The pecan weevil, Curculio caryae Horn, is an obligate nut feeder of all North American hickory (Carya) and a key pest of the pecan, C. illinoinensis Koch. This study investigated population structure of the pecan weevil. Gene flow and genetic variation was estimated for 90 pecan weevil specimens sampled from the entire Carya range. Cladistic and nested clade analyses, as well as an analysis of molecular variance (AMOVA) of mitochondrial DNA cytochrome oxidase I (mtDNA COI) were performed. The data indicate C. caryae diverged from its sister species, C. nasicus approximately 4.3 million years before present (mybp). Six-hundred and forty equally parsimonious trees of 31 haplotypes demonstrated high genetic diversity across all pecan weevil samples, and significant regional subdivision. Three clades recovered in the parsimony and nested clade analyses were strongly associated with western, eastern and central localities sampled within C. caryae's range. The current distribution of C. caryae and population structure were explained by past glaciation events. Lineage divergence between the western and eastern populations occurred during the Pleistocene (approx. 1.1 million years ago), and a more recent divergence occurred between C. caryae populations east and west of the Appalachian mountain range (870,000 yrs. ago). Haplotypes were segregated by region, but further sampling is necessary to test for gene flow among these regions.

The Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted owl. A network of late successional reserves has been established without consideration of potential for protecting overall biodiversity, including genetic diversity. Mitochondrial DNA sequences are used to examine the population structure of Acrotrichis xanthocera (Coleoptera: Ptiliidae) sampled from five late successional reserves within the Klamath-Siskiyou Ecoregion and five comparison sites from northern California. Measures of gene flow, phylogenetic analysis, and nested clade analysis are employed to infer historical demographic and phylogeographic processes. Results show that A. xanthocera populations have undergone past range expansion, but gene flow is currently limited. Individual late successional reserves do not adequately protect the genetic variation in this species. Although further research is needed, these results are likely to be congruent for other edaphic arthropod species. Improvement of the late successional reserve system is warranted for maximum protection of the genetic diversity of soil arthropod populations.

The Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted owl. A network of late successional reserves has been established without consideration of potential for protecting overall biodiversity, including genetic diversity. Mitochondrial DNA sequences are used to examine the population structure of Acrotrichis xanthocera (Coleoptera: Ptiliidae) sampled from five late successional reserves within the Klamath-Siskiyou Ecoregion and five comparison sites from northern California. Measures of gene flow, phylogenetic analysis, and nested clade analysis are employed to infer historical demographic and phylogeographic processes. Results show that A. xanthocera populations have undergone past range expansion, but gene flow is currently limited. Individual late successional reserves do not adequately protect the genetic variation in this species. Although further research is needed, these results are likely to be congruent for other edaphic arthropod species. Improvement of the late successional reserve system is warranted for maximum protection of the genetic diversity of soil arthropod populations.

Pine cone beetles (Conophthorus sp.) are serious pests of many forest ecosystems since they burrow into pine cone tissues for egg deposition, causing the death of the seeds. Management of these beetles in natural and commercial stands of pines has been problematic due to lack of understanding about species limits and distribution. This study was conducted to investigate the phylogeography and phylogenetics of the genus. Several species represented by disjunct populations appear to be monophyletic including Conophthorus edulis, C. mexicanus, C. coniperda, and C. conicollens, whereas C. ponderosae is polyphyletic with many distinct clades isolated by geography. This study explored whether host use or geography has played a greater role in the diversification of this genus, focusing on the polyphyletic C. ponderosae and the monophyletic C. edulis. In the first study, 751bp of the mtDNA CO1 gene were sequenced to reconstruct a phylogeny of the genus, and the distribution and host use were compared to investigate whether these factors were significantly associated. The second study addressed population structure and possible historical influences on the C. edulis and C. ponderosae populations using a nested clade analysis of the mtDNA haplotypes. Despite potential limitations due to sampling, several conclusions could be drawn. Three separate haplotype networks were found for the C. ponderosae haplotypes, indicating that there have been at least three lineages that have associated with P. ponderosa. Geography was significantly associated with the phylogeny at greater distances (>900km), but host use was not significant. At the species level, association with geography is variable. Population structure for C. ponderosae at the species level is minimal, and suggests that there has not been much time for lineage sorting of the haplotypes based on the nested clade analysis as compared to C. edulis.

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.

