Thesis (MSc)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: The present study aims to determine the phylogenetic relationships among the sand lizards, Pedioplanis. In addition, a single mitochondrial gene is used to investigate the geographic genetic structure of the widey distributed P. burchelli. With 11 species, Pedioplanis is the most speciose genus among the southern African genera of the family Lacertidae. All the species are restricted to the subcontinent with the exception of three (P. namaquensis, P. undata and P. benguellensis), which extend their range northwards into Angola. A total of 2200 nucleotide positions derived from two mitochondrial markers (ND2 and 16S rRNA) and one nuclear gene (RAG-1) are used to determine the phylogenetic relationships among ten of the eleven Pedioplanis species. The first well resolved gene tree for the genus, drawn from 100 individuals, is presented and this is largely congruent with a phylogeny derived from morphology. Contrary to some previous suggestions, Pedioplanis forms a monophyletic assemblage with Heliobolus and Nucras. The genus Pedioplanis is monophyletic with P. burchelli/P. laticeps forming a sister clade to all the remaining congeners. Two distinct geographic lineages can be identified within the widespread P. namaquensis; one occurs in Namibia, while the other occurs in South Africa. The “P. undata” species complex is monophyletic, but one of its constituent species, P. inornata, is paraphyletic. Relationships among the subspecies of P. lineoocellata are much more complex than previously documented. An isolated population previously assigned to P. l. pulchella is paraphyletic and sister to the three named subspecies. The phylogeny identifies two biogeographical groupings that probably diverged during the mid-Miocene. The development of the Benguella Current could have initiated isolation mechanisms associated with changes in habitat that could have generated barriers and played a role in the evolution of this group. At the lower taxonomic level, the mtDNA phylogeographic structure of the wide spread P. burchelli in South Africa reveal at least six distinct clades that are geographically partitioned. The first one is restricted to the eastern mountains along the Great Escarpment (GE). The next three are found along the Cape Fold Mountains (CFM): the north-west CFM, central CFM and eastern CFM. The fifth one shares samples from central CFM and GE. The last clade is restricted to the eastern central mountains of the GE. These six geographic groupings are genetically divergent from each other and they started separating in the early Pliocene period. Phylogeographic studies on other taxa in the region have found different levels of genetic structuring among or within taxa. The fact that P. burchelli is restricted to high altitude areas could have resulted in limited dispersal and consequently contributed to its geographic structure. However, the exact cause of the pattern obtained is not readily apparent. Habitat fragmentation in the past is probably one of the most influential factors shaping the genetic distribution of the species across South Africa. The inclusion of nuclear markers will shed more light on the evolutionary history of P. burchelli in South Africa. / AFRIKAANSE OPSOMMING: Die huidige studie stel ten doel om ‘n filogenie daar te stel vir die Sand akkedisse, Pedioplanis. ‘n Enkele mitochondriale geen is ook gebruik om die geografiese genetiese struktuur van die wydverspreide P. burchelli vas te stel. Met 11 spesies is Pedioplanis die mees spesieryke genus onder die suidelike Afrika genera wat aan die Lacertidae familie behoort. Al die spesies is beperk tot die subkontinent met die uitsondering van drie (P. namaquensis, P. undata en P. benguellensis), wat ‘n uitgebreide verspreiding het noordwaarts tot in Angola. ‘n Totaal van 2200 nukleotied posisies wat afkomstig is van twee mitochondriale merkers (ND2 en 16S rRNA) en een nukluêre geen (RAG-1) is gebruik om die filogenetiese verwantskappe tussen 10 van die 11 Pedioplanis spesies vas te stel. Die eerste goed geondersteunde geen boom vir die genus, gebasseer op 100 individue, is verkry en dit is meestal ooreenstemmend met ‘n filogenie gebasseer op morfologie. In teenstelling met sekere voorstelle van die verlede vorm Pedioplanis ‘n monofiletiese groep tesame met Heliobolus en Nucras. Die genus Pedioplanis is monofileties met P. burchelli/P. laticeps wat ‘n suster groep vorm van al die oorblywende lede van die genus. Twee herkenbare geografiese lyne kan geidentifiseer word in die wydverspreide P. namaquensis; een kom in Namibia voor, terwyl die ander een in Suid Afrika voorkom. Die “P. undata” spesies kompleks is monofileties, maar een van die spesies wat deel uitmaak van die groep, P. inornata, is parafileties. Verwantskappe tussen die subspesies van P. lineoocellata is meer kompleks as wat aanvanklik aanvaar is. ‘n Geisoleerde bevolkimg wat voorheen toegesê is aan P. l. pulchella