Coral reef diversity refutes the neutral theory of biodiversity

The global decline of coral reefs highlights the need to understand the mechanisms that regulate community structure and sustain biodiversity in these systems. The neutral theory, which assumes that individuals are demographically identical regardless of species, seeks to explain ubiquitous features of community structure and biodiversity patterns. Here we present a test of neutral-theory predictions with the use of an extensive species-level data set of Indo-Pacific coral communities. We show that coral assemblages differ markedly from neutral-model predictions for patterns of community similarity and the relative abundance of species. Within local communities, neutral models do not fit relative abundance distributions as well as the classical log-normal distribution. Relative abundances of species across local communities also differ markedly from neutral-theory predictions: coral communities exhibit community similarity values that are far more variable, and lower on average, than the neutral theory can produce. Empirical community similarities deviate from the neutral model in a direction opposite to that predicted in previous critiques of the neutral theory. Instead, our results support spatio-temporal environmental stochasticity as a major driver of diversity patterns on coral reefs.     

Explaining the excess of rare species in natural species abundance distributions

The observation that a few species in ecological communities are exceptionally abundant, whereas most are rare, prompted the development of species abundance models. Nevertheless, despite the large literature on the commonness and rarity of species inspired by these pioneering studies, some widespread empirical patterns of species abundance resist easy explanation. Notable among these is the observation that in large assemblages there are more rare species than the log normal model predicts. Here we use a long-term (21-year) data set, from an estuarine fish community, to show how an ecological community can be separated into two components. Core species, which are persistent, abundant and biologically associated with estuarine habitats, are log normally distributed. Occasional species occur infrequently in the record, are typically low in abundance and have different habitat requirements; they follow a log series distribution. These distributions are overlaid, producing the negative skew that characterizes real data sets.     

Environmental determinants of extinction selectivity in the fossil record

The causes of mass extinctions and the nature of biological selectivity during extinction events remain central questions in palaeobiology. Although many different environmental perturbations have been invoked as extinction mechanisms, it has long been recognized that fluctuations in sea level coincide with many episodes of biotic turnover. Recent work supports the hypothesis that changes in the areas of epicontinental seas have influenced the macroevolution of marine animals, but the extent to which differential environmental turnover has contributed to extinction selectivity remains unknown. Here I use a new compilation of the temporal durations of sedimentary rock packages to show that carbonate and terrigenous clastic marine shelf environments have different spatio-temporal dynamics and that these dynamics predict patterns of genus-level extinction, extinction selectivity and diversity among Sepkoski's Palaeozoic and modern evolutionary faunae. These results do not preclude a role for biological interactions or unusual physical events as drivers of macroevolution, but they do suggest that the turnover of marine shelf habitats and correlated environmental changes have been consistent determinants of extinction, extinction selectivity and the shifting composition of the marine biota during the Phanerozoic eon.     

Neutral theory: the stability of forest biodiversity

The unified neutral theory of biodiversity and biogeography provides a dynamic null hypothesis for the assembly of natural communities. It is also useful for understanding the influence of speciation, extinction, dispersal and ecological drift on patterns of relative species abundance, species-area relationships and phylogeny. Clark and McLachlan argue that neutral drift is inconsistent with the palaeorecord of stability in fossil pollen assemblages of the Holocene forests of southern Canada. We show here that their analysis is based on a partial misunderstanding of neutral theory and that their data alone cannot unambiguously test its validity.     

侏罗纪双壳类绝灭事件

侏罗纪原始大西洋的双壳类数据反映了３次区域性海生无脊椎动物绝灭事件,分别出现于Ｐｌｉｅｎｓｂａｃｈｉａｎ末期,Ｃａｌｌｏｖｉａｎ初期以及Ｔｉｔｈｏｎｉａｎ期,其中以Ｔｉｔｈｏｎｉａｎ事件规模最大,影响范围最广,海平面变化以及所伴随的环境恶化是导致绝灭主要原因。     

