Bruno Streit

Molecular ecology and evolution: approaches and applications.

I: DNA fingerprinting and behavioral ecology.- Arbitrary primer mediated fingerprinting in plants: Case studies in plant breeding, taxonomy and phylogeny.- DNA amplification fingerprinting: A general tool with applications in breeding, identification and phylogenetic analysis of plants.- The analysis of simple repeat loci as applied in evolutionary and behavioral sciences.- Multilocus DNA fingerprinting and genetic relatedness in plants: A case study with banana and tomato.- Measuring reproductive success in insects.- Unravelling the components that underlie insect reproductive traits using a simple molecular approach.- Molecular analysis of kinship in birds: Interesting questions and useful techniques.- II: Population biology.- Molecular techniques in population genetics: A brief history.- Organization of genetic variation at the molecular level: Lessons from Drosophila.- The use of microsatellite analysis in population biology: Background, methods and potential applications.- The use of microsatellites for genetic analysis of natural populations.- PCR assays of variable nucleotide sites for identification of conservation units.- Concerted evolution and RAPping in mitochondrial VNTRs and the molecular geography of cricket populations.- Molecular markers and evolutionary processes in hermaphrodite freshwater snails.- Extinction and the formation of phylogenetic lineages: Diagnosing units of conservation management in the tiger beetle Cicindela dorsalis.- Perspective on conservation genetics.- III: Molecular systematics.- Advances in the theory and practice of DNA-hybridization as a systematic method.- Allozymes in mammalian population genetics and systematics: Indicative function of a marker system reconsidered.- Analysis of DNA from natural history museum collections.- Sources of ambiguity in nucleic acid sequence alignment.- Computational problems in molecular systematics.- The comparison of morphological and molecular data in phylogenetic systematics.- Non-coding chloroplast DNA for plant molecular systematics at the infrageneric level.- Developing model systems for molecular biogeography: Vicariance and interchange in marine invertebrates.- Bridging phylogenetics and population genetics with gene tree models.- IV: Speciation, development and genome organization.- The role of molecular genetics in speciation studies.- The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium.- The evolutionary ecology of Daphnia.- Diversity within diversity: Molecular approaches to studying microbial interactions with insects.- Evolutionary analysis of genes involved in early embryonic pattern formation in Drosophila.- Developmental genes and the origin and evolution of Metazoa.- To what extent does genetic information determine structural characteristics and document homologies?.- Evolution and multi-functionality of the chitin system.- Genome evolution: Between the nucleosome and the chromosome.- Individual genes underlying quantitative traits: Molecular and analytical methods.- Perspectives on future applications of experimental biology to evolution.

Speciation and phylogeography in the cosmopolitan marine moon jelly, Aurelia sp

BackgroundThe cosmopolitan moon jelly Aurelia is characterized by high degrees of morphological and ecological plasticity, and subsequently by an unclear taxonomic status. The latter has been revised repeatedly over the last century, dividing the genus Aurelia in as many as 12 or as little as two species. We used molecular data and phenotypic traits to unravel speciation processes and phylogeographic patterns in Aurelia.ResultsMitochondrial and nuclear DNA data (16S and ITS-1/5.8S rDNA) from 66 world-wide sampled specimens reveal star-like tree topologies, unambiguously differentiating 7 (mtDNA) and 8 (ncDNA) genetic entities with sequence divergences ranging from 7.8 to 14% (mtDNA) and 5 to 32% (ncDNA), respectively. Phylogenetic patterns strongly suggest historic speciation events and the reconstruction of at least 7 different species within Aurelia. Both genetic divergences and life history traits showed associations to environmental factors, suggesting ecological differentiation forced by divergent selection. Hybridization and introgression between Aurelia lineages likely occurred due to secondary contacts, which, however, did not disrupt the unambiguousness of genetic separation.ConclusionsOur findings recommend Aurelia as a model system for using the combined power of organismic, ecological, and molecular data to unravel speciation processes in cosmopolitan marine organisms.