is parafileties en verteenwoordig ‘n suster groep van die benaamde subspesies. Die filogenie identifiseer twee biogeografiese groeperings wat moontlik gedivergeer het gedurende die middel-Miocene. Die ontwikkeling van die Benguella stroom het dalk versperrings geinisiëer as gevolg van die gesamentlike veranderinge in habitat wat dalk ook ‘n rol gespeel het in die evolusie van die groep. Op die laer taksonomiese vlak het die mtDNA filogeografiese struktuur van die wydverspreide P. burchelli in Suid Afrika ten minste ses groepe aangetoon wat geografies van mekaar geskei is. Die eerste een is beperk tot die oostelike berge wat aan die Groot Eskarpement (GE) behoort. Die volgende drie word gevind in die Kaapse Vouberge (KVB): die noord-westelike KVB, sentrale KVB en oostelike KVB. Die vyfde een deel eksemplare van beide die GE en die KVB. Die laaste groep is beperk tot die oostelike en sentrale berge van die GE. Hierdie ses geografiese groepe is geneties geskei van mekaar en hulle het begin om apart te ontwikkel gedurende die vroë Pliocene periode. Ander filogeografiese studies in die area het verskillende vlakke van genetiese struktuur vertoon tussen en binne taksa. Die feit dat P. burchelli beperk is tot hoogliggende dele kon moontlik bygedrae het tot die geografiese struktuur. Die presiese oorsaak van die patroon wat verkry is, is nie ooglopend nie. Habitat fragmentasie in die verlede is moontlik een van die mees invloedrykste faktore wat die genetiese verspreiding van die spesie in Suid Afrika beinvloed het. Die insluiting van nukluêre merkers sal meer lig warp op die evolusionêre geskiedenis van P. burchelli in Suid Afrika.

Thesis (MSc (Botany and Zoology))--University of Stellenbosch, 2006. / The role of the southern harvester termite, Microhodotermes viator, and several climatic parameters in the distribution of the group-living lizard, Cordylus cataphractus, was investigated. Microhodotermes viator is considered the most important prey item of C. cataphractus and termitophagy as the causative agent in the evolution of group-living in this species. One would therefore expect a high degree of correspondence in the ranges of C. cataphractus and M. viator. As climate will also play a role in the distribution of any species, various climatic variables were investigated to determine their influence on the distribution of C. cataphractus. Species distributions were visualized using the minimum polygon technique and the degree of overlap was determined using standard geographic information systems (GIS) techniques. A total of 53 C. cataphractus localities were investigated for the presence of termites. The climatic limits of the geographical distribution of C. cataphractus were investigated by means of three models, namely Classification Trees, General Discriminant Analysis and Logistic Regression. The range of C. cataphractus was completely included within the range of M. viator Microhodotermes viator was included in the diet of C. cataphractus at 73 % of the localities sampled within the lizard’s range. The current geographical range of C. cataphractus is mainly correlated with two climatic factors, namely the low summer rainfall and high monthly solar radiation. The restricting role of both these factors can be directly linked to the group-living nature of C. cataphractus. If termitophagy were the overarching cause of group-living in C. cataphractus, then one would expect a close relationship between termite density and lizard density and termite density and lizard group size. I investigated these relationships at both a local and regional scale. For the local scale study, 25 quadrats of 25 × 25 m were plotted at a selected site, and for the regional scale study, ten 35 × 35 m quadrats at sites throughout the lizard’s range were used. In each quadrat, a range of variables were recorded, the most important of which were lizard density, lizard group sizes, termite foraging port density, distance to nearest termite foraging ports, vegetation height and vegetation cover. I found that the density of termite foraging ports determines C. cataphractus density. Vegetation height and cover affects crevice selection by C. cataphractus groups, probably because an unobstructed view is necessary to locate termite activity at foraging ports. I also investigated possible differences in the use of termites by different sized groups of C. cataphractus during different times of the year. Faecal samples, collected once a month at Eland’s Bay from small, medium and large groups from January 2005 to December 2005, were analysed for the presence of termite head material. I found that large groups fed on termites to a greater extent than small groups during certain times of the year and there was a general tendency for this phenomenon throughout the year. The results collected in this study indicate that the southern harvester termite, M. viator, plays a central role in the ecology of the group-living lizard, C. cataphractus.

