Australian Thysanoptera – biological diversity and a diversity of studies

Abstract   Studies in Australia on thrips have had extensive impacts worldwide. In behaviour, the latest definition of eusociality is derived from work on the radiation of thrips on Acacia species in central Australia, and these Acacia thrips also having been used to develop the concept of 'model clades' for analysing the evolution of behavioural and ecological diversity. In ecology, the concept of the lack of density dependent factors in population dynamics was elaborated through studies on the plague thrips of southern Australia. In virology, thrips were first shown in Australia to be the vectors of tospoviruses, although these viruses, their vectors and the plants attacked are all non-native to this continent. Work in Australia has included the development of electronic methods of illustration, identification and information transfer about thrips, including the use of molecular methods for pest species recognition, and considerable advances have been made in Australia in our knowledge of the relationships between thrips and plants, from polyphagy to pollination.     

Ulva diversity in the Yellow Sea during the large‐scale green algal blooms in 2008–2009

In the Yellow Sea of China, large‐scale green tides have broken out for three consecutive years from 2007 to 2009. As part of the efforts to localize the algal source, two cruises were conducted in the early stage and the outbreak stage of the bloom in 2009. We analyzed the morphological and genetic diversity of drifting Ulva specimens and culture‐derived isolates from seawater sampled in different localities. For phylogenetic analyses, the nuclear encoded ribosomal DNA internal transcribed spacer region (ITS nrDNA) and the plastid encoded large subunit of ribulose‐1, 5‐bisphosphate carboxylase/oxgenase gene (rbcL) were used. Our molecular and morphological data indicate that the dominant free‐floating Ulva species in 2008 and 2009 possibly belonged to a single strain of the U. linza‐procera‐prolifera (LPP) clade. The ITS sequences from bloom‐forming algal samples with dense branches were identical to those from U. linza‐like specimens without branches derived from the Yellow Sea. Microscopic individuals of the dominant Ulva strain were detected in eight stations, revealing that spore dispersal in the water helped to enlarge biomass in the water during the outbreak stage of green tide in the Yellow Sea.     

中国哺乳动物多样性

中国哺乳动物区系有鲜明的特色:有青藏高原分布的特有种属,有第三纪孑遗动物——大熊猫科和白鱀豚科,世界一半以上的鼠兔科动物为中国特有种,中国还是世界有蹄类最丰富的国家。新世纪以来,世界哺乳动物分类体系发生了变化,中国也发现一批哺乳动物新种和新记录种。因此,有必要对中国哺乳动物多样性名录进行及时更新和完善。我们在《中国生物多样性红色名录·哺乳动物卷》的编研中,对中国哺乳动物的目级阶元采用在系统发育基因组学已经取得一致意见的方案;在科及以下阶元以《中国哺乳动物种与亚种分类名录与分布大全》和Mammal Species of the World:A Taxonomic and Geographic Reference(第3版)的分类系统为基础,有蹄类的分类采用Ungulate Taxonomy分类系统;收集整理了中国(包括台湾地区)所有哺乳动物资料,增加了截至2015年3月31日学术期刊发表的中国哺乳动物新种和新记录种,通过会议评审和通讯评审,调整了一些物种的名称和分类地位,确定了《中国哺乳动物名录(2015)》。该名录收录了中国现有哺乳动物12目55科245属673种,其中,新种18种(包括11种最近发现的或利用分子生物学方法确定的、尚有争议的新种)、新记录种18种、60个亚种提升为种。根据研究结果和专家意见,剔除了52种哺乳动物。此外,中国分类学家对新版名录中的20种啮类(Glires)的分类地位持不同意见,这些种类需要进一步研究。以《中国哺乳动物名录(2015)》收录的中国哺乳动物种数与其他国家比较,中国哺乳动物种数超过IUCN(2014)报道的世界哺乳动物排序第一的印度尼西亚(670种)。中国有150种特有哺乳动物,特有种比例为22.3%。兔形目特有种比例达43%,鼠兔科特有种比例更高达52%。劳亚食虫目的特有种比例为35%。中国灵长目、啮齿目和翼手目特有种比例约占各目总种数的1/5,翼手目特有种包括近十年发表、模式产地为中国的12个蝙蝠新种。《中国哺乳动物名录(2015)》为生物多样性研究与保护提供了最新的本底资料。     

