The origins and evolutionary expansion of the Strongylida (Nematoda)

The Strongylida are thought to have arisen from free-living rhabditoid nematodes, but the relationships between the major groupings within the Strongylida, the Strongylina, the Metastrongylina, Trichostrongylina and the Ancylostomatina are far from clear in spite of the abundance of morphological data now available for analysis. Evolutionary mechanisms including co-evolution, host switching, host dispersal, use of intermediate hosts, various sites of localisation within the definitive host and modifications of life-cycle strategies appear to have been utilised in the expansion of the Strongylida, with different mechanisms predominating in different families or superfamilies. Co-evolution appears to have been a major mode of evolution in the Strongylina, in contrast to the Trichostrongylina, which have used host dispersal and host-switching to great advantage. The phylogeny of the Ancylostomatina shows little association with host evolution, but does match the feeding preferences of the hosts. The Metastrongylina have utilised intermediate hosts and life cycle modifications including a shift to extra-intestinal sites as major means of diversification, in contrast to the other sub-orders. The review, while indicating much progress in our understanding of the phylogeny of the Strongylida, also reveals that enormous gaps still exist, and emphasises the tentative nature of many of the phylogenetic hypotheses tendered to date.     

天牛科昆虫高级分类阶元实体的进化研究(英文)

本文从生物地理学、形态学、生态学、行为学、生理学、天牛—寄主植物的相互关系、地质学、气候变迁等诸方面,探讨了天牛科高级分类阶元实体的进化证据,提出了各阶元实体进化关系的新假说。研究结果表明,沟胫天牛亚科、锯天牛亚科和天牛亚科可能于侏罗纪在冈瓦纳古陆上分化出来;花天牛亚科和幽天牛亚科于白垩纪在劳亚古陆上分化出来。各亚科的进化顺序有两种可能:(1)沟胫天牛亚科、锯天牛亚科、天牛亚科、花天牛亚科、幽天牛亚科;(2)沟胫天牛亚科、天牛亚科、锯天牛亚科;花天牛亚科、幽天牛亚科。文章最后还讨论了各亚科的系统发育关系。     

赤眼蜂属系统进化研究进展

赤眼蜂是一类重要的天敌昆虫,该属包括的种类达180多种,并且广泛地分布于世界各地。通过对形态特征的分析,赤眼蜂属的系统发育研究在不同的研究者中得到不同的分类系统。由于赤眼蜂的个体微小,仅04mm左右,现有的化石记录稀少,并且可用作系统发育研究的形态特征很少,导致该类群的系统发育研究仍有许多不清楚的地方。同时,近年来分子生物学的发展为赤眼蜂系统发育研究提供了很好的途径,也取得了一些共识。但仍然未能提出一套精确的、更可靠的分类系统。作者对近年来的赤眼蜂属系统进化研究进行了综述。     

天牛科昆虫高级分类阶元实体的进化研究

本文从生物地理学、形态学、生态学、行为学、生理学、天牛—寄主植物的相互关系、地质学、气候变迁等诸方面,探讨了天牛科高级分类阶元实体的进化证据,提出了各阶元实体进化关系的新假说。研究结果表明,沟胫天牛亚科、锯天牛亚科和天牛亚科可能于侏罗纪在冈瓦纳古陆上分化出来;花天牛亚科和幽天牛亚科于白垩纪在劳亚古陆上分化出来。各亚科的进化顺序有两种可能:(1)沟胫天牛亚科、锯天牛亚科、天牛亚科、花天牛亚科、幽天牛亚科;(2)沟胫天牛亚科、天牛亚科、锯天牛亚科;花天牛亚科、幽天牛亚科。文章最后还讨论了各亚科的系统发育关系。     

关于进化真菌学教学内容的讨论

核酸序列的比较研究使进化真菌学的面貌发生了革命性的变化,分子系统发育揭示的关系反映出真菌进化的复杂性和多样性,真菌系统学反映真菌进化关系的自然系统还有很大的距离,有赖于新物种的不断发现和分子系统发育证据的不断丰富。     

Evolution,developmental instability and the theory of acquisition

Despite major advances in the study of molecular and morphological evolution a substantial rift still exists between these two fields of endeavour. Phenotypic alteration through evolution results from a reallocation of resources which has as its origin the interplay between the production capability of the genes on the one side and the acquisitional need of the phenotype on the other. This process of allocation is coordinated through the environmental arena and is subject to mechanical, biological and economical constraints. Differences in the rates of morphological change at any level (molecular, cellular, organismal or population) depend on the level of environmental challenge, on the availability of variability and on the economics of supply and demand. Short run changes in response to severe environmental stress will be sudden and energetically expensive and will rely on stress-induced unmasking of genetic variability and loss of canalization. Long run changes will be gradual, energetically less costly and less dependent on genetic correlations.     