Dissertation (PhD)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: The taxonomic status of southern Africa’s rupicolous crag lizards (genus Pseudocordylus) was investigated. As considerable confusion exists in the literature regarding the type specimens and type localities of the various taxa, resolution of these problems were considered the starting point of the study. Examination of museum specimens allowed for the designation of lectotypes, alloparalectotypes and/or paralectotypes. Of particular relevance to this study was the rediscovery of Andrew Smith’s type specimens of P. m. melanotus and P. m. subviridis. Restriction of the type locality of P. m. subviridis, based on entries in Smith’s diary and journal, allowed for the confirmation of previous interpretations and definitions of the two taxa. The geographical distribution of the various taxa and populations was determined using an extensive locality database. Two kinds of molecular markers, namely allozymes and mitochondrial DNA, were used in an attempt to resolve taxon boundaries within the P. melanotus species complex. The allozyme analysis indicated that P. m. melanotus might be polyphyletic and comprised of two unrelated lineages. Furthermore, fixed allelic differences between parapatric populations of P. m. melanotus and P. m. subviridis, and between sympatric populations of P. m. subviridis and P. langi, suggested that all three forms might be considered full species, with the possibility of more cryptic species present in the complex. Pseudocordylus transvaalensis differed from most other populations by 1-3 fixed allelic differences, but was indistinguishable from the Nkandhla district (central KwaZulu-Natal) population of P. m. melanotus. There were no heterozygous individuals in a sample from Monontsha Pass (Qwa-Qwa), a population reportedly comprising P. m. melanotus and P. m. subviridis, as well as intermediates, and all specimens were assignable to P. m. subviridis. The allozyme study was, however, based on phenetic principles and for further taxonomic resolution a cladistic approach was required. An mtDNA analysis (16S rRNA gene) using Maximum Parsimony, Maximum Likelihood and Bayesian analyses was therefore conducted to determine phylogenetic relationships among species and subspecies and to re-assess the taxonomic status of forms in the P. melanotus species complex. The mtDNA analysis corroborated most of the results obtained in the allozyme analysis. Firstly, P. langi was again found to be basal. With the addition of P. microlepidotus and P. spinosus to the ingroup, it is now apparent that P. langi is the basal species in the genus. (Recent studies have indicated that P. capensis and P. nebulosus are not congeneric with Pseudocordylus.) Secondly, the 16S rRNA results confirm that P. m. melanotus, as presently construed, is comprised of two clades that are not sister groups. The northern populations of P. m. melanotus (Sabie and Lochiel) form a fairly deeply divergent clade that may represent a separate species. The Nkandla population was, however, found to cluster with the other southern P. m. melanotus populations and not with P. transvaalensis as was the case in the allozyme electrophoretic analysis. However, the most surprising result of the 16S rRNA analysis was the finding that both P. microlepidotus and P. spinosus are embedded within P. m. subviridis. This suggests that these two species evolved from within P. m. subviridis and may have been separated only recently, with rapid morphological divergence occurring, but with limited genetic differentiation. It is suggested that all of the above three taxa be provisionally treated as full species. There was also morphological support for the uniqueness of all groupings indicated by the mtDNA analysis. Pseudocordylus transvaalensis is characterized by its large size, unique dorsal and gular (black) colour patterns, as many as three horizontal rows of lateral temporal scales, a series of small scales posterior to the interparietal scale, and usually two subocular scales behind the median subocular on either side of the head. The various populations currently classified under the name P. melanotus are more difficult to separate, but P. m. melanotus and P. m. subviridis usually differ as follows: frontonasal divided in P. m. melanotus, undivided in P. m. subviridis (and most Northern melanotus); lateral temporals in two rows, upper more elongate versus single row of much elongated scales; longitudinal rows of dorsolaterals closely-set versus widely separated; femoral pores of females pit-like versus deep with secretory plug. Northern melanotus differs from Southern melanotus in usually having an undivided frontonasal scale and seldom having a small scale present behind the frontonasal. Pseudocordylus langi has unique dorsal and gular colour patterns (including a series of blue spots on the flanks), granular dorsals with 6-9 paravertebral rows of enlarged flat scales, high total numbers of femoral pores (25-34) and usually only five (smooth not keeled or ridged) infralabial scales on either side of the head. Pseudocordylus spinosus also has unique dorsal and gular colour patterns, spinose lateral scales, frontonasal longer than wide and excluded from the loreal scales, low total femoral pore counts (6-9), and females (not only males) have differentiated femoral scales. Both Principal Components Analysis (PCA) and Canonical Discriminant Analysis (CDA) distinguished four groups, namely P. transvaalensis, P. langi, P. spinosus and a