The domestic dog was probably the first domesticated animal, and the only one to spread to all continents in ancient times. The dog is one of the most phenotypically diverse animals, a result of human selection throughout dog history. Studies of the genetic origins and early spread of domestic dogs is important to gather information about biological and cultural mechanisms behind domestication but also to investigate early human history. The step from a hunter and gatherer lifestyle to farming is one of the most important steps in human history. In this thesis I will present work aimed at understanding both domestic dog origins and dispersal. In order to be able to investigate dog origins based on a second haploid chromosome we identified 14,437 bp of Y-chromosomal DNA sequence. Based on this we show that dogs in Asia south of Yangtze River (ASY) has the highest genetic diversity and was founded from a large number of wolf founders confirming earlier mtDNA results. Early dog dispersal is tightly coupled to human history with the dog brought along as a cultural item. We have for the first time investigated the dog dispersal into Polynesia and Australia and our data can be used as evidence for a more complex settlement of Polynesia than earlier indicated from archaeological and linguistic studies. Analysis of Y-chromosome SNPs in Australian dingoes confirms earlier mtDNA genetic studies that the dingo is part of the domestic dog phylogeny and was founded from a small population of domestic dogs. We have also for the first time investigated the dog population on Madagascar and our data strongly indicates a mainland African origin for the Madagascan dogs. Finally, we have investigated the American dog population sampled from throughout the continent and also for the first time included putative indigenous breed dogs such as Chihuahua and Pero Sín Pelo del Peru, and the free-ranging Carolina dogs from southern USA. Our data clearly indicates a primarily Old World origin for the indigenous breed dogs and also for the free-ranging Carolina dogs in USA. We can also for the first time present evidence for continuity between the ancient and extant dog population with e.g. exclusive sharing of a haplotype between a modern sample of Chihuahua and an ancient Mexican sample. / QC 20120510

The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock. In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones. Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.

The transition from a hunter-gatherer lifestyle to a farming lifestyle, i.e. the Neolithisation, is arguably the most important event in human prehistory. While the geography and dating of the Neolithisation is well known, the process is still under debate, especially if it occurred through diffusion of ideas or with migrating farmers. The process accelerated when alternative use of domesticated animals increased. Especially the use of dairy products, and the consumption of unprocessed milk, appears to be of importance. As milk consumption (lactose digestion) is dependent upon genetic components, it is debated whether the genetic disposition allowed for dairy production to evolve, or if the usages of dairy products added selection pressure that eventually lead to present day allele frequencies. Molecular genetics have the potential to solve this and similar questions, but only if the contamination problem, where authentic DNA can be distinguished from modern contaminating DNA, can be resolved. Here I investigate the nature and extent of contamination with modern human DNA in museum specimens and explore several approaches to minimise this contamination and to authenticate DNA results from ancient humans. I use real-time quantification, pyrosequencing and FLX-generated clonal sequencing assays to generate data on ancient humans and ancient dogs. I further use the techniques to study the development of lactase persistence and the nature of animal domestication. The results presented show that sample-based contamination is extensive, but can be minimised if treated with bleach. I retrieved authentic HVSI sequences from 30 Neolithic hunter-gatherers and farmers from Sweden, of which eighteen also yielded nuclear data indicating that the farmers had a higher frequency of the allele linked to lactase persistence compared to the hunter-gatherers. I conclude that genetic data from ancient humans as well as from ancient animals can be retrieved and used, but only under high stringency.

