Phylogenetic relationships among Strobilanthes s.l. (Acanthaceae): evidence from ITS nrDNA, trnL-F cpDNA, and morphology

Chloroplast trnL-F sequence data, nuclear ribosomal internal transcribed spacer (ITS) sequence data, and morphology were used to analyze phylogenetic relationships among members of the subtribe Strobilanthinae. Parsimony and maximum likelihood analyses of trnL-F indicate that the Strobilanthinae are a monophyletic group. While parsimony analysis of ITS recovers a nonmonophyletic subtribe, maximum likelihood analysis of ITS corroborates results from trnL-F and suggests that systematic error is impacting on ITS parsimony analysis. A combined ITS and trnL-F analysis strengthens the signal and also recovers a monophyletic subtribe. All analyses indicate that Hemigraphis, Sericocalyx, and Strobilanthes are nonmonophyletic. With one exception, all morphological characters included in a combined ITS and morphological analysis are homoplastic. The prospect for a new informative generic classification of the Strobilanthinae aiming to recognize and diagnose only monophyletic groups is considered. While some groups can be diagnosed, adequate diagnosis of the majority of groups remains problematic. Consequently, a single expanded genus Strobilanthes sensu lato is proposed at the level of the well-supported and monophyletic Strobilanthinae.     

Phylogenetic relationships within the harpacticoid copepod family Peltidiidae Sars, including the description of a new genus

With the discovery of Alteuthoides kootare gen. et sp. no v. , found living inside an hexactinellid sponge from offshore waters of New Zealand, and the synonymization herein of Paralteutha T. Scott with Eupelte Claus, the number of genera in the harpacticoid copepod family Peltidiidae Sars now stands at eight. In the morphology of the maxillipeds and the armature of the first leg exopods, Alteuthoides is most similar to Alteuthella (A. Scott) and Alteuthellopsis Lang. These shared apomorphies are regarded as convergent ecological specializations to a lifestyle as close associates of other marine invertebrates. Results of a cladistic analysis further assist in the interpretation of relationships within the family. Lang's speculation that Peltidium and Parapeltidium form an independent lineage from the ancestral peltidiid gains further support. Alteutha remains as the basal group to the second lineage in comparison with which all remaining genera are derived in some respect. Alteuthellopsis would appear to be the most advanced genus in the family. Because of recent additions to Neopeltopsis Hicks and Alteuthellopsis , revised diagnoses, together with a revised key to genera, are also presented.     

Substructure of the axoneme of pterygote insect spermatozoa: Phylogenetic considerations

Spermatozoa from a great number of insect species were fixed in a tannic acid-containing fixative and the ultrastructure of the flagellar axoneme was examined in a search for apomorphies. Most of the examined species, representing a majority of insect orders. have accessory tubules outside the axoneme (hence a 9 + 9 + 2 pattern), and these consist of 16 protofilaments. Some important apomorphies concern the number of protofilaments in the accessory tubules: 13 (plus 7 inner elements) in Ephemeroptera, 13 in the (elliptic) tubules of Psocoptera + Anoplura + Mallophaga (thus a synapomorphy), 13 in Tipulidae + Brachycera, 15 in the dipteran families Dixidae + Chironomidae (with a 9 + 9 + 2 axoneme) and Culicidae + Bibionidae (with a 9 + 9 + “1” axoneme), 17 in Phasmatodea, and 17–20 in Trichoptera. Other apomorphies concern the appearance of the so-called intertubular material outside the microtubular doublets, the appearance of the interior of the various microtubules, and the loss, in some taxa, of outer or inner dynein arms of both dynein arms. In some cases, the flagellum is completely abnormal; the sperm tail of Thysanoptera, for example, consists of 27 elements of 3 different kinds. The different taxa within orders Diptera and Trichoptera have sperm tail axonemes of different appearances, where those from other orders have a rather uniform appearance. The conclusions that can be drawn from this spermatological study, generally agree with data from classical studies, except with some variations, in some cases.     

Towards simultaneous analysis of morphological and molecular data in Hymenoptera

Principles and methods of simultaneous analysis in cladistics are reviewed, and the first, preliminary, analysis of combined molecular and morphological data on higher level relationships in Hymenoptera is presented to exemplify these principles. The morphological data from Ronquist et al . (1999) matrix, derived from the character diagnoses of the phylogenetic tree of Rasnitsyn (1988) , are combined with new molecular data for representatives of 10 superfamilies of Hymenoptera by means of optimization alignment. The resulting cladogram supports Apocrita and Aculeata as groups, and the superfamly Chrysidoidea, but not Chalcidoidea, Evanioidea, Vespoidea and Apoidea.     

Is the Turbellaria polyphyletic?

Within the last two decades, syntheses of both light-microscopic and ultrastructural characters have shown that there are three well-defined monophyletic groups within the Platyhelminthes: 1) the Catenulidale, 2) the Nemertodermatida-Acoela, and 3) the Haplopharyngida-Macrostomida-Polycladida-Neoophora (+ parasitic platyhelminth classes). However, the relationships among these three groups are problematic. The possible apomorphies that would unite them are either not true homologues (i.e. frontal organ), are mutually conflicting (i.e. 9+1 axoneme in spermatozoa vs. biflagellate spermatozoa, epidermal ciliary rootlet structure, and protonephridia), or are unrooted with any outgroup and hence untestable or uncertain as apomorphies (protonephridia, mode of epidermal replacement, absence of accessory centrioles on cilia). The chief obstacle to deciphering the relationships of these groups is the lack of information on them; presently available information is insufficient to test potential synapomorphies and insufficient also to allow agreement upon a narrowly defined outgroup for the Turbellaria.A view consistent with the present evidence (and admittedly an unsatisfactory view) is to regard the Turbellaria (and hence the Platyhelminthes) as polyphyletic, consisting of three separate and unrelatable groups.     

A first phylogenetic analysis of the pill millipedes of the order Glomerida,with a special assessment of mandible characters (Myriapoda,Diplopoda, Pentazonia)

The pill millipedes of the order Glomerida are a moderately diverse group with a classical Holarctic distribution pattern. Their classification is based on a typological system utilizing mainly a single character complex, the male telopods. In order to infer the apomorphies of the Glomerida, to elucidate its position in the Pentazonia, and to test the monophyly of its families and subfamilies, we conduct the first phylogenetic analysis of the order. To provide additional characters, we comparatively analyze the mandible using scanning electron microscopy. The final character matrix consists of 69 characters (11 mandible characters) and incorporates 22 species from 20 of the 34 pill millipede genera, representing all families and subfamilies, except the monotypic Mauriesiinae. Two species from each of the two other Pentazonian orders Sphaerotheriida and Glomeridesmida, as well as two Spirobolida, are included as outgroup taxa. The Glomerida are recovered as monophyletic and are supported by five apomorphies. Within the Pentazonia, the Glomeridesmida are recovered as the sister group to the classical Oniscomorpha (Sphaerotheriida + Glomerida) with weak support. The analysis provides little resolution within the Glomerida, resulting in numerous polytomies. Further morphological characters and/or the addition of molecular analyses are needed to produce a robust phylogenetic classification of the Glomerida.     

Morphological characters add support for some members of the basal grade of Asteraceae

Recent molecular studies in Asteraceae have divided tribe Mutisieae (sensu Cabrera) into 13 tribes and eight subfamilies. Each of the major clades is well supported but the relationships among them are not always clear. Some of the new taxa are easily characterized by morphological data but others are not, chief among the latter being three subfamilies (Stifftioideae, Wunderlichioideae and Gochnatioideae) and the tribe Hyalideae. To understand evolution in the family it is critical to investigate potential morphological characters that can help to evaluate the basal lineages of the Asteraceae. The data for this study were taken from 52 species in 24 genera representing the basal groups in the family. Many characters were examined but most of the useful ones were from reproductive structures. Several apomorphies supported a few of the clades. For instance, members of subfamily Wunderlichioideae (Hyalideae and Wunderlichieae) share predominantly ten‐ribbed achenes and members of Wunderlichioideae + Stifftioideae share two synapomorphies: 100–150 (200) pappus elements, arranged in (three) four or five series. These apomorphies can be viewed as an indication of a sister‐group relationship between the two subfamilies as the placement of Stifftieae was not well resolved by the molecular data. Members of Wunderlichieae are characterized by having a paleaceous receptacle, style branches that are strongly papillose above and below the bifurcation, and a pappus of scales. Hyalis and Ianthopappus (Hyalideae) share venation type and an apiculate anther appendage but these are also found in Gochnatieae. Other clades have fewer supporting characters. These characters are just a beginning. Cladograms with morphology characters plotted, illustrations and a key to the basal grade of Asteraceae are provided. © 2013 The Linnean Society of London     

Taxic Revisions

Parsimony analysis provides a straightforward way of assessing homology on a tree: a state shared by two terminals comprises homologous similarity if optimization attributes that state to all the stem species lying between those terminals. Three-taxon statements (3ts), although seemingly "exact" in that each either fits a tree or does not, do not provide a satisfactory assessment of homology, because that assessment can be internally contradictory and because 3ts systematically exclude homologous resemblance in reversed states. Modified 3ts analysis (m3ta), a method in which both plesiomorphic and apomorphic states of "paired homologue" (PH) characters (those other than presence/absence data) are regarded as "informative" (able to distinguish groups), can (obviously) group by symplesiomorphy and so form paraphyletic groups unless data are clocklike enough. Patterson's pattern analysis (ppa) has the same shortcoming, to which it adds the drawback that only characters fitting the tree perfectly are used, a restriction that can easily lead to discarding most of the structure in the data. Revised m3ta (rm3ta), a method in which plesiomorphic states are not taken as informative, can also form paraphyletic groups, because it cannot apply reversals as apomorphies. The idea that knowledge of phylogeny has been derived from classifications does not imply that nonevolutionary methods should be employed for classification, but instead means that systematic methods must be logically capable of phylogenetic interpretation. Neither m3ta nor rm3ta satisfies that requirement because of their contradictory assessments of homology.     

Toward an integrated system of clade names

Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, and apomorphies in between. An integrated system of clade names is described based on categories of clades defined with respect to lineages that have survived to the present time. In this system, the most widely known names are applied to crown clades, the names of total clades are formed by adding a standard prefix to the names of the corresponding crowns, and the names of apomorphy clades describe the specific apomorphies with which they originated. Relative to traditional approaches, this integrated approach to naming clades is both more precise concerning the associations of names with particular clades and more efficient with regard to the cognitive effort required to recognize the names of corresponding crown and total clades. It also seems preferable to five alternatives that could be used to make the same distinctions. The integrated system of clade names has several advantages, including the facilitation of communication among biologists who study distantly related clades, promoting a broader conceptualization of the origins of distinctive clades of extant organisms and emphasizing the continuous nature of evolution.     

Use of information on disease diagnoses from databases for animal health economic,welfare and food safety purposes: strengths and limitations of recordings

Many animal health, welfare and food safety databases include data on clinical and test-based disease diagnoses. However, the circumstances and constraints for establishing the diagnoses vary considerably among databases. Therefore results based on different databases are difficult to compare and compilation of data in order to perform meta-analysis is almost impossible. Nevertheless, diagnostic information collected either routinely or in research projects is valuable in cross comparisons between databases, but there is a need for improved transparency and documentation of the data and the performance characteristics of tests used to establish diagnoses. The objective of this paper is to outline the circumstances and constraints for recording of disease diagnoses in different types of databases, and to discuss these in the context of disease diagnoses when using them for additional purposes, including research. Finally some limitations and recommendations for use of data and for recording of diagnostic information in the future are given. It is concluded that many research questions have such a specific objective that investigators need to collect their own data. However, there are also examples, where a minimal amount of extra information or continued validation could make sufficient improvement of secondary data to be used for other purposes. Regardless, researchers should always carefully evaluate the opportunities and constraints when they decide to use secondary data. If the data in the existing databases are not sufficiently valid, researchers may have to collect their own data, but improved recording of diagnostic data may improve the usefulness of secondary diagnostic data in the future.     

Microbiological regulation of the biogeochemical nitrogen cycle

Most nitrogen transformations in soil are carried out by micro-organisms. An understanding of the microbiological processes is thus necessary in order for us to devise management practices in agricultural ecosystems, which will optimize plant root uptake of nitrogen and minimize nitrogen losses from the systems. Some aspects of the individual microbiological processes in the nitrogen cycle are discussed and their importance for an efficient management of agroecosystems. In soil various groups of organisms compete for available inorganic nitrogen and quantitative data are needed on the uptake kinetics for these various groups in order to be able to assess their competitive ability under different conditions. The influence of abiotic factors such as oxygen concentration, inorganic nitrogen concentration and pH is discussed in relation to the different processes. The importance of acetylene as a tool in nitrogen cycling studies is discussed briefly.     

Determination of three-dimensional protein structures from nuclear magnetic resonance data using fragments of known structures

A method to build a three-dimensional protein model from nuclear magnetic resonance (NMR) data using fragments from a data base of crystallographically determined protein structures is presented. The interproton distances derived from the nuclear Overhauser effect (NOE) data are compared to the precalculated distances in the known protein structures. An efficient search algorithm is used, which arranges the distances in matrices akin to a C alpha diagonal distance plot, and compares the NOE distance matrices for short sequential zones of the protein to the data base matrices. After cluster analysis of the fragments found in this way, the structure is built by aligning fragments in overlapping zones. The sequentially long-range NOEs cannot be used in the initial fragments search but are vital to discriminate between several possible combinations of different groups of fragments. The method has been tested on one simulated NOE data set derived from a crystal structure and one experimental NMR data set. The method produces models that have good local structure, but may contain larger global errors. These models can be used as the starting point for further refinement, e.g., by restrained molecular dynamics or interactive graphics.     

Phylogenetic relationships among the lepidopteran and trichopteran suborders (Insecta) from the embryological standpoint1

Adopting the cladistic method in comparative embryology, 27 embryonic characters were analyzed to reconstruct the phylogenetic relationships among the lepidopteran and trichopteran suborders, viz., Annulipalpia, Integripalpia, Zeugloptera, Dacnonypha, Exoporia, Monotrysia, and Ditrysia. The resultant cladogram is basically coincident with that proposed by Kristensen . The order Trichoptera and Lepidoptera constitute a monophyletic group on the basis of one synapomorphy, the presence of well developed silk glands in embryos. The Trichoptera are separable from the Lepidoptera by the states of four characters. The Trichoptera, as a whole, are quite homogenous, and embryological data provide no rational ground for the separation of this order into the Annulipalpia and Integripalpia at a subordinal level. On the contrary, the embryonic development of the Lepidoptera becomes divergent from the most primitive condition to a specialized one according to suborders. The Zeugloptera are the sister group of all other Lepidoptera, because they share two apomorphies with the latter. The Dacnonypha are the most primitive next to the Zeugloptera, and have a sister-group relationship with the Exoporia + (Monotrysia + Ditrysia), being held together with the latter by five synapomorphies. Although the Exoporia retain almost as many plesiomorphic characters as the Dacnonypha, they have a sister-group relationship with the Monotrysia + Ditrysia, as inferred on the basis of two synapomorphies. The Monotrysia and Ditrysia have a sistergroup relationship, and are the most advanced groups in the Lepidoptera judging from their shared acquisition of many apomorphic characters.     

Comparison of the Cladograms Produced by Li's Method and Farris' Method

In order to avoid producing many equally most parsimonious trees, Li (1990) developed a new cladistic method, the Median Elimination Series (MES), to construct a single cladogram for a given data set. However, we found that Li's method can produce more than one tree if two or more taxa have the same advancement index (which is the total number of apomorphies for a taxon in a given data set), because there is no objective method to decide which taxon should be connected first and different orders of connection can produce different trees. Li claimed that the result produced by his method did not apply the principle of simplicity (parsimony). Nevertheless, Zhang (1991) recognised that Li's method actually accepted the principle of parsimony. Here we demonstrated that Li's method also can produce the minimum-length trees. We conclude that Li's method could produce more than one tree and the tree(s) may be the minimum-length possible. However, the length of tree(s) depends on the order of connection of the taxa. The major problems in using Li's methodare discussed.