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第四届“中国生物系统学学术论坛” 会议报告摘要集

已有 3097 次阅读 2019-12-6 11:28 |个人分类:学术报告|系统分类:科研笔记

 

 

第四届“中国生物系统学学术论坛”

会议报告摘要集

 

 

 

主办单位:

中国昆虫学会

 

 

协办单位:

中国植物学会、中国微生物学会

中国菌物学会、中国科学院青年创新促进会

 

承办单位:

动物进化与系统学院重点实验室

动物生态与保护生物学重点实验室

 

 

 

 

 

 

 

2019126-129

北京胜利饭店


 

 

 


目  录

Benoit Guénard-Global diversity and discovery rate in insects: the case of ants

蔡晨阳-昆虫演化:分子与化石的整合

陈垒-反刍动物系统发育和适应性进化

陈之端-生命之树是二歧、多歧还是网状的?

杜宗军-细菌分离技术探索及富集分离方法的应用

高连明-被子植物及菊支基部分支的演化历史与多样化格局

郭亚龙-Transposable elements and loss-of-function mutations contribute to adaptation

韩管助-分子化石阐明逆转录类病毒的远古史和宏进化

何舜平-鱼类学的传承与创新:鱼类多样性历史的系统发育重建

胡义波-小熊猫保护基因组学研究

江廷磊-蝙蝠感官信号的特征和功能

李晨虹-基于跨物种靶基因富集技术的鲱形目系统发育基因组学研究

李虎-副新翅类昆虫线粒体基因组及其在进化研究中的应用

李猛-Asgard古菌与生命之树

李泰辉-中国食用菌多样性及其对全球产业的贡献

李学燕-Systems biology study of entomology - butterflies and fireflies as models

刘建魁-分化时间在真菌系统学研究中的应用

刘宣-从生物入侵过程探究物种时空分布规律

刘振-Convergent evolution in echolocation-related phenotypes and genotypes reveals a new echolocating genus in mammals

龙红岸-微型生物的突变

罗阿蓉-物种分子分类与进化历史研究方法评估进展

邱强-反刍动物角的起源和进化

史卫峰-三种新的虾源病毒的鉴定、分子特征及分类研究

Sudhir Kumar-Building the Grand Timetree of Life

王宝生-拟南芥近缘种Boechera stricta的群体基因组学研究

王国栋-犬科种间的基因渐渗

王年-桦木属种间进化关系及红桦的避难所

王强-桔梗科争议类群的系统学研究进展

王文-系统发育基因组学在阐释一些重要生物学问题中作用

吴爱平-病原、媒介和宿主三重视角下的系统病毒学

吴东东-高原家养动物适应性状遗传机制解析

熊杰-十种一态:隐藏在四膜虫形态种中的基因组进化

伊廷双-豆科的叶绿体系统发育基因组学

张大勇-不完全谱系筛选与种间杂交对植物系统发育重建和种群进化历史的影响

赵瑞琳-以演化时间为分类新增指标:担子菌门为例

周琦-鸭嘴兽性染色体的起源与演化

周筱帆-Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence

周旭明-哺乳动物高阶元分子系统学研究进展

苏涛-基于化石证据探讨青藏高原新生代植物多样性的演变

宋波-青藏高原有刺植物的海拔分布格局及其影响因素

李强-中国亚热带地区蚜虫DNA条形码及其种群分化

潘达-中国横断山区淡水蟹多样性进化机制的研究

 



Global diversity and discovery rate in insects: the case of ants

Speaker: Benoit Guénard

Affiliation: The University of Hong Kong

Keywords: TaxonomyBiodiversity DiscoveryGlobal TrendsAntsTaxonomist’s Productivity

Abstract:

Key question(s): Documenting Earth’s biodiversity represents one of the most challenging and pressing goals of biological sciences and conservation. Yet, previous estimates on biodiversity description completeness and their respective interpretations have greatly varied, leading to divergent conclusions on the best use of resources for the sciences describing, cataloguing and mapping species distributions. Insects are a key taxon to address such questions as their diversity represent more than 50% of global biodiversity. Yet, limited efforts have been conducted to estimate description rates in insects, taxonomic practices or taxonomists’ productivity trends over time and space.

Approach(es): Here using two novel databases on ant species taxonomy and global biogeography, I investigate 260 years of taxonomy, its evolution in practices and distribution, and compare the trends and patterns observed to other non-insect groups for which data are available.

Main group(s): Over 15,400 species of ants (Formicidae) with comparisons with vertebrates and plants.

Conclusion(s): With an average of 179 species per year since 2000, our results show that ant discovery rate is currently at its historical highest globally; but with important variations existing between biogeographic realms. Similar to other taxonomic groups, the number of active taxonomists in recent decades has strongly increased, but in contrast to vertebrate groups, this did not translate into a loss of productivity per taxonomist, contradicting previous conclusions of an erosion of new species to be discovered. Instead, our results suggest that previous conclusions did not captured a biological phenomenon but an artefact in the change of taxonomist practices over time. Finally, the biogeographic study of species discovery and taxonomic practices suggest that a major shift towards tropical regions is urgently needed.

Perspective: Our results demonstrate that recent estimates of global taxonomic completeness are underestimations and that taxonomy is more than ever needed. The study of spatial patterns of species discovery and descriptions call for an important shift of paradigm for taxonomy to fulfill its role in the modern extinction crisis.

 

 

 



 

昆虫演化:分子与化石的整合

报告人:蔡晨阳

单位:中国科学院南京地质古生物研究所;布里斯托大学

 

关键词:系统发育基因组学;模型选择;生命之树

摘要:

关键科学问题:昆虫是目前地球上生物多样性最高的动物类群,已正式描述近一百万种。昆虫的系统关系是深入了解生物进化的关键。尽管近些年在昆虫系统发育基因组领域研究取得了一系列重大进展,但许多重要支系的系统位置仍悬而未决。

主要方法:根据公开的基因组和转录组数据来推断昆虫各大支系之间的系统关系。减少数据矩阵中的噪音比例,采用位点异质混合模型(PhyloBayes软件中的CAT-GTR模型),对包含超过1400个蛋白质编码基因的氨基酸序列矩阵进行系统发育分析,得出了支持度极高的系统发生树,理清了目前争议较大类群之间的系统发育关系。

主要类群:昆虫纲

主要结论:与之前基于同质模型的系统发育研究相比,新的昆虫系统关系在很大程度上与传统的基于形态证据的系统发生以及对中生代过渡化石的解释相一致。具体而言,古翅类(包括蜻蜓目和蜉蝣目)的单系性得到确认。缺翅目是多新翅类最基干的支系,与多新翅的其他目构成姊妹群的关系。更重要的是,与昆虫化石(如二叠啮虫目和中生代巨型跳蚤)所展示的过渡性形态特征一致,证实了侧新翅类(啮虫目、缨翅目和半翅目)的单系性,啮虫目是缨翅目+半翅目的姊妹群。跳蚤(蚤目)是一类特化的长翅目昆虫,是现生南半球特有的孑遗科小蝎龄科(而不是雪蝎蛉科)的姊妹群。这项系统发育研究为昆虫演化提供了可靠的系统发育的框架,为更好地了解四亿年多来昆虫的演化历史奠定基础。

学科展望:1KITE研究团队首次提出并在时下广泛使用的昆虫系统发育基因组学方法(最大似然法,同质模型)和分子数据管理手段,很可能会得到支持极高但误解性极强的演化关系,尤其是对深部的关系而言。位点异质模型和保守的数据集很可能是系统发育基因组化时代下构建生命之树的关键。

Insect evolution: Integrating molecules and fossils

Speaker: Chenyang Cai

Affiliation: Nanjing Institute of Geology and Palaeontology, Chinese Academy of Science; University of Bristol 

Keywords: phylogenomics; model selection; tree of life

Abstract:

Key question(s): With approximately one million documented species, insects are the most speciose group of animals on Earth. The phylogenetic relationships of insects are key to understanding the evolution of life more generally. Despite significant advances in recent phylogenomic studies, the systematic positions of many major lineages remain contentious.

Approach(es): We inferred the phylogeny of insects based on published genomic and transcriptomic data. Phylogenomic analyses of filtered amino acid sequences of over 1400 protein-coding genes with a site-heterogeneous mixture model (CAT-GTR in PhyloBayes) resulted in a statistically robust tree, resolving controversial phylogenetic relationships. 

Main group(s): Insecta

Conclusion(s): In contrast with a previous phylogenomic study based on the same data but with a site-homogeneous model, our novel phylogeny of insects is largely congruent with conventional morphology-based phylogenies and the interpretations based on transitional fossils from the Mesozoic. In particular, the monophyly of Palaeoptera (Ephemeroptera + Odonata) is strongly supported, and Zoraptera (angel insects) is the basal-most lineage within the monophyletic Polyneoptera, a group that comprises earwigs, stoneflies, grasshoppers, crickets, katydids, cockroaches and their allies. More importantly, consistent with what transitional fossils such as Permopsocida and Mesozoic stem-group fleas demonstrate, the monophyly of Acercaria (true bugs, thrips, bark lice and true lice) is strongly supported, with Psocodea being the basal-most lineage. Fleas (Siphonaptera) are nested within Mecoptera (scorpionflies), sister to the relictual Southern Hemisphere endemic family Nannochoristidae. The new phylogenomic study provides a reliable backbone phylogeny for better understanding evolutionary innovations among insects over about 400 million years.

Perspective: The current prevalent approaches (maximum likelihood, site-homogeneous model) and data curation in insect phylogenomics as proposed by the 1KITE group may result in strongly supported but misleading topologies, especially for deeper nodes. The site-heterogeneous CAT model and conservative datasets may hold the key to the Tree of Life in the phylogenomic era.

反刍动物系统发育和适应性进化

报告人:陈垒

单位:西北工业大学

 

关键词:反刍动物;系统发育;适应性进化

摘要:反刍动物是大型陆地哺乳动物中最成功的一类,具有非常丰富的生物多样性特征,能够适应多样化的生存环境,并演化出极为特殊的生物性状和新器官。然而,反刍动物的系统发育关系存在诸多争议,其独特的进化特征也未得到进一步解析。我们通过大规模组装和比较反刍动物的基因组,对反刍动物的系统发育和适应性进化的遗传机制进行了深入分析。这项研究对于认识反刍动物演化和适应机制,以及未来在医学和畜牧学领域的应用具有重要意义。

关键科学问题:反刍动物的系统发育关系和进化历史;反刍动物独特性状背后的遗传机制

主要方法:结合了谱系基因组、进化和比较基因组、转录组分析方法和功能实验

主要类群:反刍亚目

主要结论:厘清了关于反刍动物在各级分类水平上的长久争议,推断了反刍动物分歧时间和群体变化动态历史;对反刍动物一些特殊性状演化的遗传机制进行了探讨

学科展望:采用大尺度、跨物种、多组学大数据分析与实验的研究思路和手段,探索开拓了研究重大生命现象的新思路、新方法;产生的大量宝贵数据,将为未来反刍动物,乃至哺乳动物和人类健康的研究提供珍贵的数据和参考。


 

The phylogeny and evolution of ruminants

Speaker: Lei Chen

Affiliation: Northwestern Polytechnical University

Keywords: Ruminants; Phylogenomics; Adaptive evolution

Abstract: The ruminants are one of the most successful mammalian lineages, exhibiting high morphological and habitat diversities. However, the phylogenetic relationship of ruminants is controversial and their unique evolutionary characteristics require further analysis. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time calibrated phylogeny to resolve topological controversies, and also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants. This study is of great significance for understanding the formation, evolution, distribution pattern and adaptation mechanism of ruminant diversity, as well as its future application in the fields of medicine and animal husbandry.

Key question(s): Phylogenetic relationship and evolutionary history of ruminants; Genetic mechanism of Ruminants distinct traits

Approach(es): Combination of phylogenomics, evolutionary and comparative genomics, transcriptome analysis methods and functional experiments.

Main group(s): Ruminantia

Conclusion(s): We created a time calibrated phylogeny to resolve topological controversies of ruminants. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expanding human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

Perspective: The large amount of data produced will provide valuable data and references for future research on ruminants, mammals and human health.

生命之树是二歧、多歧还是网状的?

报告人:陈之端

单位:中国科学院植物研究所

 

关键词命之树;水平基因转移;古杂交;杂交(渐渗);网状进化;林奈阶层系统

摘要:

关键科学问题水平基因转移、谱系筛选、基因重复或丢失、杂交(包括杂交渐渗)在陆地植物中是普遍存在的,采用与这些演化事件相关的基因建树会导致基因树之间以及基因树与物种树之间的不一致,因此,植物的系统发生和物种形成过程用二叉分支的生命之树是不能完全解释的。

主要方法:利用叶绿体基因组、线粒体基因组、核基因组、转录组和群体数据识别各种演化事件。

主要类群:角苔(水平基因转移),蔷薇类COM分支(古杂交和谱系筛选),葡萄科爬山虎属(杂交和杂交渐渗)。

主要结论:在角苔基因组中,识别出几十个从细菌或真菌中水平转移来的基因,推测陆地植物的祖先或早期陆地植物通过吞噬和其他途径从细菌中招募了一些有用基因,帮助其适应陆地生活环境。蔷薇类占所有被子植物物种的四分之一以上,包括豆类、锦葵类和COM分支三个大支,通过分析叶绿体、核和线粒体基因组数据,发现COM分支是由豆类和锦葵类的祖先经过古杂交和谱系筛选形成的。爬山虎属的三叶系包括四个种,主要分布在横断山区和喜马拉雅地区,其中有两个种是通过杂交和杂交渐渗形成的。以上举例说明:生命之树不都是简单的二歧分支,系统发生和物种形成过程通过杂交等演化事件而变得异常复杂,这些可以导致网状进化的事件发生在陆地植物各个分类阶元水平(门、纲、目、科、属、种)。

学科展望:在基因组时代,分类学数据越来越丰富,可以揭示具有网状进化的分类群的复杂演化历史,那么有两个问题值得思考:1)有没有更好的分类系统可以取代林奈阶层系统呢?2)如何利用基因组数据做分类,分类学作为实践性和经验性学科,是否是数据越多越好呢?


