Thesis (MSc)--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: This study examines the phylogeography of the southern African vlei rat, Otomys irroratus using the mtDNA cyt b gene and chromosomal data derived using G-, and C-banding, Ag-NOR staining and fluorescence in situ hybridization (FISH using flow sorts of Myotomys unisulcatus). A total of N = 102 specimens were used from the Western Cape, Eastern Cape, Northern Cape, Free State, Mpumalanga and KwaZulu-Natal provinces of South Africa. Of the N = 102, N = 55 comprised fresh material while N = 47 comprises museum material obtained from the Durban Natural Science Museum of South Africa. Cytogentic analysis of N = 55 specimens collected from seven localities in South Africa revealed intra-specific variation resulting from two rearrangements, namely pericentric inversions and heterochromatin variation. Of the 55 specimens that were analyzed 47% contained inversions or centromeric shifts on four autosomes (OIR1, OIR4, OIR6 and OIR10) which were present singly in specimens (i.e. none of the specimens contained all four inversions concurrently). These inversions were present in both homozygous and heterozygous state over a wide geographic range suggesting that they are floating polymorphisms. Given the potential role of inversions in post-mating isolation (through production of aneuploid gametes), the prevalence of inversions as floating polymorphisms in the vlei rats suggest that they are probably retained in the population through suppression of recombination in the inverted regions of the chromosomes. In addition, differences between populations is due to the presence or absence of heterochromatic arms (and not inversions), which cause variation in the NFa (40 – 49) and supernumerary B chromosomes, resulting in the variation in diploid number (2n = 28 – 32). Analysis of N = 55 specimens revealed Ag-NORs on 7 autosomal pairs 1, 2, 5, 7, 8 and 9 proximal to the centromere on the short arm of the chromosome. Pair 8 also displayed Ag-NOR at the distal end of the long arm of the chromosome in individuals from the Free State province. Pair 3 showed two Ag- NORs occurring proximal to the centromere on the short arm and on the terminal end of the long arm, respectively. I obtained 953bp of mtDNA cyt b from fresh material and 400bp from museum material. Using maximum parsimony and Bayesian inference two main clades were retrieved. Clade A specimens occur mainly in the Western and Eastern Cape provinces of South Africa. Clade B specimens occur in the Eastern Cape, Free State, KwaZulu-Natal, Northern Cape and Mpumalanga provinces of South Africa. The mean sequence divergence between the main clades (A and B) is 7.0% and between sub-clades comprising clade B is 4.8%, while within clade A the sequence divergence was 1.91%. Nested clade analysis revealed allopatric fragmentation within O. irroratus. Chromosomal characters also support the two evolutionary lineages as clade A has pericentric inversions which occur as floating polymorphisms which are absent in clade B. Clade B in turn is fixed for a complex tandem fusion rearrangement which is absent from clade A. Divergence date estimates indicate that the two clades separated around 1.1 MYA, which coincides with climate changes since the late Pliocene/Pleistocene epochs. Cladogenesis within this species complex could therefore have been influenced by habitat fragmentation. A full taxonomic review of O. irroratus is therefore warranted by this study. / AFRIKAANSE OPSOMMING: Die suider Afrikaanse vlei rot, Otomys irroratus word gekenmerk deur fenotipiese konservatisme regoor die spesie se verspreiding en het groot chromosomale variasie met diploied chromosoom getalle wat reeks vanaf 2n = 23 tot 2n = 32. Hierdie variasie binne O. irroratus het gelei tot die beskrywing van drie chromosomale groupe naamlik die A sitotipe wat gekenmerk word deur 'n akrosentriese komplement. Die tweede groep wat die B sitotipe genoem word besit ten minste agt chromosoom pare met heterokromatiese kort arms, onderwyl die derde group (die C sitotipe) vier chromosoom pare het met heterokromatiese kort arms. Hierdie studie bestudeer die bevolkings genetika struktuur van O. irroratus deur 102 monsters te analiseer wat gekollekteer was regoor die spesie se verspreiding binne Suid-Afrika en die mitochondriale merker sitokroom b sowel as chromosoom fluoressent hibridisasie te gebruik. Ek het 55 monsters van sewe lokaliteite binne Suid-Afrika sitogeneties geanaliseer deur gebruik te maak van G- en C-bandbepaling asook die hibridisasie patrone geproduseer deur die vloeisorteerde chromosoome van Myotomys unisulcatus. Die analise het gewys dat 47% van die monsters perisentromeriese inversies besit het, wat slegs aangetref was of die outosome OIR1, OIR4, OIR6 en OIR10. Hierdie inversies was nooit almal teenwoordig binne dieselfde monster nie en was gevind in beide heterosigotiese en homosigotiese vorm. Die inversies kom ook voor oor 'n wye verspreiding wat daarop aandui dat dit swerwende polymorfisme is. Omdat inversies lei tot die produksie van aneuploiede gamete speel hulle 'n belangrike rol in post-parings reproduktiewe isolasie, die verskyning van swerwende inversies binne vlei rotte dui dus daarop dat hulle onderhou word binne populasie verband deur die onderdrukking van rekombinasie in die gedeeltes van die chromosoom. Verdere verskille tussen populasies behels die voorkoms of afwesigheid van heterochromatiese kort arms wat (nie inversies) wat lei tot die variasies