Rarity facets of biodiversity: Integrating Zeta diversity and Dark diversity to understand the nature of commonness and rarity

Measuring commonness and rarity is pivotal to ecology and conservation. Zeta diversity, the average number of species shared by multiple sets of assemblages, and Dark diversity, the number of species that could occur in an assemblage but are missing, have been recently proposed to capture two aspects of the commonness‐rarity spectrum. Despite a shared focus on commonness and rarity, thus far, Zeta and Dark diversities have been assessed separately. Here, we review these two frameworks and suggest their integration into a unified paradigm of the “rarity facets of biodiversity.” This can be achieved by partitioning Alpha and Beta diversities into five components (the Zeta, Eta, Theta, Iota, and Kappa rarity facets) defined based on the commonness and rarity of species. Each facet is assessed in traditional and multiassemblage fashions to bridge conceptual differences between Dark diversity and Zeta diversity. We discuss applications of the rarity facets including comparing the taxonomic, functional, and phylogenetic diversity of rare and common species, or measuring species'' prevalence in different facets as a metric of species rarity. The rarity facets integrate two emergent paradigms in biodiversity science to better understand the ecology of commonness and rarity, an important endeavor in a time of widespread changes in biodiversity across the Earth.     

菌根多样性及其对植物生长发育的重要意义

菌根多样性是生物多样性的重要组成部分。主要包括形态多样性、物种多样性和功能多样性．大量试验表明。菌根多样性对植物物种的起源与进化、分布与生存、生长和发育等方面起着至关重要的作用。而植物多样性又决定了菌根多样性．认为菌根多样性与植物多样性是相辅相成、相互制约的。随着分子生物学技术的不断发展和完善。必将使菌根多样性的研究得到快速发展．     

Genotypic and symbiotic diversity of native rhizobia nodulating red pea (Lathyrus cicera L.) in Tunisia

Nodulation and genetic diversity of native rhizobia nodulating Lathyrus cicera plants grown in 24 cultivated and marginal soils collected from northern and central Tunisia were studied. L. cicera plants were nodulated and showed the presence of native rhizobia in 21 soils. A total of 196 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. The sequence analysis of the rrs and two housekeeping genes (recA and thrC) from 36 representative isolates identified Rhizobium laguerreae as the dominant (53%) rhizobia nodulating L. cicera. To the best of our knowledge, this is the first time that this species has been reported among wild populations of the rhizobia-nodulating Lathyrus genus. Twenty-five percent of the isolates were identified as R. leguminosarum and isolates LS11.5, LS11.7 and LS8.8 clustered with Ensifer meliloti. Interestingly, five isolates (LS20.3, LS18.3, LS19.10, LS1.2 and LS21.20) were segregated from R. laguerreae and clustered as a separate clade. These isolates possibly belong to new species. According to nodC and nodA phylogeny, strains of R. laguerreae and R. leguminosarum harbored the symbiotic genes of symbiovar viciae and clustered in three different clades showing heterogeneity within the symbiovar. Strains of E. meliloti harbored symbiotic genes of Clade V and induced inefficient nodules.     

功能、谱系多样性在机场鸟类群落研究中的应用——以扬州泰州国际机场为例

随着航空业的发展,野生动物与飞机之间的冲突愈发密集,机场鸟类群落多样性研究引起了大量关注。研究鸟类群落对生境类型的使用状况,可以掌握生境类型与鸟击风险的潜在关系,为机场环境改造提供理论依据。本研究于2019年7月至2021年11月,采用样点法对扬州泰州机场及周边8 km范围内的农田、湿地、林地和城镇4种生境中30个样点的鸟类群落进行调查。利用鸟类群落多样性指数,包括丰富度、多度、香农威纳多样性指数、辛普森多样性指数以及均匀度指数来表征群落的物种多样性,以及功能和谱系多样性,阐明机场周边4种生境的鸟类群落多样性差异。同时,基于多度加权的平均成对功能距离（MFD）和平均成对谱系距离（MPD）来表征群落的功能和谱系结构,探究群落构建机制,量化各多样性指标间的相关性。研究共记录扬州泰州国际机场鸟类88种,分别隶属于14目36科,目、科中数量最多的为雀形目（Passeriformes）和鹬科（Scolopacidae）。谱系和功能多样性在生境间差异显著,功能分散度在农田最高,城镇最低;谱系多样性指数在城镇最高,湿地最低。标准化效应值分析表明,随机生态过程影响了湿地鸟类群落功能和谱系的构建过程,农...     

