澜沧江中游水生昆虫生活史和生态学性状多样性的海拔格局: 气候和土地利用的影响

物种通过功能性状响应环境变化, 探究群落功能性状多样性的海拔格局是揭示生物多样性空间分布格局和形成机制的重要研究内容。气候变化和土地利用是影响溪流生物多样性变化及其群落构建的重要因素, 然而气候和土地利用沿海拔梯度如何影响水生昆虫功能性状垂直分布格局的系统研究仍旧比较缺乏。本文基于2016年和2018年在云南澜沧江中游1,000-3,000 m海拔共56个溪流样点的水生昆虫群落调查数据, 利用线性和二次回归模型探索并比较了生活史性状(化性、生活史快慢、成虫寿命)和生态学性状(营养习性、生活习性、温度偏好)的群落加权平均性状多样性指数沿海拔梯度的分布特征, 并通过随机森林模型解析流域尺度气候和土地利用变量对生活史和生态学性状多样性垂直分布格局的影响。结果表明: 生活史性状中, 少于1世代、无季节性、慢季节性、成虫寿命长等性状多样性沿海拔梯度呈显著的“U”型分布格局, 而快季节性和成虫寿命极短多样性呈显著的单峰型海拔格局, 成虫寿命短多样性呈显著递增的海拔格局。生态学性状中, 温度偏好多样性与海拔梯度无关, 附着者和爬行者的多样性沿海拔梯度分别呈显著的递增和“U”型格局, 滤食者、植食者和捕食者的多样性分别呈显著递增、递减和“U”型海拔格局。随机森林模型分析结果表明, 气候和土地利用对生活史性状多样性的解释量高于对生态学性状多样性的解释量, 年平均温度和农业面积百分比是共同的关键因素。综上, 水生昆虫群落功能性状多样性海拔格局存在差异, 主要受不同自然环境梯度和人类干扰因素驱动。研究结果可为制定澜沧江流域生物多样性保护对策提供理论基础。     

“2020年后全球生物多样性框架”的谈判进展以及对我国的建议

“2020年后全球生物多样性框架”是当前《生物多样性公约》谈判的焦点议题, 了解该议题的谈判进展将对我国顺利举办第15次缔约方大会(COP15)产生积极的作用。本文在梳理相关谈判进程的基础上, 分析了各方主要观点, 并就我国应对国际谈判并以东道国身份推进该框架的制定进程提出了建议。各方对制定框架的时间表、程序和一般性原则形成了较为一致的共识, 认为应尽快确定“2020年后全球生物多样性框架”的程序及时间表, 基于“爱知生物多样性目标”的执行经验、科学结论和和广泛的信息来源, 与“可持续发展目标”及其他国际进程衔接, 重视利用情景和模型, 并支持更多利益相关方参与制定过程。同时, 各方认为框架应主要包括土地利用、保护和恢复生物多样性的措施、解决生物多样性丧失的根本原因、主流化、能力建设、资源调动、国家承诺等要素。为应对国际谈判, 建议我国在《公约》谈判会议中适时提出以下观点: 重视实现可持续利用相关的目标; 提升评估指标体系的合理性; 科学制定措施。此外, 建议我国采取以下措施积极推进框架制定进程: 充分利用国际高级别会议, 提升政治重视程度; 积极与主要国际进程协作, 推进该框架深入讨论; 重视调动利益相关方积极性。     

中国苔藓植物多样性研究进展

苔藓植物是生物多样性的重要组成部分, 包括角苔植物、苔类植物和藓类植物三大类群, 其物种数量仅次于被子植物, 是高等植物的第二大类群。我国是世界苔藓植物多样性最丰富的国家。自2017年以来, 我国苔藓学者在世界范围发现了10个新属, 40个新种, 建立了新的地钱纲分类系统; 更新了我国苔藓植物物种名录, 完成了数本分类学专著, 并在苔藓系统发育基因组、苔藓植物多样性与环境关系、苔藓植物多样性保护等领域取得了可喜的进展。对未来的研究, 我们提出5点建议: (1)加强对重要生态系统、国家公园和关键类群的物种多样性调查; (2)加快基于基因组的苔藓植物多样性研究; (3)加强苔藓植物保护研究; (4)加强西北地区苔藓植物多样性研究人才的培养; (5)进一步加强国际合作, 努力构建“一带一路”国家苔藓植物多样性平台。     

