菌物分类学研究中常见的物种概念

物种是生物多样性与分类学研究的基本单元, 物种识别是生物学研究的基本问题之一。物种的划分一直以来都没有一个明确统一的标准, 这使得分类学多少带有主观的色彩, 并经常被看作艺术而不完全是科学的研究。本文简要概述了菌物分类学研究中常见的3个物种概念, 即形态学种、生物学种和系统发育学种的背景和应用现状, 并通过实例讨论了这3个物种概念的特点及应用中存在的问题, 特别是各个物种概念之间的交错, 以期为菌物分类学研究和物种概念探讨提供参考。     

木蜂属分类学研究概况

木蜂隶属于膜翅目蜜蜂总科蜜蜂科木蜂亚科木蜂族的木蜂属。其个体较大且粗壮,种类多,世界分布广泛,我国种类丰富。该物种在形态、外貌和采食行为上都与木蜂亚科的其他种类有较大差别。简述了木蜂属的分类学和系统发育学研究进展,为进一步研究、保护和利用木蜂资源奠定基础。     

文昌鱼分类学研究及展望

文昌鱼是最接近脊椎动物直接祖先的现生动物,在脊椎动物起源与演化研究中占有极其重要的位置。近年来,对文昌鱼的研究已引起越来越多的科学家的兴趣,然而作为生命科学研究的重要基础,这类动物的分类学研究相对滞后。依据已有的中国文昌鱼资源调查资料,中国沿海文昌鱼的分布应当十分广泛,即只要有适合文昌鱼栖息的沙滩,均有文昌鱼分布的可能。根据目前的分类学研究成果和动物命名法中的优先权原则,建议将产于青岛等地的文昌鱼种名Brnachiostoma belcheri tsingtauense订正为B.japonicus,南方的文昌鱼保留其原种名B.belcheri。由此,目前分布在中国沿海的鳃口文昌鱼属(Branchiostoma)至少有2种,侧殖文昌鱼属(Epigonichthys)有1～3种,漂浮文昌鱼(Amphioxides pelagicus)1种。DNA分子标记技术在文昌鱼分类学研究中将会发挥更大的作用。     

中国植物分类学中的物种问题

Nooteboom和Peter Raven都认为中国的分类学家往往持有狭隘的物种概念,而这是由于他们缺 少足够的标本,尤其是模式标本,因而不能充分研究种的变异性。Raven说这使他相信中国植物分类学 中真正的物种概念颇有模式概念的色彩。他们的说法不无道理。的确,中国的植物区系中可能有大量 的种其真实身份还有讨论的余地。根据单个性状或完全按营养器官性状来命名新种是常有的事。有些 学者甚至把发表新种作为其分类工作的主要目标。现有的、为数非常有限的关于中国植物变异式样研 究的证据证明有些“种”实际上是生态宗(Clinopodium)、地理宗(Cunninghamia和Indigofera)或呈地形 梯度变异式样的分类群(Lespedeza和Rhododendron)而已。根据表型的可塑性变化而命名的种曾经或 仍然被作为“好种”对待(Rorippa)。具各种不同叶形特性的种间杂种的分离系被命名为不同的种 (Ilex)。分类学上本来就已经很复杂的无融合生殖复合体由于新种的不断增加而变得更加复杂 (Malus)。对一个具有复杂变异式样的种的精心研究导致对25个种名的归并,其中有10个是80年代 由中国分类学家发表的(Clematoclethra)。诸如此类的例子随着研究工作的扩大而势必大量增加。传统 植物分类学主要或完全以形态性状为依据。外部形态性状具有比较容易观察和记录的优点。分类学种 概念能满足多种用途分类的需要。但如果把分类学种概念说成是完全凭分类学家个人的主观判断或甚 至偏爱而很难有是非之分就颇成问题了。现在比过去任何时候都有条件对种这个分类阶元作客观的解 释。正确的物种概念来自对植物变异式样及其分类学价值的正确和充分的理解。因此,作为标本室分 类学家,首先要研究尽可能多的标本。其次,尽可能收编来自其他方面的证据是十分可取的。这些证据 即使不是很有用的分类性状,对更好地了解或解释类群的变异式样往往具有重要的意义。分类学家可 借以发现他所寻找的分类群在表型或基因型变异上的间断。对这两种间断的合理应用将导致在许多属内种级水平的更加合理的分类。     

