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Diethard Tautz

Publications and source records attributed to Diethard Tautz.

At least 19 recordsLinked to original sources
PubMed2005

An algorithm for the determination and quantification of components of nucleic acid mixtures based on single sequencing reactions.

BACKGROUND: Determination and quantification of nucleic acid components in a mixture is usually accomplished by microarray approaches, where the mixtures are hybridized against specific probes. As an alternative, we propose here that a single sequencing reaction from a mixture of nucleic acids holds enough information to potentially distinguish the different components, provided it is known which components can occur in the mixture. RESULTS: We describe an algorithm that is based on a set of linear equations which can be solved when the sequencing profiles of the individual components are known and when the number of sequenced nucleotides is larger than the number of components in the mixture. We have implemented the procedure for one type of sequencing approach, pyrosequencing, which produces a stepwise output of peaks that is particularly suitable for the procedure. As an example we use signature sequences from ribosomal RNA to distinguish and quantify several different species in a mixture. Using simulations, we show that the procedure may also be applicable for dideoxy sequencing on capillary sequencers, requiring only some instrument specific adaptations of protocols and software. CONCLUSION: The parallel sequencing approach described here may become a simple and cheap alternative to microarray experiments which aim at routine re-determination and quantification of known nucleic acid components from environmental samples or tissue samples.

Algorithms↗
PubMed2005

An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups.

Fish abundance surveys in the Rhine system have shown in the past two decades that there is a rapid upriver invasion of a freshwater sculpin of the genus Cottus. These fish are found in habitats that are atypical for the known species Cottus gobio, which is confined to small cold streams within the Rhine drainage. Phylogeographic analysis based on mitochondrial haplotypes and diagnostic single nucleotide polymorphisms indicates that the invasive sculpins are hybrids between two old lineages from the River Scheldt drainage and the River Rhine drainage, although it is morphologically more similar to the Scheldt sculpins. Most importantly, however, the invasive population possesses a unique ecological potential that does not occur in either of the source populations from the Rhine or the Scheldt, which allows the colonization of new habitats that have previously been free of sculpins. Microsatellite analysis shows that the new lineage is genetically intermediate between the old lineages and that it forms a distinct genetic group across its whole expansion range. We conclude that hybridization between long separated groups has lead to the fast emergence of a new, adaptationally distinct sculpin lineage.

Adaptation, Physiological↗
PubMed2005

Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences.

Organisms living in or on the sediment layer of water bodies constitute the benthos fauna, which is known to harbour a large number of species of diverse taxonomic groups. The benthos plays a significant role in the nutrient cycle and it is, therefore, of high ecological relevance. Here, we have explored a DNA-taxonomic approach to access the meiobenthic organismic diversity, by focusing on obtaining signature sequences from a part of the large ribosomal subunit rRNA (28S), the D3-D5 region. To obtain a broad representation of taxa, benthos samples were taken from 12 lakes in Germany, representing different ecological conditions. In a first approach, we have extracted whole DNA from these samples, amplified the respective fragment by PCR, cloned the fragments and sequenced individual clones. However, we found a relatively large number of recombinant clones that must be considered PCR artefacts. In a second approach we have, therefore, directly sequenced PCR fragments that were obtained from DNA extracts of randomly picked individual organisms. In total, we have obtained 264 new unique sequences, which can be readily placed into taxon groups, based on phylogenetic comparison with currently available database sequences. The group with the highest taxon abundance were nematodes and protozoa, followed by chironomids. However, we find also that we have by far not exhausted the diversity of organisms in the samples. Still, our data provide a framework within which a meiobenthos DNA signature sequence database can be constructed, that will allow to develop the necessary techniques for studying taxon diversity in the context of ecological analysis. Since many taxa in our analysis are initially only identified via their signature sequences, but not yet their morphology, we propose to call this approach 'reverse taxonomy'.

Animals↗
PubMed2005

What we have also learned: adaptive speciation is theoretically plausible.