中国温带荒漠区的植物多样性及其易地保护*

^{荒漠植物多样性研究及其保护是生物多样性保护的重要组成部分。 中国荒漠区植物种类贫乏（约1000余种）,分布稀疏,生物量小,起源古老,地理成份复杂（有14个地理分布型）, 特有成份多（80余种）,珍稀濒危植物种类相对较多（50～60种）,在荒漠气候和特殊的土壤基质条件下, 形成了多种生态型和特殊的生活型,为荒漠植物多样性易地保护提供了可能性和必要性。 处于亚洲荒漠区的吐鲁番沙漠植物园的研究工作,正从传统的植物引种驯化和经济植物栽培,向荒漠区系植物多样性保护领域转移,现园内保存的荒漠区系植物成份已达42.2％,特有种和珍稀濒危植物也占相当比例。 长期适应荒漠环境的各类植物具有多种多样的抗逆性基因,因而有着潜在的开发利用前景。}     

Genomic and physiological diversity amongst strains of Thiobacillus ferrooxidans,and genomic comparison with Thiobacillus thiooxidans

Twenty-three strains of Thiobacillus ferrooxidans of known pedigree were examined. Thirteen strains survived 65° C for 5 min and 7 of these for 10 min, but sporulation was never observed. All strains grew between 25° C and 35° C and some strains grew at 5° and 40° C. They were genomically diverse, comprising 7 DNA homology groups, and the GC content varied from 55–65 mol %. Correlation between genomic group and growth temperature was noted. All strains grew on ferrous sulfate as energy source, but some failed to utilize elemental sulfur. Acidified thiosulfate supported growth of most of the strains examined but it was judged to be a poor substrate upon which to base taxonomic conclusions because of decomposition of thiosulfate in acid. Six strains of Thiobacillus thiooxidans showed negligible genomic affinity to T. ferrooxidans, and they comprised 2 DNA homology groups and their GC content varied from 52–62 mol%. Anomalies due to contaminants in cultures of T. ferrooxidans were resolved, and the contaminants were identified.     

Net primary productivity and seasonality of temperature and precipitation are predictors of the species richness of the Damselflies in the Amazon

Several hypotheses have been proposed to explain the mechanisms that generate temporal and spatial species richness patterns. We tested four common hypotheses (water, energy, climatic heterogeneity and net primary productivity) to evaluate which factors best explain patterns of Zygoptera species richness. Of these, we predicted that climatic heterogeneity would be the most important predictor for Zygoptera richness patterns. We sampled communities of adult Zygoptera in 100 small Amazonian streams. Based on generalized linear mixed models (GLMM), we found that net primary productivity and climatic heterogeneity comprised the best model of Zygoptera species richness in Amazonian streams, with an pseudo r² of 39.5%. Results indicate that species richness increases by one species per 1 kg of biomass per square meter in NPP, or with an increase of 2 °C in air temperature variability. Our work corroborates a recent study with other taxa in Brazilian Bioms. This suggests that temporal variation in climate and net primary productivity are important predictors of the macroecological patterns of richness for aquatic organisms in tropical regions.     

Stand height and cover type complement forest age structure as a biodiversity indicator in boreal and northern temperate forest management

Forest age structure is one of the main indicators of biodiversity in temperate and boreal forests worldwide. This indicator was mainly chosen for the conservation of a subset of rare or sensitive species related to the oldest age classes, not to capture variability across the entire biodiversity spectrum, but is often considered as such. In this study, we analysed alpha and beta diversity in temporary plots of western Quebec, Canada, to consider biodiversity indicators complementary to existing forest age structure targets. Our analysis revealed that considered individually, stand characteristics such as cover type and height are better predictors of changes in site-level contribution to tree beta diversity than age. We also show that plots belonging to different age classes can be similar in terms of tree alpha diversity. Height class was found to have a more significant impact on tree alpha diversity than expected: height was more important than age in coniferous forests, and in deciduous and mixedwood stands it frequently complemented age in explaining the observed diversity patterns. Our results suggest that forest age structure target levels should not be used as the sole indicator of ecosystem sustainability, and that some mature secondary stands can provide significant contributions to biodiversity. We propose that more efficient trade-offs between forest exploitation, ecosystem functioning and environmental conservation can be attained if: (i) forest age structure targets are complemented by cover type and stand height; or (ii) complementary biodiversity indicators of ecosystem sustainability are implemented.     

Previously unknown and highly divergent ssDNA viruses populate the oceans

Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.     

