Diversity of microsatellite and toll-like receptor loci in South African antelopes

Project: Research

Project Details


A major focus of conservation genetics is the evolutionary consequences of reduced genetic diversity in a population (Dalton et al. 2016). Genetic diversity can be affected by habitat loss and/or fragmentation as a result of changes in human demography and behaviour as well as increasing expansion and urbanisation (Reviewed by Ryser-Degiorgis et al., 2015). Climate change was predicted to have negative effects on the distribution range of species in taxonomic groups (Wessley et al., 2017). A number of species may lose suitable climatic conditions within protected areas and move into unprotected and human-dominated surroundings potentially increasing extinction rates (Araújo et al., 2011; Hoffmann et al., 2019). In addition, other factors such as hunting and poaching is a challenge that leads to decreased genetic diversity particularly in small and isolated population of wildlife (Zeckhausera, 2017).

Maintaining genetic diversity ensures population viability as it assists with mitigating negative effects associated with inbreeding and preserves adaptive potential to future environmental change (Ballou et al., 2010; Frankham et al., 2010; Lacy, 1997). Endangered species such as the Pale-headed Brushfinch (Atlapetes pallidiceps) has been shown to have low genetic diversity in neutral markers, which indicate a recent bottleneck and limited population size (Hartmann et al., 2014).

Genetic techniques have provided essential information in conservation biology. Ecological questions that pertain to the conservation of important species can be answered using molecular methods. Currently, several studies report on loss of heterozygosity in wildlife populations based on neutral loci such as microsatellites (Agudo et al., 2011; Kirk & Freeland, 2011), however, their utility in this regard has been debated (Meyers and Bull, 2002). Although microsatellites are powerful markers to reflect inbreeding (Townsend & Jamieson, 2013) or heterozygosity fitness correlations (Forstmeier et al., 2012) they do not necessarily represent genome-wide diversity well (Vali et al., 2008). This is due to not being actively selected for under environmental constraints (Brandies et al., 2019; Hartmann et al., 2014). Increasingly, studies are being conducted that analyse the genetic diversity at immune loci which undergo selection in a population, to complement research conducted based on neutral markers. For example, in a study conducted on water-voles undergoing a natural bottleneck event, it was reported that diversity at adaptive markers was maintained, while reflecting the bottleneck at neutral sites (Matthew & Stuart, 2012). Toll-like receptor genes (TLR) are a promising site for adaptive markers which can be used in investigating adaptive genetic diversity (Alcaide & Edwards, 2011; Grueber & Jamieson, 2013). A combination of microsatellites and TLR markers therefore allows a more comprehensive assessment of the genetic diversity in a target species.

Thus far, several studies on antelope have been conducted using neutral markers, however studies on adaptive variation in these species is limited. In order to investigate the underlying factors associated with reduced genetic diversity in antelope species, we apply an innovative approach for assessing genetic diversity in the last known populations of the species. The antelope species samples will be collected from the animal Biobank SANBI to investigate the genetic diversity, population structure and phylogeny via microsatellite and TLR markers. First, we will measure genetic diversity at neutral microsatellite loci and adaptive TLR genes. We will then compare the microsatellite and the toll-like receptor diversity. Geographic separation based on their TLR will also be evaluated.
Effective start/end date3/01/22 → …


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