Phylogenetic diversity stabilizes community biomass

Aims The relationship between biodiversity and ecological stability is a long-standing issue in ecology. Current diversity–stability studies, which have largely focused on species diversity, often report an increase in the stability of aggregate community properties with increasing species diversity. Few studies have examined the linkage between phylogenetic diversity, another important dimension of biodiversity, and stability. By taking species evolutionary history into account, phylogenetic diversity may better capture the diversity of traits and niches of species in a community than species diversity and better relate to temporal stability. In this study, we investigated whether phylogenetic diversity could affect temporal stability of community biomass independent of species diversity.Methods We performed an experiment in laboratory microcosms with a pool of 12 bacterivorous ciliated protist species. To eliminate the possibility of species diversity effects confounding with phylogenetic diversity effects, we assembled communities that had the same number of species but varied in the level of phylogenetic diversity. Weekly disturbance, in the form of short-term temperature shock, was imposed on each microcosm and species abundances were monitored over time. We examined the relationship between temporal stability of community biomass and phylogenetic diversity and evaluated the role of several stabilizing mechanisms for explaining the influence of phylogenetic diversity on temporal stability.Important findings Our results showed that increasing phylogenetic diversity promoted temporal stability of community biomass. Both total community biomass and summed variances showed a U-shaped relationship with phylogenetic diversity, driven by the presence of large, competitively superior species that attained large biomass and high temporal variation in their biomass in both low and high phylogenetic diversity communities. Communities without these species showed patterns consistent with the reduced strength of competition and increasingly asynchronous species responses to environmental changes under higher phylogenetic diversity, two mechanisms that can drive positive diversity–stability relationships. These results support the utility of species phylogenetic knowledge for predicting ecosystem functions and their stability.     

毛乌素沙地植被不同恢复阶段植物群落物种多样性、功能多样性和系统发育多样性

进入21世纪以来, 中国荒漠化恢复取得显著成效, 荒漠化、沙化土地面积持续减少, 植被覆盖度大幅提升, 但关于植被恢复过程中生物多样性如何变化的研究不足, 这制约着对荒漠化恢复成效的全面评估。本文基于群落调查和叶功能性状(叶片厚度、叶片干物质含量、比叶面积和叶片密度)的测定, 分析了毛乌素沙地不同恢复阶段(半固定沙地、固定沙地、结皮覆盖沙地和草本植物覆盖沙地)的植物群落物种多样性、功能多样性和系统发育多样性特征。结果表明: (1)多数叶功能性状的系统发育信号不显著, 表明环境因子对研究区植物功能性状的塑造作用很强。(2)对于α多样性, 结皮覆盖沙地的物种多样性(Shannon-Wiener多样性, H)、物种丰富度(S)、功能丰富度(FRic)及系统发育多样性(PD)指数均显著低于其他恢复阶段, 而其他3个阶段间无显著差异; 这些指数间均显著正相关, 表明物种多样性、功能多样性和系统发育多样性在植被恢复过程中协同变化。(3) β多样性指数随恢复阶段间隔增加而逐渐增大, 表明物种组成、功能属性及系统发育关系随植被恢复持续变化, 且半固定沙地到固定沙地的群落物种组成、功能属性及系统发育关系更替最快, 导致群落间差异最大。(4)固定沙地、结皮覆盖沙地和草本植物覆盖沙地群落系统发育结构均趋向于发散, 表明竞争排斥是群落构建的主要驱动力; 而半固定沙地群落系统发育结构无一致规律, 表明群落构建可能受到生境过滤和竞争排斥的综合作用。研究结果可为植被建设与管理提供参考, 为毛乌素沙地生态保育和生物多样性的保护提供科学依据。     

