Zooplankton samples were collected from 166 Oregon lakes. The lakes included a wide range in size, trophic status, and water quality. Lakes were located throughout the state. Zooplankton were identified using standard taxonomic keys and counted. Seventy-four species were identified from the 200 total samples, including 32 species of cladocera, 22 copepods, and 11 rotifers. Two species of copepod were recorded for the first time in Oregon: Diaptomus mississippiensis and Diaptomus pallidus. Seven species had widespread distributions throughout most of the watersheds in the state. Seventeen other species had distributions restricted to eastern, central, or western Oregon. The remaining species were either rare or had random distributions.

The prediction and analysis of changes in the numbers of biological populations rest on mathematical formulations of demographic events (births and deaths) classified by the age of individuals. The development of demographic theory when birth and death rates vary statistically over time is the central theme of this work. A study of the standard Leslie model for the demographic dynamics of populations in variable environments is made. At each time interval a Leslie matrix of survival rates and fertilities of a population is chosen according to a Markov process and the population numbers in different age classes are computed. Analytical bounds are developed for the logarithmic growth rate and the age-structure of a population after long times. For a two dimensional case, it is shown analytically that a uniform distribution results for the age-structure if the survival rate from the first to the second age-class is a uniformly distributed random quantity with no serial auto correlation. Numerical studies are made which lead to similar conclusions when the survival rate obeys other distributions. It is found that the variance in the survival parameter is linearly related to the variance in the age structure. An efficient algorithm is developed for numerical simulations on a computer by considering a time sequence of births rather than whole populations. The algorithm is then applied to an example in three dimensions to calculate a sequence of births when the survival rate from the first to the second age-class is a random parameter. Numerical values for the logarithmic growth rate and the logarithmic variance for a population and the probability of extinction are obtained and then compared to the analytical results reported here and elsewhere.

The series Californicae is a natural grouping of Iris species native to Oregon, Washington and California. Natural and experimental hybridization is characteristic of the series which has led to confusing taxonomies for some species. Populations of species belonging to this series and found on the northwestern slopes of the Siskiyou Mountains cf southwestern Oregon and adjacent California were investigated. Methods used were numerical classification techniques for morphological characters including both discriminant and K-means cluster analyses and a chemotaxonomi c analysis of flavonoid pigments using thin layer chromatography.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg. in fulfilment of the requirements tor the degree of Master of Science / This thesis develops the theoretical basis of the qualitative frame based modelling technique, a paradigm recently proposed by Starfield for the modelling of ecosystems with a multiplicity of stable states. This technique is a refinement of the State-and- Transition conceptual model of Westoby et al which involves the division of the ecosystem dynamics into a catelog of stable 'states' and a suite of transitions between these states. The frame models of Starfield associate with each stable configuration of the ecosystem a qualitative rule based model for the key processes in that stable configuration. The aims of this thesis are the following, 1. A rigorous definition of frame modelling of dynamic ecosystems is proposed, and this theoretical foundation is used to demonstrate that qualitative frame models may be used to mode! dynamic ecosystems to an arbitrary accuracy. 2. The development of implementation software. A qualitative rule based frame modelling environment is presented. and a specification for an improved environment is proposed based on the theoretical work. / Andrew Chakane 2019

Factors affecting juvenile survival are poorly known in the world’s most northern antelope, the endangered saiga (Saiga tatarica), yet they are fundamental for understanding what drives population change. For saiga neonates monitored in Sharga Nature Reserve, western Mongolia, during 2008–2010, male and single calves were heavier than those of female and twins, respectively. However, there was no significant difference in seasonal and annual survival rate between male and female or singletons and twins. Litter size and birth mass varied among years, and there was a negative relationship between these variables. Multiple regression models suggest that summer precipitation in previous years and spring mean temperature explained inter-annual variations in twinning rate, and mortality was highest during summer. Covariates providing the best model fit included year, litter size, and body weight, suggesting that environmental conditions influence twinning rates and body mass may play a key role in neonate survival rate in the first year. We identified 3 sources of mortality – predation by raptors, foxes (red and corsac, Vulpes vulpes and V. corsac), and lynx (Lynx lynx). Most predation was by raptors, such as golden eagles (Aquila chrysaetos) and cinereous vulture (Aegypius monachus). Our results point to both environmental and biotic factors affecting juvenile survival.

