Finding unknown species in the genomes of extant species

Although many species have gone extinct, their genetic components might exist in extant species because of ancient hybridization. Via advances in genome sequencing and development of modern population genetics, one can find the legacy of unknown or extinct species in the context of available genomes from extant species. Such discovery can be used as a strategy to search for hidden species or fossils in conservation biology and archeology, gain novel insight into complex evolutionary history, and provide the new sources of genetic variation for breeding and trait improvement in agriculture.     

物种概念及其界定

半世纪以来,物种概念的定义备受关注,不同研究方向的生物学家提出24种不同或至少有分歧的物种概念,根据其不同的物种概念,物种的界定和物种的数量会出现很大的差异。人们普遍认同:物种是进化分离的微居群谱系,但把谱系分离过程中获得的特征如生殖隔离、可鉴定性、单系统发生等视为鉴定物种次级特征却有不同的声音。该文提出统一的物种概念,把谱系进化分离作为物种界定的唯一而又必要的特征,把谱系分离过程中获得的次级特征作为界定谱系分离的证据。鉴于此,物种概念间的分歧就会化解。其一,物种概念化与物种界定明显分开,不再混淆;其二,谱系的次级特征只与物种界定有关,在某种程度上为谱系分离提供证据;第三,若能把合理解释的任何一个特征作为某物种客观存在的证据,这样更多的特征更能确定谱系分离;最后最重要的是,统一物种概念使我们解放思想,扬弃传统的物种界定标准,探求物种界定的新思路。     

种间作用对物种分布模拟的影响及建模方法

物种分布模型(SDMs)通过量化物种分布和环境变量之间的关系,并将其外推到未知的景观单元,模拟、预测地理空间中生物的潜在分布,是生态学、生物地理学、保护生物学等研究领域的重要工具.然而,目前物种分布模型主要采用非生物因素作为预测变量,由于数据量化和建模表达困难,生物因素特别是种间作用在物种分布模型中常被忽略,将种间作用...     

物种与物种多样性

本文首先讨论生物物种的科学概念和生物学本质，分析物种客观存在的自然属性和物种概念的局限性，认为物种的生物学属性和物种多样性的科学属性之间有着本质联系。物种多样性研究的实质是研究生物物种的生物学多样性。度量物种多样性程度有多种方法，但物种数目是物种多样性程度最直接、也是最基本的表达，估计物种多样性数目是当前国际上物种多样性研究的核心与热点内容。物种多样性产生的根源是物种形成，物种绝灭速率是维持物种多样性的关键因素。本文简要总结了物种形成与绝灭的基本模式和机制，通过分析生物地理区系与物种多样性研究的密切关系，说明物种的区系成份分析是物种多样性大尺度格局研究的重要内容。     

甘南亚高寒草甸稀有种对物种多样性和物种多度分布格局的贡献

稀有种不仅影响群落的物种多度分布格局, 同时也是α多样性的重要贡献者。本研究主要通过加性分配和Fortran软件的RAD程序包拟合的方法, 研究了甘南亚高寒草甸不同坡向物种多样性及多度分布格局的变化, 分析了物种多度分布格局及其α多样性的变化特征, 确定了稀有种在物种多度分布格局中的相对贡献。结果表明: (1)在南坡到北坡的变化中, 环境因子差异比较明显, 其中, 土壤全磷、有机碳、速效磷、碳氮比及含水量呈递增趋势; 土壤氮磷比和pH值呈递减趋势; 土壤全氮在西坡显著低于其他坡向, 而速效氮在所有坡向上差异不显著。(2)稀有种对群落物种多样性的影响在南-北坡向梯度上依次增大, 去除稀有种的影响在各坡向均高于去除非稀有种, 可见, 稀有种在甘南亚高寒草甸物种多样性中的相对贡献高于非稀有种。(3)各坡向的稀有种资源获取模式以随机分配占领模式(random fraction模型)为主, 而非稀有种则以生态位优先占领模式(geometric series模型)为主。由于稀有种有较大的扩散率, 在物种多样性较高的生态系统中, 物种之间的生态位重叠会更加明显, 从而抑制物种多样性的增加, 因此能达到维持原有物种多样性的目的。     

外来种入侵与物种多样性

在入侵生态学研究方面 ,物种多样性与生物入侵之间的关系已成为当前研究和争论的焦点。自Elton的经典假说提出以来 ,物种丰富度高的群落比物种贫乏的群落更能抵抗外来种入侵的观点得到广泛接受。一些理论模型和多样性处理实验支持了该假说。但现在越来越多的野外观测和实验研究开始对这一经典假说提出异议 ,甚至反对。同时 ,在入侵生态学广泛受到关注的今天 ,大量的实验研究也提出了一些新的观点。本文对Elton经典假说提出以来全球有关物种多样性与生物入侵关系的主要研究及其观点进行了评述 ,以期为我国有关研究工作的开展提供参考。     

