中国眼裸藻属(Euglenaria)分类学研究

为对眼裸藻属Euglenaria Karnkowska, Linton&Kwiatowski进行分类学修订,研究以采自中国的12株3种眼裸藻属物种为材料,基于形态学和分子生物学手段对眼裸藻属进行系统发育研究,鉴定了3种眼裸藻属物种,分别是尾眼裸藻Euglenaria caudata (Hubner) Karnkowska et Linton、项圈眼裸藻Euglenaria anabaena(Mainx) Karnkowska et Linton和棒形眼裸藻Euglenaria clavata (Skuja) Karnkowska et Linton,提供了它们的形态特征及分子数据。基于最大似然法和贝叶斯法构建了系统发育树,以亲缘关系较近的双鞭藻科Eutreptiaceae Hollande物种为外类群,其余的裸藻类分为扁裸藻科Phacaceae Kim, Triemer&Shin和裸藻科Euglenaceae Dujardin物种两大支,眼裸藻属位于裸藻科分支(0.84/-),共包含28株眼裸藻属物种,主要分为3个小分支,每个小支的支持率均高达99%以上,项圈眼裸藻和尾...     

中国淡水胭脂藻属植物形态及分子系统发育分析

以云南省玉溪市和河南省焦作市新采集的2株淡水胭脂藻标本为材料, 对其进行形态特征观察和分子系统发育分析, 联合我国已报道的其他胭脂藻序列信息, 构建该属植物可靠的系统发育关系。根据其现代地理分布模式, 对胭脂藻属进行了祖先地理起源重建。基于rbcL、psbA和UPA序列, 利用贝叶斯法、最大似然法和邻接法构建的系统发育树高度一致, 研究中的标本与鸡公山胭脂藻H. jigongshanensis聚合为一个独立分支, 并得到了很高的支持率, 根据分子生物学证据, 将其鉴定为鸡公山胭脂藻。通过研究中所采集2株鸡公山胭脂藻的形态特征比较, 发现传统的形态分类特征包括藻体高度和细胞直径, 在不同的环境条件下是可变的, 不适合作为胭脂藻属植物种类鉴定的依据。对于胭脂藻属这一形态结构较为简单的类群, 必须借助分子生物学证据和系统发育分析手段对其进行种类鉴定和系统发育分析。分子系统发育分析结果表明, 中国特有种鸡公山胭脂藻H. jigongshanensis形成单系类群, 其与日本胭脂藻H. japananense亲缘关系较近, 所有淡水胭脂藻种类形成一个独立的聚类群, 与海洋种类遗传差异较大。祖先地理重建的分析结果表明, 淡水胭脂藻的祖先起源地位于北美洲, 然后逐渐向东加勒比海区域、拉丁美洲和欧亚大陆扩散, 形成现代地理分布模式。胭脂藻属独特的种类地理分布特点, 可能与其较为古老的起源时间和漫长的进化历史相关, 同时淡水胭脂藻在北美洲区域起源时间较早, 进化历史漫长, 遗传多样性大, 这与该地理区域分布的种类H. angolensis为多系类群是相一致的。     

基于叶绿体psaA和psbA基因的中国熊野藻属植物系统发育分析

以中国产熊野藻属Kumanoa的两个种, 绞扭熊野藻K. intorta (=绞扭串珠藻Batrachospermum intortum), 弯形熊野藻K. curvata (=弯形串珠藻B. curvatum)和其他6种淡水红藻为实验材料, 对其psaA和psbA基因进行扩增和测序, 并与GenBank中相近序列进行比对分析, 以贝叶斯法、最大似然法和邻接法分别构建了单基因和联合基因系统发育树. 结果表明, 3种方法构建的系统树具有相似的拓扑结构, 反映的系统发育关系基本一致, 熊野藻属中的两个种聚为一支, 与串珠藻属相分离, 支持该属的建立; 中国产的熊野藻属分子学研究结果与来自南美洲及澳洲的该属植物结果一致, 说明该属的建立具有广泛的地理适用性. 系统发育树聚类结果也明确反映了熊野藻属与串珠藻属较近的亲缘关系, 根据果胞枝形态特点, 推测熊野藻属进化地位晚于串珠藻属植物, 而早于顶丝藻目和红索藻目. 此外, 胶串珠藻与其他串珠藻组植物分离, 支持将其单独分组, 红索藻目植物与串珠藻目植物分离, 支持红索藻目的建立. 同时也表明psaA和psbA基因用于淡水红藻分析, 能够较好地反映其系统发育关系.       

