食肉目哺乳动物的系统发育学研究概述

追溯生物界不同生物类型的起源及进化关系，即重建生物类群的系统发育树是进化生物学领域中一个十分重要的内容。食肉目哺乳动物位于食物链顶端，很多成员不仅在我国野生动物保护工作中占有重要地位，而且还是研究动物适应性进化遗传机制的重要模式生物。因而，食肉目物种作为物种资源中的一个重要类群，其系统发育学一直是国内外研究的热门课题。构建可靠的食肉目分子系统树，无疑将具有重要的进化理论意义和保护生物学价值。鉴于目前食肉目各科间系统发育关系仍然处于“广泛争论”的状态，本文将针对食肉目科水平上的系统发育学研究进展，包括来自于形态学特征、细胞学及分子生物学方面的证据，做简要概述，并提出目前研究中存在的问题。这对今后食肉目系统发育方面的进一步研究工作具有指导意义，并为以该类群作为模式生物开展适应性进化研究奠定基础。     

食肉目猫科物种的系统发育学研究概述

猫科动物(Felidae)是食肉目中肉食性最强的一科, 其中许多成员是人们最熟悉、最引人注目的动物, 也是各地的顶级食肉动物。目前37个现存猫科物种中有36个已经被列为濒危和稀有对象。食肉目猫科物种的进化历史是一个快速辐射和较近时期发生的物种形成事件, 使得猫科物种之间系统发育关系的重建非常困难, 一直处于广泛争论的状态。构建可靠的猫科系统发育关系, 具有重要的进化理论意义和保护生物学价值。文章对猫科物种的系统发育学研究进展, 包括来自于形态学特征、细胞学和分子生物学方面的证据做简要概述, 并提出目前研究中存在的问题。以期对今后猫科物种的系统发育方面的进一步研究工作具有指导意义, 并为该类群的生物多样性资源保护提供科学依据。     

中国兽类遗传与进化研究进展与展望

中国兽类物种丰富,且具有150个特有种。本文综述了60年来中国兽类遗传与进化的研究进展,内容涵盖系统发育关系重建、遗传多样性评估、种群遗传结构、适应性进化以及趋同进化的分子机制。本文重点概述了食肉目（大、小熊猫）、有蹄类、翼手目、灵长目、小型兽类以及海兽类等重要类群的研究进展,为中国兽类的物种保护提供了重要资料。另外,本文还对中国兽类遗传与进化研究未来的研究方向提出几点建议,包括运用各种组学技术、筛选新型遗传标记和候选基因（调控序列）、结合表观遗传学并借助进化发育生物学研究方法,以期全面深入地理解中国兽类分类地位、起源以及特异表型产生和独特适应的发育遗传学机制等,进而实现“天人合一”保护生物学的新理念和新愿景。     

麝的系统发育学研究进展

麝Moschus spp.是亚洲地区特产野生动物,具有非常重要的经济和生态价值,为我国一级重点保护物种,已被列入CITES附录Ⅰ中.麝一直为中外学者所关注.目前,麝作为独立的科已被广泛接受,但麝与新反刍下目中其他现生类群的系统发育关系长期处于"广泛争论"状态.本文从形态学、分子生物学等特征对麝的系统发育学研究进行了简要概述,总结了麝与其他新反刍下目现生类群的系统发育关系,提出了一些尚待研究的问题,并对将来的研究工作做出展望.     

