Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / The benthic habitat is the terminal destination for marine animals in terms of their reproductive lifecycle. Recruitment dynamics relating to seasonal changes in the benthic habitat may be the best source of information for predicting recruit abundance and for marine resources management. The transition from the pelagic to the benthic phases is the last stage in the connectivity between benthic populations. The transition to the benthos may be a process that dominates recruitment dynamics to the exclusion of other characteristics of larvae such as their quality and their density. Recruitment of benthic marine animals is influenced by two seasonally varying factors of the benthic habitat. First, the availability of suitable habitat for recruitment can in large part determine the survival probability for settlers, a trend that is most pronounced for low or no survival when the settlement substrate is saturated by conspecifics from a recruitment cohort. Preemption is caused by the presence of current occupants from a recruit cohort, and it influences the settlement rate or the survival probability of conspecifics. Descriptive statistics (Chapter 2) and a field experiment (Chapter 4) highlight the role of preemption on barnacle recruitment. The second factor results from seasonal changes in environmental conditions that settlers experience in the benthic habitat, which could affect the physiology and survival probability of barnacle settlers. Highly unpredictable features of recruitment dynamics also play a role, such as wind that enhances wave action in the rocky intertidal that has been linked to the rate of settlement. Day to day variability in wind may cause patterns of settlement to be highly unpredictable. Predator induced mortality is spatially aggregated, and the random pattern of mortality in space is highly unpredictable. In contrast to these high frequency sources of recruitment variability, seasonal factors that vary at lower frequencies and that often change monotonically lend great predictive ability for recruitment dynamics. It appears that barnacles have evolved to compete for suitable habitat and have mechanisms to cope with seasonally varying environmental conditions in the benthic habitat, which may be the basis for why these features dominate the barnacle recruitment dynamic. / by Jonathan N. Blythe. / Ph.D.

The Louisiana oyster industry is greatly impacted by freshwater and sediment diversions that are part of the effort to restore the state’s coastline. A habitat suitability index (HSI) proposes species-habitat relationships that can be instrumental in creating impact assessments and suitability predictions for management as new diversions are implemented. An oyster (Crassostrea virginica) HSI was developed using three variables crucial to oyster sustainability: average annual salinity, minimum monthly salinity, and average salinity during the spawning season. These Legacy HSI visualizations show annual fluctuations in the distribution of zones suitable for oyster cultivation prior to proposed diversions in Pontchartrain and Barataria Basins from 1967 to 2016. Modeling suitability based upon these variables can provide crucial information for timing the use of diversions to lessen harmful effects upon the oyster industry as well as indicate new potentially suitable areas that the diversions may create.

In ecology literature, there is much data which suggests that conspecific negative density dependence (CNDD) and abiotic disturbances increase biodiversity in forests. This thesis elucidates the notion that not only do these two forces increase diversity, but they may also interact with one another in order to achieve higher levels of biodiversity. Abiotic disturbances, like fires and hurricanes, can indirectly impact conspecific effects because when these forces remove individuals from the landscape, the role of the conspecific effects will change. The interaction of these two factors in biodiversity are explored in an agent based forest simulation through a resource surface. Several different types of abiotic disturbances are simulated with either weak or strong CNDD effects in order to establish that different disturbances and conspecific effects cause certain levels of diversity. The underlying causes for the change in impact is also examined.

Evolution occurs and can be conceptualized along a spectrum, bounded on one extreme by the relationships between deep lineages – such as phyla, classes, and orders – and on the other by the molecular dynamics of operational taxonomic units within a species, defined as population genetics. The purpose of this dissertation was to better understand the evolutionary and population dynamics of crustaceans within the Gulf of Mexico. In the second chapter of my dissertation, I provide a guide to best phylogenetic practice while reviewing infraordinal relationships within Decapoda, including the promise held by next-generation sequencing (NGS) approaches such as Anchored Hybrid Enrichment. Chapter III is a phylogenetic study of species relationships within the economically important shrimp genus, Farfantepenaeus, targeting three mitochondrial genes and uncovering an intriguing pattern of latitudinal speciation. As the first inclusive molecular phylogeny of the genus, we find support for the newly described species F. isabelae, but a lack of support for the species status of F. notialis. Additionally, our results suggest the existence of two distinct subspecies of F. brasiliensis. Chapter IV investigates the relative impacts of habitat heterogeneity and the presence of a possible glacial refugium in determining population dynamics of the Giant Deep-Sea Isopod, Bathynomus giganteus in the northern Gulf of Mexico. Through hybrid population genetics/genomics analyses and Bayesian testing of population models, we find strong evidence for habitat heterogeneity determining population dynamics for this charismatic deep-sea invertebrate. Chapter V further investigates the role of environment in determining and maintaining genetic diversity and population connectivity, specifically focused on establishing biological baselines with which we can diagnose health and resilience of the Gulf of Mexico. This was accomplished through a comparative NGS population genomics study of three species of mesopelagic crustaceans: Acanthephyra purpurea, Systellaspis debilis, and Robustosergia robusta. While diversity and connectivity differs in each species, the comparative results bespeak the importance of access to the Gulf Loop Current in determining and maintaining population dynamics. Overall, my work significantly contributes to our knowledge of Crustacea at the phylogenetic- and population genetic-level.

