Thesis (M.A.)--Humboldt State University, 2009. / Includes bibliographical references (leaves 29-31). Also available via Humboldt Digital Scholar.

Variation in morphology and genotype among individuals of the same species occurs almost everywhere in the natural world. Such variation underlies natural selection and any resulting evolution, and therefore needs to be quantified in order to predict and understand phenotypic and evolutionary dynamics. Where morphology or genotype vary non-randomly in space, structured spatial variation can arise. Such spatial variation can arise from, and cause, further evolutionary processes including local adaptation and speciation. Here, I quantify spatial variation in neutral genetics and morphology, and in selection on morphology, occurring at a very small spatial scale within a single population of European starlings (Sturnus vulgaris) resident to the Island of Fair Isle. I demonstrate weak but statistically significant genetic structure in microsatellite loci by FST comparison but that similar structure is not supported by Bayesian cluster analysis. I also show significant genetic structure between populations of starlings within the UK from England, Scotland, Colonsay, Orkney and Shetland, and show that there are two main genetic clusters supported by Bayesian cluster analysis. I show there are significant differences in weight, tarsus lengths, bill lengths, bill size and, body condition among three, spatially proximate, spatial areas within Fair Isle thereby demonstrating significant small-scale spatial variation in morphology within this island population Using capture mark recapture analysis to estimate survival probabilities I evidence the occurrence of stabilizing selection on weight and disruptive selection on tarsus length in starlings but find no evidence that selection on morphology differed between sexes or among areas within Fair Isle. I conclude that small scale spatial variation in morphology and neutral genetics can occur on small spatial scales even in species with high potential mobility and where there are no distinct differences in environment and movement is not physically inhibited.

Thesis (M.S.)--University of Wyoming, 2007. / Title from PDF title page (viewed on Feb. 10, 2009). Includes bibliographical references.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references.

Thesis (M. Sc.)--University of Canterbury, 2006. / Typescript (photocopy). Includes bibliographical references. Also available via the World Wide Web.

