URAP

Doris Bachtrog - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     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...

Doris Bachtrog - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

How do new species form? One of the major challenges in evolutionary biology is identifying the genetic changes that cause populations to stop mating with one another. We study this question in Drosophila athabasca, a group of closely related fruit fly populations that are at a very early stage of...

Annaliese Beery - Professor, Integrative Biology

Status: Current Term Now Closed     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: Current Term Now Closed     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: Current Term Now Closed     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: Current Term Now Closed     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: Current Term Now Closed     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...

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: Current Term Now Closed     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...

Seth Finnegan - Professor, Integrative Biology

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

The formation of the Isthmus of Panama separated the Caribbean Sea from the Pacific Ocean, and the marine ecosystems on either side of the isthmus have diverged substantially over the last several million years as a result of this split. Compared to the strong coastal upwelling zones present in the...

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

Lichens are partnerships of fungi, algae, and bacteria entangled in symbiosis. In two interconnected projects focused on the lace lichen (Ramalina menziesii), we are exploring how lichens persist as integrated units despite their variable habitats and symbiotic partners. We have reciprocally transplanted lace lichen from two distinct microhabitats on Santa...

Britt Koskella - Professor, Integrative Biology

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

Bacteriophages (phages) are potent bacterial predators and parasites that play a critical role in the ecology of microbial communities. While most phages immediately kill their host bacterium, some phages (prophages) allow their host to live momentarily by pausing infection and integrating into the host chromosome. While integrated, prophages can sometimes...

Britt Koskella - Professor, Integrative Biology

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

For the last 10 years the Pear project (fire blight of pear trees) has been seeking to better understand how bacteriophage viruses impact the ability of two bacterial pathogens (Erwinia amylovora and Pseudomonas syringae) to colonize and infect pear trees around the city of Berkeley. We are tracking bacteria-phage...

Britt Koskella - Professor, Integrative Biology

Status: Current Term Now Closed     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: Full- no new appr needed     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

The water-land transition of tetrapods is one of the most pivotal events in evolutionary history. This project investigates how early tetrapods (specifically temnospondyls, also considered early amphibian relatives) adapted to the novel acoustic environment of land. By using fossils, we are examining the form-function relationship of the early...

Juan Liu - Professor, Integrative Biology

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

During the Late Cretaceous period, the North American Rocky Mountain region was once part of a lost island continent called Laramidia. The eastern coastline of this landmass preserves a rich and understudied record of sharks, rays, and bony fish from the late Mesozoic and early Cenozoic Eras. The most diverse...

Cynthia Looy - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     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. We expect...

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

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

Deer mice are the primary reservoir for Sin Nombre Virus (SNV). SNV causes severe respiratory disease in humans with a case fatality of 35-50%. Those who survive the disease will eventually clear the virus from their system. However, deer mice sustain lifelong infections with minimal disease. To understand how deer...

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: Full- no new appr needed     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: Check back for status     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 in the Okamoto lab focuses on understanding the reproductive phenology of golden mussels (Limnoperna fortunei), a fast-spreading invasive species in the California river delta. Students participating in this URAP opportunity will conduct field work in the delta including mussel collections, collecting and deploying larval settlement plates...

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: Current Term Now Closed     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

Water boatmen are renowned for their remarkable adaptations for both diving and flying. However, the physical mechanisms these insects employ to overcome the constraints imposed when transitioning between aquatic and aerial environments remain poorly understood. We investigate in the lab their locomotion performance using High-speed video and fluid dynamics...

Onja Razafindratsima - Professor, Integrative Biology

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

Our research group is interested in addressing various questions related to the elevational patterns of birds in Madagascar. Over the past two years, we have collected field data on species distributions, community assemblages, and population densities along an elevational gradient in northeastern Madagascar. The student will have the opportunity to...

Onja Razafindratsima - Professor, Integrative Biology

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

Forest regeneration and seed dispersal are essential ecological processes for maintaining biodiversity, ecosystem stability, and carbon sequestration. However, these processes are being threatened by agricultural expansion and defaunation. As a first step toward understanding the importance of animal seed dispersers in forest regeneration, this project aims to assess the diversity...

Onja Razafindratsima - Professor, Integrative Biology

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

Our research group is interested in addressing various questions related to primate ecology. We have gathered data in the field for over two years about different aspects of movement and foraging ecology of three sympatric lemur species in the rainforests of Madagascar. Students will have the opportunity to develop specific...

Michael Shapira - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

Most, if not all, animals harbor extensive microbial communities, which contribute to host health and fitness. In humans, the gut microbiome holds ~100 times more genes than the host genome, encoding diverse functions. This is a theme in most animals, and raises the question of what is the significance of...