Life Sciences Commons^™

Of Rats And Men, Thomas S. Walsh

Capstones

This capstone is a data-driven investigation into New York City's rat problem. By using publicly available government data to map rat activity in NYC, I identified several socio-economic variables that correlate with rat populations at the community district, borough, and city-scale. I used these findings (mainly that rat problems are linked to lower incomes) as the basis of an investigation, which includes interviews with residents, experts, and city officials. Prof. Bobby Corrigan, urban rodentologist and formerly with the NYC Department of Health criticizes the city's efforts for the first time on the record.

https://thomasseiyawalsh.wixsite.com/ratstone

A Novel Three-Way Interaction Among A Fish, Algae, And A Parasitic Copepod, John Waldman

Publications and Research

No abstract provided.

Relative Contribution Of Neutral And Deterministic Processes In Shaping Fruit-Feeding Butterfly Assemblages In Afrotropical Forests, Kwaku Aduse-Poku, Freerk Molleman, William Oduro, Samuel K. Oppong, David J. Lohman, Rampal S. Etienne

Publications and Research

The unified neutral theory of biodiversity and biogeography has gained the status of a quantitative null model for explaining patterns in ecological (meta)communities. The theory assumes that individuals of trophically similar species are functionally equivalent. We empirically evaluate the relative contribution of neutral and deterministic processes in shaping fruit-feeding butterfly assemblages in three tropical forests in Africa, using both direct (confronting the neutral model with species abundance data) and indirect approaches (testing the predictions of neutral theory using data other than species abundance distributions). Abundance data were obtained by sampling butterflies using banana baited traps set at the forest canopy …

Cryptic Diversity And Discordance In Single‐Locus Species Delimitation Methods Within Horned Lizards (Phrynosomatidae: Phrynosoma), Christopher Blair, Robert W. Bryson Jr.

Publications and Research

Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 …

Gene Coexpression Network Analysis Of Fruit Transcriptomes Uncovers A Possible Mechanistically Distinct Class Of Sugar/Acid Ratio-Associated Genes In Sweet Orange, Liang Qiao, Minghao Cao, Jian Zheng, Yihong Zhao, Zhi-Liang Zheng

Publications and Research

Background: The ratio of sugars to organic acids, two of the major metabolites in fleshy fruits, has been considered the most important contributor to fruit sweetness. Although accumulation of sugars and acids have been extensively studied, whether plants evolve a mechanism to maintain, sense or respond to the fruit sugar/acid ratio remains a mystery. In a prior study, we used an integrated systems biology tool to identify a group of 39 acid-associated genes from the fruit transcriptomes in four sweet orange varieties (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal …

Comparative Transcriptomics Reveal Developmental Turning Points During Embryogenesis Of A Hemimetabolous Insect, The Damselfly Ischnura Elegans, Sabrina Simon, Sven Sagasser, Edoardo Saccenti, Mercer R. Brugler, M. Eric Schranz, Heike Hadrys, George Amato, Rob Desalle

Publications and Research

Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a “core” set of 6,794 transcripts – shared by all embryonic stages – which are mainly involved …

Comparative Phylogeographic, Population Genomic, And Selection Inference With Development Of Hierarchical Co-Demographic Models, Alexander Xue

Dissertations, Theses, and Capstone Projects

Comparing demographic histories across assemblages of populations, species, and sister pairs has been a focus in phylogeography since its inception. Initial approaches utilized organelle genetic data and involved qualitative comparisons of genetic patterns for evaluating hypotheses of shared evolutionary responses to past environmental changes. This endeavor has progressed with coalescent model-based statistical techniques and advances in next-generation sequencing, yet there remains a need for methods that can analyze aggregated genomic-scale data from non-model organisms within a unified framework that considers individual taxon uncertainty and variance. To this end, the aggregate site frequency spectrum (aSFS), an expansion of the site frequency …

Climate-Driven Habitat Shifts In South America: Biogeography, Historical Demography, And Population Genomics Of Anole Lizards, Ivan Prates

Dissertations, Theses, and Capstone Projects

Shifts in the geographic distribution of habitats over time can promote dispersal and vicariance, thereby influencing large-scale biogeographic patterns and ecological processes. The establishment of corridors of suitable habitat across previously disjunct yet ecologically similar regions has been widely linked to climate change over time. Such climate-mediated habitat changes may have played a key role in the assembly of tropical biotas, including those of Amazonia and the coastal Atlantic Forest in South America, two of the most diverse ecosystems on Earth. The history of biogeographic associations between tropical rainforest habitats in response to former climatic shifts, as well as their …

