Phylogeny of the Neuropterida (Insecta: Holometabola)

The Neuropterida, with about 6500 known species — living fossils in a way — at the base of the Holometabola (as a sister group of the Coleoptera), comprise Raphidioptera (about 210 species, two families), Megaloptera (about 300 species, two families) and Neuroptera (6000 species, 17 families). Megaloptera + Neuroptera is argued vs. the traditional Raphidioptera + Megaloptera. Raphidioptera are undisputedly monophyletic. Monophyly of Megaloptera is the operational hypothesis, although occasionally questioned. Sucking tubes of the larvae are the most spectacular autapomorphy of Neuroptera. The construction of larval head capsules indicates three evolutionary lines: Nevrorthiformia, and Myrmeleontiformia + Hemerobiiformia. Traditional Myrmeleontiformia is Psychopsidae + (Nemopteridae + (Nymphidae + (Myrmeleontidae + Ascalaphidae))), the present approach is (Psychopsidae + Nemopteridae) + all other Myrmeleontiformia. Hemerobiiformia are based on the ‘maxillary head’ concept. The ithonid clade Ithonidae/Rapismatidae + Polystoechothidae and the dilarid clade Dilaridae + (Mantispidae + (Rhachiberothidae + Berothidae)) are based on robust criteria. Other relationships remain unclear: Hemerobiidae + Chrysopidae (on similarity) and the ‘early offshoot’ concept of coniopterygidae (on autapomorphies) should not be perpetuated. Chysopidae + Osmylidae and (Hemerobiidae + (Coniopterygidae + Sisyridae)) + dilarid clade are discussed. Aquatic larvae, regarded as independent apomorphies of megaloptera and neuropteran Nevrorthidae and Sisyridae for a long time, are re‐interpreted as a synapomorphy of Megaloptera + Neuroptera and thus plesiomorphic within these groups. Terrestrial larvae (with cryptonephry to solve osmotic problems) are consequently apomorphic. Aquatic Sisyridae with cryptonephry of a single malpighian tubule, is conflicting, but larvae may have become secondarily aquatic, after a terrestrial intermezzo.     

Phylogenetic significance of the wing-base of the Holometabola (Insecta)

The present knowledge of the wing-base morphology of the holometabolous insects is summarized, and the value of these structures for phylogenetic analysis is demonstrated. An autapomorphy of the Holometabola is a locking mechanism composed of a knob on the basalare and a corresponding cavity on the ventral wing-base. Two synapomorphic hindwing-base characters support a sister-group relationship of Coleoptera and Neuropterida. Only few data are available on the wing-base of the Hymenoptera. An autapomorphy of the taxon is a modification of the wing locking mechanism with reduced size of the basalare and its knob. It is demonstrated that wing-base characters are helpful for the analysis of the relationships between strepsipteran families. However, characters of the wing-base support neither a relationship of Strepsiptera and Coleoptera nor of Strepsiptera and Antliophora.     

Phylogeny of the Strepsiptera based on morphological data of the first instar larvae

This investigation was the first cladistic analysis using morphological data of first instar larvae of Strepsiptera. The analysis of representatives of nearly all known families of Strepsiptera supports the division of Strepsiptera into Mengenillidia and Stylopidia. Corioxenidae and Elenchidae are placed at the base of Stylopidia. Halictophagidae is the sister group to Xeninae + Myrmecolacidae + Stylopinae. Xeninae is placed as the sister group to Myrmecolacidae + Stylopinae. Stylopidae are paraphyletic. Thus, Xenidae stat. n. is re-established. A sister-group relationship between Myrmecolacidae and Elenchidae is not supported on characters of first instar larvae.     

Phylogenetic position of the Strepsiptera: Review of molecular and morphological evidence

Molecular evidence of the monophyly of the Halteria (Strepsiptera + Diptera) is reviewed. The majority of morphological characters, which have classically been used to establish a Strepsiptera + Coleoptera sister group, are rejected, because they are based on erroneous interpretations of strepsipteran morphology. The scorings of 31 morphological characters, which directly relate to the phylogenetic position of Strepsiptera, are provided, and their distribution and optimization on the molecular + morphological tree is discussed. Of these, 13 characters specifically support the placement of Strepsiptera within the Mecopterida; seven of which are based on the optimization of inapplicable or missing data, and six of which are based on states that can be scored for Strepsiptera. Only a single character (posteromotorism) suggests a sister group relationship with the Coleoptera. The morphological and molecular data are largely congruent, and suggest that the Strepsiptera are sister group to the Diptera.     

