This study examines the reproductive and population biology of a long-lived (80-y life span) fish, Sebastes alutus (Gilbert). The objectives of the study were (i) to establish whether groups of adult S. alutus delineated by exploitation histories could be objectively identified as separate sub-populations; (ii) to identify the effects of density-independent mortality caused by exploitation, and relate them to predictions of life history theory (iii) to examine the long-term implications of this mortality pressure on the dynamics of the species; and (iv) to determine the contribution of these results to the development of management programs for this species. A lernaepodid copepod gill parasite (Neobrachiella robusta (Wilson 1912)) was used for the first time as a biological tag to delineate separate sub-populations (stocks) of a commercial fish. Intensity of infection and mean characteristics of the parasite population per fish achieved complete separation between stocks indistinguishable with morphological features. Discriminant analysis showed the parasite also functioned moderately well (34-76% correct classification) as a stock discriminator of individual fish. Use of auxilliary information on the stock identity of hosts improved the classification power of the discriminant function. The density-independent mortality of the commercial fishery on S. alutus has severely truncated the age spectrum of some stocks. Some compensatory growth changes for fish in the stocks under the strongest selection are evident. Examination of the variance structure of female length at age suggests an inverse relation of mortality and growth rate giving rise to smaller, older fish. Smaller, older fish can be accounted for using the same growth function as for the larger fish seen at younger ages, and these similar growth forms can give an aggregate appearance of quadratic growth. Growth changes do not yield significant differences in size at maturity, although age at maturity changes, implying developmental or environmental constraints on maturation. Fecundity estimation methodology was evaluated and the volumetric method previously used for this species found to be inferior to a gravimetric method. Significant differences in fecundity as a function of body variables were found among exploitation groups. Significant differences in oocyte characteristics among stocks were found, with size and age shown to have separable effects. Lightly exploited stocks had significantly higher oocyte quality (as expressed in oocyte weight), effected through differences in the oocyte diameter-oocyte weight relationship. Histological examination details the developmental sequence of oocytes and establishes the maturation period of oocytes and fish. Northern stocks were shown to have significantly larger oocytes. Follicular atresia is suggested as an alternative energy source to the embryo death which has been presented as the source for matrotrophy in this genus. Complete atresia of a ripe oocyte complement was identified in this genus for the first time. No evidence of reproductive senescence was found. The hypothesis of increasing reproductive effort with age, including the independence of age and size effects, was confirmed. No evidence of reproductive cost could be found. The hypothesis of increased reproductive effort earlier in life as a mechanism to offset increased adult mortality was supported. However, the potential of this increase, achieved by growth rate increases, is much less than is needed to compensate for the reduction in lifetime reproductive effort caused by high fishing mortality. The effects of changing mortality rates on several reproductive value indices was examined with deterministic and stochastic simulation models. Cohort reproductive value is the most sensitive of the indices examined and may be the most robust to measurement error. Reproductive value is a more sensitive index of population state than other indices in use and may play a role in determination and evaluation of optimal harvest policies. However, an experimental approach to its use will be required. / Science, Faculty of / Zoology, Department of / Graduate

Rare plant conservation efforts must utilize current genetic methods to ensure the evolutionary potential of populations is preserved. One such effort involves the Key Tree Cactus, Pilosocereus robinii, which is an endangered columnar cactus native to the Florida Keys. The populations have precipitously declined over the past decade because of habitat loss and increasing soil salinity from rising sea levels and storm surge. Next-generation DNA sequencing was used to assess the genetic structure of the populations. Twenty individuals representative of both wild and extirpated cacti were chosen for Restriction Site Associated DNA (RAD) analysis. Samples processed using the HindIII and NotIII restriction enzymes produced 82,382,440 high quality reads used for genetic mapping, from which 5,265 Single Nucleotide Polymorphisms (SNPs) were discovered. The analysis revealed that the Keys’ populations are closely related with little population differentiation. In addition, the populations display evidence of inbreeding and low genetic diversity.