in die Nfa (40 – 49). Die variasie in diploied getal (2n = 28 – 32) is eksklusief as gevolg van B chromosoome. Ag-NOR banding het ook gewys dat daar twee evolusionêre lyne binne O. irroratus voorkom. Verder het filogenetiese analise van al die monsters verkryg deur volgorde-bepaling met behulp van maksimale parsimonie en Bayesian afleiding twee klades geidentifiseer. Klade A diere kom voor in die Wes en Oos-Kaap provinsies van Suid-Afrika terwyl klade B diere voorkom in die Oos-Kaap, Vrystaat, KwaZulu-Natal, Noord-Kaap en Mpumalanga provinsies onderskeidelik van Suid-Afrika. Die gemiddelde volgorde-bepalings verskille beloop 7% tussen die twee hoof klades (A en B) en tussen sub-klades 4.8%, terwyl binne klade A die verskille slegs 1.91% beloop het. Analise van die verwantskap tussen die klades het gewys dat allopatriese fragmentasie heel waarskynlik gelei het tot die populasie genetiese struktuur binne O. irroratus. Chromosoom karakters onderskraag die twee evolusionêre lyne waar klade A slegs perisentriese inversies besit wat swerwend wat ontbreek in klade B. Klade B op sy beurt besit 'n komplekse tandemme fusie wat glad nie voorkom in klade A nie. Molekulêre datering het verder gewys dat die twee klades omtrent 1.1 miljoen jaar gelede versprei het, wat ooreenstem met die klimaats veranderinge wat sedert die Peioceen en Pleistoceen plaasgevind het. Klade vorming binne die spesies komples kan daarom as gevolg van habitat fragmentasie plaasgevind het. Hierdie studie dus noodsaak 'n volle taksonomiese ondersoek van O. irroratus ten einde vas te stel hoeveel spesies binne die komplex voorkom.

Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: South Africa's coastline is in the region of 3650kms and encompasses many different and dynamic marine environments. To enhance our current understanding of the population structure and gene flow patterns of intertidal zone marine species in this region, this study sets out to investigate the phylogeographic population structure of the Cape sea urchin, Parechinus angulosus, using mitochondrial and nuclear DNA sequence data collected in 2007 and 2008. Individuals were sampled from 18 geographic locations between southern Namibia and Durban, covering nearly the full extent of the species range. Sequence data were obtained from a 790bp region of the COI mtDNA gene (n=510) and a 182bp region of the nDNA SpREJ9 gene (n=145), respectively. The mtDNA data revealed 283 polymorphic sites (36%) defining 195 haplotypes, of which 160 were unique and 35 shared among individuals. Haplotype diversity (h) was found to be high both overall (h=0.95) and for individual localities (h=0.75-0.98), with nucleotide diversity (π) being low overall (π=0.013) as well as for individual localities (π=0.0033-0.0254). AMOVA revealed significant population structure among sampling sites in the Namaqua Province biogeographical region, as well as between three of the four respective coastal biogeographic provinces/regions. Gene flow was bi-directional among sampling sites in the south coast Agulhas and East Coast Province biogeographical regions, while gene flow in the Namaqua Province appears to be dominated by northwards movement. BAPS identified a significant break in the Cape Point region, which was also reflected in the gene flow patterns and parsimony networks. This broadly corresponds to previously identified biogeographic regions as well as genetic breaks for other marine species found along this coast. Fu's Fs statistics showed strong signal(s) of population expansion for individual sampling localities as well as for the data set as a whole, while MDIV estimated a time since expansion ranging from 7733-4759 years ago. The nDNA data revealed 54 variable sites (29.7%), defining 72 alleles of which 50 were unique and 22 shared among individuals. Many of the alleles (69.4%) were restricted to single sampling sites, with Betty's Bay on the south coast being the most diverse from a genetic viewpoint. Allelic diversity was high overall (h=0.86) while nucleotide diversity was low (π=0.025). No nuclear sub-group structure was identified by BAPS, although the parsimony network revealed shallow genetic structure between the Namaqua and Agulhas Provinces, with significant pairwise ФST values also recovered between their individual coastal localities. This points to at least one major barrier to gene flow for Parechinus angulosus along the South African coast, namely Cape Point. Several additional, smaller hindrances to gene flow along the coast were also identified, most of which are congruent with findings from studies on both other and sea urchin species. As a standalone study this research elucidated many aspects regarding the phylogeography of the Cape sea urchin, P. angulosus. However, it is when viewed in the broader context of invertebrate phylogeography along the southern African coastline that this research will provide its most critical insight. / AFRIKAANSE OPSOMMING: Geen opsomming

