Global climate change is already contributing to the extirpation of numerous species worldwide, and sensitive species will continue to face challenges associated with rising temperatures throughout this century and beyond. It is especially important to evaluate the thermal ecology of endangered ectotherm species now so that mitigation measures can be taken as early as possible. A recent study of the thermal ecology of the federally endangered Blunt-Nosed Leopard Lizard (Gambelia sila) suggested that they face major activity restrictions due to thermal constraints in their desert habitat, but that large shade-providing shrubs act as thermal buffers to allow them to maintain surface activity without overheating. We replicated this study but added a population of G. sila with no access to large shrubs to facilitate comparison of the thermal ecology of G. sila in shrubless and shrubbed populations. We found that G. sila without access to shrubs spent more time sheltering inside rodent burrows than lizards with access to shrubs, especially during the hot summer months. Lizards from a shrubbed population had higher midday body temperatures and therefore poorer thermoregulatory accuracy than G. sila from a shrubless population, suggesting that greater surface activity may represent a thermoregulatory tradeoff for G. sila. Lizards at both sites are currently constrained from using open, sunny microhabitats for much of the day during their short active seasons, and our projections suggest that climate change will exacerbate these restrictions and force G. sila to use rodent burrows for shelter even more than they do now, especially at sites without access to shrubs. The continued management of shrubs and of burrowing rodents at G. sila sites is therefore essential to the survival of this endangered species.

Picea rubens(red spruce) populations experienced a synchronous rangewide decline in growth and vigor starting in the 1960’s, which was likely caused by climate change or environmental disturbances (e.g., acid deposition); However, it is yet unknown if populations continue to decline or have recovered. In the context of global warming, red spruce is a species of concern because it is at its southern continuous range margin in Massachusetts. This study uses tree-ring data coupled with population data from permanent plots to quantify the status of red spruce in Massachusetts. Tree cores were extracted from red spruce and used to examine radial growth rates, determine a growth-climate relationship, and document disturbance events. Red spruce at these plots ranged from 90 to 184 years old, and comprised 15 to 29 m2/ha-1 basal area. Over the past 50 years, red spruce has decreased in density, basal area, and relative importance while red maple, yellow birch, and American beech have increased. Red spruce saplings persisted in some plots, but the sapling layer was comprised mostly of American beech or red maple. However, red spruce seedlings were common at red spruce dominant plots indicating that if favorable conditions occur, it could return to its more dominant position in the canopy. Dendroclimatological analyses show that red spruce is sensitive to both temperature and precipitation. Most sites are correlated with temperature, while only twoforests were correlated to precipitation. The general temperature response of the red spruce studied was positively correlated with winter temperatures while the general precipitation response was negatively correlated with precipitation. Temporal analysis of the climate-growth response indicates that red spruce here have not had a temporally-stable, climate-growth relationship. Prior to 1960, radial growth was positively correlated with temperatures from November of the previous growing season to January of the current year. After 1960, all sites showed a shift in growth responses consistent with increased summer temperature stress; narrowed tree rings were formed during warm temperatures in July and August. Precipitation remained relatively constant over the past century, while temperatures have increased up to 2˚C across the study area. Of the two precipitation-sensitive forests, one forest shifted from being positively correlated with current January precipitation to negatively correlated with previous October precipitation while the second forest showed a strong positive relationship with August precipitation. Because the radial growth of red spruce here are mostly constrained by temperatures, there has been negative growth response to regional warming and precipitation has been stable, I suggest the change in climate response is potentially due to warming and a physiological threshold response to increasing temperatures. Interestingly, disturbance frequency and intensity have increased over the same time period, which could be either a trigger or a response to the shift in the growth-climate relationship.

