戴云山物种多样性与系统发育多样性海拔梯度分布格局及驱动因子

生物多样性的海拔分布格局是生态学研究的热点。海拔作为综合性因子驱动着植物群落的物种、系统发育与功能多样性的空间分布。以戴云山南坡900-1600 m森林植物群落为研究对象,探讨物种多样性、系统发育指数与环境驱动因子的相互关系以及环境因子在群落构建与多样性维持中的重要意义。结果表明：（1）森林植物群落的系统发育多样性与物种多样性沿海拔均呈现中间高度膨胀格局。（2）物种多样性Margalef指数、Shannon-Wiener指数与系统发育多样性指数呈显著正相关,表明物种多样性越高,系统发育多样性也越高。Shannon-Wiener指数与物种多样性指数（Margalef、Pielou、Simpson指数）、系统发育多样性及系统发育结构都存在显著相关性,一定程度上Shannon-Wiener指数可以代替其他指数。Pielou指数、Simpson指数、Shannon-Wiener指数与系统发育结构NRI （Net relatedness index）指数、NTI （Net nearest taxa index）指数存在显著正相关,表明群落优势度、均匀度与系统发育结构相关性较强。（3）土壤全磷含量是影响系统发育多样性和物种多样性的主要驱动因子,土壤含水量是影响Shannon-Wiener、Pielou、Simpson指数的最显著因子,海拔是影响群落系统发育结构的主要因素。海拔是影响系统发育结构变化的主要环境因子,而土壤因子是影响物种多样性与系统发育多样性的主要因素,进一步验证了物种多样性与系统发育多样性的高度相关,结果旨在揭示物种群落空间分布规律。     

基于生态位理论研究群落构建的方法进展

理解群落构建过程可以解释生物多样性格局的形成和维持,对于生物多样性保护起到关键作用。生态位理论是群落构建研究的核心框架之一。该理论认为群落构建是生物作用和非生物作用将区域物种库中的物种选入局域群落的确定过程。近年来,随着该领域受到的关注越来越多,研究者不但从物种、谱系或功能等生物多样性维度来研究群落构建,所使用的多样性指数、零模型算法和物种库界定方式等也多种多样。本文回顾了从生物多样性不同维度研究群落构建的优势与局限,总结了群落构建过程中构建零模型和界定物种库时需要注意的一些问题,介绍了部分群落构建研究的最新方法学进展和研究成果。最后,结合近年来的研究案例提出了对未来群落构建研究的一些建议。     

An updated Chinese vascular plant tree of life: Phylogenetic diversity hotspots revisited

Large‐scale phylogenies provide a framework for interdisciplinary investigations in taxonomy, evolutionary biology, biogeography, ecology, and conservation. Integration of regional tree of life and species distribution data has greatly promoted spatial phylogenetic studies on biodiversity, floristic assembly, and biogeographic regionalization. In this study, we updated the phylogenetic tree of Chinese vascular plants by integrating data from public databases and sequences newly generated by our laboratory, to facilitate the exploration of floristic and ecological questions at a country scale. A phylogenetic tree with 15 092 tips and 14 878 species was obtained, including 13 663 species (44.0%) and 2953 genera (95.7%) native to China. Only two families (Corsiaceae and Mitrastemonaceae) and 133 genera native to China are not sampled in this study. Low proportion of sampling is detected in orders with high species diversity and those with low species diversity. The Hengduan Mountains, plus the western Qinghai–Tibet Plateau and western Xinjiang, show the greatest gap of target molecular data for angiosperms. Our phylogeny of Chinese vascular plants recovers relationships among and within major lineages that are highly congruent with published phylogenies at a broader scale. Most families (98.7%) are supported as monophyletic, and 573 genera (17.9%) are recognized as non‐monophyletic. Finally, hotspots of phylogenetic diversity for the Chinese angiosperms at both the genus and species levels are identified based on our phylogram, implicating conservation priorities for phylogenetic diversity. The updated phylogeny of Chinese vascular plants is publically available to generate subtrees through our automated phylogeny assembly tool SoTree in the DarwinTree platform ( http://www.darwintree.cn/flora-sotree-v2/index.shtml ).     