The relationship between the concepts of genetic diversity and differentiation

Summary Diversity as a measure of individual variation within a population is widely agreed to reflect the number of different types in the population, taking into account their frequencies. In contrast, differentiation measures variation between two or more populations, demes or subpopulations. As such, it is based on the relative frequencies of types within these subpopulations and, ideally, measures the average distance of subpopulations from their respective lumped remainders. This concept of subpopulation differentiation can be applied consistently to a single population by regarding each individual as a deme (subpopulation) of its own, and it results in a measure of population differentiation _T which depends on the relative frequencies of the types and the population size. _T corresponds to several indices of variation frequently applied in population genetics and ecology, and it verifies these indices as measures of differentiation rather than diversity. For any particular frequency distribution of types, the diversity is then shown to be the size of a hypothetical population in which each type is represented exactly once, i. e. for which _T =1. Hence, the diversity of a population is its differentiation effective number of types. This uniquely specifies the link between the two concepts. Moreover, again corresponds to known measures of diversity applied in population genetics and ecology. While population differentiation can always be estimated from samples, the diversity of a population, particularly if it is large, may not be. In such cases, it is recommended that population differentiation is estimated and the corresponding sample diversity merely computed. Finally, a solution to the problem of measuring multi-locus diversities is provided.     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

长湖水生植物多样性及其变化

研究了湖北省第三大湖泊长湖水生植物多样性的现状及其长期变化,并探讨了多样性丧失的机理及多样性恢复与保护的有效途径。主要结论：(1)长湖现有水生植物98种,多度最大的是微齿眼子菜(Potamogeton maackianus)、密齿苦草(Vallisneria denseserrulata)、野菱(Trapa incisa)、双角菱(T.bispinosa)、菹草(Potamogeton crispus)、紫萍(Spirodela polyrhiza)、穗花狐尾藻(Myriophyllum spicatum)、轮叶黑藻(Hydrilla verticillata)、满江红(Azolla imbricata)。(2)长湖现有水生植物群丛类型14个,群落物种多样性指数最高的是芡实 野菱 双角菱群丛(Euryale ferox Trapa incisa T.bispinosa Ass.),其次为轮叶黑藻 密齿苦草|大茨藻群丛(Hydrilla verticillata Vallisneria denseserrulata Najas marioa Ass.)与竹叶眼子菜 穗花狐尾藻群丛(Potamogeton malaianus Myriophylhum spicatum Ass.)。(3)20年来,已有6种水生植物和7个水生植物群丛类型从长湖消失,植被覆盖率下降了54．85％,全湖平均单位面积生物量下降了69．78％。(4)多样性丧失的主要原因是过度养殖、过度打草和耙捞作业,以及由此导致的湖水透明度的大幅度下降。(5)多样性恢复的有效途径是政府部门的行政干预与经济支持。     

Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity

Almost half a century after Whittaker (Ecol Monogr 30:279–338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative––depending on the organism(s) or ecosystems investigated––this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term “inventory diversity.” Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness (“key concept” vs. “abstruse concept”). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, “differentiation diversity” (first group) and “proportional diversity” (second group). Thus, we propose to use the terms “inventory diversity” for within-sample diversity, “differentiation diversity” for compositional similarity between samples, and “proportional diversity” for the comparison of inventory diversity across spatial and temporal scales. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

青藏高原禾草混播对土壤微生物多样性的影响

土壤微生物多样性的形成、维持和变化机理是生态学研究的核心内容, 已有大量研究表明土壤微生物群落构建不仅受到土壤环境的深刻影响, 也与植物群落物种多样性密切相关。由于自然群落中土壤环境和植物多样性协同影响土壤微生物, 难以区分和厘清植物多样性和土壤环境对土壤微生物多样性构建的各自影响。该研究基于在青藏高原高寒草地构建的人工草地群落, 比较分析了3种优势禾本科牧草单播和混播及施肥处理13年后, 土壤细菌和真菌物种多样性及其与植物群落和土壤理化因子的关系。主要结果: 1)与各单播处理相比, 3种牧草两两混播一致显著降低了土壤细菌群落的丰富度和多样性, 其中变形菌门和放线菌门相对丰度显著增加, 而酸杆菌门、拟杆菌门和浮霉菌门相对丰度显著减小; 牧草混播对土壤真菌多样性没有显著影响。2)牧草混播显著降低了土壤pH和土壤全氮含量, 增加了土壤全磷含量; 施肥显著降低土壤pH, 增加了土壤速效磷含量; 但这些土壤理化因子的变化不足以解释土壤细菌和真菌多样性在处理间的差异。3)施肥显著提高了植物群落地上生物量, 降低了植物物种丰富度, 土壤细菌多样性随植物物种丰富度增加而减小, 而与植物生物量变化无关。该研究在野外条件下, 通过长期控制实验揭示了高寒草地禾草混播并不增加土壤微生物多样性, 为高寒地区牧草混播人工草地实践提供了科学依据。     

