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A Long-Term Study on the Local and Regional Genetic Population Structure of the Cooperative Breeding Placid Greenbul (Phyllastrephus Placidus)

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A Long-Term Study on the Local and Regional Genetic Population Structure of the Cooperative Breeding Placid Greenbul (Phyllastrephus Placidus) Biology Department Research Group Terrestrial Ecology _____________________________________________________________________________________ A LONG-TERM STUDY ON THE LOCAL AND REGIONAL GENETIC POPULATION STRUCTURE OF THE COOPERATIVE BREEDING PLACID GREENBUL (PHYLLASTREPHUS PLACIDUS). Annelore De Ro Studentnumber: 01403714 Supervisor: Prof. Dr. Luc Lens Scientific tutor: Laurence Cousseau Master’s dissertation submitted to obtain the degree of Master of Science in Biology Academic year: 2018 - 2019 © Faculty of Sciences – research group Terrestrial Ecology All rights reserved. This thesis contains confidential information and confidential research results that are property to the UGent. The contents of this master thesis may under no circumstances be made public, nor complete or partial, without the explicit and preceding permission of the UGent representative, i.e. the supervisor. The thesis may under no circumstances be copied or duplicated in any form, unless permission granted in written form. Any violation of the confidential nature of this thesis may impose irreparable damage to the UGent. In case of a dispute that may arise within the context of this declaration, the Judicial Court of Gent only is competent to be notified. 2 TABLE OF CONTENT 1. INTRODUCTION ........................................................................................................................................... 3 2. OBJECTIVES .................................................................................................................................................. 6 3. MATERIAL AND METHODS .......................................................................................................................... 6 3.1 Study area and species .......................................................................................................................... 6 3.2 Genetic data........................................................................................................................................... 7 3.3 Genetic diversity and population structure ........................................................................................... 8 3.3.1 Genetic analyses .............................................................................................................................. 8 3.3.2 Genetic structure among fragments ................................................................................................ 9 3.3.3 Dispersal between fragments .......................................................................................................... 9 3.3.4 Regional spatial autocorrelation ...................................................................................................... 9 3.4 Local genetic patterns and sex-biased dispersal ................................................................................. 10 3.4.1 Local genetic patterns .................................................................................................................... 10 3.4.2 Sex-biased dispersal ....................................................................................................................... 10 4. RESULTS ..................................................................................................................................................... 10 4.1 Genetic diversity and population structure ......................................................................................... 10 4.1.1 Genetic diversity ............................................................................................................................. 10 4.1.2 Genetic structure among fragments .............................................................................................. 11 4.2 Fine scale genetic patterns and sex-biased dispersal .......................................................................... 16 5. DISCUSSION ............................................................................................................................................... 20 5.1 Genetic diversity .................................................................................................................................. 20 5.2 Population structure on a regional scale ............................................................................................. 21 5.3 Population structure on a local scale ................................................................................................... 23 5.4 Sex-biased dispersal ............................................................................................................................. 24 6. CONCLUSION ............................................................................................................................................. 25 7. SUMMARY ................................................................................................................................................. 26 8. SAMENVATTING ........................................................................................................................................ 29 9. TEXT FOR THE BROADER AUDIENCE .......................................................................................................... 32 10. ACKNOWLEDGMENTS ............................................................................................................................. 34 11. REFERENCES ............................................................................................................................................ 35 12. APPENDICES ............................................................................................................................................ 43 Appendix 1: The potential of genetic and demographic rescue in the Taita Apalis, a critically-endangered bird of south-east Kenya. ................................................................. 43 Appendix 2: Structure Harvester results .................................................................................................... 45 Appendix 3: BIMr results ............................................................................................................................ 45 Appendix 4: Local spatial autocorrelation graphs ..................................................................................... 46 3 1. INTRODUCTION Dispersal is an important life history trait that has an influence on several ecological scales. First, dispersal plays an important role in the dynamics of metapopulations (Hanski 1998). Colonisation of empty habitat patches depends on the dispersal capabilities of the species and can save them from (local) extinction (Kot 1996). This forms the base of several population structure theories like source-sink dynamics (Frankham et al. 2010). Dispersal is also a crucial driver of gene flow between populations which has important consequences for the population genetic structures (Van Dijk et al. 2015). There are several factors that can affect animal dispersal strategies which in turn influence population dynamics and gene flow. Habitat patch isolation will have a strong impact on the cost of dispersal between patches, making it harder for species to colonise new habitat patches (Bowler et al. 2005). Costs paid during movement between patches include factors like energy investment and exposure to predation (Travis & Dytham 1999, Bowler et al. 2005). The costs can further be increased when the matrix of the patches is inhospitable (Wiens et al. 1993). Next, temporal variation in environmental quality (e.g. decrease of food resources) may affect the carrying capacity of the patch and increase the variance of the reproductive success of individuals (Johst & Brandl 1997, Bowler et al. 2005). In such case, dispersal can be considered as a bet-hedging strategy to reduce the variance in the fitness of an individual (den Boer 1968). Next, several studies confirmed a negative correlation between patch size and emigration rate (Johst & Brandl 1997, Hill et al. 1996, Kindvall 1999, Baguette et al. 2000, Pakanen et al. 2017). A decline in patch size increases the edge to size ratio and the likelihood that an individual leaves a patch may increase when the individual is more likely to encounter the edge (Stamps et al. 1987, Kindvall & Petersson 2000). Lastly, emigration is often favoured when there is an increase in population density mainly due to an increase in competition (Bowler et al. 2005). On a local scale, restricted dispersal can have an influence on the spatial genetic structuring within populations. Both clustering of kin and sex-biased dispersal will lead to a higher level of relatedness among individuals, resulting in a positive genetic autocorrelation between them. Clustering of kin around the natal site causes an increase in the chance of inbreeding (Bengtsson 1978, Greenwood 1980, Gandon 1999) and an increase in kin competition (Hamilton & May 1977), which is often a driver for dispersal. However, high population density and clustering of kin do not always cause an increase in dispersal. Negative density- dependent emigration might be more advantageous when the presence of kin increases the fitness of the individual (Baglione et al. 2003) and the benefits of living in a group exceed the costs of competition (Bowler et al. 2005), which is the case in cooperative breeding species. Cooperative breeding is fairly common in birds species, as up to 13% of all birds species display this breeding strategy (Griesser et al.
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