P. melanotus/subviridis/microlepidotus cluster. A separate CDA of all P. melanotus populations partly distinguished between Southern melanotus and P. m. subviridis, and largely separated Northern melanotus; whereas a CDA of P. transvaalensis showed that all three allopatric populations are 100% distinguishable in morphological space. A Nested Clade Analysis indicated that fragmentation as well as range expansion played a role in the distribution of the P. melanotus species complex. This may be explained by climatic oscillations (high-low temperatures and wet-dry cycles) during the Cenozoic that caused habitat expansion and contraction. Based on the topology of the mtDNA phylogram it is apparent that the genus Pseudocordylus originated along the eastern escarpment. A P. langi-like ancestor may have had an extensive range along the eastern escarpment, with the Maloti-Drakensberg forming the southern limit of its range. During a subsequent rise in global temperatures, range contraction and fragmentation took place, leaving an isolated population in the south and one in the north. The southern population survived unchanged in the Maloti-Drakensberg refugium, but the northern population was forced to adapt to the warmer conditions. Thereafter, the northern form expanded its range again, but during a subsequent cooler period, range contraction occurred, resulting in an isolated north-eastern population in the Sabie-Lochiel area in Mpumulanga (Northern melanotus) and a western population. Relationships in the latter clade are not sufficiently resolved to allow further reconstruction of biogeographic history, but it is clear that a P. m. subviridis-like form became isolated in the south where it eventually came into contact with P. langi at high elevations. Pseudocordylus m. subviridis eventually extended its range southwestwards into the inland mountains of the Eastern Cape and Cape Fold Mountains to give rise to the P. microlepidotus complex. This cycle of range expansion and contraction may also account for the isolated populations at Suikerbosrand, Nkandhla district, and in the Amatole-Great Winterberg mountain region. Furthermore, it is suggested that P. spinosus originated from a P. m. subviridis-like ancestral population that became isolated on the lower slopes of the Drakensberg where terrestrial predation pressure resulted in a quick shift in morphology from fairly smooth body scales to a more spiny morphology. / AFRIKAANSE OPSOMMING: Die taksonomiese status van suidelike Afrika se rotsbewonende krans-akkedisse (genus Pseudocordylus) is ondersoek. Omdat daar aansienlike verwarring in die literatuur bestaan met betrekking tot die tipe monsters en die tipe lokaliteite van die verskillende taksa, is die oplossing van hierdie probleme as die beginpunt van hierdie studie geneem. Die bestudering van akkedismonsters in museums het dit moontlik gemaak om lektotipes, alloparalektotipes en/of paralektotipes aan te wys. Van besondere belang vir hierdie studie is die herontdekking van Andrew Smith se tipe monsters van P. m. melanotus en P. m. subviridis. Die beperking van die tipe lokaliteit van P. m. subviridis, gebaseer op inskrywings in Smith se dagboek en joernaal, het dit moontlik gemaak om vorige interpretasies en definisies van die twee taksa te bevestig. Die geografiese verspreiding van die verskillende taksa en bevolkings is bepaal deur middel van ’n omvattende lokaliteit databasis. Twee soorte molekulêre merkers, naamlik allosieme en mitokondriale DNS, is gebruik in ʼn poging om uitsluitsel te verkry oor die takson-grense binne die P. melanotus-spesiekompleks. Die allosiem-analise het daarop gedui dat P. m. melanotus moontlik polifileties mag wees en uit twee onverwante stamboom-vertakkings kan bestaan. Verder het vaste alleliese verskille tussen parapatriese bevolkings van P. m. melanotus en P. m. subviridis, en tussen simpatriese bevolkings van P. m. subviridis en P. langi, daarop gedui dat al drie vorme as volledige spesies beskou kan word, met die moontlikheid dat meer kriptiese spesies in die kompleks teenwoordig kan wees. Pseudocordylus transvaalensis het van die meeste ander bevolkings verskil met 1-3 vaste alleliese verskille, maar was ononderskeibaar van die bevolking van P. m. melanotus van die Nkandhla distrik (sentraal KwaZulu-Natal). Daar was slegs homosigote individue in ʼn steekproef van Monontsha Pas (Qwa-Qwa), ʼn bevolking wat volgens die literatuur P. m. melanotus en P. m. subviridis, sowel as intermediêre omvat, en alle monsters was toekenbaar aan P. m. subviridis. Die allosiemstudie is egter gebaseer op fenetiese beginsels en vir verdere taksonomiese oplossing is ʼn kladistiese benadering vereis. ʼn Mitokondriale DNS-analise (16S rRNS geen) wat gebruik maak van Maksimum Parsimonie-, Maksimum Waarskynlikheids- en Bayes-analises is daarom uitgevoer om die filogenetiese verwantskappe tussen spesies en subspesies te bepaal en om die taksonomiese status van vorme in die P. melanotus-spesiekompleks te herondersoek. Die mtDNS-analise het die meeste van die resultate van die allosiem-analise bevestig. Eerstens, P. langi is weer bevind om basaal te wees. Met die byvoeging van P. microlepidotus en P. spinosus tot die binne-groep het dit nou duidelik geword dat P. langi die basale spesie in die genus is. (Onlangse studies het aangedui dat P. capensis en P. nebulosus nie kongeneries met Pseudocordylus is nie.) Tweedens, die 16S rRNS resultate bevestig dat P. m. melanotus, soos tans vasgestel, saamgestel is uit twee klade wat nie sustergroepe is nie. Die noordelike bevolkings