Investigating genetic population structure and the role of social structure on residency, mating strategies and associations in a small population of bottlenose dolphins (Tursiops truncatus) under pressure

Thesis (PhD)--Stellenbosch University, 2021.

ENGLISH ABSTRACT: Small, range restricted populations are amongst the most vulnerable to human impacts. Species that show complicated social interactions through networks and cultural transmission of behaviours are even more vulnerable due to population substructure and behavioural specialisations. The current study combined 11 years of photographic mark-recapture (photo- ID) data and genetic data to investigate broadscale genetic population structure and phylogeography between bottlenose dolphin populations in Namibia and the North Atlantic/Mediterranean and the fine-scale influence of anthropogenic, behavioural and demographic factors to shape population social structure within Namibia. The overarching aim of the thesis is to provide critical information which can be used to support the future designation of protection to this population by the IUCN Red list. Following a general introduction, chapter two investigated genetic diversity, population structure, demographics and phylogeography. Indicating high inbreeding coefficients and low heterozygosity in the Namibian population, similar to other coastal populations, and low levels of historic geneflow between all populations. In chapter three a cost-effective, non-invasive method was developed to assign likely sexes to individual bottlenose dolphins, using the rate of change in dorsal fin features (trailing edge marks and surface features), with a high degree of consensus in sex predictions (79%) between features. This method provided additional data for social network analyses (with individual associations calculated using the half-weight indices (HWI)), where the various factors that may be influencing the social structure of the Namibian bottlenose dolphin population were explored (chapters four, five and six). Over the study period (2008 to 2019) the focal population was exposed to considerable changes in their marine habitat, associated with two harbour expansion projects. In chapter four changes in the social network and association metrics were investigated before, during and post- construction. During construction lower mean levels of association between individuals were observed, the residency of females with small calves (and the males that associate with them) declined, while the residency of females with larger calves and allied males increased. In chapter five the interplay of sex, age and social structure in this small population was investigated. Mixed sex groups were the most commonly encountered with strong and long- lasting associations within and between sexes. Males in this population are used two different mating strategies, alliances and the ‘nice guy’ mating strategy. In chapter six, using data from 2015 onwards, I determined that Namibian bottlenose dolphins, preferentially associated (HWI > 0.7) with those of a similar age class, sex and habitat preference and these factors influenced the use of a risky foraging habitat (shallow tidal lagoon where live strandings regularly occur), through the use of a socially learned foraging strategy. This specialised foraging strategy in the Namibian population may indicate a trajectory towards separation into behaviourally segregated communities, which may lead to fine-scale genetic differentiation over time. Separation of animals into distinct communities due to differential habitat use and ranging patterns can lead to differential exposure to anthropogenic impacts. Overall, this thesis provides much needed information of coastal bottlenose dolphins in Namibia, that will likely underpin future conservation of this population.

AFRIKAANSE OPSOMMING: Klein bevolkings wat beperk is tot klein areas is van die kwesbaarste vir mensgemaakte impakte. Spesies met ingewikkelde sosisiale interaksies, netwerke, en gadragspatrone wat kultureel oorgedra word, is selfs meer kwesbaar as gevolg van bevolkingsonderbou en gedragsspesialisasies binne reeds klein bevolkingsgroepe. Die huidige studie kombineer fotografiese merk-herkenning (foto-ID) data en genetiese data wat oor ‘n tydperk van 11 jaar ingesamel is, met die doel om die genetiese bevolkingstruktuur en genetiese bande tussen bottelneusdolfynpopulasies in Namibië en die in die Noord-Atlantiese Oseaan te ondersoek. Faktore (mensgemaak, gedrags, demografies) wat die sosiale struktuur van die bevolking kan beïnvloed word ook ondersoek. Die oorkoepelende doel van die data is om belangrike inligting by te dra wat gebruik kan word om toekomsitge beskermingsstatus deur die IUCN Rooidata- lys, aan hierdie bevolkingsgroep toe te wys. In hoofstuk twee het ek vasgestel dat hoë vlakke van strukturering en inteling en lae vlakke van heterosigositeit in die Namibiese bevolking teenwoordig was. Hierdie vlakke (heterosigositeit en inteling) was soortgelyk aan ander bevolkings wat naby die kus in die Noord-Atlantiese Oseaan voorkom, waarskynlik as gevolg van hul klein bevolkingsgroottes. In hoofstuk drie het ek 'n koste-effektiewe, nie-nadelige metode ontwikkel om die waarskynlikste geslag aan individuele bottelneusdolfyne toe te ken, deur gebruik te maak van die tempo van verandering in dorsalevin kenmerke (agterrandmerke en oppervlakkenmerke), met 'n hoë mate van konsensus in geslagsvoorspellings (93%) tussen kenmerke. Hierdie metode het addisionele data verskaf vir die ontleding van sosiale netwerke (met assosiasie gebaseer op halfgewig-indekse (HWI)), waartydens ons verskeie faktore wat die sosiale struktuur van die Namibiese bottelneusdolfynbevolking kan beïnvloed ondersoek het (hoofstukke vier, vyf en ses). Oor die studietydperk (2008 tot 2019) is die fokusbevolking blootgestel aan aansienlike veranderinge in hul mariene habitat, wat verband hou met twee hawe-uitbreidingsprojekte. In hoofstuk vier is veranderinge in die sosiale netwerk en assosiasie-metrieke voor, tydens, en na-konstruksie ondersoek. Tydens konstruksie is laer gemiddelde vlakke van assosiasie tussen individue waargeneem, die residensie van koeie met klein kalwers (en die mannetjies wat daarmee assosieer) het afgeneem, terwyl die residensie van vroulike diere met groter kalwers en verwante mannetjies toegeneem het. In hoofstuk vyf is die wisselwerking van geslag, ouderdom en sosiale struktuur in hierdie klein bevolking ondersoek. Gemengde geslagsgroepe was die mees algemeenste teëgekom met sterk en langdurige assosiasies binne en tussen geslagte. Mannetjies in hierdie bevolking gebruik twee verskillende paringstrategieë, alliansies en die “oulike-ou”-paringstrategie. In hoofstuk ses, met behulp van data vanaf 2015 en verder, het ek vasgestel dat Namibiese bottelneusdolfyne, wat meer gereeld assosieer (HWI > 0.7) met dié van 'n soortgelyke ouderdomsklas, geslag en habitatvoorkeur, 'n riskante habitat vir prooi-soek het (in die vlak gety waar lewendige strandings gereeld voorkom), deur gebruik te maak van 'n sosiaal aangeleerde vreetstrategie. Hierdie gespesialiseerde voedselsoekstrategie in die Namibiese bevolking kan 'n trajek aandui van ‘n skeiding in gedragsgesegregeerde gemeenskappe, wat kan lei tot fynskaalse genetiese differensiasie oor tyd. Skeiding van diere in afsonderlike gemeenskappe as gevolg van differensiële habitatgebruik en wisselende patrone kan lei tot differensiële blootstelling aan antropogeniese impakte. Oor die algemeen verskaf hierdie tesis broodnodige inligting van kusbottelneusdolfyne in Namibië, wat waarskynlik toekomstige bewaring van hierdie bevolking sal ondersteun.

Doctorate