In one study, a suite of plants from the maize genus Zea L. (Poaceae) and the specialist herbivore Dalbulus maidis (DeLong and Wolcott, 1923) (Hemiptera: Cicadellidae) were used to test the hypotheses that anti-herbivore defenses are affected by plant life-history evolution and human intervention through domestication and breeding for high yield. The suite of Zea host plants included one Mexican commercial hybrid maize Zea mays ssp. mays L., a landrace variety of maize, two populations of Balsas teosinte (Zea mays ssp. parviglumis Iltis & Doebley), and perennial teosinte (Z. diploperennis Iltis, Doebley & Guzman). This suite of host plants includes three Transitions evident within the genus Zea: life history form perennial to annual life cycle evident between perennial teosinte and Balsas teosinte, domestication transition from wild annual to domesticated annual evident between Balsas teosinte and landrace maize, and; breeding transition from landrace cultivar to a hybrid cultivar. The transitions were correlated with differences in plant defenses, as indicated by corn leafhopper performance. Results showed a performance gradient, suggesting a pattern in which plant defense is stronger in perennial than annual plants, Balsas teosinte than landrace maize, and in landraces than in hybrid maize. Furthermore, results suggested that domesticated maize would be the least defended, most suitable host for corn leafhopper. In a second study, haplotype diversity was assessed to address structuring and interconnectedness among samples of corn leafhopper collected in the southwestern region of Mexico to address microevolution. The geographic focus of the study was maintained within an area encompassing the presumed centers of radiation of Dalbulus and its host genus Zea, and of maize domestication. Samples were complemented with samples of corn leafhopper sequences available at GenBank. Results revealed seven haplotypes from three host plants within Zea: perennial teosinte, Balsas teosinte, and maize. Furthermore, genetic differentiation was present and haplotype diversity appears to correlate with differences in genetic structure between perennial teosinte and maize. One haplotype was found to be present throughout all sites, which appears to parallel the spread of maize cultivation. As maize cultivation spread beyond its area of domestication, corn leafhoppers colonized perennial teosinte, further suggesting that subsequent decreases in maize cultivation in perennial teosinte habitat created a refuge where perennial teosinte- adapted haplotypes could persist. Altogether, my research suggests that the combination of historical expansion of maize cultivation expansion and the weaker anti-herbivore defenses associated within maize domestication appears to have favored genotypes particularly adapted for exploiting maize.

"An ‘exponential growth of science’ throughout modern history has been frequently boasted by numerous narcissistic accounts of ‘modern humanity.’ Nonetheless, ‘modern science’ seems to have overwhelmingly compromised on its original promises by fitting into an ‘industrial scheme.’ With this concern, ‘molecular phylogeographics with conservational ambitions’ would look an intact ground for research efforts in a ‘school of biotechnology.’ The dog (Canis familiaris) as an earliest domestic animal has a history of conflicts over its origins and dispersal. Having those disputes addressed, valuable knowledge could be acquired on the nature and dynamics of domestication, and of human societies particularly of pre-agricultural ages. We employed two most widely-used genealogical markers, the mitochondrial DNA (mtDNA) and the non-recombining portion of the Y-chromosome (NRY), to address dog demography. Through 582 bps of mtDNA Control Region, complemented with whole mitochondrial genomes, it was established that almost all maternal lineages of the domestic dog worldwide coalesce to a population of at least 51 and perhaps many more female wolves in Asia South of Yangtze River (ASY) approximately 16,000 years before present (BP). This was based on the presence of a maximal diversity in this area, a descending gradient of diversity outward it, and a ubiquitous population structure everywhere in the world. A closer examination of this portrait in Southwest Asia (SwAsia) and the Fertile Crescent (FC), a region which has supplied persuasive evidence on early presence of the domestic dog, retrieved the same information, with implications for backbreeding with the local wolf population. Meanwhile, analyses of mtDNA dispersal showed that dogs took the long way via land to Madagascar Island, and not together with humans via sea. By the other approach, the NRY data in 14,437 bps length supplemented the mtDNA in reporting the height of diversity from ASY with a founding population of at least 13 male wolves, but expectably produced lower inter-regional differentiation by diversity. Screening of NRY by a SNP assay in the dingoes of Australia Island as a population of feral dogs revealed restricted and similar dispersal patterns for sires and dams. Prospects of ancient, multilocus and whole genome assays with the emerging high-throughput technologies has still more to promise on finer elaborations of these issues." / <p>QC 20120529</p>