头槽绦虫属的分类学研究

头槽绦虫属)Bothriocephalus Rudolphi,1808)隶属绦虫纲)Cestoidea)假叶目(Pseudophyl lidea)头槽科)Bothriocephalidae),主要寄生于海水及淡水鱼类 ,偶见于两栖类1,典型寄生部位为宿主的前肠 ,可直接影响宿主进食 ,严重时会引起宿主贫血以致死亡。该属包含的种类很多 ,仅Yamaguti21959年记载的寄生于鲤科鱼类的头槽绦虫属就有71种 ,其中危害养殖鱼类健康的多数寄生于淡水鱼类 ,B. scorpii可能是惟一危害海水经济鱼类的种类3.       

黄河中游湿地植物分类学多样性研究

在黄河中游湿地自禹门口至汾河入河口之间设置了13个样地进行植物调查,并将植物物种系统分类学中的分类学差异性指数应用到研究区域物种多样性的测度中。结果显示,样地内共记录植物75种,隶属于2门3纲18目23科61属;按所含物种数的多少统计,在门水平上主要分布在被子植物门(73种),在纲水平上主要分布在双子叶植物纲(57种),在科水平上主要集中在豆科(Leguminosae,11种)、菊科(Compositae,14种)和禾本科(Gramineae,11种),在属水平上主要集中在藜属(Chenopodium,3种)、胡枝子属(Lespedeza,3种)、蒿属(Artemisia,3种)和香蒲属(Typha,3种);一年或两年生植物最多,地上芽植物、地面芽植物和地下芽植物次之的生活型谱特征总体上反映了黄河中游湿地夏季高温多雨、冬季寒冷干旱的气候特征。用平均分类学差异指数(Δ~+)和分类学差异变异指数(Λ~+)对13个样地植物分类学多样性特征的分析表明,Δ~+和Λ~+的理论平均值分别为84.25和425.43;运用双变量分析法将Δ~+和Λ~+进行组合分析,发现汾河入河口样地(S12)的期望值较小,河津市汾河25号坝样地(S8)、闸西侧样地(S9)和万荣县西范控导工程西侧样地(S10)的期望值较大,说明样地S12的物种分类学多样性较大且物种分布较为均一,样地S8、S9、S10则与之相反。Pearson检验结果显示,平均分类学差异指数(Δ~+)、分类学差异变异指数(Λ~+)与Shannon-Wiener指数、Pielou指数、Simpson指数、Patrick指数间均无稳定的相关关系(P0.05)。     

我国涡虫纲分类学的研究

我国涡虫纲分类学的研究李光鹏（黑龙江省科学院自然资源研究所哈尔滨１５００４０）关键词涡虫，涡虫纲，分类学扁形动物门涡虫纲动物生活在海洋、淡水和潮湿的土壤中。多数营自由生活，少数为共生或寄生生活。是一类种类繁多，形态、大小、色泽和栖息环境多样性的动物［...     

科尔沁沙地蒙古族户级水平庭园植物多样性分析——以内蒙古通辽市科尔沁左翼后旗的研究为例

为了表明农户庭园在户级水平上对农业生物多样性保护的作用,在内蒙古通辽市科尔沁左翼后旗采用随机抽样和农户推荐选择20个农户,同时在邻近地区的汉族地区选择10个农户作为对比分析。在此基础上对其家庭庭园采用典型取样法设立30个样方进行调查。结果表明：巴首嘎查庭园植物有100种、哈日乌苏种畜场共有84种、公济号村有87种,包括栽培及野生蔬菜、水果、观赏、药用、饲用等植物。三个村庄庭园植物物种丰富度分析比较发现巴首嘎查的物种丰富度相对最高,而哈日乌苏种畜场的相对最低,反映巴首村对庭园物种多样性保护的贡献相对最大。这些差异是由于自然条件、庭园面积、庭园历史、庭园管理条件及庭园管理者、当地农牧民对庭园植物的传统知识和文化的认识的差异所造成。文末还对调查的三个村庄的庭园植物进行了初步编目。     