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Within southern Africa, the widely distributed four-striped mouse Rhabdomys is parasitized by, amongst others, the host-specific ectoparasitic sucking louse, Polyplax arvicanthis. The present study investigated this parasite-host association from a phylogenetic and phylogeographic perspective utilizing mitochondrial and nuclear DNA markers. The findings support the existence of four species within Rhabdomys (three distinct lineages within the previously recognized arid-adapted R. pumilio and the mesic-adapted R. dilectus). These species have distinct geographic distributions across vegetational biomes with two documented areas of sympatry at biome boundaries. Ecological niche modelling supports a strong correlation between regional biomes and the distribution of distinct evolutionary lineages of Rhabdomys. A Bayesian relaxed molecular clock suggests that cladogenesis within the genus coincides with paleoclimatic changes (and the establishment of the biomes) at the Miocene-Pliocene boundary. Strong evidence was also found that the sucking louse P. arvicanthis consists of two genetically divergent lineages, which probably represent distinct species. The two lineages have sympatric distributions throughout most of the sampled range across the various host species and also occasionally occur sympatrically on the same host individual. Further, the absence of clear morphological differences among these parasitic lineages suggests cryptic speciation. Limited phylogeographic congruence was observed among the two P. arvicanthis lineages and the various Rhabdomys species and co-phylogenetic analyses indicated limited co-divergence with several episodes of host-switching, despite the documented host-specificity and several other traits predicted to favour congruence and co-divergence. Also, despite the comparatively smaller effective population sizes and elevated mutational rates found for P. arvicanthis, spatial genetic structure was not more pronounced in the parasite lineages compared to the hosts. These findings may be partly attributed to high vagility and social behaviour of Rhabdomys, which probably promoted parasite dispersal among hosts through frequent inter-host contact. Further, the complex biogeographic history of Rhabdomys, which involved cyclic range contractions and expansions, may have facilitated parasite divergence during periods of host allopatry, and host-switching during periods of host sympatry. Intermittent contact among Rhabdomys lineages could also have prevented adaptation of P. arvicanthis to specific host lineages, thus explaining the lack of host-specificity observed in areas of host sympatry. It is thus evident that the association between Polyplax arvicanthis and Rhabdomys has been shaped by the synergistic effects of parasite traits, biogeography, and host-related factors over evolutionary time. / AFRIKAANSE OPSOMMING: Binne suidelike-Afrika word die wyd-verspreide gestreepte veldmuis, Rhabdomys, onder andere deur die gasheer-spesifieke ektoparasitiese luis, Polyplax arvicanthis, geparasitiseer. Die huidige studie het hierdie parasiet-gasheer interaksie vanuit ‘n filogenetiese en filogeografiese oogpunt ondersoek deur van beide mitokondriale en nukluêre merkers gebruik te maak. Die bevindinge dui op die bestaan van vier spesies binne Rhabdomys, waaronder drie nuwe genetiese groepe binne die voorheen erkende R. pumilio asook R. dilectus. Hierdie spesies het nie-oorvleulende geografiese verspreidings binne spesefieke plantegroei biome met twee geidentifiseerde areas van simpatriese voorkoms by bioom grense. Ekologiese nis modellering ondersteun ‘n sterk korrelasie tussen biome en die verspreiding van die evolusionêre groepe binne Rhabdomys. ‘n Bayesiaanse verslapte molekulêre klok dui daarop dat kladoginese binne die genus gedurende paleoklimatiese veranderinge, wat tot die totstandkoming van die huidige biome gelei het, by die Mioseen-Plioseen grens plaasgevind het. Sterk bewyse is ook gevind dat die parasitiese luis P. arvicanthis uit twee geneties verskillende groepe, wat heel moontlik afsonderlike spesies verteenwoordig, bestaan. Hierdie genetiese groepe het simpatriese verspreidings oor meeste van die gebestudeerde geografiese area op die verskeie gasheer spesies en mag ook soms simpatries op dieselfde gasheer individu voorkom. Verder dui die afwesigheid van duidelike morfologiese verskille tusssen die parasiet genetiese groepe op moontlike kriptiese spesiasie. Beperkte filogeografiese ooreenstemming is tussen die P. arvicanthis genetiese groepe en die Rhabdomys spesies waargeneem en die vergelykende-filogenetiese analises het aangedui dat daar beperkte gesementlike-divergensie plaasgevind het met verskeie episodes van gasheer-wisseling, ten spyte van die gasheer-spesifieke aard van die parasiete asook verskeie ander kenmerke wat veronderstel is om filogeografiese ooreenstemming en gesementlike-divergensie te bevorder. Ten spyte van die vergelykbaar kleiner effektiewe bevolking groottes en verhoogde mutasie tempo wat vir P. arvicanthis gevind is, is die geografiese genetiese struktuur nie meer gedifferensieёrd in die parasiet groepe as in die gasheer nie. Hierdie bevindinge mag deels verklaar word deur die hoё beweeglikheid asook die sosiale gedrag van Rhabdomys, wat waarskynlik parasiet beweging tussen gashere bevorder deur gereelde tussen-gasheer kontak. Die komplekse biogeografiese geskiedenis van Rhabdomys, wat sikliese inkrimping en uitsetting van die geografiese verspreiding behels het, het heel moontlik parasiet divergensie tydens tydperke van gasheer allopatrie asook gasheer-wisseling tydens tydperke van gasheer simpatrie, gefasiliteer. Tussentydse kontak tussen Rhabdomys genetiese groepe kon aanpassing van P. arvicanthis tot sekere gasheer genetiese groepe verhoed het en verklaar dus die afwesigheid van waargenome gasheer-spesifisiteit in areas van gasheer simpatrie. Dit is dus duidelik dat die assosiasie tussen P. arvicanthis en Rhabdomys deur die sinergistiese uitwerking van parasiet kenmerke, biogeografie, asook gasheer-verwante faktore oor evolusionêre tyd gevorm is. / National Research Foundation (NRF)