 

 


 

细菌分离技术探索及富集分离方法的应用

报告人:杜宗军

单位:山东大学微生物技术国家重点实验室、山东大学海洋学院

 

关键词:海洋细菌;分离技术;富集培养

摘要:利用经典的涂布平板法开展了威海近海海藻表面附生细菌的分离培养,通过2次采样从7个海藻样品分离出2030株细菌,经过16S rDNA测序及序列分析,发现这些菌株分布在723个物种,并发现358个潜在新物种,其中62个是潜在新属新种。总结本次海藻附生细菌的分离工作,得出以下几点结论:1、常规分离方法仍然能分离到大量细菌新物种;2、培养组学是细菌资源挖掘的有力手段;3、现有细菌分离方法需要改进,可行的措施包括降低有机物浓度,用结冷胶代替琼脂作为凝固剂,添加丙酮酸钠、乙酸钠等小分子有机物,添加生长因子如小分子有机酸(γ-氨基丁酸)、醌、细菌培养液等。

从威海近海采集潮间带沉积物样品,进行无氧富集培养,然后分别在有氧和无氧条件下利用涂布平板法进行细菌分离工作。有氧条件下共分离得到海洋细菌1251株,测序分析后发现其中有282个物种,包括潜在的新种97个,其中有1个新目,1个新科和16个新属;无氧条件下分离到海洋细菌650株,包括潜在新菌70余个,其中包括拟杆菌门、绿菌门、浮霉菌门、螺旋体门、互营菌门的深度分支。利用这个方法分离得到大量拟杆菌纲海洋滑动菌目的新菌,探究分离到的海洋滑动菌在富集培养过程中的丰度变化,推测部分物种是由于生理状态的改变(复苏)从而导致被分离出来。验证了富集培养可以促进VBNC状态细菌的复苏。同时,本实验设计的富集培养是一个复杂的混菌培养过程,微生物之间存在复杂的相互作用,分析了富集培养过程中海洋滑动菌与其他类群的共现关系,并初步解析了其可能的互作机制。总起来讲:1、本实验建立了高效的富集培养技术,该技术在分离培养微生物时具有很大应用潜力;2、该培养技术在培养微生物时不仅通过富集提高部分微生物丰度,还可通过复苏机制改变部分微生物的生理状态,使其容易被分离出来;3、富集培养是一种复杂的混菌培养过程,其中包含微生物间的竞争与协作,该技术有望发展成为一种模型来研究混菌培养及探索微生物暗物质。

 

 

 

 

 



 

被子植物及菊支基部分支的演化历史与多样化格局

报告人:高连明

单位:中国科学院昆明植物研究所

 

关键词:被子植物;起源与演化;系统发育基因组学;多样化历史;侏罗纪空缺

摘要:被子植物早期演化历史被认为是达尔文之谜。我们选择被子植物全部64目和85%现存科的2351种为研究对象,利用质体基因组的80个基因重建了被子植物高分辨率的系统发育树,并基于62个化石校准点估算了被子植物科级以上主要分支的分化时间。研究表明,被子植物起源于三叠纪晚期,明显早于确切的被子植物冠群最早化石年龄,首次提出被子植物化石记录与分子钟推算时间之间的侏罗纪空缺(Jurassic gap。核心被子植物五大分支之间的关系仍然没有完全解析,暗示在被子植物早期分化阶段发生了辐射分化,可能伴随着一定规模的灭绝事件。被子植物的兴起、分化并逐渐取代裸子植物在陆表植物中占据主导地位,可能与地质历史气候变化,昆虫和哺乳动物等类群的多样化过程协同演化有关。此外,我们对菊支基部类群山茱萸目和杜鹃花目的时空演化历史与多样化格局进行了对比研究,发现两个类群均起源于白垩纪并且在分化早期发生过辐射演化,但它们经历的多样化过程不同,导致两个目现今的多样性格局。本研究为今后有花植物系统演化历史相关研究提供了一个重要的框架。

关键科学问题:被子植物起源与早期快速演化是如何发生的?菊支基部两个分支的演化历史与多样化格局是否存在差异?

主要方法:系统发育重建、分化时间估算、多样化速率推断、生物地理分析

主要类群:被子植物、山茱萸目、杜鹃花目

主要结论:被子植物起源于三叠纪晚期,在早期分化阶段发生了辐射分化,可能伴随着一定规模的灭绝事件;核心被子植物五大分支之间的关系没有完全得到解析。山茱萸目和杜鹃花目均起源于白垩纪中-晚期,并经历过辐射演化,山茱萸目多样化速率随时间变化逐渐下降,而杜鹃花目整体多样化速率随时间变化有两个增高的时期。

学科展望:综合多基因组来源的组学数据,利用多重数据处理与分析方法,整合时空演化格局、地质历史事件,多类群多样化历史、生态环境与过程和基因组进化等多学科证据是解析生物演化历史与多样化格局成因的钥匙。

Transposable elements and loss-of-function mutations contribute to adaptation

Speaker: Ya-Long Guo

Affiliation: Institute of Botany, Chinese Academy of Sciences

Keywords: adaptive evolution; climate change; genetic diversity; loss-of-function mutations; natural selection; population genetics; transposable elements

Abstract: Genetic variation is the fuel for adaptive evolution. Despite rapid progress in the understanding of diverse genetic variation dynamics, what roles transposable elements (TEs) insertions and loss-of-function mutations play in the process of adaptive evolution, are largely unknown. For a long time, TEs have been regarded as junk DNA, and loss-of-function mutations (gene loss) was nearly ignored compared to gene duplication (gene gain). Based on genomics and genetics analyses using Arabidopsis and its relatives, we revealed that TEs and loss-of-function mutations play important roles in the process of adaptive evolution. Overall, our results highlight that both TE insertions and loss-of-function mutations can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.


 

 


 

分子化石阐明逆转录类病毒的远古史和宏进化

报告人:韩管助

单位:南京师范大学

 

关键词:逆转录类病毒;转座元件;系统发生分析

摘要:

关键科学问题:逆转录类病毒是如何起源和进化的?

主要方法:全基因组挖掘内源性病毒元件以及系统发生分析

主要类群:逆转录类病毒

主要结论:内源性逆转录病毒在脊椎动物基因组中广泛分布,逆转录病毒起源于远古鱼类。内源性植物拟逆转录病毒在真叶植物中基因组中广泛分布,植物拟逆转录病毒起源于远古真叶植物。昆虫的HEART转座元件是目前已知的动物拟逆转录病毒(嗜肝病毒)的最近非病毒亲属

学科展望:系统挖掘真核生物内源性逆转录类病毒以及转座元件会为逆转录类病毒的起源和进化以及真核生物基因组复杂性的进化提供新的视角。

 

 


 

Molecular fossils illuminate the deep history and macroevolution of reverse-transcribing viruses

Speaker: Guan-Zhu Han

Affiliation: Nanjing Normal University

Keywords: Reverse-transcribing viruses; transposable elements; phylogenetics

Abstract:

Key question(s): How did reverse-transcribing viruses originate and evolve?

Approach(es): Genome-wide mining of endogenous viral elements and phylogenetic analysis

Main group(s): Reverse-transcribing viruses

Conclusion(s): Endogenous retroviruses are ubiquitous within vertebrate genomes, indicating an ancient aquatic origin of retroviruses. Endogenous plant pararetroviruses are widespread within the euphyllophyte genomes, and plant pararetroviruses originated in ancient euphyllophytes. Insect HEART retroelements represent the closest non-viral relatives of animal pararetroviruses (hepadnaviruses).

Perspective: Systematic mining of endogenous reverse-transcribing viruses and transposable elements within the eukaryote genomes might provide novel insights into the origin and evolution of reverse-transcribing viruses and the evolution of genome complexity in eukaryotes.

 


鱼类学的传承与创新:鱼类多样性历史的系统发育重建

报告人:何舜平

单位:中国科学院水生生物研究所

 

 

 



 

小熊猫保护基因组学研究

报告人:胡义波

单位:中国科学院动物研究所


 


 

蝙蝠感官信号的特征和功能

报告人:江廷磊

单位:东北师范大学

 

关键词:蝙蝠;回声定位;通讯叫声;协同进化;捕食

摘要:蝙蝠是唯一真正会飞的哺乳动物,主要依赖回声定位和通讯叫声在黑暗的环境中活动,在生态系统中具有重要的价值。然而,人们对其声信号的特征和适应性功能仍知之甚少,不利于将来蝙蝠物种多样性保护。我们以蝙蝠为研究对象,通过整合声学、行为学、生态学、生理学和分子生物学等学科理论和方法,取得了以下学术成果:揭示了蝙蝠通讯叫声是诚实的激进意图信号,且具有种间识别功能;发现蝙蝠改变声信号强度和复杂性来应对环境噪声干扰,首次证实回声定位蝙蝠存在隆巴德效应;阐明了蝙蝠捕食鸟类的行为策略及其感官线索,首次揭示了相应的感官机制。研究在蝙蝠感官生态学领域取得创新性成果,并对蝙蝠物种多样性保护提供科学依据。

关键科学问题:蝙蝠声信号的功能

主要方法:声学、行为学和生态学方法

主要类群:翼手目动物

主要结论:蝙蝠声信号能传递多种信息和具有高度可塑性,并在其社群稳定、捕食和应对环境变化方面具有重要作用

学科展望:在增加蝙蝠行为生态学方面的知识具有一定贡献

 

 

 

 

 

 

 

 

 


 

The characteristics and function of sensory signals in bats

Speaker: Ting-Lei Jiang

Affiliation: Northeast Normal University

Keywords: bats; echolocation; social calls; co-evolution; predation

Abstract: Bats are the only mammals naturally capable of true and sustained flight. They mainly rely on echolocation and social calls to operate in the dark, and play an important role in ecosystems. However, so far, little is known about the characteristics and functions of acoustic signals in bats, though it be useful for conserving bat species diversity. We selected bats to investigate the function of acoustic signals by integrating the theories and methods of acoustics, ethology, ecology, physiology and molecular biology, achieving the following significant findings. Social calls are honest signals of aggressive intent in female Asian particoloured bats, and play an important role in recognition of heterospecific distress calls. Moreover, we found bats changed the amplitude and complexity of acoustic signals to cope with the interference of ambient noise, and confirmed for the first time the Lombard effect in echolocating bats. We have illuminated the behavioral strategies and sensory cues of bats for hunting on birds, and for the first time revealed relevant sensory mechanisms. The studies have made innovations in bat sensory ecology, thus providing a scientific basis for their conservation from the aspects of acoustics and behaviour.

Key question(s): The function of acoustic signals in bats

Approach(es): Acoustics, ethology, ecology

Main group(s): Bats

Conclusion(s): Acoustic signals of bats convey a lot of information and have relatively high plasticity, playing an important role in community stability, foraging and responses to environment changes. 

Perspective: To some extent, the results make an important contribution to our knowledge about behavioral ecology in bats.

 


 

基于跨物种靶基因富集技术的鲱形目系统发育基因组学研究

报告人:李晨虹

单位:上海海洋大学

关键词:鲱形目;靶基因富集;系统发育基因组学

摘要:

关键科学问题:最近关于鲱形目形态学和分子系统学的研究提出了很多新的观点,有些结果是一致的,但很多方面还存在矛盾。本研究的目的是通过系统发育基因组学研究解决鲱形目的分类和系统进化关系,评估各种系统误差对研究结果的影响,检验相关假设,如:脂眼鲱(Etrumeus)和圆腹鲱(Dussumieria)是否为姐妹类群;小沙丁鱼属(Sardinella)是否为单系;锯腹鳓科(Pristigasteridae)是否为所有鲱形目物种的姐妹群等等。

主要方法:样本包括62个鲱形目物种和7个外群;应用跨物种基因富集的方法获得4 434个单拷贝核基因位点的序列;采用连接树、物种树的方法分析结果,并研究各种系统误差对结果造成的影响。

主要类群:鲱形目(辐鳍鱼亚纲)

主要结论:鳀科(Engraulidae)是除了银带鲱属(Spratelloides)和任氏鲱属(Jenkinsia)的鲱亚目的姐妹群;脂眼鲱(Etrumeus)和圆腹鲱(Dussumieria)不是姐妹群;锯腹鳓科(Pristigasteridae)不是除齿鲱(Denticeps)外的最原始类群;锯腹鳓属(Pristigaster)是锯腹鳓科其它物种的姐妹群,支持将锯腹鳓科分成锯腹鳓亚科(Pristigasterinae)和多齿鳓亚科(Pelloninae);鳓属(Ilisha)不是单系;沙丁鱼属(Sardinella)也不是单系。

学科展望:需要基因分子、形态和化石数据提出一个更合理的鲱形目分类系统。


 

Resolving the phylogenetic interrelationships among the clupeiforms using cross-species target-gene enrichment

Speaker: Chen-Hong Li

Affiliation: Shanghai Ocean University

Keywords: Clupeiformestarget-gene enrichmentphylogenomics

Abstract:

Key question(s): New evidence and hypotheses about clupeiform phylogeny based on morphological data and from molecular analyses revealed many patterns, some confirmed by both morphological and molecular studies, but many are still controversial. The goal of this study is to resolve the relationships of the Clupeiformes using phylogenomic data, to assess the different hypotheses and to resolve the conflicts, e.g. whether Etrumeus and Dussumieria are sister-groups; Sardinella is monophyletic or not; whether Pristigasteridae is sister-group to all remaining clupeiforms, etc. The other objective is to assess whether systematic errors, i.e., GC bias, affected results.