Evolutionary Trends of External Morphology in the Marine Mite Genus Rhombognathides (Acari: Halacaridae: Rhombognathinae)

A morphology-based phylogenetic analysis of the eight species of Rhombognathides (Acari: Halacaridae) demonstrated some evolutionary tendencies of character transformation. In the course of the evolution of Rhombognathides, idiosomal plates increased in size or fused. Simple filiform setae transformed into spiniform or bipectinate setae. The number of tarsal claws, the length of median claw and leg chaetotaxy of telofemora and tibiae were reduced. The fusion or expansion of dorsal plates, transformation from filiform to other setal forms, and reduction of leg setae would have recurrently occurred in halacarid evolution. The claw structure most likely reflects adaptation to specific habitat.     

Phylogeny, Evolution and Historical Zoogeography of Ticks: A Review of Recent Progress

There has been much progress in our understanding of the phylogeny and evolution of ticks, particularly hard ticks, in the past 5 years. Indeed, a consensus about the phylogeny of the hard ticks has emerged. Our current working hypothesis for the phylogeny of ticks is quite different to the working hypothesis of 5 years ago. So that the classification reflects our knowledge of ticks, several changes to the nomenclature of ticks are imminent. One subfamily, the Hyalomminae, will probably be sunk, yet another, the Bothriocrotoninae n. subfamily, will be created. Bothriocrotoninae n. subfamily, and Bothriocroton n. genus, are being created to house an early-diverging (‘basal’) lineage of endemic Australian ticks that used to be in the genus Aponomma (ticks of reptiles). There has been progress in our understanding of the subfamily Rhipicephalinae. The genus Rhipicephalus is almost certainly paraphyletic with respect to the genus Boophilus. Thus, the genus Boophilus will probably become a subgenus of Rhipicephalus. This change to the nomenclature, unlike other options, will keep the name Boophilus in common usage. Rhipicephalus (Boophilus) microplus may still called B. microplus, and Rhipicephalus (Boophilus) annulatus may still be called B. annulatus, but the nomenclature will have been changed to reflect our knowledge of the phylogeny and evolution of these ticks. New insights into the historical zoogeography of ticks will also be presented. This revised version was published online in July 2006 with corrections to the Cover Date.     

贝叶斯推论重建乳头瘤病毒的进化系统

基于90种乳头瘤病毒的L1基因和E2基因的DNA全序列,应用似然比检验和贝叶斯推论重建病毒的系统发育树,并在此基础上讨论病毒分子系统学研究的一般原则和方法。同时比较研究贝叶斯推论和过去常用的最小进化、最大简约、最大似然三种建树算法的优劣。结果表明：乳头瘤病毒可分为4超群,不同超群的乳头瘤病毒宿主和组织特异性不同。引起人宫颈癌的高危和低危乳头瘤病毒在进化上分别具有相近的亲缘关系。高危类群起源于共同祖先。算法的比较研究表明,贝叶斯推论作为进化生物学的最新进展,在计算速度和可靠性上明显优于其它算法。     

Multiple origins of viviparity,or reversal from viviparity to oviparity? The European common lizard (Zootoca vivipara,Lacertidae) and the evolution of parity

The evolution of viviparity in squamates has been the focus of much scientific attention in previous years. In particular, the possibility of the transition from viviparity back to oviparity has been the subject of a vigorous debate. Some studies have suggested this reversal is more frequent than previously thought. However, none of them provide conclusive evidence. We investigated this problem by studying the phylogenetic relationships between oviparous and viviparous lineages of the reproductively bimodal lizard species Zootoca vivipara . Our results show that viviparous populations are not monophyletic, and that several evolutionary transitions in parity mode have occurred. The most parsimonious scenario involves a single origin of viviparity followed by a reversal back to oviparity. This is the first study with a strongly supported phylogenetic framework supporting a transition from viviparity to oviparity.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 1–11.     