This project used molecular genetic markers (microsatellites) to determine the amount of genetic diversity within populations and whether significant differentiation exists among Florida populations of the long-spined sea urchin, Diadema antillarum. Specifically, this project aimed to (1) compare genetic diversity of D. antillarum from six populations in south Florida ranging from Biscayne Bay, the Florida Keys, and Dry Tortugas, and (2) determine whether two broodstock populations of D. antillarum contain variation indicative of native Florida populations. Together, these questions can address whether broodstock populations contain the genetic variation necessary to meet the Florida Fish and Wildlife Conservation Commission’s (FWC’s) genetic policies for reintroduction throughout south Florida. Global FST among native populations was 0.0004 with a highest pairwise FST of 0.0025 between the Upper Keys and the area west of Key West, showing an overall trend of little natural differentiation between populations. Global FST for all populations inclusive of the broodstock samples was 0.0019 with a highest pairwise FST between a native population and broodstock of 0.0066 between Dry Tortuga and Mote’s broodstock, indicating little differentiation resulting from captive breeding. Average allelic richness and heterozygosity ranged from 22.6–24.4 and 0.937–0.956, respectively, for each population. Two-way ANOVAs comparing genetic diversity between native and broodstock populations showed no statistical difference in allelic richness (F= 3.892, p= 0.0535) or heterozygosity (F=1.43, p=0.237). The computer program STRUCTURE estimated the most likely number of genetic clusters to be k=1, inclusive of broodstock populations, further indicating a lack of differentiation either among native populations or between native and broodstock populations. These data suggest that captive-bred individuals of D. antillarum could be used for reintroduction as part of a plan to re-establish healthy urchin populations throughout the Florida Keys.

Mountaintop removal mining (MTR) is a notorious stressor of stream ecosystems in the Central Appalachians. Valley fills (VF) lead to reduced occupancy, abundance, and species richness of stream salamanders. Multiple factors may be responsible for these reductions, but specifically habitat fragmentation and degradation may reduce colonization rates and increase local extinction rates. From 2013-2015, repeated counts of salamanders were conducted in stream reaches impacted by MTR/VF and compared to counts in reference reaches to answer the question: do stream salamander population dynamics differ between stream reaches impacted by MTR/VF and reference stream reaches? I also investigated dynamics of stream habitat using measures relevant to stream salamander persistence. Accordingly, I examined number of cover objects, percent detritus, hydroperiod, and specific conductance. From the salamander capture data, colonization and survival probabilities were lower in MTR/VF reaches than reference reaches. MTR/VF reaches also had fewer cover objects, higher percent detritus, constant stream flow, and elevated specific conductance. Although specific conductance was increased in MTR/VF reaches, it was not strongly correlated with colonization and survival. I suggest reduced rates of colonization and survival in MTR/VF stream reaches are driven by inhibited dispersal and reduced individual survival due to degraded terrestrial and aquatic environments.

Phylogeographic studies have relied on surveying neutral genetic variation in natural populations as a way of gaining better insights into the evolutionary processes shaping present day population demography. Recent emphasis on understanding putative adaptive variation have brought to light the role of epigenetic variation in influencing phenotypes and the mechanisms underlying local adaptation. While much is known about how methylation acts at specific loci to influence known phenotypes, there is little information on the spatial genetic structure of genome-wide patterns of methylation and the extent to which it can extend our understanding of both neutral and putatively adaptive processes. This research examines spatial genetic structure using paired nucleotide and methylation genetic markers in the Sonoran bark beetle, Araptus attenuatus, for which we have a considerable knowledge about its neutral demographic history, demography, and factors influencing ongoing genetic connectivity. Using the msAFLP approach, we attained 703 genetic markers. Of those, 297 were polymorphic in both nucleotide (SEQ) and methylation (METH) were assayed from 20 populations collected throughout the species range. Of the paired SEQ and METH locis, the METH were both more frequent (16% vs. 7%), maintained more diversity (Shannon IMeth = 0.361 vs. ISeq=0.272), and had more among-population genetic structure (ΦST; Meth = 0.035 vs. ΦST; Seq= 0.008) than their paired SEQ loci. Interpopulation genetic distance in both SEQ and METH markers were highly correlated, with 16% of the METH loci having sufficient signal to reconstruct phylogeographic history. Allele frequency variation at five loci (two SEQ and three METH) showed significant relationships with at-site bioclimatic variables suggesting the need for subsequent analysis addressing non-neutral evolution. These results suggest that methylation can be as informative as nucleotide variation when examining spatial genetic structure for phylogeography, connectivity, and, identifying putatively adaptive genetic variance.