Obtaining accurate estimates of animal abundance is made difficult by the fact that most animal species are detected imperfectly. Early attempts at building likelihood models that account for unknown detection probability impose a simplifying assumption unrealistic for many populations, however: no births, deaths, migration or emigration can occur in the population throughout the study (i.e., population closure). In this dissertation, I develop likelihood models that account for unknown detection and do not require assuming population closure. In fact, the proposed models yield a statistical test for population closure. The basic idea utilizes a procedure in three steps: (1) condition the probability of the observed data on the (unobserved) period- specific abundances; (2) multiply this conditional probability by the (prior) likelihood for the period abundances; and (3) remove (via summation) the period- specific abundances from the joint likelihood, leaving the marginal likelihood of the observed data. The utility of this procedure is two-fold: step (1) allows detection probability to be more accurately estimated, and step (2) allows population dynamics such as entering migration rate and survival probability to be modeled. The main difficulty of this procedure arises in the summation in step (3), although it is greatly simplified by assuming abundances in one period depend only the most previous period (i.e., abundances have the Markov property). I apply this procedure to form abundance and site occupancy rate estimators for both the setting where observed point counts are available and the setting where only the presence or absence of an animal species is ob- served. Although the two settings yield very different likelihood models and estimators, the basic procedure forming these estimators is constant in both. / Graduation date: 2012

Butternut (Juglans cinerea L.), a lesser-known relative of black walnut (Juglans nigra L.), is a native tree species beneficial for wildlife, valuable for timber, and part of the great diversity of species in the eastern forests of North America. Populations of butternut are being devastated by butternut canker disease, caused by the fungus Sirococcus clavigignenti-juglandacearum (V.M.G. Nair, Kostichka, & Kuntz), which is thought to be introduced to North America. The disease causes multiple branch and stem cankers that eventually girdle trees. Small population sizes, lack of sprouting, and shade intolerance exacerbates the disease and results in permanent losses of butternut across the native range. Fortunately, healthy, canker-free butternut trees have been found proximal to diseased trees, indicating that a breeding approach could be a feasible strategy for producing and reintroducing resistant butternuts. A successful restoration program will require an understanding of genetic variation in open-pollinated seedlings, genetic basis of disease resistance, seedling establishment procedures, site requirements, and a greater understanding of disease development over time. This dissertation is divided into six parts, with the overall goal of insight into butternut ecology and management techniques which could be used to guide restoration decisions for this important species. The first two parts are an introduction and a literature review. In the third section, butternut seedlings were propagated in nursery progeny plantings to determine the genetic and phenotypic variability among one-year-old seedlings in a controlled environment. Part four outlines the disease development of butternut seedlings across progeny in resistance screening plantings at various locations. Part five aims at aiding restoration techniques by determining the impact of phenotypic and genetic variables on establishment success across various planting sites with different silvicultural treatments. Part six describes the dynamics of a large population of healthy and diseased butternut trees including disease development across temporal scales. The information gained from this research will be directly used in gene conservation strategies, the construction of disease resistant breeding orchards, and in determining appropriate restoration techniques.

