Metaves,Mirandornithes, Strisores and other novelties – a critical review of the higher‐level phylogeny of neornithine birds

Recent hypotheses on the higher‐level phylogeny of modern birds are reviewed, and areas of agreement and major conflict are detailed, with emphasis being put on congruence among independent molecular and morphological data sets. Although molecular data significantly contributed to a better understanding of avian phylogeny, they do not seem to be free of homoplasy and caution is warranted in the interpretation of some results. The recently proposed ‘Metaves’ clade is likely to be an artefact of the β‐fibrinogen gene, and current molecular data do not yield well‐supported phylogenies for some groups whose interrelationships can be resolved with morphological evidence. There exists, however, congruent and strong molecular evidence for several novel clades that were not recognized by morphologists before, and to ease future discussions the terms Picocoraciae (non‐leptosomid ‘Coraciiformes’ and Piciformes) and Aequornithes (‘waterbird assemblage’) are introduced. Molecular studies further congruently recover some clades, which have not yet been adequately appreciated and are outlined in the present review.     

A multidisciplinary approach to the fine-systematics within Tisbe - an evaluation of morphological and molecular methods

Six species from the species-rich taxon Tisbe (Copepoda, Harpacticoida) were selected that could be reared in the laboratory as mass cultures. Phylogenetic relationships among these species were assessed by morphological studies of adults and larvae, DNA restriction site polymorphisms, allozymic, immunological distance, and lipid composition. Limits of scope and practicability of these analyses became apparent, as well as their potential and importance for future work in zoological systematics.     

Molecular phylogeny of Gastrotricha on the basis of a comparison of the 18S rRNA genes: Rejection of the hypothesis of a relationship between Gastrotricha and Nematoda

Gastrotricha are the small meiobenthic acoelomate worms whose phylogenetic relationships between themselves and other invertebrates remain unclear, despite all attempts to clarify them on the basis of both morphological and molecular analyses. The complete sequences of the 18S rRNA genes (8 new and 7 known) were analyzed in 15 Gastrotricha species to test different hypotheses on the phylogeny of this taxon and to determine the reasons for the contradictions in earlier results. The data were analyzed using both maximum likelihood and Bayesian methods. Based on the results, it was assumed that gastrotrichs form a monophyletic group within the Spiralia clade, which also includes Gnathostomulida, Plathelminthes, Syndermata (Rotifera + Acanthocephala), Nemertea, and Lophotrochozoa. Statistical tests rejected a phylogenetic hypotheses considering Gastrotricha to be closely related to Nematoda and other Ecdysozoa or placing them at the base of the Bilateria tree, close to Acoela or Nemertodermatida. Among gastrotrichs, species belonging to the orders Chaetonotida and Macrodasyida form two well-supported clades. The analysis confirmed monophyly of the families Chaetonotidae and Xenotrichulidae from the order Chaetonida, as well as the families Turbanellidae and Thaumastodermatidae from the order Macrodasyida. Lepidodasyidae is a polyphyletic family, because the genus Mesodasys forms a sister group for Turbanellidae; genus Cephalodasys forms a separate branch at the base of Macrodasyida; and Lepidodasys groups with Neodasys between Thaumastodermatidae and Turbanellidae. To confirm these conclusions and to get an authentic view of the phylogeny of Gastrotricha, it is necessary to study more Gastrotricha species and to analyze some other genes.     

On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.     

On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.

Zusammenfassung

Ein fundamentaler Unterschied zwischen der einzelnen Sequenzposition oder auch numerischen Merkmalen und komplexen morphologischen Merkmalen ist ihr Informationsgehalt. Merkmalsreihen komplexer Strukturen enthalten meist genügend Information, um a priori die Bestimmung der Lesrichtung zu ermöglichen. Die Feststellung des Ursprunges eines Dendrogramms ist somit ohne kladistischen Außengruppenvergleich möglich, während Bäume (Topologien), die auf wenig informativen Merkmalen beruhen, allgemein nur mit dem kladistischen Außengruppenvergleich 'gewurzelt' werden können. Die Qualität der insgesamt verwendeten Information ist entscheidend für die Wahl zwischen alternativen Verwandtschaftshypothesen. Numerische Methoden der Rekonstruktion der Phylogenese sind nützlich bei Verwendung einer gro β en Zahl informationsarmer Merkmale; das Hennigsche Verfahren ist für komplexe Merkmale vorzuziehen.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

The anostracan genus Branchinella (Crustacea: Branchiopoda), in need of a taxonomic revision; evidence from penile morphology

Three morphologically different penile types discovered in branchinellids from Botswana are compared with literature information on congeners. The striking differences among penile structures in Branchinella ondonguae, B. ornata and the halobiontic B. spinosa raise doubts about their congeneric status. Penis morphology in B. ondonguae corresponds with the most common configuration in branchinellids, but it is largely deviant in the other two. Branchinella ornata shares penile structures with Dendrocephalus , while basal parts in B. spinosa reflect affinity with chirocephalids. A considerable general morphological variability in Branchinella , not met in any other anostracan genus, may reflect the antiquity of the group, or else poor taxonomy. Large intra-branchinellid variability and vague generic boundaries, even when considering the usually conservative penile structures, stress the need of a thorough revision of the entire family of the Thamnocephalidae.     

