Organization of the Mitochondrial Genome of Mantis Shrimp Pseudosquilla ciliata (Crustacea: Stomatopoda)

We determined the nearly complete mitochondrial genome of Pseudosquilla ciliata (Crustacea, Stomatopoda), including all protein-coding genes and all but one of the transfer RNAs. There were no gene rearrangements relative to the pattern shared by crustaceans and hexapods. Phylogenetic analysis using concatenated amino acid sequences of the mitochondrial protein-coding genes confirmed a basal position of Stomatopoda among Eumalacostraca. Pancrustacean relationships based on mitogenomic data were analyzed and are discussed in relation to crustacean and hexapod monophyly and hexapod affinities to crustacean subtaxa.     

被子植物系统发育深层关系研究: 进展与挑战

被子植物系统发育学是研究被子植物及其各类群间亲缘关系与进化历史的学科。从20世纪90年代起, 核苷酸和氨基酸序列等分子数据开始被广泛运用于被子植物系统发育研究, 经过20多年的发展, 从使用单个或联合少数几个细胞器基因, 到近期应用整个叶绿体基因组来重建被子植物的系统发育关系, 目、科水平上的被子植物系统发育框架已被广泛接受。在这个框架中, 基部类群、主要的5个分支(即真双子叶植物、单子叶植物、木兰类、金粟兰目和金鱼藻目)、每个分支所包含的目以及几个大分支包括的核心类群等都具有高度支持。与此同时, 细胞器基因还存在一些固有的问题, 例如单亲遗传、系统发育信息量有限等, 因此近年来双亲遗传的核基因在被子植物系统发育研究中的重要性逐渐得到关注, 并在不同分类阶元的研究中都取得了一定进展。但是, 被子植物系统发育中仍然存在一些难以确定的关系, 例如被子植物5个分支之间的关系、真双子叶植物内部某些类群的位置等。本文简述了20多年来被子植物系统发育深层关系的主要研究进展, 讨论了被子植物系统发育学常用的细胞器基因和核基因的选用, 已经确定和尚未确定系统发育位置的主要类群, 以及研究中尚存在的问题和可能的解决方法。     

谈系统发生树建立的分子标准

随着进化生物学以及生物信息学的发展 ,研究不同物种间进化关系的方法也有了新的进展。其中分子进化方法使得系统发生树的建立更加简便和精确。几种系统发生树的建树方法及相关分子标准目前比较流行。。     

A congruent solution to arthropod phylogeny: phylogenomics,microRNAs and morphology support monophyletic Mandibulata

While a unique origin of the euarthropods is well established, relationships between the four euarthropod classes—chelicerates, myriapods, crustaceans and hexapods—are less clear. Unsolved questions include the position of myriapods, the monophyletic origin of chelicerates, and the validity of the close relationship of euarthropods to tardigrades and onychophorans. Morphology predicts that myriapods, insects and crustaceans form a monophyletic group, the Mandibulata, which has been contradicted by many molecular studies that support an alternative Myriochelata hypothesis (Myriapoda plus Chelicerata). Because of the conflicting insights from published molecular datasets, evidence from nuclear-coding genes needs corroboration from independent data to define the relationships among major nodes in the euarthropod tree. Here, we address this issue by analysing two independent molecular datasets: a phylogenomic dataset of 198 protein-coding genes including new sequences for myriapods, and novel microRNA complements sampled from all major arthropod lineages. Our phylogenomic analyses strongly support Mandibulata, and show that Myriochelata is a tree-reconstruction artefact caused by saturation and long-branch attraction. The analysis of the microRNA dataset corroborates the Mandibulata, showing that the microRNAs miR-965 and miR-282 are present and expressed in all mandibulate species sampled, but not in the chelicerates. Mandibulata is further supported by the phylogenetic analysis of a comprehensive morphological dataset covering living and fossil arthropods, and including recently proposed, putative apomorphies of Myriochelata. Our phylogenomic analyses also provide strong support for the inclusion of pycnogonids in a monophyletic Chelicerata, a paraphyletic Cycloneuralia, and a common origin of Arthropoda (tardigrades, onychophorans and arthropods), suggesting that previous phylogenies grouping tardigrades and nematodes may also have been subject to tree-reconstruction artefacts.     

