Thesis (M.S.)--Virginia Polytechnic Institute and State University, 2001. / Title from PDF t.p. (viewed Dec. 17, 2005). Vita. Includes bibliographical references (p. 33-41).

Thesis (M.S.)--Ohio University, June, 2008. / Title from PDF t.p. Includes bibliographical references.

Project (M.S.)--Brigham Young University. Dept. of Biology, 2007. / Includes bibliographical references (p. 29-36).

No description available.

Thesis (PhD)--Stellenbosch University, 2013. / Australian Acacia species are an important group of invaders and are known to form dense monospecific cultures in invaded habitats. Despite the ecological and economic importance of invasive acacias, little is known about their invasive biology both from an ecological and evolutionary perspective. Molecular genetic methods have increasingly become important in identifying source populations for invasive species and determining the population genetic structure of these populations. This thesis applied molecular tools to understand the invasion ecology of Acacia pycnantha and its rhizobial symbionts as a model system of Australian Acacia introductions. Specific objectives were to: reconstruct the molecular phylogeny of invasive and native populations of populations of Acacia pycnantha and identify the native provenance of A. pycnantha; identify microsatellite markers for Acacia pycnantha and other invasive Australian acacias based on transferring microsatellite markers developed for A. mangium, A. saligna, Paraserianthes lophantha and universal chloroplast microsatellites developed from tobacco; assess the introduction dynamics of Acacia pycnantha in South Africa and identify the source populations in the species’ native range ; and determine which nitrogen fixing symbionts nodulate A. pycnantha and determine whether A. pycnantha brought its symbionts along from its native range or acquired them in the invasive range. Nuclear and chloroplast DNA sequence data were used to reconstruct phylogeographic relationships between native and invasive A. pycnantha populations. The chloroplast phylogeny showed that Australian populations of A. pycnantha are geographically structured into two previously informally recognized lineages (representing wetland and dry land forms). Habitat fragmentation is probably the result of cycles of aridity and abundant rainfall during the Pleistocene0. The invasive population in Portugal was found to be the wetland form while South African populations were found to be predominantly wetland form although some dryland forms were identified. Thirty microsatellites out of the forty nine tested microsatellites successfully amplified across all species tested (A. implexa, A. longifolia, A. melanoxylon, A. pycnantha and A. podalyriifolia). High Transfer rates varied between 85% for microsatellites developed for A. mangium to 50% for those developed in A. saligna. Although transfer rates were high only twelve microsatellites (24%) out of the fifty tested were polymorphic while the chloroplast microsatellites showed no polymorphism. The low level of polymorphic loci calls for development of more microsatellites in this genus especially for species that have high commodity value. Nuclear microsatellites revealed three genetic groupings with substantial admixture in the native range (1. wetland Victoria and South Australia populations; 2. dryland Victoria and Flinders Range population; and 3. New South Wales). Admixture in the native range may have occurred as a result of reforestation exercises. Acacia pycnantha has been widely used in rea forestation projects in Australia because of its fast growth rate and ease of germination. Admixed populations were most - likely introduced to South Africa thus establishment of A. pycnantha may have been facilitated by already admixed propagules in the invasive range. Extensive admixture in the native range made it difficult to identify source populations of invasive A. pycnantha found in South Africa. The rhizobial symbionts of A. pycnantha were identified, showing that this species utilizes a wider suite of symbionts in its invasive range than its native range and there is support for both the co-introduction and host jumping hypotheses. This creates substantial opportunities for horizontal gene transfer between previously allopatric bacterial lineages, with as yet unknown consequences for plant and bacterial invasions.