Dominant species maintain ecosystem function with non-random species loss

Loss of species caused by widespread stressors, such as drought and fragmentation, is likely to be non‐random depending on species abundance in the community. We experimentally reduced the number of rare and uncommon plant species while independently reducing only the abundance of dominant grass species in intact, native grassland. This allowed us to simulate a non‐random pattern of species loss, based on species abundances, from communities shaped by natural ecological interactions and characterized by uneven species abundance distributions. Over two growing seasons, total above‐ground net primary productivity (ANPP) declined with reductions in abundance of the dominant species but was unaffected by a threefold decline in richness of less common species. In contrast, productivity of the remaining rare and uncommon species decreased with declining richness, in part due to loss of complementary interactions among these species. However, increased production of the dominant grasses offset the negative effects of species loss. We conclude that the dominant species, as controllers of ecosystem function, can provide short‐term resistance to reductions in ecosystem function when species loss is nonrandom. However, the concurrent loss of complementary interactions among rare and uncommon species, the most diverse component of communities, may contribute to additional species loss and portends erosion of ecosystem function in the long term.     

Confronting species distribution model predictions with species functional traits

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day⁻¹. Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = −0.26, 95% CI (−0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.     

外来树种对本地林业虫害的诱发作用

白蜡窄吉丁、萧氏松茎象、光肩星天牛、黄斑星天牛、云斑天牛和桑天牛等林业害虫均为我国本地林业生态系统中的昆虫种类,在北美白蜡树、北美松树和北美黑杨派杨树等外来树种引入和大量栽培之前,一直没有形成严重的危害,以至于白蜡窄吉丁和萧氏松茎象都没有引起人们的关注。这些重要林业害虫在我国的发生都是伴随着敏感外来树种的引进和大量不合理的种植而逐渐严重起来的。本文对外来树种的引进与本地林业虫害的发生之间的关系进行了分析,提出了外来树种的不合理引进可能诱发本地林业新虫害的观点,并对其发生机理以及相应的研究和治理对策进行了讨论。     

No universal scale-dependent impacts of invasive species on native plant species richness

A growing number of studies seeking generalizations about the impact of plant invasions compare heavily invaded sites to uninvaded sites. But does this approach warrant any generalizations? Using two large datasets from forests, grasslands and desert ecosystems across the conterminous United States, we show that (i) a continuum of invasion impacts exists in many biomes and (ii) many possible species–area relationships may emerge reflecting a wide range of patterns of co-occurrence of native and alien plant species. Our results contradict a smaller recent study by Powell et al. 2013 (Science 339, 316–318. (doi:10.1126/science.1226817)), who compared heavily invaded and uninvaded sites in three biomes and concluded that plant communities invaded by non-native plant species generally have lower local richness (intercepts of log species richness–log area regression lines) but steeper species accumulation with increasing area (slopes of the regression lines) than do uninvaded communities. We conclude that the impacts of plant invasions on plant species richness are not universal.     

森林群落物种组成对凋落物组成的影响

在海南铜鼓岭山麓灌木林和季雨矮林固定大样地的基础上,通过收集凋落物,比较两林型的凋落物数量及其器官组成、凋落叶物种组成,探讨森林群落物种组成与凋落物组成的关系。结果表明:(1)两林型的凋落物总量及其器官组成不同,山麓灌木林(6.227 t/hm~2)比季雨矮林的年凋落量大(5.636 t/hm~2);凋落叶是凋落物的主要组成部分,能反映凋落物的凋落情况。(2)山麓灌木林凋落物优势种和主要物种为贡甲、林仔竹、橄树等15个物种,凋落叶总量占77.72%;季雨矮林的凋落物优势种和主要物种为方枝蒲桃、肖蒲桃、贡甲等17个物种,凋落叶总量占71.84%;山麓灌木林中凋落物优势种和主要物种的叶凋落量与其组成物种的株数、总断面积、树冠面积极显著正相关而季雨矮林的凋落物优势种和主要物种的叶凋落量与其组成物种的株数极显著正相关。山麓灌木林中两者的Jaccard相似性系数为20%,季雨矮林为25.93%,两林型的群落物种组成与凋落叶物种组成不一致,热带森林群落优势种不一定是凋落物优势种。     

萼花臂尾轮虫种复合体内三个姐妹种的形态差异

应用单因子方差分析和判别分析方法,分别比较了采自芜湖市3个自然水体的萼花臂尾轮虫种复合体内3个姐妹种(分别以克隆HE1和HE5、克隆HE3和SE1、克隆LE9为代表)的成体和幼体的形态差异。结果表明,克隆HE3成体的各形态参数均最小,而克隆HE1和LE9成体的各形态参数间无显著的差异;克隆HE1和HE3幼体的前中棘刺间距离和后侧棘刺长度、克隆LE9和HE1幼体的前侧棘刺间距离以及前中棘刺和侧棘刺间距离均无显著性差异,轮虫幼体的其它形态参数均以克隆LE9最长,克隆HE1次之,克隆HE3最短。对克隆HE1、HE3和LE9幼体有明显差异的形态参数所作的分布图显示,它们的分布区有很高程度的重叠。以判别分析建立的判别函数对3姐妹种成体的综合判别率中形态分析Ⅰ为47.8%,形态分析Ⅱ为55.6%;对3姐妹种幼体的综合判别率中形态分析Ⅰ和Ⅱ均为71.1%;两种形态分析对克隆HE1判别准确率均较低,分别为0-76.7%和0-74.2%;依据形态特征无法准确甄别萼花臂尾轮虫姐妹种。     