In North America 72% of freshwater mussel species are endangered, threatened, or of special concern due to factors such as habitat loss and degradation, biological invasion, and land use change. Propagation of freshwater mussels has been considered a necessary conservation strategy for population restoration where threats have been mitigated but small population sizes limit population viability. Yellow lampmussel is a species of freshwater mussel that is endangered, threatened, or imperiled throughout its range; therefore, I evaluated laboratory techniques (probiotic supplements and secondary rearing designs) to improve culture of yellow lampmussel for population restoration. Several aquaculture facilities commonly use probiotics; thus, I used commercial probiotics to determine if 1) probiotic concentration and 2) type of probiotic mixture improved growth or survival of juvenile mussels during primary culture. I further asked whether probiotics affected mussels by reducing ammonia, thereby improving water quality. Some probiotics increased survival (and, in one experiment, increased growth) of juvenile mussels, regardless of concentration, but results were variable by experiment and probiotic type. Probiotics did not significantly reduce ammonia concentrations, so this was unlikely the mechanism of benefit. I also investigated the effect of different secondary rearing systems at two culture facilities on growth and survival of juvenile mussels in two size classes (5.0 mm). I used five different secondary culture systems that were either indoors (dogpans and baskets) or outdoors (trough, airlift upweller, tank upweller, baskets), where water was either recirculating or flow-through. Survival was exceptional in all larger size class rearing systems, and the baskets in the ponds had the greatest growth rates. Smaller mussels had lower survival than the larger mussels, indicating that when deploying juvenile mussels into outdoor culture systems mussels size should be greater than 5.0 mm. Results of this project will inform future rearing yellow lampmussel in New England and more broadly add to the limited literature on probiotic use and secondary rearing designs in freshwater mussel culture.

Though the American marten (Martes americana) is widely distributed across northern North America, habitat use and population abundance vary widely across the range. Due to its status as a furbearer, the species has been extensively researched, resulting in a large body of knowledge about the species’ ecology, distribution, and abundance, as well as drivers of population structure and dynamics. More recently, marten research has shifted focus to genetics, habitat associations, and estimation of population state variables. The rapid increase in estimation of states such as occupancy, abundance, and density has likely been driven by the increasing accessibility of noninvasive field technology, such as noninvasive genetic sampling and remote camera trapping, and by the statistical development of ecological hierarchical models. This convergence of advances in field and analytical methods is most apparent in the now widespread application of spatial capture-recapture, an approach that produces robust estimates of population densities and abundance that can be compared across time and space. These new models are especially valuable near the edges of marten distribution where populations are often recovering from historic overexploitation, and expanding into areas they have previously been absent from. In these areas, detailed, landscape-scale understanding of marten populations is necessary in order to establish current conditions, effectively monitor changes, and predict what effect management actions may have on marten populations. I utilized these models to study marten populations in New Hampshire where marten are a species of management interest, and recent recovery has led to their removal from the state endangered species list. Through a collaborative effort with New Hampshire Fish and Game Department in the winters of 2017 and 2018, marten were surveyed across northern New Hampshire using a novel camera trap design that allows for the identification of individuals. These data were analyzed using spatial capture-recapture models, allowing me to evaluate habitat associations that explain spatial variation in marten density and provide a population status assessment for the New Hampshire marten population. Marten densities are highest in the White Mountain National Forest, though other protected lands in northern New Hampshire also appear to support larger populations. The greatest population densities coincided with deeper snows, increased canopy closure, and intermediate boreal biomass. These results provide additional support for several hypotheses explaining marten habitat use across their range while also providing novel insight that will inform active management of both marten and the habitat they occur in. In addition to the population status assessment, I evaluated the relationship between estimates of occupancy and density in New Hampshire. Though utility of non-invasive methodology can decrease research costs, the need for individual identification in spatial capture-recapture models represents a cost increase over occupancy models. My results suggest that the two are positively correlated; however, occupancy is a poor predictor of the entire range of density, especially because the variables used to predict each of the state variables are different. Thus, occupancy is likely not a good proxy for density in New Hampshire, however it could be used to track general trends through time so long as density is re-evaluated periodically.