New world crocodilians constitute a monophyletic group comprising four species: Crocodylus rhombifer (Cuban crocodile), Crocodylus acutus (American crocodile), Crocodylus intermedius (Orinoco crocodile), and Crocodylus moreletii (Morelet’s crocodile). All of these are in the IUCN Red list of Threatened Species and exhibit geographic distributions covering small to widespread ranges across the Americas and insular Caribbean. With the overarching goal of generating relevant information for the conservation of endangered new world crocodilians, this dissertation integrates genetic and ecological information to provide a context spanning a scale from the species level to specific populations, to analyses of mating systems and breeding strategies in Crocodylus. In addition, my research applies tools of ecological inference to model the influence of environmental factors and natural habitat disturbances in the reproductive success of Crocodylus using a long-term dataset. This work uses C. intermedius and C. acutus as model species to explore four focal questions organized in distinct chapters related to the biology and ecology of crocodilians. In Chapter I, I compare previously reported reproductive traits among C. acutus populations across its geographic range. This comparative analysis reveals a high degree of variability in reproductive traits across C. acutus range and provides potential adaptive explanations for the patterns observed. Crocodylus acutus appears to be one of the most adaptable of crocodilians in terms of nesting requirements, total nests per breeding season, nest mode (hole vs. mound), timing of egg-laying, female minimum reproductive size, clutch size, female nest defence behavior, and female parental care. Besides regional comparisons, this chapter focuses on the largest nesting population of C. acutus located in southeastern Cuba, where the species still occurs at its natural population numbers. In Chapter II, I use molecular tools to elucidate the mating system of the Orinoco crocodile in a reintroduced population in the Llanos of Venezuela. Analyzing 17 polymorphic microsatellite loci from 20 clutches I found multiple paternity in C. intermedius, with half of the clutches fathered by two or three males. Sixteen mothers and 14 fathers were inferred by reconstruction of multilocus parental genotypes. Results showed skewed paternal contributions to multiple-sired clutches in four of the clutches (40%), leading to an overall unequal contribution of offspring among fathers with six of the 14 inferred males fathering 90% of the total offspring, and three of those six males fathering more than 70% of the total offspring. Results of this chapter provide the first evidence of multiple paternity occurring in the Orinoco crocodile and confirm the success of reintroduction efforts of this critically endangered species in Venezuela. In Chapter III, I apply generalized linear mixed models to infer the effect of tropical cyclones and environmental variability on the nesting success of C. acutus in the largest nesting population of the species in southeastern Cuba for a period of 21 years. Results of this chapter report the highest-density nesting for the species documented to date, and one of the highest densities of nesting in relation to other crocodilian species, with an average of 164 nests per year and a density of 17 nests per hectare. Two of the five analyzed nesting sites had consistently higher nests and higher nesting success for the whole 21-year period. Much of the temporal variation in nesting success could be explained by the occurrence of tropical cyclones. I found that occurrence of tropical cyclones within a nesting season negatively affected nesting success, whereas the occurrence of tropical cyclones one or two years before the nesting season positively affected nesting success. Additionally, results of this chapter suggest that higher ambient temperature negatively affected nesting success. Higher-intensity tropical cyclones are expected to strike the coasts of Cuba due to climate change, potentially devastating C. acutus nests if they occur during the nesting season. As the recruitment of C. acutus populations in Cuba heavily rely on nesting success, we propose incorporating information on crocodilian’s nesting success and density, as well as the impact of tropical cyclones on the latter, as key components of coastal resilience when designing plans for coastal adaptation in the context of climate change. In the last chapter, I employed data on mitochondrial DNA (mtDNA) control region and 12 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus between and among localities in South America, North America, Central America and the Greater Antilles. All analyses for both mtDNA and nuclear markers show evidence of strong population genetic structure in the American crocodile, with unique populations in each of the sampling localities. My research results reinforce previous findings showing the greatest degree of genetic differentiation between the continental C. acutus and the Greater Antillean C. acutus. Three new haplotypes unique to Venezuela were reported. These were considerably less distant from Central and North American haplotypes than Greater Antillean haplotypes. Overall evidence of this chapter suggests that Cuban and Jamaican C. acutus share a mtDNA haplotype but currently represent at least two different genetic populations when using nuclear, faster evolving, microsatellite markers. Findings of this chapter offer the first evidence of genetic differentiation among the populations of Greater Antillean C. acutus, the first ever reported haplotypes for the species in Venezuela, and provide important information for the regional planning and in-situ conservation of the species. In conclusion, research findings of my dissertation are the product of combining ecological data collected in the field, genetic data generated in the lab, and the use of a suite of classic and inference-based methodological approaches to gain a better understanding of the behavior and evolution of crocodilians. The dissertation presents the first genetic research on C. intermedius, shows the importance of coastal mangrove conservation for the persistence of C. acutus in Cuba, and depicts phylogeographic linkages among distinct C. acutus populations across the Americas and Greater Antilles. The outcomes of this research provide science-based information to influence decision-making processes for the conservation of threatened crocodilians and their habitats across the study areas.

Philosophiae Doctor - PhD / The systematic and population genetic relationships were characterised for three ecologically related euphausiid species: Euphausia lucens, E. recurva and E. vallentini. These species have different geographical distributions and life histories. All three species have a circumpolar distribution in the Southern Hemisphere while E. recurva is also distributed in the North Pacific. DNA sequence variation was determined for three regions of mitochondrial DNA and a single nuclear gene. It was conclusively demonstrated that both E. lucens and E. vallentini represent valid taxonomic species with fixed differences observed in both the nuclear and mitochondrial genes and that the low divergences previously reported for these species with 16SrRNA and CO1 resulted from a species misidentification. It was also shown that previous attempts to date the divergence between Antarctic and Sub-Antarctic euphausiid species based on 16SrRNA distances suffer from a large overestimation due to a calculation error. / South Africa

