Doctor of Philosophy / Department of Biology / Donald W. Kaufman / Glennis A. Kaufman / Little is known about nightly activity patterns of nocturnal small mammals under natural conditions, and how these activity patterns might be affected by photoperiod, season, and sex, age, and reproductive status of individuals. The main objectives of this research were: 1) to find an appropriate method for marking individual deer mice (Peromyscus maniculatus) so that their activity could be monitored remotely; 2) to design a portable activity-monitoring system to investigate temporal patterns of shelter use by deer mice under natural conditions; 3) to determine the influence of environmental conditions such as photoperiod and season on nightly activity of deer mice; and 4) to compare effects of demographic or physiological factors such as sex, age, and reproductive status on nightly activity of deer mice at artificial burrows in tallgrass prairie. In general, commencement of activity was correlated positively with timing of sunset, and time of retirement to the burrow was correlated positively with sunrise. Among adults, males first emerged from the burrow earlier and made more trips of shorter duration in a night than did females, although total duration of trips was similar. Return visits and subsequent stays typically were shorter for males than females, but total time spent in the burrow and retirement time relative to sunrise were similar for both sexes. Young deer mice emerged significantly later, made more trips of shorter duration, spent less total time outside, and retired to their burrow earlier than adults. Reproductive females emerged later, made fewer trips of generally longer duration, and spent shorter total amounts of time away from the burrow each night than non-reproductive females. Return visits of reproductive females were of longer duration than non-reproductives, but total time spent inside and time of retirement for the night did not differ relative to reproductive status. From parturition through lactation, activity of females showed a number of directional trends. Results suggest that under natural conditions, activity patterns of deer mice are highly variable but responsive to both the changing physical environment and internal conditions related to sex-specific maximization of fitness.

Master of Science / Department of Biology / Brett K. Sandercock / Samantha Wisely / In birds, the offspring of females in socially monogamous species can be sired not only by their social partner (within-pair mating) but also by other males (extra-pair mating), resulting in broods of mixed paternity. Several hypotheses have been proposed which attempt to explain the adaptive significance of this behavior, including the genetic diversity hypothesis, the good genes hypothesis, the genetic compatibility hypothesis and the fertility insurance hypothesis. I report results of a 5 year population study of the Upland Sandpiper (Bartramia longicauda) at Konza Prairie Biological Station in northeast Kansas. My objective was to determine the genetic mating system of this socially monogamous shorebird, and determine which of the genetic hypotheses best explains the patterns of extra-pair paternity (EPP) in the population. As part of the analysis, I optimized laboratory protocols for genetic sexing of our monomorphic study species. Potential errors in molecular sexing have been previously described but usually result in females being misidentified as males. Here, I report evidence that events in PCR reactions can lead to the opposite error, with males misidentified as females. I recommend the use of multiple primer sets and large samples of known-sex birds for validation when designing protocols for molecular sex analysis. I genotyped birds and tested for the existence of EPP in 58 family groups of Upland Sandpipers. I found 15% of chicks and 30% of broods were the result of extra-pair paternity in this population, which is high in comparison to other socially monogamous shorebirds. Only 2% of chicks and 2% of broods were attended by females unrelated to the young. I tested ecological covariates known to influence EPP in other birds including relatedness of mated pairs, morphology of the within-pair male, and nest initiation date, as well as variables which signify genetic benefits, including morphology of the offspring and offspring heterozygosity, but found no significant relationships. None of the prevailing genetic hypotheses can fully explain the high rates of EPP in this population of Upland Sandpipers. However, the discovery of fine-scale genetic structure in female birds, but not in males, suggests female natal philopatry or male-biased dispersal. This sex-specific genetic structure could be a mechanism of inbreeding avoidance, thereby eliminating the need for females to choose mates based on relatedness. This study provides the first estimates of EPP for the socially monogamous Upland Sandpiper, and provides evidence that the inbreeding avoidance mechanism of engaging in extra-pair copulations does not seem to be as important in Upland Sandpipers as in other socially monogamous shorebirds. Future research should include the identification of extra-pair males and the determination of offspring fitness after departure from the nest.