Throughout the eastern United States, the spread of the hemlock woolly adelgid, Adelges tsugae Annand, has caused high mortality of eastern hemlocks Tsuga canadensis (L.). We recorded overwintering survival and fecundity of A. tsugae, and tree new growth at sites in the northeastern and southeastern United States and in a common garden experiment in Massachusetts. Overwintering mortality of A. tsugae was much higher in the north (87%) than the south (37%) in 2009, and showed significantly positive density-dependence in the north only. In 2010, overwintering mortality decreased in both regions but remained higher in the north (54%) than the south (34%), and, unlike 2009, density-dependent mortality was strongly negative in the north, and positive in the south. In both years, sistens fecundity was significantly higher in the south than the north, but we observed no density-dependent trends, and fecundity measurements were similar in the two years. The regional discrepancies in fecundity suggested the possibility of an evolutionary trade-off between overwintering mortality and sistens fecundity. However, when we reared samples in a common garden, we found that source region had no effect on either sistens fecundity or overwintering mortality, which suggests observed regional differences can be attributed to environmental factors rather than genetic differences. In our regional studies, branch samples from the north had significantly more new growth than those from the south in both 2009 and 2010, even though A. tsugae densities were comparable. This difference persisted in the common garden wherein branches inoculated with northern-derived A. tsugae had significantly higher new growth than those infested with southern-derived A. tsugae. These findings raise the possibility that A. tsugae may be evolving towards reduced virulence. If true, these findings may help explain why A. tsugae is killing hemlocks much more slowly now in New England than it did when it first invaded this region more than 20 years ago, or as it is doing now in more recently invaded regions in the southern United States.

Researchers have investigated several factors that could alter fetal growth, including nutrient restriction (Valiente et al., 2021), hair shedding (Gray et al., 2011), and extreme hot and cold temperatures (Davidson et al., 2022). Hot temperatures and increased humidity percentages in the southeast United States caused researchers to investigate the hair coats of Angus cattle in the commercial production setting. An improvement in fiber digestibility and calf birth and weaning weights has been observed in Angus dams that shed 50% of the winter hair coat by May (Gray et al., 2011; Burnett et al., 2021). Our objective of this experiment was to investigate the nutrient digestibility of Angus calves born to cows that on average, shed early compared to calves from cows that shed later. Newly weaned, purebred Angus bull calves (early; n = 6, late; n = 6) were housed in metabolism crates for 10 d. Prior to the trial, calves had a 14 d adaption period to a 14% CP textured feed (CPC 14% Developer, CPC Commodities, Fountain Run, KY) and offered ad libitum Cynodon dactlyon hay and water. After 3 d crate acclimation period, urine, feces, orts, and hay samples were collected for 7 d. Concentrate was offered at 0.25% of average BW. Approximately 5% samples were taken of feces, and urine samples had 1-1.5% of 25% metaphosphoric acid added to prevent ammonia volatilization, and both collections were composited by animal. Orts were collected at 0600 h daily, dried, and composited by animal. Laboratory analysis included dry matter (DM), organic matter (OM), Ash, neutral detergent fiber (NDF), acid detergent fiber (ADF), Kjeldahl N (CP), and fat. Data were analyzed using the GLM procedure of SAS 9.4 in a completely randomized design with calf as the experimental unit. Significant (P ≤ 0.05) means were separated using Fischer’s protected LSD. The model for intake included average daily DM and OM (kg) and adjusted by body weight (BW%). For digestibility analysis, the model included: DM, OM, ash, NDF, ADF, hemi-cellulose (HC), CP, and fat. The N retention model included: N retained (g/d), N retained/consumed (%), and N retained/DM intake (%). There were no differences between early or late calves for DM intake (5.502 ± 0.2774 kg/d; 2.251 ± 0.1247 %BW), or OM intake (5.199 ± 0.2591 kg/d; 2.128 ± 0.1166 %BW). There were no differences in digestibility for either group for DM, OM, Ash, NDF, ADF, HC, CP, or fat (Table 1.). There were also no differences in N retention in either group of calves (3.686 ± 2.0242 g/d; 4.366 ± 2.3964 %; 0.064 ± 0.0355 %). Replication and further research are needed in this area to adequately understand factors influencing nutrient digestibility in calves born from early and late shedding dams.