Approach(es): Sampling: 62 Clupeiformes species of 5 families, including 38 samples from the Clupeidae; 8 species from the Pristigasteridae; 14 Engraulidae; 1 Denticepitidae and 1 Chrocentridae, 7 species were used as outgroups. Data collection: cross-species gene capture was applied to collect sequence data from 4,434 single-copy nuclear loci. Analysis: concatenated analyses and specie tree analyses were enacted, with different approaches to examine the effects of systematic errors.

Main group(s): The Clupeiformes (Actinopterygii)

Conclusion(s): Engraulidae (s.l.) are sister-group to the remaining Clupoidei (i.e. Spratelloides and Jenkinsia would jump one node higher); Etrumeus and Dussumieria are sister-groups (both share a unique scute-type); Pristigasteridae is not sister-group to all remaining clupeiforms (except Denticeps). Pristigaster is sister to all other Pristigasteridae, reflecting the present division in two subfamilies Pristigasterinae and Pelloninae; Ilisha is not monophyletic; Sardinella is not monophyletic.

Perspective: A new classification of the Clupeiformes should be formulated with molecules, morphology and fossil evidence.


 

副新翅类昆虫线粒体基因组及其在进化研究中的应用

报告人:李虎

单位:中国农业大学

 

关键词:副新翅类昆虫;线粒体基因组;基因组裂化;系统发育

摘要:副新翅类是不完全变态类昆虫的最大类群,包括啮虫目、虱目、缨翅目及半翅目4个目,不少种类是重要的农林和卫生害虫、天敌以及资源昆虫,在农林业生产和人类日常生活中起着重要作用。其形态多样,习性复杂,高级阶元的系统发育关系至今仍存在不同的观点。副新翅类昆虫线粒体基因组还是昆虫中最为独特的,部分类群具有高度的基因重排和线粒体基因组的裂化现象,是研究昆虫线粒体基因组进化的重要类群。近几年,我们通过利用比较基因组学、系统发育基因组学、整合分类学等研究方法,从线粒体基因组数据层面为副新翅类昆虫中各类群高级阶元间的系统发育关系提供了重要的证据;并以物种系统进化关系为基础,重点研究了半翅目昆虫物种多样性形成机制以及副新翅类昆虫线粒体基因组结构的多样性与进化规律,特别是线粒体基因组裂化和基因重排的进化,发现部分寄生虱线粒体基因组的裂化现象可能与其寄生习性进化过程中的宿主选择有关,为深入研究昆虫线粒体基因组裂化的形成机制提供了新的思路。

关键科学问题:副新翅类昆虫高级阶元间的进化关系及其线粒体基因组的进化规律

主要方法:高通量测序、比较线粒体基因组学、进化树重建、进化分歧时间推算、原始特征重建

主要类群:副新翅类昆虫(啮虫总目、半翅目、缨翅目)

主要结论:1)利用基于贝叶斯混合异质性模型的进化树构建方法,能够较为有效地降低由于线粒体基因组数据异质性导致的系统偏好性,较好地解析了副新翅类昆虫中各类群高级阶元间的系统发育关系;2)利用线粒体基因组数据,解析了半翅目高级阶元间的系统进化关系,揭示了关键特征的适应性进化有利于异翅亚目昆虫不同食性的多次独立转换以及占据水生环境的多次演化,促进了其物种多样性的分化;3)首次在虱目兽羽虱科发现了线粒体基因组的裂化现象,并综合线粒体基因组结构、DNA序列、宿主等多方面的证据,肯定了真兽类哺乳动物的寄生虱(兽羽虱科、象虱亚目、吸虱亚目)为一单系群,而线粒体基因组的裂化很可能与寄生虱进化过程中的宿主选择有关。

学科展望:随着高通量测序方法的快速发展,昆虫线粒体基因组的获取效率显著提升,测序成本越来越低,并且对样品标本质量的要求远没有转录组或基因组测序那么高。线粒体基因组数据在基于大尺度物种取样的进化研究中可操作性更强,未来将在系统发育、物种形成、种群遗传、食物网重建以及生物多样性监测等研究领域发挥重要作用。此外,部分副新翅类昆虫线粒体基因组存在高度的基因重排和基因组裂化,是研究昆虫线粒体基因组进化的理想类群。但目前的研究多是基于小规模物种取样的比较线粒体基因组学研究,缺乏相关功能研究的基础,由此得出的结论往往存在局限性,相关进化机理尚待深入探究。未来也应在较完善的物种系统进化框架下,结合多组学和相关基因功能的研究,重点研究副新翅类昆虫线粒体基因组加速进化的功能适应机制。

 


 

Mitochondrial genome of paraneopteran insects and its application in evolutionary studies

Speaker: Li Hu

Affiliation: China Agricultural University

Keywords: paraneopteran insects; mitochondrial genome; genome fragmentation; phylogenetics

Abstract: Paraneoptera, which comprise orders Psocoptera, Phthiraptera, Thysanoptera and Hemiptera, is the largest superorder of insects with incomplete metamorphism. Many lineages of this superorder are of great economic and cultural significance, affecting human life through agriculture, public health and environments. To date, phylogenetic relationships within Paraneoptera remain controversial, with debates arising primarily on the relationships among higher taxa. Compared to other hexapod lineages, paraneopteran insects possess a mitochondrial genome with remarkably high level of gene rearrangement and fragmentation, making them an ideal model to study mitochondrial genome evolution. In recent years, by using methods of comparative genomics, phylogenomics and integrative taxonomy and mitochondrial genomic data, we provide important evidence for the higher-level relationships among paraneopteran insects. With a robust phylogeny, we then explored mechanisms underlying species diversification in Hemiptera, and examined possible drivers of fragmentation and gene rearrangement in the paraneopteran mitochondrial genome. Data from parasitic lice suggests that genome fragmentation is likely to be associated with host switch events during paraneopteran lineage diversification. Our study thus brings new insights into mechanisms driving insect mitochondrial evolution and raises new hypotheses regarding insect mitochondrial genome fragmentation that merit future examination.

Key question(s): the higher-level phylogeny and the evolution of mitochondrial genome of paraneopteran insects.

Approach(es): next-generation sequencing, comparative genomics, reconstruction of phylogenetic trees, divergence time estimation and ancestral character state reconstruction.

Main group(s): Paraneopteran insects (Psocodea, Thysanoptera, Hemiptera)

Conclusion(s): 1) Compared to other models, Bayesian inference with site-heterogeneous mixture models are better at resolving the higher-level Paraneoptera phylogeny by effectively reducing the effect of systematic bias caused by the compositional heterogeneity of mitochondrial genome sequences; 2) Using mitochondrial genome sequences, we obtained a high resolution phylogeny among higher hemipteran taxa and reveal some key morphological innovations that have facilitated multiple independent shifts among diverse feeding habits and multiple independent colonizations of aquatic habitats, which have driven the diversification of heteropteran and hemipteran insects; 3) We discovered mitochondrial genome fragmentation in Trichodectidae (Phthiraptera: Ischnocera) for the first time. Combining evidences from mitochondrial genome structure, DNA sequences and hosts strongly support a novel clade of the eutherian mammal lice (Trichodectidae+ (Anoplura + Rhynchophthirina)), and suggest a link between mt genome fragmentation and the host switch from birds to mammals in parasitic lice.

Perspective: New high-throughput sequencing techniques have enabled rapid and low-cost sequencing of large sets of mitochondrial genomes. Compared to transcriptome or genome analysis, the sample size and quality required for mitochondrial sequencing can be much lower. These make mitochondrial genome better suited for evolutionary studies that involve large-scale taxon sampling, including but not limited to phylogenetics, speciation, population genetics, food web reconstruction, and biodiversity monitoring. Furthermore, high levels of gene rearrangement and genome fragmentation of paraneopteran mitochondrial genomes make them an ideal model for the study of mitochondrial genome evolution in insects. Nevertheless, our understanding of insect mitochondrial genome evolution is impeded by several factors, such as a lack of comprehensive taxon sampling and functional studies. With a more robust and comprehensive phylogenetic framework, future studies that integrate multi-omic and functional genomic data would allow a deeper understanding of mechanisms driving accelerated evolution of paraneopteran mitochondrial genomes.

 

 


 

Asgard古菌与生命之树

报告人:李猛

单位:深圳大学高等研究院

 

关键词:生命之树;Asgard古菌;系统发育

摘要:核生物的起源是决定地球生命进化树基本形态的关键,也是生物学界亟待解决的焦点问题。阿斯加德(Asgard)古菌是近年新发现的古菌超门,包括洛基古菌(Lokiarchaeota)、索尔古菌(Thorarchaeota)、奥丁古菌(Odinarchaeota)、海姆达尔古菌(Heimdallarchaeota)和海拉古菌(Helarchaeota)等。由于Asgard古菌基因组中含有大量与真核生物相似的功能基因,且在系统发育树中与真核生物聚在同一分支,被认为是真核生物的祖先,这由此引发了科学界的广泛关注,并迅速成为研究热点。本研究将介绍Asgard古菌的相关研究进展,着重讨论Asgard古菌和真核生物起源之间的关系,进一步阐明Asgard古菌在生命之树的特殊位置。

关键科学问题:真核生物起源与Asgard古菌的关系

主要方法:系统发育分析,16S/18S rRNA genes, Ribosomal proteins

主要类群:Asgard 古菌,真核生物

主要结论:真核生物极有可能起源于Asgard古菌。

学科展望:生命之树的二域论和三域论的争论被再次激发,Asgard古菌的发现撼动了地球生命之树,三域论或将被二域论战胜。

 

 

 

 

 

 

 


 

 


 

中国食用菌多样性及其对全球产业的贡献

报告人:李泰辉

单位:广东省微生物研究所

 


 


 

Systems biology study of entomology - butterflies and fireflies as models

报告人:李学燕

单位:中国科学院昆明动物研究所

 

关键词:系统生物学(Systems Biology);多次数据整合;昆虫学;蝴蝶;发光甲虫

摘要:

关键科学问题:昆虫学是生命科学中历史悠久引人入胜的重要学科。纵观中西方昆虫学史,昆虫学的发展方兴未艾;但横比生物学各学科,它的发展尚未站上时代前沿。近年来兴起的系统生物学(Systems Biology)试图跳出传统还原论和学科过于细化分隔的藩篱,从整体论、多层次理解生命现象。鉴于纷繁复杂的昆虫世界,我们以昆虫分类作为基础,近年来一直循着系统生物学的思路,以具有特殊表型特征的萤火虫(生物荧光)和蝴蝶(形态多样性)等昆虫为起始对象,探讨昆虫的一些重要生命现象,试图在厘清昆虫系统发育关系的同时,解决重要的昆虫学生物学问题。

主要方法:以分类学为基础,综合形态学、基因组学、转录组和ATAC-seq组、蛋白组、CRISPR/Cas9基因编辑功能验证和细胞实验验证等系统生物学(Systems Biology)的研究思路和方法。

主要类群:以具有特殊表型特征的萤火虫(生物荧光)和蝴蝶(形态多样性)等昆虫为起始对象。

要结论:介绍近我们近期在昆虫学的系统生物学(Systems Biology)研究框架下的一些进展。

以蝴蝶为例,为了探讨形态多样性的遗传分子机制,自2010年开始发展蝴蝶为作为研究模式。我们在2015年完成所有蝴蝶模式种金凤蝶及其近缘种柑橘凤蝶两种凤蝶基因组和以蝴蝶为例成功实现野生昆虫基因编辑(Li et al., 2015, Nature Communications),建立蝴蝶作为研究模式的基础上,一方面继续以这两种为模式通过基因编辑方法探讨基因对形态的影响(Li et al., 2017, Insect Science; Liu et al, in preparation),另一方面于2017年启动了蝴蝶系谱基因组计划,旨在系统发育框架下获得一些具有重要表型特征的代表种类的高质量基因组并进一步探讨表型特征进化的分子遗传机制。为此,我们测定了667种蝴蝶的C值并组装了他们的线粒体基因组,结合已知的线粒体基因组和基因组大小的数据,探讨了蝴蝶基因组大小的系统进化(Liu et al., Systematic Entomology已修回);在此基础上,我们获得了近50种蝴蝶的基高质量的全基因组;其中两种已获得色体水平的参考基因组(Lu et al., 2019, GigaScience; Yang et al., submitted);同时,我们对其中一些物种的重要发育阶段进行了ATAC测序(Wan et al., In preparation)。

以萤火虫等发光甲虫研究为例,为了探讨生物荧光的起源与进化,我们自2002年开始以萤火虫等发光甲虫为研究对象,一直循着物种分类和系统发育、发光基因和发光的分子体系展开相关的研究。最近,我们发现了亚洲首例发光叩甲,组装了其线粒体基因组,综合分子和形态数据确立该种作为叩甲科的一个新亚科新属新种(He et al., 2019, Mitochondrial DNA-B; Bi et al., 2019, Zookeys),为甲虫生物荧光的多次起源提供了重要的证据;通过综合形态和分子数据,我们对分布于喜马拉雅及邻近区域的扁萤属(Lamprigera)进行了研究,发现3个新种(Dong et al., submitted);利用线粒体基因组数据和核基因标记,我们探讨了亚洲1523种萤火虫的系统发育关系(Chen et al., 2019, MPE);为了探讨发生物荧光进化,我们克隆了中国分布的一些萤火虫物种的荧光酶基因并分析了酶学特征(Liu et al., Photochem Photobiol., 2019; Liu et al., Photochem Photobiol., 2019; Liu et al., in preparation);为了从组水平探讨生物荧光起源与进化,我们测定了14种萤火虫的C值和探讨了基因大小进化(Liu et al., 2017, Zoological Research),在此基础上,组装了基中部分种类的高质理基因组,并对生物荧光的起源进行了挖掘(Zhang et al., in preparation)。

学科展望:利用系统生物学(Systems Biology)的方法和思路进行昆虫学研究,整合从形态到组学到功能验证多层次数据,把昆虫学研究提升到现代系统生物学的前沿水平,探索开拓现代昆虫学研究的新范式。

 


 

Systems biology study of entomology -butterflies and fireflies as models 

Speaker: Xueyan Li

Affiliation: Kunming Institute of Zoology, Chinese Academy of Sciences

Keywords: Systems BiologyIntegration of multi-level dataEntomologyButterflies; Fireflies

Abstract:

Key question(s): Entomology is an important and fascinating field with a long history in life science. To review the history of Entomology in China and the West, we might perceive great progress in Entomology. Compared with other branches in life science, however, it still falls behind, showing a big imbalance with the diversity of insects, their ecological significance and economic value to human life and production. In recent decades, our knowledge of the foundation of living organisms in terms of various components of cells, tissues and organ systems has been greatly expanded due to advances in technologies for high-throughput genomics, transcriptomics, proteomics and metabolomics. The availability of such multiscale information has catalyzed the formation of Systems Biology as a discipline in biomedical sciences. Systems Biology is an integrative discipline connecting the molecular components within a single biological scale and also among different scales (e.g. cells, tissues and organ systems) to physiological functions and organismal phenotypes through quantitative reasoning, computational models and high-throughput experimental technologies. With the background of insect taxonomic work, we are now using butterflies and fireflies as models to clarify diverse intriguing scientific issues in Entomology in the context of phylogeny, following the principles and methodology of Systems Biology. 