Family Pinguipedidae belong to the class Actinopterygii, subclass Neopterygii, order Perciformes, suborder Trachinoidei. Currently the interrelationships of the genera within this family and among the families in the Trachinoidei remain unequivocal. Also, whether the Cheimarrichthys should be included in the family Pinguipedidae has also been a controversial issue. This study aimed to reconstruct phylogenetic hypotheses in order to resolve these questions. Species of the Parapercis and Kochichtys in the family Pinguipedidae occur Taiwan. This study used osteological characters, 16S rRNA and Cyt b sequences to conduct phylogenetic analysis such that hypotheses can be proposed. The results revealed the monophyly of Parapercis, a taxonomic view consistent to the prevailary classification. Summarizing all the results, the 17 Parapercis species analysed can be divided into 4 groups. They are (1) Parapercis aurantiaca¡BP. decemfasciata¡BP. mimaseana¡BP. multifasciata¡BP. muronis¡Btwo morphotypes of P. sexfasciata¡F(2) P. cephalopunctata¡BP. clathrata¡BP. hexophthalma¡BP. kamoharai¡BP. tetracantha¡BP. xanthozona¡F(3) P. cylindrica and P. snyderi¡F(4) P. maculata¡BP. ommatura and P. somaliensis. Two color morphotypes have been shown for Parapercis sexfasciata. Data of the present study revealed that the ¡§ autapomorphic¡¨ osteological character known only in Kochichtys also occurred in three Parapercis species. This result supports a close relationship between these species. However, it also challenges the validity of the generic status of Kochichtys. About the dabate of the phylogenetic position of Cheimarrichthys, it should be put into its own family, Cheimarichthyide, rather than placed in the Pinguipedidae. The hypothesis for the sister group of Pinguipedidae to the Cheimarichthyide is not supported by all the data in this study completely. Morphological and molecular evidences are incongruence for closest phylogenetic relationship. Similar results were also obtained when the molecular sequences were analysed using different methods. More data analyses are needed for complete and reliable results. The present study suggests that the Trachinoidei is not a monophyletic group.

Der plötzliche Kindstod (engl. Sudden Infant Death Syndrome-SIDS) ist die häufigste Todesursache bei Säuglingen innerhalb des ersten Lebensjahres. Die zugrundeliegenden pathophysiologischen Veränderungen sowie die genaue Todesursache sind bis dato ungeklärt. Viele Forschungsbereiche setzen sich intensiv mit der Klärung dieses „Phänomens“ auseinander. Ein Schwerpunkt liegt auf dem genetischen Gebiet und der Betrachtung verschiedener Polymorphismen. Ein Fokus wird hierbei auf die genetischen Polymorphismen der mitochondrialen DNA (mtDNA) gesetzt. In der vorliegenden Arbeit wurden daher drei Polymorphismen der mtDNA und mögliche Risikofaktoren im Bezug zu SIDS-Fällen untersucht. Die Folge eines mitochondrialen Polymorphismus kann beispielsweise die verminderte Genexpression der Untereinheiten der Atmungskette zur Folge haben. Daraus kann ein Defizit in der ATP (Adenosintriphosphat)-Produktion resultieren. Der physiologische Kreislauf einer menschlichen Zelle ist durch dieses Defizit nur eingeschränkt gewährleistet. Im Rahmen der Forschungsarbeit wurden die SNPs G3010A, T16519C und C7028T der mtDNA in Hinblick auf einen möglichen Zusammenhang mit dem SIDS untersucht. Schon 2003 untersuchten Divne et al. (2003) einen möglichen Zusammenhang der SNPs G3010A und C7028T im Zusammenhang mit SIDS, jedoch ohne signifikantes Ergebnis. Boles et al. (2010) konnten eine Assoziation zwischen den Polymorphismen G3010A und T16519C mit dem plötzlichen Kindstod herstellen. Da bislang jedoch keine ausführliche Publikation zu dieser Frage vorliegt, wurde mit der vorliegenden Arbeit die Rolle der Polymorphismen G3010A und T16519C in Bezug auf den plötzlichen Kindstod gemeinsam mit der (bei Europäern) häufigsten Variation C7028T untersucht. Die DNA von 176 SIDS-Fällen und einer Kontrollgruppe von 113 Erwachsenen wurde mittels Singleplex-PCR und RFLP-Analyse genotypisiert. Anhand der Genotypisierung konnten die SNPs quantifiziert und im Hinblick auf einen möglichen Unterschied zwischen SIDS-Fällen und der Kontrollgruppe untersucht werden. Bei Betrachtung der einzelnen SNPs G3010A, T16519C und C7028T lassen sich keine signifikanten Unterschiede zwischen den SIDS-Fällen und der Kontrollgruppe feststellen. Das gehäufte Vorliegen einer erhöhten Mutationsrate in einem Individuum bei SIDS-Fällen im Vergleich zur Kontrollgruppe, sowie die von Opdal et al. (1999) geäußerte Annahme, dass beim Vorliegen einer Mutation in der D-Loop-Region weitere Mutationen im kodierenden Bereich vorkommen, konnten durch diese Arbeit bestätigt werden.

