal distribution shifts and seven of their traits, and examined whether the observed shifts can be explained by three main hypotheses on potential drivers. Results showed that at least 60 species (58%) seasonally changed their distributions along elevations. While most of them (42 species) tended to move downhill in winter, a considerable number of species (14) tended to move uphill. While the species breeding at high or low elevations tended to move downhill in winter, those breeding at medium‐low elevations tended to move or extend their distributions to higher elevations. Our regression models suggested that seasonal variations in climates and food availability could be major drivers of the behavior. However, the three hypotheses can only partially explain the observed downhill migration patterns and none of them can well explain the uphill patterns, indicating an important knowledge gap. This study investigated avian altitudinal migration from a new perspective with a novel and generalizable approach, and revealed interesting patterns that could be difficult to identify with conventional approaches. It demonstrated the power of citizen science data to provide new insights into this behavior by characterizing the general patterns and mechanisms across a large number of species.     

New insights into the pathological mechanisms of cerebrotendinous xanthomatosis in the Taiwanese using genomic and proteomic tools

Cerebrotendinous xanthomatosis (CTX) is an autosomal recessive lipid-storage disorder caused by a deficiency of the mitochondrial sterol 27-hydroxylase. Genetic analysis utilizing SSCP and direct DNA sequencing identified a new mutation. One base-pair of cytosine was deleted at codon 326 on exon 2 of CYP27 in all CTX patients while their father was heterozygotic. This novel point deletion predicts a frameshift in mRNA (Pro(102) -->Leu) and results in the appearance of a premature termination codon (TGA) to substitute for Val(106) (GTG). To characterize the pathological mechanism of CTX patients, the protein profiles of serum and leukocytes extracted from these subjects were presented by means of proteomic technologies including 2-DE and MALDI-TOF analysis. According to the results, the amount of vinculin, ABP-280, talin and vimentin in leukocytes of CTX patients had changed significantly, reflecting the changes in membrane dynamics concerning cholestanol accumulation. The expression of target proteins in CTX patients and control was further verified by western blotting which indicated the same tendency as 2-DE data. This is the first paper to integrate both genomic and proteomic concepts for analyzing the possible mechanism of CTX and provides more information for related study in the future.     

Polyphyly of the fern family Tectariaceae sensu Ching: insights from cpDNA sequence data

Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL and atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria and Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with and should be included within the newly-defined Dryopteridaceae, and Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix, and Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae and to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.     

Population genetics of New World screwworm from the Caribbean: insights from microsatellite data

Abstract.  Diseases affecting livestock can have a significant impact on animal productivity and on trade of live animals, meat and other animal products, which, consequently, affects the overall process of economic development. The New World screwworm, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae), is an important parasitic insect pest in Neotropical regions. This species has been successfully eradicated from North and most of Central America by the sterile insect technique, but continues to affect the development of the livestock sector in most Caribbean economies. Here, we provide some insight into the patterns of genetic variation and structure and gene flow of C. hominivorax populations from the Caribbean. Analysis of populations from 10 geographical sites in four islands revealed a moderate genetic variability within the populations. Surprisingly, a high population differentiation was found even in intra-island comparisons between populations. This observation can reflect either highly structured populations resulting from a lack of gene flow or a source–sink dynamic. Our study also suggests that New World screwworm populations can recover very rapidly from population contractions. This is valuable information that should be required prior to any investment in large-scale efforts aiming at controlling this pest.