Approach(es): we are constructing a Systems Biology methodology and platform by integrating multi-level data from morphology, taxonomy and phylogeny, multi-omics, to gene function experiments (gene editing, cell level, etc.), which is helpful to explore intriguing and long-standing questions in Entomology and also in Evolutionary Biology.

Main group(s): We used butterflies (with morphological diversity) and fireflies (with bioluminescence) as pilot models.

Conclusion(s): Here, we introduce some progress on butterfly and firefly researches based on principles of Systems Biology.

Butterflies are a promising system to explore the genetics, evolution, and development of morphological diversification and speciation because of their extraordinarily diverse wing patterns and also other diverse traits in virtually all aspects of their biology. To develop butterfly as a model for exploring the genetic and molecular architecture underling morphological evolution, we focused on butterflies since 2010. We dissected the reference genomes of two butterflies, i.e. Papilio machaon (as type species for all butterflies by Linnaeus in his System Nature) and its close relative P. xuthus, two highly heterozygous species that differ in host plant affiliations, and adult and larval color patterns, and for this first time, developed an efficient CRISPR/Cas9 gene editing method in butterflies, providing valuable genomic and technological resources for butterflies and unlocking their potential as a genetic model system (Li et al., 2015, Nature Communications). With this platform, we investigated the function of Abd-B gene in P. machaon (Li et al., 2017Insect Science) and the function of some pigment-related genes in P. xuthus (Liu et al., In preparation). We also continue to explore genome evolution in a phylogenetic context. Firstly, we explore genome size evolution of butterflies in a newly inferred mitogenomic phylogeny by measuring genome C-value using Flow cytometry (Liu et al., Systematic Entomology, Revised); then, we selected about 50 species to sequencing the genomes of using Pacbio technology; based on third-generation DNA sequencing and Hi-C analysis, we have finished two chromosomal-level genome assemblies of the Chinese peacock butterfly (Papilionidae: Papilio bianor), an ideal model to explore population subdivision and the origin of combined (pigmentary and structural) wing color (Lu et al., 2019, GigaScience), and of the dead leaf butterfly (Nymphalidae, Kallima inachus), commonly cited example of protective resemblance of organisms (i.e. masquerade)Yang et al., submitted; we also finished ATAC-seq of some developmental stages for some important butterfly species (Wan et al., In preparation). Our data provide not only key insights into genome characteristics of butterflies and but also an important datasource for the butterfly community. 

Bioluminescence is a particularly intriguing phenomenon which evolved independently many times in various organisms, and its origin and evolution has fascinated biologists since Charles Darwin. Fireflies (Lampyridae) and other luminous beetles (Rhagophthalmidae, Phengodidae and some Elateridae), all in the superfamily Elateroidea, are one of the best-known luminescent organisms since Aristotle, and are thus an important subject of scientific studies, especially related to their bioluminescent behavior and biochemistry. Also attracted by bioluminescence of fireflies (and other luminous beetles), we have studied luminous beetles since 2002, from originally focusing on their basic taxonomy and phylogeny, luciferase, to bioluminescence origin and evolution by multi-omics data. We discovered the first record of a luminous click-beetle in Asia and provided important evidence for the multiple origin of bioluminescence in Elateridae (He et al., 2019, Mitochondrial DNA-B; Bi et al., 2019, Zookeys). We found a rich species diversity in China for such Asia-distributing genera asLamprigera (Dong et al., submitted). We sequenced the mitogenomes of 23 Asian fireflies in 15 genera, and explored their phylogenetic relationship with emphasis on those subfamilies and genera in Lampyridae (Chen et al., 2019, Molecular Phylogeny and Evolution).We also cloned luciferase from some important Chinese fireflies and investigated their enzymatic charisteristics (Liu et al., Photochem Photobiol., 2019; Liu et al., Photochem Photobiol., 2019; Liu et al., in preparation). We also explored genome size variation of different Chinese firefly genera by measuring their C-value (Liu et al., 2017, Zoological Research, and further finished the reference genome assembly of two representative fireflies with different light signal pattern (glow or flash signal) and different morphology and the structure of their luminous organs (Zhang et al., in preparation). All these data provide important insights into the phylogeny if luminous beetles and the origin and evolution of their bioluminescence.

Perspective: With butterflies and fireflies as models, our ultimate objective is to provide a valuable paradigm of Systems Biology study in Entomology.

分化时间在真菌系统学研究中的应用

报告人:刘建魁

单位:电子科技大学生命科学与技术学院

 

关键词:子囊菌;系统学;分化时间;座囊菌纲;分类学

摘要:

The current classification system of fungi, especially at high-ranking levels, is subjective. With the development of molecular approaches and the availability of fossil calibration data, the use of divergence times as a universally standardized criterion for ranking taxa has now become possible. We can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of Dothideomycetes. We chose Dothideomycetes, the largest class of the phylum Ascomycota, which contains 32 orders, to establish ages at which points orders have split; and Pleosporales, the largest order of Dothideomycetes contains 55 families, to establish family divergence times. Our results indicate that divergence times (crown age) for most orders (20 out of 32, or 63%) are between 100 and 220 Mya, while divergence times for most families (39 out of 55, or 71%)) are between 20 and 100 Mya. We believe that divergence times can provide additional evidence to support establishment of higher level taxa, such as families, orders and classes. Taking advantage of this approach, we can strive towards establishing a standardized taxonomic system both within and outside Fungi. To get more reliable calibrations, we also carry out a modern review of estimations regarding ancient lineages of Ascomycota, and we summarize a historical fossil outline with a reliable minimum age for 16 calibrating points. A scheme of Ascomycota ancient lineages is also provided in order to improve divergence time estimations.

关键科学问题:在真菌系统分类中寻找和探索新的分类依据,使其更趋于自然的分类方法和结果。

主要方法:通过分子数据,结合BEAST等软件分析,以已发现的化石作为时间校准点,建立不同分类阶元的分化时间,进而利用其作为新的证据应用到真菌系统分学研究中。

主要类群:子囊菌、座囊菌纲、

主要结论:分化时间的建立可以作为真菌系统学研究的一个新的证据,特别是在其高阶元分类上(目、纲、亚门等高阶元)。


 

从生物入侵过程探究物种时空分布规律

报告人:刘宣

单位:中国科学院动物研究所

 

关键词:入侵种;陆栖脊椎动物;种群建立;分布区扩展;动物地理

摘要:入侵种由于在新环境中摆脱了原产地专性天敌、竞争者和病菌的束缚,通常能够快速高效地在入侵区建立种群并完成分布区的扩张,因而生物入侵过程被誉为探索物种时空分布规律的天然实验室。同时,入侵种是当今全球化时代生物多样性的重大威胁,了解入侵过程及其影响因素对发展早期入侵风险预测框架至关重要。2007年以来,以生物入侵过程为主线,通过对美洲牛蛙等全球性入侵种在我国舟山群岛等地十余年野外工作,并结合跨类群的原产地和不同入侵地分析,较系统的研究了入侵两栖爬行动物种群建立-动态-扩展-危害及其对全球动物地理格局的影响。研究发现,外来两栖爬行动物可以快速适应入侵区的气候,表现出生活史特征和气候生态位的快速漂移,但在高温耐受性方面表现出极强保守性,极端高温和季节性降水等气候变化敏感性生态位是塑造入侵物种组成的重要气候过滤因子;同时,贸易和人为引种等繁殖体压力大小、与当地系统发育关系相近物种的丰富度以及人为协助二次扩散等对解释入侵种分布区的快速扩张也非常重要;除了大尺度气候和人为活动影响,局域尺度多个同域分布入侵种与当地种之间也会产生复杂的多营养级互作关系,并在长时间尺度上调节着入侵种的种群动态变化及其对当地种的密度制约性危害。最终,在上述研究基础上,综合气候-人为活动-种间互作等决定不同入侵阶段的重要因素,探讨了816种陆栖脊椎动物外来种在全球121个亚非拉欧经济发展体和生物多样性热点地区的早期入侵风险,为全球入侵热点地区提出了具体的科学防控建议。

关键科学问题:环境过滤等基础生态因素和迁移及局域扩散限制等中性过程对解释外来种入侵成功和种群动态的相对重要性及其时空变化,如何结合影响生物入侵过程的重要因素来预测外来物种的早期入侵风险。

主要方法:野外研究和地理信息系统、空间地统计分析、生态位动态量化框架等宏生态学研究方法相结合。

主要类群:陆栖脊椎动物(主要以两栖爬行类为研究对象)。

主要结论:气候、植被等基础生态位因素和繁殖体压力、人为活动、种间互作等影响物种迁移扩散的因素在塑造外来种入侵成功和分布规律上具有时空异质性,不同因素的相对重要性随生物入侵阶段也会发生改变,并在长时间尺度上调节着入侵种的种群动态变化及其对当地种的危害。

学科展望:1. 生态位理论结合系统发育信号解释外来种入侵成功规律,2. “人类世时代外来物种入侵如何重塑传统土著群落的谱系结构,3. 综合野外微生境选择、模拟自然的人工受控实验、并结合生理机制性模型的构建,发展全方位的新一代入侵风险预测框架。

Exploring species distribution dynamics from biological invasions

Speaker: Xuan Liu

Affiliation: Institute of Zoology, Chinese Academy of Sciences

Keywords: invasive species; terrestrial vertebrate; population establishment; range expansion; zoogeography

Abstract: The process of alien species invasion not only provides an ideal natural experiment system exploring the spatio-temporal dynamics of species distributions, but also is an urgent conservation concern for directing management and policy to prevent new invasions. Invasive alien species are one major factor causing rapid decline of native amphibians and reptiles, which are among the most threatened vertebrate taxa. Since 2007, combining long-term field work on the invasive American bullfrog (Lithobates catesbeianus = Rana catesbeiana) and native anurans in Zhoushan Archipelago, China, with collected information at both native and invaded ranges across taxa at the global scale, we explored the feral population establishment, dynamics, expansion, impact and influence on global zoogeographical patterns. We found that the alien amphibians and reptiles can rapidly adapt to novel climates in invaded ranges, representing the shift of realized climatic niches, but show strong conservatism in high temperatures. High temperature extremes and seasonal precipitation, which are two hallmarks of ongoing climate change, are the two most important climatic filters of modern-day species assemblage after invasions. Except for climate, factors associated with propagule pressure, the richness of congener diversity, topographic heterogeneity and human-assisted dispersal are also crucial predictors of alien herpetofauna spread rates across the globe. At a regional scale, based on data from 10-year field surveys of 157 water bodies in the Zhoushan Archipelago, China, we observed that the dynamics of invasive bullfrog populations are modulated by antagonistic interactions with other co-occurring invaders such as the red swamp crayfish (Procambarus clarkii) and native anurans. By linking various key predictors of invasion, we finally explored invasion potentials of 816 alien terrestrial vertebrates in 121 economic development entities and biodiversity hotspots. We identified those invasion hotspots with specific suggestions to prevent early introductions of those problematic species in high-risk areas.

Key question(s): the relative importance of fundamental niches such as climatic and habitat variables, and neutral and meta-community processes such as dispersal and propagule pressure in explaining alien species invasion success, and how it can be applied to prediction and prevention of alien species invasions

Approach(es): long-term field work and macro-ecological methods

Main group(s): terrestrial vertebrates particularly focusing on amphibians and reptiles that are declining globally and are among the most threatened vertebrate taxa on Earth.

Conclusion(s): The fundamental niche (FN) factors such as climate, vegetation and factors reflecting species dispersal and propagule pressure (PP) jointly shape the invasion success and population dynamics across spatial-temporal scales, which then modulate the invasive population dynamics, species assemblage and biogeography

Perspective: how to capture the phylogenetic signals in successful invaders, how biological invasions may modify future community phylogeny, and how to link field work, mesocosm experiments, and physiological mechanistic models to develop framework of predicting alien species invasions.

