PhD theses 0607
On this page you find a selection of PhD theses from the academic year 2006-2007. If you would like to have your PhD thesis added to this list, please send an e-mail to Pleuni Pennings.
Name: Steffen Beisswanger
Title: Selection and population structure in Drosophila melanogaster
Supervisor: Prof Stephan
Abstract: In this thesis I scrutinized a specific region of the X chromosome of Drosophila melanogaster for evidence of positive directional selection. In addition, I analyzed the structure of six Southeast (SE) Asian populations of this species.
In the first chapter, I analyzed a region that showed no polymorphism in a previous scan of the X chromosome in a European D. melanogaster population. This region, which I named the wapl region, is located on the distal part of the X chromosome, in cytological division 2C10 – 2E1. I observed a 60.5 – kb stretch of DNA encompassing the genes ph-d, ph-p, CG3835, bcn92, Pgd, wapl and Cyp4d1 that almost completely lacks variation in the European sample. Loci flanking this region show a skewed frequency spectrum at segregating sites, strong haplotype structure, and high levels of linkage disequilibrium. Neutrality tests revealed that these patterns of variation are unlikely under the neutral equilibrium model or simple bottleneck scenarios. In contrast, newly developed likelihood ratio tests suggest that strong positive selection has acted recently on the region under investigation, resulting in a selective sweep. Evidence is presented that this sweep may have originated in an ancestral population in Africa.
In the second chapter, I revisited the center of the wapl region analyzed in chapter 1. I concentrated on the African D. melanogaster sample, as the valley of reduced variation found in the previous study was much narrower in the African sample than in the European one, which should help to pinpoint the target of selection. About 80% of the valley of reduced nucleotide variation was sequenced. This valley is located between the genes ph-d and Pgd. I therefore termed this part the ph-d – Pgd region. The new results confirm previous conclusions about selection having shaped nucleotide variability in this part of the D. melanogaster genome. Moreover, by sequencing the center of the selective sweep I was able to establish the haplotype structure in that region and to infer the historical context of the sweep. Most likely a positively selected substitution occurred at ph-p and was fixed before the out-of-Africa expansion of D. melanogaster, possibly >30,000 years ago. This substitution might be associated with the specialization of ph-p in gene regulation. In addition, the results obtained from the European sample indicate that sequence variation was not affected by demography alone. In fact, it was found that selection affected nucleotide diversity in the ph-d – Pgd region of the European sample as well. Since heterozygosity across the whole wapl region is substantially reduced, I propose that an additional selective sweep occurred at a different site in the European population. This is supported by an analysis regarding the time since the fixation of the (first) beneficial mutation at ph-p, which points toward a substitution in D. melanogaster before the colonization of Europe.
In chapter 3, I obtained sequence data from six SE Asian samples for ten putatively neutrally evolving X-linked loci. Population genetic parameters were estimated and compared to those previously obtained from the European and the African sample. I observe substantially lower levels of nucleotide diversity in SE Asia than in either Africa or Europe. In particular, samples taken from more peripheral populations (e.g. Manila and Cebu, located on the Philippines) show a paucity of haplotypes. Common summary statistics indicate that genetic drift had a significant impact on these populations, which also led to considerable population substructure. One sample, i.e. Kuala Lumpur, however, shows rather high levels of heterozygosity among all SE Asian samples and is on average least differentiated from these. This indicates that the Kuala Lumpur population is ancestral to the other SE Asian populations, which is supported by a high amount of shared polymorphic sites. Finally, I revisited the wapl region, as analyzed in the first chapter, and find evidence that the selective sweep is older in Kuala Lumpur than in Europe.
Name: Michaela Harbeck
Title: Molecular biological parameters of bone diagenesis - Implications for archaeometric analysis
Supervisor: Prof Grupe
Bone material is often the only bodily relic of deceased individuals and therefore constitutes a most important source of information. Today, several analytical methods are available for retrieving the kind of information necessary for the historical or forensic context. For example, analysis of stable isotopes evidences individual dietary preferences and/or migration patterns (Lösch et al. 2006; Montgomery et. al. 2005), while analysis of preserved DNAmolecules permits for a genetical fingerprint and hence the reconstruction of kinship (Dissing et al. 2007; Dudar et al. 2003).