Sequence variation of a 238 bp segment of the mitochondrial control region was analyzed for 1,568 Steller sea lions (2.8% of the estimated species population) sampled from 50 rookeries representing nearly every locality at which Steller sea lions are known to breed in significant numbers. Haplotype diversity (H = 0.9164 ± 0.0035) was high and nucleotide diversity (π = 0.00967 ± 0.00586) was moderate. No evidence was observed for significant genetic bottleneck effects. Rookeries were grouped into regions and stocks to examine structure at different spatial scales. F- and Φ-statistics were computed for all pairwise comparisons of rookeries, regions and stocks. Significant (P<0.05) divergence of eastern stock (southeastern Alaska to California) animals from western stock animals was supported in analyses at all spatial scales. Likewise, rookeries and regions from Asia were found to be significantly different from all other western stock rookeries. This was most clearly demonstrated using Φ-statistics at the regional level. The Commander Islands clearly associate with Alaskan western stock rookeries, not with the Asian rookeries. Within each of the three stocks there is significant isolation by distance among rookeries. This relationship does not hold for inter-stock comparisons indicating that there are important barriers to gene flow among stocks. Mitochondrial DNA analysis supports the recognition of three stocks for appropriate conservation of the species. The currently recognized eastern stock is unaffected, but the western stock is now partitioned west of the Commander Islands yielding a western stock which ranges from Prince William Sound west to the Commander Islands, and an Asian stock including rookeries from the Kamchatka Peninsula, Kuril Islands, and Sea of Okhtosk.

OPA1 regulates cristae structure and mitochondrial DNA (mtDNA) maintenance. Recently, our lab identified ATAD3A and SLC25 proteins as OPA1 interactors. After validating these interactions by co-immunoprecipitation, the role of these proteins in OPA1 function was examined. Previously, ATAD3A was implicated in mtDNA maintenance. However, no change in mtDNA content or nucleoid number was observed in my studies following long-term and short-term ATAD3A knockdown suggesting that OPA1 maintains mtDNA independently of ATAD3A. Previous data from our lab demonstrates that OPA1 oligomerization and cristae structure is altered by nutrients. SLC25 proteins transport nutrients into mitochondria. Therefore, OPA1 oligomerization and cristae structure was analyzed following SLC25 protein inhibition and knockdown. Decreased OPA1 oligomerization and cristae remodeling was observed following SLC25 protein inhibition and OGC knockdown. In addition these changes correlate with decreased ATP synthase monomers and oligomers suggesting that cristae remodeling may affect metabolism. Overall, these studies enhance our understanding of OPA1 function.