十四种凤仙花属植物种皮微形态特征及其分类学意义

通过扫描电镜对凤仙花属(Impatiens)14种植物的种子表皮微形态特征进行了观察。根据种皮表面纹饰及衍生物的特点,将该属植物的种皮微形态特征划分为4种类型,即光滑型、颗粒型、网状型和隆起型,后两者又可细分为若干亚型,其中负网状亚型和网状-丘状隆起亚型为首次报导。研究表明,14种凤仙花属植物种子表皮微形态特征差异显著,它们作为属内种的分类鉴别特征具有重要价值;种子表皮的微形态学特征与其植物体的部分表型特征具有相关性,在一定程度上反映了属内类群的分化。     

我国直翅目昆虫细胞分类学研究现状

从研究材料、研究方法、染色体研究在昆虫分类上的应用 3个方面对我国昆虫尤其是直翅目昆虫的细胞分类学研究情况作了简要的概述 ,并着重论述了直翅目昆虫的核型及带型的研究现状 ,同时对我国直翅目昆虫分类学的发展前景进行了展望     

Integrative taxonomy uncovers hidden species diversity in the rheophilic genus Potamometra (Hemiptera: Gerridae)

The genus Potamometra Bianchi, 1896 represents big rheophilic semi-aquatic bugs that typically inhabit middle-altitude mountainous streams. Here, we integrated molecular and morphological data for delimiting species boundaries and understanding the evolutionary history of the genus Potamometra. Twenty-seven complete mitochondrial genomes of Potamometra were sequenced, with samples representing most of the known geographically distributed locations around the Sichuan Basin. The results of different species delimitation methods (ABGD, bPTP, GMYC and BPP) based on the monolocus or multilocus data strongly supported the existence of two cryptic new species (Potamometra anderseni Zheng, Ye & Bu, sp. nov. and Potamometra zhengi Zheng, Ye & Bu, sp. nov.) although more entities were found in the tree-based delimitation methods. The two new species were successfully validated using morphological characters within a detailed taxonomic framework. Phylogenetic analyses supported the reciprocal monophyly of the seven highly node-supported clades, which were matched with the five known species and two new taxa. A novel gene arrangement pattern that two trnF (trnF1 and trnF2) genes separated by an intergenic spacer (IGS) were found in all the species except the sister group of Potamometra berezowskii Bianchi, 1896 and Potamometra linnavuorii Chen, Nieser & Bu, 2016. This gene rearrangement event could be explained by the tandem duplication and random loss (TDRL) model. Our study emphasized that the combination of molecular sequence data, morphological characters and mitochondrial structural information could improve the accuracy of species delimitation.     

中国沙拐枣属植物的数值分类研究

选择了中国19种沙拐枣属（CalligonumL.)植物,共测定及引用了35个形态分类指标,应用单因素方差分析（MANOVA）和主成分分析（PCA）,分别对形态因子进行了单元和多元分析。结果表明,所有的种间形态指标均差异显著,冠幅（BC）,木质枝枝节长度（LKWB）,果实直径（DF）,雄蕊长度（SL）,同化枝枝节长度（LKAS）和同化枝化枝角度（ARAS）指标在沙拐枣属植物的数值分类上,具有很强的差异性分析意义。依据平方欧氏距离,应用类平均法（UPGMA）将19种沙拐枣植物聚为5类,系统聚类结论与主成分分析的三维排序结果基本一致,与传统的形态分类结果有一定的差异。     

Take up the challenge! Opportunities for evolution research from resolving conflict in integrative taxonomy