However, bone is a complex biological material and is subject to a variety of pre-depositional and post-depositional processes (diagenesis), resulting in physical and chemical alterations which will destroy information, complicate analysis or may even lead to false positive results. It is therefore of outstanding importance to evaluate which kind of diagenetic changes could have taken place and how they influence the analysis and the results. Furthermore, the success of archaeometric analyses is highly dependent on the degree of preservation of bone. In this context it is necessary to stress that the diagenetic history of an excavated bone has to be deduced from its current status quo.
This study aimed at an examination of the processes and the relationships of the diagenetic changes on different organizational levels of the bone substance (microstructure, biomolecules and mineral crystals), in order to evaluate how the various diagenetic processes will be capable of biasing archaeometric results and how these biases can be detected. In the following, existing relationships between the degrees of preservation of the different organizational levels of the bone structure were statistically assessed to formulate indicators capable of predicting the probable success of archaeometrical methods to be applied. The evaluation of such indicators is highly desirable since archaeometrical analyses are both costly and time consuming.
The study was carried out by use of 127 excavated human bones of known archaeological age (from 11500 to 400 years). Analysis included microstructural parameters (Oxford Histological Index, birefringence), UV-fluorescence, collagen preservation (weight percent) and especially its quality (percentage of carbon and nitrogen, molar C/N ratio, amino acid profile), amino acid racemisation, preservation of DNA (extraction and amplification success), and finally the integrity of the mineral matrix (Ca/P mass ratio, chemical composition). In addition, a sample of modern cremated bones was also examined to assess which archaeometrical methods will lead to valid results obtained on this special bone material. Finally, in vitro ageing experiments were carried out on 28 modern bones to directly observe isolated chemical diagenetic processes.
The major results of this study was that the the excavated bones could be categorized into only three diagenetic types (well preserved bones, microbially degraded bone, and bone characterized by an altered mineral fraction), which were related to three different diagenetic pathways due to time elapsed after inhumation, and environmental parameters. While the examination of UV-fluorescence is used by forensic scientists for an assessment of time since death of skeletal finds (e.g. Knight & Lauder 1969; Verhoff & Kreutz 2004), own preliminary investigations (Harbeck 2002) on archaeological material could not verify such a correlation with time. The results of the PhD study confirmed that the fluorescence quality rather depends on the degree of preservation, and is therefore also suggested an indicator for the degree of diagensis.
The statistically significant relationships between the examined parameters permitted the formulation of indicators for the success of biomolecular archaeometric analysis. Microstructural features and the Ca/P mass ratio are capable of predicting the success of archaeometric analysis of bone collagen or DNA. With a somewhat smaller probability, it is possible to estimate the success of archaeometric analysis of biomolecules with regard to the diagenetic type. Microscopical preservation, and, as expected, the fluorescence of bone, are particularly good indicators.
This study revealed the likelihood of false positive results occurring in the course of biomolecular analysis (DNA and collagen), and how difficult it is to avoid them. It could be shown that many of the identification criteria commonly agreed upon for the assessment of the state of preservation of extractable biomolecules are indeed not suitable, and the list of criteria has to be extended e.g. by the necessity of establishing amino acid profiles of extractable collagen. Preserved DNA unexpectedly amplifyable from modern cremated material was identified as false positive results due to contamination most likely already derived from the crematorium. Contrary to some recent publications, forensic DNA-analysis ofcremated material cannot be recommended. Also, collagen could no more be retrieved from cremated material. Stable isotope analysis of the cremated mineral fraction lead to so far unexplained isotopic fractionation due to thermal exposure.