Seasonal fire effects on the diversity patterns,spatial distribution and community structure of forbs in the Northern Mixed Prairie,USA

The effects of fire season on forb diversity patterns, density, and composition were determined for a northern Mixed Prairie site, USA. Repeated spring burns (dormant season), summer burns, fall burns (dormant season), and unburned treatments were compared over a 3-yr period characterized by wet and dry moisture conditions. Alpha and beta diversity were highest on unburned and summer burn treatments, while landscape mosaic diversity was highest on fall burns. Forb density was highest on fall and spring burn sites. Nine forb species comprised 82% of total densities and were significantly affected by fire season and year to year variations in moisture. Forb composition for unburned and spring burn treatments was similar, but both treatments were different from the summer burn and fall burn treatments which were similar to each other. Fire alone did not appear to be an intense enough disturbance to initiate drastic changes in the forb component of vegetation patches. Specific fire seasons did appear to either mask or enhance forb structure arising from other disturbance(s). Fire season also affected the scales of forb organization in the landscape. Contrasting spatial characteristics of the forb component of prairie plant communities may provide a diagnostic technique for exposing the interaction of disturbances at different temporal and spatial scales.     

Plant species richness, endemism, and genetic resources in Namibia

Namibia is a floristically diverse, arid to mesic country, with several highly distinct taxa. Including naturalized plants, there are about 4334 vascular plant species and infraspecific taxa within the country's borders, a substantial increase from the existing major reference work. Dominant families are the Poaceae (422species), Fabaceae (377), Asteraceae (385) and Mesembryanthemaceae (177). Freshwater algae and most other groups of lower plants remain poorly known. Concentrations of plant species richness are found in the Succulent Karoo biome, Kaokoveld, Otavi highland/Karstveld area, Okavango Basin, and Khomas highlands. Recent studies have led to a new estimate of 687 endemic plant species, defined as those contained wholly within Namibia's borders, amounting to about 17% of the Namibian flora. At least a further 275 species are Namib Desert endemics shared between the Kaokoveld and southern Angola (75spp.) and between the Succulent Karoo and northwestern South Africa (200spp.). Research on plant genetic resources is focused on species of potential or actual agricultural importance, such as pearl millet, Pennisetum glaucum, and cucurbits. Many wild plants have considerable genetic diversity and development potential. Primary threats to plant diversity fall in the category of poor land management and inappropriate development.     

龙凤湿地与珰奈湿地底泥细菌古菌多样性及其对环境因子的响应

【背景】城市湿地和天然湿地受到人为扰动影响的程度显著不同。【目的】研究2种不同类型湿地底泥微生物多样性及种类的差异。【方法】采集冬夏两季城市湿地(龙凤湿地)和天然湿地(珰奈湿地)的底泥样品,使用16S rRNA基因测序技术测定底泥中细菌和古菌群落结构,分析2种湿地底泥的细菌、古菌差异及环境因素与微生物的相关性。【结果】龙凤湿地底泥中的硫杆菌属(Thiobacillus)、芽孢杆菌属(Bacillus)和鞘氨醇单胞菌属(Sphingomonas)丰度显著高于珰奈湿地(P<0.05);Methanoregula在珰奈湿地底泥中的丰度高于龙凤湿地;冬季厌氧绳菌属(Anaerolinea)和甲烷八叠球菌属(Methanosarcina)在珰奈湿地底泥中的丰度显著高于龙凤湿地(P<0.05)。【结论】龙凤湿地与珰奈湿地的差异主要影响湿地底泥中参与元素循环的细菌和产甲烷古菌的丰度,人为干扰和低温会降低湿地中微生物的多样性,pH、盐分和碱性磷酸酶是显著影响微生物多样性的环境因素。     

Diversity and family: an inquiry into the effects of ethnic,linguistic, and religious fractionalization on family values

This article focuses on the connection between three forms of diversity – religious, ethnic, and linguistic – and family values. The article builds on the idea that diversity challenges social identity and people react by returning to traditional family values in order to protect their social identity and the in-group culture. The paper aims at contributing to the sociological debate about the effect of diversity on social life and investigates how different types of diversity connect with traditional family values because individuals want to protect their in-group culture that is mainly transmitted within family. The paper tests the research hypotheses employing multilevel regression models and using data from the ISSP IV from 2012. Religious diversity associates with traditional attitudes regarding marriage and gender roles, ethnic diversity goes together with lower support for marriage, but has no connection with attitudes towards gender role, while linguistic diversity is not associated with attitudes family values.