Phylogenetic community patterns suggest Central Indian tropical dry forests are structured by montane climate refuges

Aim

We used an eco-phylogenetic approach to investigate the diversity and assembly patterns of tropical dry forests (TDFs) in Central India. We aimed at informing conservation and restoration practices in these anthropogenically disturbed forests by identifying potential habitats of conservation significance and elements of regional biodiversity most vulnerable to human impact and climate change.

Location

Tropical dry forests of Madhya Pradesh, Central India.

Methods

We analysed the species richness, stem density, basal area and phylogenetic structure (standardized effect size of MNTD, MPD, PD and community evolutionary distinctiveness cED) of 117 tree species assemblages distributed across a ~230 to ~940 m elevational gradient. We examined how these community measures and taxonomic (Sørensen) and phylogenetic (UniFrac) beta diversity varied with elevation, precipitation, temperature and climatic stress.

Results

Species richness, phylogenetic diversity, stem density and basal area were positively correlated with elevation, with high-elevation plots exhibiting cooler temperatures, higher precipitation and lower stress. High-elevation assemblages also trended towards greater phylogenetic dispersion, which diminished at lower elevations and in drier, more stressful plots. Phylogenetic turnover was observed across the elevation gradient, and species evolutionary distinctiveness increased at lower elevations and under harsher abiotic conditions.

Main Conclusions

Harsher abiotic conditions at low elevations may act as a selective filter on plant lineages, leading to phylogenetically clustered low-diversity assemblages. These assemblages contained more evolutionarily distinct species that may contribute disproportionately to biodiversity. Conversely, milder abiotic conditions at high elevations may serve as refuges for drought-sensitive species, resulting in more diverse assemblages. Conservation practices that prioritize both high- and low-elevation habitats could promote the persistence of evolutionarily distinct species and areas of high biodiversity within the Central Indian landscape. Establishing connectivity between these habitats may provide a range of climatic conditions for species to retreat to or persist within as climates change.     

Species‐time‐area and phylogenetic‐time‐area relationships in tropical tree communities

The species‐area relationship (SAR) has proven to be one of the few strong generalities in ecology. The temporal analog of the SAR, the species‐time relationship (STR), has received considerably less attention. Recent work primarily from the temperate zone has aimed to merge the SAR and the STR into a synthetic and unified species‐time‐area relationship (STAR) as originally envisioned by Preston (1960). Here we test this framework using two tropical tree communities and extend it by deriving a phylogenetic‐time‐area relationship (PTAR). The work finds some support for Preston's prediction that diversity‐time relationships, both species and phylogenetic, are sensitive to the spatial scale of the sampling. Contrary to the Preston's predictions we find a decoupling of diversity‐area and diversity‐time relationships in both forests as the time period used to quantify the diversity‐area relationship changes. In particular, diversity‐area and diversity‐time relationships are positively correlated using the initial census to quantify the diversity‐area relationship, but weakly or even negatively correlated when using the most recent census. Thus, diversity‐area relationships could forecast the temporal accumulation of biodiversity of the forests, but they failed to “back‐cast” the temporal accumulation of biodiversity suggesting a decoupling of space and time.     