The diversity of FtsY‐lipid interactions

The bacterial signal recognition particle (SRP) receptor FtsY forms a complex with the SRP Ffh to target nascent polypeptide chains to the bacterial inner membrane. How FtsY interacts with lipids and associates to the membrane is unclear. Here, we show that vesicle binding leads to partial protection against proteolytic degradation and a change in secondary structure, which differs depending on whether the lipids are simple mixtures of zwitterionic and anionic lipids, mimics of Escherichia coli lipids, or lysolipids. Lipid binding alters the stability of FtsY. Thermal unfolding of FtsY in buffer shows two transitions, one occurring at ～60°C and the other at ～90°C. The thermal intermediate accumulating between 60 and 90°C has structural features in common with the state induced by binding to E. coli lipids. E. coli lipid extract induces a single transition around 70°C, anionic lipids have no effect while cooperative unfolding is completely removed in lysolipids. Thus, the lipid environment profoundly influences the dynamic properties of FtsY, leading to three different kinds of FtsY‐lipid interactions with different effects on structure, proteolytic protection, and stability, and is driven both by hydrophobic and electrostatic interactions. Trypsin digestion experiments highlight the central role of the N‐domain in lipid contacts, whereas the A‐ and G‐domains appear to play a more minor part. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 595–606, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Measuring beta‐diversity from taxonomic similarity

Question: The utility of beta (β‐) diversity measures that incorporate information about the degree of taxonomic (dis)similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of β‐diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot‐to‐plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher‐level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify β‐diversity from taxonomic dissimilarities is discussed. Results: The proposed measure of taxonomic β‐diversity incorporates not only species richness, but also information about the degree of higher‐order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of β‐di‐versity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80% of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher‐order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot‐to‐plot similarity is only needed if we are interested in the residual system's variation that is related to the higher‐order taxonomic structure of a pair of species plots.     

Pyrodiversity begets plant–pollinator community diversity

Fire has a major impact on the structure and function of many ecosystems globally. Pyrodiversity, the diversity of fires within a region (where diversity is based on fire characteristics such as extent, severity, and frequency), has been hypothesized to promote biodiversity, but changing climate and land management practices have eroded pyrodiversity. To assess whether changes in pyrodiversity will have impacts on ecological communities, we must first understand the mechanisms that might enable pyrodiversity to sustain biodiversity, and how such changes might interact with other disturbances such as drought. Focusing on plant–pollinator communities in mixed‐conifer forest with frequent fire in Yosemite National Park, California, we examine how pyrodiversity, combined with drought intensity, influences those communities. We find that pyrodiversity is positively related to the richness of the pollinators, flowering plants, and plant–pollinator interactions. On average, a 5% increase in pyrodiversity led to the gain of approximately one pollinator and one flowering plant species and nearly two interactions. We also find that a diversity of fire characteristics contributes to the spatial heterogeneity (β‐diversity) of plant and pollinator communities. Lastly, we find evidence that fire diversity buffers pollinator communities against the effects of drought‐induced floral resource scarcity. Fire diversity is thus important for the maintenance of flowering plant and pollinator diversity and predicted shifts in fire regimes to include less pyrodiversity compounded with increasing drought occurrence will negatively influence the richness of these communities in this and other forested ecosystems. In addition, lower heterogeneity of fire severity may act to reduce spatial turnover of plant–pollinator communities. The heterogeneity of community composition is a primary determinant of the total species diversity present in a landscape, and thus, lower pyrodiversity may negatively affect the richness of plant–pollinator communities across large spatial scales.     

