The impact of host genetic diversity on virus evolution and emergence

Accumulating evidence indicates that biodiversity has an important impact on parasite evolution and emergence. The vast majority of studies in this area have only considered the diversity of species within an environment as an overall measure of biodiversity, overlooking the role of genetic diversity within a particular host species. Although theoretical models propose that host genetic diversity in part shapes that of the infecting parasite population, and hence modulates the risk of parasite emergence, this effect has seldom been tested empirically. Using Rabies virus (RABV) as a model parasite, we provide evidence that greater host genetic diversity increases both parasite genetic diversity and the likelihood of a host being a donor in RABV cross‐species transmission events. We conclude that host genetic diversity may be an important determinant of parasite evolution and emergence.     

Conflicts in maintaining biodiversity at multiple scales

Biodiversity consists of multiple scales, including functional diversity in ecological traits, species diversity and genetic diversity within species, and is declining across the globe, largely in response to human activities. While species extinctions are the most obvious aspect of this, there has also been a more insidious loss of genetic diversity within species. While a vast literature concerns each of these scales of biodiversity, less is known about how different scales affect one another. In particular, genetic and species diversity may influence each other in numerous ways, both positively and negatively. However, we know little about the mechanism behind these patterns. In this issue of Molecular Ecology, Nestmann et al. (2011) experimentally explore the effect of species and functional diversity and composition of grassland plant communities on the genetic structure of one of the component species. Increasing species richness led to greater changes in the genetic composition of the focal populations over 4 years, primarily because of genetic drift in smaller population sizes. However, there were also genetic changes in response to particular plant functional groups, indicating selective differences driven by plant community composition. These results suggest that different levels of biodiversity can trade-off in communities, which may prove a challenge for conservation biologists seeking to preserve all aspects of biodiversity.     

遗传多样性的取样策略

合理取样是生物多样性有效保护、利用和研究所面临的最基本问题 ,它在很大程度上受到植物自身的生物学特性、环境条件和取样目的的影响。遗传多样性的取样策略是指对一定地理分布范围内的生物个体取样时 ,使样本具有代表性和包含尽可能多的遗传变异的最佳取样方法 ,包括了取样数目 (一个给定区域的居群数和一个居群的个体数 )以及取样方式。包括“哈迪 温伯格平衡 (Hardy WeinbergEquilibrium)”定律在内的居群遗传学基本原理是研究取样策略的理论基础 ,在此基础上可以对居群内的取样个体数及应获取的居群数进行理论计算 ,同时还可以根据物种居群的遗传结构特点和环境条件的异质性来决定取样的方式。因此 ,应该依据研究对象本身的特点和取样的目的来确定某一特定区域的居群取样数 ,以及某一居群内的样本数及取样方式。     

Analysis of biodiversity across levels of biological organization: a problem of defining traits

Biodiversity is a term that comprises the appearance, structure and function of all levels of biological organization, including genes, species and ecosystems. The vast majority of measures of biodiversity (usually termed ‘diversity indices’) considers only number, proportion and distribution of species which belong to a specified group and exist in a defined area or ecosystem. Genetic diversity as a part of biodiversity within species (or populations) was either not regarded in this respect or was treated (by geneticists) as a separate entity of diversity quantified with separate measures. Little attention has been given to the integration of both types of diversity, within and among species, in a single measurement (termed ‘transspecific’ diversity). In order to attain this integration on a general basis, an operational trait concept is developed which allows the determination of variation in traits observable in members not only of the same species but also of different species. The concept rests on methods of investigation that can be adapted to a broader range of organisms without modification of their characteristics. Once a trait is specified on this basis, any meaningful measure of diversity can be applied to assess biodiversity across levels of biological organization. The utility of the concept is demonstrated by application to the results of an earlier study on associations between species and genetic diversity in a forest tree community. Attributes of isozymes which are visible in electrophoresis are used as a transspecific genetic trait.     

Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus

The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here, we combine genome scans, population genetics and sequence-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a sampling design encompassing five major Amazonian rivers, three hydrochemical settings, 352 nuclear markers and two mitochondrial DNA genes, we assess the influence of environmental gradients as biodiversity drivers in Amazonia. We identify strong divergent natural selection with gene flow and isolation by environment across craton (black and clear colour)- and Andean (white colour)-derived water types. Furthermore, we find that heightened selection and population genetic structure present at the interface of these water types appears more powerful in generating diversity than the spatial arrangement of river systems and vicariant biogeographic history. The results from our study challenge assumptions about the origin and distribution of adaptive and neutral genetic diversity in tropical ecosystems. In addition, they have important implications for measures of biodiversity and evolutionary potential in one of the world's most diverse and iconic ecosystems.     

Genetic and community similarities are correlated in endemic-rich springs of the northern Chihuahuan Desert

Aim Species diversity and genetic diversity within a taxon are intrinsic parts of global biodiversity. These two levels of biodiversity can show strong correlation due to a variety of reasons (i.e. parallel processes affecting both communities and populations, genotypes of a numerically or functionally dominant species affecting community composition, a species assemblage selecting for a particular genotype by affecting its selection regime). We examined correlations between species and genetic biodiversity in four isolated endemic‐rich spring systems in a hot desert and their potential link to environmental variables and physical isolation. Location Chihuahuan Desert spring systems in the Pecos River basin of New Mexico and Texas, USA. Methods We compared species richness of fish and benthic macroinvertebrate communities to within‐population allelic richness of amphipods (monophyletic Gammarus spp.) and Pecos gambusia (Gambusia nobilis) using Mantel tests. We also compared pairwise community similarities with pairwise genetic identities of populations among the same groups. We tested correlations among diversity, similarity and environmental variables after controlling for the effects of spatial distances using partial Mantel tests. We partitioned genetic and species diversity into three spatial scales (i.e. individual springs, individual spring systems, the entire region) using AMOVA and partition . Results We found strong correlations between invertebrate species richness and mosquitofish allelic richness. We found even stronger correlations of amphipod and gambusia genetic identities with fish and invertebrate community similarities; these were best explained by geographic distance rather than abiotic environmental factors. Most of the taxa and communities exhibited the largest proportion of diversity at the regional level. Main conclusions Our results suggest that drift and migration are the mechanisms that best explain our observations, and although α‐diversity among genes and species may not be strongly correlated, the pattern of species and allelic complementarity among these groups seems to be concordant at the regional level.     

杨属遗传多样性研究进展

 生物多样性的研究和保护是目前全世界普遍关注的问题,其中研究较多的是遗传多样性、物种多样性及生态系统多样性,遗传多样性作为生物多样性的重要组成部分,是生态系统多样性和物种多样性的基础方面。杨树是世界各国普遍种植的木本植物,研究其遗传多样性具有重要的理论和实践意义,国内外都开展了广泛研究。本文综述了杨属(Populus)植物的派、种及无性系等在表型、染色体、蛋白质及DNA水平的遗传多样性的研究进展。其表型多样性主要体现在不同水平上的种群大小、形态特征、物候期、材性以及对生物或非生物逆境的抗性等方面;在杨属植物中已发现有天然的三倍体及三倍体/非整倍体的杂交种存在;蛋白质的多态性主要集中于同工酶的研究,用于不同杨属植物的遗传差异,无性系或品种的特征、分化和遗传研究;DNA多态性是研究最多的,RFLP、RAPD、AFLP和SSR等分子标记已广泛用于杨属的遗传多样性研究中,根据不同的研究目的所选择的DNA（nDNA, cpDNA或mtDNA）也不同。并根据国内的研究现状,提出了几点建议。     

Genetic diversity and phylogenetic analysis of native mountain ponies of Britain and Ireland reveals a novel rare population

