介形纲丽足目和速足目及相关类群18S rDNA分子系统发育的研究

文中分析现生介形类 (Ostracoda) 4目 2 1科 2 9属的 18SrDNA部分序列 ,采用最大似然法 (ML)、邻接法 (NJ)和最大简约法 (MP) ,尝试构建介形类的分子系统树 ;结合介形类的形态特征和化石记录 ,主要对速足目(Podocopida)、丽足目 (Myodocopida)及其超科级分类阶元的系统发生关系进行探讨。 3种分析方法均支持形态学上Podocopida ,Myodocopida和海萤超科 (Cypridinacea)的界定 ;但对Podocopida目土菱介超科 (Bairdiacea)的系统地位提出质疑 ,该类群可能不是单系发生的自然类群。上述分析显示 ,Podocopida,Myodocopida,Platycopida和Halo cypridina组成一个单系群 ;介形类在目、超科、科和属的水平上可能发生过多次辐射分化     

松辽盆地D80井嫩一段介形类化石壳体特征及生物地层

松辽盆地嫩江组一段富含介形类化石,是系统研究Santonian期陆相介形类的理想层位。论文对中央坳陷区D80井嫩一段的介形类化石进行了系统的分类、生物地层和壳体特征分析。鉴定出介形类化石11属30种,划分出6个介形类化石带,并与前人的研究结果进行了对比;描述了该段介形类化石的壳体结构,共识别出4种壳饰类型,8种壳形结构,基于介形类壳体特征和其他证据,初步探讨了该时期湖盆湖平面的变化特征,显示出嫩一段时期松辽湖盆湖平面经历了由深逐渐变浅的过程。     

介形类的形态学及其环境、功能和分类学意义

化石介形类分类依据--壳体形态,包括壳体的大小、形状、装饰和诸如毛孔、叠覆、似犁状构造、喙、铰合构造等构造特征都与介形类的栖息环境,包括地理、气候(季节、纬度等)、水体的深度、化学性质和稳定程度,食物的富集程度和群落的组成及个体数量以及性别息息相关.因此,正确理解介形类的形态学特征及其功能学,不仅能揭示介形类的生活习性,推测化石介形类的生活环境,从而为古环境和古群落生态重建提供依据,而且可以提高化石介形类个体发育、系统分类和演化研究结果的可靠性.     

同种介形类壳体的多态性兼及化石介形类的物种鉴定

介形类个体发育过程中壳体形状及各种构造的多态性,以及各种外界环境因素对分形类壳体各种分类特征形态变化的影响是十分明显的。该文较系统地阐述了在介形类个体发育中壳体形状、大小、肌痕、边缘毛细管带、边庭、铰合构造及纹饰的变化,并介绍了成年期雌、雄性壳体及左、右壳瓣在形态上的差异;列举了环境因素(主要是水体温度、含盐度、深度)对介形类壳体各分类特征形态变化的影响。基于以上事实,提出了古生物工作者在介形类化石鉴定中应注意的一些问题并讨论了某些描述术语的具体标准。     

速足目主要类群系统发育的分子证据

文章基于速足目现生主要类群18S rDNA、28S rDNA和COI基因序列,采用贝叶斯法、邻接法和最大简约法,尝试构建速足目的分子系统树;结合形态特征和化石记录,主要对速足目各超科级分类阶元的系统发育关系进行探讨。结果表明,速足目现生超科Bairdiacea、Darwinulacea、Cypridacea和Cytheracea均为单系群,支持形态学上关于上述4个超科的的界定;3种基因均支持形态学上Darwinulacea和Cypridacea具有较近的亲缘关系的观点。18S rDNA序列分析在较显著水平上支持Darwinulacea和Bairdiacea为姐妹群,Darwinulacea可能从Bairdia-cea中的一支演化而来;Bairdiacea和Darwinulacea组成的分支是Cypridacea的姐妹群,支持将三者合并为Bairdio-copina亚目的观点;Cytheracea是Cypridacea(Darwinulacea Bairdiacea)的姐妹群,可提升为Cytheracopina亚目。     

