Patterns of genetic diversity in vervet monkeys (Chlorocebus aethiops) from the south eastern regions of South Africa
Abstract
English: Vervet monkeys (Chlorocebus aethiops) are one of the most widely distributed
primate species in Africa. The aim of this study was to determine the level of genetic
differentiation among conspecific vervet monkey populations in the south-eastern
regions of South Africa, as part of a bigger project to determine levels of
differentiation across South Africa. For this purpose, samples were taken from four
localities in the Free State Province (Soetdoring Nature Reserve (NR), Gariep Dam
NR, Sandveld NR and the Parys area), four Eastern Cape locations (Tsolwana NR,
Baviaanskloof NR, Shamwari Private Game Reserve (PGR) and the Nelson Mandela
Metropolitan University (NMMU) campus, Port Elizabeth), three Kwa-Zulu Natal
location (St. Lucia area) and one Limpopo Province locality. Genetic differentiation
was quantified using sequence data from a portion of the mtDNA control region.
Twelve Haplotypes were identified within the total sample group. The nucleotide
diversity for each grouping was calculated over all loci. Nucleotide diversity ranged
from 0 to 0.038% ±0.02. Haplotype frequencies distribution among samples was
calculated. An analysis of Molecular Variance (AMOVA) test was conducted and
population pairwise FST values were estimated. The AMOVA test revealed that the
majority of the genetic diversity occurred among the different groups (52.5%), with
only 4.9% of the variation found within populations. The populations were assigned
to groups according to geographic origins. The pairwise analysis identified
significant levels of genetic variation among populations, with an average FST value
of 0.851. These haplotypes were found to coincide with the geographical borders of
Provinces. A ML tree was constructed using the haplotype data, and results showed
clustering corresponding to geographical borders. A phylogenetic network was
constructed, and this showed clustering similar to that found with the ML tree
analysis. According to these results it is clear that there is genetic structuring among
vervet monkey populations in South Africa. This clustering of populations can be
potentially explained by female philopatry and geographical barriers. Female
philopatry is a well known occurrence amongst Cercopithecine primates. The
occurrence of geographical barriers, such as rivers and mountains had influence on
migration rates and genetic structuring. This clustering pattern observed with
mtDNA analysis contradicts results from previous studies working with nuclear DNA
markers. This can be caused by various factors. Except for female philopatry
having an effect on mtDNA differentiation patterns, it should be noted that the faster
evolutionary rate of mtDNA vs. nuclear DNA can also cause different genetic
patterns. The effective population size of mtDNA is also four-fold smaller than that of
nuclear genes, and will also cause skewed results when comparing mtDNA data with
nuclear DNA data. No reliable recommendations can be made toward the release of
rehabilitated vervet monkeys, as further analysis is needed. It is thus suggested to
use both genetic markers in follow-up studies. An increase in sample size from a
broader geographical range is also recommended. In addition to further work on
patterns of genetic variation, the adaptive significance of observed genetic
differences should also be investigated. Afrikaans: Blouape (Chlorocebus aethiops) is een van die mees wyd-verspeide primaat spesies
in Afrika. Die doel van hierdie studie was om die vlak van genetiese differensiasie
tussen blouaap bevolkings in die suidoostelike gebiede van Suid-Afrika te
identifiseer. Hierdie studie vorm deel van 'n groter projek wat gefokus is op die
genetiese variasie van blouape regoor Suid-Afrika. Biologiese monsters was
versamel vanaf vier areas in die Vrystaat (Soetdoring Natuurreservaat (NR), die
Gariep dam area, Sandveld NR en die Parys area), vier areas in die Oos-Kaap
(Tsolwana NR, die Baviaanskloof area, Shamwarie Privaat Wildreservaat en die
NMMU kampus, Port Elizabeth) en drie Kwa-Zulu Natal areas (Blythedale Beach,
Thorny Park Estate en St. Lucia area). 'n Gedeelte van die mtDNS kontrole gebied
was gebruik vir die analiese van genetiese variasie deur middel van ONS volgorde
bepaling. "n Analiese van die Molekulêre Variasie (AMOVA) toets was gedoen en
tussen-bevolking FST waardes was bepaal. Die AMOVA toets het gewys dat die
meerderheid van die genetiese diversiteit tussen die verskillende groepe voorkom
(52.47%) en dat net 4.87% van die diversiteit binne elke populasie voorkom. Die
groepe was volgens hul geografiese oorsprong (provinsies) gegroepeer.