绣球属(Hydrangea L.)植物分子系统学及系统发育分析

该研究基于对绣球属(Hydrangea L.)的大尺度取样,选取国内外61种绣球属和近缘属植物,分别基于核基因片段(ITS)和叶绿体基因片段(rbcL,trnL-F,atpB)重建了绣球属及其近缘种属的系统发育关系。结果表明:(1)核基因与叶绿体基因树之间在树形上没有明显的冲突,进而基于核基因和叶绿体基因联合数据重建了绣球属及其近缘种属的系统发育关系。(2)基于联合数据构建的系统树确认了2个大分支,并得到了果实顶端截平与否这一形态学证据的强力支持;每个大分枝又分为4个类群,共确定了8个类群。部分类群也得到了广义宏观形态性状的支持,如第1类群得到了叶形、花粉以及种子形态的支持。因此,该系统发育关系的重建对于全面理解绣球属及其近缘种属的演化关系具有重要的启发。     

基于种皮形态和叶绿体trnL-F对菘蓝属（十字花科）的系统学位置研究

利用种皮微形态观察与叶绿体DNA的trnL内含子和trnL-F基因间隔区序列测定分析相结合,对十字花科菘蓝属植物及其相关属种的系统学关系进行了探讨.研究结果表明原属独行菜族的菘蓝属植物,其种皮特征与原属鸟头荠族的舟果荠属植物相似,同属一类型.而与独行菜族的模式属独行菜属植物、大蒜芥族的模式属大蒜芥属植物以及鸟头荠族的模式属鸟头荠属植物种皮微形态差异显著;在基于叶绿体DNA的trnL内含子和trnL-F基因间隔区序列所构建的系统发育树中,菘蓝属植物与舟果荠属植物距离最近,而与独行菜属、大蒜芥属、鸟头荠属植物具有一定的间隔,结合形态特征,本研究认为,菘蓝属与舟果荠属植物具有较近的亲缘关系,而不是同族的独行菜属植物.     

藻类植物叶绿体基因组研究进展

藻类植物的cpDNA结构复杂,普遍缺失反向重复序列IR,且存在IR的藻类植物种类的cpDNA也有IR变短退化迹象.藻类植物的cpDNA包含的基因一般比高等植物要多,编码能力更强.藻类植物cpDNA全序列的测定方法主要是Fosmid文库构建,配合使用Long-PCR技术.该文对国内外有关藻类植物叶绿体基因组结构、叶绿体编码基因、叶绿体基因组在藻类系统发育中的应用以及藻类植物叶绿体基因组的提取和序列测定方法等进行综述,为藻类植物的系统发育和叶绿体起源以及功能基因组学的研究提供理论依据.     

裸藻类植物的分支系统学研究

本文选取了裸藻类的33个属级分类单位,以及它们的35个性状,利用分支系统学的原理和方法,对性状的演化极性进行了分析,同时对性状间的极性关系进行了和谐性分析,使性状间极性关系处在较为合理的状态,然后建立了分支分析的数据矩阵。应用徐克学建立的“演化极端结合法”进行微机运算．得简约系数远小于1(o．2159)的分支谱系图。根据分支诺系图对裸藻类的系统发育关系进行了探讨,井与已有的关于裸藻类分类系统和演化假设进行了比较。在此基础上按照裸藻类的亲缘关系及单系原则,对裸藻类的分类等级进行了划分,初步提出了建立1门1纲5目的分类系统。按照在分支谱系中的演化地位,认为裸藻属的5个亚属,明显地都应是独立的属。同时对裸藻类的共生起源与演化的关系也进行了讨论。     