The structuring of Atlantic salmon (Salmo salar L.) into discrete, genetically differentiated populations both within and between river catchments is well documented. The utilisation of this knowledge has proved valuable in a variety of evolutionary, ecological, managerial and conservation contexts. In this thesis, the genetic structuring of Atlantic salmon populations in northwest Europe was assessed in two catchments of very different sizes, using a range of molecular and associated population genetic methods; findings from the catchment level research are set in context by a broader phylogeographic study of post-glacial colonisation of the region. A regional study into the glacial origins and post-glacial colonisation routes of Atlantic salmon in northwest Europe was explored by analysing a pre-existing microsatellite dataset and supplementing it with haplotype data from mtDNA PCR-RFLP analysis of the same samples (N=702). Evidence from allele permutation tests undertaken on the microsatellite data alongside mtDNA haplotype frequencies suggested that there was a cryptic northern refuge in northwest France, with colonisation of the British Isles and Ireland occurring from this and the long-known Iberian Peninsula refuge. Catchment level studies were undertaken on the river Dart and river Tweed, involving 1151 fish being genotyped with 14 microsatellite loci with a subset of 211 fish being genotyped by mtDNA PCR-RFLP. In both catchments, populations were found to be weakly differentiated genetically, and were most consistent with the meta-population theory of evolution. Similarly, individual spatial autocorrelation analysis indicated that each major tributary within the catchments could be considered as a distinct management or conservation unit. In the Tweed dataset, however, limitations in the sample coverage across the catchment reduced the robustness of some findings. Historical stocking of the river Dart with fish from Scotland and Iceland is well-documented. The long-term implications of these activities on contemporary Dart populations were assessed by genotyping 177 fish from the donor populations using scale samples taken in the 1960s and comparing them to contemporary Dart populations by undertaking admixture analysis. Overall, admixture between the donor and recipient populations was low and appeared to reflect natural underlying levels of genetic relationships. However, increased admixture of donor stocks with one extant Dart population was apparent, indicating some potentially long-term localised success of the stocked fish through hybridisation with the native populations; nevertheless, with the population continuing to decline, this should not be viewed as a successful supplementation programme. Two tributaries on the river Tweed, the Gala and Leader, were inaccessible to salmon for long periods due to the construction of barriers to migration. On both tributaries, fish passes were installed in the 1940s and re-colonisation of the tributaries was possible. Assignment analysis was undertaken and indicated that, contrary to findings for between catchment studies, salmon straying from the most proximate tributaries (i.e. the Ettrick and Caddon) did not appear to be the principal colonisers of the current Gala and Leader populations. Rather, the highest proportion of Gala samples assigned to the Teviot (42%), with the Leader populations assigning to many tributaries across the catchment (Ettrick 28%; Upper 21%; Teviot 19%). However, given the relatively weak differentiation of the baseline samples and limitations inherent in the dataset, the correct self-assignment of baseline samples was very low (average 26%; range 0-47%), hence interpretation must be undertaken with caution. Nevertheless, the findings suggest that the Gala population may have reached a temporally stable state in the 60 years since it has been accessible to salmon. Whilst the relatively small scale of these studies is acknowledged, the application of the findings in management and conservation of the species are discussed in a wider context. These studies would support the following recommendations: to include information on the historic (refugial) origin of contemporary populations in regional management strategies; to treat each major tributary as a distinct unit as an appropriate scale for catchment level management; and, with stocking and supplementation programmes appearing to have no significant long-term success, coupled with the relative speed with which extirpated tributaries appear to be naturally re-colonised, the use of stocking and supplementation programmes should be discouraged.