Abstract Sequence variation of the atpB-rbcL noncoding spacer region of the chloroplast DNA was used to reconstruct the phylogeography of Tetraena mongolica.T. mongolica (Zogophylaceae) is a relict species of a monotypic genus of in Inner Mongolia of China. It has been listed as seriously endangered plants that only distributed on the Ordos plateau of Inner Mongolic. The area is a refuge of many relict Asian Plants. Reproduction of T. mongolica is mainly by seed but a reproduction is anther way under the stress. A total of 880 bp of the atpB-rbcL spacer of cpDNA was sequenced from 8 populations of T. Mongolic. According to the cpDNA data, the level of gene flow (Nm:0.04-2.01), and population differentiation (Fst:0.199-0.895) were indicated, and the ¡§isolation by distance¡¨ model was not supported (R2 =0.0024). Based on minimum spanning network and nested clade analysis, the past fragmentation is the main phylogeographic factor affecting the population structure of T. mongolica .We suggested the deluges of Yellow River and isolation of Gianlishan Mountain cased the population fragmentation of T. mongolica. Keywords: phylogeography, Tetraena mongolica, gene flow, population differentiation, nested clade analysis, past fragmentation

Understanding the mechanisms that generate shared morphologies across closely related taxa is important when identifying distinct evolutionary lineages using morphological characters. Desmognathus salamanders are an ideal group for testing hypotheses concerning the correlation between morphological similarity and genetic exchange within and among nominal species due to a pattern of high discordance between the two. Phylogeographic hypotheses are tested for populations of the D. quadramaculatus species complex throughout southern Appalachia by combining phylogenetic and population genetic methods with geographical information. Phylogenetic and phylogeographic inferences are then assessed in conjunction with morphological characteristics that have traditionally diagnosed taxonomic entities to understand the genetic basis of shared morphology in this complex, and to assess species boundaries. A history of fragmentation followed by range expansion is suggested as a recurrent pattern that has shaped the current population structure within this complex. The current taxonomy is found to unite populations that share similar morphologies due to parallel evolution rather than ancestry. We suggest revisions in taxonomy that will better reflect the evolutionary history of these lineages. Appreciation of the hidden genetic variation and homoplasious morphological variation often present in and among salamander species can foster the implementation of more appropriate methods for detecting and recognizing the complex history of these organisms.

No description available.

A key component to conservation is an accurate understanding of genetic subdivision within a species. Despite their ecological and economic importance, relatively little is understood about the genetic structuring of Yellowstone cutthroat trout in Yellowstone National Park. Here, we use traditional (Fst, Rst, Nm, and AMOVA) and modern (Bayesian assignment tests, coalescent theory, and nested clade analysis) analytical approaches to describe the population genetic subdivision of cutthroat trout spawning populations in Yellowstone Lake and to identify genetically distinct population segments throughout Yellowstone National Park. Evidence for restricted gene flow between spawning populations within Yellowstone Lake was detected using nested clade analysis. This is the first molecular evidence for restricted gene flow between spawning populations in Yellowstone Lake. In contrast, traditional methods such as Fst and Rst as well as the Bayesian clustering program STRUCTURE v2.0 failed to detect evidence for restricted gene flow. Across our sampling range within Yellowstone National Park, eleven genetically distinct cutthroat trout population segments were detected. These showed a general pattern of small, isolated populations with low genetic diversity in headwater streams and wide-spread, genetically diverse populations in higher-order rivers. We recommend populations be managed to maintain current levels of genetic diversity and gene flow. Based on the recent decline of and distinct morphological, behavioral, and genetic nature of cutthroat trout in Yellowstone Lake, we recommend the Yellowstone Lake spawning populations collectively be recognized as an evolutionarily significant unit.

Marine turtle conservation is most successful when it is based on sound data incorporating life history, historical population stability, and gene flow among populations. This research attempts to provide that information through two studies. In chapter I, I identify historical patterns of gene flow, population sizes, and contraction/expansion during major climatic shifts. In chapter II, I reveal a life history characteristic of loggerhead turtles previously undocumented. I identify a pattern of juvenile recruitment to foraging grounds proximal to their natal nesting beach. This pattern results in a predictable recruitment pattern from juvenile foraging ground aggregations to local rookeries. This research will provide crucial information to conservation managers by demonstrating how sensitive marine turtles are to global climate change. In the second component of my research, I demonstrate how threats posed to juvenile foraging grounds will have measurable effects on rookeries proximal to those foraging grounds. The addition of this basic life history information will have dramatic effects on marine turtle conservation in the future, and will serve as the basis for more thorough, forward-looking recovery plans.