van P. m. melanotus (Sabie en Lochiel) vorm ʼn redelik diep divergente klaad wat ʼn afsonderlike spesie mag verteenwoordig. Dit is egter bevind dat die Nkandla bevolking saamgegroepeer het met die ander suidelike P. m. melanotus-bevolkings en nie met P. transvaalensis soos wat die geval was in die allosiem-elektroforetiese analise nie. Die mees verbasende resultaat van die 16S rRNS-analise was egter die bevinding dat beide P. microlepidotus en P. spinosus genestel was binne P. m. subviridis. Dit dui daarop dat hierdie twee spesies kon ontwikkel het vanuit P. m. subviridis en slegs onlangs van mekaar geskei het, toe vinnige morfologiese splitsing voorgekom het, maar met beperkte genetiese differensiasie. Dit word voorgestel dat al drie die bogenoemde taksa voorlopig as volledige spesies beskou word. Daar was ook morfologiese steun vir die uniekheid van al die groeperings wat die mtDNS-analise uitgewys het. Pseudocordylus transvaalensis kan uitgeken word aan sy bogemiddelde grootte, unieke dorsale en (swart) kleurpatrone op die keel, so veel as drie horisontale rye lateraaltemporale skubbe, ʼn reeks klein skubbe agter die interpariëtale skub, en gewoonlik twee subokulêre skubbe agter die middelste subokulêre skub op beide kante van die kop. Die verskillende bevolkings wat tans geklassifiseer word as P. melanotus is moeiliker om van mekaar te skei, maar P. m. melanotus en P. m. subviridis verskil gewoonlik soos volg: frontonasale skub in twee gedeel in P. m. melanotus, heel in P. m. subviridis (en in die meeste Noordelike melanotus); lateraal-temporale skubbe in twee rye, die boonste ry met verlengde skubbe teenoor ʼn enkele ry verlengde skubbe; longitudinale rye van dorsolaterale skubbe naby aan mekaar teenoor ver uit mekaar; femorale porieë van wyfies klein en vlak teenoor diep met sekreterende proppe. Noordelike melanotus verskil van Suidelike melanotus deurdat hulle gewoonlik ʼn heel frontonasale skub het en daar selde ʼn klein skub teenwoordig is agter die frontonasale skub. Pseudocordylus langi het unieke dorsale en keel-kleurpatrone (wat ʼn reeks blou kolle op die sye insluit), granulêre dorsale skubbe met 6-9 rye vergrote plat skubbe langs die rugsteen, ʼn groot totale aantal femorale porieë (25-34), en gewoonlik net vyf (glad, ongerif) infralabiale skubbe op elke kant van die kop. Pseudocordylus spinosus het ook unieke dorsale en keel-kleurpatrone, skerp laterale skubbe, frontonasale skub langer as wyd en nie in kontak met die loreale skubbe nie, klein totale aantal femorale porieë (6-9), en wyfies (nie net mannetjies nie) het gedifferensieerde femorale skubbe. Die Hoof-komponent Analise (HKA) en die Kanonieke Diskriminant Analise (KDA) het albei vier groepe geïdentifiseer, naamlik P. transvaalensis, P. langi, P. spinosus en ʼn P. melanotus/subviridis/microlepidotus groepering. ʼn Aparte KDA van alle P. melanotus bevolkings het gedeeltelik onderskei tussen Suidelike melanotus en P. m. subviridis, en die Noordelike melanotus is grootliks van die ander onderskei; terwyl ʼn KDA van P. transvaalensis daarop gedui het dat al drie allopatriese bevolkings 100% onderskeibaar in morfologiese ruimte is. ʼn Genestelde Klaad-Analise het aangedui dat fragmentasie, sowel as gebiedsuitbreiding, ʼn rol gespeel het in die verspreiding van die P. melanotus-spesiekompleks. Dit kan moontlik verklaar word deur die klimaatswisselinge (hoë-lae temperature en nat-droë siklusse) gedurende die Senosoikum wat habitat-uitbreiding en –verkleining veroorsaak het. Gebaseer op die topologie van die mtDNS filogram is dit duidelik dat die genus Pseudocordylus al langs die oostelike platorand ontstaan het. ʼn Voorouer soortgelyk aan P. langi kon ʼn uitgebreide gebied al langs die oostelike platorand gehad het, met die Maloti-Drakensberg wat die suidelike limiet van hierdie gebied gevorm het. Gedurende ʼn daaropvolgende toename in globale temperature het gebiedsverkleining en fragmentasie plaasgevind, wat ʼn geïsoleerde bevolking in die suide en een in die noorde tot gevolg gehad het. Die suidelike bevolking het onveranderd oorleef in die Maloti-Drakensberg skuilplek (“refugium”), maar die noordelike bevolking is geforseer om aan te pas in die warmer toestande. Daarna het die noordelike vorm se gebied weer uitgebrei, maar gedurende ʼn daaropvolgende koeler periode het gebiedsverkleining weer plaasgevind, met die gevolg dat daar ʼn geïsoleerde noord-oostelike bevolking in die Sabie-Lochiel-area in Mpumalanga (Noordelike melanotus) en ʼn bevolking in die weste was. Verwantskappe in die laasgenoemde klaad is nie voldoende opgelos om verdere rekonstruksie van die biogeografiese geskiedenis moontlik te maak nie, maar dit is duidelik dat ʼn vorm soortgelyk aan P. m. subviridis geïsoleer geraak het in die suide waar dit eindelik op hoë liggings in kontak gekom het met P. langi. Die gebied van P. m. subviridis is ook later suidweswaarts uitgebrei tot in die binnelandse berge van die Oos-Kaap en Kaapse Plooiberge om tot die ontstaan van die P. microlepidotuskompleks aanleiding te gee. Hierdie siklus van gebiedsuitbreiding en verkleining kan ook ʼn verklaring bied vir die geïsoleerde bevolkings by Suikerbosrand, Nkandhla distrik, en in die Amatole-Groot Winterberg-streek. Verder word voorgestel dat P. spinosus ontstaan het uit ʼn voorouerlike bevolking soortgelyk aan P. m. subviridis wat geïsoleerd geraak het op die laer hange van die Drakensberg waar die druk van aardsbewonende roofdiere tot ʼn vinnige verandering in morfologie vanaf redelik gladde liggaamskubbe tot ʼn meer skerppuntige morfologie gelei het.