Phylogeny,extinction and conservation: embracing uncertainties in a time of urgency

Evolutionary studies have played a fundamental role in our understanding of life, but until recently, they had only a relatively modest involvement in addressing conservation issues. The main goal of the present discussion meeting issue is to offer a platform to present the available methods allowing the integration of phylogenetic and extinction risk data in conservation planning. Here, we identify the main knowledge gaps in biodiversity science, which include incomplete sampling, reconstruction biases in phylogenetic analyses, partly known species distribution ranges, and the difficulty in producing conservation assessments for all known species, not to mention that much of the effective biological diversity remains to be discovered. Given the impact that human activities have on biodiversity and the urgency with which we need to address these issues, imperfect assumptions need to be sanctioned and surrogates used in the race to salvage as much as possible of our natural and evolutionary heritage. We discuss some aspects of the uncertainties found in biodiversity science, such as the ideal surrogates for biodiversity, the gaps in our knowledge and the numerous available phylogenetic diversity-based methods. We also introduce a series of cases studies that demonstrate how evolutionary biology can effectively contribute to biodiversity conservation science.     

Altitudinal biodiversity patterns of seed plants along Gongga Mountain in the southeastern Qinghai–Tibetan Plateau

The mechanisms underlying elevation patterns in species and phylogenetic diversity remain a central issue in ecology and are vital for effective biodiversity conservation in the mountains. Gongga Mountain, located in the southeastern Qinghai–Tibetan Plateau, represents one of the longest elevational gradients (ca. 6,500 m, from ca. 1,000 to 7,556 m) in the world for studying species diversity patterns. However, the elevational gradient and conservation of plant species diversity and phylogenetic diversity in this mountain remain poorly studied. Here, we compiled the elevational distributions of 2,667 native seed plant species occurring in Gongga Mountain, and estimated the species diversity, phylogenetic diversity, species density, and phylogenetic relatedness across ten elevation belts and five vegetation zones. The results indicated that species diversity and phylogenetic diversity of all seed plants showed a hump‐shaped pattern, peaking at 1,800–2,200 m. Species diversity was significantly correlated with phylogenetic diversity and species density. The floras in temperate coniferous broad‐leaved mixed forests, subalpine coniferous forests, and alpine shrublands and meadows were significantly phylogenetically clustered, whereas the floras in evergreen broad‐leaved forests had phylogenetically random structure. Both climate and human pressure had strong correlation with species diversity, phylogenetic diversity, and phylogenetic structure of seed plants. Our results suggest that the evergreen broad‐leaved forests and coniferous broad‐leaved mixed forests at low to mid elevations deserve more conservation efforts. This study improves our understanding on the elevational gradients of species and phylogenetic diversity and their determinants and provides support for improvement of seed plant conservation in Gongga Mountain.     

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。     

Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups

Identifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple taxonomic groups can be used jointly to map diversity and endemism. Here, we demonstrate how to apply different phylogenetic approaches to assess biodiversity across multiple taxonomic groups. We map spatial patterns of phylogenetic diversity/endemism to identify concordant areas with the greatest representation of biodiversity across multiple taxa and demonstrate the approach by applying it to the Murray–Darling basin region of southeastern Australia. The areas with significant centers of phylogenetic diversity and endemism were distributed differently for the five taxonomic groups studied (plant genera, fish, tree frogs, acacias, and eucalypts); no strong shared patterns across all five groups emerged. However, congruence was apparent between some groups in some parts of the basin. The northern region of the basin emerges from the analysis as a priority area for future conservation initiatives focused on eucalypts and tree frogs. The southern region is particularly important for conservation of the evolutionary heritage of plants and fishes.     

A taxonomic and phylogenetic perspective on plant community assembly along an elevational gradient in subtropical forests

亚热带森林植物群落沿海拔梯度的分类与系统发育研究 生物多样性沿海拔梯度的分布格局已受到广泛关注。然而,生物多样性格局沿海拔梯度的变异及其潜在机制尚不清楚。整合生物多样性的多维度信息为理解群落构建机制提供了新思路。本研究在我国东部亚热带森林沿海拔270–1470 m的梯度上设置了17个木本植物固定样地,分析了沿海拔梯度植物群落 构建的生态和进化驱动力。基于样地内物种出现(0–1数据)和多度信息,计算群落内被子植物的物种和系统发育alpha和beta多样性、系统发育结构等,并量化多样性指标与微气候和地形之间的关系。研究发现,不论多度加权与否,物种alpha多样性均沿海拔升高而增加,物种和系统发育的相似性随海拔距离的增加而呈衰减趋势。然而,多度加权与否会形成不同的系统发育alpha多样性格局。对于系统发育结构而言,沿海拔增加并无明显趋势。地形和微气候是多样性格局和系统发育结构的主要驱动力。与未考虑物种多度的多样性指标相比,多度加权的指标与坡度和胸高断面积相关性更高。这些结果表明,由局域物种多度介导的确定性过程对沿海拔梯度的植物群落构建具有一定影响。     