Doctor of Philosophy / Department of Biology / Philip S. Gipson / Understanding factors that influence genetic variability, demographic vital rates, and resource selection is important for conservation and management of wildlife populations. I examined factors influencing microsatellite variability, demographic vital rates, and habitat use for a reintroduced elk (Cervus elaphus) population at Fort Riley, Kansas based on data collected from 2003 – 2007. Levels of allelic richness, observed heterozygosity, and expected heterozygosity for the Fort Riley population were intermediate to other North American elk populations. Genetic variability in restored North American elk populations was not well explained by founding population size, number of founding populations, or number of years since the last translocation. I examined the influence of demographic vital rates on the rate of population change to test the hypothesis that variability in calf survival has a greater influence on rates of population change than adult survival. Survival for prime-age adult elk had the highest stage-specific elasticity value, but life-stage simulation analysis indicated that variation in calf survival had the highest correlation with variation in population growth rate. These results suggest that calf survival varies temporally and is the vital rate most directly related to variation in population growth rate for this population. I assessed the relative influence of risk-related and resource-related factors on elk habitat selection by comparing predictor variables included in top resource selection function models at the landscape and home range scales. All predictor variables, with the exception of fall and spring prescribed burns, were included in top models across seasons at both spatial scales. Elk selected low elevation areas, gentle slopes, edge habitat, and areas close to streams at both spatial scales. At the landscape scale, elk generally avoided roads and preferred areas on or near Fort Riley. At both spatial scales, elk used riparian woodlands more frequently than grasslands and selected for agricultural crops when seasonally available. These findings do not support the idea that risk-related factors are the primary determinant of elk habitat use at the landscape scale as has been found for ungulates in areas with natural predators.

Beaked whales (family Ziphiidae) are one of the least known of all mammalian groups. The majority of species have been described from only a handful of specimens. Found in deep ocean waters, these species are widespread and often sexually dimorphic. Little is known of intra-specific variation in morphology, and many species are very similar in external appearance. A reference database of mitochondrial DNA sequences was compiled for all 20 recognised ziphiid species to aid in species identification. All reference sequences were derived from validated specimens, which were often represented only by bone or teeth. DNA was obtained from this ‘historic’ material using ‘ancient’ DNA methods. For three species, holotypes were sampled. Phylogenetic analyses using this database led to the discovery of a new, previously unrecognised species of beaked whale (Mesoplodon perrini), new specimens of Longman's beaked whale (Indopacetus pacificus), a species known previously from only two partial skulls and the synonymy of a third (M. traversii = M. bahamondi). Phylogenetic reconstructions based on sequence data from three mitochondrial and two nuclear loci (total, 2815 bp) using neighbour joining, parsimony, and maximum likelihood methods, resolved many of the sister-species relationships in this group. Inferred relationships among Mesoplodon beaked whales indicated that cranial and tooth morphology may be far more variable between closely related species than previously assumed. No support was found for a linear-progression of tooth form as suggested by Moore (1968) in his phenetic evaluation of relationships among the Ziphiidae. The geographic distribution of Mesoplodon species with similar or divergent tooth morphology is likely due to a combination of sexual selection and selection for species recognition. Both hypotheses predict similar patterns, such as dissimilar tooth morphology among species with sympatric or parapatric distributions. However, only sexual selection appears to offer an explanation for why there are so many Mesoplodon beaked whales. Investigation of mtDNA diversity among a number of beaked whale species indicated that nucleotide diversity was generally lower in this group than in other wide-ranging oceanic cetaceans. The cause of this low diversity was not clear but may be indicative of overall low abundance. Particularly low levels of diversity were found in Baird's beaked whale Berardius bairdii , Arnoux's beaked whale B. arnuxii and the northern bottlenose whale Hyperoodon ampullatus. Strong geographic structure in haplotype frequencies was observed among a worldwide sample of Cuvier's beaked whales Ziphius cavirostris. / Subscription resource available via Digital Dissertations only.

Beaked whales (family Ziphiidae) are one of the least known of all mammalian groups. The majority of species have been described from only a handful of specimens. Found in deep ocean waters, these species are widespread and often sexually dimorphic. Little is known of intra-specific variation in morphology, and many species are very similar in external appearance. A reference database of mitochondrial DNA sequences was compiled for all 20 recognised ziphiid species to aid in species identification. All reference sequences were derived from validated specimens, which were often represented only by bone or teeth. DNA was obtained from this ‘historic’ material using ‘ancient’ DNA methods. For three species, holotypes were sampled. Phylogenetic analyses using this database led to the discovery of a new, previously unrecognised species of beaked whale (Mesoplodon perrini), new specimens of Longman's beaked whale (Indopacetus pacificus), a species known previously from only two partial skulls and the synonymy of a third (M. traversii = M. bahamondi). Phylogenetic reconstructions based on sequence data from three mitochondrial and two nuclear loci (total, 2815 bp) using neighbour joining, parsimony, and maximum likelihood methods, resolved many of the sister-species relationships in this group. Inferred relationships among Mesoplodon beaked whales indicated that cranial and tooth morphology may be far more variable between closely related species than previously assumed. No support was found for a linear-progression of tooth form as suggested by Moore (1968) in his phenetic evaluation of relationships among the Ziphiidae. The geographic distribution of Mesoplodon species with similar or divergent tooth morphology is likely due to a combination of sexual selection and selection for species recognition. Both hypotheses predict similar patterns, such as dissimilar tooth morphology among species with sympatric or parapatric distributions. However, only sexual selection appears to offer an explanation for why there are so many Mesoplodon beaked whales. Investigation of mtDNA diversity among a number of beaked whale species indicated that nucleotide diversity was generally lower in this group than in other wide-ranging oceanic cetaceans. The cause of this low diversity was not clear but may be indicative of overall low abundance. Particularly low levels of diversity were found in Baird's beaked whale Berardius bairdii , Arnoux's beaked whale B. arnuxii and the northern bottlenose whale Hyperoodon ampullatus. Strong geographic structure in haplotype frequencies was observed among a worldwide sample of Cuvier's beaked whales Ziphius cavirostris. / Subscription resource available via Digital Dissertations only.