Thesis (MSc)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: This study investigated the evolution of the genus Palinurus at the higher and lower taxonomic levels. The population genetics of the spiny lobster, Palinurus delagoae, was investigated by making use of a portion of the mitochondrial DNA (mtDNA) control region (547 base pairs) that was sequenced for 285 lobsters from the southeastern coast of Africa (six sites) and 49 lobsters from Walters Shoals (one site), a submerged seamount on the Madagascar Ridge. Lobsters from these two areas shared no haplotypes and differed by at least 27 mutational steps. An analysis of molecular variance showed significant genetic partitioning, and pairwise comparisons suggested that lobsters from Walters Shoals are distinct from those of other sampling areas. Along the south east African coastline there was shallow genetic partitioning between four southern sites (South Africa) and two northern (Mozambique) sites, suggesting two Management Units along the African coast. Female gene flow along the African coast may be propagated by larval dispersal in the Mozambique and Agulhas Currents and counter-current migrations by benthic juveniles along the shelf, but the mtDNA data strongly suggest that larvae at Walters Shoals have been, or are currently still retained by other oceanographic processes. The magnitude of mtDNA divergence among lobsters from the southeastern coast of Africa and those at Walters Shoals, together with the absence of any shared haplotypes between these regions, strongly suggested that these two taxa represent distinct species. The molecular data of the large subunit ribosomal RNA, 16S rRNA (481 bp), and cytochrome oxidase subunit I, COI (520 bp) were then used for a higher level phylogenetic analysis of the genus. A total of 33 individuals (five representatives from each of the six species), and two outgroups (Projasus parkeri and Palinustus unicornutus), were subjected to maximum parsimony, maximum likelihood and Bayesian inference analyses. All analyses were conducted on both the separate data sets as well as a combination of the two genes. Bootstrap analyses of the 16S rRNA data resulted in >70% support for the monophyly of all six Palinurus species but no support could be obtained for any of the interspecific associations. Likewise, individual analyses of the COI gene resulted in strong support for the monophyly of the species. The combined data (parsimony analyses) increased the resolution considerably and apart from the monophyly of all six species, good bootstrap support was also obtained for associations among species. The topology for the maximum likelihood analyses displayed a more resolved and well supported tree when the basal ingroup taxon P. elephas was used to root the tree. The combined Bayesian analyses did not result in a well resolved topology and no significant posterior probabilities could be obtained reflecting the associations among species. / AFRIKAANSE OPSOMMING: Hierdie studie het die evolusie van die genus Palinurus by hoë en laer taksonomiese vlakke ondersoek. Die bevolkingsgenetika studie op die kreef, Palinurus delagoae, is ondersoek deur gebruik te maak van 'n gedeelte van die mitokondriale (mtDNA) kontrole-area (547 basispare) waarvan die volgorde bepaal is vir 285 krewe van die suidoos-kus van Afrika (afkomstig van ses verskillende gebiede) en 49 krewe afkomstig van Walters Shoals (een gebied), 'n ondersese berg op die Madagaskar Rand. Krewe van hierdie twee areas deel geen haplotipes nie en verskil met ten minste 27 mutasiestappe. 'n Analise van die molekulêre variansie toon dat daar 'n beduidende genetiese verdeling tussen die twee groepe is en 'n gepaarde vergelyking toon dat krewe afkomstig van Walters Shoals verskil beduidend van krewe uit ander gebiede. Volgens die vlak genetiese verdeling tussen die vier suidelike (Suid-Afrika) en twee noordelike (Mosambiek) gebiede van die suidoos-kus van Afrika wil dit voorkom of daar twee bestuurseenhede langs die kuslyn van Afrika is. Vroulike geenvloei langs hierdie kuslyn kan dalk bevarder word deur larwale verspreiding in die Mosambiek- en Agulhas- Seestrome en teenstroom migrasie van jong bodemwonende krefies op die kontinentale plaat. Die mtDNA data stel egter voor dat kreeflarwes by Walters Shoals deur ander oseanografiese prosesse steeds (of tot onlangs toe) behou word. Die grootte van mtDNA divergering tussen krewe van die suidoos-kus van Afrika en die by Walters Shoals, sowel as die afwesigheid van enige gemeenskaplike haplotipes tussen die twee gebiede, toon met beduidende sekerheid aan dat hierdie twee taksa twee unieke spesies verteenwoordig. Die molekulêre data van die 16S-rRNA (481bp) van die groot ribosomale-subeenheid en die sitochroom oksidase subeenheid, COI (520bp) is gebruik om 'n hoër resolusie filogenetiese analise van die genus te bepaal. Data van 33 individue (vyf individue uit elk van die ses spesies) en twee buitegroepe (Projasnus parkeri en Palinustus uniconutus) is geanaliseer deur gebruik te maak van die maksimum-parsimonie, die maksimum-waarskynlikheid en die Bayes-inferensie metodes. Alle analises is uitgevoer op beide die afsonderlike datastelle sowel as op die gekombineerde data van die twee gene. Analise van die 16S-rRNA data deur die skoenlusmetode (steekproefhersteekproef- metode) toon meer as 70% steun vir die monofilie van al ses Palinurus spesies maar dit toon geen steun vir enige van die interspesifieke assosiasies nie. Net so toon individuele analise van die COI geen beduidende steun vir die monofilie van die spesies. Die gekombineerde data (parsimonie) het 'n aansienlike verhoging in die resolusie teweeg gebring en behalwe vir die monofilie van al ses die spesies was daar ook goeie steun deur die skoenlusmetode vir die assosiasie tussen spesies verkry. Die topologie vir die maksimum-parsimonie het 'n goed gesteunde en hoër resolusie boom vir die gekombineerde datastel (sonder die buitegroepe) getoon. Die gekombineerde Bayesanalise het nie 'n soortgelyke boom opgelewer nie en die assosiasie tussen die spesies is nie ondersteun nie aangesien geen beduidende a posteriori-waarskynlikheid verkry kon word nie.