Periodically-harvested fisheries closures (PHCs) are a widespread form of community-based marine spatial management used throughout the Indo-Pacific that also is currently being intensively advocated by conservation organizations for supporting productive fisheries and healthy marine ecosystems. However, local implementation of PHCs has historically been designed to support occasional and efficient exploitation of fish stocks, and not necessarily sustainable fisheries yields and stock conservation. The efficacy of PHCs for achieving their historical cultural objectives of periodicity and efficiency of harvest, simultaneously with achieving contemporary fisheries objectives of fisheries productivity and conservation is undetermined. As a result, the utility of PHCs for supporting contemporary ecosystem-based fisheries management is uncertain given environmental, social and climate change. We developed a biological-economic fisheries model of PHCs to test the value of this form of marine resource management for achieving cultural, fisheries and conservation objectives under sustainable and overfishing scenarios. Our results reveal PHCs to be more effective at achieving the multiple objectives than either non-spatial or fully-protected area management when fisher impact on fish behavior is considered. These results describe the performance of PHCs in general when fish behavior is considered, but does not provide detailed guidance for a particular PHC. Thus, we modified and calibrated our biological-economic fisheries model with empirical data from Nakodu Village on Koro Island in Fiji. The calibrated model allowed us to estimate the effectiveness of Nakodu Village’s current PHC management and predict consequences of future management actions. Results suggest that 5-year PHC closures are optimal for simultaneously achieving fisheries productivity and conservation goals in Nakodu Village. These findings challenge the dogma that PHCs are simply a cultural legacy and warrant further investigation of the utility of PHCs for supporting ecosystem-based management beyond the Indo-Pacific.

Successful reproduction in salamanders is driven by behavioral, environmental, and temporal interactions among adults. While much of our understanding of salamander mating systems is based upon either courtship behavior of both sexes or aspects of female choice, the decisions made by males regarding where to place spermatophores is much less quantified. In this study, we mapped male spermatophore placement in the spotted salamander (Ambystoma maculatum) with respect to ecological and spatial locations within a vernal pool complex in Charles City County, Virginia. The overall goal was to use the spatial and ecological placement of spermatophores to determine if individuals deposit spermatophores randomly within the vernal pool or if males exhibited specific preferences for deposition. Using comprehensive surveys of the vernal pools and individual spermatophores within a 0.5m2 grid and terrestrial LIDAR, a total of 218 spermatophores were identified and mapped. We repeated these surveys for two successive breeding seasons. Placement occurred at an intermediate depth and an intermediate distance to the edge. Males also preferred to place spermatophores on leaf substrate as opposed to sticks or conifer needles. The physical placement of spermatophores exhibited autocorrelation in space during single reproductive events as well as across breeding seasons. These results suggest that males actively select for specific locations within a pool for spermatophore placement-a proverbial Goldilocks zone-which may be consistent with increased reproductive success. This information is key to understanding salamander mating system parameters in this species and may contribute to developing more effective management strategies.

Circadian clocks enable coordination of essential biological and metabolic processes in relation to the 24-hour light cycle. However, there are many habitats that are not subject to this light cycle, such as the deep sea, arctic regions, and cave systems. This study analyzes the circadian pattern of isolated populations of a subterranean spider, Meta ovalis from two Tennessee caves and five Indiana caves. Locomotor activity was recorded with TriKinetics LAM50 Locomotor Activity Monitor under a 12-hour light (L), 12-hour dark (D) (LD 12:12) cycle preceding total darkness (DD). Significant differences were found within and among populations found in Tennessee cave systems in average free running period and onset of locomotor activity. Selection, drift, and genetic fixation are explored as the causes of variation in the present study, using M. ovalis as the model organism. All five caves in Indiana show little variation, whereas both Tennessee caves show large interindividual variation.

Continental scale studies on ungulate crown heights in relation to climate and habitat changes have revealed a correlation between increasing hypsodonty and a shift to more arid environments. Small mammals have been shown to adapt to changing habitats millions of years earlier than larger mammals. In this study I examined fossil localities throughout the last 37 Ma across North America. Diversity of rodents and lagomorphs were analyzed through this time period, with examination of community structure characterized by relative percentages of taxa with different crown heights. Overall, a decrease in precipitation and temperature was found across North America from 37 Ma to the present. The Mid Miocene Climatic Optimum (around 15 Ma) was an pronounced period of warming, comparable to the warming we see today. Nebraska and California showed increases in crown height before Oregon. Overall, these findings help demonstrate how communities react at different time scales to climate change.