Mammal species often live in social groups, but the factors that promote group cohesion can be difficult to analyze due to the prevalence of strong group affiliations. Feral horses maintain stable harems of one or two males and several females, and harem stability is strongly related to individual fitness. Anecdotal evidence and an early study in the non-breeding season suggest that management of the Shackleford Banks island horses with immunocontraception reduces harem stability in the population, providing an opportunity to study the factors that influence harem stability. I investigated the effects of the immunocontraceptive PZP on harem stability during the breeding season and examined mare activity budgets and harassment rates to determine if these factors influence harem stability. I hypothesized that 1) immunocontraception would increase the rates at which mares changed harems during the breeding season 2) activity budgets of contracepted individuals would differ significantly from those of uncontracepted individuals, and 3) contracepted mares would experience greater levels of harassment associated with changing harems than uncontracepted mares. I found that the immunocontraceptive does increase harem changes during the breeding season. I also found that contracepted mares have different activity budgets than uncontracepted mares; as predicted, contracepted mares grazed less and moved more than uncontracepted controls. The factors that influence mare activity budgets included immunocontraception, harem stallion, number of individuals in the harem, number of mares in the harem and body condition of the mare, as well as some interactions between factors. I found that high harassment rates by both harem stallions and other mares in the harem are correlated with higher harem change rates and that contracepted mares are harassed more than uncontracepted mares. These results indicate that the immunocontraceptive does influence harem stability in this feral horse population, potentially through alterations in activity budgets and harassment rates.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, in fulfilment of the requirements for the degree of Master of Science. Johannesburg, 2017. / With an increase in opportunistically-collected data, statistical methods that can accommodate unstructured designs are increasingly useful. Spatial capturerecapture (SCR) has such potential, but its applicability for species that are strongly gregarious is uncertain. It assumes that average animal locations are spatially random and independent, which is violated for gregarious species. I used a data set for African elephants (Loxodonta africana) and data simulation to assess bias and precision of SCR population density estimates given violations in location independence. I found that estimates were negatively biased and likely too precise if non-independence was ignored. Encounter heterogeneity models produced more realistic precision but density estimates were positively biased. Lowest bias was achieved by estimating density of groups, group size, and then multiplying to estimate overall population density. Such findings have important implications for the reliability of population density estimates where data are collected by unstructured means. / LG2017