Evolutionary morphology of whip spiders: towards a phylogenetic system (Chelicerata: Arachnida: Amblypygi)*

The aim of this study is to present a cladogram and phylogenetic system and to use this to discuss the phylogeny and biogeography of the Amblypygi. A total of 29 morphological structures were studied, their plesiomorphic and apomorphic characters or character states were identified, and the resulting data matrix was analysed. As a result, the ‘old’Charontidae or Pulvillata emerge as a paraphyletic group; the genus Paracharon is the sister group of all other amblypygids, which are now termed Euamblypygi. The ‘new’Charontidae (sensu Quintero: the genera Stygophrynus and Charon) are the sister group of the Phrynida or Apulvillata; together they form the Neoamblypygi. The relationships of the genera of the Charinidae cannot be resolved with the available data. They may be a paraphyletic group. The genus Catageus is a possible candidate for being the sister group of the Neoamblypygi. The new system allows a discussion of the phylogeny and biogeography of whip spiders. It also points to unresolved taxa and thus indicates the questions future research should address.     

Examination of subfamilial phylogeny in Bromeliaceae using comparative sequencing of the plastid locus ndhF

Parsimony analysis of 31 sequences of the chloroplast locus ndhF was used to address questions of subfamilial phylogeny in Bromeliaceae. Results presented here are congruent with those from chloroplast DNA restriction site analysis in recognizing a clade containing Bromelioideae and Pitcairnioideae, and in resolving Tillandsioideae near the base of the family. Placements of several taxonomically difficult genera (e.g., Glomeropitcairnia and Navia) corroborate those of traditional treatments; however, these data suggest that Brocchinia (Pitcairnioideae) is the sister group to the remainder of Bromeliaceae. Further evidence for the paraphyly of Pitcairnioideae includes the resolution of Puya as the sister group to Bromelioideae. Implications for taxonomic realignment at the subfamily level are considered.     

Evolution of genes and taxa: a primer

The rapidly growing fields of molecular evolution and systematics have much to offer to molecular biology, but like any field have their own repertoire of terms and concepts. Homology, for example, is a central theme in evolutionary biology whose definition is complex and often controversial. Homology extends to multigene families, where the distinction between orthology and paralogy is key. Nucleotide sequence alignment is also a homology issue, and is a key stage in any evolutionary analysis of sequence data. Models based on our understanding of the processes of nucleotide substitution are used both in the estimation of the number of evolutionary changes between aligned sequences and in phylogeny reconstruction from sequence data. The three common methods of phylogeny reconstruction – parsimony, distance and maximum likelihood – differ in their use of these models. All three face similar problems in finding optimal – and reliable – solutions among the vast number of possible trees. Moreover, even optimal trees for a given gene may not reflect the relationships of the organisms from which the gene was sampled. Knowledge of how genes evolve and at what rate is critical for understanding gene function across species or within gene families. The Neutral Theory of Molecular Evolution serves as the null model of molecular evolution and plays a central role in data analysis. Three areas in which the Neutral Theory plays a vital role are: interpreting ratios of nonsynonymous to synonymous nucleotide substitutions, assessing the reliability of molecular clocks, and providing a foundation for molecular population genetics.     

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。     

Identification of apomorphies and the role of groundpatterns in molecular systematics

Putative apomorphic character states are the only relevant phylogenetic signal contained in sets of sequence data. Using the sequence position as a character, a way to identify putative apomorphies prior to phylogenetic analysis is proposed. It is shown that distance-matrix methods use trivial characters. The concept of the asymmetrical split is presented for determination of character polarity. It is furthermore argued that groundpatterns (node sequences) should be reconstructed prior to the study of relationships between taxa of high phylogenetic age. The 'evolutionary noise'contained in groundpatterns can be illustrated with a network of distances using a split-decomposition analysis.     

Trigonometric analysis of the Human Median Sagittal Plane and its applications in reconstruction and phylogeny

By means of a new method of measurement which defines a total of eight measuring points along the median sagittal plane of the skull, methodical aspects are explained. The advantages of this method consist in its easy use and exact reproducibility of the calculated data thus obtained. On account of the fact that it permits to obtain the median sagittal plane of the skull by means of points of a cartesian system of coordinate, phylogenetic comparison, standardisable on optional points of reference respectively planes of reference is possible. The specific trigonometric construction enables extensive interpretation of single angles, distances and parts of surface, the amount of detail of which exceeds that of method in use.     

Molecular biological study on speciation and phylogeny of the order Entomobryomorpha (Collembola: Hexapoda)

In order to elucidate the phylogenetic relationship among groups of the order Entomobryomorpha (Collembola), the sequences on the ITS 1 to ITS 2 fragments of the rRNA gene were analyzed in 11 species of three families. In order to avoid the potential risks and inconsistencies of a single method or data set, the phylogenetic reconstructions were based on three different approaches: methods of maximum parsimony, maximum likelihood and neighbor joining. The inferred phylogenies supported monophyly of the order Entomobryomorpha. The relationships between families were different, but the orders of branching within each family were the same. Entomobryidae and Isotomidae were paraphyletic, whereas Tomoceridae was monophyletic. Tomoceridae was subdivided into two branches; the molecular analysis provided results distinctive enough to separate the two genera by the high bootstrap value. On the other hand, two different populations of putative Homidia koreana appeared to be different species, although their chaetotaxy is identical. A wide coverage of characters, including not only morphological characters but also genetic data such as allozymes and DNA sequences, will give a more accurate picture of the classification and phylogeny of the studied group.     

A molecular perspective on the phylogeny of placental mammals based on mitochondrial 12S rDNA sequences,with special reference to the problem of the Paenungulata

Part of the 12S rDNA gene was amplified and sequenced for 11 placental mammals, 3 marsupials, and 2 monotremes. Multiple alignments for these sequences and nine additional placental sequences taken from GenBank were obtained using CLUSTAL. Phylogenetic analyses were performed using standard parsimony, transversion parsimony, and Lake's method of invariants. All of our analyses uniteLoxodontia withDugong. Procavia, in turn, is a sister group to these taxa, thus supporting the monophyly of the Paenungulata. Perissodactyls are a sister group to paenungulates when transitions and transversions are both included but not when transitions are omitted. Likewise, cetaceans are a sister group to artiodactyls on minimum length trees under standard parsimony but not under transversion parsimony. Rodent monophyly and bat monophyly also receive mixed support, as does a putative alliance between primates and lagomorphs. Interestingly, the percentage divergence between the echidna and the platypus is less than for the rat and mouse.     

Molecular phylogeny of leeches: Congruence of nuclear and mitochondrial rDNA data sets and the origin of bloodsucking

Complete 18S rDNA sequences and sequences of domain III of mitochondrial 12S rDNA were obtained to assess phylogenetic relationships among major suprageneric taxa of leeches and the possibly closely related clitellate taxa Branchiobdellida and Acanthobdellida. The monophyly of the families Erpobdellidae, Piscicolidae, and Glossiphoniidae, the suborders Erpobdelliformes and Hirudiniformes, and the order Arhynchobdellida have been confirmed by parsimony and maximum likelihood phylogenetic analysis of separate and combined data sets. Both the nuclear 18S rDNA sequences and the mitochondrial 12S rDNA sequences were consistent in not supporting a monophyletic order Rhynchobdellida, represented by the families Piscicolidae and Glossiphoniidae. A topology with the Piscicolidae as the first branch in the leech tree followed by the Glossiphoniidae received the highest support in terms of taxonomic, character, and outgroup congruence. According to this topology, the putative apomorphies of the Rhynchobdellidae (e.g. the proboscis) can be parsimoniously explained as plesiomorphies already present in the ancestral leech. This common ancestor was probably a bloodsucking leech with a proboscis rather than an unspecialized ectocommensal, as suggested by previous hypotheses. During the course of leech evolution, a reduction of the proboscis could have taken place in predatory arhynchobdellid ancestors to enable swallowing of larger prey. A second gain of sanguivory by the jawed Hirudiniformes could have been facilitated by pre-adaptations to ectoparasitic blood feeding. The 18S rDNA analysis further indicates a close relationship between the clitellate groups Branchiobdellida and Acanthobdellida, although this relationship is not strongly supported.     

Diagnosis and phylogeny of the new world streptocephalidae (Branchiopoda: Anostraca)

We present an updated diagnosis of 13Streptocephalus species of North America. Three new species are included. A key to the species is provided.The phylogeny of the group is discussed on the basis of (1) a systematic approach (Maeda-Martinezet al., 1995; this volume), which considers the entire distal antennal outgrowth, the frontal appendage, and the morphology of the ovaries as essential in defining different genetic lineages or species-groups, and (2) a cladistic analysis. We suggest that of nine monophyletic groups, three are represented in both the Old and New World. Thus, contrary to former disparsalist hypotheses, we argue that the New World species represent relict forms of ancestral groups fragmented by continental drift (vicariance model).