A recent Perspectives article by Gavrilets (2003) on the theory of speciation ignored advances in understanding processes of adaptive speciation, in which the splitting of lineages is an adaptation caused by frequency-dependent selection. Adaptive, or sympatric, speciation has been modeled since the 1960s, but the large amount of attention from both empirical and theoretical biologists that adaptive speciation has received in recent years goes far beyond what was described in Gavrilets' paper. Due to conceptual advances based on the theory of adaptive dynamics, adaptive speciation has emerged as a theoretically plausible evolutionary process that can occur in many different ecological settings.

Adaptation, Biological↗
PubMed2004

Introducing "Frontiers in Zoology"

As a biological discipline, zoology has one of the longest histories. Today it occasionally appears as though, due to the rapid expansion of life sciences, zoology has been replaced by more or less independent sub-disciplines amongst which exchange is often sparse. However, the recent advance of molecular methodology into "classical" fields of biology, and the development of theories that can explain phenomena on different levels of organisation, has led to a re-integration of zoological disciplines promoting a broader than usual approach to zoological questions. Zoology has re-emerged as an integrative discipline encompassing the most diverse aspects of animal life, from the level of the gene to the level of the ecosystem.The new journal Frontiers in Zoology is the first Open Access journal focussing on zoology as a whole. It aims to represent and re-unite the various disciplines that look at animal life from different perspectives and at providing the basis for a comprehensive understanding of zoological phenomena on all levels of analysis. Frontiers in Zoology provides a unique opportunity to publish high quality research and reviews on zoological issues that will be internationally accessible to any reader at no cost.

Journal Article↗
PubMed2004

her11 is involved in the somitogenesis clock in zebrafish.

Somitogenesis requires an intricate process of pre-patterning, which is driven by an oscillator mechanism consisting of the Delta-Notch pathway and hairy- (h) and Enhancer of split- [E(spl)] related genes. With the aim of unravelling the complex mechanism of somite pre-patterning, we have conducted an extensive search for h/E(spl)-related genes in the third release of the Danio rerio genomic sequence. We identified 14 new h/E(spl) genes and analysed them by in situ hybridisation for their potential role in the somitogenesis process. We describe here the functional analysis of one of these genes, which we have named her11. her11 is a paralogue of her1 and, similar to her1, is arranged in a head to head fashion with another her gene, namely the previously described her5. It shares an expression in the midbrain-hindbrain boundary with her5, but is in addition cyclically expressed in patterns overlapping those of her1 and her7 and complementary to those of hey1. Furthermore it is expressed in the anterior half of the most caudally formed somites. We show that Delta-Notch pathway genes and fused somites ( fss) are necessary for the control of her11 expression. However, some aspects of the her11 regulation suggest that at least one additional as yet unknown gene of the Delta-Notch cascade is required to explain its expression. Morpholino-oligonucleotide-mediated knockdown of her11 shows that it is involved in the zebrafish somitogenesis clock via an interaction with her1 and her7. We have also studied the role of hey1 by morpholino injection, but could not find a direct function for this gene, suggesting that it reflects the output of the clock rather than being a core component of the mechanism.

Amino Acid Sequence↗
PubMed2004

Separable stripe enhancer elements for the pair-rule gene hairy in the beetle Tribolium.

Pair-rule genes in Drosophila integrate the positional information provided by the transcription factor gradients of gap genes and set the framework for the expression of the segment polarity genes. Pair-rule genes are also expressed during the segmentation of the short germ-band embryo of the flour beetle Tribolium, although this occurs under cellular conditions that should not allow the generation of transcription factor gradients by passive diffusion. To analyse the regulation of the pair-rule gene hairy in Tribolium, we have used germline transformation with reporter gene constructs based on the piggyBac vector. We can identify an upstream fragment that drives the full expression of the eight pair-rule stripes, which are sequentially generated during embryogenesis. Further experiments with smaller fragments reveal separable regions driving stripes three to five, and one region driving stripe three only. Our results suggest that the generation of pair-rule stripes in Tribolium is comparable to that in Drosophila despite the cellular versus syncytial mode of embryogenesis.

Animals↗
PubMed2004

Correlated evolution of synonymous and nonsynonymous sites in Drosophila.