O objetivo deste trabalho foi caracterizar aspectos biológicos e ecológicos de Austinixa aidae, um caranguejo simbionte em galerias construídas pelo Thalassinidea Callichirus major, na Praia do Perequê-Açu, Ubatuba, litoral Norte do Estado de São Paulo. As coletas foram realizadas por meio de bombas de sucção manual na região intermareal da praia arenosa, de Maio/2005 a Setembro/2006. Nesta dissertação foram apresentados, em três capítulos distintos, a Estrutura Populacional, o Crescimento Relativo e as Estratégias Reprodutivas deste caranguejo. No Capítulo I, sua população foi estudada com ênfase em aspectos estruturais como abundância sazonal, freqüência de indivíduos em classes de tamanho, razão sexual, densidade e incidência nas galerias de seus hospedeiros, os períodos reprodutivo e de recrutamento. Além disso, foram avaliadas as correlações entre sua densidade e seu tamanho com o tamanho de seus respectivos hospedeiros. Foi constatado que as espécies do gênero Austinixa possuem aspectos ecológicos e biológicos semelhantes, mesmo em casos de localidades muito distantes geograficamente, corroborando o que foi postulado por outros autores quanto à similaridade destes parâmetros entre os membros do grupo. No Capítulo II, devido ao forte dimorfismo sexual e uma série de adaptações morfológicas atribuídas ao estilo de vida simbionte destes caranguejos, foram estudadas as características corporais, o crescimento relativo, a maturidade e o dimorfismo sexual destes indivíduos. Os adultos de A. aidae possuem a largura da carapaça em média 2,4 vezes o seu comprimento, essas características foram sugeridas como sendo adaptações ao estilo de vida simbionte. O crescimento relativo evidenciou que alterações morfológicas processadas ao longo da ontogenia dos animais estão relacionadas à maturidade sexual da espécie. No Capítulo III, o objetivo foi conhecer a estratégia reprodutiva relacionada à fecundidade, determinando-se o número de ovos produzidos pelas fêmeas ovígeras de distintos tamanhos e em diferentes períodos, além do desenvolvimento dos ovos, seu diâmetro e volume. A. aidae apresentou uma estratégia reprodutiva com padrões característicos de outros crustáceos Decapoda, com evidências de eficiência reprodutiva no local onde esta população está instalada. Considerando a ausência de estudos populacionais e reprodutivos para esta espécie, esta dissertação visou suprir esta demanda na literatura científica. / The biological and ecological aspects of Austinixa aidae, a symbiotic crab inhabiting burrows of the Thalassinidea ghost shrimp Callichirus major, from Perequê-Açu beach, Ubatuba, North shore of State of São Paulo, Brazil, were studied. The samples were conducted bimonthly with manual suction pumps in the intertidal region of the sand beach, from May/2005 to September/2006. This project was subdivided into three chapters: Population Structure, Relative growth and Reproductive Strategies. In Chapter I, the population of A. aidae was determined in terms of seasonal abundance, size frequency distribution, sex ratio, density and incidence in the burrows of the thalassinids, reproductive and recruitment periods. In addition, were evaluated the correlations between its density and size with size of their respective hosts. Was found that Austinixa species posses similar biological and ecological aspects, even in distant localities. In Chapter II, due to sexual dimorphism and the morphological adaptations assigned to symbiotic life style, body features, relative growth, maturity and sexual dimorphism were studied. Adults of A. aidae have the carapace width on average 2.4 times the carapace length. Relative growth revealed that morphological changes are related to sexual maturity of this species. In Chapter III, the goal was to know the reproductive strategy related to production of eggs, to determine the fecundity of ovigerous females of different sizes and different periods, conditions of the development of eggs, and their parameters (diameter and volume). A. aidae presented patterns of reproductive strategy similar to other Decapoda crustaceans, with evidence of reproductive efficiency where this population is established. Due to a lack of population and reproductive studies for this species, this study aimed to supply this demand in the scientific literature.

A population of the rare Southern Appalachian endemic species Lilium grayi, (Gray’s lily) Roan Mountain, TN/NC was monitored for 2 years to determine the cause and impact of an early season collapse. High concentrations of the Lilium spp. host-specific fungal phytopathogen, Pseudocercosporella inconspicua (G. Winter) U. Braun were associated with 19/20 symptomatic and 0/30 asymptomatic plants. Strength of the association between pathogen and disease and the replication of disease symptoms in 4/4 healthy hosts showed that P. inconspicua was the causal agent of the disease referred to as lily leaf spot. Disease had a severe impact on the population with 59% of mature and 98% of adolescent plants undergoing early senescence. Only 32% of mature plants produced capsules and they were frequently diseased. A recurring spatiotemporal pattern typical of an infectious disease suggested that the lily leaf spot disease is capable of causing sequential annual epidemics of unknown long-term consequences to the stability of the host population.

The future of Lake Baikal’s biodiversity is uncertain in response to climate change. Unlike its diverse benthos, Lake Baikal’s zooplankton is species poor, with up to 96% of its biomass being composed of a single Calanoid copepod species, Epischura baikalensis. This study characterizes the genetic differentiation and differential gene expression of E. baikalensis. Using partial-transcriptome sequences obtained by 454 Rosche and Illumina sequencing technologies, the genetic differentiation at inferred single nucleotide polymorphism (SNP) sites and differential gene expression in populations sampled from various parts of the lake were analyzed. The functional genomics of genes showed significant differential expression among the lake’s regions with some genes being highly up-or down-regulated. High genetic differentiation among regions suggests isolated subpopulations. Moreover, significantly differentially expressed transcripts were significantly more genetically differentiated than transcripts exhibiting no differential expression. These results suggest high potential phenotypic plasticity and adaptability in response to climate change, e.g., temperature.