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: The genus Seriola includes several important commercial fish species, yet the phylogenetic relationships between species have not been fully investigated to date. This study reports the first molecular phylogeny for this genus based on two mitochondrial (Cytb and COI) and two nuclear gene (RAG1 and Rhod) fragments for all extant Seriola species (nine species, n = 27). The phylogenetic patterns resolved three main lineages: a ((S. fasciata and S. peruana), S. carpenteri) clade, a (S. dumerili and S. rivoliana) clade and a (S. lalandi and S. quinqueradiata) clade. The closure of the Tethys Sea (12 - 20 MYA) coincides with divergence of the ((S. fasciata and S. peruana), S. carpenteri) clade from the rest of the Seriola species; while the uplifting of the Isthmus of Panama (± 3 MYA) played an important role in speciation between S. fasciata and S. peruana. The climate and water temperature fluctuation in the Pliocene played important roles during the divergence of the remainder of the Seriola species. This study is also the first to describe the evolutionary history of the commercially important species Seriola lalandi across its distribution range. Global patterns of genetic variation within S. lalandi (n = 190) were examined using three genes fragments (mitochondrial DNA COI, Cytb and nuclear RAG1). Three distinct clades were identified, corresponding to three different geographic regions (North-western Pacific - Japan, North-eastern Pacific - USA, and the southern hemisphere clade). These groupings correspond with the previously identified subspecies of S. lalandi (North-western Pacific – S. lalandi aureovittata, North-eastern Pacific – S. lalandi dorsalis, and the southern hemisphere clade - S. lalandi lalandi). AMOVA results and pairwise FST values revealed significant population differentiation between these groups. The population subdivision between these clades in all probability is maintained by biogeographic or oceanographic barriers (such as the equator and East Pacific Barrier) that disrupt gene flow. The southern hemisphere clade comprised of samples from the southern Pacific (AUS, NZL and Chile) and the southern Atlantic (SA). No haplotypes were shared between these areas in the southern hemisphere. This southern hemisphere clade was further investigated with six microsatellite markers. The analyses revealed the South African populations as genetically distinct from populations of the South Pacific oceans (AMOVA, FCA and STRUCTURE results). In summary, the South African and southern Pacific grouping could be the result of recent vicariant events during the Pleistocene glacial / interglacial periods and / or contemporary oceanographic forces acting on these populations. Further population differentiation was found within the South African samples, but not in the South Pacific. In the southern Pacific clade this lack of population structure is the result of high gene flow (analysed with MIGRATE) between the sampling localities. This is the first report on the genetic structure of this commercial important species for South African populations. Five sampling localities from the west- to the east coast of South Africa were sampled (n = 201). The microsatellite analyses revealed two potentially genetically distinct groups. AMOVA, FST and FCA results suggest small but significant differentiation between populations from the west coast and from the south- and east coast, suggesting a potential genetic break in the Cape Point region (BARRIER). However, the program STRUCTURE showed a high level of admixture along the South African coast and the migration results (MIGRATE and BAYESASS) also suggest a high degree of gene flow between these regions. / AFRIKAANSE OPSOMMING: Die genus Seriola bevat verskeie kommersieel belangrike vis spesies, tog is filogenietiese verwantskap tussen species is nog nie ten volle bestudeer nie. Hierdie studie is die eeste molekulêre filogenietiese studie vir die genus gebaseer op twee mitochondriale DNA (Cytb en COI) en twee nukleêre DNA fragmente (RAG1 en Rhod) vir al die bestaande Seriola spesies (nege spesies, n = 27). Drie beranglike filogenitiese patrone is geïdentifiseer: ‘n ((S. fasciata en S. peruana), S. carpenteri) groep, ‘n (S. dumerili en S. rivoliana) groep en ‘n (S. lalandi en S. quinqueradiata) groep. Die diversifikasie van die ((S. fasciata en S. peruana), S. carpenteri) groep van die ander Seriola spesies stem oor een met die sluiting van die Tethys See (12 - 20 MYA). Terwyl die opligging van die Isthmus van Panama (± 3 MYA) ‘n belangrike rol gespeel het in die spesiasie tussen S. fasciata en S. Peruana. Die veranderlike klimaat toestande en water temperature tydens die Pliocene help met die diversifikasie van die res van die Seriola spesies. Hierdie studie is die eerste om verslag te doen op die evolusionêre geskiedenes van kommersiele belangrike vis spesies Seriola lalandi oor sy hele verspreidings gebied. Die globale patrone van genetiese variasie binne S. lalandi (n = 190) is ondersoek deur gebruik te maak van mitokondriale (Cytb en COI) en nukleêre (RAG1) DNA volgorde data. Drie groepe geassosieer met geografie is geïdentifiseer (Noord-westelike Stille Oseaan - Japan, Noord-oostelike Stille Oseaan - FSA en die suidelike hemisfeer groep). Hierdie groepeerings stem oor een met