<p>The systematic and population genetic relationships were characterised for three ecologically related euphausiid species: Euphausia lucens, E. recurva and E. vallentini. These species have different geographical distributions and life histories. All three species have a circumpolar distribution in the Southern Hemisphere while E. recurva is also distributed in the North Pacific. DNA sequence variation was determined for three regions of mitochondrial DNA and a single nuclear gene. It was conclusively demonstrated that both E. lucens and E. vallentini represent valid taxonomic species with fixed differences observed in both the nuclear and mitochondrial genes and that the low divergences previously reported for these species with 16SrRNA and CO1 resulted from a species misidentification. It was also shown that previous attempts to date the divergence between Antarctic and Sub-Antarctic euphausiid species based on 16SrRNA distances suffer from a large overestimation due to a calculation error.</p>

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references. / The overarching goal of this thesis was to investigate marine benthic invertebrate phylogenetics and population genetics, focused on the phylum Annelida. Recent expansions of molecular methods and the increasing diversity of available markers have allowed more complex and fine-scale questions to be asked at a variety of taxonomic levels. At the phylogenetic level, whole mitochondrial genome sequencing of two polychaetes (the deep-sea tubeworm Riftia pachyptila and the intertidal bamboo worm Clymenella torquata) supports the placement of leeches and oligochaetes within the polychaete radiation, in keeping with molecular evidence and morphological reinvestigations. This re-interpretation, first proposed by others, synonomizes "Annelida" and "Polychaeta", and lends further support to the inclusion of echiurids, siboglinids (previously called vestimentiferans) within annelids, and sipunculans as close allies. The complete mt-genome of C. torquata was then rapidly screened to obtain markers useful in short timescale population genetics. / (cont.) Two quickly evolving mitochondrial markers were sequenced from ten populations of C. torquata from the Bay of Fundy to New Jersey to investigate previous hypotheses that the Cape Cod, MA peninsula is a barrier to gene flow in the northwest Atlantic. A barrier to gene flow was found, but displaced south of Cape Cod, between Rhode Island and Long Island, NY. Imposed upon this pattern was a gradient in genetic diversity presumably due to previous glaciation, with northern populations exhibiting greatly reduced diversity relative to southern sites. These trends in C. torquata, combined with other recent short time scale population genetic research, highlight the lack of population genetics models relevant to marine benthic invertebrates. To this end, I constructed a model including a typical benthic invertebrate life cycle, and described the patterns of genetic differentiation at the juvenile and adult stages. Model analysis indicates that selection operating at the post- settlement stage may be extremely important in structuring genetic differentiation between populations and life stages. Further, it demonstrates how combined genetic analysis of sub-adult and adult samples can provide more information about population dynamics than either could alone. / by Robert M. Jennings. / Ph.D.