基于DNA条形码评估西双版纳国家级自然保护区对樟科植物进化历史的保护

为评估西双版纳国家级自然保护区对樟科这一重要植物类群进化潜力的保护情况, 揭示将物种进化历史纳入生物多样性保护评估的重要性, 本研究通过对西双版纳地区长期的野外调查并查阅标本记录与文献资料, 整理出该地区樟科13属121种物种的具体分布信息, 以植物条形码ITS序列作为分子标记构建了反映整个西双版纳地区樟科植物系统发育关系的系统发育树。我们以此为基础, 从物种层面分析了各物种的进化特异性(evolutionary distinctiveness, ED), 从区域层面分析了自然保护区内、外以及32个行政乡镇的系统发育多样性(phylogenetic diversity, PD), 并结合物种丰富度(species richness, SR)与物种濒危等级, 综合探讨了西双版纳国家级自然保护区对樟科植物进化历史的保护情况。研究发现, 西双版纳国家级自然保护区仅拥有整个西双版纳地区54.5%的樟科物种数, 却保护了该地区樟科植物约88.8%的进化历史, 没有被列入保护范围但却拥有高系统发育多样性的区域有打洛镇、易武乡等。就物种而言, 进化特异性相对较高的19个物种中, 有5种(26.3%)在自然保护区内没有分布; 濒危等级高的54个物种中, 有20种(37.0%)在自然保护区没有分布, 同时拥有高进化特异性和濒危等级的物种仅有1种不在保护区内分布。结果表明, 虽然西双版纳国家级自然保护区对樟科这一植物类群的系统发育多样性以及高保护价值物种的保护较好, 但仍有部分重要樟科植物的进化历史没有涵盖在现有自然保护区范围内; 按照传统方法设定的自然保护区虽能在一定程度上保护樟科物种的进化历史, 但仍然存在与标准化系统发育多样性保护策略相矛盾的地方。因此, 今后在建立自然保护区时, 应将系统发育多样性考虑在内, 以保护生物多样性应对环境变化的潜力。     

贝叶斯推论及其在百合目分子系统学中的应用

贝叶斯推论作为进化生物学的最新进展,在适用复杂模型、大型数据集、计算速度和结果容易解释等方面明显优于其它算法。本文简要介绍了贝叶斯推论原理及其在分子进化和系统发育研究中的重要性,并使用该方法对百合目主要类群的系统发育关系进行了重建。结果显示,百合目rbcL基因最适合的DNA进化模型为GTR I G,贝叶斯法与距离法和最大简约法构建的系统发育树拓扑结构相似,没有显著差异,但是分辨率和支持率明显比后者高。贝叶斯分析结果显示,百合目内划分的7个科,除Smilacaceae科外,其余各科均为高后验概率(PP=1·0)支持的单系类群;文中作者还对各科间的系统关系进行了探讨。     

拟南芥及其近缘种的适应性进化研究

植物如何适应环境变化从而生存繁衍,即适应性进化,是一个自达尔文时代起就备受关注的生物学核心科学问题.随着测序技术的快速发展,植物中各个主要类群均有物种完成了全基因组测序,并且每个物种里有许多样品完成了重测序.除了基因组外,不同维度的组学数据也得到解析,如转录组、甲基化组、小RNA组及蛋白质组等.海量的多维组学数据极大地促进了适应性进化的研究,基于多维组学数据来研究植物适应性进化的过程及机制已成为植物学研究的一个重要领域.十字花科的拟南芥是植物遗传学及分子生物学研究的模式物种,所有的研究结果及各种资源和数据使拟南芥及其近缘种也成为研究进化生物学问题的模式体系.因此,本文综述了围绕拟南芥及其近缘种近年来在植物适应性进化方面取得的重要进展,并在此基础上探讨该领域仍亟待解决的核心科学问题及未来的研究方向.     