Phylogenetic relevance of the genital sclerites of Neuropterida (Insecta: Holometabola)

Abstract Segment 9 of male Raphidioptera, comprising tergite, sternite, gonocoxites, gonostyli and gonapophyses, is a benchmark for homologies in the male and female terminalia of the three Neuropterida orders Raphidioptera, Megaloptera and Neuroptera. The segments relating to genitalia are 9, 10 and 11 in males and 7, 8 and 9 in females. Results from holomorphological and recent molecular cladistic analyses of Neuropterida agree in supporting the sister‐group relationships between: (1) the Raphidioptera and the clade Megaloptera + Neuroptera, and (2) the suborder Nevrorthiformia and all other Neuroptera. The main discrepancy between the results of these studies is the nonmonophyly of the suborder Hemerobiiformia in the molecular analysis. The monophyly of the Megaloptera (which has been repeatedly questioned) is further corroborated by a hitherto overlooked ground pattern autapomorphy: the presence of eversible sacs within the complex of the fused gonocoxites 11 in Corydalidae and Sialidae. The recently discovered paired complex of gonocoxites 10 (parameres) in Nipponeurorthus (Nevrorthidae) indicates that the curious apex of sternite 9 of Nevrorthus and Austroneurorthus is the amalgamation of the sclerites of gonocoxites 10 with sternite 9, interpreted as synapomorphic. In the molecular study, the Nevrorthidae, Sisyridae and Osmylidae branch off in consecutive splitting events, a result that is supported by the analysis of male genital sclerites reported here. Extraordinary parallel apomorphies (e.g. excessive enlargement and modification of gonocoxites 10 ending in a thread‐like ‘penisfilum’) in derived representatives of Coniopterygidae, Berothidae, Rhachiberothidae and Mantispidae corroborate the dilarid clade of the morphological analysis and leads us to hypothesize a sister‐group relationship of the Coniopterygidae with the dilarid clade. A re‐interpretation of the tignum of Chrysopidae as gonocoxites 11 means that the structure previously called the gonarcus represents the fused gonocoxites 9. In Hemerobiidae, the corresponding sclerite is consequently also homologized as fused gonocoxites 9. The enlargement of the lateral wings of the gonocoxites in both families is interpreted as a synapomorphy. Excessive enlargement of gonostyli 11 in the Polystoechotid clade and Myrmeleontiformia supports a sister‐group relationship of these two clades. The occurrence of certain serial homologues of female genitalia structures (gonocoxites and gonapophyses), such as the digitiform processus together with the flat appendices in segment 8 of certain Myrmeleontidae, or the wart‐like processus together with the flat circular sclerites in segment 7 of certain Berothidae, as well as the presence of gonocoxites 8 as pseudosternites in certain Nemopteridae and Coniopterygidae, are probably character reversals. The digitiform processus of tergite 9 (pseudogonocoxites) in Rhachiberothidae and Austroberothella (Berothidae) are either independently developed acquisitions with a function in oviposition, or are homologous sclerites, possibly of epipleurite origin.     

饶氏藻系统位置的研究

用18S rDNA基因序列分析饶氏藻属(Jaoa)与相关藻类的亲缘关系。结果表明:饶氏藻18S rDNA的长度为1632 bp,GC%为50.6%,泡状饶氏藻18S rDNA的长度为1639 bp,GC%为50.3%。用最大简约法与饶氏藻上一级分类单元(目)构建的系统树表明有4个大的分支。两种饶氏藻与石莼目的 Ulva curvata、U.rigida、Enteromorpha intestinalis和Monostroma grevillei构成很强的支持分支(分支B),它们之间的核苷酸趋异性最低仅0.041,而与胶毛藻目的 Chaetophora incrassata的趋异性则很显著,达0.112,因此,饶氏藻应属于石莼目的一个类群,且饶氏藻和泡状饶氏藻构成一单系起源的分支,这两个物种的趋异性仅0.002,显示出它们具有非常紧密的亲缘关系,很可能是1种1变种而不是2种。     