珠江三角洲PRD16孔微体生物记录与晚更新世以来的古环境重建

对珠江三角洲PRD16孔的微体动物群进行了分析,共发现底栖有孔虫12属24种,介形类9属13种,它们可分别划分为3种生态类型。根据有孔虫和介形类微体动物群的分布特征、并结合岩性和沉积粒度特征,推断PRD16孔研究区晚更新世以来沉积环境演化经历了5个阶段:①34 600 cal a BP以前为河流相环境,形成了研究区最早的第四纪河床相砂砾沉积;②34 600～23 900 cal a BP推测为河口湾环境;③23 900～7 960 cal aBP受末次盛冰期影响,研究区暴露地表遭受风化剥蚀,形成花斑黏土;④7 960～2 810 cal a BP为全新世大海侵时期,研究区为河口海湾环境,发育以广盐性有孔虫和中盐-多盐性介形类为主的微体动物群,其间发生了2次小规模海平面波动,受地块区域沉降作用影响,研究区在3 873 cal a BP左右水深达到最大,主要有孔虫和介形类属种的丰度达到全新世最高值;⑤2 810 cal a BP以来海平面持续下降,研究区由潮坪环境变为河口砂坝,随后河流作用增强,又逐渐变为河流冲积-潮上带环境。     

Extinction risk depends strongly on factors contributing to stochasticity

Extinction risk in natural populations depends on stochastic factors that affect individuals, and is estimated by incorporating such factors into stochastic models. Stochasticity can be divided into four categories, which include the probabilistic nature of birth and death at the level of individuals (demographic stochasticity), variation in population-level birth and death rates among times or locations (environmental stochasticity), the sex of individuals and variation in vital rates among individuals within a population (demographic heterogeneity). Mechanistic stochastic models that include all of these factors have not previously been developed to examine their combined effects on extinction risk. Here we derive a family of stochastic Ricker models using different combinations of all these stochastic factors, and show that extinction risk depends strongly on the combination of factors that contribute to stochasticity. Furthermore, we show that only with the full stochastic model can the relative importance of environmental and demographic variability, and therefore extinction risk, be correctly determined. Using the full model, we find that demographic sources of stochasticity are the prominent cause of variability in a laboratory population of Tribolium castaneum (red flour beetle), whereas using only the standard simpler models would lead to the erroneous conclusion that environmental variability dominates. Our results demonstrate that current estimates of extinction risk for natural populations could be greatly underestimated because variability has been mistakenly attributed to the environment rather than the demographic factors described here that entail much higher extinction risk for the same variability level.     

Coherent ecological dynamics induced by large-scale disturbance

Aggregate community-level response to disturbance is a principle concern in ecology because post-disturbance dynamics are integral to the ability of ecosystems to maintain function in an uncertain world. Community-level responses to disturbance can be arrayed along a spectrum ranging from synchronous oscillations where all species rise and fall together, to compensatory dynamics where total biomass remains relatively constant despite fluctuations in the densities of individual species. An important recent insight is that patterns of synchrony and compensation can vary with the timescale of analysis and that spectral time series methods can enable detection of coherent dynamics that would otherwise be obscured by opposing patterns occurring at different scales. Here I show that application of wavelet analysis to experimentally manipulated plankton communities reveals strong synchrony after disturbance. The result is paradoxical because it is well established that these communities contain both disturbance-sensitive and disturbance-tolerant species leading to compensation within functional groups. Theory predicts that compensatory substitution of functionally equivalent species should stabilize ecological communities, yet I found at the whole-community level a large increase in seasonal biomass variation. Resolution of the paradox hinges on patterns of seasonality among species. The compensatory shift in community composition after disturbance resulted in a loss of cold-season dominants, which before disturbance had served to stabilize biomass throughout the year. Species dominating the disturbed community peaked coherently during the warm season, explaining the observed synchrony and increase in seasonal biomass variation. These results suggest that theory relating compensatory dynamics to ecological stability needs to consider not only complementarity in species responses to environmental change, but also seasonal complementarity among disturbance-tolerant and disturbance-sensitive species.     

环境扰动对钦州港潮间带大型底栖动物群落的影响

为了了解钦州港海洋生态环境质量,于2001年春夏两季在钦州港码头区两侧的无名岛和旧营盘,及距离稍远的鸡墩头和鹿耳环的潮间带滩涂,对大型底栖动物状况进行调查。共设置4条断面,每个断面设2～3个站位,用样方方法定量采集动物样品。应用种类相似性指数、生物多样性指数和丰度生物量比较法分析大型底栖动物群落间差异及生态质量状况。结果表明：该海域滩涂潮间带上发现有大型底栖动物70种,包括软体动物贝类38种,甲壳类18种,多毛类5种,鱼类4种,及其他类群的动物5种。生境的相似导致在钦州港码头区两侧的2个断面潮间带动物群落间的相似性最大。在种群水平上,珠带拟蟹守螺(Cerithidea cingulata)为丰度和生物量上的主要优势种。在类群水平上,贝类为主要的优势类群。应用丰度生物量比较法发现码头区两侧的2个断面潮间带动物群落受到扰动,显然是由于环境经常变动导致的。同时,从4个断面的潮间带动物物种数及3个生物多样性指数的比较也得到同样的结论。     