植物生命之树重建的现状、问题和对策建议

生命之树的概念源自1859年达尔文的《物种起源》, 但利用分子数据重建植物生命之树的研究则在20世纪90年代才开始兴起。近年来, 随着测序技术、分析方法和计算能力的快速发展, 植物生命之树重建研究取得了显著成果。本文首先概述了当前以及未来很长一段时间内植物生命之树重建工作的重点, 包括植物属级和种级水平的系统发育研究、植物系统发育基因组学研究、分子和形态数据联合分析、包括灭绝与现存植物类群的生命之树重建, 以及超大植物生命之树重建等5个方面; 然后简要概括国内植物生命之树重建研究的现状, 指出了我国在植物生命之树重建领域发展中所存在的问题, 并从“类群研究体系、学科评价体系、国家顶层设计, 以及拓展国际合作”等方面对学科未来的发展提出了一些对策建议。     

分子生物学技术在双翅目实蝇科昆虫系统发育研究中的应用

分子生物学技术如同工酶电泳、RFLP、RAPD、核酸序列分析、微卫星DNA和探针杂交等,在实蝇科昆虫系统发育研究中具有重要作用。利用这些技术对实蝇种群进行系统发育研究,揭示其亲缘及进化关系,从生命本质上寻找实蝇种群间的内在联系。文章综述上述几种分子生物学技术在实蝇科昆虫核酸结构、种内和种间的亲缘及进化关系等方面的研究进展,分析在应用中存在的问题,展望这些分子生物学技术在实蝇科昆虫系统发育中的应用前景。     

Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)

Drosophila is the genus responsible for the birth of experimental genetics, but the taxonomy of drosophilids is difficult because of the overwhelming diversity of the group. In this study, we assembled sequences for 358 species (14 genera, eight subgenera, 57 species groups, and 65 subgroups) to generate a maximum‐likelihood topology and a Bayesian timescale. In addition to sampling an unprecedented diversity of Drosophila lineages, our analyses incorporated a geographical perspective because of the high levels of endemism. In our topology, Drosophila funebris (Fabricius, 1787) (the type species of Drosophila) is tightly clustered with the pinicola subgroup in a North American clade within subgenus Drosophila. The type species of other drosophilid genera fall within the Drosophila radiation, presenting interesting prospects for the phylogenetic taxonomy of the group. Our timescale suggests that a few drosophilid lineages survived the Cretaceous–Palaeogene (K‐Pg) extinction. The drosophilid diversification began during the Palaeocene in Eurasia, but peaked during the Miocene, an epoch of drastic climatic changes. The most recent common ancestor of the clades corresponding to subgenera Sophophora and Drosophila lived approximately 56 Mya. Additionally, Hawaiian drosophilids diverged from an East Asian lineage approximately 26 Mya, which is similar to the age of the oldest emerging atoll in the Hawaiian–Emperor Chain. Interestingly, the time estimates for major geographical splits (New World versus Asia and Africa versus Asia) were highly similar for independent lineages. These results suggest that vicariance played a significant role in the radiation of fruit flies. © 2013 The Linnean Society of London     

直翅目昆虫线粒体基因组研究进展

本文总结了本实验室对40余种直翅目昆虫的线粒体基因组序列的研究方法和主要结果.直翅目线粒体基因组研究中最重要的发现包括：（1）在直翅目昆虫线粒体基因组中发现了3种基因排列次序.蝗亚目除蜢总科外都具有DK排列.蜢总科的变色乌蜢为KD 排列,与蝗亚目其他总科不同,而与螽亚目昆虫的排序方式相同.已测出的螽亚目大多数昆虫的KD 排列顺序与典型节肢动物的完全相同,但在黄脸油葫芦Teleogryllus emma发生了tRNA^Glu,tRNA^Ser和tRNA^Asn的倒置;（2）在疑钩额螽Ruspolia dubia中发现了一种到目前为止具有最短控制区（70 bp）的线粒体基因组;（3）采用多种方法分析了昆虫A+T富集区存在的调控序列和二级结构特征,获得了昆虫A+T富集区保守序列的一致结构.采用Z曲线分析蝗虫的A+T富集区,表明也存在与原核生物复制起点类似的信号;（4）构建了30种蝗虫12S rRNA和16S rRNA的二级结构.在昆虫线粒体基因组非编码链中发现了一些类tRNA结构和tRNA异构体;（5）构建了基于线粒体基因组数据的直翅目昆虫主要亚科以上分类单元之间的系统发育关系.     