Functional and phylogenetic diversity determine woody productivity in a temperate forest

Understanding the relationships between biodiversity and ecosystem productivity has become a central issue in ecology and conservation biology studies, particularly when these relationships are connected with global climate change and species extinction. However, which facets of biodiversity (i.e. taxonomic, functional, and phylogenetic diversity) account most for variations in productivity are still not understood very well. This is especially true with regard to temperate forest ecosystems. In this study, we used a dataset from a stem‐mapped permanent forest plot in northeastern China exploring the relationships between biodiversity and productivity at different spatial scales (20 × 20 m; 40 × 40 m; and 60 × 60 m). The influence of specific environmental conditions (topographic conditions) and stand maturity (expressed by initial stand volume and biomass) were taken into account using the multivariate approach known as structural equation models. The variable “Biodiversity” includes taxonomic (Shannon), functional (FDis), and phylogenetic diversity (PD). Biodiversity–productivity relationships varied with the spatial scales. At the scale of 20 × 20 m, PD and FDis significantly affected forest biomass productivity, while Shannon had only indirect effects. At the 40 × 40 m and 60 × 60 m scales, biodiversity and productivity were weakly correlated. The initial stand volume and biomass were the most important drivers of forest productivity. The local environmental conditions significantly influenced the stand volume, biomass, biodiversity, and productivity. The results highlight the scale dependency of the relationships between forest biodiversity and productivity. The positive role of biodiversity in facilitating forest productivity was confirmed at the smaller scales. Our findings emphasize the fundamental role of environmental conditions in determining forest ecosystem performances. The results of this study provide a better understanding of the underlying ecological processes that influence specific forest biodiversity and productivity relationships.     

Environment differentially affects the functional and phylogenetic structures of plant communities in a dry evergreen Afromontane tropical forest

Testing how local environmental conditions influence plant community assembly is important to understand the underlying mechanisms that promote and/or maintain biodiversity. Functional traits are used to find the broad spectrum of resource use strategies that plants use to respond to environmental variation. The patterns and drivers of plant community assembly through the lens of traits and phylogeny; however, remain to be studied in a uniquely biodiversity rich but poorly known fragmented dry Afromontane forest of Ethiopia. Here, we combined trait and community phylogenetic data from thirty sampling plots of 20 × 20 m size to determine the functional and phylogenetic structures and their drivers in a fragmented, human-dominated dry evergreen Afromontane forest. We found phylogenetic and functional clustering of plants in which the effect of environment was found to be trait specific. A weak phylogenetic signal for traits was detected suggesting that species resource use strategies may not be inferred using species phylogenetic distance. Additionally, we found functional traits to be weak in predicting species abundance distribution. Overall, while this study shows a non-random community assembly pattern, it also highlights the importance of deterministic processes being trait specific.     