为何要信达尔文的演化论——论《物种起源》的二十五重简约美

科学理论的本质较量是解释力之简约美的较量, 其使得科学革命成为可能。本文通过整理与剖析达尔文的《物种起源》的论述, 展示了生命科学史上最伟大革命的内在理性, 即, 演化论相对于神创论的25重简约性优势, 分别体现在解释: (1)驯化品种的产生、(2)驯化品种在内外性状层面的多样性的差异性、(3) (杂交的子代的)遗传性状的变化、(4)杂种与混血在健康度与生殖力方面的差异、(5)杂种与混血在性状变化上的差异、(6)生物形态分布的簇状格局、(7)生物形态分化在不同分类阶元内部的不均等性、(8)不同性状分化的不均等性、(9)物种间性状差别的渐变性、(10)伴随环境变化的形态变化、(11)相对环境变化的形态惯性、(12)生物间竞争强度分布的不均等性、(13)不同物种间的形态同似性、(14)个体间的形态差异随着个体发育而变大的现象、(15)生物的痕迹构造、(16)生物地理分布的系统差异性(贯穿诸生物分类阶元的稳定偏向的差异性)、(17)物种的“等级性”与其地理分布范围的关系、(18)生物地理分布的“岛屿”现象、(19)岛屿物种的总丰度低而土著物种丰度高的特征、(20)岛屿生物的类别构成特征、(21)岛屿生物与相邻大陆的生物间的相似度关系、(22)物种迁移与物种灭绝的地域差异性、(23)物种灭绝的渐变模式、(24)古生物与现存生物在形态上的关系、(25)胚胎形态与古生物形态间的相似关系。正是这25重简约美, 铸造了《物种起源》作为最伟大的科学著作的底色, 并奠定了现代生命科学研究的大方向与总方法——“范式”。这一剖析亦有助于我们理解科学发展的真精神以及把握当代科学研究的进展。     

大气CO2浓度和气温升高对麦田节肢动物群落的影响

为了预测气候变化对麦田节肢动物群落多样性的影响, 本研究在麦田开放环境中设置4种处理, 分别是高温(高于当时气温2℃和当前CO₂浓度)、高CO₂浓度(500 μL/L和当时气温)、高温+高CO₂浓度和对照(当前CO₂浓度和气温)等, 采用定期随机抽样方法调查节肢动物群落的多样性, 用经典的多样性指数对整体节肢动物群落以及不同食性节肢动物群落多样性进行分析。共采到节肢动物3纲10目42科52种。仅“高温”和“高温+高CO₂”处理显著增大节肢动物群落的均匀度, 其余处理均无显著影响。“高温+高CO₂”处理的影响随小麦生长发育期不同而略有差异, 在苗期可增大Shannon-Wiener多样性指数, 而在后期使该指数减小; “高温+高CO₂”与“高温”处理的群落多样性较为相似。对不同食性节肢动物群落的分析表明, 与对照相比, 植食性昆虫群落在“高CO₂”下丰富度显著增大; 寄生性昆虫群落的多度在“高温”下显著增大; 腐食性等节肢动物群落的多度在“高CO₂+高温”和“高温”处理下有所增大、均匀度在“高温”下略降低, 但均未达统计上的显著水平; 捕食性节肢动物群落不受影响。本研究说明, CO₂浓度和气温升高不同程度地影响麦田节肢动物群落的物种多样性, 两类因素同时升高与各自单独升高的影响不完全一致。     