Convergent evolution in echolocation-related phenotypes and genotypes reveals a new echolocating genus in mammals

报告人:刘振

单位:中国科学院昆明动物研究所


 


 

微型生物的突变

报告人:龙红岸1  Michael Lynch2

单位:1中国海洋大学海洋生物多样性与进化研究所

2The Biodesign Institute, Arizona State University, Tempe, AZ, US

 

关键词:自发突变;环境诱导突变;基因组演化;单细胞生物

摘要:突变是生物多样性的终极源泉,也是多种疾病的元凶。绝大多数物种的全基因组自发突变率和突变谱在本研究开始之前均属未知,突变率的演化规律也因突变数据集的缺乏而少有研究,环境诱导突变的规律也更无从谈起。本研究利用全基因组深度测序和突变积累技术,跨度八年的时间,破解了23种真原核单细胞生物的突变率和突变谱,探讨了突变率和基因组核苷酸组成的演化规律,量化了不同邻近核苷酸组成对碱基替换突变率的影响,揭示了各种环境因素对生物突变的影响。

关键科学问题:多种微型生物的自发突变率和突变谱的测算与变化规律;生物基因组构成的演化决定因素;不同环境因子对生物突变的诱导作用。

主要方法:组学和生物信息学、微生物学、突变积累实验。

主要类群:原生动物、酵母、细菌。

主要结论:单细胞生物的碱基替换突变率多在10-1210-8之间,纤毛虫原生动物具有最低的碱基替换突变率,一个物种的突变率下限可能由有效种群数量决定;单细胞生物碱基替换,此前研究认为均倾向于产生A/T碱基,而抗辐射双球菌则是第一个例外;一个核苷酸上下游邻近碱基的G/C含量越高,其突变率越高,而突变发生后被修复的机率也直接受G/C含量的影响;突变倾向性、自然选择、基因转换等演化作用力对基因组的核苷酸组成构成直接影响;抗生素诺氟沙星可以通过激活应急响应线性提升大肠杆菌突变率,pH降低则会降低突变率,除草剂草柑膦则对突变率没有影响。

学科展望:未来的微型生物突变研究将采用新的培养和分析方法,验证之前的假说和提出新的突变率进化解释,最终揭示微型生物在自然环境中的突变规律。

 

 


 

Microbial mutations

Speaker: Hongan Long1, Michael Lynch2

Affiliation: 1Institute of Evolution and Marine Biodiversity

2The Biodesign Institute, Arizona State University, Tempe, AZ, US

Keywords: Spontaneous mutations; Environment-induced mutations; Genome evolution; Unicellular organisms

Abstract: Biodiversity ultimately originates from mutations, as do many diseases. Mutation rates and spectra of most microbial organisms were not available before the start of this study. Using deep, whole-genome sequencing and mutation accumulation experiments (up to 8 years), this study deciphered mutation rates and spectrums of 23 unicellular prokaryotic and eukaryotic organisms, explored evolutionary mechanisms of mutation rate and genome-wide nucleotide composition, quantified mutation rate variation with different nucleotide-context, and revealed the influence of environmental factors on mutation rate.

Key question(s): Measuring mutation rate/spectrum and their variation; Evolutionary determinants of genome architecture; How environmental factors influence mutation rate

Approach(es): -omics and bioinformatics, microbiology, mutation accumulation experiments

Main group(s): Protozoa, yeasts, bacteria

Conclusion(s): Mutation rate varies between 10-12 to 10-8, with ciliated protozoa having the lowest mutation rate, and its lower limit might be determined by the effective population size; mutations are not universally biased to A/T, with D. radiodurans as the first exception; mutation rate of a focal nucleotide is influenced by the G/C composition of neighboring nucleotides: the higher the G/C content the higher the mutation rate, so does the repair efficiency of the DNA mismatch repair system; genomic nucleotide composition is influenced by mutation bias, natural selection and gene conversion; the fluoroquinolone antibiotic norfloxacin could elevate E. coli mutation rate by enhancing the expression of the stress response, pH decrease could reduce mutation rate and the herbicide glyphosate does not influence bacterial mutation rate.

Perspective: Future mutation studies on microbial organisms should use new culturing and analyzing methods to test previous hypotheses and explore new mutational mechanisms. The mutation rate of microbes in nature would be eventually revealed.

物种分子分类与进化历史研究方法评估进展

报告人:罗阿蓉

单位:中国科学院动物研究所

 

关键词:分子分类;系统发育树;分子钟;支端定年

摘要:关键科学问题:物种是自然界的基本实体单元之一,对其多样性和进化历史的探究一直是本学科长期关注的重点科学问题。发展至今,已经有各种方法可以用于该领域的研究,比如分子分类领域广泛应用的GMYCPTPBPP等,估算物种分化时间的节点定年法和支端定年法。同时,我们在具体类群研究中,还会面临如分子分类取样大小、分子钟模型等系列策略抉择问题。所有这些都会给最终的分析结果产生重要的影响。因此,有必要对该领域相关方法及其内部理论依据开展深入的分析研究。

主要方法:方法的研究一般需要以真实模型作为参考,因此我们的研究中注重采用大量的模拟数据。同时,我们也会尝试将相关的方法或结论应用到具体的动物类群。具体到分子分类方法研究中,我们根据五种物种形成理论模型进行分子序列模拟,同时也借鉴统计学中假阳性错误等设计对结果进行分析的评判标准;在物种进化历史研究中,我们则突出在物种树基础上对化石发生和不同进化速率的序列数据等的模拟。

主要类群:模拟类群、蜜蜂总科、熊属

主要结论:在现有的广泛应用的分子分类方法中,BPP相比GMYCPTP可以更加准确的进行物种分类;种间的基因流对它们均产生明显的负面作用;作为主要影响因素,当物种种群大小和物种分化时间的比率较高时,该三种方法的功效均有所降低。相比节点定年用于物种进化历史研究,支端定年不仅克服了诸多弊端,同时其能比较准确和精确的估算类群重要历史时间点,如根部时间点等;但是其在准确重建现生物种系统拓扑关系的同时,化石的系统发育位置存在一定的误差。

学科展望:测序技术的发展将为物种多样性和进化历史研究提供大量的数据。但是,大量数据的涌现将使本学科的分析方法面临挑战和机遇。因此,优化与发展系统基因组研究的分析方法应该是本学科的重要发展方向之一。

 

 


 

Progresses on methods for molecular species delimitation and evolutionary history

Speaker: Arong Luo

Affiliation: Institute of Zoology, Chinese Academy of Sciences

Keywords: molecular species delimitation, phylogeny, molecular clock, tip-dating

Abstract:

Key question(s): Species are one of the fundamental units in nature. Light has been shed on species diversity and evolutionary history for a long time. Till now, various methods exist in this field, such as GMYC, PTP, and BPP for molecular species delimitation, and node-dating and tip-dating for evolutionary timescales. In practice, we can also encounter a series of strategy options such as sampling size for species delimitation and molecular-clock models. Different methods/options would induce important impacts on the results we are interested in. Thus, it is necessary to investigate the efficacy of methods as well as their hidden theory in this field. 

Approach(es): True values/models are indispensable for studying methods. So, a large number of simulated datasets were adopted in our studies. What is more, we should apply some method or conclusion to real animals. For molecular species delimitation in particular, we simulated molecular sequences based on five speciation models, and devised criteria for judging the methods based on statistical indices (e.g., the false positive). We highlighted simulations of fossils occurrences and sequences of evolutionary rate variation based on simulated species trees in our dating analysis.

Main group(s): simulations, Apoidea, and Ursus

Conclusion(s): BPP showed higher accuracy in species delimitation than GMYC and PTP. Gene flow between species exerted negative influences on all of the three widely used methods. When the ratio of population size to divergence time, which was found to be the main factor, was relatively high, efficacy of the three methods all decreased. For estimating evolutionary timescales, tip-dating which overcomes many drawbacks of node-dating, was found to estimate time points (e.g., root age) with high accuracy and precision. Tip-dating can also reconstruct evolutionary relationships of extant taxa well; however, phylogenetic positions of fossils are usually problematic. 

Perspective: Next generation sequencing will provide huge data for studying species diversity and evolution, which also brings challenges and opportunities for methods analyzing the data. Therefore, it should be one of the important issues to optimize/develop phylogenomic methods in this field.


 

反刍动物角的起源和进化

报告人:邱强

单位:西北工业大学

 

关键词:反刍动物;角;再生与抑癌

摘要:反刍动物独有的骨质角是动物进化史上器官性状创新的奇迹,鹿角又是哺乳动物中唯一能完全再生的器官,其细胞分裂速度是癌细胞增殖速度的30倍,但鹿科物种的癌症发生率却比其他哺乳动物低5倍。基于多层次组学数据,提出反刍动物的角具有相同的细胞起源和基因调控通路,阐明了反刍动物角具有单一进化起源和发生发育机制。在此基础上,发现肿瘤发生相关基因可能介导鹿角的快速再生,而大量抑癌基因受到强烈的自然选择又能在调控鹿茸快速生长的同时抑制癌症发生。

关键科学问题:反刍动物角的起源和发育的遗传基础,鹿茸再生和避免癌化的遗传分子机制。

主要方法:进化和比较基因组学。

主要类群:反刍亚目。

主要结论:揭示了反刍动物角的进化,发育和组织学起源以及鹿角再生的遗传机制。

学科展望:继续深入研究鹿角再生的机制和鹿抗癌能力的机制,对再生医学、肿瘤生物学,以及培育新品种家畜都有重要意义。

 

 

 


 

 


 

三种新的虾源病毒的鉴定、分子特征及分类研究

报告人:史卫峰

单位:山东第一医科大学(山东省医学科学院)

 

关键词:新病毒发现;布尼亚病毒目;戊肝病毒;黄病毒;分子特征;病毒分类

摘要:

关键科学问题:我国养殖虾体内携带哪些新病毒并不清楚。

主要方法:对我国部分省份采集的虾进行转录组测序,通过与公共数据库进行比对,从虾体内发现了多种新病毒。

主要类群:病毒。

主要结论:课题组从不同种类的病虾中鉴定出三种新的病毒,分属布尼亚病毒目白纤病毒科,戊型肝炎病毒科和类黄热病毒。特别地,新的布尼亚病毒的基因组结构可能与白纤病毒科的已知病毒均不相同。系统发育分析表明,这些病毒分别属于一个新近命名的属和两个尚未划分的属。特别地,虾源类黄热病毒可能与我国养殖虾性早熟和减产有关。

学科展望:我国节肢动物物种多样性极其丰富,通过高通量测序可以从节肢动物中发现大量的新病毒。

 


 

Identification, molecular characterizations and taxonomy of three novel viruses from shrimps

Speaker: Wei-Feng Shi

Affiliation: Shandong First Medical University & Shandong Academy of Medical Sciences

Keywords: Novel virus discovery; Bunyavirales; Hepatitis E virus; Flavivirus; molecular characterization; virus taxonomy

Abstract:

Key question(s): The viruses existing in Chinese shrimps remain poorly understood.

Approach(es): Next generation sequencing (NGS) was performed for shrimp collected from several provinces in China. Multiple novel viruses were identified from shrimp via blasting our NGS results against public databases.

Main group(s): Viruses

Conclusion(s): Three novel viruses were identified from different shrimp species, which belonged to Phenuiviridae (Bunyavirales), Hepeviridae and Flaviviridae. These shrimp-origin viruses shared low identities with previously described viruses. In particular, the novel bunyavirus probably had a different genomic organization from known bunyaviruses of the Phenuiviridae. Phylogenetic analysis revealed that they might belong to a recently classified genus of Wenrivirus and two unclassified genera within each family, respectively. Remarkably, the shrimp-origin flavivirus might be related to infectious precocity syndrome and production cuts in farmed shrimps in China.

Perspective: The biodiversity of arthropods is extremely high in China and metagenomic sequencing would identify many novel viruses from arthropods.

 

 

 

 


 

Building the Grand Timetree of Life

Speaker: Sudhir Kumar

Affiliation: Institute for Genomics and Evolutionary Medicine (iGEM), Temple University

EDITOR-IN-CHIEF, Molecular Biology and Evolution

Molecular phylogenies scaled to time (timetrees) are fundamental to understanding the origin and diversification of species and strains. Timetrees are key to revealing micro- and macro-evolutionary processes, including the role of geologic history in shaping the evolution of life, temporal patterns of biological diversity, coevolution of hosts and pathogens, and origin of pathogenic strains. We have developed many innovative methods (RelTime), tools (MEGA), and resources (www.TimeTree.org) to assemble the grand timetree of life. The RelTime approach is theoretically sound, requires fewest prior assumptions, and computes quickly for very large datasets.  The newest release of MEGA presents RelTime and associated methods to select models (CorrTest) and estimate confidence intervals by incorporating multiple clock calibrations and probability densities during the inference of divergence times. Our TimeTree.org resource makes the knowledge of published species divergence times in over 4000 research articles easily accessible to experts and non-experts alike. Our synthesis of thousands of timetrees has produced the largest time Timetree of Life, containing >100,000 species, which has revealed a clock-like speciation process. Therefore, our methods, tools, and resources are revealing fundamental patterns, and underlying processes, of molecular and species evolution.