Bacterial Diversity Impacts As A Result Of Combined Sewer Overflow In A Polluted Waterway, Olga Calderón, Holly Porter-Morgan, Joby Jacob, Willis Elkins

Publications and Research

Newtown Creek is an industrial waterway and former tidal wetland in New York City. It is one of the most polluted water bodies in the United States and was designated as a superfund site in 2010. For over a century, organic compounds, heavy metals, and other forms of industrial pollution have disrupted the creek’s environment. The creek is also impacted by discharges from twenty combined sewer overflow pipes, which may deposit raw sewage or partially treated wastewater directly into the creek during heavy or sustained rain events. Combined sewer overflow events and associated nutrient over-enrichment at the creek drive eutrophication …

Walking As Ontological Shifter: Thoughts In The Key Of Life, Bibi (Silvina) Calderaro

Dissertations, Theses, and Capstone Projects

With walking as ontological shifter I pursue an alternative to the dominant modernist episteme that offers either/or onto-epistemologies of opposition and their reifying engagements. I propose this type of walking is an intentional turning towards a set of radical positions that, as integrative aesthetic and therapeutic practice, brings multiplicity and synchronicity to experience and being in an expanded sociality. This practice facilitates the conditions of possibility for recurring points of contact between the interiority perceived as ‘body’ and the exteriority perceived as ‘world.’ While making evident the self’s at once incoherence with it-self, it opens to a space beyond the …

Climate Matching Drives Spread Rate But Not Establishment Success In Recent Unintentional Bird Introductions, Pedro Abellán, José L. Tella, Martina Carrete, Laura Cardador, José D. Anadón

Publications and Research

Understanding factors driving successful invasions is one of the cornerstones of invasion biology. Bird invasions have been frequently used as study models, and the foundation of current knowledge largely relies on species purposefully introduced during the 19th and early 20th centuries in countries colonized by Europeans. However, the profile of exotic bird species has changed radically in the last decades, as birds are now mostly introduced into the invasion process through unplanned releases from the worldwide pet and avicultural trade. Here we assessed the role of the three main drivers of invasion success (i.e., event-, species-, and location-level factors) on …

The Influence Of Phylogeny And Niche Differentiation On The Diets Of Malagasy Primates, Rebekka S. Hughes

Theses and Dissertations

Previous studies have shown that haplorhine diet is affected by phylogeny; however, until now studies in Malagasy strepsirrhines were lacking. The evolution of differences in Malagasy primates’ diets appears to differ from the pattern shown in haplorhines. My results indicate that niche differentiation may be a stronger predictor of diet.

Ecological Niche Modeling Of The Genus Papio, Amanda J. Fuchs

Theses and Dissertations

Ecological niche modeling investigates how climatic variables have influenced taxonomic diversity in Papio. Models performed well suggesting climatic variables influence the distribution of baboon species. Niche overlap among all possible pairs of taxa determined that species exhibited significantly different niches. The results of these models support a parapatric speciation scenario.

Large-Scale Differences In Microbial Biodiversity Discovery Between 16s Amplicon And Shotgun Sequencing, Michael Tessler, Johannes S. Neumann, Ebrahim Afshinnekoo, Michael Pineda, Rebecca Hersch, Luiz Felipe M. Velgo, Bianca T. Segovia, Fabio A. Lansac-Toha, Michael Lemke, Rob Desalle, Christopher E. Mason, Mercer R. Brugler

Publications and Research

Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles …

Memory For Stimulus Sequences: A Divide Between Humans And Other Animals?, Ghirlanda Stefano, Johan Lind, Magnus Enquist

Publications and Research

Humans stand out among animals for their unique capacities in domains such as language, culture and imitation, yet it has been difficult to identify cognitive elements that are specifically human. Most research has focused on how information is processed after it is acquired, e.g. in problem solving or ‘insight’ tasks, but we may also look for species differences in the initial acquisition and coding of information. Here, we show that non-human species have only a limited capacity to discriminate ordered sequences of stimuli. Collating data from 108 experiments on stimulus sequence discrimination (1540 data points from 14 bird and mammal …

Ecology, Evolution, And Sexual Selection In The Invasive, Globally Distributed Small Indian Mongoose (Urva Auropunctata), M. Aaron Owen

Dissertations, Theses, and Capstone Projects

Introduced species provide rare opportunities to test evolutionary hypotheses in situ by creating so-called natural experiments. Natural experiments are situations in nature that resemble laboratory studies by allowing for comparisons of a “control” group (i.e., a species’ native range) with “experimental” groups (i.e., a species’ introduced range). In particular, introduced animals allow us to investigate evolutionary dynamics in complex, long-lived organisms in ways that would otherwise be impossible in a laboratory setting. One such introduced animal is the small Indian mongoose (Urva auropunctata, formerly Herpestes auropunctatus). Native to South Asia, the small Indian mongoose’s introduction to more …