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

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Assembling the lophotrochozoan (=spiralian) tree of life

The advent of numerical methods for analysing phylogenetic relationships, along with the study of morphology and molecular data, has driven our understanding of animal relationships for the past three decades. Within the protostome branch of the animal tree of life, these data have sufficed to establish its two main side branches, the moulting Ecdysozoa and the non-moulting Lophotrochozoa. In this review, I explore our current knowledge of protostome relationships and discuss progress and future perspectives and strategies to increase resolution within the main lophotrochozoan clades. Novel approaches to coding morphological characters are needed by scoring real observations on species selected as terminals. Still, methodological issues, for example, how to deal with inapplicable characters or the coding of absences, may require novel algorithmic developments. Taxon sampling is another key issue, as phyla should include enough species so as to represent their span of anatomical disparity. On the molecular side, phylogenomics is playing an increasingly important role in elucidating animal relationships, but genomic sampling is still fairly limited within the lophotrochozoan protostomes, for which only three phyla are represented in currently available phylogenies. Future work should therefore concentrate on generating novel morphological observations and on producing genomic data for the lophotrochozoan side of the animal tree of life.     

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.     

Molecular Markers and Concepts of Plant Evolutionary Relationships: Progress,Promise, and Future Prospects

In just the past 20 years systematics has progressed from the sequencing of individual genes for a few taxa to routine sequencing of complete plastid and even nuclear genomes. Recent technological advances have made it possible to compile very large data sets, the analyses of which have in turn provided unprecedented insights into phylogeny and evolution. Indeed, this narrow window of a few decades will likely be viewed as a golden era in systematics. Relationships have been resolved at all taxonomic levels across all groups of photosynthetic life. In the angiosperms, problematic deep-level relationships have either been largely resolved, or will be resolved within the next several years. The same large data sets have also provided new insights into the many rapid radiations that have characterized angiosperm evolution. For example, all of the major lineages of angiosperms likely arose within a narrow window of just a few million years. At the population level, the ease of DNA sequencing has given new life to phylogeographic studies, and microsatellite analyses have become more commonplace, with a concomitant impact on conservation and population biology. With the wealth of sequence data soon to be available, we are on the cusp of assembling the first semi-comprehensive tree of life for many of the 15,000 genera of flowering plants and indeed for much of green life. Accompanying these opportunities are also enormous new computational/informatic challenges including the management and phylogenetic analysis of such large, sometimes fragmentary data sets, and visualization of trees with thousands of terminals.     

Genome‐wide survey of nuclear protein‐coding markers for beetle phylogenetics and their application in resolving both deep and shallow‐level divergences

Beetles (Coleoptera) are the most diverse and species‐rich insect group, representing an impressive explosive radiation in the evolutionary history of insects, and their evolutionary relationships are often difficult to resolve. The amount of ‘traditional markers’ (e.g. mitochondrial genes and nuclear rDNAs) for beetle phylogenetics is small, and these markers often lack sufficient signals in resolving relationships for such a rapidly radiating lineage. Here, based on the available genome data of beetles and other related insect species, we performed a genome‐wide survey to search nuclear protein‐coding (NPC) genes suitable for research on beetle phylogenetics. As a result, we identified 1470 candidate loci, which provided a valuable data resource to the beetle evolutionary research community for NPC marker development. We randomly chose 180 candidate loci from the database to design primers and successfully developed 95 NPC markers which can be PCR amplified from standard genomic DNA extracts. These new nuclear markers are universally applicable across Coleoptera, with an average amplification success rate of 90%. To test the phylogenetic utility, we used them to investigate the backbone phylogeny of Coleoptera (18 families sampled) and the family Coccinellidae (39 species sampled). Both phylogenies are well resolved (average bootstrap support >95%), showing that our markers can be used to address phylogenetic questions of various evolutionary depth (from species level to family level). In general, the newly developed nuclear markers are much easier to use and more phylogenetically informative than the ‘traditional markers’, and show great potential to expedite resolution of many parts in the Beetle Tree of Life.     