The origins of graptolites and other pterobranchs: a journey from ‘Polyzoa’

The graptolites, known only from fossils, have been convincingly allied to the pterobranch hemichordates, a group of tiny, mostly colonial marine invertebrates bearing feeding arms. The phylogenetic position of pterobranchs has been subject to debate and revision for over a century. Their colonial lifestyle and feeding arms were originally seen as evidence placing them among the bryozoans, until later and more careful anatomical studies revealed more characters in common with acorn worms. Pterobranchs and acorn worms are now grouped as the phylum Hemichordata. For many decades, it was thought that pterobranchs were closer to the ancestral form of hemichordates, particularly because ‘lophophorate’ invertebrates also possess feeding arms, notably the phoronids and bryozoans, as do crinoid echinoderms. This traditional view has been challenged by recent molecular evidence. First, there is strong molecular evidence to indicate that lophophorates are very distant from hemichordates and echinoderms, in a different major branch of the animal phylogenetic tree. Therefore, similarities between the feeding structures must be due to convergent evolution. Second, there is strong evidence that hemichordates and echinoderms form a clade (Ambulacraria) within the deuterostomes, rather than hemichordates being closer to chordates. Third, there is weaker evidence that pterobranchs may be derived from acorn worms, and hence that the vermiform body plan may be ancestral within hemichordates. This suggestion warrants further testing. Here we review the evidence for these conclusions, highlight strengths and weaknesses in the data and analyses, and consider the implications for the origins of pterobranchs and graptolites.     

Description of a new long‐snouted beaked whale from the Late Miocene of Denmark: evolution of suction feeding and sexual dimorphism in the Ziphiidae (Cetacea: Odontoceti)

A new genus and species of Ziphiidae, Dagonodum mojnum gen. nov., sp. nov., from the upper Miocene Gram Formation (c. 9.9–7.2 Ma) represents the first occurrence of the family in Denmark. This long‐snouted ziphiid is characterized by two pairs of mandibular tusks, the Eustachian outlet that approximately levels with the dorsalmost margin of the posterior portion of the involucrum, and the left trapezoid nasal with a posteromedial projection into the frontal. A phylogenetic analysis including 25 species and 69 characters was conducted. Dagonodum mojnum is placed in a basal ziphiid clade as the sister taxon of Messapicetus. The specimen is probably a male, because it has enlarged tusks. Alternatively, females could also be involved in fights and develop erupted tusks as in the extant Berardius. Although less well supported, this interpretation proposes that aggressive interactions were not restricted to males in stem‐ziphiids. With a thickened thyrohyal and the presence of a precoronoid crest, D. mojnum was able to use suction feeding, but was less specialized to it compared to extant ziphiids. The elongated neck of D. mojnum less optimized to perform deep dives, and the shallow depth at which the Gram Formation was deposited corroborates the hypothesis that at least part of the stem‐ziphiids were not regular deep divers.     

The evolutionary expansion of the Spirurida

The possible origins of the 12 superfamilies of the Spirurida are considered, based on comparative morphology, host and geographic distributions. The available evidence suggests a complex origin of these nematodes, some families being derived from the Seuratoidea, and others from the Cosmocercoidea (Ascaridida). The spirurid radiation is an old one and seems to have occurred primarily in the Secondary or early Tertiary eras. Since then, expansion has occurred with host capture as a prominent mechanism. The Dracunculoidea Procamallanidae and Camallanidae are probably derived from the Chitwoodchabaudiidae and the Rictularioidea from the Schneidernematidae. The Seuratidae may have given rise to the Gnathostomatoidea, the Physalopteroidea, the Thelazioidea, the Habronematoidea, the Spiruroidea and the Acuarioidea. The filarioid nematodes appear to have several origins with the Diplotriaenoidea derived from the Spiruroidea, while constituents of the Aproctoidea derived from the Cystidicolinae, the Seuratoidea and the Spiruroidea. The Filarioidea are thought to have arisen from the Spiruroidea and the Thelazioidea. The evolution of tissue parasitism as a secondary phenomenon is considered in various groups.     

The morphology and systematics of Mammalodon colliveri (Cetacea: Mysticeti), a toothed mysticete from the Oligocene of Australia

Mammalodon colliveri is an unusual toothed archaic mysticete (Cetacea) from the Upper Oligocene Jan Juc Formation of south‐east Australia. The morphology of the holotype skull and postcrania are described in detail. Superimposed on the generally plesiomorphic archaeocete‐like morphology of Mammalodon are subtle mysticete synapomorphies. Derived features of Mammalodon include a short and bluntly rounded rostrum, reduced premaxillae, and anterodorsally directed orbits. Within Mysticeti, this suite of features is unique. The aberrant rostral morphology of Mammalodon suggests specialization for suction feeding. Janjucetus hunderi is placed in an expanded family Mammalodontidae. Phylogenetic analysis corroborates the monophyly of Basilosauridae, Neoceti, Odontoceti, and Mysticeti, and yields a novel hypothesis of toothed mysticete relationships: a basal clade of undescribed toothed mysticetes from South Carolina, a Llanocetidae + Mammalodontidae clade, and monophyletic Aetiocetidae are posited as successive sister taxa to edentulous baleen whales (Chaeomysticeti). Toothed archaic mysticetes clearly employed diverse prey capture strategies, with exaptations for filter feeding evolving sequentially in stem group Mysticeti. A stratigraphically calibrated phylogeny implies that the initial diversification of Mysticeti occurred during the Late Eocene. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 367–476.     