The bull shark, Carcharhinus leucas, is an important euryhaline predator that is exploited throughout its range for meat and fins. This species is taxonomically paired with the pigeye shark, C. amboinensis. Validity of this group has not been directly tested using molecular markers. Genetic variation and phylogeny was examined with concatenated datasets of mitochondrial genes (cytb, cox1 and 12stRNA16s) for nineteen species, from three families within the order Carcharhiniformes. Whilst there were indications of species pairings within the genus, there was no evidence to suggest that the bull and pigeye sharks should be considered a species group. Phylogenetic analysis failed to resolve Carcharhinus, but confirmed Negaprion as a sister taxon and placed Prionace glauca within Carcharhinus. It remains unclear if the family Sphyrnidae, arose from a Rhizoprionodon or Scoliodon ancestor and future revision of this complex group of sharks is required. Like other large carcharhinid species, C. leucas exhibits a low reproductive rate and long generation times. It is susceptible to localised depletions and such declines have been documented. The global stock structure was assessed by analysing the mitochondrial control region in 245 individuals sampled from eight populations in three ocean basins. The bull shark exhibits relatively high haplotype diversity (0.896 ± 0.010) when compared to other globally-distributed sharks and the nucleotide diversity was similar to others from the genus (0.00465 ± 0.00014). There was significant stock structure found among populations (ΦST=0.736, p<0.00001) and among ocean basins (ΦCT=0.527, p=0.00653). Geneflow between the US Atlantic coastline and Gulf of Mexico was sufficient to consider the area to be a single panmictic population. Coalescent analyses suggest an Indian Ocean origin with population divergences associated with warm interglacials and increased habitat with drop in sea level during the recent Wisconsin glaciation. Seven discrete stock management units for bull sharks are proposed.