 

拟南芥近缘种Boechera stricta的群体基因组学研究

报告人:王宝生

单位:中国科学院华南植物园

 

关键词:祖先多态;多态位点分选;平衡选择;基因组分化;物种形成

摘要:

遗传分化产生,导致生殖隔离并最终形成新物种的过程,是进化生物学研究关注的热点问题。随着全基因组测序技术的飞速发展,越来越多的研究发现遗传变异在基因组上的分布是不均匀的,存在变异很高的岛屿区域。但是导致基因组遗传多态性不均匀分布的原因至今尚不清楚。通过对拟南芥近缘属物种Boechera stricta500多个个体进行全基因组测序分析,证实了祖先群体中受到平衡选择的多态性位点可以通过随机漂变在不同的后代群体中固定,从而产生后代群体间高度分化的基因组区域。同时,该研究还发现平衡选择作用于抗性基因,促使祖先单倍型在后代群体中得到保留,从而在基因组上形成高度遗传多态性区域。这一工作解析了多种中性和选择因素在基因组分化过程中的作用,证实了平衡选择是维持基因组变异的重要力量,加深了我们对适应性分化和物种形成过程的理解。

关键科学问题基因组变异模式的产生机制。

主要方法:全基因组重测序,溯祖模拟。

主要类群:Boechera stricta(十字花科)。

主要结论:1)祖先多态性位点通过随机偏选在不同的后代群体中固定,产生基因组间高度分化的岛屿区域。(2)祖先多态位点受到平衡选择保留在后代群体中,形成基因组高多态性的区域。

学科展望:基因组变异受到多种中性和非中性因素的影响,未来利用新的测序技术和群体遗传学模型,将有可能揭示各种因素的基因组分化和物种形成过程中的相对作用。


 

 


 

犬科种间的基因渐渗

报告人:王国栋

单位:中国科学院昆明动物研究所

 

关键词:基因渐渗;犬科;迁移;基因组

摘要:

关键科学问题:1)犬科物种间是否存在基因渐渗?其强度和广度如何?2)家犬在驯化后随人类走向世界各地,是否和当地犬科物种存在基因交流?3)博物馆样品可为我们提供怎样的启示?

主要方法:基因组,二代测序,群体基因组,群体结构的分析方法(PCAadmixture等),系统发育树,基因渐渗的分析方法(treemixF3 testD test等)。

主要类群:犬科(Canidae):狼(Canis lupus),狗(Canis lupus familiaris),郊狼(Canis latrans),金豺(Canis aureus),豺(Cuon alpinus),赤狐(Vulpes vulpes)等。

主要结论:犬亚科和薮犬亚科之间和内部存在广泛的基因交流,例如埃塞尔比亚狼和非洲金豺,狼和郊狼,豺和狼,豺和非洲野狗等。家犬在跟随人类走向世界各地并定居的过程中和当地犬科物种亦存在广泛的基因交流,例如非洲家犬和非洲金豺。澳洲野狗从东南亚到澳大利亚后野化,成为当地的顶级掠食者。欧洲人登陆后带来了欧洲支系的家犬,和它之间存在基因交流。中国南方狼是一个单独的支系,并和一支未知的犬科物种见有基因交流。

学科展望:1)这种广泛存在的基因交流背后的生物学机制是什么?2)古DNA的方法对我们了解古老的基因交流提供了广阔的前景。


 

Gene flow among Canidae

Speaker: Guo-Dong Wang

Affiliation: Kunming Institute of Zoology, Chinese Academy of Sciences

Keywords: gene flow; Canidae; migration; genome

Abstract:

Key question(s): 1) Do species in Canidae have gene flow? What about the intensity and extensity? 2) Dogs spread around the world quickly following human beings. Do they have gene flow with the local Canidae? 3) How about based on the specimens in museums?

Approach(es): Genome, sequencing, population genomics, approaches on the population structure, phylogeny, and gene flow, etc.

Main group(s): Canidae: Canis lupusCanis lupus familiarisCanis latransCanis aureusCuon alpinus, etc.

Conclusion(s): There is interspecific Gene Flow among Canidae, for instance, with the Ethiopian wolf and African golden wolf, grey wolf and coyote, dhole and African hunting dog, etc. There is extensive gene flow among dogs and local Canis, for instance, with African golden wolf. Intestingly, Dingoes had gene flow with dogs from Europe. Furthermore, the Gray wolf from South China is a separate lineage, with the gene flow on unknown Canids.

Perspective: 1) What is the biological mechanism of the extensive and interspecific Gene Flow among Canidae? 2) How do the specimens from museum shed the new light on the field of the gene flow?


 

桦木属种间进化关系及红桦的避难所

报告人:王年

单位:山东农业大学

 

关键词:系统发育基因组学;桦木属;RADseq;红桦;避难所;微卫星标记

摘要:桦木属有65个种和亚种,广泛分布与北半球,具有极高的经济价值和生态价值。由于频繁的种间杂交、多倍化及形态性状的连续变化,桦木属种间进化关系一直未得到解决。本研究利用RADseq,以垂枝桦全基因组作为参考,通过超级矩阵及ASTRAL解决了桦木属的种间进化关系。此外作者研究了红桦的群体遗传学,STRUCTURE结果表明红桦分为具有遗传分化的两个支系,即南方支系和北方支系,两个支系在川西北混合; 种群遗传多样性及杂合度在北纬32-26度之间呈现由北往南逐渐降低的趋势; 生态位模型表明在末次冰期,川西北及秦岭地区适合红桦的生存。这些结果表明红桦在川西及秦岭等存在多个避难所,且红桦有局部扩散的趋势。

关键科学问题:桦木属的种间进化关系;红桦在南方和北方是否存在多个避难所

主要方法:RADseq及微卫星标记

主要类群:桦木属

主要结论:桦木属的种间进化关系同传统的分类不一致,不一致的原因有形态性状的趋同进化及种间杂交等。红桦具有多个避难所,过去气候变化可能是导致红桦种内分化的原因。

学科展望: 桦木属植物性状趋同进化及不同适应性的分子基础。


 


 

桔梗科争议类群的系统学研究进展

报告人:王强

单位:中国科学院植物研究所

 

关键词:党参属;多萼参属;分类系统;系统学位置

摘要:

关键科学问题:1.党参属的界定2.党参属与近缘属的关系3.多萼参属的系统学位置。

主要方法: 基于形态学和微形态学、孢粉学、细胞分类学、分子系统学的综合系统学分析方法。

主要类群:狭义桔梗科党参属、幅冠参属、须弥参属、山南参属、多萼参属等。

主要结论:1.传统的党参属界定不合理,与近缘属的关系需要修正;2.基于综合的系统学证据,桔梗科内新发现三个新属;3.多萼参属并不成立,应该归并入茄科红丝线属。

学科展望:对于大多数区域性的志书而言,类群界定和分类系统通常是基于形态学分析。但是,单方面的证据通常无法揭示类群间的内在关系。本报告讨论了桔梗科的大麻烦”—党参属的界定,以及著名的桔梗科之谜”—多萼参属的系统学位置。这一类研究揭示,基于分子系统学证据与形态学、孢粉学等多学科证据的综合系统学分析是研究复杂的类群关系的重要手段。

 


 

Systematic studies of problematic taxa of the family Campanulaceae

Speaker: Qiang Wang

Affiliation: Institute of Botany, Chinese Academy of Sciences

Keywords: Codonopsis; Numaeacampa; taxonomic system; systematic position

Abstract:

Key question(s): 1. Circumscription of Codonopsis; 2. Relationship of Codonopsis and allied genera; 3. Systematic position of Numaeacampa

Approach(es): Integrative systematic analysis based on Morphology, Micro-Morphology, Palynology, Cytotaxonomy, and Molecular Systematics.

Main group(s): Campanulaceae (CodonopsisPseudocodonHimalacodonPankycodonNumaeacampa)

Conclusion(s): 1. The circumscription and relationships of Codonopsis and allied genera should be revised; 2. Three new genera are described based on integrative systematic analysis; 3. The genus Numaeacampa should be reduced to a synonym of Lycianthes of Solanaceae.

Perspective: For most regional flora, taxon delimitation and taxonomic system are usually based on morphology. However, one-sided evidence usually can not reveal complex relationships. In this presentation, we discussed the ‘big problem’ of Campanulaceae about the circumscription of Codonopsis, and the well-known ‘Campanulaceae puzzle’ of Numaeacampa. These case studies show that integrative systematic analysis based on Molecular Systematics, Palynology, and evidence from other subjects is important and efficient for revealing complicated relationships within taxa.

 


 

系统发育基因组学在阐释一些重要生物学问题中作用

报告人:王文

单位:西北工业大学生态与环境保护学院

 

关键词:系统发育基因组学;重要性状的阐释;反刍动物

摘要:

各种类群的生物构成了多姿多彩的生命世界,但长期来各种野生生物类群及其独特性状的形成和演化机制大多是谜团。随着基因组学及大数据分析方法的飞速发展,目前已经可能大尺度、跨物种针对一个高级分类阶元进行全基因组水平的分析比较研究,在构建可靠系统发育基因组树澄清各种分类争议的同时,还能揭示该类生物独特特征的遗传变异基础。这些结果不仅解决了反刍动物自身进化的大量问题,也为再生医学、肿瘤防治、骨质疏松和睡眠障碍等人类关心的健康问题提供了全新的启示。

关键科学问题:高级分类阶元生物类群及其独特性状形成和演化的分子机制

主要方法:系统发育基因组学,基因组学,计算生物学,实验生物学

主要类群:反刍亚目

主要结论:对反刍亚目全部6个科近一半属进行的基因组解析,结合大量转录组和部分功能验证实验,澄清了长期以来有争议的反刍亚目各级分类阶元的分类进化关系,并鉴定了一些与多胃室、角起源、独特牙齿结构、快速奔跑能力、鹿角快速再生和鹿科动物低癌发生率以及驯鹿适应北极地区等的分子遗传基础。

学科展望:可以预见,未来一些年内,类似的系统发育基因组学研究将会在各类生物类群里大量涌现。

 

 


 

Deciphering evolutionary history and mechanism of a high taxonomic unit and its distinct traits by phylogenomics

Speaker: Wen Wang

Affiliation: Northwestern Polytechnical University

Keywords: phylogenomics; distinct traits; ruminants

Abstract: The ruminants are one of the most successful mammalian lineages exhibiting extensive morphological and ecological diversity, and containing several key livestock species such as cattle, buffalo, yak, sheep and goat. Ruminants have also evolved a number of remarkable distinct traits. By including more than 50 ruminant species genomes, covering about half the genera and all the six extant Ruminantia families, together with transcriptomic data of more than 900 samples from more than 60 tissues of 4 species and experimental tests, we conducted a phylogenomic study for Ruminantia. We not only successfully clarified long-term controversies in  the family and different taxonomic levels, but also identified many genetic features correlated with the evolution of distinct traits of ruminants.

Key question(s): Deciphering evolutionary history and mechanism of a high taxonomic unit and its distinct traits.

Approach(es): phylogenomics, genomics, computational biology, experimental biology

Main group(s): Ruminantia

Conclusion(s): We constructed a new well-supported ruminant phylogenetic tree, resolving previous controversies over the deep branches of ruminant families. Further analysis revealed that incomplete lineage sorting played the dominant role in the incongruence of Ruminantia phylogeny. Under this highly reliable phylogenetic context, together with other omics and experimental evidence, we identified many genomic changes that are associated with the multi-chambered stomach, headgear, rapid regeneration of deer antler, low cancer rate in cervids, vitamin D and fat metabolism, body size variation, cursorial locomotion, dentition pattern, and so on.

Perspective: It is conceivable that many similar phylogenomic studies in other high taxonomic units will appear in the coming years.


 

病原、媒介和宿主三重视角下的系统病毒学

报告人:吴爱平

单位:中国医学科学院苏州系统医学研究所

 

关键词:病毒;高通量测序;进化;媒介;宿主

摘要:

关键科学问题:新发再发病毒的起源追溯、变异分化和宿主免疫

主要方法:1)基于高通量技术的媒介病毒组、病原基因组和宿主转录组测序;2)基于进化推断的病毒溯源和变异分化路径构建;3)基于机器学习方法的多源组学数据整合建模用于宿主感染后的免疫信号定量。

主要类群:病毒;黄病毒属;寨卡病毒;流感病毒;

主要结论:1)媒介层面,病毒组学测序揭示云南地区库蠓比蚊子携带有更多样的病毒组成,带有更多潜在对人或动物致病病毒,特别是库蠓中发现了大量新型黄病毒属成员;2)病原层面发现了季节性流感病毒抗原变异的关键性突变机制,以及新发禽流感病毒H7N9的重配事件;3)宿主层面建立了系列基于宿主组织转录组数据的免疫细胞组分推断模型,成功用于流感病毒和寨卡病毒感染后的动态免疫信号监测。

学科展望:二代测序技术能够在病原、宿主和媒介等多个层面给出高通量分子数据,捕捉基因组、转录组和表观组等全面的组学信息。这些分子组学数据,结合传染病流行学监测和功能检测数据等,通过数据整合和计算建模,将为病毒性疾病研究提供从分子到表型的全面刻画,促进传染病应急防控政策的制定、药物研发以及疫苗设计评估等,推动系统病毒学这一新型交叉领域的快速发展。

 


 

Systems virology from views of pathogens, hosts and vectors

Speaker: Ai-Ping Wu

Affiliation: Suzhou Institute of Systems Medcine, Chinese Academy of Medical Sciences

Keywords: VirusSequencing; Evolution; Vector; Host

Abstract:

Key question(s): The early warnings, origins, divergent evolution and host immune patterns for emerging and re-emerging viruses.

Approach(es): 1) Virome, genome and transcriptome with high-throughput sequencing; 2) Virus origins and mutational pathway with evolutionary analysis; 3) Quantification of host immune response signatures from multi-omics data via machine learning methods. 