Currently, a variety of methods are available to monitor anurans, and little standardization of methods exists. New methods to monitor anurans have become available over the past twenty years, including PVC pipe arrays used for tree frog capture and Automated Digital Recording Systems (ADRS) used to remotely monitor calling activity. In addition to ADRS, machine-learning computer software, automated vocalization recognition software (AVRS), has been developed to automatically detect vocalizations within digital sound recordings. The use of a combination of ADRS and AVRS shows the promise to reduce the number of people, time, and resources needed for an effective call survey program. However, little research exists that uses the described tools for wildlife monitoring, especially for anuran monitoring. In the study, there were two problems addressed relating to AVRS. The first was the poorly understood relationship between auditory survey methods and physical survey methods. I tested this problem by using current auditory monitoring methods, ADRS and the AVRS Song Scope© (v.3.1), alongside more traditional physical monitoring methods that included drift fences, a PVC pipe array, and visual encounter transects. No significant relationship between physical and auditory community population measures was found. Auditory methods were also effective in the detection of call characteristic differences between urban and rural locations, further suggesting an influence of noise pollution. The second problem addressed was the call identification errors found in auditory survey methods. I examined the influence of treatments including the ADRS location, listener group, species, and season on the error rates of the AVRS Song Scope© (v.3.1) and groups of human listeners. Computer error rates were higher than human listeners, yet less affected by the treatments. Both studies suggested that AVRS was a viable method to monitor anuran populations, but the choice of methods should be dependent upon the species of interest and the objectives of the study.

Effects of herbivory, fire, and tree harvesting on Acacia drepanolobium were studied using plant population dynamics as the philosophical basis of research. Specifically, growth rates, chrono-sequence of re-growth, biomass and charcoal yield, herbivory, flowering, seed production, germination, mortality and the ants of Acacia drepanolobium were studied in the black cotton ecosystem of Mpala Research Centre, Laikipia, Kenya, between September 1995 and December 2000. Acacia drepanolobium was the most abundant tree or shrub with densities ranging from 80% to 98% of all the overstorey species, but it was the least browsed of all the trees and shrubs in the black cotton ecosystem, ranging from a mean of 7.2% to 9% of the individuals browsed. The tree is inhabited by four Acacia ant species, Crematogaster mimosae, Crematogaster sjoestedti, Crematogaster nigriceps, and Tetraponera penzigi, which are believed to be obligate, and which probably play a role in the low browsing rates observed. Six herbivore treatments replicated three times (no herbivores - O; only cattle - C, all herbivores allowed - MWC {control}, mega-herbivores {elephants and giraffe} and wildlife {W} – MW only, wildlife – W - only {all wildlife except mega-herbivores} and wildlife and cattle only - WC) was the main experimental design used in understanding the dynamics of the tree species under influence of different herbivores. Mean annual height growth of A. drepanolobium trees was 24.9 cm yr-1, while the mean Relative Growth Rates ranged from 14.6 x 10 –3 cm cm-1 yr-1 to 18.7 x 10 –3 cm cm-1 yr-1. Growth rates were different among the herbivore treatments and between seasons. Shoots of the tree grew by a mean range of 6.8 cm to 9.1 cm, were similar among the treatments but differed among the seasons. Canopy volume increased over time although it fluctuated with seasons, suggesting an increase in bushiness of A. drepanolobium in the ecosystem. Trees occupied by different ant species showed differences in shoot density (number of new shoots per twig), being greater in Crematogaster nigriceps occupied trees compared with the other ant species. Swollen thorn (gall) density per unit of twig length was greatest in treatments with megaherbivores; these galls were significantly larger on trees occupied by the ant Crematogaster nigriceps. Treatments with herbivores were more spinescent than the total exclusion treatment. Spine lengths ranged from 0.8 to 2.4 cm, and recorded a progressive reduction of up to 36.36.7% in treatments without browsers suggesting a relaxation of induced defence in A. drepanolobium. Flowering in A. drepanolobium was low and staggered over the study period ranging from 0.8% to 2.0% of the trees with no differences among the treatments suggesting that the level of herbivory was not sufficient to influence reproduction of the tree in the experimental site. Consequently, seedling recruitment was very low within the experimental site. However, a nearby site recorded flowering of between 22.7% and 93.5%. Mean pod production, mean number of seeds per tree and mean weight of pods and seeds had a positive linear relationship with tree density (R2=0.77, 0.81 and 0.81 respectively). Trees occupied by Crematogaster mimosae were the most likely to flower (68%) compared with C. nigriceps (5.8%), again suggesting that ants had an effect on the tree’s reproduction. Mortality of A. drepanolobium trees averaged 0.9% to 4.2% over the study period, being significantly greater in treatments with mega-herbivores. Seedling survival ranged from 42% to 75%, being greatest in the cattle only treatment. Between 30% and 100% (mean 67.2%), of A. drepanolobium seeds were attacked by a bruchid beetle (Bruchus sp.). Seeds attacked by bruchid beetles had significantly lower germination rates. Similarly, seeds passed through a fire also recoded significantly low germination rates compared with normal seeds. Fire (3.4%) and bruchid beetles (20.7%) germination compared with (control) undamaged seeds (84%) play an important role in the population dynamics of A. drepanolobium. Fewer A. drepanolobium seeds (33%) were recovered from the surface compared with buried (72%) seeds after a fire, indicating seed loss from the effect of fire and predation. In the burn experiment, fire top-killed 16% of A. drepanolobium trees but no tree or seedling was killed. On the other hand, fire significantly reduced the density of non-A. drepanolobium trees by between 50% and 100%, with none of them showing signs of coppicing after the fire unlike top-killed A. drepanolobium trees. Woody biomass from A. drepanolobium was strongly related to stem diameter (Y = 3.77x + 1.17, R2 = 0.96, P < 0.001). Mean charcoal production from earthen kilns was 2.83 Mg ha- 1. Height and stem diameter in coppicing stands increased at a mean rate of 28.6 cm yr-1 and 0.7 cm yr-1 respectively. Biomass in coppicing stands accumulated at a mean rate of 1.3 Mg ha-1 yr-1 in a 14-year period, yielding dry biomass of 18.26 Mg ha-1 useable wood that can produce a minimum of 3.0 Mg ha-1 of charcoal. This study shows that Acacia drepanolobium populations are affected by several factors including herbivory, fire and ants. The population dynamics of this tree shows that it can be harvested for sustainable charcoal yield over a 14-year cycle. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2007.