There is an increasing interest in the use of autonomous recording units as an alternative survey method to point count surveys conducted by human observers; however, questions remain about whether or not these recording units perform similarly to point count surveys and produce valid, comparable results. The use of individual listeners to transcribe the acoustic data collected by autonomous recording units is a common method for the analysis of recorded acoustic data, but potential variability among transcribers raises questions about the standardization of listening protocols to decrease inconsistencies in transcription results. Autonomous recording units have been used to monitor birds in and around Brimfield State Forest in Brimfield, Massachusetts since 2012, after a tornado severely damaged a large area of the forest and surrounding properties. In 2016 and 2017, I conducted 71 10-minute point count surveys while simultaneously recording the survey with an autonomous recording unit in three habitat types in and around Brimfield State Forest in Brimfield, Massachusetts. I transcribed the acoustic data from the recordings and compared it to the results of the point count surveys to determine if autonomous recording units performed as well as point count surveys. To assess variability among listeners, four listeners transcribed the same sample of 30 recordings and a sub-sample of 6 of those recordings that were created during the 2014 field season using two different listening protocols. The first protocol instructed listeners to play each recording straight through without stopping, and the second protocol instructed listeners to stop and replay any part of the recording they needed to and also use outside sources to aid in species identification. I compared the number of species, individuals, distant individuals, and mean counts (uncorrected abundance), corrected abundance and detectability of focal species between both survey methods, among all listeners using both listening protocols, and where possible between habitat types to assess differences in method performance and listener variability. I tested for correlation between autonomous recording units and point counts using the uncorrected and corrected abundance estimates. The number of species and number of individuals detected did not differ between survey methods overall and for each habitat individually; however, in each habitat type, more individuals were classified as distant by autonomous recording units overall for all habitats. The number of species detected did not differ between listeners overall and for in each habitat using either listening protocol. The number of individuals and distant individuals detected differed significantly between listeners and within certain habitats using the first listening protocol. There were no differences in the number of species, individuals, or distant individuals detected overall between listeners using the second listening protocol, but there were significant differences in individuals and distant individuals detected between habitats by listeners. Corrected and uncorrected abundance estimates between autonomous recording units and point count surveys were highly correlated, and there were no differences in detection probabilities for the focal 23 species between survey methods and among habitat types. Only 2 out of 18 focal species indicated a significant difference in detection probability between listeners using both listening protocols. Based on the results of my study, I conclude that autonomous recording units perform at least as well as human observers conducting point count surveys, and that multiple listeners transcribing the same acoustic data do not show high levels of variation in the results of their transcriptions.

Marine shellfish play a vital role in intertidal ecosystems and coastal communities, but many of these fisheries are small-scale and lack the necessary monitoring to ensure long-term sustainability. Effective management often requires information on key demographic parameters, such as population status, reproduction and growth. Pismo clams (Tivela stultorum) are a culturally important and iconic species in California, which supported a thriving commercial and recreational fishery throughout much of the 1900’s. However, Pismo clam populations have declined statewide in recent decades and are attributed to human harvest and predation by California sea otters (Enhydra lutris); However, no studies have examined their populations, population drivers, or life history for at least 40 years. Managers require updated and expanded information on populations, habitat associations, reproduction and growth rates to effectively manage, regulate, and recover Pismo clam in California. In Chapter 1, we investigated current Pismo clam population levels in California and examined the role of abiotic and biotic factors as correlates of clam abundance. We quantified Pismo clam presence, density and biomass at 38 sites in California during 2018 and 2019. Our results indicate that while human population density does not appear to drive clam populations, median sediment grain size is an important predictor for Pismo clams on open coast beaches. As median grain size increases, the probability of clam presence, density, and biomass decreases, suggesting that the composition of beach habitat is a critical factor regulating Pismo clam populations. Additionally, clam density and biomass are significantly higher on beaches north of Point Conception compared to beaches south. This suggests that Pismo clam population declines are more complicated than conventional wisdom suggests. Overall, Pismo clam densities are lower and size structures are shifted towards smaller sizes than historical accounts. This study is the most comprehensive set of population surveys to date and identifies key factors associated with Pismo clam abundance, which may be used to inform management and guide restoration and recovery of this once iconic species. In Chapter 2, we examined life history characteristics of Pismo clams in California. Specifically, we investigated the annual reproductive cycle of Pismo clams in California, pairing multiple metrics within a single study to describe the sex ratio, gonad development stages, body condition index, and length at sexual maturity. Further, we examine age-length relationships across California to provide estimates of age structure and growth rate, which will better inform recovery timelines for the recreational fishery in California. Our results indicate that the sex ratio is 1:1, peak spawning occurred in late summer, and clams can spawn in their first year (<20 >mm). Cycles of body condition were influenced primarily by mean monthly sea surface temperature, but mean monthly chlorophyll-a concentration, photoperiod, clam size, and year were also important. Body condition was significantly correlated with the proportion of clams in the Ripe stage. Thus, body condition has the potential to be a rapid, inexpensive proxy for monitoring reproduction in Pismo clams, potentially providing useful information about changes in reproductive patterns. Finally, examination of age-length relationships for Pismo clams suggest that clams may require over 13 years to reach a legally harvestable size (114 mm across most of California). The estimated age at legal size is substantially older than historical estimates, which suggested that Pismo clams could reach legally harvestable size in as few as 6 years. Collectively, this work represents a significant advance in our knowledge of the biology and ecology of this iconic and culturally important species. Furthermore, it provides vital information on the current population status, reproduction, and growth rates to inform management, regulation, and potential recovery of Pismo clams in California.