voorheen geïdentifiseerde subspesies van S. lalandi (Noord-westelike Stille Oseaan - S. lalandi aureovittata, Noord-oostelike Stille Oseaan - S. lalandi dorsalis en die suidelike hemisfeer groep - S. lalandi lalandi). AMOVA en FST resultate bevestig die hoë graad van genetiese struktuur tussen groepe. Hierdie populasie groepeerings is moonlik die oorsaak van - en onderhou deur giogeografiese and oseaanografiese grense (soos the ewenaar en EPB) wat geen vloei ontwrig. Die suidelike hemisfeer groep kan verder verdeel word in ‘n suidelike Stille Oseaan (AUS, NZL en Chile) groep en ‘n suidelike Atlantiese groep (SA). Geen haplotiepes word gedeel deur hierdie twee groepe. Hiedie suidelike hemisfeer groep was verder ondersoek met ses mikrosatelliet merkers. Die analises bevestig dat die Suid Afrikaanse populasies geneties verskillend is van die suidelike Stille Oseaan groep (AMOVA, FCA and STRUCTURE). Verdere genetiese struktuur kan verkry word binne die Suid Afrikaanse monsters, maar nie in die suidelike Stille Oseaan nie. In die suidelike Stille Oseaan hiere gebrek aan populasie struktuur is as gevolg van die hoë geen vloei (MIGRATE) tussen die lokaliteite. Hierdie is ook die eerste studie oor die genetiese structure van S. lalandi vir Suid Afrikaanse populasies. Monsters (n = 201) was geneem by vyf lokaliteite vanaf wes tot oos kus van Suid Afrika. Die mikrosatelliet analises dui op twee moontlike genetiese groepe. AMOVA, FST en FCA dui ‘n klein maar betekenisvolle differensiasie tussen populasies van die wes kus en die van die suid en oos kus. Dit dui aan op moontlike breek in die Kaap Punt omgewing (BARRIER). STRUCTURE analises toon egter ‘n bymengsel van twee groepe langs die Suid Afrikaanse kus en migrasie resultate (MIGRATE en BAYESASS) toon ook ‘n hoë graad van gene vloei tussen hierdie gebiede.

Estimates from radiocarbon-dated packrat middens indicate that the high elevation woodland communities of the Madrean Sky Islands were continuous as recently as 8,000 to 12,000 years ago. A number of population studies on a diverse collection of taxa have investigated the extent to which the Madrean Sky Island system has limited gene flow among mountain ranges. The results of several of these studies indicate that population divergences may be more ancient than the Holocene. Yarrow’s spiny lizards, Sceloporus jarrovii, were sampled from eight sites representing seven mountain ranges. The populations of S. jarrovii are host to the malarial parasite, Plasmodium chiricahuae. DNA sequences from the lizards and their malarial parasites were used to reconstruct the evolutionary relationships and estimate the ages of the populations for both host and parasite. The findings of these analyses indicate that the sky island populations of S. jarrovii have been isolated for hundreds of thousands of years and did not experience gene flow during the last woodland expansion. In contrast, the results indicate that the malarial infection occurred more recently, possibly during the Holocene woodland expansion. In addition, the prevalence of the malarial infection was compared to multiple attributes of the lizards. This analysis revealed a negative relationship between the genetic diversity of the lizard populations and the prevalence of infection. Furthermore, lizard populations with lower prevalence of infection have a lower frequency of multiclonal infections.

The American beaver, the largest rodent of North America, is distributed in ponds, lakes, and streams from Alaska to northern Mexico. This semi-aquatic mammal is considered an ecosystem engineer because beavers modify the landscape by cutting trees and by creating dams and ponds that have important effects on the aquatic community structure, providing habitat for aquatic invertebrates, fish, and birds. The American beaver has played an important socioeconomic role in the history of North America due to beavers' fur value, which caused the near extirpation of this mammal at the beginning of the 1900s due to overharvest by early Europeans. Because of the highly specific habitat requirements of beavers, this mammal also suffers the effects of habitat loss in some areas where riparian ecosystems are now scarce. My objectives in this study were to assess how climatic and geological events affected the current distribution of the American beaver in North America, and how the management actions to restore and control beaver populations have affected the genetic structure and conservation of beaver populations. Specifically, I addressed four aspects of the management and conservation genetics of the beaver: 1) a literature review of the management of beavers in the past 100 years; 2) the development of novel microsatellite DNA markers to address the population genetic structure aspects of the study; 3) the use of these microsatellite DNA markers to assess genetic diversity of current populations of beavers and to detect past population bottlenecks; and 4) the use of two mitochondrial DNA genes to resolve the current phylogeography of the American beaver in order to better understand how historical factors have affected the beaver's current distribution and genetic structure in North America. The results from this study provide information of the effects that management actions and climatic events can have on the genetic structure of beavers. This information can be used by wildlife biologists, and land managers, to develop future strategies for management and conservation of the American beaver.

Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: South Africa is known for its high marine invertebrate diversity but the evolutionary histories of these species are largely unknown. The present study contributes to the growing body of phylogeographic studies of southern African coastal species. The main aim is to better understand the colonization and diversification of South African barnacles. To investigate the phylogeographic pattern in the southern African volcano barnacle, Tetraclita serrata, 410 individuals from 20 sampling localities were analyzed. In addition, to understand the colonization and diversification patterns of South African barnacle species, nine taxa were included in a molecular phylogeny derived from the nuclear gene, 18S rRNA. With only a limited number of 18S sequences available on GenBank, a separate phylogenetic tree, for the mitochondrial gene, was constructed to determine whether the genus Tetraclita is monophyletic. Restricted gene flow in some geographical areas was hypothesized for T. serrata based on oceanic circulation patterns; known biogeographic regions; and features such as the Agulhas Bank, which has shaped the population genetic structure of several other South African marine organisms. The population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (CO1) and nuclear internal transcribed spacer 1 (ITS1) genes. Phylogenetic and population genetic analyses of the CO1 gene revealed two distinct genetic clades with overlapping distributions. The nuclear ITS1 data performed on a subset of individuals drawn from both mtDNA clades revealed a single lineage. The pattern observed can be ascribed to a historical event that may have been responsible for the formation of allopatric lineages that have since come into secondary contact. On the other hand, the pattern observed may be as result of incomplete sorting of nDNA alleles, in which case, given that the two mtDNA clades are not geographically isolated, could be explained by selective pressures acting on the species due to ecological constraints. No clear phylogeographic structure was found within each of these clades and the direction of gene flow of T. serrata individuals can be linked to the oceanographic features found along the South African coast. In contrast to most other South African marine species studied to date, the haplotype network, mismatch distributions and time since expansion suggest that the effective population size of T. serrata was not severely affected by the Last Glacial Maximum. It is proposed that further investigations into the phylogeography of coastal marine species, particularly obligatory sessile species such as barnacles, are required to determine whether the patterns observed in T. serrata is a rare history, or not. Neighbour-joining, maximum parsimony and Bayesian analyses on the CO1 gene provide evidence for the monophyly of the genus Tetraclita; however, Tetraclita species found in South Africa do not share a common ancestry suggesting multiple colonization events. This study has also accidently led to the discovery of an introduced species, Balanus perforatus, native to Europe, and I discuss the potential of the alien becoming invasive on the east coast of South Africa where it was found. / AFRIKAANSE OPSOMMING: Suid-Afrika is bekend vir sy hoë mariene ongewerwelde diversiteit, maar die evolusionêre geskiedenis van hierdie spesies is grootliks onbekend. Hierdie studie is gedoen om by te dra tot die filografiese studies van suider Afrikaanse kus spesies en om die kolonisasie en diversifikasie van die Suid-Afrikaanse eendmossels beter te verstaan. Om die genetiese struktuur van die bevolkings van die vulkaan eendmossel, Tetraclita serrata, wat langs die Suid-Afrikaanse kuslyn voorkom, te bestudeer, was 410 individue van 20 lokaliteite ontleed. Daarbenewens, om die kolonisasie en diversifikasie van Suid-Afrikaanse eendmossels te verstaan, was nege spesies ingesluit in 'n molekulêre filogenie wat gebaseer is op die kern geen, 18s rRNA. Met slegs 'n beperkte aantal 18s DNS volgordes beskikbaar op GenBank,is 'n aparte filogenetiese boom, vir die mitochondriale geen COI, gekonstrueer om te bepaal of die genus Tetraclita monofileties is. Beperkte geen-vloei in sommige geografiese gebiede was verwag vir T. serrrata gebaseer op oseaniese sirkulasiepatrone; bekende biogeografiese streke, en kenmerke soos die Agulhas Bank, wat die filogeografiese struktuur van verskeie ander Suid- Afrikaanse mariene organismes beïnvloed het. Die genetiese struktuurvan die bevolkings is geondersoek met behulp van die mitochondriale sitochroom oksidase subeenheid 1 (COI) en kern interne getranskripeerde spasieërder 1 (ITS1) gene. Geen duidelike bevolkings genetiese struktuur is gevind nie en die rigting van geenvloei van T. serrata individue kan gekoppel word aan die oseanografiese kenmerke wat langs die Suid-Afrikaanse kus voorkom. Filogenetiese en bevolking genetiese ontleding van die COI geen openbaar twee afsonderlike klades maar met oorvleuelende geografiese verspruidings. Die ITS1 data-analise wat uitgevoer was op 'n subset van individue wys op 'n enkele spesie. Die waargenome patroon dui op 'n belangrike historiese verskil tussen die twee klades. 'n Geskiedkundige gebeurtenis was dalk verantwoordelik vir die vorming van twee evolusionêre lyne wat sederdien sekondêre kontak het. Aan die ander kant, kan die patroon waargeneem word as gevolg van die onvolledige sortering van nDNA allele, in welke geval, gegee dat die twee mtDNA clades nie geografies geïsoleer is nie, dit verduidelik kan word deur selektiewe druk wat op die spesie was as gevolg van fisiologiese of ekologiese beperkings. Die statistiese parsimonie netwerk, ongelyksoortige verspreidings en tyd sedert die bevolkingsuitbreiding dui daarop dat T. serrata die laaste ysagtige maksimum tydperk oortleef het. Tot op hede het geen Suid- Afrikaanse mariene spesies so 'n patroon gewys nie. So, verdere ondersoeke in die filogeografie van die kus mariene spesies, veral verpligte sittende spesies soos eendmossels, word vereis om te bepaal of die patroon waargeneem in T. serrata 'n seldsame geskiedenis het, of nie. Buur-aansluiting, maksimum parsimonie en Bayesian afleiding op die CO1 geen het bewyse verskaf vir die monofiletiese afkoms van die genus Tetraclita, maar Tetraclita spesies wat in Suid Afrika gevind is, deel nie ‘n gemeenskaplike afkoms nie, wat weer bewyse verskaf vir verskeie kolonisasie gebeure. Hierdie studie het gelei tot die ontdekking van 'n eksotiese spesie, Balanus perforatus, inheems aan Europa, en die potensiaal van die indringer om ontwykend te raak aan die ooskus van Suid-Afrika waar dit gevind is word bespreek. / The South African National Research Foundation (NRF) and Stellenbosch University

This thesis explores the potential of new substrates for ancient DNA studies and addresses novel questions that can now be asked. It also highlights an additional use of ancient DNA extracted from a traditional source.