推动中国企业参与《生物多样性公约》全球伙伴关系的机制建设

党的十九大首次提出了中国要成为全球生态文明建设引领者的新要求。生物多样性保护是中国生态文明建设和全球生态文明建设的重要内容, 也是构建人与自然生命共同体、人类命运共同体、清洁美丽世界的集中体现。本文系统总结了推动《生物多样性公约》倡导的“企业与生物多样性全球伙伴关系” (GPBB)的主要国际经验, 提出了中国推动落实“中国企业与生物多样性伙伴关系”倡议(简称CBBP)的政策建议, 为中国政府更好地引导企业参与, 撬动社会资源合力加强生物多样性保护提供参考。通过分析德国、印度、加拿大、秘鲁、澳大利亚、南非、日本和韩国构建企业参与GPBB的实践, 发现各国经验主要有以下特点: (1)政府作用重要且方式多样, 或提供管理、或提供资金或实物等; (2)组织方式多样, 常见的为组建跨部门的决策机构并下设秘书组; (3)成员加入, 一般需要签署协约, 有的偏重特定行业, 有的重视机构会员; (4)在服务上, 政府一般提供法律政策解读、知识信息传播、政策指引等服务; (5)在资金来源上, 有的主要靠缴纳会费, 有的包括实物捐赠、志愿服务、PPP (公私合营)项目合作等方式。各国经验的主要启示有: (1)根据论坛会议沟通和实际工作交流, 大量企业表现出参与生物多样性伙伴关系倡议的积极意愿; (2)推动企业参与的国际资源网络已基本建立; (3)受限于规模和资金, 绝大多数企业的参与需要本国政府更为有力的引导和支持。2015年, 中国正式加入GPBB。截至目前, 虽然中国已开展了许多推动GPBB的相关工作, 但仍然存在和面临许多问题与挑战: (1)由于中国倡议CBBP相关文件仍未通过审批, 因此, 尽管根据调研已有许多企业非常有意愿成为中国伙伴关系成员单位, 但仍无章可循, 无法加入; (2)中国尚未建立健全的推动CBBP倡议行动的组织模式和资金机制; (3)《生物多样性公约》第15次缔约方大会将于2020年在北京召开, 这对中国在促进CBBP的管理运行也提出更高和更为紧迫的要求。对此, 本文建议CBBP倡议可实施“两步走”战略: (1)成立并发起CBBP联盟倡议; (2)加大国际公约建设和国家履约谈判支持。     

“自然对人类的贡献”的实现、发展趋势和启示

生物多样性和生态系统服务政府间科学政策平台(IPBES)的目标是加强科学政策对生物多样性和生态系统服务的影响。为了更好地理解和展示IPBES目标的基本要素及其相互关系, 在千年生态系统评估(MA)的基础上, IPBES融合多种知识体系, 不断完善、创新, 逐步形成了以“自然对人类的贡献” (NCP)为核心的概念框架。本文首先梳理了NCP的发展历程, 论述了NCP与生态系统服务的关系, 指出两者均关注人类福祉, 但与生态系统服务不同的是, NCP涵盖了自然对人类生活的消极影响, 强调社会文化因素、传统知识和土著居民的地位以及人与自然共同作用的重要性。其次, 本文阐述了人与自然共同实现NCP进而影响人类良好生活质量的机制, 并分析了NCP大幅下降的全球趋势, 提出世界各国应不断推动生物多样性保护主流化, 增加国际交流与合作, 致力实现“人与自然和谐共生”的2050年愿景。最后, 本文讨论了NCP在IPBES评估和《生物多样性公约》磋商谈判中的应用前景, 为今后NCP理论研究和实践提供科学支持。     

