URAP

Doris Bachtrog - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Sex chromosomes are expected to segregate equally during meiosis, but in many species they show signs of genetic conflict. In Drosophila, certain genes are found in unusually high copy number on the X or Y chromosome, suggesting they may act as “meiotic drivers” that bias their own transmission at the...

Annaliese Beery - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Research in our laboratory is focused on factors that influence affiliative social behavior in two species of voles. This project involves working with a graduate student training voles to press a lever to gain access to social rewards, and testing how social reward varies under different circumstances...

Annaliese Beery - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

We maintain breeding colonies of meadow voles and prairie voles for social behavior research. This project builds on basic husbandry (covered by staff) to track lineages, wean new litters and determine pup sexes to maintain the long term health and robustness of our breeding program and provide voles for research...

Mike Boots - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Our research group in the Department of Integrative Biology researches the dynamics of infectious disease evolution and population biology in multiple insect systems, including Lepidopteran hosts (moths and butterflies). We are currently working on two interconnected projects: The first project investigates host heterogeneity by examining how environmental factors (such as...

Mike Boots - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Our research group in the Department of Integrative Biology researches the dynamics and evolution of infectious disease. Pairwise host–parasite relationships are typically embedded in broader networks of ecological interactions, which have the potential to shape parasite evolutionary trajectories. Understanding this ‘community context’ of pathogen evolution is vital for wildlife...

Mike Boots - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

The Boots' lab in the Department of Integrative Biology studies disease ecology and evolution across multiple systems, with research ranging from theory to empirical to field biology. This project focuses on the honey bee – native bee – virus field system. Each year managed honey bees in the USA face high overwintering...

Mike Boots - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 3-5 hrs     Location: On Campus

Our research group in the Department of Integrative Biology studies the dynamics, ecology, and evolution of infectious diseases through various systems. Almonds are majorly grown in California and require mass imports of honeybees for their pollination. However, honeybees used for mass agriculture also suffer from constant exposure to pathogens. RNA...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

We are working on a project to study the adaptation and evolutionary history of hummingbirds and sunbirds. Hummingbirds and sunbirds are two groups of birds that have independently adopted nectar as a major component of their diet and have evolved to be morphologically similar. Our project aims to explore whether...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

My lab is involved with a large collaborative project to study disease transmission within and among species of wild birds. As part of this project, swabs of a variety of bird species are being collected to study their microbial communities (i.e. their microbiome). Lab studies suggest that microbial diversity can...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Students can assist with several ongoing research projects that investigate geographic variation and species limits in birds and integrate these data with quantification of prevalence of disease vectors such as bird malaria and trypanosome infections...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Nest structures are widespread across animals including insects, fish, amphibians, and most conspicuously, birds. Despite their ubiquity, nests remain one of the most understudied components of avian life history. Some of the most remarkable examples of elaborate nest design are within the passerine weaverbirds (family Ploceidae). Weaverbirds are an Old...

Cara Brook - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

The Brook lab runs a longterm field research project, capturing and collecting biological samples for molecular analyses of zoonotic viruses from three species of wild fruit bat endemic to the island nation of Madagascar. The lab seeks a student researcher to carry out data cleaning, curation, and visualization when new...

Robert Dudley - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Flying insects are the most diverse and abundant form of animal life in the terrestrial biosphere. However, the origins of insect flight remain obscure given the absence of a transitional fossil record. This project will involve construction of a small robot that mimics the likely morphology of early insects, and...

Robert Dudley - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Hummingbirds are only found in the Americas, but in Africa and Asia some members of a different bird family (the sunbirds, Nectariniidae) can also hover, albeit for relatively short durations. This behavior has never been systematically characterized, however, and this project will survey existing video sequences from on-line ornithological...

Moisés Expósito-Alonso - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

The global climate is changing at an unprecedented rate due to human activities, threatening global biodiversity and food security. A fundamental question in evolutionary biology is: What enables or limits species to rapidly evolve and adapt to changing climates? In this project, we will use natural ecotypes of Arabidopsis to...

Moisés Expósito-Alonso - Professor, Integrative Biology

Status: Check back for status     Weekly Hours: to be negotiated     Location: On Campus

Description: Spontaneous mutations fuel the rate of evolutionary change by increasing the amount of genetic variation across the green tree of life. Genetic variation is utilized within natural populations to improve fitness, therefore, knowledge of the historical bias of mutation rates and spectra across a genome and across populations will...

Moisés Expósito-Alonso - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Why do some plants thrive while others face extinction? While the International Union for the Conservation of Nature (IUCN) tracks species risk, they often overlook a critical factor: genetic diversity. Genetic diversity is the "fuel" for adaptation; without it, plants cannot evolve to survive climate change or new diseases. Our...

Moisés Expósito-Alonso - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

International conservation policies including the Kunming-Montreal Global Biodiversity Framework now consider genetic diversity of wild species in their targets. However, scalable, theory-driven tools to assess and predict genetic diversity loss are still emerging, limiting their use in conservation planning. Analogous to the species-area relationship, recent work has...

