The Francolins constitute the largest genus in the Galliform family Phasianidae. There is little accord concerning the taxonomic classification of its members. In the past, information on this group has been provided by morphological and palaeontological evidence. An investigation into the molecular history of this group is presented, using mitochondrial DNA (mtDNA) as an evolutionary tool. A comparison of mtDNA restriction fragment lengths has been used to help define the phylogenetic relationships between 13 southern African Francolin species and a selected outgroup, the Japanese Quail. Both cladistic and distance-based analytical methods have been used to construct phylogenies from the molecular fragment data. The trees relating the Francolins are in general agreement with the traditional classification based on morphological, behavioural and morphometric studies, but differ in the branching order of two species, F. levaillantii and F. hartlaubi. A recent proposal for the partitioning of the genus into two monophyletic assemblages of quail-like "partridges" and pheasant-like "francolins" is supported by mtDNA fragment data, with the exception of the two aberrant taxa. On the basis of the initial fragment size comparison, F. hartlaubi and F. levaillantii constitute part of an unresolved quadrichotomy at the base of the tree. A restriction endonuclease site mapping approach has been utilized to provide a deeper resolution for the molecular phylogeny. Detailed mtDNA restriction endonuclease maps of F. levaillantii, F. hartlaubi, two species representing the "partridge" and "francolin" monophyletic groups respectively, and also of the Madagascar Partridge, have been constructed. Phylogenetic analysis of this data has helped to resolve the problematic placement of the two aberrant taxa by showing an early separation of F. levaillantii from the "partridge" lineage, and of F. hartlaubi from the "francolin" lineage. The Madagascar Partridge was anticipated to be a likely sister-taxon to the whole group, but instead appears to have close relationships within the "partridge" lineage.

Yu Man Him. / Thesis (M.Sc.)--Chinese University of Hong Kong, 2000. / Includes bibliographical references (leaves 45-50). / Abstracts in English and Chinese. / Abstract --- p.ii / Acknowledgement --- p.ii / Chapter 1. --- Introduction / The mitochondrion --- p.1 / The mitochondrial genome --- p.3 / Mitochondrial DNA and diseases --- p.7 / Circulating plasma DNA --- p.8 / Project aims --- p.8 / Chapter 2. --- Materials and Methods / Choice of gene quantification system --- p.9 / Real time quantitative PGR --- p.11 / 7700Sequence Detection System --- p.14 / The LightCycler ´ؤ an alternative fast analyzer --- p.15 / Quatntitation of starting copy number using real time PCR --- p.17 / Primer and probe design rules --- p.18 / Hot start PCR technique --- p.19 / Other anti-contamination measures --- p.20 / Test subjects --- p.21 / Sample processing --- p.23 / DNA extraction --- p.24 / Chapter 3. --- System Development / Choice of primer and probe sequences --- p.28 / Optimization of PCR conditions --- p.30 / Imprecision of TaqMan assays --- p.33 / MTRNR2 vs. MTCYB probes --- p.33 / Construction of standard curve --- p.35 / Chapter 4. --- Research Application / The trauma model --- p.37 / Plasma DNA as a marker for trauma severity --- p.37 / Results --- p.38 / Disussion --- p.41 / Chapter 5. --- Conclusion --- p.44 / Chapter 6. --- References --- p.45

Thesis (doctoral)--Lund University, 1996.

Thesis (doctoral)--Lund University, 1996.