Main group(s): Virus; Flavivirus; Zika Virus; Influenza virus;

Conclusion(s): 1In view of vectors, we found Culicoides take more pathogenic viruses than mosquitoes for human or animals and have higher viral diversity. 2) In view of pathogens, we found the dominant mutation mechanism underlying the antigenic evolution of seasonal influenza viruses, and the reassortment mechanism of human-infecting H7N9 virus. 3) In view of hosts, we developed a set of methods to infer immune cell compositions from tissue transcriptomes and successfully transferred them into the infections of influenza viruses and zika viruses. 

Perspective: With the development of next-generation sequencing (NGS) technologies, large quantities of omics data have been accumulated concerning pathogens, hosts, and even vectors in viral diseases. These data could be integrated with traditional surveillance and functional data together for better description of viral diseases from genotype to phenotype. Also, omics data plays an important role in the development of policy for viral prevention and control, development of anti-viral drugs and design of vaccines. The introduction of omics technology into viral diseases has already re-shaped the research paradigm of virology and will push it into the era of systems virology in the near future.


 

高原家养动物适应性状遗传机制解析

报告人:吴东东

单位:中国科学院昆明动物研究所

 

关键词:高原适应;趋同进化;基因组进化;家养动物

摘要:生活在青藏高原丰富多样的家养动物为研究极端环境适应的遗传机制提供了非常好的素材。基于大规模基因组数据,我们解析了青藏高原家鸡、藏獒、马、家牛、绵羊、山羊以及家猪高原适应遗传机制的异同,发现较高水平的趋同进化现象,尤其是EPAS1基因在很多家养动物中都发生了快速进化。同时我们也发现基因交流在藏黄牛、藏獒高原适应中起到非常重要的作用。尤其是藏黄牛基因组中的低氧诱导通路基因EGLN1EGLN2HIF3a从牦牛中获得,这也提示,藏黄牛通过拿来主义从牦牛中快速获得适应高原低氧环境的遗传变异。


 


 

十种一态:隐藏在四膜虫形态种中的基因组进化

报告人:熊杰

单位:中国科学院水生生物研究所

 

关键词:四膜虫;形态种;大、小核;基因组;转座子

摘要:A morphospecies is defined as a taxonomic species based wholly on morphology, but often morphospecies consist of clusters of cryptic species that can be identified genetically or molecularly. The nature of the evolutionary novelty that accompanies speciation in a morphospecies is an intriguing question. Morphospecies are particularly common among ciliates, a group of unicellular eukaryotes that separates two kinds of nuclei, the silenced germline nucleus (micronucleus) and actively expressed somatic nucleus (macronucleus), within a common cytoplasm. Because of their very similar morphologies, members of the genus Tetrahymena are considered a morphospecies. We explored the hidden genomic evolution within this genus by performing a comprehensive comparative analysis of the somatic genomes of ten species and the germline genomes of two species of Tetrahymena. These species show high genetic divergence; phylogenomic analysis suggests that the genus originated about 300 My ago. Seven universal protein domains are preferentially included among the species-specific (i.e., the youngest) Tetrahymena genes. In particular, leucine-rich repeat (LRR) genes make the largest contribution to the high level of genome divergence of the ten species. LRR genes can be sorted into three different age groups. Parallel evolutionary trajectories have independently occurred among LRR genes in the different Tetrahymena species. Thousands of young LRR genes contain tandem arrays of exactly 90-bp exons. The introns separating these exons show a unique, extreme phase 2 bias, suggesting a clonal origin and successive expansions of 90-bp exon LRR genes. Identifying LRR gene age groups allowed us to document a Tetrahymena intron length cycle. The youngest 90-bp exon LRR genes in T. thermophila are concentrated in pericentromeric and subtelomeric regions of the five micronuclear chromosomes, suggesting these regions act as genome innovation centers. Copies of a Tetrahymena LINE-like retrotransposon are very frequently found physically adjacent to 90-bp exon/intron repeat units of the youngest LRR genes. We propose that Tetrahymena species have used a massive exon-shuffling mechanism, involving unequal crossing-over possibly in concert with retrotransposition, to create the unique 90-bp exon array LRR genes.

关键科学问题:形态种是如何进化的?

主要方法:比较基因组学。

主要类群:原生动物纤毛虫。

主要结论:形态高度相似的十种四膜虫以小核染色体近着丝粒和亚端粒区域为基因组的创新中心,以转座子为重要介质,创造大量与四膜虫环境适应相关的大核新基因。

学科展望:不同真核生物类群中形态种进化机制的异同。



 

豆科的叶绿体系统发育基因组学

报告人:伊廷双

单位:中国科学院昆明植物所

 


 


 

不完全谱系筛选与种间杂交对植物系统发育重建和种群进化历史的影响

报告人:张大勇

单位:北京师范大学

 


 


 

以演化时间为分类新增指标:担子菌门为例

报告人:赵瑞琳 贺茂强

单位:中国科学院微生物研究所

 

关键词:系统学;分子钟;进化基因组;系统发育;大型真菌

摘要:

关键科学问题:单系进化支序的分类等级认定中,由于表型特征的多样性导致特定的表型特征往往缺乏普遍适用性,这是引起分类系统不稳定的主要原因之一。因此,引入演化时间作为命名新增指标对构建稳定的分类系统具有重要价值。而担子菌门真菌在10年来,大量新分类单元发表,有必要利用演化时间等标准对其分类系统进行修订。

主要方法:我们集结近十年来担子菌门分类的最新进展,选取539个种(18纲,3亚纲,62目,183科,392)构建了担子菌门基于6个基因(LSU, SSU, 5.8s, rpb1, rpb2, ef1)的系统发育图谱;116个种(17纲,54目)基于396个直系同源基因的系统基因组进化的系统发育图谱;及771个种(60个目、185科)的分子钟分析,展示了各个分类单元的系统发育关系,并对科和科以上的分类阶元的演化时间进行估算。此外在系统发育研究基础上,联合27个国家,60个机构,70位真菌学家对担子菌门中的已知的所有3198个属进行了梳理,通过文献查阅等认定其中1261个属为异名,保留合格属1928个;并对每个合格属的分类地位、包含物种数、模式种、生活类型、生境、分布地及DNA系统发育信息等进行整理。

主要类群:担子菌门(物种占真菌界1/3),是大型真菌,尤其是食药用菌的主要构成,同时也包含锈菌和黑粉菌等重要植物病原菌及酵母菌等微真菌。

主要结论:通过上述研究,担子菌门内各单系分类阶元及其系统发育关系被认定;分别估算担子菌门内亚门、纲、目、科的演化时间范围分别为406-490 Mya245-393 Mya120-290 Mya27-222 Mya,并建议把这些演化时间作为建立相应分类等级的新增依据。结合分析结果,新认定亚门Wallemiomycotina;发现担子菌门中1个目由于过于年轻的演化时间建议废除;2个科具有的古老演化时间,分别正式提升为2个目。结合其它分类信息把这些合格属依次归入241个科,68个目,18个纲和4个亚门中,最终形成并修订了整个担子菌门分类系统。

学科展望:本项工作提供了完整的担子菌门分类系统,将有力推动目前的真菌分类工作,同时为后续不断完善并逐渐形成更为稳定可靠的担子菌门分类体系奠定基础。此外,本研究系统性提供了科及科以上分类阶元的演化时间,这作为命名分类阶元的一个新增指标将为解决具体类群的分类问题提供线索和参考。

Reconstruction of taxonomic system used an additional criterion of divergence times: case of Basidiomycota

Speaker: Rui-Lin Zhao, Mao-Qiang He

Affiliation: Institute of Microbiology, Chinese Academy of Sciences

Keywords: Systematics; molecular clock; phylogenomics; phylogenetics; macrofungi

Abstract:

Key question(s): In modern taxonomy, ranking taxa is mainly based on the combination of phylogenetic monophyly and diagnosed phenotypes. However, the diversity of phenotypes make it unqualified to be a universal criterion and this assumes the main responsibility for the unstable taxonomic system nowadays. Using divergence time as an additional criterion for ranking could help to build a robust taxonomic system. In the past ten years, numerous new taxa were published in Basidiomycota, thus it is essential to revise the system by using divergence time as an additional criterion.

Approach(es): Based on the studies of Basidiomycota in the past ten years, we build the system for Basidiomycota and estimated divergence times from subphylum to family level in Basidiomycota by: multi-gene phylogenetic analyses including six-genes (LSU, SSU, 5.8s, rpb1, rpb2, ef1) from 539 species which represented 18 classes, 3 subclasses, 62 orders, 183 families and 392 genera; phyloproteomics analyses including 396 orthologous genes from 116 species which represented 17 classes and 54 orders; molecular dating analyses including 771 species from 60 orders and 185 families. Furthermore, united with 70 mycologists from 27 countries (60 institutions), we untangled the taxonomic status of 3198 genera in Basidiomycota, verified 1928 valid genera and provided an outline for these genera in Basidiomycota. The outline includes 1928 currently used genera names with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information.

Main group(s): Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers only to the Ascomycota. It embraces most of the edible and medicinal mushrooms, the pathogenic group including rust and smut and the industrial important group such as yeast, etc.

Conclusion(s): The systematic relationships above family level of Basidiomycota are presented. Divergence times are provided to the family level as: subphyla are 406–430 Mya, classes are 211–383 Mya, orders are 99–323 Mya and families are 27–222 Mya. We suggest these divergence time ranges as additional criteria for ranking taxa in Basidiomycota. Our results reveal a new subphylum (Wallemiomycotina) and two new orders (raised from two known families) according to their relatively older divergence times; abolished an order according to its relatively younger divergence time. Combined with information from other aspects, we classified all the valid genera in 241 families, 68 orders, 18 classes and 4 subphyla. Finally, we built and revised the taxonomic system of Basidiomycota.

Perspective: The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. The Outlines of the Fungi provide essential taxonomic information which are easy to use by workers in various disciplines incorporating mycological fields. It is becoming a stable system with continual updates, reaching a consensus for the classification of all of the Fungi. Besides, the divergence times we provided in this study could be a new clue and a reference to resolve problems in the ranking and naming of taxa.

鸭嘴兽性染色体的起源与演化

报告人:周琦

单位:浙江大学

 

关键词:鸭嘴兽;性染色体;染色体水平基因组序列

摘要:鸭嘴兽是很早与其他兽亚纲哺乳类分化的单孔目哺乳类,却兼具鸟类,爬行类,和哺乳类的形态行为特征,一直是令进化生物学家着迷的类群。它有独特的独立起源的五对通过头尾配对的性染色体,但由于之前基因组质量的问题,其性染色体的起源和演化一直是个谜。我们通过与丹麦哥本哈根大学的张国捷研究小组的合作,通过第三代基因组测序技术拼装了高质量的鸭嘴兽染色体序列,将超过95%以上的基因组组装成了染色体。我们发现鸭嘴兽的性染色体特征与鸟类而不是哺乳类更接近:五对性染色体中最长的一条与鸟类的性染色体同源,而并没有任何染色体与人类的X染色体同源。整个性染色体系统没有剂量补偿机制,而且我们进一步揭示现今观察到的头尾相配的性染色体链很可能起源于独特的环状染色体构象。这一独特的性染色体起源与演化模式挑战了经典的性染色体演化模型,为性染色体的一般演化规律提供了新的认识。

关键科学问题:动物性染色体演化。

主要方法:基因组学。

主要类群:鸭嘴兽。

主要结论:鸭嘴兽的链状性染色体起源于祖先的环状构象。

学科展望:这为全面理解性染色体演化的一般规律和独特的单孔目哺乳类的研究提出了新的方向。


 

Origin and evolution of platypus sex chromosomes

Speaker: Qi Zhou

Affiliation: Zhejiang University

Keywords: platypus; sex chromosomes; chromosome-level genome assembly

Abstract: Platypus are diverged from most therian mammals and combines features of birds, reptiles and mammals. They have fascinated evolutionary biologists also for their unique five pairs of sex chromosomes that pair with each other in a head-to-tail manner. The origin and evolution of such a unique sex chromosome complex remain unclear because of the low quality of the previous version of genome assembly. By collaborating with Guojie Zhang’s group at University of Copenhagen, we applied third-generation sequencing technology and anchored over 95% of the genome sequences into chromosomes. We report that the sex chromosomes of platypus are more similar to those of birds, rather than to those of mammals. The longest sex chromosome is homologous to the Z chromosome of birds, not to the X chromosome of human. There is no global dosage compensation in the platypus sex chromosomes. We also found that the chain sex chromosome complex of platypus probably originated from an ancestral ring configuration. Our results challenge the classic paradigm of sex chromosome evolution, and offered new insights into the general principles of sex chromosome evolution.

Key question(s): evolution of animal sex chromosomes

Approach(es): genomics

Main group(s): platypus

Conclusion(s): The chain sex chromosomes of playpus originated from an ancestral ring structure

Perspective: Our results challenged the classic paradigm of sex chromosome evolution, offering new insights into the general principles of sex chromosome evolution.


 

Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence

Speaker: Xiao-Fan Zhou

Affiliation: South China Agricultural University

Keywords: phylogenetics; phylogenomics; phylogenetic conflict

Abstract:

Key question(s): Incongruence, or topological conflict, is prevalent in genome-scale data sets. Internode certainty (IC) and related measures were recently introduced to explicitly quantify the level of incongruence of a given internal branch among a set of phylogenetic trees and complementary regular branch support measures (e.g., bootstrap, posterior probability) that instead assess the statistical confidence of inferences. Since most phylogenomic studies contain data partitions (e.g., genes) with missing taxa and IC scores stem from the frequencies of bipartitions (or splits) on a set of trees, IC score calculation typically requires adjusting the frequencies of bipartitions from these partial gene trees. However, when the proportion of missing taxa is high, the scores yielded by current approaches that adjust bipartition frequencies in partial gene trees differ substantially from each other and tend to be overestimates.

Approach(es): To overcome these issues, we developed three new IC measures based on the frequencies of quartets, which naturally apply to both complete and partial trees.