O morcego Desmodus rotundus é uma das três espécies de morcegos hematófagos existentes. Possui ampla distribuição, ocorrendo do sul do México até Argentina e Chile. Além de seu hábito alimentar incomum, esta espécie possui particular interesse por ser transmissor da raiva bovina. Apesar dos métodos de controle da população, estudos estimaram em até 33 milhões de dólares ao ano os prejuízos causados por esta espécie a pecuária no Brasil. Ao mesmo tempo, segundo dados oficiais, cerca de 200.000 indivíduos da espécie podem ter sido mortos no Estado de São Paulo no ano de 2000 através dos métodos de controle populacional. Além deste controle não surtir o efeito desejado (o número de casos de raiva não diminuiu no período), não se conhece qual o efeito desta matança nas populações naturais do morcego. Apesar de sua ampla distribuição e reconhecida variação morfológica, nenhum estudo foi realizado para procurar entender como a variabilidade genética desta espécie está distribuída geograficamente. Este estudo se propôs a estudar a filogeografia do morcego vampiro comum analisando um marcador mitocondrial, dois marcadores nucleares e morfometria de crânio. O marcador mitocondrial identificou cinco clados monofiléticos sem haplótipos compartilhados nem zonas de contato, cada um representando uma região geográfica diferente. São eles: Mata Atlântica sul (MAS), Mata Atlântica norte (MAN), Amazônia e Cerrado (AMC), América Central (AC) e Pantanal (PAN), sendo que os clados da Mata Atlântica formam um clado monofilético a Leste, se contrapondo aos demais clados a Oeste. Os índices de divergência entre estes clados são comparáveis a distâncias descritas para espécies congenéricas. Os tempos de divergência estimados entre os clados através de métodos coalescentes e não-coalescentes apontam para uma divergência pleistocênica, além de testes de neutralidade apoiarem a idéia de fragmentação por refúgios. O padrão biogeográfico descrito para D. rotundus possui um paralelo em uma série de outros organismos. Os marcadores nucleares por sua vez mostraram baixa variabilidade, e extenso compartilhamento de haplótipos entre as localidades pertencentes a distintos clados mitocondriais, num padrão que contrasta com os resultados descritos anteriormente. Simulações coalescentes foram realizadas com os parâmetros calculados para o gene nuclear RAG2 e mostraram compatibilidade entre os dados observados e vicariância pleistocênica para um marcador nuclear com o Ne calculados para D. rotundus. Os dados de morfometria de crânio mostraram que existe pouca diferenciação ao longo de toda a distribuição da espécie. Dados de Fst, funções discriminantes e variáveis canônicas mostram uma grande afinidade entre indivíduos dos clados AC e AMC, que juntos formam a distribuição de uma antiga subespécie atribuída a este táxon, Desmodus rotundus murinus. As análises de distância de Mahalanobis também são concordantes com os resultados obtido para o marcador mitondrial. Por fim, uma análise realizada com o software treescan mostra existir uma correlação estatisticamente significativa entre a árvore de DNA mitocondrial e os dados multivariados de crânio. Assim, por fim propõe-se que se reconheçam duas linhagens hoje atribuídas a D. rotundus como espécies distintas: uma a Leste (Mata Atlântica) e uma a Oeste. Uma amostragem mais cuidadosa do interior do Brasil e do restante da América do Sul deve determinar corretamente a área de ocorrência de cada espécie. / The bat Desmodus rotundus is one of the three extant vampire bat species. It has a broad distribution, occurring from southern México until Argentina and Chile. Besides its unique feeding habit, this species is of particular interest for being the main vector of cattle rabies. Even with population control methods, studies have estimated in 33 million dollars per year the damage caused by this bat to cattle farming in Brazil. At the same time 200.000 specimens might have been killed in São Paulo state in the year 2000 using the population control methods. Besides the fact that this control did not diminish the number of rabies cases, the impact of this killing in the bats\' natural populations is unknown. Although this species has a broad distribution and recognized morphological variation, no effort was made thus far to understand how this species\' genetic variability is distributed geographically. This work is aimed at studying the common vapire bats\' phylogeographic pattern using a mitochondrial marker, two nuclear markers and skull morphometrics. The mitochondrial marker identified five monophiletic clades without shared haplotypes or contact zones. Each clade represents a distinct geographic region: South Atlantic Forest (SAF), North Atlantic Forest (NAF), Amazon and Cerrado (AMC), Central America (CA) and Pantanal (PAN). The Atlantic Forest clades form an Eastern monophiletic clade opposing the other clade that lies westwards. The nucleotide divergence between these clades is similar to the one described to congeneric species. The divergence times estimated by coalescent and non-coalescent methods point to a Pleistocene vicariant event. The neutrality tests also point to refugia allopatric fragmentation. The biogegraphic pattern described for D. rotundus has a parallel in many other organisms. The nuclear markers showed low variability and sharing of haplotypes among all localities, contrasting with the previous results. Coalescent simulations were carried with populational parameters estimated for the nuclear gene RAG2 and showed compatibility between the observed data and Pleistocene vicariance effect on a neutral nuclear marker. Skull morphometrics showed low differentiation throughout the bats\' distribution. Data on Fst, discriminant functions and canonic variables shows affinity between CA and AMC clades. These two clades together form the distribution of a subspecies previously described to this taxon, Desmodus rotundus murinus. The Mahalanobis distance analyses are also congruent with the results obtained withn the nuclear marker. The analysis done with the software treescan shows a statistic significant correlation between the mtDNA tree and the skull multivariate data. On the basis of the results presented, it is proposed that two lineages currently atributed to D. rotundus are to be recognized as different species: one to the east (Atlantic Forest) and one to the west. A detailed sampling of the Brazilian and South American country will determine the exact range of each species.