净多样化速率和进化时间对虎耳草目科间物种多样性差异的影响

不同生物类群包含的物种数目常存在巨大差异,这是生态学和生物学研究中普遍观察到的现象。然而,这一现象产生的原因仍然是未解之谜。从宏观进化的角度,进化时间假说和多样化速率假说是两个比较流行的假说。进化时间假说认为类群的演化时间越长,积累的物种丰富度越高; 而多样化速率假说认为类群的净多样化速率越快,则其物种丰富度越高。为验证这两个假说,该文以一棵包含1 539个物种化石定年的虎耳草目系统发育树为基础,通过宏观进化分析获取了虎耳草目内15个科的物种形成和灭绝速率,并计算了每个科的平均多样化速率。结果表明:(1)虎耳草目的物种多样化速率有着增加的趋势,并且多样化速率的增加主要出现在温带和高山类群,如茶藨子科、景天科和芍药科等。(2)采用系统发育广义最小二乘模型(PGLS)和线性回归模型(LM)结果表明,虎耳草目15个科的物种丰富度与科的分化时间和科内物种的最近共同祖先年龄都没有显著相关关系,而与净多样化速率显著正相关(R² =0.380,P<0.05)。该研究支持了多样化速率假说,认为不同科的净多样化速率的差异是导致虎耳草目科间物种数目差异的主要原因之一。全球气候变冷可能为虎耳草目中草本、落叶乔木和灌木等能够适应寒冷环境的类群提供了分布范围扩张和物种快速多样化的机会。该研究表明在温带和高山扩张类群中,物种净多样化速率可能是导致不同类群物种数目差异的主要原因。     

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。     

区域生命之树及其在植物区系研究中的应用

区域生命之树是对一个区域内的所有物种进行生命之树重建,在最近10年已成为生命科学领域的研究热点。生命之树反映了物种间的亲缘关系和进化信息,可以将生物区系形成与发展过程中的进化和生态因素联系起来,是揭示区系来源和演化规律的有效手段。本文从3个方面总结了区域生命之树在植物区系研究中的应用:(1)在时间维度上,通过生命之树类群分化时间和进化速率估算,反映区系演化历史,揭示区系的时间分化格局;(2)在空间维度上,结合系统发育信息与物种分布数据,揭示区系内生物多样性的空间格局,并在此基础上进行区系分区;(3)整合生物地理信息和气候环境数据,分析区系中生物类群对古地理事件以及气候变化的响应机制,以揭示形成现存生物多样性格局的生态、地理和历史因素。此外,我们阐述了区域生命之树与全球生命之树之间的关系;指出由于类群取样不全而造成的时间估算偏差是区域生命之树研究中需要注意的问题;建议对生物多样性热点地区从不同尺度进行大数据的整合分析。     

Dogs,cats, and kin: A molecular species-level phylogeny of Carnivora

Phylogenies underpin comparative biology as high-utility tools to test evolutionary and biogeographic hypotheses, inform on conservation strategies, and reveal the age and evolutionary histories of traits and lineages. As tools, most powerful are those phylogenies that contain all, or nearly all, of the taxa of a given group. Despite their obvious utility, such phylogenies, other than summary ‘supertrees’, are currently lacking for most mammalian orders, including the order Carnivora. Carnivora consists of about 270 extant species including most of the world’s large terrestrial predators (e.g., the big cats, wolves, bears), as well as many of man’s favorite wild (panda, cheetah, tiger) and domesticated animals (dog, cat). Distributed globally, carnivores are highly diverse ecologically, having occupied all major habitat types on the planet and being diverse in traits such as sociality, communication, body/brain size, and foraging ecology. Thus, numerous studies continue to address comparative questions within the order, highlighting the need for a detailed species-level phylogeny. Here we present a phylogeny of Carnivora that increases taxon sampling density from 28% in the most detailed primary-data study to date, to 82% containing 243 taxa (222 extant species, 17 subspecies). In addition to extant species, we sampled four extinct species: American cheetah, saber-toothed cat, cave bear and the giant short-faced bear. Bayesian analysis of cytochrome b sequences data-mined from GenBank results in a phylogenetic hypothesis that is largely congruent with prior studies based on fewer taxa but more characters. We find support for the monophyly of Carnivora, its major division into Caniformia and Feliformia, and for all but one family within the order. The only exception is the placement of the kinkajou outside Procyonidae, however, prior studies have already cast doubt on its family placement. In contrast, at the subfamily and genus level, our results indicate numerous problems with current classification. Our results also propose new, controversial hypotheses, such as the possible placement of the red panda (Ailuridae) sister to canids (Canidae). Our results confirm previous findings suggesting that the dog was domesticated from the Eurasian wolf (Canis lupus lupus) and are congruent with the Near East domestication of the cat. In sum, this study presents the most detailed species-level phylogeny of Carnivora to date and a much needed tool for comparative studies of carnivoran species. To demonstrate one such use, we perform a phylogenetic analysis of evolutionary distinctiveness (EDGE), which can be used to help establish conservation priorities. According with those criteria, and under one of the many possible sets of parameters, the highest priority Carnivora species for conservation of evolutionary diversity include: monk seals, giant and red panda, giant otter, otter civet, Owston’s palm civet, sea otter, Liberian mongoose, spectacled bear, walrus, binturong, and the fossa.     