中国草原/荒漠植物多样性监测网 模式植物群落监测方案

“模式群落”是指能够反映某种植被分类单元基本特征, 并可作为准确描述该植被类型“标准”的典型植物群落。中国生物多样性监测网络——草原/荒漠植物多样性监测网旨在统一监测方法和技术规范的基础上, 在草原/荒漠植被主要群系分布的典型地段建立模式植物群落监测固定样方, 定期复查, 长期监测草原和荒漠的植物多样性变化。文章强调了典型植物群落监测是生物多样性监测的重要组成部分, 阐述了模式群落的概念, 介绍了草原/荒漠植物多样性监测网的总体思路和布局, 以及主要监测内容、方法、指标和预期产出。     

生物多样性起源与进化研究进展

生物多样性的起源与进化是生命科学领域最重要的科学问题之一。多组学数据的积累和相关分析技术的发展, 极大地推动了人们对生物多样性起源与进化的理解和研究, 使得阐明生物进化事件发生的过程与机制成为可能。值此《生物多样性》创刊30周年之际, 本文简要回顾生物多样性起源与进化相关研究在近年来取得的重要研究进展, 以期帮助读者了解该研究方向的发展现状。过去10年中, 生物多样性起源与进化相关研究在生命之树重建、生物多样性时空分布格局、物种概念、物种形成与适应性进化以及新性状起源与多样化等方面取得了许多重要进展, 并在此基础上厘清了许多分类单元间的系统发育关系、揭示了生物多样性分布格局的部分历史成因、提出了新的物种概念和物种形成模型、阐明了新性状和新功能发生的部分分子机制。我们认为, 更精准地重建生命之树、深入挖掘基因组数据以及多学科交叉融合将是今后生物多样性研究的主要趋势。     

中国生物多样性相关传统知识调查与评估指标体系构建

基于调查获得的数据开展生物多样性相关传统知识评估, 明确面临的主要压力和保护空缺, 可为相关管理部门决策提供科学依据。指标是开展评估的主要工具, 但是目前尚未有关于生物多样性相关传统知识评估指标体系的文献报道。我们基于压力-状态-响应(pressure-state-response, PSR)模型, 充分考虑生物多样性相关传统知识的基本特征、主要威胁因子、保护和传承措施, 初步构建了区域和国家尺度的生物多样性相关传统知识评估指标体系。然后通过专家咨询, 确定了30项指标, 其中压力指标7项、状态指标14项、响应指标9项。这些指标不仅可以用于生物多样性相关传统知识的综合评估, 还可以对其基本状况、受威胁状况、保护与传承状况、相关遗传资源进行单独评价。此外, 基于评估参数计算的数据需求, 我们借鉴国内外民族植物学和生物多样性相关传统知识调查的主要研究成果, 建立了“全国生物多样性相关传统知识调查技术方法体系”, 并通过试点调查进行修改完善。 “全国生物多样性相关传统知识调查”以关键人物访谈、问卷调查和参与观察为主, 并辅以生物学和生态学调查; 采用滚雪球抽样法对目标群体进行抽样, 确定访谈对象。     

Old trees, new trees--is there any progress?

The amount of comparative data for phylogenetic analyses is constantly increasing. Data come from different directions such as morphology, molecular genetics, developmental biology and paleontology. With the increasing diversity of data and of analytical tools, the number of competing hypotheses on phylogenetic relationships rises, too. The choice of the phylogenetic tree as a basis for the interpretation of new data is important, because different trees will support different evolutionary interpretations of the data investigated. I argue here that, although many problematic aspects exist, there are several phylogenetic relationships that are supported by the majority of analyses and may be regarded as something like a robust backbone. This accounts, for example, for the monophyly of Metazoa, Bilateria, Deuterostomia, Protostomia (= Gastroneuralia), Gnathifera, Spiralia, Trochozoa and Arthropoda and probably also for the branching order of diploblastic taxa (“Porifera”, Trichoplax adhaerens, Cnidaria and Ctenophora). Along this “backbone”, there are several problematic regions, where either monophyly is questionable and/or where taxa “rotate” in narrow regions of the tree. This is illustrated exemplified by the probable paraphyly of Porifera and the phylogenetic relationships of basal spiralian taxa. Two problems span wider regions of the tree: the position of Arthropoda either as the sister taxon of Annelida (= Articulata) or of Cycloneuralia (= Ecdysozoa) and the position of tentaculate taxa either as sister taxa of Deuterostomia (= Radialia) or within the taxon Spiralia. The backbone makes it possible to develop a basic understanding of the evolution of genes, molecules and structures in metazoan animals.     