Estudos morfológicos constataram que a espécie Tropidurus torquatus apresenta dois morfotipos geograficamente distintos ao longo da área ocupada pela espécie. Um com preferência por ambientes saxícolas, situado mais para o interior do continente e, outro, mais costeiro, ocupando predominantemente os solos arenosos de dunas e restingas. Estes morfotipos possuem características morfológicas externas distintas associadas a estes ambientes. Porém, estas diferenças morfológicas observadas não foram determinantes para um estudo mais conclusivo dos padrões de diferenciação e da história zoogeográfica da espécie em questão. Dentro deste contexto teórico, este trabalho abordou a história das populações de T. torquatus com o uso de dados moleculares mostrando como a variabilidade genética da espécie esta distribuída geograficamente. Esta espécie se mostrou muito mais diversa do que se imaginava inicialmente. Quatro diferentes linhagens foram recuperadas na maioria das análises e apresentam relação com a geografia. Os resultados mostraram que esta espécie está se expandido e que possivelmente pode ocorrer uma diferenciação intraespecífica. Também mostrou que pode estar ocorrendo fluxo gênico não só dentro desta espécie, mas como entre as outras espécies do gênero, porém somente uma filogenia mais robusta poderá elucidar a relação entre elas / Morphological studies have showed that Tropidurus torquatus presents two geographically distinct morphotypes along the area occupied by the species. The first morphotype is saxicolous and exhibits a preference for rocky environments located farther inland, and the other morphotype is located in more coastal areas, occupying predominantly sandy soils of dunes and sandbanks. These morphotypes have distinct external morphological traits associated with the environments they occupy. However, these differences were not observed morphological determinants for a more conclusive study of the differentiation patterns of differentiation and zoogeographical history of the species. Within this theoretical context, this work addressed the history of T. torquatus populations using molecular data, in order to understand the geographical distribution of genetic variability. Results showed that this species is far more diverse than initially hypothesized. Four different lineages were recovered in most analyzes, each one related to its intrinsic distributional pattern. Besides, this study shows that this species is expanding its distribution area and for this reason a differentiation among populations is likely to occur, potentially with formation of new species. Also results show that gene flow may be occurring not only within the species, but also between other Tropidurus species. Nonetheless, only a more robust phylogeny may elucidate the relationship between these species

Pionus maximiliani é uma espécie de psitacídeo amplamente distribuída que ocorre do nordeste do Brasil até o norte da Argentina, e compreende quatro subespécies: Pionus maximiliani maximiliani (Kuhl, 1820), P. m. siy Souancé, 1856, P. m. melanoblepharus Miranda-Ribeiro, 1920 e P. m. lacerus (Heine, 1884). Embora alguns estudos tratando a história filogenética deste grupo tivessem sido conduzidos, não foram propostas novas classificações taxonômicas e além disso, a filogeografia deste grupo nunca foi analisada. Os objetivos deste trabalho foram: 1) definir o limite de espécies no complexo Pionus maximiliani, integrando caracteres morfológicos, vocais e moleculares; e 2) inferir a história evolutiva e biogeográfica deste complexo através de uma análise filogeográfica. Os resultados das análises morfológicas e moleculares são congruentes, suportando a existência de dois grupos consistentes que correspondem às populações do leste e oeste da distribuição. Portanto, as populações que devem ser consideradas espécies plenas de acordo com o conceito filogenético de espécie são: Pionus maximiliani (Kuhl, 1820) e Pionus siy Souancé, 1856. O tempo de divergência estimado entre estes grupos sugere que a sua separação tenha ocorrido durante o Pleistoceno. Além disso, o ciclo de expansão e retração das florestas na região do norte da Argentina durante este período provavelmente permitiu a dispersão e posterior divergência entre as duas populações / Pionus maximiliani is a widely distributed species of parrot that is distributed from northeastern Brazil to northern Argentina, and comprises four subspecies: Pionus maximiliani maximiliani (Kuhl, 1820), P. m. siy Souancé, 1856, P. m. melanoblepharus Miranda-Ribeiro, 1920 and P. m. lacerus (Heine, 1884). Although some works have been conducted recently on the phylogenetic history of this group, no formal taxonomic classification has been proposed. Furthermore, the phylogeography of this group has never been analyzed. The objectives of this study were 1) to define species limits within the Pionus maximiliani complex by integrating morphological, vocal, and molecular characters; and 2) to infer the evolutionary and biogeographic history of the complex following a phylogeographic approach. Morphological and molecular results are congruent, supporting the existence of two consistent groups which corresponds to eastern and western populations. Thus, these populations could be considered as full species under the phylogenetic species concept: Pionus maximiliani (Kuhl, 1820) and Pionus siy Souancé, 1856. Estimated divergence times between these groups suggest that the split occurred during the Pleistocene. Further, cycles of forest expansion and retraction in northern Argentina during this period probably allowed the dispersion and posterior divergence between these two populations