What's in a species? The multiple connotations of the question tend to lack simple answers, and not surprisingly so. For example, speciation is a gradual process. Can we say when exactly a child has become an adult? We have precocious youngsters and late bloomers, and often, adults are in some ways childish. There are many triggers for and routes to adolescence. All this holds for speciation, and delimiting species can therefore be a tricky task. Recently, the field of integrative taxonomy has emerged—species delimitation based on multiple sources of evidence. Given that we expect species to exhibit peculiarities in at least one or a few aspects, might it be their alleles of a gene, their morphology, chemistry, behaviour, ecology, reproductive compatibility, or whatever, investigating not just one but several of these aspects makes it more likely that we capture such peculiarities. If the same pattern is found multiply, we talk about agreement among disciplines, and species delimitation is easy. But what if different disciplines tell different stories? Such disagreement makes species delimitation more difficult but is also an opportunity for evolutionary biology (Schlick‐Steiner et al. 2010). In this issue of Molecular Ecology, Andújar et al. (2014) present a comprehensive integrative‐taxonomic case study of Mesocarabus ground beetles including nomenclatural consequences. They resolve extensive disagreement among disciplines by invoking evolutionary explanations, and the process of conflict resolution thus advances knowledge on species boundaries and evolutionary processes simultaneously.     

我国及周边地区松属白松亚组系统学研究进展和保护现状

合理的物种划分和深入的系统学研究对理解物种的进化历史、物种编目以及生物多样性保护具有重要意义。松属(Pinus)是裸子植物中最大的一个属, 也是北半球针叶林的重要组成成分。白松亚组(Subsect. Strobus)隶属于松属白松亚属(Subg. Strobus)五针松组(Sect. Quinquefoliae), 是松属物种数目最多的亚组之一, 其中半数以上物种分布在我国及周边地区。白松亚组(又称五针松亚组)所有物种针叶均为五针一束, 由于形态相近、种间遗传分化小和野外调查不充分, 这些五针松的物种界定和种间关系一直存在很多争议。此外, 亚热带地区大多数五针松物种的地理分布非常狭窄或群体片断化严重, 已有多个物种被IUCN评估为受威胁物种。在2021年9月我国新发布的《国家重点保护野生植物名录》中, 大别山五针松(Pinus dabeshanensis)和毛枝五针松(P. wangii)也由原国家二级保护野生植物调升为国家一级保护野生植物。近年来, 得益于系统发育基因组学在裸子植物等大基因组的木本植物类群中的成功应用, 我国及周边地区五针松的种间关系和群体历史得到初步解析。本文主要回顾和总结了我国及周边地区的五针松在系统分类、群体遗传及物种保护等方面取得的进展和存在的不足, 提出未来应当充分重视基础研究和野外调查, 并加强学科交叉以及新技术和新方法在相关研究中的应用以实现濒危物种的精准保护。     

Employing statistical learning to derive species-level genetic diversity for mammalian species

1. The patterns of genetic diversity in several genomic regions have been used in mammalian systematics for decades. For instance, when studying closely related species, it is generally assumed that the mitochondrial cytochrome b gene (cytb) exhibits significant information that can be used for differentiation between intraspecies and interspecies variation in mammals. Because of sampling limitations, early analyses of this proposition were conducted mainly on rodents and bats.
2. Currently, more than 57000 cytb sequences are available covering all major lineages of mammals, and sequencing of several individuals per species is common practice in molecular systematics. We were thus prompted to carry out a large-scale analysis of the utility of cytb genetic variation as a predictor of whether a pair of sequences came from within-species or between-species comparisons.
3. Using predetermined species-level assignments, we employed standard methods from statistical learning to calculate the cut-off values able to classify genetic distances in either intraspecies or interspecies categories; we then measured the performance of such statistical classifiers to predict the species-level taxonomic rank as defined by experts.
4. Depending on the classifier, our results showed that when adopting cytb distance cut-off values of 7.3% and 5.5% for small mammals (Metatheria, Rodentia, Chiroptera, and Eulipotyphla) and 4.3% and 3% for medium-sized to large mammals (Primates, Carnivora, and Artiodactyla), the frequency of incorrect assignment of within-species divergences to the between-species category (type I error) varied from 7 to 11%.
5. In order to avoid over-splitting by future researchers, we calculated cut-off values using a more conservative evaluation and provided a list of mammalian species that are likely to consist of complexes of cryptic species. We show that our supervised method can provide practical guidelines to improve the performance of unsupervised algorithms for species delimitation. Finally, we discuss limitations of large-scale approaches (e.g. effects of misclassification in databases and the need for case-by-case evaluation of cryptic species complexes) and their consequences for conservation policies.