The conservation of unique populations of animals is critical in order to preserve valuable genetic diversity and, where populations are free‐living, maintain their irreplaceable influence upon habitat ecology. An accurate assessment of genetic diversity and structure within and between populations is crucial in order to design and implement conservation strategies in natural and domesticated species. Moreover, where it is possible to identify relic populations that are related to a structured breed an ideal opportunity presents itself to model processes that reveal historical factors that have shaped genetic diversity. The origins of native UK mountain and moorland ponies are uncertain, but they may have directly descended from prehistoric populations and potentially harbour specific adaptations to the uplands of Britain and Ireland. To date, there have been no studies of population structure and genetic diversity present within a free‐living group of ponies in the Carneddau mountain range of North Wales. Herein, we describe the use of microsatellites and SNPs together with analysis of the mitochondrial control region to quantify the extent and magnitude of genetic diversity present in the feral Carneddau pony and relate this to several recognised British and Irish pony breeds. Our results establish that the feral Carneddau ponies represent a unique and distinctive population that merits recognition as a defined population and conservation priority. We discuss the implications for conservation of this population as a unique pool of genetic diversity adapted to the British uplands and potentially of particular value in maintaining the biodiversity of these habitats.     

酵母生物多样性开发及工业应用

酵母是一类包括酿酒酵母和非常规酵母在内的多种单细胞真菌的总称,其中酿酒酵母是应用较多的重要工业微生物,广泛应用于生物医药、食品、轻工和生物燃料生产等不同生物制造领域。近年来,研究者从不同生态环境中分离了大量的酵母菌株,鉴定了多个新种,也发现了抗逆性不同以及具有多种活性产物合成能力的菌株,证明天然酵母资源具有丰富的生物多样性和功能多样性。利用基因组挖掘以及转录组、蛋白组等多组学分析研究,可进一步开发利用酵母遗传多样性,获得酶和调节蛋白的基因以及启动子等遗传元件改造酵母菌株。除了利用酵母的天然遗传多样性,还可通过诱变、驯化、代谢工程改造及合成生物学等技术产生具有多种非天然多样性的菌株。此外,对天然遗传元件也可以进行突变和定向进化,所产生的新遗传元件可用于有效提升菌株的性能。开发利用酵母的生物多样性,对构建高效酵母细胞工厂,生产生物酶、疫苗以及多种活性天然产物等产品具有重要意义。文中对酵母生物多样性的研究现状进行综述,并对未来高效开发利用酵母菌株资源和遗传资源的研究进行了展望。文中所总结的研究方法和思路也可为研究其他工业微生物的多样性及进行高效菌株的选育提供参考。     

Connections between species diversity and genetic diversity

Species diversity and genetic diversity remain the nearly exclusive domains of community ecology and population genetics, respectively, despite repeated recognition in the literature over the past 30 years of close parallels between these two levels of diversity. Species diversity within communities and genetic diversity within populations are hypothesized to co‐vary in space or time because of locality characteristics that influence the two levels of diversity via parallel processes, or because of direct effects of one level of diversity on the other via several different mechanisms. Here, we draw on a wide range of studies in ecology and evolution to examine the theoretical underpinnings of these hypotheses, review relevant empirical literature, and outline an agenda for future research. The plausibility of species diversity–genetic diversity relationships is supported by a variety of theoretical and empirical studies, and several recent studies provide direct, though preliminary support. Focusing on potential connections between species diversity and genetic diversity complements other approaches to synthesis at the ecology–evolution interface, and should contribute to conceptual unification of biodiversity research at the levels of genes and species.     

Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products

To further explore possible avenues for accessing microbial biodiversity for drug discovery from natural products, we constructed and screened a 5,000-clone "shotgun" environmental DNA library by using an Escherichia coli-Streptomyces lividans shuttle cosmid vector and DNA inserts from microbes derived directly (without cultivation) from soil. The library was analyzed by several means to assess diversity, genetic content, and expression of heterologous genes in both expression hosts. We found that the phylogenetic content of the DNA library was extremely diverse, representing mostly microorganisms that have not been described previously. The library was screened by PCR for sequences similar to parts of type I polyketide synthase genes and tested for the expression of new molecules by screening of live colonies and cell extracts. The results revealed new polyketide synthase genes in at least eight clones. In addition, at least five additional clones were confirmed by high-pressure liquid chromatography analysis and/or biological activity to produce heterologous molecules. These data reinforce the idea that exploiting previously unknown or uncultivated microorganisms for the discovery of novel natural products has potential value and, most importantly, suggest a strategy for developing this technology into a realistic and effective drug discovery tool.     

Habitat variability correlates with duplicate content of Drosophila genomes

The factors limiting the habitat range of species are crucial in understanding their biodiversity and response to environmental change. Yet the genetic and genomic architectures that produce genetic variation to enable environmental adaptation have remained poorly understood. Here we show that the proportion of duplicated genes (P(D)) in the whole genomes of fully sequenced Drosophila species is significantly correlated with environmental variability within the habitats measured by the climatic envelope and habitat diversity. Furthermore, species with a low P(D) tend to lose the duplicated genes owing to their faster evolution. These results indicate that the rapid relaxation of functional constraints on duplicated genes resulted in a low P(D) for species with lower habitat diversity, and suggest that the maintenance of duplicated genes gives organisms an ecological advantage during evolution. We therefore propose that the P(D) in a genome is related to adaptation to environmental variation.     

Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota

Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.     

Strengthening desert plant biotechnology research in the United Arab Emirates: a viewpoint

The biotechnology of desert plants is a vast subject. The main applications in this broad field of study comprises of plant tissue culture, genetic engineering, molecular markers and others. Biotechnology applications have the potential to address biodiversity conservation as well as agricultural, medicinal, and environmental issues. There is a need to increase our knowledge of the genetic diversity through the use of molecular genetics and biotechnological approaches in desert plants in the Arabian Gulf region including those in the United Arab Emirates (UAE). This article provides a prospective research for the study of UAE desert plant diversity through DNA fingerprinting as well as understanding the mechanisms of both abiotic stress resistance (including salinity, drought and heat stresses) and biotic stress resistance (including disease and insect resistance). Special attention is given to the desert halophytes and their utilization to alleviate the salinity stress, which is one of the major challenges in agriculture. In addition, symbioses with microorganisms are thought to be hypothesized as important components of desert plant survival under stressful environmental conditions. Thus, factors shaping the diversity and functionality of plant microbiomes in desert ecosystems are also emphasized in this article. It is important to establish a critical mass for biotechnology research and applications while strengthening the channels for collaboration among research/academic institutions in the area of desert plant biotechnology.     

The structure of cross-cultural musical diversity

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations.     

珞珈山东亚三角头涡虫群体遗传多样性贫乏的RAPD证据

无脊椎动物是在生物多样性中占优势的类群,生物多样性研究还未受人们重视。遗传多样性研究是生物多样性研究的重要方面,采用RAPD技术分析了取样于武汉大学珞珈山的一个东亚三角头涡虫群体,该群体多态位点比例为11.3%,遗传相似度0.9505～1.0000,平均遗传相似度为0.9784,Shannon多样性指数为0.180,UPGMA聚类分析显示该群体分为两个大的分支,各项参数显示该群体的遗传多样性贫乏。根据RAPD分析结果,该东亚三角头涡虫群体遗传多样性贫乏与其周围生境退化有关,也可能与东亚三角头涡虫具有无性生殖和有性生殖这一独特的繁殖方式相关。     

Genetic variation among populations of the Antarctic toothfish: evolutionary insights and implications for conservation