基于rbpL片段对瑞香科沉香基原植物系统发育研究

以NCBI数据库中瑞香科植物叶绿体rbpL基因为目标片段,构建该科植物的系统发育关系树,并结合已报道的沉香基原植物对瑞香科中潜在结香树种进行探讨。研究明确了结香树种在瑞香科系统发育关系中的地位,同时也获得与结香树种亲缘关系较近的种属(Octolepis、Lethedon、Arnhemia、Daphnopsis、Solmsia、 Deltaria),为扩大结香树木种质资源提供依据。     

衣藻属的系统发育分析——基于形态形状和nrDNA ITS序列

通过实验分析莱茵衣藻 ( Chlamydomonas reinhardtii) 1个种和互连网获得衣藻属 1 5个种及丝藻属 1个种 ( Ulothrix zonata) ,共 1 7个种的 nr DNA ITS序列 ,并以 U.zonata为外类群 ,采用计算机分析软件包对其进行分析及构建分子系统发育树图。同时以 1 2个传统分类性状 ,对此 1 6种衣藻构建数据矩阵 ;以 U.zonata动孢子的相应性状为外类群原始性状 ,用Wagner法在计算机上对其进行分枝分析 ;然后比较并分析分子系统树和表征性状分支分析树的异同。初步尝试以 ITS分子序列系统发育分析作为传统性状分析的补充来研究衣藻种间的亲缘关系。     

囊裸藻属与陀螺藻属囊壳微细结构及元素组成比较

对采自自然水体中囊裸藻属(Trachelomonas)的8种和陀螺藻属(Strombomonas)的两种藻类的囊壳微细结构和元素组成进行了比较分析,并探讨了这两个属的系统演化关系.结果表明:组成囊壳的矿质元素主要是铁和硅,在陀螺藻和表面粗糙的囊裸藻中,硅的含量较高,铁的含量相对较低;在大多数囊裸藻中,尤其是表面致密、光滑的种类中,铁的含量较高,硅的含量较低,矿质元素的组成与囊壳的颜色无直接关系.建议将陀螺藻属(Strombomonas)撤消,原陀螺藻属的种作为囊裸藻属(Trachelomonas)中的一个种组(Group),它们是裸藻科中最原始的具囊壳的类群.     

Phylogenetic and Morphological Evolution of Green Euglenophytes Based on 18S rRNA

Green euglenophytes are a group of eukaryotes with ancient origin. In order to understand the evolution of the group, it is interesting to know which characteristics are more primitive. Here, a phylogenetic tree of green euglenophytes based on the 18S rRNA gene was constructed, and ancestral states were reconstructed based on eight morphological characters. This research clarifies the phylogenetic relationships of green euglenophytes and provides a basis for the study of the origin of these plants. The phylogenetic tree, which was constructed by Bayesian inference, revealed that: Eutreptia and Eutreptiella were sister groups and that Lepocinclis, Phacus, and Discoplastis were close relatives; Euglena, Cryptoglena, Monomorphina, and Colacium were closely related in addition to Trachelomonas and Strombomonas; and Euglena was not monophyletic. An ancestral reconstruction based on morphological characters revealed seven primitive character states: ductile surface, spirally striated, slightly narrowing or sharp elongated cauda, absence of a lorica, chloroplast lamellar, shield or large discoid, pyrenoid with sheath, and with many small paramylon grains. However, the ancestral state of the length of the flagellum could not be inferred. Euglena and Euglenaria, which both possessed all of the ancestral character states, might represent the most ancient lineages of green euglenophytes.     

Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon‐rich Analyses of Five Genes

Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions of three nuclear‐encoded genes (nSSU, nLSU, hsp90), one chloroplast‐encoded gene (cpSSU) and one nuclear‐encoded chloroplast gene (psbO) to estimate phylogenetic relationships among 59 photosynthetic euglenid species. Our results were consistent with previous works; most genera were monophyletic, except for the polyphyletic genus Euglena, and the paraphyletic genus Phacus. We also analyzed character evolution in photosynthetic euglenids using our phylogenetic tree and eight morphological traits commonly used for generic and species diagnoses, including: characters corresponding to well‐defined clades, apomorphies like presence of lorica and mucilaginous stalks, and homoplastic characters like rigid cells and presence of large paramylon grains. This research indicated that pyrenoids were lost twice during the evolution of phototrophic euglenids, and that mucocysts, which only occur in the genus Euglena, evolved independently at least twice. In contrast, the evolution of cell shape and chloroplast morphology was difficult to elucidate, and could not be unambiguously reconstructed in our analyses.     