One-way escape gates and earthen escape ramps are structures used to enable deer to exit the highway right-of-way along fenced roads. I compared the use of one-way escape gates and earthen escape ramps by mule deer on two highways in Utah to determine if deer exhibited a preference for either structure. Results showed that earthen escape ramps were used by mule deer 8-11 times more frequently than one-way gates. Highway mortality data suggest that the installation of the escape ramps likely reduced mortality of mule deer in both study locations, because we could not attribute reductions in mortality to decreased population densities of mule deer in either location. Because they provide a topographic solution for exiting the right-of-way, escape ramps may reduce deer mortality along other game-fenced highways throughout the United States. Management recommendations that address the placement and spacing of escape ramps will help wildlife and highway personnel implement the use of these ramps in other locations. A cost-benefit analysis was conducted to determine if the cost of ramp installation was offset within a reasonable time period by the monetary savings associated with reduced deer-vehicle collisions. The cost-effectiveness of installing the earthen escape ramps at both locations was determined by using the number of successful ramp crossings and potential deer mortality levels to generate projected monetary losses associated with varying mortality levels. The assumption was made that at least some of these deer that crossed successfully would have been involved in a deer-vehicle collision had the ramps not been in place. Six arbitrary levels of potential mortality (from 2% to 15%) were generated based on those assumptions. These percentages were multiplied by the number of successful deer crossings at each location to generate potential deer mortality numbers. The number of deer mortalities was then multiplied by the average economic loss of a deer-vehicle collision ($3,845) to obtain an estimate of the mitigated benefits of installing the ramps through 1999. These values were compared to the cost of installing ramps at each location to determine the amortization period. Results showed that the cost of installation of earthen escape ramps is very rapidly offset by the benefits gained in deer survival and reduced automobile collisions. At the 2% mortality level, the cost of ramp installation in both locations was offset by the monetary savings associated with reduced deer-vehicle collisions by the second year. Heavy use of the escape ramps as well as reduction in mortality observed at both study sites indicate that the mitigation benefits may be much greater than those projected at the 2% mortality level. Installing earthen escape ramps on big-game fenced highways is a very cost-effective way to further reduce deer mortalities along roadways.

Population biology of the black-tailed jackrabbit population on a 250-square-mile area in Curlew Valley, northern Utah, was studied from 1962-70. During this period the fall population density index increased from 40.0 in 1962, to 60.6 in 1963, decreased progressively to a low of 21.2 in 1967, then increased the following 3 years to a high of 185.0 in 1970. Breeding was synchronous with four conception periods each year; in some years a fifth conception period was evident. The first conception period occurred about the last half of January; other periods followed at 40-day intervals indicating a 40-day gestation period and postpartum estrus with subsequent conception. Over the 9 years of study, the mean percentages of females breeding during the five conception periods were 88, 99, 100, 70, and 11 percent, respectively. The mean number of ova ovulated per breeding female for the five periods was 1.9, 5.1, 6.4, 4.9, and 3.6, respectively. During the period of decreasing density, 1963-67, the yearly mean number of ova ovulated per female surviving the breeding season ranged from 13.2-19.3, but varied independently of density. During the 3 consecutive years of density increase, 1968-70, however, the number of ova ovulated per female decreased progressively from 19.8 in 1968 to 14.2 in 1970. Mortality rates of the total population from October-March remained relatively constant (mean: 63 percent) during the years of population decline, but dropped to 33 percent during the first year of population increase (1968). March-October mortality of adults decreased to 9 percent during the first year of population increase from a previous mean of 73 percent, and juvenile mortality from parturition to fall census, decreased from a mean of 68 percent to 38 percent. The effects of variations in mortality rates on population density have overshadowed the effects of the relatively less extreme variations in natality rates. As a result the pattern of density change was almost entirely a result of changes in mortality rates. Changes in mortality rates of adults and juveniles were well correlated with the coyote/rabbit ratio on the study area. Exceptions occurred with juvenile mortality rates at the relatively high rabbit densities observed in 1969-70. During these two years, juvenile mortality rates from parturition to fall census (61 and 68 percent, respectively) were greater than could be accounted for by coyote predation. The factor or factors responsible for the increased juvenile mortality are not known. Observed annual density changes were described with the mathematical model: Nt+4 = Nt (1 - 37.8 - 988x1) (1 + 11.2 - 1130x2 - 0.0581x3 + 42000x22 + 0.00115x32) where Nt is the number of animals at the end of October, Nt+1 is the number of animals at the end of the following October, x1 is the coyote/rabbit ratio from October-March, x2 is the coyote/rabbit ratio from March-October, and x3 is the mean number of rabbits per square mile from March-October. The model accounts for 99 percent of the observed change in rabbit density from 1968-70.