Dudar, J.C.; Waye, J.S.; Saunders, S. R. (2003): Determination of a kinship system using ancient DNA, mortuary practice, and historic records in an upper canadian pioneer cemetery. International Journal of OSteoarchaeology 13: 232-243
Dissing, J.; Binalden, A.; Hansen, A.; Sejrsen, B.; Willerslev, E.; Lynnerup, N. (2007): The last Viking King: A royal maternity case solved by ancient DNA analysis. Forensic Science International 166: 21-27
Harbeck, M. (2002): Morphologische und molekularbiologische Aspekte der Knochenalterung: Untersuchungen zur Liegezeitbestimmung. Diplomarbeit, Christian-Albrechts-Universität zu Kiel
Knight, B.; Lauder, I. (1969): Methods of dating skeletal remains. Human Biology 41: 322-341 Lösch, S.; Grupe, G.; Peters, J. (2006): Stable isotopes and dietary adaptions in humans and animals at prepottery Neolithic Nevali Cori, southeast Anatolia. American Journal of Physical Anthropology. 131: 181-193
Montgomery, J. Evans, J.A.; Powlesland, D.; Roberts, C.A. (2005): Continuity or colonization in Anglo-Saxon England? Isotope evidence for mobility, subsistence practice and status at West Heserton. American Journal of Physical Anthropology 126: 126-138
Verhoff, M.H.; Kreutz, K. (2004): Forensischer Osteologie, Humanspezifität, Liegezeit und Verletzungsspuren. Rechtsmedizin 14: 417-430
Name: Kristina Pfannes
Title: CHARACTERIZATION OF THE SYMBIOTIC BACTERIAL PARTNERS IN PHOTOTROPHIC CONSORTIA
Supervisor: Prof Overmann
Bacterial interactions play a major role in nature, but are poorly understood, because of the lack of adequate model systems. Phototrophic consortia represent the most highly developed type of interspecific bacterial association due to the precise spatial arrangement of phototrophic green sulfur bacteria (GSB) around a heterotrophic central bacterium. Therefore, they are valuable model systems for the study of symbiosis, signal transduction, and coevolution between different bacteria. This thesis summarizes a series of laboratory experiments with the objective of elucidating the molecular, physiological and phylogenetical properties of the two bacterial partners in the symbiotic phototrophic consortium "C. aggregatum".
The central bacterium of “C. aggregatum” had been identified as a Betaproteobacterium, however, it could not be characterized further due to the low amount of consortia in enrichment cultures. In this work a suitable method for enrichment and isolation of DNA of the central bacterium of "C. aggregatum" has been established using cesium chloridebisbenzimidazole equilibrium density gradient centrifugation (Chapter 3). In density gradients, genomic DNA of the central bacterium of “C. aggregatum” formed a distinct band, which could be detected by real-time PCR. Using this method, the GC-content of the central bacterium was estimated to be 55.6%. Furthermore, its precise phylogenetic position was determined and it was shown to represent a novel and phylogenetically isolated lineage of the Comamonadaceae within the b-subgroup of the Proteobacteria.
Chapter 4 describes the detection of a new, highly diverse subcluster of Betaproteobacteria, which contains several central bacteria of phototrophic consortia. Genomic DNA of the central bacterium of “C. aggregatum” was enriched several hundred fold by employing a selective method for growth of consortia in a monolayer biofilm followed by a purification of the central bacterial genome by density gradient centrifugation. A combination of molecular methods revealed that two rrn operons of the central bacterium are arranged in a tandem fashion. This rare gene order was exploited to screen various natural microbial communities. A diverse and previously unknown subgroup of Betaproteobacteria was discovered in the chemocline of Lake Dagow, Eastern Germany. All 16S rRNA gene sequences recovered are related to that of the central bacterium of “C. aggregatum”. Phylogenetic analyses showed, that the central, chemotrophic symbionts of phototrophic consortia have a polyphyletic origin, just like their phototrophic counterparts. This indictates that not only different GSB but also different Betaproteobacteria have adapted to life in this type of symbiosis.
Chapter 5 focuses on the isolation of the epibiont of “C. aggregatum” from a consortia enrichment culture and its description as Chlorobium chlorochromatii strain CaD. It represents a novel species within the genus Chlorobium and is characterized by physiological properties typical for GSB. However, the symbiotic strain differs from free-living GSB in the distribution of its chlorosomes and the presence of a conspicuous additional structure at the attachment-site to the central bacterium. Its capability to grow in pure culture indicates that it is not obligately symbiotic.