Demographic changes, through immigration/emigration (or death) can affect the social and community structure of a population. This study reports on the effects of demographic changes following 2 intense hurricanes on two sympatric delphinid species: Atlantic bottlenose dolphins, Tursiops truncatus, and Atlantic spotted dolphins Stenella frontalis. Thirty percent of the bottlenose population was lost after the hurricanes, with an influx of roughly the same number of immigrants. The stable community split into two cohesive units. Preferences in association in relation to reproductive status and sex remained. Immigrants assimilated well into the population, especially males. There is a conflict of interest between resident males and females in accepting immigrants and often females find more resistance than males. Long-term analysis of spotted dolphins revealed a community structure defined by long-term site fidelity, natal philopatry of both sexes and three social clusters. / Female associations were influenced by reproductive status and social familiarity within clusters. Males formed long-term alliances and shorter-term coalitions. Some movement between clusters occurred. Alliance formation crystallized in adulthood. Mating strategies and sex were the primary factors shaping social structure. Thirty-six percent of the spotted dolphin population was lost after the hurricanes with no influx of immigrants. The spotted dolphin community differed little from long-term analysis, including definitive social clusters and sex preferences. Social cohesion increased within units and across age classes. Some juveniles had associations of alliance level. Loss of individuals resulted in subtle changes in social structure. Interspecies associations reveal striking differences in association patterns between species. Group sizes and re-sightings of spotted dolphins were larger than for bottlenose dolphins, particularly for aggressive encounters. / Male alliances and coalitions were prevalent for spotted dolphins, but not for bottlenose dolphins. After the hurricanes lower re-sighting and group sizes for spotted dolphin males and less aggressive behavior documented, indicates a re-structuring period of relationships between the species. This study shows that environmental variations may alter the structure of mammal societies through demographic upheaval and survival of populations may depend on their social structure and the social adaptability of the species. / by Cindy Rogers Elliser. / Thesis (Ph.D.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

This study investigated a resident community of Atlantic spotted dolphins (Stenella frontalis) on Little Bahama Bank (LBB) in the Bahamas utilizing a noninvasive molecular approach. Genetic template material was collected and extracted from fecal material of S. frontalis. Fine-scale population structure was found within LBB according to mitochondrial DNA (mtDNA) and microsatellites (Fst = 0.25317, P < 0.0001 and Fst = 0.04491, P < 0.0001, respectively). Three main social clusters (North, Central, South/Roam) exist on LBB and all clusters were found to be genetically distinct according to microsatellite analyses. Mitochondrial haplotypes revealed North and South/Roam were not differentiated, but Central was different from both. When separated by sex, males were less genetically structured than females. Males showed no evidence of structure according to Ost or Rst. / Females of all clusters were differentiated according to microsatellites whereas mtDNA revealed the same pattern in females as was seen for the total population. The structuring patterns of the sexes clearly indicate a pattern of male dispersal and female philopatry for the LBB population. Genetic investigation of mating revealed patterns in the mating system of S. frontalis on LBB. Genotypes of females and offspring were analyzed and revealed that more than two males were required to explain the progeny arrays, indicating promiscuous mating among females. In addition, paternity assessment assigned seven males as fathers to ten of 29 mother-calf pairs. A pattern of reproductive skew according to age was revealed because reproductively successful males were in the oldest age class at the estimated time of conception of the calves. / Patterns in social cluster mating revealed that males from the Central cluster sired offspring with females from both the Central and North clusters, while Roaming males sired offspring with South and Central females indicating that males mate within their social cluster or with females from the next closest cluster. The study has important implications for cetacean research, specifically delphinids. Fine-scale population structure and mating patterns of male and female S. frontalis were revealed through noninvasive methodology presenting a valuable genetic framework with which to support ongoing investigations of life history, behavior, communication and social structure. / by Michelle Lynn Green. / Vita. / Thesis (Ph.D.)--Florida Atlantic University, 2008. / Includes bibliography. / Electronic reproduction. Boca Raton, FL : 2008 Mode of access: World Wide Web.