Molecular phylogeny,analysis of character evolution,and submersible collections enable a new classification of a diverse group of gobies (Teleostei: Gobiidae: Nes subgroup), including nine new species and four new genera

The Nes subgroup of the Gobiosomatini (Teleostei: Gobiiformes: Gobiidae) is an ecologically diverse clade of fishes endemic to the tropical western Atlantic and eastern Pacific oceans. It has been suggested that morphological characters in gobies tend to evolve via reduction and loss associated with miniaturization, and this, coupled with the parallel evolution of adaptations to similar microhabitats, may lead to homoplasy and ultimately obscure our ability to discern phylogenetic relationships using morphological characters alone. This may be particularly true for the Nes subgroup of gobies, where several genera that are diagnosed by ‘reductive characters’ have been shown to be polyphyletic. Here we present the most comprehensive phylogeny to date of the Nes subgroup using mitochondrial and nuclear sequence data. We then evaluate the congruence between the distribution of morphological characters and our molecular tree using maximum‐likelihood ancestral state reconstruction, and test for phylogenetic signal in characters using Pagel's λ tree transformations (Nature, 401 , 1999 and 877). Our results indicate that all of the characters previously used to diagnose genera of the Nes subgroup display some degree of homoplasy with respect to our molecular tree; however, many characters display considerable phylogenetic signal and thus may be useful in diagnosing genera when used in combination with other characters. We present a new classification for the group in which all genera are monophyletic and in most cases diagnosed by combinations of morphological characters. The new classification includes four new genera and nine new species described here, many of which were collected from rarely sampled deep Caribbean reefs using manned submersibles. The group now contains 38 species in the genera Carrigobius gen. nov., Chriolepis, Eleotrica, Gobulus, Gymneleotris, Nes, Paedovaricus gen. nov., Pinnichthys gen. nov., Psilotris, and Varicus. Lastly, we provide a key to all named species of the Nes subgroup along with photographs and illustrations to aid in identification.     

Cladistic analysis of blue-green procaryote interrelationships and chloroplast origin based on 16S rRNA oligonucleotide catalogues

Oligonucleotide catalogues from 16S rRNA have been a major source of information for phylogenetic reconstruction among procaryotes. Several large procaryote groups have been analyzed and phylogenies presented. Catalogues are also available for many chloroplasts. The hypotheses of phylogeny are derived mainly from similarity (phenetic) comparisons of the catalogues and the extent of the homoplasy (parallelisms and reversals) involved has not been estimated properly. Although catalogues are currently being superseded by complete sequence data, an evaluation of the strength of catalogue data, and hence of the strength of the extensive phylogenetic hypotheses derived from them, is in order. Cladistic analysis of 16S rRNA oligonucleotide catalogues from three blue-green procaryotes, Prochloron, and chloroplasts of a red alga, Euglena, a green alga and two flowering plants shows that there is extensive homoplasy in the catalogues and several phylogenetic trees are possible. The corresponding consensus trees indicate that little or nothing can be said about interrelationships and chloroplast origin on the basis of these particular catalogues, except that Prochloron may be more closely related to the blue-greens than to chloroplasts.     

Phylogenetic position and delimitation of the moss family Plagiotheciaceae in the order Hypnales