Discriminating Micropathogen Lineages and Their Reticulate Evolution through Graph Theory-Based Network Analysis: The Case of Trypanosoma cruzi,the Agent of Chagas Disease

Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease, to identify major lineages and to unravel their past history of divergence and possible recombination events. At the scale of T. cruzi subspecific diversity, graph theory-based networks applied to 22 isoenzyme loci (262 distinct Multi-Locus-Enzyme-Electrophoresis -MLEE) and 19 microsatellite loci (66 Multi-Locus-Genotypes -MLG) fully confirms the high clustering of genotypes into major lineages or “near-clades”. The release of the dichotomic constraint associated with phylogenetic reconstruction usually applied to Multilocus data allows identifying putative hybrids and their parental lineages. Reticulate topology suggests a slightly different history for some of the main “near-clades”, and a possibly more complex origin for the putative hybrids than hitherto proposed. Finally the sub-network of the near-clade T. cruzi I (28 MLG) shows a clustering subdivision into three differentiated lesser near-clades (“Russian doll pattern”), which confirms the hypothesis recently proposed by other investigators. The present study broadens and clarifies the hypotheses previously obtained from classical markers on the same sets of data, which demonstrates the added value of this approach. This underlines the potential of graph theory-based network analysis for describing the nature and relationships of major pathogens, thereby opening stimulating prospects to unravel the organization, dynamics and history of major micropathogen lineages.     

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

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Deep Phylogeny��How a Tree Can Help Characterize Early Life on Earth

The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history.

“You know, a tree is a tree.  How many more do you need to look at?”–Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966

The following article addresses a period in life most removed from life’s origins compared with other articles in this collection. The article discusses an advanced form of life that seems to have lived on the order of 3.5–4.0 billion years ago, around the time when life as we know it began to diversify in a Darwinian sense. The life from this geological period is located deep within an illustrated taxonomic tree of life. The hope is that by understanding how early life evolved, we can better understand how life originated. In this sense, the article attempts to travel backwards in time, starting from modern organisms, to understand life’s origin.The Darwinian concept of evolution suggests that all modern life shares a single common ancestor, often referred to as the last universal common ancestor (LUCA). Throughout evolutionary history, this ancestor has for the most part generated descendants as successive bifurcations in a tree-like manner. This so called Tree of Life, and phylogenetics in general provides much of the framework for the field of molecular evolution. Taxonomic trees allow us to better understand relationships and commonalities shared by life. For instance, a tree may tell us whether a trait or phenotype shared between two organisms is the result of shared-common ancestry (termed homologous traits) or whether the trait has evolved multiple times independent of ancestry (analogous traits such as wings).Taxonomic trees can be built using diverse sources of information. These can include morphological and phenotypic data at the macro-level down to DNA and protein sequence data at the micro-level. Ideally, trees built from multiple sources of input have identical taxonomic relationships and branching patterns, and such trees are said to be congruent. In practice, however, trees built from morphological data (say, presence or absence of wings) are often different than a tree built from molecular data (DNA or protein sequences). This requires the biologist to determine which of the two data sets is misleading and/or which taxonomic tree-building algorithm is most appropriate to use for a particular data set. Such an artform is common in the field of molecular evolution because rarely are trees congruent when built from two sources of input data.In light of this fact, we have provided the quote at the beginning of this article as a reflection about the field of molecular evolution and its interpretations of taxonomic trees. Although Reagan was not speaking about taxonomic trees in his quote, the same sort of disconnect exists between evolutionary biologists and molecular biologists (Woese and Goldenfeld 2009), as it did between conservationists and Ronald Reagan. A molecular biologist may be inclined to say that once you have seen one phylogenetic tree, you have seen them all. And in fairness, there is some validity to such a notion because historically a phylogenetic tree could not help a molecular biologist to better describe their system. An evolutionary biologist, however, will argue that individual trees have nuances that can dramatically alter our interpretation of evolutionary processes.We intend to show in this article that not all (taxonomic) trees look similar and describe identical evolutionary scenarios. We will discuss how our concept of the Tree of Life has changed over the past couple of decades, how trees can be interpreted, and what a tree can tell us about early life. In particular, the article will focus on the temperature conditions of early life because this topic has received much attention over the past few years as a direct result of improved DNA sequencing technology and a better understanding of molecular evolutionary processes. We will also describe how trees can be used to guide laboratory experiments in our attempt to understand ancient life. Lastly, we will discuss how phylogenetic trees will serve as the foundation for an “evolutionary synthetic biology” that should allow us to better understand the evolution of cellular pathways, macromolecular machines such as the ribosome, and other emergent properties of early life.     