Worldwide research of bottlenose dolphins (Tursiops truncatus) has led to varied definitions and terminology regarding ways to group dolphins for study and management. An understanding of the demographic history and population structure of bottlenose dolphins residing within the Indian River Lagoon Estuary System (IRLES), Florida, is needed to help define the IRLES dolphin population: ecotype, population, or community. Using mitochondrial DNA sequencing and microsatellite genotyping, this study detected: (1) genetic differentiation between estuarine and coastal individuals (FstmtDNA=0.414, Fstmsat=0.057; p<0.05; K=2), (2) genetic differentiation between the Indian River Lagoon (IRL) and Mosquito Lagoon (ML) (FstmtDNA=0.0201, Fstmsat=0.0234; p<0.09), and (3) minute undefined sub-structure within the IRLES (FstmtDNA=-0.00 -0.0379, Fstmsat=0.00 - vii 0.0445; p>0.1). Additionally, within ML this study detected non-mixing cohabitation of two potential ecotypes, estuarine and coastal. These findings raise many questions regarding how dolphins are presently categorized and managed which are critical to population assessments including abundance, vital rates, and health. / by Sarah E. Rodgers. / Thesis (M.S.)--Florida Atlantic University, 2013. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.

The Major Histocompatibility Complex (MHC) encodes proteins critical to the vertebrate immune response; therefore MHC diversity is an indicator of population health. I have (1) Isolated exon 2 of the class II gene DQA in Tursiops truncatus in the North Indian River Lagoon (IRL) (n=17), South IRL (n=29) and adjacent Atlantic waters (n=20), (2) assessed genetic variability between groups, (3) developed a method to genotype individuals, (4) typed 11 unique alleles in 66 individuals, (5) detected geographic patterns of diversity between estuarine and coastal individuals (FST=0.1255, p<0.05), (6) found evidence of positive selection centered in the binding pockets P1, P6 and P9 of the peptide binding region (w=2.08), (7) found that patterns of polymorphism did not closely match patterns of diversity in neutral markers, (8) performed a pilot study with Orcinus orca. The initial findings highlight the need for further comparative work and suggest that silent mutations are not neutral. / by Tatiana Ferrer. / Thesis (M.S.)--Florida Atlantic University, 2013. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.

This study examines the spatial and temporal distribution and life history of the "offshore" component of the Northeastern Pacific spiny dogfish (Squalus acanthias) population. Distribution was examined in relation to latitude, depth, the Columbia River plume and large-scale climate changes. Fishery and survey data indicate that the Northeastern Pacific spiny dogfish population has a broad range along the Washington and Oregon coasts, with the highest abundance occurring off the northern Washington and central Oregon coasts. Catches, however, were patchy throughout the 37-year period of available survey data. In terms of depth, the greatest abundances of spiny dogfish were captured in shallow waters (55-184 m). An examination of the influence of the Columbia River plume using a generalized additive model (GAM) indicated that the fish were influenced significantly by the salinity, chlorophyll and surface temperature patterns associated with the plume, preferring the oceanic zone to the plume zone. In contrast, there was no indication that the catch-per-unit-effort of spiny dogfish was influenced by the Pacific Decadal Oscillation (PDO) or the El-Niño (ENSO) over 24-year period of the National Marine Fisheries (NMFS) triennial shelf groundfish survey (1977-2001). The multi-cohort age structure of the population, due to the spiny dogfish's late age at maturity and long lifespan, as well as the low fecundity make it difficult to detect the loss of a single cohort or two when examining abundance trends. Moreover, effects on abundance may be time-lagged, especially if, as is likely, the youngest cohort(s) is the most vulnerable life stage. Their absence would not become evident until they were large enough to have been captured by the survey gear. Sensitive abundance data and/or age-structured data would be needed to identify a pattern. I quantified the age, maturation and fecundity of the spiny dogfish and use these data to develop an age-structured matrix model to examine the sensitivity of the population's growth rate to changes in mortality (i.e. fishing). Female spiny dogfish in this population have an average age at 50% maturity of 28 years and males 20 years. Average length at 50% maturity was 85.0 cm for females and 71.5 cm for males. Female fecundity was extremely low, averaging eight pups per clutch biennially and ranging from four to 14. The number of pups increased with length, but not age. Using these data, a deterministic, female-based model was developed. Asymptotic population growth rate (λ) was determined to be very low, 1.01, and comparable to population growth rates calculated for "coastal" populations. When fishing mortality was incorporated into the model, the fishery was only sustainable when exploitation was low and strict size limits enforced. When fecundity was doubled, the population growth rate increased from 1% to 3% per year. This 33% increase in population growth was equivalent to the effect of a decrease in the age at first maturity of three years. Given that responses to changes in population demographics through shifts in fecundity or spawning frequency are likely constrained, responses would then seem likely to involve changes in age at maturity. These life history traits translate into a low potential population growth and as a consequence high susceptibility to overfishing. My findings indicate that the Northeastern Pacific spiny dogfish are relatively slow growing, late to mature, and have low fecundity and a patchy distribution, with large catches occurring off the northern Washington and central Oregon coasts in shallow waters (55-184 m). These life history traits and distributional patterns are useful in the development of population models to predict responses to environmental fluctuations or increased mortality and thus the management of the population. It is evident from my findings that periodic monitoring is necessary to track possible catch declines off the northern Washington and central Oregon coasts and prevent collapse of the population should it be targeted by a fishery and overfishing occur. / Graduation date: 2005