Introduction. Extent, processes and evolutionary impact of interspecific hybridization in animals

Since the time of Charles Darwin, studies of interspecific hybridization have been a major focus for evolutionary biologists. Although this phenomenon has often been viewed as problematic in the fields of ecology, taxonomy and systematics, it has become a primary source of data for studies on speciation and adaptation. Effects from genetic/evolutionary processes, such as recombination and natural selection, usually develop over extended periods of time; however, they are accelerated in cases of hybridization. Interspecific hybrids exhibit novel genomes that are exposed to natural selection, thus providing a key to unravel the ultimate causes of adaptation and speciation. Here we provide firstly a historic perspective of hybridization research, secondly a novel attempt to assess the extent of hybridization among animals and thirdly an overview of the reviews and case studies presented in this theme issue.

Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species

Biodiversity studies require species level analyses for the accurate assessment of community structures. However, while specialized taxonomic knowledge is only rarely available for routine identifications, DNA taxonomy and DNA barcoding could provide the taxonomic basis for ecological inferences. In this study, we assessed the community structure of sediment dwelling, morphologically cryptic Chironomus larvae in the Rhine‐valley plain/Germany, comparing larval type classification, cytotaxonomy, DNA taxonomy and barcoding. While larval type classification performed poorly, cytotaxonomy and DNA‐based methods yielded comparable results: detrended correspondence analysis and permutation analyses indicated that the assemblages are not randomly but competitively structured. However, DNA taxonomy identified an additional species that could not be resolved by the traditional method. We argue that DNA‐based identification methods such as DNA barcoding can be a valuable tool to increase accuracy, objectivity and comparability of the taxonomic assessment in biodiversity and community ecology studies.

From sea to land and beyond – New insights into the evolution of euthyneuran Gastropoda (Mollusca)

BackgroundThe Euthyneura are considered to be the most successful and diverse group of Gastropoda. Phylogenetically, they are riven with controversy. Previous morphology-based phylogenetic studies have been greatly hampered by rampant parallelism in morphological characters or by incomplete taxon sampling. Based on sequences of nuclear 18S rRNA and 28S rRNA as well as mitochondrial 16S rRNA and COI DNA from 56 taxa, we reconstructed the phylogeny of Euthyneura utilising Maximum Likelihood and Bayesian inference methods. The evolution of colonization of freshwater and terrestrial habitats by pulmonate Euthyneura, considered crucial in the evolution of this group of Gastropoda, is reconstructed with Bayesian approaches.ResultsWe found several well supported clades within Euthyneura, however, we could not confirm the traditional classification, since Pulmonata are paraphyletic and Opistobranchia are either polyphyletic or paraphyletic with several clades clearly distinguishable. Sacoglossa appear separately from the rest of the Opisthobranchia as sister taxon to basal Pulmonata. Within Pulmonata, Basommatophora are paraphyletic and Hygrophila and Eupulmonata form monophyletic clades. Pyramidelloidea are placed within Euthyneura rendering the Euthyneura paraphyletic.ConclusionBased on the current phylogeny, it can be proposed for the first time that invasion of freshwater by Pulmonata is a unique evolutionary event and has taken place directly from the marine environment via an aquatic pathway. The origin of colonisation of terrestrial habitats is seeded in marginal zones and has probably occurred via estuaries or semi-terrestrial habitats such as mangroves.

RAPD identification of microsatellites in Daphnia.

Simple sequence repeats (SSRs, or microsatellites) have been constantly gaining importance as single‐locus DNA markers in population genetics and behavioural ecology. We tested a PCR‐based strategy for finding microsatellite loci in anonymous genomes, which avoids genomic library construction and screening, and the need for larger amounts of DNA. In the first step, parts of a genome are randomly amplified with arbitrary 10mer primers using RAPD fingerprinting. Labelled SSR‐oligonucleotides serve as probes to detect complementary sequences in RAPD products by means of Southern analyses. Subsequently, positive RAPD fragments of suitable size are cloned and sequenced. Using GA and GT probes, we applied this approach to waterfleas (Daphnia) and revealed 37 hybridization signals in 20 RAPD profiles. Thirteen positive RAPD fragments from three Daphnia species and two hybrid ‘species’ were cloned and sequenced. In all cases simple sequence repeats were detected. We characterized seven perfect repeat loci, which were found to be polymorphic within and between species.