The natural habitat of GSB and phototrophic consortia is the chemocline of stratified lakes. Therefore, the physiological response to oxygen exposure of the epibiont and the freeliving GSB Chlorobium limicola has been investigated (Chapter 6). It was shown that GSB are able to survive oxygen exposure and have developed several strategies for oxygen detoxification. Genome annotation revealed the presence of several enzymes involved in oxygen detoxification in all currently sequenced GSB genomes. Phylogenetic analyses showed that most of these enzymes likely were present in the common ancestor of this group. The activity of some of those enzymes could be confirmed. Since carotenoids can also act as antioxidants, the carotenoid composition of the epibiont was investigated. In contrast to all other GSB it lacks chlorobactene, the major carotenoid in green-coloured GSB. In addition, 7,8-dihydro-g-carotene has been identified in the epibiont as a novel carotenoid in nature. Substantial progress has been made in the course of this study not only with the establishment of a method facilitating genome sequencing of the central bacterium of “C. aggregatum”, but also with the developement of a molecular screening tool for central bacteria of phototrophic consortia. The resulting sequences will enable the direct comparison of the phylogeny of both bacterial partners in different phototrophic consortia and hence will provide the unique opportunity to assess for the first time the process of the coevolution of a bacteria-bacteria-symbiosis.
Name: Alexander Varzari
Title: Population History of the Dniester-Carpathians: Evidence from Alu Insertion and Y-Chromosome Polymorphisms
Supervisor: Prof Weiss
The Dniester-Carpathian region has attracted much attention from historians, linguists, and anthropologists, but remains insufficiently studied genetically. We have analyzed a set of autosomal polymorphic loci and Y-chromosome markers in six autochthonous Dniester-Carpathian population groups: two Moldavian, one Romanian, one Ukrainian and two Gagauz populations. To gain insight into the population history of the region, the data obtained in this study were compared with corresponding data for other populations of Western Eurasia.
The analysis of 12 Alu human-specific polymorphisms in 513 individuals from the Dniester-Carpathian region showed a high degree of homogeneity among Dniester-Carpathian as well as southeastern European populations. The observed homogeneity suggests either a common ancestry of all southeastern European populations or a strong gene flow between them. Nevertheless, tree reconstruction and principle component analyses allow the distinction between Balkan-Carpathian (Macedonians, Romanians, Moldavians, Ukrainians and Gagauzes) and Eastern Mediterranean (Turks, Greeks and Albanians) population groups. These results are consistent with those from classical and other DNA markers and are compatible with archaeological and paleoanthropological data.
Haplotypes constructed from Y-chromosome markers were used to trace the paternal origin of the Dniester-Carpathian populations. A set of 32 binary and 7 STR Y-chromosome polymorphisms was genotyped in 322 Dniester-Carpathian Y-chromosomes. On this basis, 21 stable haplogroups and 171 combination binary marker/STR haplotypes were identified. The haplogroups E3b1, G, J1, J2, I1b, R1a1, and R1b3, most common in the Dniester-Carpathian region, are also common in European and Near Eastern populations. Ukrainians and southeastern Moldavians show a high proportion of eastern European lineages, while Romanians and northern Moldavians demonstrate a high proportion of western Balkan lineages. The Gagauzes harbor a conspicuous proportion of lineages of Near Eastern origin, comparable to that in Balkan populations. In general, the Dniester-Carpathian populations demonstrate the closest affinities to the neighboring southeastern and eastern European populations. The expansion times were estimated for 4 haplogroups (E3b1, I1b, R1a1, and R1b3) from associated STR diversity. The presence in the studied area of genetic components of different age indicates successive waves of migration from diverse source areas of Western Eurasia.
Neither of the genetic systems used in this study revealed any correspondence between genetic and linguistic patterns in the Dniester-Carpathian region or in Southeastern Europe, a fact which suggests either that the ethnic differentiation in these regions was indeed very recent or that the linguistic and other social barriers were not strong enough to prevent genetic flow between populations. In particular, Gagauzes, a Turkic speaking population, show closer affinities not to other Turkic peoples, but to their geographical neighbors.