The Cerulean Warbler (Setophaga cerulea) is a mature forest obligate and one of the fastest declining songbird species in the United States. This decline may be related to a lack of disturbance within contemporary forests; however, the consequences of disturbance on the species have not been rigorously evaluated. Thus, we assessed multiple responses by Cerulean Warblers to a range of experimental forest disturbances across the core of their breeding range in the Appalachian Mountains. We quantified individual and population responses to these manipulations, and assessed the potential consequences of disturbance on the sexual signaling system. Male ceruleans were strongly attracted to intermediate and heavy disturbances at the stand scale. Despite attraction to disturbed habitats, nest success declined in these conditions, particularly in the highly productive Cumberland Mountains of northern Tennessee. Taken together, these opposing responses suggest that anthropogenically-disturbed forests may act as local ecological traps, but the impact of these local traps on the global population is dependent on several unestimated parameters. At a finer scale, selection for habitat features varied spatially. Males consistently selected for territories near canopy gaps and on productive slopes, but they displayed inconsistent territory selection in regards to tree diameter, basal area, overstory canopy cover, and canopy height. Females were more consistent in their selection of features within territories, selecting nest patches with large, well-spaced trees near disturbances. Floristically, female ceruleans consistently selected for sugar maples (Acer saccharum), white oaks (Quercus alba), and cucumber magnolias (Magnolia acuminata) as nest trees and they selected against red maples (A. rubrum) and red oaks (Q. rubra). Disturbances had little effect on male age structure, but males that occupied disturbed forest habitat were in better condition than those in undisturbed habitat. Parental behavior differed among disturbances, with birds in more highly disturbed habitats provisioning their young at greater rates, but bringing smaller food loads, potentially helping to explain the decrease in nest survival in disturbances. Finally, we found that male ceruleans displayed various plumage ornaments that signaled individual quality. However, the relationship between breast band width and body mass was contingent on habitat, and only existed in intermediate disturbances.

[Truncated abstract] Amidst concern over the global phenomenon of declining amphibians, there is an increasing appreciation of the importance of understanding population dynamics at both local and regional scales. Data on the viability and persistence of species in landscapes altered by humans are scarce but an understanding of these dynamics is essential for enabling long-term species conservation in a modified world. Habitat loss, fragmentation and ensuing salinisation are of particular concern for species in Australia’s temperate agricultural regions where the rapid conversion of continuously vegetated landscapes to small fragments has occurred in less than 200 years. This thesis investigated the local and metapopulation structure of Heleioporus albopunctatus to determine the current population structure and likely future of this species in a highly degraded landscape: the wheat and sheep growing areas of southwestern Australia ... The life-history attributes of H. albopunctatus, including high fecundity, high adult longevity and low to moderate dispersal contribute to a robust regional metapopulation, responsive to changes, but with a strong chance of persistence over the long-term. H. albopunctatus appears to have adjusted to a radically modified landscape but its long-term persistence may be dependent on the existence of a small number of source populations that recruit in most years.