The phylogenetic position and generic composition of the moss family Plagiotheciaceae were explored using DNA sequence data from three genomes: plastid trnL‐F and rps4, mitochondrial nad5 intron and nuclear ITS1‐5.8S‐ITS2. Our phylogenetic analyses included 35 terminals from Plagiotheciaceae and 71 outgroup taxa from a representative set of hypnalean moss families. The family Plagiotheciaceae is resolved in the early‐diverging Hypnales grade, together with Fontinalaceae, Habrodontaceae and several genera which are mainly distributed in the area of the former Gondwanan supercontinent. However, monophyly of the family can only be attained if the three Southern Hemisphere genera, Acrocladium, Catagonium and Rhizofabronia, are excluded. Ancestral state reconstruction for eight morphological characters reveals that many characters used to delimit the family, such as a lack of pseudoparaphyllia and rhizoids inserted in the leaf axils, were already present in the ancestor of Hypnales. Dispersal–vicariance analysis suggests that Plagiotheciaceae and Fontinalaceae have their ancestral distributions in the area of the former Laurasian supercontinent. As the analyses also reveal a Gondwanan distribution for the ancestor of Hypnales in general, Plagiotheciaceae and Fontinalaceae represent the first diverging Laurasian lineages in the order. © 2013 The Linnean Society of London     

Cytological Characterization of a Giant Strain of Euglena gracilis Obtained from Dark-starved Cultures

Euglena gracilis green cells were dark-starved for four months. After this period almost the entire population died, while a few giant, viable cells appeared in the culture. The giantism was maintained after repeated subcultures in growth medium in light or dark conditions. However, the phenomenon was not permanent, and the morphological characteristics of the wild-type Euglena were gradually restored. In giant cells nuclei enlarged greatly, DNA content increased and the Golgi apparatus greatly proliferated. Chloroplasts and mitochondria increased in number and size and often presented structural modifications when compared with normal Euglena. Importantly, in the giant cells that were maintained in darkness in resting or growth conditions chloroplasts persisted as structured organelles which appeared red-fluorescent under UV illumination. Whether giantism is a phenotypic or a genotypic change is still debated. In our case, the evolution of this phenomenon, chiefly the enhanced DNA content, suggests that teratism is a multiploid mutation with the possibility of a return to the normoploid condition. Constitutive chloroplasts are present in most algae, except for a few species, among which is Euglena gracilis. The persistence of differentiated plastids in darkness in giant Euglena is considered to be a return to an ancestral condition and may, therefore, be phylogenetically important.     

Phylogeny of the neotropical rove beetle genus Nordus (Coleoptera: Staphylinidae) with a special reference to the evolution of coloration and secondary sexual characters

Abstract. A phylogenetic analysis for Nordus is provided; the monophyly of the genus is established and the phylogenetic relationships of its thirty-eight species are resolved. Analysis of eighty-seven morphological characters, including two coloration characters, produced four equally most-parsimonious trees (tree length = 365, consistency index = 0.38, retention index = 0.66). The coloration of the head and thorax is examined in the context of the reconstructed phylogeny and the evolution of heterochromy is discussed. Golden-orange coloration of the head and thorax evolved in the ancestor of Nordus. Black coloration of the head evolved at least five times, and black coloration of the thorax at least six times within the genus. The evolution of secondary sexual structures in Nordus is also examined in the context of the phylogeny. In males, a medial emarginate abdominal sternum VIII is the ancestral condition. The presence of a single large median lobe on sternum VIII or the presence of two elongate median lobes with a medial emargination on sternum VIII each represent independent evolution of modifications to the male sternum VIII in different lineages. In females, an unmodified abdominal sternum VIII is the ancestral condition. Evolution of an emargination, small lobe or pointed lobe on the margin of sternum VIII in females occurred in different lineages.     

TESTING FOR UNEQUAL AMOUNTS OF EVOLUTION IN A CONTINUOUS CHARACTER ON DIFFERENT BRANCHES OF A PHYLOGENETIC TREE USING LINEAR AND SQUARED-CHANGE PARSIMONY: AN EXAMPLE USING LESSER ANTILLEAN ANOLIS LIZARDS