海南岛热带天然针叶林主要树种的空间格局及关联性

天然针叶林在热带地区虽较为少见, 但其对维持热带地区的生物多样性和生境异质性具有特殊意义。在我国热带天然针叶林集中分布面积最大的海南霸王岭林区, 作者选择伴生阔叶树种优势度不同的两种典型南亚松(Pinus latteri)天然林(简称纯林和混交林), 采用点格局法分析了其林冠层、亚林层和林下层主要树种的空间分布格局及其关联性。结果表明: (1)纯林中林冠层的南亚松主要为聚集分布, 混交林中在较小尺度上为聚集分布, 在较大尺度上为随机分布。(2)纯林中亚林层树种在较小尺度上为聚集分布, 在较大尺度上为随机分布, 在混交林中主要为聚集分布。(3)纯林中林下层树种主要呈现为随机分布, 而在混交林中主要为聚集分布。(4)随着尺度的增加, 林冠层与其他两个层次的树种, 在纯林中表现出从空间无关联到正关联的变化趋势, 而在混交林中则表现出从空间无关联到负关联的变化趋势。(5)亚林层与林下层树种在各个尺度上都表现为空间正关联。由此可见, 热带天然针叶林中优势种南亚松对伴生阔叶树种的分布格局具有重要影响。     

Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions

The evolution of specific seed traits in scatter-hoarded tree species often has been attributed to granivore foraging behavior. However, the degree to which foraging investments and seed traits correlate with phylogenetic relationships among trees remains unexplored. We presented seeds of 23 different hardwood tree species (families Betulaceae, Fagaceae, Juglandaceae) to eastern gray squirrels (Sciurus carolinensis), and measured the time and distance travelled by squirrels that consumed or cached each seed. We estimated 11 physical and chemical seed traits for each species, and the phylogenetic relationships between the 23 hardwood trees. Variance partitioning revealed that considerable variation in foraging investment was attributable to seed traits alone (27–73%), and combined effects of seed traits and phylogeny of hardwood trees (5–55%). A phylogenetic PCA (pPCA) on seed traits and tree phylogeny resulted in 2 “global” axes of traits that were phylogenetically autocorrelated at the family and genus level and a third “local” axis in which traits were not phylogenetically autocorrelated. Collectively, these axes explained 30–76% of the variation in squirrel foraging investments. The first global pPCA axis, which produced large scores for seed species with thin shells, low lipid and high carbohydrate content, was negatively related to time to consume and cache seeds and travel distance to cache. The second global pPCA axis, which produced large scores for seeds with high protein, low tannin and low dormancy levels, was an important predictor of consumption time only. The local pPCA axis primarily reflected kernel mass. Although it explained only 12% of the variation in trait space and was not autocorrelated among phylogenetic clades, the local axis was related to all four squirrel foraging investments. Squirrel foraging behaviors are influenced by a combination of phylogenetically conserved and more evolutionarily labile seed traits that is consistent with a weak or more diffuse coevolutionary relationship between rodents and hardwood trees rather than a direct coevolutionary relationship.     