Betekenisvolle variasie was tussen die bvolkings gevind, met 'n gemiddelde FST
waarde van 0.851. Die nukleotied diversiteit was vir elke populasie bepaal en was
tussen 0 tot 0.038% ±0.02. Haplotiepe frekwensie verspreiding was ook bepaal.
Twaalf haplotiepes was tussen die totale proef groep gevind. Die haplotiepe
groepering was in lyn met die geografiese grense van Suid-Afrika. "n ML
filogenetiese boom was opgestel deur gebruik te maak van die bepaalde haplotiepe
data. Hierdie resultate was meer en deels in lyn met die bogenoemde haplotiepe
frekwensie data. Die konstruksie van "n haplotiep netwerk het die ML boom resultate
ondersteun. Hierdie resultate wys na defnitiewe genetiese strukturering tussen die
blouaap populasies in Suid-Afrika. Hierdie groeperings patrone kan deur twee hoof
meganismes beskryf word, naamlik vroulike trop-gebondenheid (philopatry) en
geografiese skeidings. Cercopithecine primate is bekend daarvoor dat vroulike
individue gebondenheid tot hul trop van oorsprong toon. Die tempo van migrasie en
genetiese strukturering kan ook deur geografiese skeidings, soos berge en riviere,
beïnvloed word. Die groeperings patrone wat deur mtDNS analiese waargeneem
was is teenstrydig met vorige werk wat op kern DNA gefokus het. Die vinniger
evolusionêre tempo van mtDNS teenoor kern ONS kan ook 'n invloed op genetiese
patrone hê. Die effektiewe bevolkingsgrootte van mtDNS is ook vier keer kleiner as
dié van kern ONS, en kan oneweredige resultate verskaf indien mtDNS data met
kern DNS data vergelyk word. Tot op datum kan geen betroubare aanbevelings ten
opsige van die vrylating van gerehabiliteerde blouape dus gemaak word nie,
aangesien verdere inligting benodig word. Dit word dus voorgestel dat altwee tipes
genetiese merkers vir toekomstige studies gebruik word, asook 'n groter proef groep
wat 'n groter geografiese gebied dek. Behalwe vir die addisionele werk wat op die
patrone van genetiese variasie gedoen moet word, moet die adaptiewe betekenis
van die waargenome genetiese variasie ook ondersoek word.
Collections
Related items
Showing items related by title, author, creator and subject.
-
Genetic management of the baboon population in the Suikerbosrand Nature Reserve
Bubb, Annesca (University of the Free State, 2012-10-12)Genetic management has become a critical part of the overall management of nonhuman primate populations. This dissertation describes a genetic analysis of the chacma baboon population at the Suikerbosrand Nature Reserve. ... -
Cross-species microsatellite markers for the detection of hybrids in the genus connochaetes
Wessels, Letecia (University of the Free State, 2013-07)Black wildebeest (Connochaetes gnou), a species endemic to South Africa, experienced two bottlenecks in the last century and the number of animals ultimately decreased to approximately 300. These bottlenecks led to a ... -
The application of new technologies in conservation genetics
Labuschagne, Christiaan De Jager (University of the Free State, 2016-01)English: Over the past decade, the development of high-throughput DNA techniques has expanded the scope of conservation genetics and molecular markers have become indispensable tools for the management of wildlife species ...