Field Museum Semester: Research in Natural History

Title: Gene flow and local adaptation in a tropical avifauna

Mentor: Abhimanyu Lele, Scientific Affiliate, Field Museum of Natural History

Brief description: The evolutionary history of a species is fundamentally affected by the degree to which it adapts to varying conditions across its range. Local adaptation affects range boundaries responses to environmental change, and ecological speciation. It is thus of both theoretical and applied interest. Critical gaps remain in our understanding of local adaptation, particularly in tropical ecosystems, and among endotherms: in particular, the relationship between gene flow and local adaptation remains incompletely understood, with theoretical and empirical support for both negative and positive relationships between gene flow and local adaptation. We propose to investigate the relationship between intraspecies variation, local adaptation, and gene flow, using comparative methods to explore spatial variation in phenotypic and genotypic traits across a suite of species.

 

Title: The domestication and evolution of the coca crops part II: Genome resequencing of key clades

Mentor: Dawson White, Postdoc, Grainger Bioinformatics Center, Field Museum of Natural History

Brief description: This project aims to complete whole-genome shotgun sequencing for representative samples of key coca clades, new E. gracilipes samples from Peru and Colombia, and new Ecuador samples. Phylogeographic and demographic analyses will significantly improve our understanding of the locations, timing, and evolution of the coca crops. This project will sample Field Museum herbarium collections, use the DNA lab for genomic DNA isolation and library preparation, and utilize the Grainger computer servers for analyses. Interns might also be involved in collecting leaf hyperspectral reflectance scans.

 

Title: Whole genome sequencing of neglected coronavirus diversity recovered from Afrotropical bats

Mentor: Holly Lutz, Scripps Research; Scientific Affiliate, Field Museum of Natural History

Brief description: This proposed project will expand availability of publicly available coronavirus genomes from the underrepresented region of East Africa, which will be achieved by leveraging samples collected as part of the previously NSF-funded Bat Microbiome Project (BMP). As part of the BMP, rectal and oral swabs from ~450 bats were preserved in RNAlater for viral discovery. Preliminary analyses using RT-PCR and Sanger sequencing targeting the RdRp gene have identified four novel Alpha and Betacoronavirus lineages out of 50 randomly assorted individuals screened. Based on these results, we anticipate that given an ~8% rate of positive infections, we will identify approximately 36 novel CoV lineages upon completion of these initial screens.

 

Title: Grounding the evolution of the mammalian middle ear: morphological integration and the role of auditory bone-conduction in a major evolutionary transition

Mentor: Spencer Hellert, Scientific Affiliate, Field Museum of Natural History

Brief description: Over roughly 150 million years, mammalian middle ear bones changed their shape, location, and function, resulting in an iconic mammalian feature seen in no other tetrapods and a prime example of gradual evolution of complex systems. The unique functionality of the Definitive Mammalian Middle Ear (DMME) is made possible in large part by the incorporation of postdentary bones into the middle ear. Why the synapsid lineage was the only tetrapod clade to incorporate parts of the mandible into the middle ear remains virtually unstudied. In a first-of-its-kind study, we will use cutting-edge 3D imaging technology and innovative geometric morphometric (GMM) methods to investigate if mammal ancestors could “hear” by picking up vibrations in the ground through their jaw bones, which prompted the extraordinary evolution of the mammalian middle ear.

 

Title: Chromosome evolution & Recombination Landscape of Pyrrhura cruentata and Pyrrhura griseipectus

Mentor: Taylor Hains, Scientific Affiliate, Field Museum of Natural History

Brief description: The proposed project will quantify the differences in the recombination landscape of parrots in comparison to published data from passerines, confirm or reject the loss of PRDM9 in parrots, and study how the presence or absence of PRDM9 is affecting comparative recombination rates between parrots and Passeriforms. This will be done by generating chromosome-level genome assemblies using both linked-reads and chromatin-conformation capture data as well as long-read transcriptome data for two species of Pyrrhura with accessible sampled captive populations: Pyrrhura cruentata and Pyrrhura griseipectus.