Recent work has shown that Drosophila melanogaster genes with fast-evolving nonsynonymous sites have lower codon usage bias. This pattern has been attributed to interference between positive selection at nonsynonymous sites and weak selection on codon usage. Here we have looked for this correlation in a much larger and less biased dataset, comprising 630 gene pairs from D. melanogaster and D. yakuba. We confirmed that there is a negative correlation between the rate of nonsynonymous substitutions (d(N)) and codon bias in D. melanogaster. We then tested the interference hypothesis and other alternative explanations, including one involving gene expression. We found that d(N) indeed correlates with the level of gene expression. Given that gene expression is a strong determinant of codon bias, the relationship between d(N) and codon bias might be a by-product of gene expression. However, our tests show that none of the hypotheses we consider seem to explain the data fully.

Amino Acid Substitution↗
PubMed2004

Segmentation.

The three major taxa with metameric segmentation (annelids, arthropods, and chordates) appear to use three very different molecular strategies to generate segments. However, unexpected similarities are starting to emerge from characterization of pair-rule patterning and segmental border formation. Moreover, the existence of an ancestral segmentation clock based on Notch signaling has become likely. An old concept of comparative anatomy, the enterocoele theory, is compatible with a single origin of segmentation mechanisms and could therefore provide a conceptual framework for assessing these molecular similarities.

Animals↗
PubMed2004

Of statistics and genomes.

Higher organisms have more genes and larger genomes than simple organisms. This statement sounds almost too trivial to ask the question: why? But there are at least two different answers. Either there is an inherent necessity to increase genome size when more complexity is required or genome size increases because of other reasons that then enable complexity to "latch on". Recently, an article by Lynch and Conery, which used arguments of evolutionary population dynamics, proposed that low population size leads to larger genomes. This then provides the opportunity to generate more complex organisms.

Algorithms↗
PubMed2004

Adaptive divergence vs. environmental plasticity: tracing local genetic adaptation of metamorphosis traits in salamanders.

In order to assess the significance of local adaptation relative to environmental plasticity on the evolution of life history traits, we analysed the possible genetic basis of differences between pond- and stream-breeding fire salamanders (Salamandra salamandra) in Germany. These salamanders typically deposit their larvae in small streams, where they grow until they are sufficiently large to metamorphose. However, some populations in Western Germany use ponds as larval habitat. Because habitat quality of streams differs from that of ponds one expects life history differences in the pond animals, which may result either from a plastic response or through genetic differentiation (i.e. local adaptation). Using a phylogeographical analysis of mitochondrial D-loop sequences, we show that both stream and pond populations in Western Germany are derived from a single lineage that recolonized following the last glaciation. This finding suggests that pond breeding originated very recently. Our studies of habitat quality and metamorphic behaviour of larvae in natural ponds and streams disclosed that pond larvae experience a significantly reduced food supply and greater risk of drying than do stream larvae. Pond larvae metamorphose earlier at the cost of reduced mass. Common-environment experiments with pond and stream larvae show that metamorphic behaviour of pond larvae under limited-food conditions is determined genetically and is not simply a plastic response to the differing habitat conditions. These results show that phenotypic plasticity is less important than local adaptation in explaining differences in ecological diversification within this species and suggests the possibility of rapid evolution of genetic adaptations when new habitats are exploited.

Adaptation, Physiological↗
PubMed2003

Prospero and Snail expression during spider neurogenesis.

Analysis of early neurogenesis in the spider Cupiennius salei (Chelicerata, Aranea, Ctenidae) has shown that the cells of the central nervous system are recruited from clusters of cells that invaginate from the neuroectoderm. This is in contrast to Drosophila, where only single cells delaminate and become neuroblasts, the stem cells of the nervous system. In order to compare the processes further, we have cloned homologues of the pan-neural Drosophila genes prospero and snail from the spider and have analysed their RNA and protein expression pattern. We find that snail expression is transient and only a subset of neural cells expresses Snail protein at any given time, making it difficult to assess whether it is indeed a pan-neural gene in the spider. Prospero protein expression, on the other hand, is seen in all invaginating cells and continues throughout differentiation of the neurons. In contrast to Drosophila, asymmetric localization cannot be detected, even in cells that still divide. Our results provide no evidence for neuroblasts or stem cells in the spider, although there are a limited number of mitoses in the cells that are derived from the invaginating clusters. These aspects of spider neurogenesis are more similar to the neurogenesis process known from vertebrates.