Beaked whales (family Ziphiidae) are one of the least known of all mammalian groups. The majority of species have been described from only a handful of specimens. Found in deep ocean waters, these species are widespread and often sexually dimorphic. Little is known of intra-specific variation in morphology, and many species are very similar in external appearance. A reference database of mitochondrial DNA sequences was compiled for all 20 recognised ziphiid species to aid in species identification. All reference sequences were derived from validated specimens, which were often represented only by bone or teeth. DNA was obtained from this ‘historic’ material using ‘ancient’ DNA methods. For three species, holotypes were sampled. Phylogenetic analyses using this database led to the discovery of a new, previously unrecognised species of beaked whale (Mesoplodon perrini), new specimens of Longman's beaked whale (Indopacetus pacificus), a species known previously from only two partial skulls and the synonymy of a third (M. traversii = M. bahamondi). Phylogenetic reconstructions based on sequence data from three mitochondrial and two nuclear loci (total, 2815 bp) using neighbour joining, parsimony, and maximum likelihood methods, resolved many of the sister-species relationships in this group. Inferred relationships among Mesoplodon beaked whales indicated that cranial and tooth morphology may be far more variable between closely related species than previously assumed. No support was found for a linear-progression of tooth form as suggested by Moore (1968) in his phenetic evaluation of relationships among the Ziphiidae. The geographic distribution of Mesoplodon species with similar or divergent tooth morphology is likely due to a combination of sexual selection and selection for species recognition. Both hypotheses predict similar patterns, such as dissimilar tooth morphology among species with sympatric or parapatric distributions. However, only sexual selection appears to offer an explanation for why there are so many Mesoplodon beaked whales. Investigation of mtDNA diversity among a number of beaked whale species indicated that nucleotide diversity was generally lower in this group than in other wide-ranging oceanic cetaceans. The cause of this low diversity was not clear but may be indicative of overall low abundance. Particularly low levels of diversity were found in Baird's beaked whale Berardius bairdii , Arnoux's beaked whale B. arnuxii and the northern bottlenose whale Hyperoodon ampullatus. Strong geographic structure in haplotype frequencies was observed among a worldwide sample of Cuvier's beaked whales Ziphius cavirostris. / Subscription resource available via Digital Dissertations only.

Beaked whales (family Ziphiidae) are one of the least known of all mammalian groups. The majority of species have been described from only a handful of specimens. Found in deep ocean waters, these species are widespread and often sexually dimorphic. Little is known of intra-specific variation in morphology, and many species are very similar in external appearance. A reference database of mitochondrial DNA sequences was compiled for all 20 recognised ziphiid species to aid in species identification. All reference sequences were derived from validated specimens, which were often represented only by bone or teeth. DNA was obtained from this ‘historic’ material using ‘ancient’ DNA methods. For three species, holotypes were sampled. Phylogenetic analyses using this database led to the discovery of a new, previously unrecognised species of beaked whale (Mesoplodon perrini), new specimens of Longman's beaked whale (Indopacetus pacificus), a species known previously from only two partial skulls and the synonymy of a third (M. traversii = M. bahamondi). Phylogenetic reconstructions based on sequence data from three mitochondrial and two nuclear loci (total, 2815 bp) using neighbour joining, parsimony, and maximum likelihood methods, resolved many of the sister-species relationships in this group. Inferred relationships among Mesoplodon beaked whales indicated that cranial and tooth morphology may be far more variable between closely related species than previously assumed. No support was found for a linear-progression of tooth form as suggested by Moore (1968) in his phenetic evaluation of relationships among the Ziphiidae. The geographic distribution of Mesoplodon species with similar or divergent tooth morphology is likely due to a combination of sexual selection and selection for species recognition. Both hypotheses predict similar patterns, such as dissimilar tooth morphology among species with sympatric or parapatric distributions. However, only sexual selection appears to offer an explanation for why there are so many Mesoplodon beaked whales. Investigation of mtDNA diversity among a number of beaked whale species indicated that nucleotide diversity was generally lower in this group than in other wide-ranging oceanic cetaceans. The cause of this low diversity was not clear but may be indicative of overall low abundance. Particularly low levels of diversity were found in Baird's beaked whale Berardius bairdii , Arnoux's beaked whale B. arnuxii and the northern bottlenose whale Hyperoodon ampullatus. Strong geographic structure in haplotype frequencies was observed among a worldwide sample of Cuvier's beaked whales Ziphius cavirostris. / Subscription resource available via Digital Dissertations only.