This thesis describes the results of an investigation into the population genetic structure of the blue swimmer crab, Portunus pelagicus, in Australian waters. P. pelagicus is an Indo-West Pacific species, with adults and juveniles that inhabit sheltered benthic coastal environments and a planktonic phase (of modest duration) in its life cycle. The investigation was done by examining the patterns of variation at six microsatellite loci and in a 342 bp portion of the cytochrome oxidase subunit I (COI) gene in the mitochondrial DNA in samples of Portunus pelagicus from a total of 16 different assemblages/waterbodies. Overall, the samples were collected from throughout the geographical range of this species in Australian waters, i.e. from the western seaboard, from the eastern seaboard, from Darwin on the north coast and from South Australia on the south coast. The samples sizes ranged from 4 to 57 individuals, depending on the sample and the genetic assay. The population genetic structure of P. pelagicus was analysed from both a traditional population structure perspective and from a phylogeographical and historical demography perspective. The traditional assessment of the population genetic structure of Portunus pelagicus indicates that this species exhibits a significant amount of genetic heterogeneity in Australian waters (e.g. FST for microsatellite data = 0.098; ¥èST for COI data = 0.375 and ¥ÕST for COI data = 0.492). This assessment also indicates that P. pelagicus exhibits varying degrees of genetic heterogeneity within and between geographical regions in Australian waters, as follows. (1) The genetic compositions of the samples from the different coastlines (i.e. north, south, east and west) invariably showed statistically significant differences for at least two microsatellite loci, although the differences between the samples from the eastern seaboard, Darwin and those from the western seaboard to the north of Port Denison were not as great as those within the western seaboard samples or within South Australian samples. (2) The genetic compositions of the samples from the assemblages on the eastern seaboard of Australia, which ranged from Mackay (21¨¬06¡ÇS) to Port Stephens (32¡Æ40¡ÇS), were essentially homogeneous. (3) The samples from the assemblages on the western seaboard of Australia, which ranged from Broome (17¡Æ58¡ÇS) to Geographe Bay (33¡Æ35¡ÇS), exhibited significant levels of genetic heterogeneity. Furthermore, those from south of Port Denison formed a highly distinctive (but not invariant) group compared to those from elsewhere. (4) The samples from South Australia were also highly genetically distinctive compared to those from elsewhere, although they also showed significant heterogeneity amongst themselves. The above findings were more or less suggested by both the microsatellite and COI markers, although the former generally provided a higher resolution picture of the population structure of P. pelagicus than did the latter. The main findings of the investigation into the phylogeography and recent demographic history of Portunus pelagicus in Australian waters were as follows. (1) A phylogeny constructed from COI sequence variation was shallow, with the lineages showing varied geographical distributions. (2) The results of a nested clade analysis of this variation indicate that range expansion has been a predominant influence on the historical demography of P. pelagicus in Australian waters. (3) The samples from the assemblages on the western seaboard to the south of Port Denison contained low levels of genetic diversity, a sub-set of the diversity present in the samples from lower latitude sites on the western seaboard, and microsatellite-based evidence of having coming from assemblages that have undergone a bottleneck (or founder effect) followed by an expansion in size. (4) The samples from the assemblages in South Australia contained low levels of genetic diversity, phylogenetic affinities with samples from the eastern seaboard, and microsatellite-based evidence of having coming from assemblages that have undergone a bottleneck (or founder effect) followed by an expansion in size. The two major interpretations to stem from the results of this investigation are as follows. (1) Overall, Portunus pelagicus has undergone a recent (in an evolutionary sense) range expansion, from a single source, within Australian waters. At a finer-scale, this species appears to have colonised south-western Australia from a lower latitude site(s) on the western seaboard and probably colonised South Australia from the southern margins of its range on the eastern seaboard. Regardless, there has been limited penetrance of genetic variation into temperate waters on the western seaboard and into South Australia, presumably due one or more of the barriers to gene flow listed below. (2) P. pelagicus experiences significant restrictions to gene flow within its present-day geographical range in Australian waters due to (i) geographic distance per se; (ii) discontinuities in the distribution of the sheltered coastal environments; (iii) hydrological barriers to dispersal and (iv) possibly low temperatures in the temperature margins of the range.