Paul Fine - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 3-5 hrs     Location: On Campus

High in the rainforest canopy, epiphytic plants face the challenge of obtaining the nutrients they need without having contact with the soil. This project investigates nutrient acquisition challenges and strategies between epiphytic plants found in two different forest types in the Peruvian Amazon: relatively nutrient-rich forests with a clay...

Paul Fine - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 3-5 hrs     Location: On Campus

Near infrared spectroscopy (FT-NIR) is a fast, cost-effective technology that measures the irradiation of organic molecules inside of a leaf. The spectrometer makes chemical bonds vibrate and generate a wave response that corresponds to the leaf’s internal chemical composition (both qualitative and quantitative). These signals have been shown...

Paul Fine - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

There are many missing taxa in the molecular phylogeny of Burseraceae. Some of these missing taxa are endemic to extremely remote geographic locations and far away from their closest putative relatives. We will extract DNA from dried leaves, and get samples ready for genomic sequencing...

Seth Finnegan - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

For tens of millions of years large parts of California’s Central Valley were flooded by the ocean, creating an inland sea with a unique ecosystem including now-extinct species of clams, snails, sand dollars, corals, and other groups familiar from modern California beaches. Some of the species that lived in...

Seth Finnegan - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Besides coral, marine reefs are made up of many other strange invertebrates, including the little-known “moss animal”, or bryozoan. These abundant, microscopic filter-feeders grow in colonies and build elaborate domes, lacework, and tree-like structures on the ocean floor, from the intertidal to the abyss, from the poles...

Seth Finnegan - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Death assemblages’ are the actively accumulating shelly remains of organisms living at the bottom of the ocean. Because death assemblages accumulate over 100s to 1,000s of years, they are powerful tools to estimate past biodiversity. By comparing the ecological composition of living communities and death assemblages, we can assess recent...

Stephen Gaughran - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

The California coast is home to more than two dozen marine mammal species. Our state is also a highly productive agricultural center for the country, producing not just food but also agricultural runoff that flows into the ocean. This runoff carries nutrients and microbes from fertilizer and livestock waste, which...

Stephen Gaughran - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Monk seals are the world’s only tropical seals, with two distinct species living in Hawaii and the Mediterranean Sea. Despite intensive conservation efforts, only about 1,000 individuals survive in each species. My lab is using whole genome sequencing data from hundreds of individuals and population genetic analyses to study the...

Stephen Gaughran - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

The platypus is one of the only surviving species of monotremes, a clade of egg-laying mammals. These animals live in rivers and streams of eastern Australia and Tasmania, and show many unusual phenotypes including egg laying, electrolocation, venom production, and adaptations to aquatic life. The species is also of...

Britt Koskella - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Microbiomes change over time, often with important functional consequences for their hosts. But the ecological drivers of microbiome succession are poorly understood. We are studying the role that microbial interactions play in this process by examining the constituents of the digestive microbiome of the insectivorous California pitcher plant (Darlingtonia californica...

Britt Koskella - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Phage, viruses that infect and kill bacteria, are ubiquitous, yet their impacts on beneficial bacteria that colonize plants are not well understood. Phage are abundant in the soil and therefore soil-dwelling bacteria must hone defenses against phage in order to survive. Likewise, phage must hone their capacity to infect...

Britt Koskella - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

We are building a new system (fire blight of pear trees) to better understand how bacteriophage viruses might impact the ability of a bacterial pathogen (Erwinia amylovora) to colonize and infect pear trees. We are tracking bacteria-phage interactions through time by isolating individual phages from each of 25 diseased...

Britt Koskella - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

In natural systems, microorganisms interact with myriad other microbial populations which influence their evolution and ecology. When associated with a eukaryotic host, these complex microbial communities (known as microbiomes) also interact with and impact their host’s ecology and evolution, nutrient acquisition, and pathogen susceptibility. Despite the microbiome's vast importance on...

Juan Liu - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Lateral line sensory system, or lateral line organ, or simply the lateral line, is a system of sensory organs found in fish and some tetrapods (four-legged vertebrates). The lateral line enables those vertebrates to detect and perceive the hydrodynamic and physical environment they inhabit including movement, vibration, and pressure...

Juan Liu - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Scientific illustration is art in the service of science by drawing, painting, or rendering images of scientific subjects to accurately inform and communicate sciences. Research in fossil fishes (paleoichthyology) is at the junction of paleontology and ichthyology, and therefore, possesses characteristics of both —-- the incomplete nature of fossil preservations and...

Juan Liu - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Our study aims to explore the intricate details of mammalian hearing, with a specific emphasis on the function and evolution of the middle ear, with comparative anatomy with fish hearing apparatus. This critical aspect of auditory anatomy plays a pivotal role in the way mammals perceive and interpret sound. By...

