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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 [mailto:pennings@lmu.de Pleuni Pennings].

===Name: Steffen Beisswanger===

'''Title: Selection and population structure in Drosophila melanogaster

'''Supervisor: Prof Stephan

'''CV: [http://www.zi.biologie.uni-muenchen.de/evol/CV/Beisswangercurriculumvitae.htm link]

'''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

'''CV: [http://www.biologie.uni-muenchen.de/ou/anthropologie/Personen/Seiten/Assistentin.htm link]

'''Abstract:

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===
[[Image:Pfannes2.jpg]]

'''Title: CHARACTERIZATION OF THE SYMBIOTIC BACTERIAL PARTNERS IN PHOTOTROPHIC CONSORTIA

'''Supervisor: Prof Overmann

'''Abstract: 

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

'''CV: [[Alexander Varzari| link]]

'''Abstract:

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.
Return to PhD theses 0607.
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