Conservation biology of Malagasy strepsirhines: a phylogenetic approach

The phylogenetic diversity of extant lemurs represents one of the most important but least studied aspects of the conservation biology of primates. The phylogenetic diversity of a species is inversely proportional to the relative number and closeness of its phylogenetic relatives. Phylogenetic diversity can then be used to determine conservation priorities for specific biogeographic regions. Although Malagasy strepsirhines represent the highest phylogenetic diversity among primates at the global level, there are few phylogenetic data on species-specific and regional conservation plans for lemurs in Madagascar. Therefore, in this paper the following questions are addressed for extant lemurs: 1) how does the measure of taxonomic uniqueness used by Mittermeier et al. (1992 Lemurs of Madagascar; Gland, Switzerland: IUCN) equate with an index of phylogenetic diversity, 2) what are the regional conservation priorities based on analyses of phylogenetic diversity in extant lemurs, and 3) what conservation recommendations can be made based on analyses of phylogenetic diversity in lemurs? Taxonomic endemicity standardized weight (TESW) indices of phylogenetic diversity were used to determine the evolutionary component of biodiversity and to prioritize regions for conserving lemur taxa. TESW refers to the standardization of phylogenetic diversity indices for widespread taxa and endemicity of species. The phylogenetic data came from recent genetic studies of Malagasy strepsirhines at the species level. Lemur species were assigned as being either present or absent in six biogeographic regions. TESW indices were combined with data on lemur complementarity and protected areas to assign conservation priorities at the regional level. Although there were no overall differences between taxonomic ranks and phylogenetic rankings, there were significant differences for the top-ranked taxa. The phylogenetic component of lemur diversity is greatest for Daubentonia madagascariensis, Allocebus trichotis, Lepilemur septentrionalis, Indri indri, and Mirza coquereli. Regional conservation priorities are highest for lemurs that range into northeast humid forests and western dry forests. Expansion of existing protected areas in these regions may provide the most rapid method for preserving lemurs. In the long term, new protected areas must be created because there are lemur species that: 1) are not found in existing protected areas, 2) exist only in one or two protected areas, and 3) are still being discovered outside the current network of protected areas. Data on the population dynamics and feeding ecology of phylogenetically important species are needed to ensure that protected areas adequately conserve lemur populations in Madagascar.     

Community disassembly under global change: Evidence in favor of the stress‐dominance hypothesis

Ecological theory suggests that communities are not random combinations of species but rather the results of community assembly processes filtering and sorting species that are able to coexist together. To date, such processes (i.e., assembly rules) have been inferred from observed spatial patterns of biodiversity combined with null model approaches, but relatively few attempts have been made to assess how these processes may be changing through time. Specifically, in the context of the ongoing biodiversity crisis and global change, understanding how processes shaping communities may be changing and identifying the potential drivers underlying these changes become increasingly critical. Here, we used time series of 460 French freshwater fish communities and assessed both functional and phylogenetic diversity patterns to determine the relative importance of two key assembly rules (i.e., habitat filtering and limiting similarity) in shaping these communities over the last two decades. We aimed to (a) describe the temporal changes in both functional and phylogenetic diversity patterns, (b) determine to what extent temporal changes in processes inferred through the use of standardized diversity indices were congruent, and (c) test the relationships between the dynamics of assembly rules and both climatic and biotic drivers. Our results revealed that habitat filtering, although already largely predominant over limiting similarity, became more widespread over time. We also highlighted that phylogenetic and trait‐based approaches offered complementary information about temporal changes in assembly rules. Finally, we found that increased environmental harshness over the study period (especially higher seasonality of temperature) led to an increase in habitat filtering and that biological invasions increased functional redundancy within communities. Overall, these findings underlie the need to develop temporal perspectives in community assembly studies, as understanding ongoing temporal changes could provide a better vision about the way communities could respond to future global changes.     

Evolutionary constraints on regional faunas: whom, but not how many

The latitudinal diversity gradient has been hypothesized to reflect past evolutionary dynamics driven by climatic niche conservation during cladogenesis, i.e. the tropical conservatism hypothesis. Here we show that the species diversity of treefrogs (Hylidae) across the western hemisphere is actually independent of evolutionary niche dynamics. We evaluated three key predictions of the tropical conservatism hypothesis that relate to the relationships between climate, species richness and the phylogenetic structure of regional treefrog faunas across the continental Americas. Species composition was dependent on the inability of some lineages to evolve cold tolerance, but the actual number of species in a region was strongly predicted by precipitation, not temperature. Moreover, phylogenetic structure was independent of precipitation. Thus, species in low-richness areas were no more closely related than species in highly diverse regions. These results provide no support for the tropical conservatism hypothesis. Instead, they show that regional species composition and richness are constrained by different climatic components, demonstrating that global biodiversity gradients can be independent of niche stasis during cladogenesis.     