甘肃玉门下沟地区早白垩世下沟组介形类

甘肃玉门下沟地区下沟组介形类化石十分丰富,该地区下沟组介形类化石共计9属4亚属,21种,本文描述了其中4新种,即Cypridea(Cyamocypris)xiagouensissp.nov.,Cypridea(Cypridea)subunicostatasp.nov.,Stenestroemiasubpeculiarissp.nov.和Stenestroemiaxiagouensissp.nov.。该介形类化石组合尤以Cypridea最为繁盛,通过分析介形类属种的形态特征和化石组合特征并结合岩性特征,推断下沟组的地质时代为早白垩世巴列姆期;并认为下沟组为水动力较弱的淡水-微咸水河湖相沉积。     

介形类内模眼窦及其它微细结构的研究意义

本文较为详细地介绍由Kontrovitz首先使用的介形类人工内模的铸型方法。基于某些海生或淡水现生、化石介形类Echinocythereis margaritifera,Actinocythereis thompsoni, Henryhowella florienensis 和Cytherissa lacustris内模的电子扫描显微镜观察,介绍了其中具眼窦介形类的跟窦结构及术语;报道了它的形态特点和差异;讨论了服窦形态在介形类分类、个体发育,尤其是利用它在判断生物生活水体深度的潜在意义。首次报道了淡水介形类Cytherissa lacustris内模上垂直毛细管及边缘毛细管的形态特点,这些微细结构过去也难以在电镜下清楚地观察和研究。介形类人工内模的研究,为现生或化石介形类的深入研究开辟了一条新途径。     

石松类卷柏科地史时期和现代地理分布格局的形成

卷柏科仅含一属,全球分布,具有宽幅生态适应性,属于维管植物基部类群石松类植物,现生约700种。卷柏科起源于泥盆纪,化石记录遍布自石炭纪至今的各地质时期。目前,现代卷柏属亚属的分类方案基本稳定,但对于化石卷柏的亚属分类、以及地质历史时期的时空分布问题还缺乏相关研究。本文全面总结了卷柏科化石记录的时代和地理分布,并结合分子系统学探讨其地理分布格局的演化,为该科植物的分类与进化研究提供参考。根据现有研究基础,结合最新的卷柏科系统分类研究成果和化石记录,本文对该类群化石的系统分类进行归纳和厘定,并对化石类群的卷柏亚属Selaginella、Hexaphyllum亚属及rhizophoric clade物种的分化和地理分布格局的形成进行了讨论。本文认为,卷柏科起源于古生代的欧美植物区,不晚于二叠纪,其后伴随着泛大陆解体扩散至华夏植物区及冈瓦纳植物区。化石亚属Hexaphyllum是rhizophoric clade的基部类群,在石炭纪末灭绝。化石证据表明,从古生代末期起,rhizophoric clade已成为卷柏科的优势类群,并在中生代形成了全球分布的格局。     

云南宁蒗大槽子泥盆纪介形类—古足目类

本文描述和图解介形类化石１０属、４亚属和１４种,包括１新属（Ｐａｒａｕｌｒｉｃｈｉａ）和６新种。其中古足目类８属、３亚属和１２种;豆石目类１属、１亚属和１种;显壳亚目类１属和１种。这些介形类化石分别采自云南宁蒗大槽子泥盆系剖面大槽子组和碳山坪组。根据介形类组合特征,大槽子组的地质时代为晚埃姆斯期,碳山坪组下、中部的地质时代可能属晚埃姆斯期。介形类生态组合属古足目－平足目集群,代表局限的碳酸盐台地环境。在生物地理上,与泥盆纪华南介形类动物地理区系一致。     