The human-abetted introduction of commensal species (i.e. those that opportunistically exploit the anthropogenic environment for food and shelter, e.g. rats, cockroaches etc.) to new areas has occurred throughout history. This has resulted in detrimental ecological changes worldwide but, from a viewpoint of human knowledge, a beneficial corollary of these translocations is that the species in question can be used as proxies to study the movement of the humans who transported them. I reconstruct colonisation histories of three widespread commensal mammalian species in the Western Indian Ocean, the black rat Rattus rattus, house mouse Mus musculus and Asian house shrew Suncus murinus, through phylogeographic studies (the geographic distribution of genetic lineages) of maternally-inherited mitochondrial markers, and zooarchaeological data. The DNA analyses are conducted on samples largely derived from museum specimens collected up to 110 years ago, and from archaeological bones (in the case of rats). I show considerable cryptic diversity in all three species, particularly in mice for which we find a potential major new lineage. Certain lineages within each species predominantly reveal long-distance translocations within the Indian Ocean, but high resolution geographic and genetic clustering is also evident, particularly in Asian house shrews. Phylogeographic structuring of the three species in East Africa and the southern Indian Ocean region (e.g. Madagascar, Reunion, etc.) indicate connections with Arabia, the Middle East, and India in the Islamic period from the first millennium AD, and later European connections during the Age of Exploration. Closer to the origins of the three species (the Indian subcontinent in all cases), range expansions in Eurasia and nearby islands relate to early to mid Holocene human populations, but also with signals of later secondary colonisations. Through ancient DNA studies I found genetic continuity between temporally separated populations of black rats suggesting population persistence, and high levels of diversity in Songo Mnara, a Swahili stonetown in Tanzania. Knowledge of the colonisation history and genetic diversity of an introduced species is essential to understand their resilience in novel landscapes, and to identify pathways of invasion and, by proxy, human trade and exchange networks that facilitated their dispersal. My research contributes significantly to that end for three socially, economically and ecologically important species that are well-established in the Indian Ocean region and beyond.

Le plateado ou dorado - Brachyplatystoma rousseauxii (Pimelodidae, Siluriformes) est un grand poisson-chat Amazonien d’intérêt commercial, qui présente un des cycles de vie les plus surprenants et énigmatiques, avec la plus grande migration connue en eaux douces, entre l’estuaire de l'Amazone et les têtes de fleuves en Amazonie occidentale. Le but de ce travail était de déterminer, au niveau moléculaire, la position phylogénétique du plateado dans la famille Pimelodidae ainsi que sa structure génétique dans le Haut Madera (Villa Bella–VB, Cachuella Esperanza–CE, Puerto Maldonado–PM, Rurrenabaque–RU, Puerto Villarroel–PV) et ouest de l'Amazonie (Iquitos–IQ) bassins (Bolivie et Pérou). Les relations phylogénétiques ont été définies par une analyse du maximum de vraisemblance (ML) des séquences nucléotidiques de deux gènes mitochondriaux (Région de Contrôle–RC, ~ 900 pb, 32 taxons; Cytochrome Oxydase 1-CO1, ~ 650 pb, 61 taxons), et d’un gène nucléaire (F-reticulon4–RTN4, ~ 1700 pb, 38 taxons). La structure génétique des populations a été évaluée par le polymorphisme de longueur de neuf microsatellites (284 inds) et par les variations de séquence de la RC (461 inds + 45 en provenance du Brésil, disponibles dans GenBank). Les variations de fréquences des microsatellites ont été utilisées pour identifier les unités panmictiques (clusters) les plus probables dans l'ensemble des données, à travers une approche bayésienne (BAPS), après avoir démontré une déviation significative à l'équilibre de Hardy-Weinberg (HWE) quand l’ensemble des données étaient analysé comme faisant partie d’une seule unité.L’analyse phylogénétique concaténée (ML) a montré que la famille Pimelodidae était un groupe monophylétique. Les résultats les plus notables de la phylogénie sont la monophylie peu soutenue (77%) de la tribu Brachyplatystomatini et la non-monophylie des Brachyplatystoma. Seul le sous-genre Malacobagrus (B. rousseauxii + (B. filamentosum + B. capapretum)), défini morphologiquement, s’est avéré monophylétique. Ces résultats suggèrent que le genre Brachyplatystoma pourrait contenir Platynematichthys ou pourrait être limité au sous-genre Malacobagrus.L'analyse des microsatellites sur l'ensemble des échantillons (ouest Amazone + haut Madera) a montré un écart significatif á la panmixia, ainsi que sur l'ensemble des échantillons du haut Madera. A la lumière de ces résultats, l’approche bayésienne a été développée, montrant qu'au moins trois clusters (1, 2, 3) sont présents dans les bassins du haut Madera et de l'ouest de l'Amazone, avec des répartitions qui se chevauchent partiellement. En parallèle á l'identification des clusters, il a été mis en évidence une