Field parameterization and experimental test of the neutral theory of biodiversity

Ecologists would like to explain general patterns observed across multi-species communities, such as species-area and abundance-frequency relationships, in terms of the fundamental processes of birth, death and migration underlying the dynamics of all constituent species. The unified neutral theory of biodiversity and related theories based on these fundamental population processes have successfully recreated general species-abundance patterns without accounting for either the variation among species and individuals or resource-releasing processes such as predation and disturbance, long emphasized in ecological theory. If ecological communities can be described adequately without estimating variation in species and their interactions, our understanding of ecological community organization and the predicted consequences of reduced biodiversity and environmental change would shift markedly. Here, I introduce a strong method to test the neutral theory that combines field parameterization of the underlying population dynamics with a field experiment, and apply it to a rocky intertidal community. Although the observed abundance-frequency distribution of the system follows that predicted by the neutral theory, the neutral theory predicts poorly the field experimental results, indicating an essential role for variation in species interactions.     

冶勒地区大熊猫种群生存力分析

采用种群生存力分析（ＰＶＡ） 软件———漩涡软件（ｖｏｒｔｅｘ ｖ６ ．３） ,用４ 种不同的初始参数模拟了冶勒地区大熊猫在１００ ａ 内的变动趋势。模拟结果显示：在不考虑灾变和近亲抑制的理想状态下,种群数量有一个缓慢增长;当加入很小的近亲繁殖参数时,种群在第９０ 年绝灭,而加入１７６ ％ 的灾变机率时,种群在第６０ 年绝灭。     

Two episodes of microbial change coupled with Permo/Triassic faunal mass extinction

Microbial expansion following faunal mass extinctions in Earth history can be studied by petrographic examination of microbialites (microbial crusts) or well-preserved organic-walled microbes. However, where preservation is poor, quantification of microbial communities can be problematic. We have circumvented this problem by adopting a lipid biomarker-based approach to evaluate microbial community changes across the Permo/Triassic (P/Tr) boundary at Meishan in South China. We present here a biomarker stratigraphic record showing episodic microbial changes coupled with a high-resolution record of invertebrate mass extinction. Variation in the microbial community structure is characterized by the 2-methylhopane (2-MHP) index (a ratio of the abundance of cyanobacterial biomarkers to more general bacterial biomarkers). Two episodes of faunal mass extinction were each preceded by minima in the 2-MHP index, followed by strong maxima, likely reflecting microbial responses to the catastrophic events that caused the extinction and initiated ecosystem changes. Hence, both cyanobacterial biomarker and invertebrate fossil records provide evidence for two episodes of biotic crisis across the P/Tr boundary.     

Predicting distributions of known and unknown reptile species in Madagascar

Despite the importance of tropical biodiversity, informative species distributional data are seldom available for biogeographical study or setting conservation priorities. Modelling ecological niche distributions of species offers a potential solution; however, the utility of old locality data from museums, and of more recent remotely sensed satellite data, remains poorly explored, especially for rapidly changing tropical landscapes. Using 29 modern data sets of environmental land coverage and 621 chameleon occurrence localities from Madagascar (historical and recent), here we demonstrate a significant ability of our niche models in predicting species distribution. At 11 recently inventoried sites, highest predictive success (85.1%) was obtained for models based only on modern occurrence data (74.7% and 82.8% predictive success, respectively, for pre-1978 and all data combined). Notably, these models also identified three intersecting areas of over-prediction that recently yielded seven chameleon species new to science. We conclude that ecological niche modelling using recent locality records and readily available environmental coverage data provides informative biogeographical data for poorly known tropical landscapes, and offers innovative potential for the discovery of unknown distributional areas and unknown species.     