Cloning of Arctic lamprey Lethenteron camtschaticum cd9 with roles in the immune response

In this study, the cd9 gene, a member of the tetraspanin superfamily and involved in various cellular processes, was cloned from Lethenteron camtschaticum. Both real-time PCR and immunohistochemical assays showed broad distribution of cd9 in various L. camtschaticum tissues. In addition, expression levels of Cd9 mRNA were up-regulated in the liver and heart after stimulation by lipopolysaccharide. Flow cytometric analyses demonstrated that cd9 was detected on the leukocytes and that the expression level was higher on granulocytes than on lymphocytes, which implied that cd9 was mainly involved in innate immunity.     

Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers

Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.     

Coding of intraspecific nucleotide polymorphisms: A tool to resolve reticulate evolutionary relationships in the ITS of beech trees (Fagus L., Fagaceae)

The internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA (rDNA) have recently been found to display remarkable intraspecific polymorphism, a feature suggested as limiting their value for phylogenetic reconstructions. A comparative study of oligonucleotide motives and intraindividual nucleotide variability across all species of the tree genus Fagus (beech) shows, however, that this intraspecific ITS polymorphism follows a particular pattern, which can be used to detect reticulation and ancient polymorphism within the genus. Coding ITS polymorphisms as phylogenetically informative characters, moreover, resulted in better‐resolved phylogenies than traditional ‘base‐per‐base’ maximum parsimony and maximum likelihood analyses.     

Phylogenetic implications of the Crustacean nauplius

The plesiomorphic mode of crustacean development is widely accepted to be via a larva called the nauplius. Extant taxa like the Cephalocarida, Branchiopoda, Ostracoda, Mystacocarida, Copepoda, Cirripedia, Ascothoracida, Facetotecta, Euphausiacea and Penaeidea hatch from an egg as a free-living nauplius. Other crustaceans show an embryonic phase of development suggestive of a naupliar organization. Several features of the nauplius larva have been proposed as diagnostic characters for the Crustacea: a median (nauplius) eye; at least three pairs of head appendages (antennules, antennae, mandibles); a posteriorly directed fold (the labrum) extending over the mouth and a cephalic (nauplius) shield. The relationship between trilobite protaspis with at least four appendages and the crustacean nauplius remains unclear, but reports of a copepod orthonauplius with four appendages are rejected. Swimming is suggested to represent the underived mode of locomotion for the crustacean nauplius, and that naupliar swimming directly results in naupliar feeding which also is underived.     

How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets

We analyzed 12 combined mitochondrial and nuclear gene datasets in seven orders of insects using both equal weights parsimony (to evaluate phylogenetic utility) and Bayesian methods (to investigate substitution patterns). For the Bayesian analyses we used relatively complex models (e.g., general time reversible models with rate variation) that allowed us to quantitatively compare relative rates among genes and codon positions, patterns of rate variation among genes, and substitution patterns within genes. Our analyses indicate that nuclear and mitochondrial genes differ in a number of important ways, some of which are correlated with phylogenetic utility. First and most obviously, nuclear genes generally evolve more slowly than mitochondrial genes (except in one case), making them better markers for deep divergences. Second, nuclear genes showed universally high values of CI and (generally) contribute more to overall tree resolution than mitochondrial genes (as measured by partitioned Bremer support). Third, nuclear genes show more homogeneous patterns of among-site rate variation (higher values of alpha than mitochondrial genes). Finally, nuclear genes show more symmetrical transformation rate matrices than mitochondrial genes. The combination of low values of alpha and highly asymmetrical transformation rate matrices may explain the overall poor performance of mitochondrial genes when compared to nuclear genes in the same analysis. Our analyses indicate that some parameters are highly correlated. For example, A/T bias was positively and significantly associated with relative rate and CI was positively and significantly associated with alpha (the shape of the gamma distribution). These results provide important insights into the substitution patterns that might characterized high quality genes for phylogenetic analysis: high values of alpha, unbiased base composition, and symmetrical transformation rate matrices. We argue that insect molecular systematists should increasingly focus on nuclear rather than mitochondrial gene datasets because nuclear genes do not suffer from the same substitutional biases that characterize mitochondrial genes.