Comparing the efficacy of morphologic and DNA-based taxonomy in the freshwater gastropod genus Radix (Basommatophora, Pulmonata)

BackgroundReliable taxonomic identification at the species level is the basis for many biological disciplines. In order to distinguish species, it is necessary that taxonomic characters allow for the separation of individuals into recognisable, homogeneous groups that differ from other such groups in a consistent way. We compared here the suitability and efficacy of traditionally used shell morphology and DNA-based methods to distinguish among species of the freshwater snail genus Radix (Basommatophora, Pulmonata).ResultsMorphometric analysis showed that shell shape was unsuitable to define homogeneous, recognisable entities, because the variation was continuous. On the other hand, the Molecularly defined Operational Taxonomic Units (MOTU), inferred from mitochondrial COI sequence variation, proved to be congruent with biological species, inferred from geographic distribution patterns, congruence with nuclear markers and crossing experiments. Moreover, it could be shown that the phenotypically plastic shell variation is mostly determined by the environmental conditions experienced.ConclusionContrary to DNA-taxonomy, shell morphology was not suitable for delimiting and recognising species in Radix. As the situation encountered here seems to be widespread in invertebrates, we propose DNA-taxonomy as a reliable, comparable, and objective means for species identification in biological research.

The impact of human-made ecological changes on the genetic architecture of Daphnia species

The overenrichment (eutrophication) of aquatic ecosystems with nutrients leading to algal blooms and anoxic conditions has been a persistent and widespread environmental problem. Although there are many studies on the ecological impact of elevated phosphorus (P) levels (e.g., decrease in biodiversity and water quality), little is known about the evolutionary consequences for animal species. We reconstructed the genetic architecture of a Daphnia species complex in 2 European lakes using diapausing eggs that were isolated from sediment layers covering the past 100 years. Changes in total P were clearly associated with a shift in species composition and the population structure of evolutionary lineages. Although environmental conditions were largely re-established after peak eutrophication during the 1970s and 1980s, original species composition and the genetic architecture of species were not restored but evolved along new evolutionary trajectories. Our data demonstrate that anthropogenically induced temporal alterations of habitats are associated with long-lasting changes in communities and species via interspecific hybridization and introgression.

Bioaccumulation processes in ecosystems

The fate of environmental pollutants — the various isotopes of elements, and inorganic or organic compounds — is a fundamental aspect of ecology and ecotoxicology, and bioaccumulation is a phenomenon often discussed in this context. Human activities have drastically altered natural concentrations of many substances in the environment and added numerous new chemicals. An understanding of the processes of bioaccumulation is important for several reasons. 1) Bioaccumulation in organisms may enhance the persistence of industrial chemicals in the ecosystem as a whole, since they can be fixed in the tissues of organisms. 2) Stored chemicals are not exposed to direct physical, chemical, or biochemical degradation. 3) Stored chemicals can directly affect an individuals health. 4) Predators of those organisms that have bioaccumulated harmful substances may be endangered by food chain effects. While former theories on the processes of bioaccumulation focused on single aspects that affect the extent of accumulation (such as the trophic level within the food chain or the lipophilicity of the chemical), modern theories are based on compartmental kinetics and the integration of various environmental interactions. Concepts include results from quantitative structure-activity relationships (QSAR), pharmacokinetics, ecophysiology and general biology, molecular genetic aspects and selection, and finally the structure of communities and man-made alterations in them.

Isolation by Distance in a Population of a Small Land Snail Trochoidea geyeri: Evidence from Direct and Indirect Methods

Population structure was estimated in a continuous population of a small land snail (Trochoidea geyeri). Mark–recapture experiments and randomly amplified polymorphic DNA analyses indicate that the population structure can be described by the isolation by distance model of Wright (1946). Estimates of density and dispersal suggest a neighbourhood size of 70–208 individuals on an area of 13–21 m2. A principal component analysis of the randomly amplified polymorphic DNA data reveals clinal variation of genetic composition across the population, as predicted by the neighbourhood concept. An analysis of molecular variance indicates substantial genetic structuring. Comparisons of the genetic distances, expressed as euclidean distances among individuals, versus the geographic distance between sampling sites yield a highly significant positive correlation (Mantel test: r = 0.567, p < 0.0001). The revealed pattern of populational subdivision on a microgeographic scale seems to be one of the principal processes generating and maintaining genetic diversity within populations of small land gastropods.