植物生命之树重建的现状、问题和对策建议

生命之树的概念源自1859年达尔文的《物种起源》, 但利用分子数据重建植物生命之树的研究则在20世纪90年代才开始兴起。近年来, 随着测序技术、分析方法和计算能力的快速发展, 植物生命之树重建研究取得了显著成果。本文首先概述了当前以及未来很长一段时间内植物生命之树重建工作的重点, 包括植物属级和种级水平的系统发育研究、植物系统发育基因组学研究、分子和形态数据联合分析、包括灭绝与现存植物类群的生命之树重建, 以及超大植物生命之树重建等5个方面; 然后简要概括国内植物生命之树重建研究的现状, 指出了我国在植物生命之树重建领域发展中所存在的问题, 并从“类群研究体系、学科评价体系、国家顶层设计, 以及拓展国际合作”等方面对学科未来的发展提出了一些对策建议。     

Are our phylomorphospace plots so terribly tangled? An investigation of disorder in data simulated under adaptive and nonadaptive models

Contemporary methods for visualizing phenotypic evolution, such as phylomorphospaces, often reveal patterns which depart strongly from a naïve expectation of consistently divergent branching and expansion. Instead, branches regularly crisscross as convergence, reversals, or other forms of homoplasy occur, forming patterns described as “birds’ nests”, “flies in vials”, or less elegantly, “a mess”. In other words, the phenotypic tree of life often appears highly tangled. Various explanations are given for this, such as differential degrees of developmental constraint, adaptation, or lack of adaptation. However, null expectations for the magnitude of disorder or “tangling” have never been established, so it is unclear which or even whether various evolutionary factors are required to explain messy patterns of evolution. I simulated evolution along phylogenies under a number of varying parameters (number of taxa and number of traits) and models (Brownian motion, Ornstein–Uhlenbeck (OU)-based, early burst, and character displacement (CD)] and quantified disorder using 2 measures. All models produce substantial amounts of disorder. Disorder increases with tree size and the number of phenotypic traits. OU models produced the largest amounts of disorder—adaptive peaks influence lineages to evolve within restricted areas, with concomitant increases in crossing of branches and density of evolution. Large early changes in trait values can be important in minimizing disorder. CD consistently produced trees with low (but not absent) disorder. Overall, neither constraints nor a lack of adaptation is required to explain messy phylomorphospaces—both stochastic and deterministic processes can act to produce the tantalizingly tangled phenotypic tree of life.     

Using directed phylogenetic networks to retrace species dispersal history

Methods designed for inferring phylogenetic trees have been widely applied to reconstruct biogeographic history. Because traditional phylogenetic methods used in biogeographic reconstruction are based on trees rather than networks, they follow the strict assumption in which dispersal among geographical units have occurred on the basis of single dispersal routes across regions and are, therefore, incapable of modelling multiple alternative dispersal scenarios. The goal of this study is to describe a new method that allows for retracing species dispersal by means of directed phylogenetic networks obtained using a horizontal gene transfer (HGT) detection method as well as to draw parallels between the processes of HGT and biogeographic reconstruction. In our case study, we reconstructed the biogeographic history of the postglacial dispersal of freshwater fishes in the Ontario province of Canada. This case study demonstrated the utility and robustness of the new method, indicating that the most important events were south-to-north dispersal patterns, as one would expect, with secondary faunal interchange among regions. Finally, we showed how our method can be used to explore additional questions regarding the commonalities in dispersal history patterns and phylogenetic similarities among species.