Amino Acid Sequence↗
PubMed2003

The expression of the proximodistal axis patterning genes Distal-less and dachshund in the appendages of Glomeris marginata (Myriapoda: Diplopoda) suggests a special role of these genes in patterning the head appendages.

The genes Distal-less, dachshund, extradenticle, and homothorax have been shown in Drosophila to be among the earliest genes that define positional values along the proximal-distal (PD) axis of the developing legs. In order to study PD axis formation in the appendages of the pill millipede Glomeris marginata, we have isolated homologues of these four genes and have studied their expression patterns. In the trunk legs, there are several differences to Drosophila, but the patterns are nevertheless compatible with a conserved role in defining positional values along the PD axis. However, their role in the head appendages is apparently more complex. Distal-less in the mandible and maxilla is expressed in the forming sensory organs and, thus, does not seem to be involved in PD axis patterning. We could not identify in the mouthparts components that are homologous to the distal parts of the trunk legs and antennnae. Interestingly, there is also a transient premorphogenetic expression of Distal-less in the second antennal and second maxillary segment, although no appendages are eventually formed in these segments. The dachshund gene is apparently involved both in PD patterning as well as in sensory organ development in the antenna, maxilla, and mandible. Strong dachshund expression is specifically correlated with the tooth-like part of the mandible, a feature that is shared with other mandibulate arthropods. homothorax is expressed in the proximal and medial parts of the legs, while extradenticle RNA is only seen in the proximal region. This overlap of expression corresponds to the functional overlap between extradenticle and homothorax in Drosophila.

Animals↗
PubMed2003

Chordate evolution in a new light.

Gene expression studies in embryos often provide insights into evolutionary relationships across phyla. In this issue of Cell, Lowe et al. examine the patterning of the bilaterian nervous system by studying gene expression in a hemichordate, the acorn worm. Although these animals have an unstructured nervous system, they show surprisingly conserved gene expression domains, shedding new light on the evolution of the central nervous system and the phylogenetic placement of chordates.

Animals↗
PubMed2003

The role of Suppressor of Hairless in Notch mediated signalling during zebrafish somitogenesis.

Suppressor of Hairless (Su(H)) codes for a protein that interacts with the intracellular domain of Notch to activate the target genes of the Delta-Notch signalling pathway. We have cloned the zebrafish homologue of Su(H) and have analysed its function by morpholino mediated knockdown. While there are at least four notch and four delta homologues in zebrafish, there appears to be only one complete Su(H) homologue. We have analysed the function of Su(H) in the somitogenesis process and its influence on the expression of notch pathway genes, in particular her1, her7, deltaC and deltaD. The cyclic expression of her1, her7 and deltaC in the presomitic mesoderm is disrupted by the Su(H) knockdown mimicking the expression of these genes in the notch1a mutant deadly seven. deltaD expression is similarly affected by Su(H) knockdown like deltaC but shows in addition an ectopic expression in the developing neural tube. The inactivation of Su(H) in a fss/tbx24 mutant background leads furthermore to a clear breakdown of cyclic her1 and her7 expression, indicating that the Delta-Notch pathway is required for the creation of oscillation and not only for the synchronisation between neighbouring cells. The strongest phenotypes in the Su(H) knockdown embryos show a loss of all somites posterior to the first five to seven ones. This phenotype is stronger than the known amorphic phenotypes for notch1 (des) or deltaD (aei) in zebrafish, but mimicks the knockout phenotype of RBP-Jkappa gene in the mouse, which is the homologue of Su(H). This suggests that there is some functional redundancy among the Notch and Delta genes. This fact that the first five to seven somites are only weakly affected by Su(H) knockdown indicates that additional genetic pathways may be active in the specification of the most anterior somites.

Animals↗