In arid and semi-arid deserts, soils are commonly covered with biological soil crusts. The study of arid biocrusts and their ecological function has become increasingly common in the literature over the last several decades. Interestingly, no mention is made of biological soil crusts in forested ecosystems, raising the question as to whether they exist in these areas and if they do, why they have yet to be recognized as such? Through the use a parallel logic, this study finds that biocrusts do indeed exist in forests, a novel relationship in forest ecology and seeks to determine if there exist ecophysical explanations for the abundance and distribution throughout the forest landscape. This study examined the effects of climate variables and substrate types on the abundance, distribution and overall cover of forest soil biocrust at fifty-two sites in southern Oregon, U.S.A. Sites were randomly selected within established buffer zones in the Siuslaw, Rogue-Sisikyou, Umpqua, and Fremont-Winema National Forests. The methods of Belnap et al 2001 were tested and then modified for application in forested ecosystems. Data were collected on the relative abundance and distribution of biocrust morphological groups across available substrates, community biocrust morphology, aspect, elevation and soil texture, pH and organic matter content. Site-specific data on average annual precipitation and minimum/maximum temperatures was collected using the PRISM Climate Model. This study found substrate colonization by specific morphological groups mixed across the study; though dominant communities were observed for each substrate present, substrate availability appears to be confounded by a number of variables (climate, stand age and structure and litter layer) not controlled for in this study. Biocrust community morphologies varied across sites, primarily influenced by the surface texture of the substrate and morphology of the individual. Relatively smooth surfaces (rock, bare soil) often resulted in smooth biocrust morphologies, whereas rough surfaces (dead wood, bare soil) tended to result in a rolling morphology. Litter layer directly influenced the relative proportion of substrates colonized, notably affecting dead wood and mineral soil biocrusts. Total biocrust cover increased as precipitation increased as did biocrust preference for dead wood substrates while mineral soil remained unchanged and rock surfaces were negatively represented. Aspect generally followed the anticipated distribution of total biocrust cover with the highest cover on N and NW aspects and lowest on the W aspect. Increases in elevation were negatively related to overall biocrust cover. Soil texture was not found to be directly related to overall biocrust cover, attributed in part to the highly adaptive nature of the biocrust community. Soil organic matter (SOM) influenced total biocrust cover with positive correlations between total cover and increasing SOM content. Soil pH increased as expected across the precipitation range (17 to 159 in/yr) of the transect. Total biocrust cover was found to trend with soil pH, but is believed to be attributed to the parallel relationship between precipitation and pH, rather than pH alone given the relative moderate pH range (4.39 to 6.54) of the study. The distribution and abundance of forest soil biocrusts is strongly influenced by precipitation. The confounding influence of precipitation to litter layer depth and organic matter content (through gradients of vegetative productivity) and soil pH further are concluded to influence substrate preference by morphological groups. Across the variables examined, similarities between the two communities (arid and forest) in response to climate and soil chemistry show parallel relations, justifying the formal establishment of biological soil crust community in forested regions. The differences between communities related to the presence of trees validate the establishment of forest soil biocrusts as distinct community in both form and ecological function with the forests. / Graduation date: 2013

A new sampling method that decouples spatial and environmental correlations was developed and applied to a temperate forest understory. Data were used to contrast niche theory with neutral theory, and only showed support for niche theory. A spatial and environmental partitioning analysis indicated that the effects of dispersal are primarily important within the spatial extent of environments suitable for a given species. The same sampling data were used to test correlates of non-native species invasion at a species level and as a group. The distributions of non-native plant species are also better explained by the niche model; however, non-native species do not appear to negatively impact native species, nor to be negatively impacted by native species. Together, these results suggest that the forest understory is strongly niche-structured, but likely not saturated. Diversity in this forest appears to be primarily determined by regional processes, and only secondarily by local species interactions.