Managing Monarch butterfly overwintering groves: making room among the eucalyptus Proper management and conservation of the coastal California overwintering sites used by western Monarch butterflies (Danaus plexippus L.) is critical for continued use of these sites by monarchs. Many management efforts are currently concentrating on eucalyptus-only sites because of the prevailing notion that monarchs prefer eucalyptus over native tree species. Yet, whether a preference exists or not has never been tested. Herein, we test the “eucalyptus preference” hypothesis with data from five overwintering sites comprised of blue gum eucalyptus (Eucalyptus globulus) and at least one other native tree species from fall 2009 to spring 2012. We found that when monarchs clustered disproportionately on a tree species relative to its availability, they clustered significantly more than expected on native trees and significantly less than expected on eucalyptus. Also, in years when the overwintering population was highest, monarchs clustered disproportionately on native conifers, and they often switched from clustering on eucalyptus in the early winter to native conifers in the middle or late winter. Our results suggest that overwintering groves should be managed to include a mixture of tree species. We cannot recommend simply planting more eucalyptus. At overwintering sites in central coastal California, native conifers such as Monterey cypress (Hesperocyparis macrocarpa) and pitch canker-resistant Monterey pine (Pinus radiata) should be planted as replacements for blue gum eucalyptus in areas where trees are likely to fall, and around the perimeter of groves. Testing the Monarch butterfly eucalyptus preference hypothesis at California overwintering sites Western Monarch butterflies (Danaus plexippus L.) overwinter in groves of native and non-native trees along the California coast. Eucalyptus is abundant in coastal counties, and overwintering monarchs utilize this type of tree more than any other. This has led to the belief that monarchs prefer eucalyptus. Yet whether a preference exists has never been tested. We tested the “eucalyptus preference” hypothesis at five California overwintering sites with canopies comprised of eucalyptus and at least one native conifer species. We found that at no time over the course of three years did monarchs cluster on trees in proportion to their availability in the canopy. Overall, they did not cluster on one tree species significantly more frequently than another, indicating that monarchs do not prefer eucalyptus—or any tree species—all of the time. However, more often than not monarchs clustered significantly more than expected on native trees, particularly at midseason when the weather was most inclement. They also clustered disproportionately on native conifers when the overwintering population size was highest. At most sites monarchs exhibited tree switching, shifting from eucalyptus to native conifers in the middle or late winter. Based on these results, we reject the “eucalyptus preference” hypothesis. In its place, we propose the “conditional preference hypothesis”, wherein monarchs are predicted to prefer cluster trees according to microclimate conditions and prefer alternate trees within a site as climatic conditions change. Rejection of the eucalyptus preference hypothesis suggests that sites comprised exclusively of eucalyptus may not offer monarchs a suitable range of microhabitats, and further suggests we should rethink “eucalyptus-centric” management. Monarch butterflies overwintering in coastal California: low site fidelity and high intersite movement Western monarch butterflies (Danaus plexippus L.) overwinter in large aggregations at hundreds of sites along the California coast. Management plans and census methods are both founded on the assumption that individual monarchs arrive at an overwintering site in the fall and stay at that site for the winter. Though populations potentially coalesce en masse from autumnal sites onto climax overwintering sites, very little individual movement between sites is inferred. Monarch movement is therefore thought to be primarily into sites (as opposed to out of or among them). We refer to this assumption and inference as the accrual hypothesis. In light of previous studies that provide evidence for movement among sites, we propose that overwintering monarchs may belong to a superpopulation. The existence of a superpopulation comprised of individuals moving in and out of sites would force us to rethink our ideas of landscape-level resource use by monarchs, our site-centric (rather than landscape-level) management strategies, and our abundance estimation techniques, which employ closed population models. We tested the closed population model, the accrual hypothesis, and the superpopulation model at three California overwintering sites using a mark-resight study design. We found that a large proportion of the monarchs at a site moved among (into and out of) monitored sites, both while the population size increased in October and November, and while the population appeared to exhibit an equilibrium winter maximum. The pattern of abundance of both tagged and untagged monarchs at monitored sites leads us to reject the closed population model and the accrual hypothesis. We found that monarchs at all three study sites are part of a larger superpopulation, though the sites do not contribute to the superpopulation equally. We determined that mark-resight is a viable alternative to existing population estimation techniques, though mark-resight methods would need to be explored further before being applied routinely. Our results suggest we need to move away from site-based management and manage instead for landscape-level overwintering (superpopulation) dynamics.