différence significative au sein de B. rousseauxii entre l’ouest de l'Amazonie et le haut Madera bassin.L'analyse généalogique (ML) des séquences de la RC a montré une topologie en peigne, sans groupe d'haplotypes montrant une histoire commune. En revanche, l'analyse des fréquences haplotypiques a révélé l’existence de 4 haplogroupes, liés à la géographie. Un haplogroupe a été identifié le long de l'axe principal de l’Amazonas-Solimões (Belem-Brésil et Iquitos-Pérou) et 3 autres dans le haut Madera (VB; CE+MD; RU+PV), organisés selon une tendance aval - amont. Ainsi, nous observons d’un coté 3 populations (clusters) avec une distribution géographique partiellement chevauchante, et de l’autre quatre haplogroupes positionnés selon une logique géographique. Le scenario le plus probable implique un comportement de homing des individus du cluster 1 (homing à l’échelle des grands sous-bassins), qui préfèrent ou tendent à retourner dans le sous-bassin du Madera. Les 3 populations coexisteraient alors dans le haut Madera en se reproduisant à des périodes (phénologie) ou à des endroits différents (ségrégation spatiale). Enfin, les résultats sont discutés à la lumière des résultats précédemment publiés dans le bassin de l'Amazone et des menaces qui pèsent sur l'espèce dans le bassin du Madera. / The Plateado or Dorado - Brachyplatystoma rousseauxii (Pimelodidae, Siluriformes) is a commercial migratory catfish species with one of the most surprising and enigmatic life histories in the Amazon basin, involving the largest migration known for a freshwater species, between the estuary and the head waters in the Andean piedmont. The aim of the present work was to determine the molecular phylogenetic position of the Plateado in the Pimelodidae family and its population genetic structure in the Upper Madera (Villa Bella – VB, Cachuella Esperanza – CE, Puerto Maldonado – PM, Rurrenabaque – RU, Puerto Villarroel - PV) and Western Amazon (Iquitos - IQ) basins (Bolivia and Peru). The phylogenetic relationships were defined through a Maximum Likelihood (ML) analysis of nucleotide sequences of two mitochondrial (Control Region – CR, ~ 900 pb, 32 taxa; Cytochrome Oxidase 1 – CO1, ~ 650 bp, 61 taxa), and a nuclear fragment (F-reticulon4 - RTN4, ~1700 bp, 38 taxa). The population genetic structure was evaluated through the length polymorphism of nine microsatellites (284 inds) and CR sequence variations (461 inds + 45 from Brazil available in GenBank). Microsatellites frequencies variations were used to identify through a Bayesian approach (BAPS) the most probable panmictic units (clusters) in the whole data, after previous demonstration of a deviation to Hardy-Weinberg Equilibrium (HWE). The ML phylogenetic concatenated analysis showed the Pimelodidae family as a monophyletic group, with the genera Phractocephalus and Leiarius as basal lineages. The most notable results in the phylogeny were the not well-supported monophyly (77%) of the tribe Brachyplatystomatini and the non-monophyly of Brachyplatystoma. Only the morfologically defined subgenus Malacobagrus (B. rousseauxii + (B. filamentosum + B. capapretum)) was recovered as monophyletic. These results suggest that Brachyplatystoma could contain Platynematichthys or be restricted to the subgenus Malacobagrus, and the other species be related to distinct (earliest) genera, in agreement with another study carried out in parallel with other markers.Microsatellite analysis of the whole data (Western Amazon + Upper Madera) showed a significant departure of the HWE expectations, as well as the analysis of the whole data from the Upper Madera region. In the light of these results, the Bayesian approach has been implemented, showing that at least three clusters (1, 2, 3) are present in the Upper Madera and Western Amazon basins with partial overlapping distribution.To the margin of the cluster identification, it was evident the significant difference between Western Amazon (Iquitos region) and the Upper Madera basin.The genealogical analysis (ML) of the CR sequences showed a generalized comb-like topology without group of haplotypes with common ancestry. On the other hand, CR frequency analysis showed the conformation of four haplogroups associated to geography. One haplogroup was identified along the main axis of the Amazonas-Solimões, from Belem (Brazil) to Iquitos (Peru), and three other haplogroups were observed in the Upper Madera basin (VB; CE+PM; RU+PV), positioned in a downstream - upstream pattern.Hence, we observed on the one hand three genetic populations (clusters), distributed in partially overlapping geographical areas, and on the other hand four haplogroups, positioned according to a geographical pattern. The most probable scenario involves a homing behavior of individuals from cluster 1 (homing at the scale of large watersheds), which prefer or tend to return to the Madera basin, with the three populations coexisting within the upper Madera because they reproduce at different moments (phenology) or different places (spatial segregation). Finally, the results are discussed in the light of previous results in the Amazon basin and the threats to the species in the Madera basin (p.e. fragmentation by dams, overfishing, climate variability, among other).