PCA and Clustering Reveal Alternate mtDNA Phylogeny of N and M Clades

Phylogenetic trees based on mtDNA polymorphisms are often used to infer the history of recent human migrations. However, there is no consensus on which method to use. Most methods make strong assumptions which may bias the choice of polymorphisms and result in computational complexity which limits the analysis to a few samples/polymorphisms. For example, parsimony minimizes the number of mutations, which biases the results to minimizing homoplasy events. Such biases may miss the global structure of the polymorphisms altogether, with the risk of identifying a "common" polymorphism as ancient without an internal check on whether it either is homoplasic or is identified as ancient because of sampling bias (from oversampling the population with the polymorphism). A signature of this problem is that different methods applied to the same data or the same method applied to different datasets results in different tree topologies. When the results of such analyses are combined, the consensus trees have a low internal branch consensus. We determine human mtDNA phylogeny from 1737 complete sequences using a new, direct method based on principal component analysis (PCA) and unsupervised consensus ensemble clustering. PCA identifies polymorphisms representing robust variations in the data and consensus ensemble clustering creates stable haplogroup clusters. The tree is obtained from the bifurcating network obtained when the data are split into k = 2,3,4,...,kmax clusters, with equal sampling from each haplogroup. Our method assumes only that the data can be clustered into groups based on mutations, is fast, is stable to sample perturbation, uses all significant polymorphisms in the data, works for arbitrary sample sizes, and avoids sample choice and haplogroup size bias. The internal branches of our tree have a 90% consensus accuracy. In conclusion, our tree recreates the standard phylogeny of the N, M, L0/L1, L2, and L3 clades, confirming the African origin of modern humans and showing that the M and N clades arose in almost coincident migrations. However, the N clade haplogroups split along an East-West geographic divide, with a "European R clade" containing the haplogroups H, V, H/V, J, T, and U and a "Eurasian N subclade" including haplogroups B, R5, F, A, N9, I, W, and X. The haplogroup pairs (N9a, N9b) and (M7a, M7b) within N and M are placed in nonnearest locations in agreement with their expected large TMRCA from studies of their migrations into Japan. For comparison, we also construct consensus maximum likelihood, parsimony, neighbor joining, and UPGMA-based trees using the same polymorphisms and show that these methods give consistent results only for the clade tree. For recent branches, the consensus accuracy for these methods is in the range of 1-20%. From a comparison of our haplogroups to two chimp and one bonobo sequences, and assuming a chimp-human coalescent time of 5 million years before present, we find a human mtDNA TMRCA of 206,000 +/- 14,000 years before present.     

Phylogenetic Ordinal Placement Based on rDNA Sequences of the Freshwater Genera Ophioceras and Pseudohalonectria

Chen, W., Shearer, C. A., and Klopp, J. 1995. Phylogenetic ordinal placement based on rDNA sequences of the freshwater genera Ophioceras and Pseudohalonectria. Experimental Mycology 19, 191-201, The ordinal placement of two closely related freshwater genera, Ophioceras and Pseudohalonectria , was assessed by using phylogenetic analysis of morphological characters, partial sequences of the large subunit ribosomal DNA and restriction site variations in the internal transcribed spacer (ITS). The two genera have some morphological features that are used to define taxa in both the Sordariales and Diaporthales, and, hence, their phylogenetic relationships are unclear. Equally weighted analyses of thirty-eight morphological characters produced unresolved phylogenetic trees and unequivocal conclusions could not be drawn based on the morphological data. The polymcrase chain reaction-amplified ITS region was variable in length between the two genera and restriction sites in the ITS region were determined. Analysis of variation in restriction sites in the ITS region placed Ophioceras and Pseudohalonectria in one clade with taxa sampled from Sordariales. About 350 basepairs of DNA sequence from the 5′ end of the large subunit rDNA were also determined. In phylogenetic analysis of the sequence data with Hypocrea lutea and Nectria cinnabarina as outgroups, Ophioceras and Pseudohalonectria showed a closer relationship to Neurospora crassa , Schizothecium sp., and Sordaria fimicola of the Sordariales than to Cryphonectria parasitica and Endothia gyrosa of the Diaporthales.     

Phylogeny and evolution of Rab7 and Rab9 proteins

Background  

An important role in the evolution of intracellular trafficking machinery in eukaryotes played small GTPases belonging to the Rab family known as pivotal regulators of vesicle docking, fusion and transport. The Rab family is very diversified and divided into several specialized subfamilies. We focused on the VII functional group comprising Rab7 and Rab9, two related subfamilies, and analysed 210 sequences of these proteins. Rab7 regulates traffic from early to late endosomes and from late endosome to vacuole/lysosome, whereas Rab9 participates in transport from late endosomes to the trans-Golgi network.     

