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General Introduction
The evolutionary history of species and populations is the product of processes occurring over two time scales: evolutionary time – being based on broad-scale changes under specific environmental conditions with associated selective pressures and ecological time – over which population processes (e.g., demographic changes, migration, local extinction and colonisation) occur (Martin and Simon, 1990; Carroll et al., 2007). Evolutionary biology aims at unraveling these interactions and assessing the importance of the processes. Understanding evolutionary processes is brought about through the study of closely related taxa (Martin and Simon, 1990). Genetic structure of a population can therefore be correlated with both biogeographical factors as well as ecological and
demographic processes (Carisio et al., 2004). Our understanding of species formation is based on population level comparisons; by examining the variation among these populations, their historical associations and the processes of genetic restructuring that may have lead to speciation can often be revealed (Knowles 2004; Knowles and Maddison 2002; Wright, 1931).
Biological diversity can be meaningfully divided into least common evolutionary denominators, namely, the ‘species’ (Hendry et al., 2000). Delineating distinct species is often problematic but most biologists agree with Mayr (1957) that “the living world comprises more or less distinct entities that we call species”. Taxonomic groups have historically been identified using morphological criteria but over the last couple of decades molecular techniques have provided a powerful tool for evaluating the validity of taxonomic units (Avise and Walker, 1999). Avise and Walker (1999) used patterns of mitochondrial DNA (mtDNA) variation to argue that mtDNA discontinuities and traditional taxonomic designations tend to converge which in turn may reveal real biotic units.
Speciation has been described as the evolutionary process by which new biological species arise (Mayr, 1942). Geographic models of speciation in nature have been described based on the extent to which populations are geographically isolated: allopatric (physical barrier separates populations), peripatric (species are formed in isolated, small peripheral populations that are prevented from exchanging genes with the main population) parapatric (zones of two diverging populations are separate but do overlap) and sympatric (population sharing a geographic location is forced by environmental factors to diverge).
The large genetic and phenotypic diversity observed within species is necessary for evolution to create new reproductively isolated species (Härdling et al., 2009). Although most biologist believe that reproductive isolation is the driving force behind species, it has been shown that reproductive isolation alone is not sufficient to permit coexistence of two species at the same locality (Mayr, 1949). Species should also be different in their ecological requirements to avoid competition (Crombie, 1947). Speciation then means the evolution of reproductive isolation as well as of ecological differentiation between populations. To this day, processes and mechanisms involved in speciation are still much debated.
There are many species concepts such as the phylogenetic species concept (PSC), the biological species concept (BSC), the evolutionary species concept (ESC), the cohesion species concept (CSC), the ecological species concept (ESC), the genetics species concept (GSC) and many others (Cracraft, 1989; Dobzhansky, 1940; Mayr, 1940; Mayr, 1942; Simpson, 1961; Schluter, 1998; Schluter, 2001; Templeton, 1989; Wiley, 1978)
Regardless of the species concept (reviewed by De Queiroz, 2007; Mayden, 1997) chosen, biologists are confronted with the question of how much difference (or amount of isolation) defines a species (Hendry et al., 2000). The BSC states that “species are groups of interbreeding populations which are reproductively isolated from other such groups” (Mayr, 1940). If 100% reproductive isolation is used as a criterion for applying the BSC, then the identification of species would be relatively straight-forward (Hendry et al., 2000). On the other hand, if the BSC was universally adopted, many of the current taxonomic species would no longer be recognised due to hybridisation and introgression (see Petit and Excoffier, 2009) in populations in the wild (Hendry et al., 2000; Niemiller et al., 2008; Nosil, 2008).
While the analysis of geographic variation in widely distributed species may lead to the recognition of distinct aggregates of local populations, a problem arises in deciding whether such aggregates represent species or subspecies (Mayr, 1997; Mayr and Ashlock, 1991). The problem is exacerbated by the numerous definitions that have been proposed to define species as mentioned above. For example, the BSC defines species as “interbreeding natural populations that are reproductively isolated form other suc populations” (Dobzhansky, 1940; Mayr, 1942), while the PSC (Cracraft, 1989) considers a species as “a cluster of organisms, diagnosably distinct from other such clusters”. The cohesion species concept (CSC) on the other hand, defines species as “the most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms” (Templeton, 1989). Ecological speciation states that natural selection on traits between populations in different environments leads to the evolution of reproductive isolation and as a consequence species (Schluter, 2001). The genetic species concept defines a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other groups (Baker and Bradley, 2006). The GSC differs from the BSC that the focus is rather on generic isolation than reproductive isolation (Baker and Baker, 2006). The BSC and its variations, is the most widely used in mammals and are thus followed in this study.
CHAPTER 1: GENERAL INTRODUCTION
1. General
2. African Rock Rats
3. Molecules and Phylogeny
4. Phylogeograph
5. Aims of Study
6. Research Questions
6. Relevance of Stud
7. Thesis Outline
8. General Notes
9. References
CHAPTER 2: THE MICAELAMYS NAMAQUENSIS (RODENTIA: MURIDAE) SPECIES COMPLEX FROM SOUTHERN AFRICA: PATTERNS OF MITOCHONDRIAL DNA VERSUS MORPHOLOGICAL DIVERSITY
Abstract
1. Introduction
2. Materials and Methods
3. Results
4. Discussion
5. Conclusion
6. Acknowledgements
References
Appendices
CHAPTER 3: PHYLOGENETIC RELATIONSHIPS WITHIN MICAELAMYS NAMAQUENSIS (RODENTIA: MURIDAE) FROM SOUTHERN AFRICA AS INFERRED FROM MITOCHONDRIAL AND NUCLEAR GENES
1. Introduction
2. Materials and Methods
3. Results
4. Discussion
5. Conclusion
6. Acknowledgements
References
Appendices
CHAPTER 4: PHYLOGEOGRAPHY OF MICAELAMYS NAMAQUENSIS (RODENTIA: MURIDAE) FROM THE EASTERN KALAHARI BUSHVELD BIOREGION OF SOUTH AFRICA
1. Introduction
2. Materials and Methods
3. Results
4. Discussion
5. Conclusio
6. Acknowledgements
References
Appendix
CHAPTER 5: GENERAL CONCLUSIONS