川东中侏罗统新田沟组介形类化石壳体方解石化特征及元素成分初步分析

首次利用扫描电子显微镜观察川东新田沟组介形类化石的保存情况,并利用X射线能谱分析部分化石的元素含量及分布。研究发现新田沟组介形类壳体绝大部分方解石化,不同层位介形类壳质方解石化有所不同,且方解石化特点显示其可能与有机质作用有关。通过与前人研究结果对比发现,新田沟组壳体保存处在介形虫壳体埋藏作用的第二阶段和第三阶段。     

Origin of the Ostracoda and their maxillopodan and hexapodan affinities

There are Cambrian fossils attributed to the Ostracoda but the extant subclasses Podocopa and Myodocopa do not appear until the Ordovician. At this time the morphologically similar, free-living ancestors of the now sedentary Thecostraca (Ascothoracida, Acrothoracica and Cirripedia) may have still been extant, and from an ecological point of view it seems likely that, by and large, ostracods replaced them. However, living ostracods have an abbreviated, direct development, and some key aspects of their morphology, such as the nature of the maxillary segment and abdomen, are conjectural. Thus the affinities between these and related taxa remain uncertain; e.g., while some contemporary carcinologists place Ostracoda as a taxon coordinate with the Branchiopoda, Remipedia, Cephalocarida, Maxillopoda, Malacostraca, others tentatively or unequivocally ally them with the Maxillopoda (generally Mystacocarida, Copepoda, Tantulocarida and Thecostraca, and sometimes Branchiura and Pentastomida). Others, largely involved with fossils, have stretched the definition of the Maxillopoda even further, to the point where it seems even less likely a monophyletic taxon. Until recently cladistic analyses utilizing genetic (largely 18S rDNA) as well traditional morphological characteristics have given confusing results regarding the affinities between these taxa, and an important one suggested the Ostracoda might even be diphyletic. Furthermore, a very recent genetic study utilizing protein encoding genes places a podocopine ostracod among the most primitive of the extant crustaceans (Branchiopoda, Cephalocarida Remipedia and Mystacocarida), and then generally at the base of a lineage leading to the Malacostraca, a lineage giving rise to copepods and cirripeds along the way. This indicates these so-called maxillopodan taxa evolved independently from a malacostracan-like ancestor, and if so they are convergent. And finally, from genetic studies it is not only becoming well documented the Crustacea rather than Myriapoda gave rise to the Hexapoda, but it appears the Hexapoda stem from among the lower rather than the higher crustaceans, possibly even from the Ostracoda. Whether there were terrestrial ostracods at the time hexapods appeared in the Lower Ordovician is unknown, but the modest diversity of terrestrial ostracods today are podocopines which also first appeared in the Lower Ordovician. Thus, if current interpretations of living ostracodan and fossil hexapodan body plans are largely correct, it can be hypothesized the Ostracoda are close to the ancestor of the Hexapoda.     

Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic

Recent molecular analyses indicate that crustaceans and hexapods form a clade (Pancrustacea or Tetraconata), but relationships among its constituent lineages, including monophyly of crustaceans, are controversial. Our phylogenetic analysis of three protein-coding nuclear genes from 62 arthropods and lobopods (Onychophora and Tardigrada) demonstrates that Hexapoda is most closely related to the crustaceans Branchiopoda (fairy shrimp, water fleas, etc.) and Cephalocarida + Remipedia, thereby making hexapods terrestrial crustaceans and the traditionally defined Crustacea paraphyletic. Additional findings are that Malacostraca (crabs, isopods, etc.) unites with Cirripedia (barnacles, etc.) and they, in turn, with Copepoda, making the traditional crustacean class Maxillopoda paraphyletic. Ostracoda (seed shrimp)--either all or a subgroup--is associated with Branchiura (fish lice) and likely to be basal to all other pancrustaceans. A Bayesian statistical (non-clock) estimate of divergence times suggests a Precambrian origin for Pancrustacea (600 Myr ago or more), which precedes the first unambiguous arthropod fossils by over 60 Myr.     