Main group(s): A general phylogenetic method that can be applied on various groups.

Conclusion(s): Comparison of our new quartet-based measures to previous bipartition-based measures on simulated data shows that: (1) on complete data sets, both quartet-based and bipartition-based measures yield very similar IC scores; (2) IC scores of quartet-based measures on a given data set with and without missing taxa are more similar than the scores of bipartition-based measures; and (3) quartet-based measures are more robust to the absence of phylogenetic signal and errors in phylogenetic inference than bipartition-based measures. Additionally, the analysis of an empirical mammalian phylogenomic data set using our quartet-based measures reveals the presence of substantial levels of incongruence for numerous internal branches.

Perspective: Overall, our results suggest that our newly developed quartet-based IC measures are useful for more accurately quantifying phylogenetic incongruence. An efficient open-source implementation of these quartet-based measures is freely available in the program QuartetScores (https://github.com/lutteropp/QuartetScores).


 

哺乳动物高阶元分子系统学研究进展

报告人:周旭明

单位:中国科学院动物研究所

 

关键词:哺乳动物;系统学;分歧时间;科级阶元

摘要:

关键科学问题哺乳动物高级阶元的系统关系,尤其是科级阶元的系统关系目前仍存有争议或未被关注。同时关于第三次生物大灭绝事件(大约发生在Cretaceous-PaleogeneKPg,约65百万年前)所产生空余的生态位是否促进哺乳动物科级阶元多样性的形成,目前也同样存疑且亟需更多数据的验证。

主要方法通过大范围的合作采样和PCR扩增,完善目前最通用构建哺乳动物科级阶元系统树的核基因数据集,计划补充其~85%以上的数据漏洞。随后利用最新的系统发育重建和分化时间估算的方法来进行哺乳动物科级阶元系统关系的重建和分歧时间估计。

主要类群哺乳动物约150个科级阶元。

主要结论本研究从全基因组序列,稀有基因组变异及染色体涂染等几个方面简要介绍了现生哺乳动物分子系统学研究的主要进展和结论,综合已有的研究归纳整理了胎盘亚纲的总目及目间的系统发育关系,总结了哺乳动物科级阶元的研究现状和数据整理情况。本文还分析了哺乳动物系统学目前所面临的主要问题及未来的发展前景及报道了我们在科级阶元系统关系重建方面的进展。

学科展望哺乳动物目级阶元的系统发育已经趋于稳定,部分类群的争议和命名已经得到基因组数据的确认。科级阶元的关系是下一步分子系统学研究的热点,相关结果对于阐述哺乳动物的演化和辐射历史至关重要。

 

 


 

Review of the mammalian phylogenetics

Speaker: Xu-Ming Zhou

Affiliation: Institute of Zoology, Chinese Academy of Sciences

Keywords: Mammals; Molecular systematics; Divergences; Family

Abstract:

Key question(s): The evolutionary history of mammals is a hot topic in the areas of zoology and evolutionary biology. However, the relationship between origin timing and adaptive radiation of Placentalia mammals and KPg (Cretaceous-Paleogene boundary) is controversial and currently four evolutionary models, i.e., “Soft explosive model”, “Hard explosive model”, “Long fuse model” and “Short fuse model” have been suggested by preliminary studies.

Approach(es): Via large scale sampling and PCR amplification, we aimed to fill the ~85% gaps of the largest nuclear alignment that is popularly used by current studies. Then, using phylogenetic tools and molecular dating with fossil calibrations, this project will reconstruct the family-level phylogenetic relationships of mammals, enabling divergence time estimates of the main groups.

Main group(s): ~150 families of mammals.

Conclusion(s): In this paper, we reviewed the interordinal mammalian phylogeny from previous studies, which are resolved phylogenetic relationships of mammals based on whole genome sequences, rare genomic changes, and chromosome painting. A phylogenetic tree for 19 orders was presented and some potential problems and future perspectives for phylogenomics were also addressed. We also provided our progress in building the phylogenetic tree for mammalian families.

Perspective: The interordinal mammalian phylogeny has been extensively investigated via whole genome data and most of controversial nodes have been resolved. However, the phylogenetics of families could be the next hot area for molecular systematics and key to clarification of mammalian diversification and adaptive radiations.

 


 

基于化石证据探讨青藏高原新生代植物多样性的演变

苏涛

中国科学院西双版纳热带植物园热带森林生态学重点实验室

 

印度板块向北漂移与欧亚板块碰撞(55±10 Ma),形成了全球海拔最高、面积最大的高原青藏高原。由于抬升导致的环境效应,地质时期曾分布于高原的众多植物类群在该地区已经不复存在,因此植物化石是探讨这些植物类群分布历史乃至高原植物多样性演变过程的唯一直接证据。我们团队近十年来在青藏高原持续不断地开展相关的野外考察,采集到涵盖古新世至上新世的植物化石标本1万余件,并结合年代地层学证据确定了化石植物群可靠的地质年代。研究结果表明:(1)青藏高原在地质时期(特别是古近纪)具有远远高于现在的植物多样性;(2)青藏高原中部至少在早始新世(~50 Ma)到晚渐新世(~25 Ma)存在高山峡谷地貌,南面为冈底斯山,北面为羌塘山脉,两山之间的低地孕育了众多的植物类群,如绝灭类群兔耳果属(Lagokarpos)、椿榆属(Cedrelospermum)、似浮萍叶属(Limnobiophyllum)等,现生类群如臭椿属(Ailanthus)、栾树属(Koelreuteria)、萝藦亚科(Asclepiadoideae)等;(3)青藏高原对其周边地区,如我国西南、东南亚的植物多样性现代化面貌格局具有重要贡献;(4)由于冈底斯山和喜马拉雅山脉的阻挡,青藏高原和印度板块的植物区系交流较少;(5)青藏高原在古近纪和亚洲乃至整个北半球的植物区系都有着密切的联系。今后需要继续结合古植物学、构造地质学、分子生物学、模型模拟等多学科证据,从而深入理解青藏高原的植物多样性演变历史及其成因。

 

*本研究得到国家自然科学基金(4192201041661134049)、中科院前沿科学与教育局重点研究计划项目(QYZDB-SSW-SMC016)和中国科学院先导专项(XDA20070301XDB26000000)的联合资助。


 


 

青藏高原有刺植物的海拔分布格局及其影响因素

报告人:宋波

单位:中国科学院昆明植物研究所

 

关键词:海拔;植物防御;植物与植食性动物相互作用;刺

摘要:

关键科学问题:海拔啃食防御假说预测,由于更有利的环境条件,低海拔区域动物多样性与丰富度更高,意味着低海拔的植物可能遭受植食性动物啃食的压力更大,生长在这里的植物应当进化出更高水平的防御。刺是一个进化上比较稳定的性状,主要功能在于防御植食性哺乳动物的啃食。因此,我们探讨了青藏高原有刺植物的海拔分布格局及与植食性哺乳动物的关系。

主要方法:利用中国植物志、横断山维管植物名录以及西藏植物志等资料搜集青藏高原分布的1万余种被子植物和200余种植食性哺乳动物的海拔分布数据(600-6000米)。采用逻辑斯蒂回归分析有刺植物与海拔以及植食性哺乳动物的关系。

主要类群:被子植物。

主要结论:研究结果并不支持海拔啃食防御假说:中海拔有刺植物的比例最高(单峰格局)。而且,生活型对刺的分布格局具有显著的影响:单峰格局只出现在多年生草本植物、灌木与乔木类群,一年生有刺植物的分布没有显著的海拔变化规律。进一步分析该区域植食性哺乳动物的分布发现,中海拔的植食性哺乳动物丰富度最高,并且植食性哺乳动物的丰富度与有刺植物的比例在海拔上呈现出显著的正相关关系。结果说明,植食性哺乳动物的丰富度在海拔上的变化可能是驱动有刺植物海拔分布格局变化的主要因素。由于动物丰富度在中海拔最高的分布格局是一个全球范围广泛存在的现象,这种植物防御水平在中海拔最高的分布格局可能也是广泛存在的,而植物与植食性动物之间的防御与反防御协同进化(军备竞赛)可能在一定程度上导致中海拔区域植物与动物的高度分化,为理解全球植物多样性在中海拔最高的分布格局提供了新的视角。

学科展望:研究尺度对研究结果具有显著的影响,标本数据为开展大尺度研究提供了新的思路。


 

Elevational pattern of spinescent plants in Qinghai-Tibetan Plateau

Speaker: Bo Song

Affiliation: Kunming Institute of Botany, Chinese Academy of Sciences

Keywords: elevation; plant defence; plant-animal interaction; spine

Abstract:

Key question(s): In response to higher herbivore pressure, due to higher herbivore diversity and richness because of more favorable environmental conditions, greater investment in plant defences is predicted to occur in the lowlands. Spinescence is considered to evolve primarily as a defence against herbivorous mammals. We tested the elevational variation in spinescent plants in Qinghai-Tibetan Plateau.

Approach(es): We collated binary spinescence data for 10622 angiosperm species ranging from 600 to 6000 m a.s.l. Logistic regression was used to quantify the elevational pattern in spinescence and the association between spinescence and mammalian herbivore richness. 

Main group(s): Angiosperms

Conclusion(s): We found a unimodal relationship between elevation and spinescence, with the highest proportion of spinescent species occurring at mid-elevations. This unimodal relationship was present in perennial herbs, shrubs and trees, but not in annual herbs. Herbivorous mammal richness also showed a unimodal elevational pattern. A positive association between herbivorous mammal richness and the incidence of spinescent species suggests that elevational variation in herbivore pressure from mammals might drive elevational variation in spinescence. Our findings further call into question the elevational herbivory defence hypothesis and shed new light on the potential causes of elevational gradients in plant diversity.

Perspective: Our findings highlight the importance of quantifying geographical gradients in plant defence (and only other traits) over broad gradients, and thus specimen data provides opportunities for large-scale study. 


 

中国亚热带地区蚜虫DNA条形码及其种群分化

李强,邓鋆,陈翠,曾凌达,姚佳敏,林小兰,黄晓磊*

闽台作物有害生物生态防控国家重点实验室,福建农林大学植物保护学院

 

关键词:蚜虫;DNA条形码;鉴定;种群分化;系统发育

摘要:中国亚热带地区具有复杂的地质地貌、气候条件以及非常高的生物多样性,很多蚜虫类群分布在这里,其中包括一些重要的农林业害虫,给农林业生产带来巨大的损失。对于蚜虫的鉴定仍然主要基于形态和生态特征,然而由于蚜虫的表型可塑性以及生态上的复杂性,想要快速而准确地鉴定和划分蚜虫物种存在困难。基于线粒体细胞色素氧化酶亚基ICOI)基因片段的DNA条形码技术越来越被广泛地用来鉴定动物特别是昆虫类群以及划分其分子分类单元(MOTUs)。本研究主要利用DNA条形码技术探究中国亚热带地区蚜虫物种多样性及其种群分化现状,我们对中国亚热带地区10个省份进行广泛地样品采集,涉及244种寄主植物,共获得1581条蚜虫COI序列。基于形态和生态鉴定特征,共鉴定出13亚科146种蚜虫。在DNA条形码分析中,共有117个形态种(82%)成功匹配上三种物种划分方法(ABGDGMYCbPTP)所划定的MOTUs。另外,我们还发现由于寄主植物、地理分布以及一些其他因素的差异,亚热带地区可能存在10个隐存种,我们分别对其描述并讨论可能的诱导原因。本研究也证明了DNA条形码技术能够快速而有效的对蚜虫物种进行鉴定和划分。

 

通讯作者:huangxl@fafu.edu.cn


 


 

中国横断山区淡水蟹多样性进化机制的研究

潘达、史博洋、王儒晓、孙红英*

南京师范大学

 

关键词:淡水蟹;物种多样性;快速多样化;分子系统学;系统地理学

摘要:物种的多样化对现今生物多样性的格局形成起着关键的作用,物种多样化的机制一直是进化生物学中的热点问题。淡水蟹俗称溪蟹或原生淡水蟹(Primary freshwater crab,指整个生活史大都在陆地淡水环境中度过的蟹类隶属软甲纲(Malacostraca)、十足目(Decapoda)、短尾下目(Brachyura)。中国是全球淡水蟹物种多样性最高的国家已描述物种总数达249330种,其区系组成主要为溪蟹科成份(47301种)。横断山区是全球生物多样性的热点地区,在这一地区也有着中国数量最多的淡水蟹物种。然而,淡水蟹在横断山区多样性发生的机制一直缺乏系统调查和研究。

关键科学问题:横断山区淡水蟹物种多样化的机制。

主要方法:1)基于野外调查和形态描述新物种发现与物种分类界定;(2)线粒体基因组进化研究;(3)基于多分子标记的系统地理学和系统进化研究。

主要类群:溪蟹科淡水蟹。

主要结论:1)系统发生重建显示多个溪蟹科的属为非单系;(2)横断山区溪蟹科淡水蟹的线粒体基因组经历了多次的重排,可能与其物种多样化相关;(3)淡水蟹的在横断山区的多样化可能是由多因素导致的,包括由青藏高原隆起导致的地理隔离和形态上对气候的适应并由此导致的生殖隔离。

学科展望:1)继续开展深入的野外调查,摸清中国淡水蟹的物种多样性,为淡水蟹生物多样性保护提供依据;(2)基于系统基因组学研究横断山区淡水蟹物种的系统发生关系;(3)通过转录组和全基因组测序深入了解物种历史种群动态以及物种形成机制和适应进化的分子机制。

 

*通讯作者:sunhongying@njnu.edu.cn

**本研究获得国家自然科学基金项目(项目批准号:31772427)的资助

 


 

 



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