Twenty-five years of change in scleractinian coral communities of Daya Bay （northern South China Sea） and its response to the 2008 AD extreme cold climate event

Coral reefs worldwide are becoming increasingly and detrimentally impacted upon by a variety of factors including significant climate changes, such as global warming and increased El Nino-Southern Oscillation activity. Generally, the persistence of coral reefs, especially at low-latitudes, is governed, in part, by sea surface temperatures not exceeding the critical limit （-30℃） at which mass mortality can occur. Thus, it is thought that corals living at high-latitudes （i.e., currently cooler sea surface temperatures） will likely respond more favourably to hypothesized future temperature increases than corals living at low-latitudes （i.e., currently warmer sea surface temperatures）. Consequently, high-latitude coral communities may have the potential to act as regions of refugia for many coral species in the face of potential future global warming. The Daya Bay （22°31′--22°50′N）, northern South China Sea, contains several high-latitude non-reefal coral communities and represents one of the most northerly distributions of scleractinian corals within the region. Significantly, Daya Bay has experienced dramatic warming in both air and sea surface temperatures throughout the past 50 years. In this paper, we analyze 25 years of change in the Daya Bay coral communities, based both on historic surveys and our latest 2006--2008 regional ecological surveys. Our results suggest that, contrary to predictions, there have been significant declines in coral cover within the Daya Bay during the past 25 years （i.e., 76.6% coral cover in 1983/1984 to only 15.3% coral cover by 2008）. Such changes also reflect a significant shift in the most abundant coral species, from Acropora pruinosa to Favites abdita. Most of the modern coral communities became established between 15 and 30 years ago, corresponding to a period of increased winter sea surface temperature. However, very few colonies have become established within the last 15 years, despite a more intense period of warming. By taking into account additional factors, we hypothesize that direct anthropogenic impacts, rather than climatic events, have both restricted the development, and drove the decline, of Daya Bay coral communities in the last 15 years. The Daya Bay has also been subjected to occasional extreme cold events during the past 50 years, with the most recent occurring in early 2008 （13 January-13 February）. During the 2008 cold event, the lowest air temperature reaches only 6.6℃, and the mean sea surface temperature for February fall to 〈 14℃, including six continuous days at 12.3℃. Significantly, the sea surface temperatures fall below the hypothesized critical lower temperature threshold （-13℃） that commonly leads to mass mortality in scleractinian coral communities. Surprisingly, our coral community surveys, conducted both before （August 2007） and after （late February 2008） the extreme 2008 cold event, demonstrate that the Daya Bay coral ecosystems are barely impacted upon during the cold period. Those observations suggest that the Daya Bay scleractinian coral communities have developed adaptations to low sea surface temperatures. Overall, our data support the hypothesis that high-latitude coral communities, such as Daya Bay, have the potential to act as areas of refugia for scleractinian corals in the advent of potential future global warming.     

东北三江平原地区水位梯度对湿地植被群落生态特征的影响

【目的】探究三江平原湿地水文因子与湿地植被群落类型的关系以及水位梯度与湿地植被生态特征的耦合关系,分析水文情势对湿地植被群落的影响,为湿地生态恢复与生态系统的科学管理提供依据。【方法】以东北三江平原洪河国家级自然保护区湿地为研究区,基于野外调查选取水位梯度明显的9条样线共90个样点数据,建立以物种为横坐标、样点为纵坐标的21×90的矩阵。采用PC-ORD 5对矩阵数据进行双向指示种分析(TWINSPAN),对保护区湿地植被群落进行数量分类并分析群落类型与水位梯度的关系,使用CANOCO 5对矩阵数据进行除趋势对应分析(DCA),探究湿地植被群落分布与水位梯度的关系。最后利用Origin 2018对典型湿地植被的株高及生物量与水位数据进行高斯拟合,探究水文梯度变化对湿地植被生态特征的影响。【结果】TWINSPAN结果显示,洪河自然保护区湿地植被可划分为12个群落类型,群丛类型沿水文梯度的变化体现了植被类型由湿生植被向旱生植被演替的变化趋势,表明水位变化对湿地植被群落的演替与分布具有重要作用。样地DCA分析结果表明,湿地植被群丛的分布呈现一定的规律,植被群落类型及分布主要受水位梯度的影响。物种DCA排序结果显示,湿生植被、湿中生植被、旱生植被在排序图上均有明显的分布范围和界限,影响植被分布的主要环境因子是水位梯度。高斯拟合结果表明,3种典型湿地植被的高度和生物量随水位的变化趋势均为先增加后减少。小叶章(Calamagrostis angustifolia)、毛果苔草(Carex lasiocarpa)、漂筏苔草(Carex pseudocuraica)的最适水位生态幅分别为:[4.46 cm,20.04 cm]、[8.30 cm,28.40 cm]和[40.87 cm,48.71 cm],3种湿地植被的高度及生物量对应最大水位排序均为:小叶章<毛果苔草<漂筏苔草,此结果与分类和排序结果相符合。小叶章的高度及生物量对水位梯度的变化最敏感。【结论】水位梯度为洪河国家级自然保护区湿地植被群落类型与分布的首要环境因子,优势种的分布体现了所属植被群落的分布特征,并且具有指示生境的作用。水位梯度对湿地植被的生态特征有极显著影响,不同湿地植被对淹水水位适应性的差异导致其最适水位生态幅的差异明显。     