Spatial phylogenetics of the native woody plant species in Hainan,China

To better identify biodiversity hotspots for conservation on Hainan Island, a tropical island in southern China, we assessed spatial variation in phylogenetic diversity and species richness using 18,976 georeferenced specimen records and a newly reconstructed molecular phylogeny of 957 native woody plants. Within this framework, we delineated bioregions based on vegetation composition and mapped areas of neoendemism and paleoendemism to identify areas of priority for conservation. Our results reveal that the southwest of Hainan is the most important hot spot for endemism and plant diversity followed by the southeast area. The distribution of endemic species showed a scattered, rather than clustered, pattern on the island. Based on phylogenetic range‐weighted turnover metrics, we delineated three major vegetational zones in Hainan. These largely correspond to natural secondary growth and managed forests (e.g., rubber and timber forests) in central Hainan, old‐growth forests and natural secondary growth forest at the margins of Hainan, and nature reserves on the island (e.g., Jianfeng and Diaoluo National Nature Reserves). Our study helps to elucidate potential botanical conservation priorities for Hainan within an evolutionary, phylogenetic framework.     

Phylogenetic Autocorrelation Analysis of Extinction Risks and the Loss of Evolutionary History in Felidae (Carnivora: Mammalia)

Phylogeny provides a natural measurement of biodiversity by allowing the computation of indexes that express the amount of phylogenetic diversity that are, in principle, independent of species counts and provides an objective measurement to evaluate the amount of biodiversity lost under the ongoing extinction crisis. In this note, we analyzed patterns of phylogenetic autocorrelation in extinction risks in Felidae (Mammalia: Carnivora) and estimated, using simulation procedures, the amount of phylogenetic diversity loss if k species are preserved in this clade. The simulations showed that loss of phylogenetic diversity based on the IUCN list for extinction threats in Felidae is within the expected values based on the simulated random model, a result also confirmed by the absence of phylogenetic autocorrelation in extinction risks, indicating that extinction threats are randomly distributed across the phylogeny. So, we confirm that loosing species will not necessarily generate a direct proportional loss of phylogenetic information and, consequently, that alternative measures of biodiversity could be used to establish conservation priorities under the common restriction of resources.     

Eutrophication,biodiversity loss,and species invasions modify the relationship between host and parasite richness during host community assembly

Host and parasite richness are generally positively correlated, but the stability of this relationship in response to global change remains poorly understood. Rapidly changing biotic and abiotic conditions can alter host community assembly, which in turn, can alter parasite transmission. Consequently, if the relationship between host and parasite richness is sensitive to parasite transmission, then changes in host composition under various global change scenarios could strengthen or weaken the relationship between host and parasite richness. To test the hypothesis that host community assembly can alter the relationship between host and parasite richness in response to global change, we experimentally crossed host diversity (biodiversity loss) and resource supply to hosts (eutrophication), then allowed communities to assemble. As previously shown, initial host diversity and resource supply determined the trajectory of host community assembly, altering post‐assembly host species richness, richness‐independent host phylogenetic diversity, and colonization by exotic host species. Overall, host richness predicted parasite richness, and as predicted, this effect was moderated by exotic abundance—communities dominated by exotic species exhibited a stronger positive relationship between post‐assembly host and parasite richness. Ultimately, these results suggest that, by modulating parasite transmission, community assembly can modify the relationship between host and parasite richness. These results thus provide a novel mechanism to explain how global environmental change can generate contingencies in a fundamental ecological relationship—the positive relationship between host and parasite richness.