Commercial fishing is having an increasingly negative impact on marine biodiversity, with over 70% of the world's fish stocks being fully exploited and, in many cases, overexploited. On top of this, the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) has granted commercial fishing permits in the most remote marine environment on earth, the high-latitude Southern Ocean. The primary target of these new commercial fishing ventures is the large pelagic piscivorous predator, the Antarctic toothfish (Dissostichus mawsoni). Unfortunately, little information is available on the demography, genetics, or life history of this large fish. Without such information we have little idea as to the effects of commercial fishing on the population structure and survival of this species. In this study, we focus on patterns of genetic diversity within and between geographically disparate populations of the Antarctic toothfish, using randomly amplified polymorphic DNA markers. Results of our study showed high levels of genetic similarity within and between populations. Despite high levels of genetic similarity, genetic analyses detected significant population structure, including fixed differences among populations, a significant fixation index (Fst) and between-population differentiation via a Mantel test. From a conservation perspective, low levels of genetic diversity may be indicative of relatively small populations that would not be able to withstand heavy commercial fishing pressures. Given that there is evidence for significant genetic structure, it will be important to manage these fisheries in a manner that will help prevent the loss of unique genetic variation from regional overfishing.     

中国稻区的生物多样性

中国稻区生物多样性是指该区域各种生命形式的资源总和,包括遗传多样性、物种多样性、生态系统多样性及与此相关的各种生态过程。本文阐述了中国栽培稻、野生稻遗传资源及稻区生境动植物的多样性,初步探讨了稻区生物多样性丧失的原因及其保护措施。     

Environmental change and predator diversity drive alpha and beta diversity in freshwater macro and microorganisms

Global biodiversity is eroding due to anthropogenic causes, such as climate change, habitat loss, and trophic simplification of biological communities. Most studies address only isolated causes within a single group of organisms; however, biological groups of different trophic levels may respond in particular ways to different environmental impacts. Our study used natural microcosms to investigate the predicted individual and interactive effects of warming, changes in top predator diversity, and habitat size on the alpha and beta diversity of macrofauna, microfauna, and bacteria. Alpha diversity (i.e., richness within each bromeliad) generally explained a larger proportion of the gamma diversity (partitioned in alpha and beta diversity). Overall, dissimilarity between communities occurred due to species turnover and not species loss (nestedness). Nevertheless, the three biological groups responded differently to each environmental stressor. Microfauna were the most sensitive group, with alpha and beta diversity being affected by environmental changes (warming and habitat size) and trophic structure (diversity of top predators). Macrofauna alpha and beta diversity was sensitive to changes in predator diversity and habitat size, but not warming. In contrast, the bacterial community was not influenced by the treatments. The community of each biological group was not mutually concordant with the environmental and trophic changes. Our results demonstrate that distinct anthropogenic impacts differentially affect the components of macro and microorganism diversity through direct and indirect effects (i.e., bottom‐up and top‐down effects). Therefore, a multitrophic and multispecies approach is necessary to assess the effects of different anthropogenic impacts on biodiversity.     

Evidence for selection at cytokine loci in a natural population of field voles (Microtus agrestis)

Individuals in natural populations are frequently exposed to a wide range of pathogens. Given the diverse profile of gene products involved in responses to different types of pathogen, this potentially results in complex pathogen-specific selection pressures acting on a broad spectrum of immune system genes in wild animals. Thus far, studies into the evolution of immune genes in natural populations have focused almost exclusively on the Major Histocompatibility Complex (MHC). However, the MHC represents only a fraction of the immune system and there is a need to broaden research in wild species to include other immune genes. Here, we examine the evidence for natural selection in a range of non-MHC genes in a natural population of field voles (Microtus agrestis). We concentrate primarily on genes encoding cytokines, signalling molecules critical in eliciting and mediating immune responses and identify signatures of natural selection acting on several of these genes. In particular, genetic diversity within Interleukin 1 beta and Interleukin 2 appears to have been maintained through balancing selection. Taken together with previous findings that polymorphism within these genes is associated with variation in resistance to multiple pathogens, this suggests that pathogen-mediated selection may be an important force driving genetic diversity at cytokine loci in voles and other natural populations. These results also suggest that, along with the MHC, preservation of genetic variation within cytokine genes should be a priority for the conservation genetics of threatened wildlife populations.