Assessing microbial diversity using recent lake sediments and estimations of spatio‐temporal diversity

Aim Recent papers have used large palaeolimnological datasets to reveal the biodiversity patterns of aquatic microorganisms. However, scant attention has been paid to the influence of time on these patterns. Where lake surficial sediment samples are used as integrals of diversity, the time interval of each sample varies according to differences in sediment accumulation rates. This paper aims to test the reliability of using lake surface sediments to measure and to compare microbial diversity when the potential influences of the species–time relationships are taken into account. Location Alpine lakes in Europe. Methods We analysed microorganism (siliceous microalgae) assemblages in three European Alpine lakes using short sediment cores (²¹⁰Pb‐dated) and annual sediment trap samples from 12 UK lakes. The same number of individuals was pooled for each sample 500 times to avoid sampling effort effects and to standardize species diversity estimation. The influence of time on the diversity score was assessed by simulating an increase of time span for surface sediment samples by cumulatively adding in successive sediment core samples (from the most recent to the oldest). We used species richness (S) and the exponential of the bias‐corrected Shannon entropy index (exp(H_b‐c)) to estimate diversity. Results Increasing the time interval represented by a surficial sediment sample did not affect the diversity results. The estimation of diversity was similar for cumulative and non‐cumulative samples. Diversity estimation was only altered in lakes experiencing high community turnover due to strong environmental forcing during the time period spanned by the cumulative sample. Main conclusions The use of surface lake sediments is suitable for estimating the average site diversity of free‐living microorganisms. Diversity is integrated in a single sample and species assemblage composition is derived from microbial communities living in distinct lake microhabitats. Species remains, accumulated in a single sample over several years of environmental variability, represent a diversity integral that captures a spatio‐temporal component equivalent to the γ‐diversity measure.     

Non‐genetic diversity modulates population performance

Biological functions are typically performed by groups of cells that express predominantly the same genes, yet display a continuum of phenotypes. While it is known how one genotype can generate such non‐genetic diversity, it remains unclear how different phenotypes contribute to the performance of biological function at the population level. We developed a microfluidic device to simultaneously measure the phenotype and chemotactic performance of tens of thousands of individual, freely swimming Escherichia coli as they climbed a gradient of attractant. We discovered that spatial structure spontaneously emerged from initially well‐mixed wild‐type populations due to non‐genetic diversity. By manipulating the expression of key chemotaxis proteins, we established a causal relationship between protein expression, non‐genetic diversity, and performance that was theoretically predicted. This approach generated a complete phenotype‐to‐performance map, in which we found a nonlinear regime. We used this map to demonstrate how changing the shape of a phenotypic distribution can have as large of an effect on collective performance as changing the mean phenotype, suggesting that selection could act on both during the process of adaptation.     

On the origins,rapid expansion and genetic diversity of native Americans from hunting‐gatherers to agriculturalists

Given the importance of Y‐chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y‐chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai‐Tai, Kungurtug, and Toora‐Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post‐migration population growth in the ubiquitous and diverse Y‐STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural‐ and trade‐based subsistence adopted during the Pre‐Classic, Classic and Post‐Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median‐joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y‐ STR average gene diversity indices. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

A quantitative review of MHC‐based mating preference: the role of diversity and dissimilarity

Sexual selection hypotheses stipulate that the major histocompatibility complex genes (MHC) constitute a key molecular underpinning for mate choice in vertebrates. The last four decades saw growing empirical literature on the role of MHC diversity and dissimilarity in mate choice for a wide range of vertebrate animals, but with mixed support for its significance in natural populations. Using formal phylogenetic meta‐analysis and meta‐regression techniques, we quantitatively review the existing literature on MHC‐dependent mating preferences in nonhuman vertebrates with a focus on the role of MHC diversity and dissimilarity. Overall, we found small, statistically nonsignificant, average effect sizes for both diversity‐ and dissimilarity‐based mate choice (r = 0.113 and 0.064, respectively). Importantly, however, meta‐regression models revealed statistically significant support regarding female choice for diversity, and choice for dissimilarity (regardless of choosy sex) only when dissimilarity is characterized across multiple loci. Little difference was found among vertebrate taxa; however, the lack of statistical power meant statistically significant effects were limited to some taxa. We found little sign of publication bias; thus, our results are likely to be robust. In light of our quantitative assessment, methodological improvements and fruitful future avenues of research are highlighted.     