 

Title: Where are these big lichens coming from and why? An investigation of the Parmotrema reticulatum invasion of the Chicagoland area

Mentor: Todd Widhelm, Collection Manager Fungi, Field Museum of Natural History

Brief description: Parmotrema reticulatum was not common in the Chicagoland area in the past. A 1998 checklist of the Palos Region of the Forest Preserves of Cook County did not report this species, but recent collections in Palos Region this summer found P. reticulatum to be fairly common there today. Where are these new colonizers coming from? P. reticulatum is found on every continent besides Antarctica and is known to contain cryptic lineages. Which cryptic genetic groups are colonizing the Chicagoland area? Identifying which lineages are present in Chicagoland will help to answer where the new colonizers are coming from.

 

Title: Who’s hanging out with who? Characterizing symbiotic interaction networks in lichens

Mentor: Matthew Nelsen, Ph.D., Research Scientist, Field Museum of Natural History

Brief description: While lichens—symbiotic associations between fungi and algae—are classic models of symbiosis, our understanding of them is limited. DNA barcoding (Illumina MiSeq) will be used to characterize symbiont diversity, and understand the roles environment, traits and evolutionary history play in structuring fungal-algal associations—ultimately providing insight into their stability and potential responses to disturbances like climate change. This position will provide experience in DNA sequencing, scripting in R, lichen biology, and scientific communication.

 

Title: Accelerating the pace of scientific discovery: Uncovering hidden biodiversity using machine learning

Mentor: Matt Von Konrat, Ph.D., Head of Botanical Collections; Rick Ree, Curator of Flowering Plants and Head of Life Sciences;  Beth McDonald, MS, Machine Learning Engineer, Field Museum of Natural History

Brief description: Machine Learning (ML) is affecting all aspects of modern society with broad applications from banking to medicine. Only recently has this technology been applied to natural history collections achieving impressive performance on a variety of predictive tasks, e.g., species identification and plant species distribution. The study will apply this rapidly expanding technology using images rendered from large-scale digitization efforts. Broad hypotheses can be tested and have the potential for supporting biodiversity research and natural history collection management. Questions might include 1) Investigating the utility of ML to detect phenotypic structures, morphological landmarks, and reproductive structures in selected species; 2) testing taxonomic and evolutionary hypotheses regarding morphologically cryptic species. Skills acquired would include development of computer-aided tools, coding, digital microscopy, herbarium skills, morphometrics, plant systematics.

 

Title: Comparative Population Dynamics and Morphometrics of Brown Rats (Rattus norvegicus) vs Squirrels across the Chicagoland Region to Understand Urban Species Adaptation

Mentor: Noé De La Sancha, Ph.D., Associate Professor, Chicago State University; Research Associate, Field Museum of Natural History

Brief description: We are currently in the middle of the fifth mass extinction on the planet, the Anthropocene. The main driver for this mass stems from the reshaping of natural environments into urban habitats and other highly anthropogenic landscapes, such as agriculture. The proposed study will answer the following questions: What makes some species better adapted to coexistence with humans in urban environments? How did urban adaptation shape the genomes of native and invasive urban species? How do native vs exotic species populations react to urbanization (i.e., population numbers)?

 

Title: Rapid Inventory biodiversity data from the Amazon: making data more accessible

Mentor: Michelle Thompson, Ph.D., Conservation Ecologist/Herpetologist, Field Museum of Natural History

Brief description: Since 1999, the Field Museum Keller Science Action Center’s rapid inventory team has carried out 24 scientific expeditions to unexplored landscapes in South America’s Andes-Amazon region. These rapid inventories have had major conservation and scientific impacts. The intern will 1) work with conservation biologists to digitize, archive, and publish plant and animal observations collected from the Andes- Amazon, 2) along with their mentor, develop a research question and analysis using the biodiversity data. Potential research themes include aiming to better understand the patterns and processes of diversity in the Amazon or identifying gaps in biodiversity data and/or data accessibility.

 

Title: Evolutionary walks through ornamental phenotype space: Understanding constraint and innovation in diverse acoustic and visual phenotypes of kingfishers

Mentor: Chad M. Eliason, Ph.D., Field Museum of Natural History

Brief description: With diverse color patterns and vocal behaviors, kingfishers provide a powerful opportunity to study the genetic and physical mechanisms underpinning signal diversity. The proposed project combines genomic data with digitization of interior signaling structures to reveal how genetic constraints and mechanisms of signal production limit or enable the evolution of novel ornamental phenotypes. The internship will also engage in “virtual collection experiences” to train and communicate our science to diverse audiences.