关于生态居住小区的内涵及其评估指标体系的研究

随着城市化进程的加剧，城市生态环境问题日益突出，建设生态居住小区对改善城市环境具有重要作用．通过对沈阳市8个典型的居住小区的实地调查，应用生态学原理提出了生态居住小区的内涵，并制定了生态居住小区的评估指标体系．     

四种蔬菜土壤真菌群落组成与多样性

土壤真菌群落多样性是评价耕作土壤环境质量与健康的重要指标。以山东四种重要的蔬菜作物大葱、姜、草莓、黄瓜种植土壤为研究对象，采用qPCR和基于扩增子测序的高通量测序技术，结合土壤理化性质分析，研究了不同作物土壤真菌的群落组成及其多样性差异。结果表明：大葱土壤中以真菌ITS拷贝数为指标的总真菌丰度最低，且与草莓、黄瓜和姜土壤总真菌丰度具有显著差异(P<0.05);大葱和姜土壤真菌群落香农指数和操作分类单元指数高，多样性较丰富；黄瓜和草莓土壤真菌香农指数和操作分类单元指数低，多样性较差；土壤中子囊菌、担子菌、被孢菌门等相对丰度占比较高，其中在发病土壤中子囊菌门真菌相对丰度更高；土壤真菌类群受环境因子的影响，其中pH和有效磷对真菌群落构成的影响最大。这些结果为厘清不同真菌群落多样性与蔬菜土壤环境质量关系，为蔬菜土壤环境质量改善提供了理论依据。     

Neutral metacommunity models predict fish diversity patterns in Mississippi-Missouri basin

River networks, seen as ecological corridors featuring connected and hierarchical dendritic landscapes for animals and plants, present unique challenges and opportunities for testing biogeographical theories and macroecological laws. Although local and basin-scale differences in riverine fish diversity have been analysed as functions of energy availability and habitat heterogeneity, scale-dependent environmental conditions and river discharge, a model that predicts a comprehensive set of system-wide diversity patterns has been hard to find. Here we show that fish diversity patterns throughout the Mississippi-Missouri River System are well described by a neutral metacommunity model coupled with an appropriate habitat capacity distribution and dispersal kernel. River network structure acts as an effective template for characterizing spatial attributes of fish biodiversity. We show that estimates of average dispersal behaviour and habitat capacities, objectively calculated from average runoff production, yield reliable predictions of large-scale spatial biodiversity patterns in riverine systems. The success of the neutral theory in two-dimensional forest ecosystems and here in dendritic riverine ecosystems suggests the possible application of neutral metacommunity models in a diverse suite of ecosystems. This framework offers direct linkage from large-scale forcing, such as global climate change, to biodiversity patterns.     

Effects of biodiversity on the functioning of trophic groups and ecosystems

Over the past decade, accelerating rates of species extinction have prompted an increasing number of studies to reduce species diversity experimentally and examine how this alters the efficiency by which communities capture resources and convert those into biomass. So far, the generality of patterns and processes observed in individual studies have been the subjects of considerable debate. Here we present a formal meta-analysis of studies that have experimentally manipulated species diversity to examine how it affects the functioning of numerous trophic groups in multiple types of ecosystem. We show that the average effect of decreasing species richness is to decrease the abundance or biomass of the focal trophic group, leading to less complete depletion of resources used by that group. At the same time, analyses reveal that the standing stock of, and resource depletion by, the most species-rich polyculture tends to be no different from that of the single most productive species used in an experiment. Of the known mechanisms that might explain these trends, results are most consistent with what is called the 'sampling effect', which occurs when diverse communities are more likely to contain and become dominated by the most productive species. Whether this mechanism is widespread in natural communities is currently controversial. Patterns we report are remarkably consistent for four different trophic groups (producers, herbivores, detritivores and predators) and two major ecosystem types (aquatic and terrestrial). Collectively, our analyses suggest that the average species loss does indeed affect the functioning of a wide variety of organisms and ecosystems, but the magnitude of these effects is ultimately determined by the identity of species that are going extinct.