Richness‐dependence of phylogenetic diversity indices

Phylogenetic diversity indices are widely used to characterize the structure and diversity of ecological communities. Most indices are based on a metric that is expected to vary with species richness, so they are standardized to remove this richness‐dependence. With this standardization, values of 0 are consistent with random phylogenetic structure, while phylogenetic clustering is associated with either negative or positive values (depending on the index). One common interpretation of phylogenetic clustering is that it indicates some combination of environmental and biological filtering that restricts the species that can be present in a community. Increasingly, studies are comparing phylogenetic indices along environmental gradients to infer differences in the factors structuring communities. This comparison implicitly assumes that index values are comparable among communities with different numbers of species. Using a set of simulations, I show here that this assumption is incorrect. Holding the strength of filtering constant, communities composed of more species show larger absolute index values. This problem is most pronounced when the environmental filter favors a moderate‐sized clade strongly over others and when using the net relatedness index (NRI) to measure clustering. This bias potentially casts doubt on studies studying phylogenetic index patterns along gradients where richness also varies. Fortunately, the arising generality that more stressful environments have lower species richness and stronger clustering is opposite to this bias and therefore robust. I also show that a simple rarefaction can remove the richness‐dependence of these indices, at the expense of increased error.     

极地陆域微生物多样性研究进展

极地是指高纬度、高海拔地区,包括南极(60°S以南)、北极(60°N以北)和被称为“第三极”的青藏高原地区(平均海拔4,500 m).这些地区气温极低、养分极度贫乏,生态系统非常脆弱,对全球气候变化极为敏感,该地区生态系统一旦破坏将很难恢复.尽管极地地区自然条件恶劣,但在这些极端环境中栖息着大量微生物,是元素生物地球化学循环的主要驱动者,对极地生态系统的构建和维持具有非常重要的作用.本文综述了极地土壤、湖泊和冰川等陆域环境微生物研究进展.在这些极地环境中,目前已发现了Acidobacteria,Actinobacteria,Bacteroidetes,Cyanobacteria和Firmicutes等类群,这些微生物具有嗜盐/耐盐及耐低温等特征.我国在极地微生物生态学研究方面落后于发达国家,建议优先发展较易到达的青藏高原地区微生物生态学长期定位观测,这将有助于较快提升我国极地微生物多样性研究水平,深入了解极端生命过程及其生态学效应.     

A resource-based conceptual model of plant diversity that reassesses causality in the productivity–diversity relationship

Biogeographical studies frequently reveal positive correlations between species richness and estimates of environmental water and/or energy. A popular interpretation of this relationship relates the supply of water and energy to productivity, and then, in turn, to richness. Productivity–diversity theories are now legion, yet none has proved sufficiently intuitive to gain broad acceptance. Like productivity, heterogeneity is known to influence diversity at fine spatial scales, yet the possibility that richness might relate to water–energy dynamics at coarse spatial scales via a heterogeneity‐generating mechanism has received little attention. In this paper we outline such a conceptual model for plants that is internally consistent and testable. We believe it may help to explain the capacity of environments receiving different inputs of water and energy to support variable numbers of species at a range of spatial scales, the pervasive correlation between productivity and richness, some exceptions to the productivity–diversity relationship, the form of productivity–diversity curves and the link between richness and environmental ‘harshness’. The model may also provide an answer to one of the most venerable puzzles in the field of diversity studies: why high inputs of water and energy correspond to more species rather than simply more individuals.