Juan Liu - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Catfishes (Siluriformes) are remarkable among hearing specialist fishes in their possession of the Weberian apparatus, a conductive multi-ossicle chain linking the inner ear and swim bladder that is analogous to the middle ear ossicles of the mammalian tetrapods. Work with laboratory animals has produced considerable insight into the role...

Cynthia Looy - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 3-5 hrs     Location: On Campus

Pollinators are essential components of a healthy ecosystem and provide vital benefits to both plants and animals. The student-run pollinator garden on the south side of the Valley Life Science Building (VLSB) supports native insects, spiders, and other wildlife and is an environmental education resource for students. Our goal...

Cynthia Looy - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Plants are adapted to the physical conditions in their environments, including temperature, precipitation, atmospheric CO2 concentrations, and light level. In cooler and drier habitats, leaves tend to be smaller with condensed venation and toothed margins. While under warmer and wetter conditions, leaves tend to be larger, have ‘drip tips’, and...

Michael Nachman - Professor, Museum of Vertebrate Zoology, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Within ~500 years, house mice (Mus musculus domesticus) have expanded into a wide variety of habitats across North and South America. House mice can be found from the tropics to the arctic, and populations inhabiting these different environments have adapted to different thermal regimes. This project will focus on the...

Michael Nachman - Professor, Museum of Vertebrate Zoology, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Within ~500 years, house mice (Mus musculus domesticus) have expanded into a wide variety of habitats across North and South America. House mice can be found from the tropics to the arctic, and populations inhabiting these different environments have adapted to different thermal regimes. Mice from cold regions are larger...

Michael Nachman - Professor, Museum of Vertebrate Zoology, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

A fundamental challenge in evolutionary biology is to understand how new species arise. The California vole is a widespread Californian rodent that appears generally uniform and is currently classified as a single species. However, recent studies have shown that the California vole forms two genetically distinct groups with reproductive isolation...

Rasmus Nielsen - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Understanding how species interact with their environment and how climate influences where species occur is integral to ecology. We work on questions about what factors influence the spatial distribution of species, which can be determined using mathematical models called 'species distribution models' or 'environmental niche models'. The data that go...

Rasmus Nielsen - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     

The Fluorescence In Situ Hybridization (FISH) technique is a molecular cytogenetic method used to detect and localize the presence or absence of specific DNA sequences on chromosomes. It is widely used for karyotyping to visualize and map chromosomal abnormalities such as translocations, deletions, duplications, and aneuploidies. In Nielsen lab, we've...

Daniel Okamoto - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Climate change is dramatically altering the oceans. These changes include increases in sea surface temperature, pH, dissolved oxygen, and primary productivity. We use experiments and field data to assess how these changes affect the physiology, growth, reproduction, and behavior of marine animals. We have numerous samples from past experiments and...

Daniel Okamoto - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

In kelp forests, food resources are a key contributor to a kelp forest inhabitant’s fitness. Recently, sea urchin herbivory has been shown to rapidly reshape the food landscape within these forests, converting areas of high productivity to desert-like ‘urchin barrens’. We aim to study food assimilation as it relates...

Daniel Okamoto - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

This URAP opportunity focuses on the energetics of host-parasite interactions in a model zooplankton-fungal parasite system. Over the course of Fall 2025- Spring 2026, we will conduct several experiments that test how variable food resources shape host and parasite fitness. Students will have the opportunity to connect and...

Daniel Okamoto - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Seaweeds (e.g., kelp, nori) are important primary producers, food sources, and essential fish habitat around the globe. While many species are resilient to climate change, many important species are also exhibiting declines in recent years and especially in response to marine heatwaves. We are conducting laboratory experiments and fieldwork focused...

Victor Ortega Jimenez - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Marangoni effect is used by water striders (Veliidae) and rove beetles (Staphylinidae) to induce an ultrafast escape response against inter- or intra-specific predators. However, it is unclear if the surfactants secreted by these insects, that reduce surface tension of water, can also affect predator’s locomotion during the chasing...

Victor Ortega Jimenez - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Phantom crane flies (Bittacomorpha clavipes) are one of the most mysterious fliers in the insect world because it has been suggested that they are able to use their legs and body to generate aerodynamic forces and still keep a tight aerial control. Our research can be applied to micro aerial...

Victor Ortega Jimenez - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Helicopters seeds (Samaras) are remarkable for their aerodynamic capabilities with insects wings. We Investigate the aerodynamics and kinematics of samaras in a vertical wind tunnel. The goal of this project is to understand the unsteady mechanisms they have to fly on unsteady flow conditions...

Victor Ortega Jimenez - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Flying predator and their prey are commonly challenged to interact under unstable flow conditions. However, the effects produced by non-steady flows on predator-prey relationships, which demand acute aerial control and maneuvering, remain unclear. Particularly, because aerial predators are generally larger than preys, which can bias the locomotory effects...