The unusual adaptive expansion of pancreatic ribonuclease gene in carnivora

Pancreatic ribonuclease (RNASE1) is a digestive enzyme that has been recognized to be one of the most attractive model systems for molecular evolutionary studies. The contribution of RNASE1 gene duplication to the functional adaptation of digestive physiology in foregut-fermenting herbivores, mostly in ruminants, has been well documented. However, no one has ever done a comprehensive study on the carnivores, which are sister to the artiodactyls. Here, we sequenced this gene from 15 species of the superfamily Caniformia in order Carnivora, which all have a relatively simple digestive system and lack the microbial digestion in rumen or cecum typical of most herbivores. In contrast to our initial expectation that only a single RNASE1 gene is present in these carnivores, we observed a "birth (gene duplication)-and-death (gene deactivation)" process for the evolution of RNASE1 genes in all 3 species of Mustelidae family examined here, adding the growing diversity of RNASE1 gene family evolution. In addition, bursts of positive selection have been shown to contribute the enigmatic diversification of these RNASE1 genes in Mustelidae. The finding of the adaptive expansion of RNASE1 in animals without foregut fermentation provides another opportunity for further studies of the structure, function, and evolution of this gene, raising the possibility that new tissue specificity or other functions of RNASE1 genes might have developed in these species.     

Mandible shape in marsupial and placental carnivorous mammals: a morphological comparative study using geometric morphometrics

We analysed mandible shape of the orders Dasyuromorpha, Didelphimorphia, and Carnivora using two‐dimensional geometric morphometrics, in order to explore the relationship between shape, size, and phylogeny. We studied 541 specimens, covering most of the genera of the terrestrial Carnivora (115 species) and a wide sample of marsupials (36 species). The observed shape variation had an ecological component. As an example, omnivorous carnivores have thick mandibles and large talonids in the carnassials, while hypercarnivores possess short mandibles and reduced talonids. There is also a discrimination between different taxonomic groups (i.e. marsupials and Carnivora), indicating some kind of constraint. Size explains a large percentage of total variance (large species had shorter and stronger mandibles, with anteriorly displaced carnassials), was significant when phylogeny was taken into account with a comparative method, but not when size and shape were optimized on the phylogeny. Carnivora presents a larger disparity and variation in body size, which could be related to the difference in teeth replacement. The optimization of mandible shape on the phylogenetic tree indicates that functional aspects, such as diet, are a key factor in the evolution of the carnivore mandible, but also that there is a phylogenetic pattern that cannot be explained by differences in diet alone. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 836–855.     

FGF gene family characterization provides insights into its adaptive evolution in Carnivora

Fibroblast growth factors (FGFs) encoded by the FGF gene family can regulate development and physiology in animals. However, their evolutionary characteristics in Carnivora are largely unknown. In this study, we identified 660 sequences of three types of FGF genes from 30 unannotated genomes of Carnivora animals (before 7th May 2020), and the FGF genes from 52 Carnivora species were analyzed through the method of comparative genomics. Phylogenetic and selective pressure analyses were carried out based on the FGF genes of these 52 Carnivora species. The phylogenetic analysis results demonstrated that the FGF gene family was divided into 10 subfamilies and that FGF5 formed one clade rather than belonging to the subfamilies of FGF4 and FGF6. The evolutionary analysis results showed that the FGF genes were prominently subjected to purifying selection and were highly conserved in the process of Carnivora evolution. We also carried out phylogenetic comparative analyses, which indicated that the habitat was one of the factors that shaped the evolution of Carnivora FGF genes. The FGF1 and FGF6 genes were positively selected in the Carnivora animals, and positive selection signals were detected for the FGF19 gene in semiaquatic Carnivora animals. In summary, we clarified the phylogenetic and evolutionary characteristics of Carnivora FGF genes and provided valuable data for future studies on evolutionary characterization of Carnivora animals.     