A new 'great-appendage' arthropod from the Lower Cambrian of China and homology of chelicerate chelicerae and raptorial antero-ventral appendages

The uniramous ‘great appendages’ of several arthropods from the Early to Middle Cambrian are a characteristic pair of pre‐oral limbs, which served for prey capture. It has been assumed that the morphological differences between the ‘great‐appendage’ arthropods indicate that raptorial antero‐ventral and anteriorly pointing appendages evolved more than once in arthropod phylogeny. One set of Cambrian ‘great‐appendage’ arthropods has, however, very similar short antero‐ventral appendages with a peduncle of two segments angled against each other (elbowed) and with stout distally or medio‐distally directed spines or long flexible flagellate spines on each of the four distal segments. Moreover, the head appendages of all these forms comprise the ‘great appendages’ and three pairs of biramous limbs. To this set of taxa we can add a new form from the Lower Cambrian Maotianshan Shale of southern China, Haikoucaris ercaiensis n. gen. and n. sp. It is known from three specimens, possibly being little abundant in the faunal community. It can be distinguished from all other taxa by the prominence of the proximal claw segment of its ‘great appendages’ and by only three distal spines (one on each of the distal segments). The similarity of the short, spiky ‘great appendages’ of Haikoucaris with the chelicera of the Chelicerata leads us to hypothesize that this particular type of ‘great appendages’ was the actual precursor of the chelicera. Homeobox gene and developmental data recently demonstrated the homology between the antenna of ateloceratans and the antennula of crustaceans on one side and the chelicera of chelicerates on the other. To this we add palaeontological evidence for the homology between the chelicerae of chelicerates and the ‘short great appendages’ of certain Cambrian arthropods, which leads us to hypothesize that the evolutionary path went from the ‘short great appendages’, by progressive compaction, toward the chelicera with only a two‐spined chela. The new form from China is regarded as the possible latest offshoot, whereas the other ‘great appendages’ arthropods with similar short grasping limbs were derivatives of the stem lineage of the crown‐group Chelicerata. Consequently, the chelicera with a chela with one fixed and one mobile finger is an autapomorphy of the crown group of Chelicerata, whereas a raptorial, but more limb‐like antenna, with more distal spine‐bearing segments, characterized the ground pattern of Chelicerata. Further taxa having ‘great appendages’, including the large Anomalocarididae, are also discussed in the light of their possible affinities to the Chelicerata and possible monophyly of all of these arthropods with raptorial anterior appendages.     

LZ complexity distance of DNA sequences and its application in phylogenetic tree reconstruction

DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet （A, C, T, G）. As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals （Eutheria） with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.     

Hydrodynamics and sliding posture analysis of the Cambrian arthropod Ercaicunia multinodosa

Dynamic mechanical analysis offers the opportunity to explore the motility and feeding strategies of extinct organisms, but the prerequisite is to have an accurate recovery engineering model. As shown with micro-computed tomography (CT) scanning, fossils of the bivalved arthropod Ercaicunia multinodosa from the Cambrian (Series 2, Stage 3) Chengjiang biota of China have well-preserved three-dimensional (3D) morphological details with a certain degree of compression. Here, we propose a palaeontological restoration method using computational fluid dynamics (CFD) to analyse multiple hypothetical models based on the fossil information to obtain a reasonable restoration model. Furthermore, we carry out hydrodynamic experiments to verify the palaeontological restoration results. Our simulation and experimental results suggest that, a dorsally convex and ventrally straight body shape with the valves opening at an angle of approximately 120° works best for E. multinodosa to overcome resistance, and in the meantime obtain most lift while sliding in the water column. The combination of three-dimensional reconstruction, CFD simulation, and hydrodynamic experiments provides a useful method for restoring the morphologies of extinct animals and exploring their palaeoecology.     

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.     

Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone

While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea, and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca, and Typha), a water lily (Nuphar), a ranunculid (Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein data sets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiosperm phylogeny. However, their relative positions proved to be dependent on the method of analysis, with parsimony favoring Amborella as sister to all other angiosperms and maximum likelihood (ML) and neighbor-joining methods favoring an Amborella + Nymphaeales clade as sister. The ML phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single-gene phylogenies, estimated divergence dates, and conflicting indel characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiosperm phylogeny. Molecular dating analyses provided median age estimates of 161 MYA for the most recent common ancestor (MRCA) of all extant angiosperms and 145 MYA for the MRCA of monocots, magnoliids, and eudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction might mislead genome-scale phylogenetic analyses.