Naturally-Derived Molecular Ensembles In Medicine, Materials Science And Evolutionary Biology: An Interdisciplinary Study, Silvio Panettieri

Dissertations, Theses, and Capstone Projects

The first chapter will introduce the work carried out in collaboration with the Govind laboratory at CCNY. Our quest was set forth to investigate the intimate relationship lying between chronic inflammation and tumor development. For at least the last fifteen years much research has been conducted on this topic; yet, the level of complexity arising from exceedingly interwoven biochemical pathways in mammals has resulted in slow advancements in this field. This is why we resorted to a simple yet powerful immunogenetic model organism, the fruit fly Drosophila melanogaster, in combination with the administration of the most common anti-inflammatory drug, …

Lichen Conservation In Eastern North America: Population Genomics, Climate Change, And Translocations, Jessica Allen

Dissertations, Theses, and Capstone Projects

Conservation biology is a scientific discipline that draws on methods from diverse fields to address specific conservation concerns and inform conservation actions. This field is overwhelmingly focused on charismatic animals and vascular plants, often ignoring other diverse and ecologically important groups. This trend is slowly changing in some ways; for example, increasing number of fungal species are being added to the IUCN Red-List. However, a strong taxonomic bias still exists. Here I contribute four research chapters to further the conservation of lichens, one group of frequently overlooked organisms. I address specific conservation concerns in eastern North America using modern methods. …

Characterizing The Impacts Of Contaminants On Fish Embryogenesis And Revealing An Alternate Molecular Mechanism Of Ahr Mediated Cardiac Defects, Corinna Singleman

Dissertations, Theses, and Capstone Projects

There is a long history of damage to natural ecosystems from environmental pollution. Many environmental contaminants are man-made and have been released with abandon over the last 100 years including dioxins, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and polychlorinated biphenyls (PCBs). These chemicals act on similar cellular processes and cause skin lesions, cancer, learning disabilities and reproductive problems in many vertebrates. There are many studies exploring various aspects of TCDD and PCB exposure on model and wild organisms. Few studies however, have compared effects of PCB mixtures on ecosystems to effects of individual PCBs in the lab. The first aim of this thesis is …

Oldest Skeleton Of A Plesiadapiform Provides Additional Evidence For An Exclusively Arboreal Radiation Of Stem Primates In The Palaeocene, Stephen B. Chester, Thomas E. Williamson, Jonathan I. Bloch, Mary T. Silcox, Eric J. Sargis

Publications and Research

Palaechthonid plesiadapiforms from the Palaeocene of western North America have long been recognized as among the oldest and most primitive euarchontan mammals, a group that includes extant primates, colugos and treeshrews. Despite their relatively sparse fossil record, palaechthonids have played an important role in discussions surrounding adaptive scenarios for primate origins for nearly a half-century. Likewise, palaechthonids have been considered important for understanding relationships among plesiadapiforms, with members of the group proposed as plausible ancestors of Paromomyidae and Microsyopidae. Here, we describe a dentally associated partial skeleton of Torrejonia wilsoni from the early Palaeocene (approx. 62Ma) of New Mexico, which …

African Wild Dog, Lycaon Pictus, Coloration Patterns And Social Aggregation, Ayong J. Kim

Theses and Dissertations

Packs of African wild dogs, Lycaon pictus, were analyzed for coloration patterns and social aggregation tendencies. Mapped locations determined if the coat patterns followed a geographic distribution that corresponded to Southern or Eastern phenotypic forms. Social aggregation tendencies were observed to determine grouping behavior presumably related to individuals’ roles.

Does Genotype Correlate With Phenotype? Evaluating Ruffed Lemur (Varecia Spp.) Color Vision Using Subject Mediated Automatic Remote Testing Apparatus (Smarta), Raymond Vagell

Theses and Dissertations

Ruffed lemur (Varecia spp.) color vision research was conducted using a multidisciplinary approach: psychophysics, genetic analysis, technology, and animal training. The behavioral manifestation of Varecia spp. trichromacy was shown using a touchscreen apparatus (SMARTA). Trichromats performed better than dichromats when discriminating red from green (G₂ = 78.10, p < 0.001).