Testing for local species saturation with nonindependent regional species pools

Identifying the factors controlling local community structure is a central problem in ecology. Ecologists frequently use regression to test for a nonlinear saturating relationship between local community richness and regional species pool richness, suggesting that species interactions limit the number of locally coexisting species. However, communities in different regions are not independent if regions share species. We present a Monte Carlo test for whether an observed local-regional richness relationship is significantly different from that expected when regions are nonindependent and species interactions do not limit community membership. We illustrate this test with data from experimental microcosm communities. A conventional F -test suggests a significant saturating relationship between realized community richness and species pool richness. However, the Monte Carlo test fails to reject the null hypothesis that species interactions do not affect community richness. Strong species interactions do not necessarily set an absolute upper limit to the number of locally coexisting species.     

Separating effects of species identity and species richness on predation,pathogen dissemination and resistance to invasive species in tropical ant communities

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生物多样性事业需要科学、可操作的物种概念

物种概念(species concept)是生物学家们持续关注的中心问题。物种概念决定物种划分, 而物种划分的合理性关系到生物多样性的研究、保护和可持续利用。本文把现有较流行的物种概念分为6类, 并对它们予以述评后指出: 虽然生物学物种概念、遗传学物种概念、进化物种概念、系统发生物种概念等从不同方面认识了物种的客观真实性和物种的本质, 但在实践中都难以操作。绝大多数物种是由分类学家划分的, 但目前所有的分类学物种概念都包含有不同程度的主观因素, 从而造成物种划分的人为性, 对生物多样性研究造成负面影响。因此, 生物多样性事业需要科学、可操作的物种概念。本文在吸收了生物学物种概念、遗传学物种概念、进化物种概念以及系统发生物种概念等的长处, 也分析了它们的不足和问题的基础上提出一个新的物种概念, 即形态-生物学物种概念。最后, 以芍药属(Paeonia)几个物种的处理为例, 说明这一新的物种概念是可操作的, 划分的物种在形态上区别分明, 易于鉴别。更重要的是, 其结果得到基于25或26个单拷贝或寡拷贝核基因DNA序列所作的系统发生分析的强有力支持。各个物种在系统发生树上形成单系和独立的谱系, 表明其间各自形成独立的基因库, 没有基因交换, 它们独立进化, 有各自的生态位和独立的分布区。因此, 利用这一新的物种概念能够达到预期目标。     

The problem of species revisited

Hypothetical-deductive analysis is an alternative to both induction and deduction, the difference between which is considered less important. The hypothetical-deductive approach requires a scientist to abandon the synthetic theory of evolution in favor of the epigenetic theory. This latter treats species as a discrete level of biodiversity and, particularly, the one where sympatric biparental groups show reproductive independence. In the case of uniparental (asexual and parthenogenetic groups), as well as in bisexual allopatric groups, the species level of divergence is identifiable by analogy to sympatric biparental relatives. The biological and evolutionary species concepts are disproved: the former contradicts observation, and the latter is non-operational.     

评世界保护联盟新的物种受威胁分类系统草案

为了进一步了解物种受威胁的情况和发展,以加强物种保护工作,世界保护联盟制定了一个新的物种受威胁分类系统草案,把物种受威胁的程度分为９个级别,即绝灭种、野生状态下的绝灭种、极危种、濒危种、渐危种、敏感种、安全的／危险性小的种、不充分了解的种和未估价的种。本文对这个分类系统草案作了简略的评介。     

The local introduction of strongly interacting species and the loss of geographic variation in species and species interactions

Species introductions into nearby communities may seem innocuous, however, these introductions, like long-distance introductions (e.g. trans- and intercontinental), can cause extinctions and alter the evolutionary trajectories of remaining community members. These 'local introductions' can also more cryptically homogenize formerly distinct populations within a species. We focus on several characteristics and the potential consequences of local introductions. First, local introductions are commonly successful because the species being introduced is compatible with existing abiotic and biotic conditions; many nearby communities differ because of historical factors and the absence of certain species is simply the result of barriers to dispersal. Moreover, the species with which they interact most strongly (e.g. prey) may have, for example, lost defences making the establishment even more likely. The loss or absence of defences is especially likely when the absent species is a strongly interacting species, which we argue often includes mammals in terrestrial communities. Second, the effects of the introduction may be difficult to detect because the community is likely to converge onto nearby communities that naturally have the introduced species (hence the perceived innocuousness). This homogenization of formerly distinct populations eliminates the geographic diversity of species interactions and the geographic potential for speciation, and reduces regional species diversity. We illustrate these ideas by focusing on the introduction of tree squirrels into formerly squirrel-less forest patches. Such introductions have eliminated incipient species of crossbills (Loxia spp.) co-evolving in arms races with conifers and will likely have considerable impacts on community structure and ecosystem processes.