Although a large body of work investigating tests of correlated evolution of two continuous characters exists, hypotheses such as character displacement are really tests of whether substantial evolutionary change has occurred on a particular branch or branches of the phylogenetic tree. In this study, we present a methodology for testing such a hypothesis using ancestral character state reconstruction and simulation. Furthermore, we suggest how to investigate the robustness of the hypothesis test by varying the reconstruction methods or simulation parameters. As a case study, we tested a hypothesis of character displacement in body size of Caribbean Anolis lizards. We compared squared-change, weighted squared-change, and linear parsimony reconstruction methods, gradual Brownian motion and speciational models of evolution, and several resolution methods for linear parsimony. We used ancestor reconstruction methods to infer the amount of body size evolution, and tested whether evolutionary change in body size was greater on branches of the phylogenetic tree in which a transition from occupying a single-species island to a two-species island occurred. Simulations were used to generate null distributions of reconstructed body size change. The hypothesis of character displacement was tested using Wilcoxon Rank-Sums. When tested against simulated null distributions, all of the reconstruction methods resulted in more significant P-values than when standard statistical tables were used. These results confirm that P-values for tests using ancestor reconstruction methods should be assessed via simulation rather than from standard statistical tables. Linear parsimony can produce an infinite number of most parsimonious reconstructions in continuous characters. We present an example of assessing the robustness of our statistical test by exploring the sample space of possible resolutions. We compare ACCTRAN and DELTRAN resolutions of ambiguous character reconstructions in linear parsimony to the most and least conservative resolutions for our particular hypothesis.     

Evolution of life history and behavior in Hominidae: Towards phylogenetic reconstruction of the chimpanzee–human last common ancestor

The origin of the fundamental behavioral differences between humans and our closest living relatives is one of the central issues of evolutionary anthropology. The prominent, chimpanzee-based referential model of early hominin behavior has recently been challenged on the basis of broad multispecies comparisons and newly discovered fossil evidence. Here, we argue that while behavioral data on extant great apes are extremely relevant for reconstruction of ancestral behaviors, these behaviors should be reconstructed trait by trait using formal phylogenetic methods. Using the widely accepted hominoid phylogenetic tree, we perform a series of character optimization analyses using 65 selected life-history and behavioral characters for all extant hominid species. This analysis allows us to reconstruct the character states of the last common ancestors of Hominoidea, Hominidae, and the chimpanzee–human last common ancestor. Our analyses demonstrate that many fundamental behavioral and life-history attributes of hominids (including humans) are evidently ancient and likely inherited from the common ancestor of all hominids. However, numerous behaviors present in extant great apes represent their own terminal autapomorphies (both uniquely derived and homoplastic). Any evolutionary model that uses a single extant species to explain behavioral evolution of early hominins is therefore of limited use. In contrast, phylogenetic reconstruction of ancestral states is able to provide a detailed suite of behavioral, ecological and life-history characters for each hypothetical ancestor. The living great apes therefore play an important role for the confident identification of the traits found in the chimpanzee–human last common ancestor, some of which are likely to represent behaviors of the fossil hominins.     

PHYLOGENY OF EUGLENOPHYCEAE BASED ON SMALL SUBUNIT rDNA SEQUENCES: TAXONOMIC IMPLICATIONS1

Small subunit rDNA sequences of 42 taxa belonging to 10 genera were used to infer phylogenetic relationships among euglenoids. Members of the phototrophic genera Euglena, Phacus, Lepocinclis, Colacium, Trachelomonas, and Strombomonas plus the osmotrophs Astasia longa, Khawkinea quartana, and Hyalophacus ocellatus were included. Six major clades were found in most trees using multiple methods. The utility of Bayesian analyses in resolving these clades is demonstrated. The genus Phacus was polyphyletic with taxa sorting into two main clades. The two clades correlated with overall morphology and corresponded in large part to the previously defined sections, Pleur‐ aspis Pochmann and Proterophacus Pochmann. Euglena was also polyphyletic and split into two clades. In Bayesian analyses species with less plastic pellicles and small disk‐like chloroplasts diverged at the base of the tree. They grouped into a single clade which included the two Lepocinclis spp., which also are rigid and bear similar chloroplasts. The metabolic Euglena species with larger plastids bearing pyrenoids and paramylon caps arose near the top of the tree. The loricates Strombomonas and Trachelomonas formed two well‐ supported, but paraphyletic, clades. The strong support for the individual clades confirmed the value of using lorica features as taxonomic criteria. The separation of the osmotrophic species A. longa, K. quartana, and H. ocellatus into different clades suggested that the loss of the photosynthetic ability has occurred multiple times.