Rhizobial 16S rRNA and dnaK Genes: Mosaicism and the Uncertain Phylogenetic Placement of Rhizobium galegae

The phylogenetic relatedness among 12 agriculturally important species in the order Rhizobiales was estimated by comparative 16S rRNA and dnaK sequence analyses. Two groups of related species were identified by neighbor-joining and maximum-parsimony analysis. One group consisted of Mesorhizobium loti and Mesorhizobium ciceri, and the other group consisted of Agrobacterium rhizogenes, Rhizobium tropici, Rhizobium etli, and Rhizobium leguminosarum. Although bootstrap support for the placement of the remaining six species varied, A. tumefaciens, Agrobacterium rubi, and Agrobacterium vitis were consistently associated in the same subcluster. The three other species included Rhizobium galegae, Sinorhizobium meliloti, and Brucella ovis. Among these, the placement of R. galegae was the least consistent, in that it was placed flanking the A. rhizogenes-Rhizobium cluster in the dnaK nucleotide sequence trees, while it was placed with the other three Agrobacterium species in the 16S rRNA and the DnaK amino acid trees. In an effort to explain the inconsistent placement of R. galegae, we examined polymorphic site distribution patterns among the various species. Localized runs of nucleotide sequence similarity were evident between R. galegae and certain other species, suggesting that the R. galegae genes are chimeric. These results provide a tenable explanation for the weak statistical support often associated with the phylogenetic placement of R. galegae, and they also illustrate a potential pitfall in the use of partial sequences for species identification.     

Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola

We present the largest morphological character set ever compiled for Holometabola. This was made possible through an optimized acquisition of data. Based on our analyses and recently published hypotheses based on molecular data, we discuss higher‐level phylogeny and evolutionary changes. We comment on the information content of different character systems and discuss the role of morphology in the age of phylogenomics. Microcomputer tomography in combination with other techniques proved highly efficient for acquiring and documenting morphological data. Detailed anatomical information (356 characters) is now available for 30 representatives of all holometabolan orders. A combination of traditional and novel techniques complemented each other and rapidly provided reliable data. In addition, our approach facilitates documenting the anatomy of model organisms. Our results show little congruence with studies based on rRNA, but confirm most clades retrieved in a recent study based on nuclear genes: Holometabola excluding Hymenoptera, Coleopterida (= Strepsiptera + Coleoptera), Neuropterida excl. Neuroptera, and Mecoptera. Mecopterida (= Antliophora + Amphiesmenoptera) was retrieved only in Bayesian analyses. All orders except Megaloptera are monophyletic. Problems in the analyses are caused by taxa with numerous autapomorphies and/or inapplicable character states due to the loss of major structures (such as wings). Different factors have contributed to the evolutionary success of various holometabolan lineages. It is likely that good flying performance, the ability to occupy different habitats as larvae and adults, parasitism, liquid feeding, and co‐evolution with flowering plants have played important roles. We argue that even in the “age of phylogenomics”, comparative morphology will still play a vital role. In addition, morphology is essential for reconstructing major evolutionary transformations at the phenotypic level, for testing evolutionary scenarios, and for placing fossil taxa.
© The Willi Hennig Society 2010.     

The morphology and evolution of the female postabdomen of Holometabola (Insecta)

In the present article homology issues, character evolution and phylogenetic implications related to the female postabdomen of the holometabolan insects are discussed, based on an earlier analysis of a comprehensive morphological data set. Hymenoptera, the sistergroup of the remaining Holometabola, are the only group where the females have retained a fully developed primary ovipositor of the lepismatid type. There are no characters of the female abdomen supporting a clade Coleopterida + Neuropterida. The invagination of the terminal segments is an autapomorphy of Coleoptera. The ovipositor is substantially modified in Raphidioptera and distinctly reduced in Megaloptera and Neuroptera. The entire female abdomen is extremely simplified in Strepsiptera. The postabdomen is tapering posteriorly in Mecopterida and retractile in a telescopic manner (oviscapt). The paired ventral sclerites of segments VIII and IX are preserved, but valvifers and valvulae are not distinguishable. In Amphiesmenoptera sclerotizations derived from the ventral appendages VIII are fused ventromedially, forming a solid plate, and the appendages IX are reduced. The terminal segments are fused and form a terminal unit which bears the genital opening subapically. The presence of two pairs of apophyses and the related protraction of the terminal unit by muscle force are additional autapomorphies, as is the fusion of the rectum with the posterior part of the genital chamber (cloaca). Antliophora are supported by the presence of a transverse muscle between the ventral sclerites of segment VIII. Secondary egg laying tubes have evolved independently within Boreidae (absent in Caurinus) and in Tipulomorpha. The loss of two muscle associated with the genital chamber are likely autapomorphies of Diptera. The secondary loss of the telescopic retractability of the postabdomen is one of many autapomorphies of Siphonaptera.     