Beaked whales (family Ziphiidae) are one of the least known of all mammalian groups. The majority of species have been described from only a handful of specimens. Found in deep ocean waters, these species are widespread and often sexually dimorphic. Little is known of intra-specific variation in morphology, and many species are very similar in external appearance. A reference database of mitochondrial DNA sequences was compiled for all 20 recognised ziphiid species to aid in species identification. All reference sequences were derived from validated specimens, which were often represented only by bone or teeth. DNA was obtained from this ‘historic’ material using ‘ancient’ DNA methods. For three species, holotypes were sampled. Phylogenetic analyses using this database led to the discovery of a new, previously unrecognised species of beaked whale (Mesoplodon perrini), new specimens of Longman's beaked whale (Indopacetus pacificus), a species known previously from only two partial skulls and the synonymy of a third (M. traversii = M. bahamondi). Phylogenetic reconstructions based on sequence data from three mitochondrial and two nuclear loci (total, 2815 bp) using neighbour joining, parsimony, and maximum likelihood methods, resolved many of the sister-species relationships in this group. Inferred relationships among Mesoplodon beaked whales indicated that cranial and tooth morphology may be far more variable between closely related species than previously assumed. No support was found for a linear-progression of tooth form as suggested by Moore (1968) in his phenetic evaluation of relationships among the Ziphiidae. The geographic distribution of Mesoplodon species with similar or divergent tooth morphology is likely due to a combination of sexual selection and selection for species recognition. Both hypotheses predict similar patterns, such as dissimilar tooth morphology among species with sympatric or parapatric distributions. However, only sexual selection appears to offer an explanation for why there are so many Mesoplodon beaked whales. Investigation of mtDNA diversity among a number of beaked whale species indicated that nucleotide diversity was generally lower in this group than in other wide-ranging oceanic cetaceans. The cause of this low diversity was not clear but may be indicative of overall low abundance. Particularly low levels of diversity were found in Baird's beaked whale Berardius bairdii , Arnoux's beaked whale B. arnuxii and the northern bottlenose whale Hyperoodon ampullatus. Strong geographic structure in haplotype frequencies was observed among a worldwide sample of Cuvier's beaked whales Ziphius cavirostris. / Subscription resource available via Digital Dissertations only.

Doctor of Philosophy / Department of Biology / Brett K. Sandercock / The reproductive strategies of avian brood parasites and the behavioral responses of their hosts have served as a model of co-evolution in nature. Host adaptations to reduce the costs of parasitism are countered with novel parasite behaviors that increase the success of the parasite and thereby decrease host productivity. Not all host species possess anti-parasite defense behaviors, and parasitism by Brown-headed Cowbirds (Molothrus ater) may cause population declines in some species. Bell’s Vireo (Vireo bellii) is a small-bodied cowbird host that fails to fledge young if successfully parasitized. Although vireos desert naturally parasitized nests, the cues that cause desertion have not been identified. Understanding how parasitism affects vireo productivity is important because cowbird removal is an integral component of the recovery efforts for the endangered Least Bell’s Vireo (V. b. pusillus) in California. However, it is generally unknown how cowbird removal affects vireo productivity. To address these issues, I monitored the productivity of vireos nesting in Kansas at the Konza Prairie Biological Station, conducted a clutch manipulation experiment, and experimentally removed cowbirds. In addition, I used stable isotope analysis to determine if recently fledged cowbird young could be assigned to habitats or host species. I found that vireos did not desert nests due to the presence of a cowbird egg; rather egg removal by cowbirds caused desertion, which is a generalized response in many taxa of birds. Cowbird removals decreased parasitism of vireo nests by approximately 36% and led to a 2-fold increase in vireo productivity per pair. Cowbird productivity from vireo pairs increased because fewer parasitized nests were deserted and parasitized nests on removal plots had a higher probability of success. No cowbird removal study has reported an increase in cowbird productivity in response to trapping. Cowbird nestlings from prairie plots and shrub plots differed in carbon and nitrogen isotope compositions, and 87% of locally produced juvenile cowbirds were classified with nestlings from shrub plots. Thus, the continued expansion of woody plants into tallgrass prairie may result in local increases in cowbird productivity.