A thesis submitted to the Faculty of Medicine, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. / The subject of this thesis is mitochondrial DNA (mtDNA) variation in southern African populations. The purpose of this study was twofold. Firstly, mtDNA variations were used to investigate the genetic affinities of Negroid, Khoisan, Caucasoid and "Coloured" populations in an attempt to refine theories on southern African population affinities and prehistory. MtDNA variations were detected using two different methods. The first method makes use of restriction fragment length polymorphisms (RFLPs) detected with the restriction enzymes Hpal, BamUI, Haell, Mspl, Avail and Hindi in 795 unrelated individuals from twenty ethnic groups within the Khoisan, Negroid, Caucasoid and "Coloured" populations from South Africa and Namibia. The combinations of the various restriction enzyme patterns (morphs) for the enzymes Hpal, Bam HI, Hae II, Mspl, Avail and Hindi (in this order), were used to derive the mtDNA type for each individual studied. This resulted in the discovery of 52 distinct mtDNA types: 30 of which had been previously reported, 28 out of 32 resulted from new combinations of enzyme morphs and 4/32 were due to the discovery of new enzyme morphs (MspI-17 in the Ashkenazi Jewish population and AvaII-31, AvaII-32 and AvaII-33 in the South African "Coloured" population). The second method involves sequencing approximately 750 base pairs of mtDNA contained within the two hypervariable segments within the non-coding control region of the mtDNA molecule in 144 individuals, most of whom where investigated for mtDNA RFLP variations. Pairwise comparisons of mtDNA sequences revealed 119 variant sites which gave rise to 129 unique mtDNA types. / WHSLYP2017

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karol Inst., 2003. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karololinska institutet, 2006. / Härtill 5 uppsatser.

Thesis (Ph. D.)--University of Washington, 2008. / Vita. Includes bibliographical references (p. 91-99).

The classification of the family Felidae (cats) is problematical due to the conservative nature of their morphology. Some workers classify the family into as many as 20 genera (Ewer, 1973) while others divide it into three genera (Walker et al., 1964). Such studies have largely been based on morphological and behavioural characters. Recently, molecular studies, namely, protein albumin immunological distances (Collier and O'Brien, 1985) and protein electrophoresis (Randi and Ragni, 1991) have been used to try and resolve the problems underlying this family. To complement the previous studies, in the present study we use mitochondrial (mt) DNA to construct a· phylogeny of eight members of the southern African Felidae namely, African wild cat, Felis lybica; domestic cat, Felis catus; caracal, Caracal caracal; European wild cat, Felis sylvestris; leopard, Panthera pardus; lion, Panthera leo; and cheetah, Acynonyx jubatus. Mitochondrial DNA (mt DNA) was utilized instead of nuclear DNA since it accumulates point mutations at a rate which is 5 to 10 times as fast as the nuclear DNA and is therefore particularly useful for studying more closely related organisms between sub-species, species and genera. Its apparent potential to be used as a tool for constructing genealogical trees and time scales makes it a method of choice in evolutionary studies. We used the restriction mapping approach to generate data for phylogenetic analysis. Restriction mapping was utilized since it gives good resolution at the species and genus level and evolutionary estimates derived from this method are considered more accurate than those obtained by methods such as the restriction fragment size comparison. We have also attempted to develop the methodology for sequencing part of the cytochrome b region of mt DNA following polymerase chain reaction (PCR) amplification. Both cladistic and distance approaches were used for phylogenetic construction. This study will be both of academic value and may have relevance to practical conservation management since these molecular approaches help to identify or confirm specific status especially with respect to the relationship between the domestic cat and the African and the European wild cats. Furthermore, such approaches can be used at the intraspecific level to address problems in biogeography and population genetics. Our results are in concordance with the previously determined morphological studies and albumin immunological distance studies. The restriction maps for the African wild cat and the domestic cat are identical, emphasizing their close relationship and the African origin of the domestic cat. The European wild cat showed a slight variation with the African wild cat or the domestic cat with four different restriction sites and a sequence divergence of 0.9. This suggests that the common ancestral mt DNA of these cats existed about 450 000 years ago. The lion and the leopard are monophyletic in both cladistic and distance approaches. The precise placement of caracal has yet to be resolved but it is deeply rooted in the phylogenetic analysis which would be more consistent with a separate generic status of the latter species rather than its inclusion within either Felis or Panthera. The distance analyses are consistent with the placement of the cheetah as the most distantly related species amongst the eight Felid species examined.