Genomic and morphological evidence converge to resolve the enigma of Strepsiptera

The phylogeny of insects, one of the most spectacular radiations of life on earth, has received considerable attention. However, the evolutionary roots of one intriguing group of insects, the twisted-wing parasites (Strepsiptera), remain unclear despite centuries of study and debate. Strepsiptera exhibit exceptional larval developmental features, consistent with a predicted step from direct (hemimetabolous) larval development to complete metamorphosis that could have set the stage for the spectacular radiation of metamorphic (holometabolous) insects. Here we report the sequencing of a Strepsiptera genome and show that the analysis of sequence-based genomic data (comprising more than 18 million nucleotides from nearly 4,500 genes obtained from a total of 13 insect genomes), along with genomic metacharacters, clarifies the phylogenetic origin of Strepsiptera and sheds light on the evolution of holometabolous insect development. Our results provide overwhelming support for Strepsiptera as the closest living relatives of beetles (Coleoptera). They demonstrate that the larval developmental features of Strepsiptera, reminiscent of those of hemimetabolous insects, are the result of convergence. Our analyses solve the long-standing enigma of the evolutionary roots of Strepsiptera and reveal that the holometabolous mode of insect development is more malleable than previously thought.     

Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

Principal components analysis (PCA) and hierarchical clustering are two of the most heavily used techniques for analyzing the differences between nucleic acid sequence samples taken from a given environment. They have led to many insights regarding the structure of microbial communities. We have developed two new complementary methods that leverage how this microbial community data sits on a phylogenetic tree. Edge principal components analysis enables the detection of important differences between samples that contain closely related taxa. Each principal component axis is a collection of signed weights on the edges of the phylogenetic tree, and these weights are easily visualized by a suitable thickening and coloring of the edges. Squash clustering outputs a (rooted) clustering tree in which each internal node corresponds to an appropriate “average” of the original samples at the leaves below the node. Moreover, the length of an edge is a suitably defined distance between the averaged samples associated with the two incident nodes, rather than the less interpretable average of distances produced by UPGMA, the most widely used hierarchical clustering method in this context. We present these methods and illustrate their use with data from the human microbiome.     

河南发现刘氏石龙子及该物种系统位置分析

2018年8月下旬,在河南省南阳市桐柏山采集到11号石龙子科（Scincidae）蜥蜴标本。经形态比较鉴定,该批标本均为刘氏石龙子（Pleistiodon liui）,是河南省爬行动物分布新记录种,也是该物种在长江以北地区首次被发现。通过形态学分析,发现刘氏石龙子可能存在雌雄性二态。基于COI基因658 bp序列的系统发育分析显示,大渡石龙子（P. capito）和黄纹石龙子（P. tunganus）聚在一起,然后再与刘氏石龙子聚成一支系,支持先前基于形态数据的黄纹石龙子种组的单系性。     

Selection of Orthologous Genes for Construction of a Highly Resolved Phylogenetic Tree and Clarification of the Phylogeny of Trichosporonales Species

The order Trichosporonales (Tremellomycotina, Basidiomycota) includes various species that have clinical, agricultural and biotechnological value. Thus, understanding why and how evolutionary diversification occurred within this order is extremely important. This study clarified the phylogenetic relationships among Tricosporonales species. To select genes suitable for phylogenetic analysis, we determined the draft genomes of 17 Trichosporonales species and extracted 30 protein-coding DNA sequences (CDSs) from genomic data. The CDS regions of Trichosporon asahii and T. faecale were identified by referring to mRNA sequence data since the intron positions of the respective genes differed from those of Cryptococcus neoformans (outgroup) and are not conserved within this order. A multiple alignment of the respective gene was first constructed using the CDSs of T. asahii, T. faecale and C. neoformans, and those of other species were added and aligned based on codons. The phylogenetic trees were constructed based on each gene and a concatenated alignment. Resolution of the maximum-likelihood trees estimated from the concatenated dataset based on both nucleotide (72,531) and amino acid (24,173) sequences were greater than in previous reports. In addition, we found that several genes, such as phosphatidylinositol 3-kinase TOR1 and glutamate synthase (NADH), had good resolution in this group (even when used alone). Our study proposes a set of genes suitable for constructing a phylogenetic tree with high resolution to examine evolutionary diversification in Trichosporonales. These can also be used for epidemiological and biogeographical studies, and may also serve as the basis for a comprehensive reclassification of pleomorphic fungi.