雪豹保护遗传学和基因组学研究进展

雪豹 (Panthera uncia) 隶属于食肉目猫科豹属,是生活在青藏高原及其周边地区的旗舰物种。随着分子生物学和高通量测序技术的发展,雪豹保护遗传学和保护基因组学研究得到快速的发展,其中非损伤性遗传取样法显著推动了雪豹保护遗传学研究。本文综述了非损伤性遗传取样法在雪豹物种鉴定、个体识别和性别鉴定等研究中的应用,雪豹的系统发生地位、系统地理格局和种群遗传结构及其亚种争议、演化历史、适应性演化和基因组特征等保护遗传学和基因组学方面的研究现状和进展,并对雪豹保护遗传学和基因组学未来发展趋势进行了展望,以期促进雪豹保护生物学研究和保护对策的科学制定。     

Spots, stripes, tail tips and dark eyes: Predicting the function of carnivore colour patterns using the comparative method

Animal colour patterns are adaptive for three reasons: camouflage, communication and physico-physiological functions. This study proposes a conceptual framework for predicting the main adaptive function of carnivore colour patterns based on three factors: visibility, shape and location on the body, as well as, their behavioural ecological correlates. Using a comparative phylogenetic approach, the colour patterns present on the body, the tail and the eyes of 200 species of mammalian carnivores were analysed. Their evolutionary history was reconstructed using MacClade and Maddison's concentrated-changes test was used to test the association between species' colour patterns and their behavioural ecology on a composite phylogeny for all the Carnivora. The results for dark spots, vertical stripes, horizontal stripes, ringed tails, black tail tips, white tail tips, dark eye contour and dark eye patches, are presented. The comparative analyses indicate that spotted, vertically striped and horizontally striped coats evolved for camouflage. Tail markings seem to have evolved for intra- and/or inter-specific communication, while dark markings near and around the eyes are associated with variables consistent with a physico-physiological function. These findings suggest that both the physical environment and animal behaviour are important selective factors driving the evolution of animal colour patterns and that both need to be taken into consideration in future studies of animal coloration.     

Diversification on an ecologically constrained adaptive landscape

We used phylogenetic analysis of body-size ecomorphs in a crustacean species complex to gain insight into how spatial complexity of ecological processes generates and maintains biological diversity. Studies of geographically widespread species of Hyalella amphipods show that phenotypic evolution is tightly constrained in a manner consistent with adaptive responses to alternative predation regimes. A molecular phylogeny indicates that evolution of Hyalella ecomorphs is characterized by parallel evolution and by phenotypic stasis despite substantial levels of underlying molecular change. The phylogeny suggests that species diversification sometimes occurs by niche shifts, and sometimes occurs without a change in niche. Moreover, diversification in the Hyalella ecomorphs has involved the repeated evolution of similar phenotypic forms that exist in similar ecological settings, a hallmark of adaptive evolution. The evolutionary stasis observed in clades separated by substantial genetic divergence, but existing in similar habitats, is also suggestive of stabilizing natural selection acting to constrain phenotypic evolution within narrow bounds. We interpret the observed decoupling of genetic and phenotypic diversification in terms of adaptive radiation on an ecologically constrained adaptive landscape, and suggest that ecological constraints, perhaps acting together with genetic and functional constraints, may explain the parallel evolution and evolutionary stasis inferred by the phylogeny.     

Modeling body size evolution in Felidae under alternative phylogenetic hypotheses

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that "good" phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies.