Speciation within genomic networks: a case study based on Steatocranus cichlids of the lower Congo rapids

Hybridization in animals is a much more common phenomenon as previously thought and may have profound implications for speciation research. The cichlid genus Steatocranus (Teleostei: Cichlidae), a close relative to members of the East African cichlid radiations, radiated under riverine conditions in the lower Congo rapids and produced a small species flock. Previous phylogenetic analyses suggested that hybridization occurred and contributed to speciation in this genus. A re-analysis of an already published 2000 loci-AFLP data set explicitly testing for patterns of ancient gene flow provided strong evidence for a highly reticulate phylogenetic history of the genus. We provide, to our knowledge, the first example of a complex reticulate network in vertebrates, including multiple closely related species connected through ancient as well as recent gene flow. In this context, the limited validity of strictly bifurcating tree hypotheses as a phylogenetic basis for hypothesis testing in evolutionary biology is discussed.     

An Empirical Analysis of mt 16S rRNA Covarion-Like Evolution in Insects: Site-Specific Rate Variation Is Clustered and Frequently Detected

The structural and functional analysis of rRNA molecules has attracted considerable scientific interest. Empirical studies have demonstrated that sequence variation is not directly translated into modifications of rRNA secondary structure. Obviously, the maintenance of secondary structure and sequence variation are in part governed by different selection regimes. The nature of those selection regimes still remains quite elusive. The analysis of individual bacterial models cannot adequately explore this topic. Therefore, we used primary sequence data and secondary structures of a mitochondrial 16S rRNA fragment of 558 insect species from 15 monophyletic groups to study patterns of sequence variation, and variation of secondary structure. Using simulation studies to establish significance levels of change, we found that despite conservation of secondary structure, the location of sequence variation within the conserved rRNA structure changes significantly between groups of insects. Despite our conservative estimation procedure we found significant site-specific rate changes at 56 sites out of 184. Additionally, site-specific rate variation is somewhat clustered in certain helices. Both results confirm what has been predicted from an application of non-stationary maximum likelihood models to rRNA sequences. Clearly, constraints on sequence variation evolve and leave footprints in the form of evolutionary plasticity in rRNA sequences. Here, we show that a better understanding of the evolution of rRNA sequences can be obtained by integrating both phylogenetic and structural information.     

Molecular evolution of a Y-chromosomal repetitive sequence family in the genus Mus

A 522-base-long Y-chromosomal sequence was isolated from a BALB/c genomic library and was designated "BF046." It is repeated about 200 times in the male genome, and a difference was detected between the Mus musculus musculus and the M. m. domesticus type Y chromosomes. BF046- related sequences were present over the entire length of the Y chromosome as visualized by in situ hybridization. Southern blot analysis against DNAs isolated from eight species in the genus Mus showed that BF046-related sequences were amplified in the Y chromosomes of three closely related species: M. musculus, M. spicilegus, and M. spretus. To gain insight into the stability of the BF046 sequence family, we isolated 18 additional clones from these three mouse species and compared their sequences. The M. musculus sequences differed from the M. spicilegus and M. spretus sequences by two indels. The remaining parts of the sequences were very similar, but both parsimony and distance-based analytical methods divided the sequences into the same four subgroups, with each species having its own subgroup(s). Thus, the Y chromosomes of M. musculus, M. spicilegus, and M. spretus can be distinguished from one another.      

Heterochronic differences of Hoxa-11 expression in Xenopus fore- and hind limb development: Evidence for lower limb identity of the anuran ankle bones

 The wrist (carpus) and ankle (tarsus) of most tetrapods, as well as the wrist of anurans, contains relatively small nodular skeletal elements. The anuran tarsus, however, comprises a pair of long bones, the proximal tarsals tibiale and fibulare, which resemble the lower leg bones, tibia and fibula (zeugopodium). In this paper we investigate whether the proximal tarsals of Xenopus are of zeugopodial character identity, i.e. whether they develop under the influence of the same genes that pattern the lower limb. We compare Hoxa-11 expression in the forelimb bud with that in the hind limb bud by whole-mount in situ hybridization. Hoxa-11 has been implicated in the development of the lower limb. In Xenopus we note three differences between Hoxa-11 expression in fore- and hind limb buds: (1) Hoxa-11 expression is maintained until the hind limb bud reaches a larger size (2 mm) than that of the forelimb bud (1.5 mm); (2) Hoxa-11 expression is maintained over larger spatial domains than in the forelimb; and (3) Hoxa-11 expression has a pronounced posterior polarity in the hind limb, but not in the forelimb. Hind limb expression of Hoxa-11 can be understood as a heterochronic prolonging of the expression dynamic in the forelimb. Finally we found that the proximal tarsals start to develop within the expression domain of Hoxa-11, while in the forelimb the lower arm elements reach the distal expression limit of Hoxa-11. The gene expression data presented here support the notion of a zeugopodial identity of the proximal tarsal elements in Xenopus. Received: 20 January 1998 / Accepted: 27 March 1998     

The lactosylceramide binding specificity of Helicobacter pylori

The possible role of glycosphingolipids as adhesion receptors for the human gastric pathogen Helicobacter pylori was examined by use of radiolabeled bacteria, or protein extracts from the bacterial cell surface, in the thin-layer chromatogram binding assay. Of several binding specificities found, the binding to lactosylceramide is described in detail here, the others being reported elsewhere. By autoradiography a preferential binding to lactosylceramide having sphingosine/phytosphingosine and 2-D hydroxy fatty acids was detected, whereas lactosylceramide having sphingosine and nonhydroxy fatty acids was consistently nonbinding. A selective binding of H. pylori to lactosylceramide with phytosphingosine and 2-D hydroxy fatty acid was obtained when the different lactosylceramide species were incorporated into liposomes, but only in the presence of cholesterol, suggesting that this selectivity may be present also in vivo . Importantly, lactosylceramide with sphingosine and hydroxy fatty acids does not bind in this assay. Furthermore, a lactosylceramide-based binding pattern obtained for different trisaccharide glycosphingolipids is consistent with the assumption that this selectivity is due to binding of a conformation of lactosylceramide in which the oxygen of the 2-D fatty acid hydroxyl group forms a hydrogen bond with the Glc hydroxy methyl group, yielding an epitope presentation different from other possible conformers. An alternative conformation that may come into consideration corresponds to the crystal structure found for cerebroside, in which the fatty acid hydroxyl group is free to interact directly with the adhesin. By isolating glycosphingolipids from epithelial cells of human stomach from seven individuals, a binding of H.pylori to the diglycosylceramide region of the non-acid fraction could be demonstrated in one of these cases. Mass spectrometry showed that the binding-active sample contained diglycosylceramides with phytosphingosine and 2-D hydroxy fatty acids with 16-24 carbon atoms in agreement with the results related above.      

On quality of evidence in phylogeny reconstruction: a reply to Zrzavý's defence of the 'Ecdysozoa' hypothesis

Zrzavý’s arguments against the critical analyses of data supporting the Ecdysozoa hypothesis (Wägele et al., J. Zool. Syst. Evol. Res. 37, 211–223, 1999) are discussed. Zrzavý does not understand that the same basic principle of a priori weighting can be applied to sequence data as well as to morphological characters. Quality of evidence is the same as probability of homology, which is estimated from the number of discernible identical details. In sequences it is the number of identical nucleotides. Spectral analyses, dismissed by Zrzavý, visualize patterns of putative homologies present in alignments and also the number of positions supporting splits by chance alone. In cases in which old phylogenetic signals for a given monophylum are eroded in a gene, plesiomorphies and chance patterns will have strong influence on tree topologies and spectra. If plesiomorphies are a cause of errors, the addition of taxa that shorten internal branches is a remedy, although, in many cases such taxa may be extinct. The place of a priori estimations of data quality in a sequence of steps necessary for a phylogenetic analysis is shown. Morphological complexity is used as a proxy for a complex genetic basis and is used as a major criterion to compare characters of the Ecdysozoa and the Articulata. The details associated with the character ‘complex cuticle’ are discussed. Neither moulting nor the known components of the cuticle are novelties occurring only in Ecdysozoa. A published total evidence analysis is used to show that the number of coded characters does not necessarily reflect the quality of the data set. Zrzavý’s misunderstanding of the role of evolutionary scenarios is clarified and the importance of the use of additional biological data for plausibility arguments is explained. Plausibility arguments in favour of the Articulata hypothesis rely on facts found in functional morphology and in the fossil record. Zrzavý’s critique follows the actual mainstream but does not uncover logical mistakes or erroneous data analyses in the work of 86 . It is concluded that the Articulata hypothesis is a well‐founded alternative to the Ecdysozoa; it is based on much better morphological evidence and supported by plausibility arguments that currently do not exist for the Ecdysozoa.     

Metazoa-level USCOs as markers in species delimitation and classification

Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.     

Efficacy assessed in follow-ups of clinical trials: methodological conundrum

Increasingly, we see papers describing the long-term follow-up results of randomised clinical trials. Sometimes, like the article by Rantalaiho and colleagues in the previous issue of Arthritis Research & Therapy, the follow-up extends to more than 10 years. It is not uncommon that authors of such articles describe their results as a comparison of the original treatment groups in the original randomised clinical trial. Methodologically, such a comparison is fallible for several reasons. In this editorial, two important sources of bias that may jeopardise the results of such follow-up studies are discussed: confounding by indication and confounding by trial completion.