Conserved Patterns Of Integrated Developmental Plasticity In A Group Of Polyphenic Tropical Butterflies, Erik Van Bergen, Dave Osbaldeston, Ullasa Kondandaramaiah, Oskar Brattström, Kwaku Aduse-Poku, Paul M. Brakefield

Publications and Research

Background: Developmental plasticity is thought to have profound macro-evolutionary effects, for example, by increasing the probability of establishment in new environments and subsequent divergence into independently evolving lineages. In contrast to plasticity optimized for individual traits, phenotypic integration, which enables a concerted response of plastic traits to environmental variability, may affect the rate of local adaptation by constraining independent responses of traits to selection. Using a comparative framework, this study explores the evolution of reaction norms for a variety of life history and morphological traits across five related species of mycalesine butterflies from the Old World tropics.

Results: Our data …

Egg Discrimination Along A Gradient Of Natural Variation In Eggshell Coloration, Daniel Hanley, Tomáš Grim, Branislav Igic, Peter Samaš, Analía V. López, Matthew D. Shawkey, Mark E. Hauber

Publications and Research

Accurate recognition of salient cues is critical for adaptive responses, but the underlying sensory and cognitive processes are often poorly understood. For example, hosts of avian brood parasites have long been assumed to reject foreign eggs from their nests based on the total degree of dissimilarity in colour to their own eggs, regardless of the foreign eggs’ colours. We tested hosts’ responses to gradients of natural (blue-green to brown) and artificial (green to purple) egg colours, and demonstrate that hosts base rejection decisions on both the direction and degree of colour dissimilarity along the natural, but not artificial, gradient of …

The Paucity Of Frugivores In Madagascar May Not Be Due To Unpredictable Temperatures Or Fruit Resources, Sarah Federman, Miranda Sinnott-Armstrong, Andrea L. Baden, Colin A. Chapman, Douglas C. Daly, Alison R. Richard, Kim Valenta, Michael J. Donoghue

Publications and Research

The evolution of ecological idiosyncrasies in Madagascar has often been attributed to selective pressures stemming from extreme unpredictability in climate and resource availability compared to other tropical areas. With the exception of rainfall, few studies have investigated these assumptions. To assess the hypothesis that Madagascar's paucity of frugivores is due to unreliability in fruiting resources, we use statistical modeling to analyze phenology datasets and their environmental correlates from two tropical wet forests, the Réserve Naturelle Intégrale Betampona in Madagascar, and Kibale National Park in Uganda. At each site we found that temperature is a good environmental predictor of fruit availability. …

A Phylogenetic And Environmental Analysis Of Brazilian Placosoma Lizards, Kai A. Farje-Van Vlack

Dissertations and Theses

Placosoma is a genus comprised of the Brazilian spectacled lizards P. champsonotus, P. cipoense, P. cordylinum, P. glabellum, and P. limaverdorum. While P. champsonotus, P. cordylinum, and P. glabellum occupy the southern coast of Brazil, P. cipoense is found in the montane grasslands north of that range, and P. limaverdorum was recently discovered in forest isolates that persist within the semi-arid Caatinga. This study elucidates the ecological and evolutionary relationships among these morphologically similar lizards. Using mitochondrial and nuclear gene sequences, genus-wide phylogenies were inferred through Bayesian inference and a species tree approach, …

Are Weevils Picky Eaters? Community Structure And Host Specificity Of Neotropical Saproxylic Beetles (Coleoptera: Curculionidae), Jhunior A. Morillo

Dissertations and Theses

Abstract Primary saproxylic beetles play a major role in forest nutrient cycling and making deadwood accessible to other decomposers. Understanding beetle host preferences and patterns of community assembly is critical for their conservation, and for predicting which species might become invasive. This project aims to investigate the ecological and host specificity, as well as the community composition of curculionids in a mosaic of old-growth (OG) and secondary forest on the Osa Peninsula, Costa Rica. The subfamily Scolytinae was expected to be the most species-rich and abundant. Ambrosia beetles were expected to have more generalist species than other curculionids. Old growth …

Large-Scale Surveillance Of Captive Naked Mole-Rat Colonies Shows Caste Differences In Space Utilization, Michael Kress, Edward F. Meehan, Dan Mccloskey

Publications and Research

African naked mole-rats are eusocial mammals that provide unique opportunity to study complex mammalian social behavior and large-group dynamics in a controlled vivarium setting. Previous reports of captive and wild naked mole-rats have identified a division of labor among non-reproductive colony members along a size polyethism, with large animals specializing in defense behaviors, and small animals performing foraging, nest building, and caretaking functions. This study utilized radio frequency identification (RFID) and advanced computational approaches to monitor the activity patterns and place preferences of all members in two naked mole-rat colonies (N = 36 and 37 animals) for a period of …