Early fossils illuminate character evolution and interrelationships of Lampridiformes (Teleostei,Acanthomorpha)

Lampridiformes is a peculiar clade of pelagic marine acanthomorph (spiny‐rayed) teleosts. Its phylogenetic position remains ambiguous, and varies depending on the type of data (morphological or molecular) used to infer interrelationships. Because the extreme morphological specializations of lampridiforms may have overwritten the ancestral features of the group with a bearing on its relationships, the inclusion of fossils that exhibit primitive character state combinations for the group as a whole is vital in establishing its phylogenetic position. Therefore, we present an osteological data set of extant (ten taxa) and fossil (14 taxa) acanthomorphs, including early Late Cretaceous taxa for which a close relationship with extant Lampridiformes has been suggested: ?Aipichthyoidea, ?Pharmacichthyidae, and ?Pycnosteroididae. We find that all three taxa plus Lampridiformes form a clade that we call Lampridomorpha. Under this hypothesis, ?Aipichthyoidea is paraphyletic. The inclusion of fossils in the analysis changes the topology, highlighting their critical importance in phylogenetic studies of morphological characters. When fossils are included, Lampridomorpha is sister to Euacanthomorpha (all other extant acanthomorphs), concurring with most previous anatomical studies, but conflicting with most molecular results. Lampridomorpha as a whole was a major component of the earliest acanthomorph faunas, notably in the Cenomanian. © 2014 The Linnean Society of London     

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.     

Myodocopa (Crustacea: Ostracoda) as models for evolutionary studies of light and vision: multiple origins of bioluminescence and extreme sexual dimorphism

Evolutionists often use phylogeny to examine independent evolutionary events in search of generality. Therefore, groups of organisms rich in such independent character transitions are particularly valuable for the study of evolution. With respect to eyes, vision, and light-related characters, one such group is Ostracoda (Crustacea). Phylogenies of ostracods, derived from DNA sequence data and morphological characters, are presented. These inferred relationships largely agree with previous assessments of ostracod phylogeny, with the exception of paraphyletic Philomedidae. Based on methods of character reconstruction using these inferred relationships, different groups of ostracods probably evolved both bioluminescence and extreme sexual dimorphism (females lack eyes, males have large eyes) multiple times. Furthermore, myodocopid ostracods may have evolved compound eyes independently of other arthropods. For these and other reasons, it is proposed that the Ostracoda are an exceptionally important group for studying the evolution of vision- and light-related characters.     

Species and paleoanthropology

The biotic world is self-evidently “packaged” into units, of which the most basic is the species. It is necessary to develop an accurate understanding of what species are and how they are to be identified before we can proceed to more complex analyses of the evolutionary histories and relationships of extinct and extant taxa at all levels of the systematic hierarchy. In this article, we review the major species concepts current today among paleoanthropologists, and examine the limitations of their applicability to practical studies of extant and extinct faunas. The primary such limitation for paleoanthropologists is the fact that all major species definitions stress reproductive continuity (whether by exclusionary or inclusionary mechanisms), a quality that is inferential at best among forms known only as fossils (and, in many cases, in the extant fauna as well). The only reliable signal as to species status in the fossil record is morphology, yet speciation carries with it no specifiable quantity of morphological innovation. Some groups with autapomorphies are not species, and some species do not bear autapomorphies. How, then, are we to recognize species in the hominid and other fossil records? Noting that osteodental differences among congeneric primate species tend to be subtle, and that when consistent identifiable “morphs” can be found at least as many species are present, we recommend equating morphs based on several characters with species—realizing that only one or two distinctive characters may not make a morph. In this way, our views of the phylogenetic histories of higher taxa may be oversimplified, but their essential patterns will not be distorted.     

Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae

The identification and application of reliable fossil calibrations represents a key component of many molecular studies of evolutionary timescales. In studies of plants, most paleontological calibrations are associated with macrofossils. However, the pollen record can also inform age calibrations if fossils matching extant pollen groups are found. Recent work has shown that pollen of the myrtle family, Myrtaceae, can be classified into a number of morphological groups that are synapomorphic with molecular groups. By assembling a data matrix of pollen morphological characters from extant and fossil Myrtaceae, we were able to measure the fit of 26 pollen fossils to a molecular phylogenetic tree using parsimony optimisation of characters. We identified eight Myrtaceidites fossils as appropriate for calibration based on the most parsimonious placements of these fossils on the tree. These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (matK and ndhF) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera. Three additional analyses were calibrated by placing pollen fossils using geographic and morphological information (eight calibrations), macrofossils (five calibrations), and macrofossils and pollen fossils in combination (12 calibrations). The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae. Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages. This study illustrates the potential of including pollen-based calibrations in molecular studies of divergence times.     

Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers

Recent attempts to address the long-debated 'origin' of the angiosperms depend on a phylogenetic framework derived from a matrix of taxa versus characters; most assume that empirical rigour is proportional to the size of the matrix. Sequence-based genotypic approaches increase the number of characters (nucleotides and indels) in the matrix but are confined to the highly restricted spectrum of extant species, whereas morphology-based approaches increase the number of phylogenetically informative taxa (including fossils) at the expense of accessing only a restricted spectrum of phenotypic characters. The two approaches are currently delivering strongly contrasting hypotheses of relationship. Most molecular studies indicate that all extant gymnosperms form a natural group, suggesting surprisingly early divergence of the lineage that led to angiosperms, whereas morphology-only phylogenies indicate that a succession of (mostly extinct) gymnosperms preceded a later angiosperm origin. Causes of this conflict include: (i) the vast phenotypic and genotypic lacuna, largely reflecting pre-Cenozoic extinctions, that separates early-divergent living angiosperms from their closest relatives among the living gymnosperms; (ii) profound uncertainty regarding which (a) extant and (b) extinct angiosperms are most closely related to gymnosperms; and (iii) profound uncertainty regarding which (a) extant and (b) extinct gymnosperms are most closely related to angiosperms, and thus best serve as 'outgroups' dictating the perceived evolutionary polarity of character transitions among the early-divergent angiosperms. These factors still permit a remarkable range of contrasting, yet credible, hypotheses regarding the order of acquisition of the many phenotypic characters, reproductive and vegetative, that distinguish 'classic' angiospermy from 'classic' gymnospermy. The flower remains ill-defined and its mode (or modes) of origin remains hotly disputed; some definitions and hypotheses of evolutionary relationships preclude a role for the flower in delimiting the angiosperms. We advocate maintenance of parallel, reciprocally illuminating programmes of morphological and molecular phylogeny reconstruction, respectively supported by homology testing through additional taxa (especially fossils) and evolutionary-developmental genetic studies that explore genes potentially responsible for major phenotypic transitions.     

Distinguishing heat from light in debate over controversial fossils

Fossil organisms offer our only direct insight into how the distinctive body plans of extant organisms were assembled. However, realizing the potential evolutionary significance of fossils can be hampered by controversy over their interpretation. Here, as a guide to evaluating palaeontological debates, we outline the process and pitfalls of fossil interpretation. The physical remains of controversial fossils should be reconstructed before interpreting homologies, and choice of interpretative model should be explicit and justified. Extinct taxa lack characters diagnostic of extant clades because the characters had not yet evolved, because of secondary loss, or because they have rotted away. The latter, if not taken into account, will lead to the spurious assignment of fossils to basally branching clades. Conflicting interpretations of fossils can often be resolved by considering all the steps in the process of anatomical analysis and phylogenetic placement, although we must accept that some fossil organisms are simply too incompletely preserved for their evolutionary significance to be realized.     

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.