The Survival of the Central American Squirrel monkey (Saimiri oerstedi): the habitat and behavior of a troop on the Burica Peninsula in a conservation context

The conservation status of Central American Squirrel monkeys (Saimiri oerstedi) on the far southern coast of Peninsula Burica in Panama was assessed over the course of a 13 day study period. Four troops of squirrel monkeys (67 individuals) were located on the southern coast of Peninsula Burica. Using information from local sources it can be estimated that up to 7 troops (157 individuals) live in the 7-8 km2 study site. These troops are sharing an estimated 80 ha of habitat which compared to past studies is a fairly low amount of habitat. One troop of squirrel monkeys which is fed at an eco-lodge (Mono Feliz), was assessed in depth for behavioral characteristics, habitat-use, and membership distribution. The Mono Feliz troop had 32 members the preponderance of which appeared to be males. During the study period, no females were conclusively identified during monitoring or feeding times. The troop had similar behavioral characteristics to other troops studied in the past (lack of play behavior, urine washing, chasing, genital sniffing etc…) except demonstrated intense resource-based aggression, unusual in Saimiri oersted, in response to being fed bananas. Because the study occurred in the late wet season and fruit and arthrpod abundance were at their minimum, the rest of the troop´s diet consisted of Huevo de Mono and insects. The monkeys were seen eating ants, katydids, moths, and spiders during the study period. The troop spent 8% of its time exclusively traveling and 29% of its time juggling travel and forage. Stationary rest and forging took up the majority of the troop’s time (43%) while stationary foraging consumed only 19% of the day. The troop almost never exclusively rested during the day (1%). In these activities the troop utilized a total of 28.9 ha of habitat during the study period and spent 29% of their time within 1 ha of Mono Feliz which the troop returned to multiple times per day. The daily feeding of the monkeys was therefore found to constrict foraging circuits to the area around the central location of Mono Feliz. The forests that the monkeys utilized contained large patches of early secondary growth forest, corridors of exclusively cultivated trees, an older secondary growth ridge (crowns 30-35 m), and mixed forests containing scattered larger trees as well as dense undergrowth. The average tree height of the areas sampled was 10.6 m high. There were several places within the troops normal routes were habitat bottle-necked and the monkeys had to run along the ground or make a very difficult arboreal crossing one by one. The largest conservation challenges in the areas go hand in hand. Hunting presents a genuine threat to the populations of squirrel monkeys around Punta Burica due to good prices (5-25 dollars) and the ease of catching one. The reason the babies can be caught by hand is because the monkeys must descend to the ground to connect together their habitat due to their fragmented foraging areas. Hunting is probably at least contributing to the lack of female monkeys in the area and could possibly be much of the reason for their decline. There are two contrastingly different eco-tourism/ private reserve projects developed and in development in the area. This projects have the potential to substantially help the monkeys of the area by creating habitat, educating visitors and locals, and connecting together isolated fragments of land, but much care must be taken with projects especially large-scale ones because unintended consequences can easily render the projects harmful rather than helpful

Quantitative Trait Loci Associated with the "Shade Avoidance" Type Response in A. thaliana when Grown under Oscillating Daily Summer Temperatures

A poster discussing "shade avoidance" in A. thaliana plants

The role of Phytochrome A in the heat stress response of Arabidopsis thaliana: Linkage or gene regulation?

A poster discussing the role of Phytochrome A in the heat stress response of Arabidopsis thaliana

Combining GWAS and Population Genomic Analyses to Characterize Coevolution in a Legume-rhizobia Symbiosis

The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype-by-genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts

The Influence of Genetic and Environmental Factors on the Phenology and Life-Cycle Expression of Arabidopsis thaliana

<p>This dissertation examines the processes that generate phenotypic variation in life cycles in seasonal environments. Collectively, a life cycle describes the stages an organism passes through during a generation. The timing, or phenology, of these transitions is often influenced by both environmental and allelic variation. Using the model organism Arabidopsis thaliana and both empirical and modeling approaches, I examine how correlations between life-cycle transitions, environment-dependent allelic effects, and epistasis generate patterns of life-cycle variation both within and between generations. In my first chapter, I use experiments to determine that many combinations of genetic, environmental, and developmental factors can create similar germination phenotypes, that maternal effects can influence phenotypes more than genetic differences, and that cross-generational effects can reduce variation in germination timing despite variation in flowering and dispersal time. In my second chapter, I use a modeling approach to consider the entire life cycle. I find that environmental variation is a major driver of phenotypic variation, and that considering the known geographic distribution of allelic variation across the range improves the match of model predictions to phenotypes expressed in natural populations. Specifically, variation in dormancy generated in the previous generation is predicted to cause life-cycle differences within a location, and the geographic distribution of allelic variation in dormancy interacts with local climatic environments to canalize an annual life history across the range. Finally, I test if allelic and environmental variation that affects early life stages can influence the environment experienced during reproduction. This environment determines both the time available for reproduction and the environment experienced during senescence. By implementing simple survival rules for flowering plants in the model, I show that time available for a plant to reproduce depends on earlier phenological traits and varies widely from year to year, location to location, and genotype to genotype. If reproductive trade-offs that underlie the evolution of senescence are environmentally sensitive, these results suggest that genetic variation in earlier life-stage transitions might shape senescence rates and whether they are environmentally responsive. In sum, my dissertation demonstrates the importance of pleiotropy, environment-dependent allelic expression, and epistasis in defining life-cycle variation, and proposes a novel way of predicting these relationships and complex life cycles under seasonal conditions.</p>Dissertatio

Strain frequencies from first sequencing run

Strain frequencies of 101 rhizobial strains in pools of Medicago nodules inferred from high coverage WGS data. Raw data used to calculate strain frequencies are on NCBI (Accessions SRR6029825–SRR6029912) with code in a previous Dryad repository ( https://doi.org/10.5061/dryad.fp1bg)

Strain frequencies from second sequencing run

Strain frequencies of 101 rhizobial strains from pools of Medicago nodules inferred from high coverage WGS data. Raw data used to calculate strain frequencies are on NCBI (Accessions SRR6029825–SRR6029912) with code in a previous Dryad repository (https://doi.org/10.5061/dryad.fp1bg)

Main R code: statistical analysis and figures

R code to recreate all figures and analysis included in the Evolution paper. This file takes as inputs freq1.tsv, freq2.tsv, and SingleStrain_phenotype_summary.tsv

Plant phenotypes from single strain experiment

Plant phenotype data from a previously published single strain experiment (Burghardt et al, 2018, PNAS, https://doi.org/10.1073/pnas.1714246115). This file is also found in the Dryad repository for that publication ( https://doi.org/10.5061/dryad.fp1bg). The file is used as input for calculations of plant benefit of strain communities in the main R code