     

Integrative taxonomy of the primitively segmented spider genus Ganthela (Araneae: Mesothelae: Liphistiidae): DNA barcoding gap agrees with morphology

Species delimitation is difficult for taxa in which the morphological characters are poorly known because of the rarity of adult morphs or sexes, and in cryptic species. In primitively segmented spiders, family Liphistiidae, males are often unknown, and female genital morphology – usually species‐specific in spiders – exhibits considerable intraspecific variation. Here, we report on an integrative taxonomic study of the liphistiid genus Ganthela Xu & Kuntner, 2015, endemic to south‐east China, where males are only available for two of the seven morphological species (two known and five undescribed). We obtained DNA barcodes (cytochrome c oxidase subunit I gene, COI) for 51 newly collected specimens of six morphological species and analysed them using five species‐delimitation methods: DNA barcoding gap, species delimitation plugin [P ID(Liberal)], automatic barcode gap discovery (ABGD), generalized mixed Yule‐coalescent model (GMYC), and statistical parsimony (SP). Whereas the first three agreed with the morphology, GMYC and SP indicate several additional species. We used the consensus results to delimit and diagnose six Ganthela species, which in addition to the type species Ganthela yundingensis Xu, 2015, completes the revision of the genus. Although multi‐locus phylogenetic approaches may be needed for complex taxonomic delimitations, our results indicate that even single‐locus analyses based on the COI barcodes, if integrated with morphological and geographical data, may provide sufficiently reliable species delimitation. © 2015 The Linnean Society of London     

Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South-East Asian waters

The decapod family Penaeidae comprises most of the economically important marine shrimp species. Its members are widespread throughout the world, with its highest species diversity centred in the Indo-West Pacific region. Despite this importance, their taxonomy, classification and phylogeny are not yet settled due in part to incongruence among hypotheses proposed from molecular versus morphological studies. In this study, using a thorough taxonomic sampling of especially the South-East Asian species, we aim to (a) utilize a reconstructed phylogeny to test the monophyly of the Penaeidae and its currently recognized genera and (b) explore its species diversity in South-East Asian waters. To infer the phylogeny, a combined gene data set (including 109 ingroup and six outgroup taxa) of mitochondrial genes, COI and 16S rRNA, and two nuclear genes, NaK and PEPCK, was utilized. To explore its diversity, another data set that included 371 COI gene sequences (231 newly generated and 140 retrieved from public sources) was compiled and subsequently analysed with two different tools (ABGD and bPTP) for species delimitation. Other than supporting the non-monophyly of the Penaeidae with the Sicyoniidae nested within the penaeid tribe Trachypenaeini, the genera Penaeus, Mierspenaeopsis and Parapenaeopsis were also revealed to be polyphyletic. Our species delimitation analysis inferred that 94 putative species actually existed within the 71 morphospecies reviewed, indicating an underestimated biodiversity in this family and the potential presence of new species within the following morphospecies: Kishinouyepenaeopsis cornuta, K. incisa, Mierspenaeopsis sculptilis, M hardwicki, Parapenaeopsis coromandelica and Penaeus monodon.     

Primate taxonomy: Species and conservation

Primatology as a discrete branch of science involving the study of primate behavior and ecology took off in the 1960s after discovery of the importance of primates as models for biomedical research and the realization that primates provide insights into the evolutionary history of humans. Osman Hill's unfortunately incomplete monograph series on the comparative anatomy and taxonomy of the primates¹ and the Napiers' 1967 A Handbook of Living Primates² recorded the world's view of primate diversity at this time. This taxonomy remained the baseline for nearly three decades, with the diversity of each genus being represented by some species, but extensively as subspecies.