A teacher showing two students a marine organism
0

The Academy's Summer Systematics Institute and Biological Illustration internships will be offered from June 10 to August 9, 2019.

Application deadline: February 15, 2019

Since 1995, the California Academy of Sciences' Summer Systematics Institute (SSI), with support from NSF's Research Experiences for Undergraduates (REU) initiative and the Academy's Robert T. Wallace endowment, has addressed critical issues like worldwide threats to biodiversity, the origins and diversification of life, phylogenetic systematics, and evolutionary biology.

SSI is a nine-week paid research internship at our state-of-the-art research facility and museum in San Francisco’s Golden Gate Park. This world-renowned venue continues to offer undergraduates important insights into the contributions that museum-based research can make to issues facing society today. The program accommodates up to 10 undergraduate students. This internship is made possible by the National Science Foundation and a generous gift from the Robert T. Wallace Endowment for undergraduate research experiences. One internship in Biological Illustration is integrated with the SSI program.

Program Curriculum

Participants will conduct research with their chosen advisor on a project relating to the discipline of the advisor and student. The program begins with a week-long field trip to the Pepperwood Preserve in Sonoma County where students will participate in workshops on natural history field methods and science communication, before traveling to the coast to participating in the annual Snapshot Cal Coast Bioblitz.

Throughout the program, participants also take part in a museum-based curriculum that includes lectures and lab exercises on phylogenetics and systematics, molecular techniques, biodiversity, evolutionary biology, global change, and other contemporary issues in the natural sciences. Other activities include collections tours, popular writing, and science communication workshops, and time out on the museum floor directly communicating with the public.

The program culminates with a research symposium, where participants have an opportunity to communicate their summer research findings with the Academy community. Following their summer internship, participants are also invited (and encouraged) to attend a scientific meeting to present their findings in the form of a talk or poster.

0

Duration & Location

The Summer Systematics Institute is a full-time program (40 hours/week) for nine weeks, from June 10 through August 9, 2019. The first week of the program will be spent at Pepperwood Preserve, with the remainder of the time spent in San Francisco at the California Academy of Sciences.

0

How to Apply

  1. The application process is entirely online. You will need to complete the application form.

  2. The online form will ask you to prepare a statement of interest in working at the Academy, as well as some background information that tells us how you became interested in biology.

  3. Complete the advisor selection portion of the application form after consulting the advisors and projects listed at the bottom of this page.

  4. You will need to find two references and provide their contact information. At least one must be a science professor or academic professional (such as an instructor or teaching assistant) who knows your school work well enough to address that in their recommendation. You should speak to these people before submitting their information to be sure they are willing to potentially write a letter of recommendation on your behalf.

Deadline: February 15, 2019. Applications received after midnight on February 15, 2019, will not be reviewed.

0

Notification

Applicants will be notified by email sometime in mid-March or early-April and should note that because of the schedules of potential mentors reviewing applications, and the possible need to contact applicants on reversion lists, there cannot be a firm deadline on our part. Due to the volume of applicants, we cannot give individual confirmation for application materials received. We hope that applicants can be patient as we make our final decisions. In general, successful applicants will know earlier in the process.

0

Eligibility

Any U.S. citizen or resident alien (green card) who is an undergraduate student, and who will not have graduated before fall of 2018, is welcome to apply. That is, you must be enrolled in an undergraduate program at the time of the internship. We encourage applications from groups under-represented in the sciences. An excellent academic record and participation in a wide range of campus activities are highly regarded, but not the sole criteria for the selection process.

0

Housing & Stipend

A $5,175 ($575/week) stipend will be awarded to each intern. Travel to and from San Francisco will be provided. Housing will be provided in dormitories in San Francisco, with details to be provided upon selection of interns. Personal stipends may be subject to federal and/or state income taxes.

 

0

2019 SSI/BI Advisors

Click the + next to each advisor's name to learn more.

Rebecca Albright

ralbright@calacademy.org

Dr. Albright is a coral reef biologist with expertise in coral reproduction, physiology, and biogeochemistry. Her research focuses on the capacity of coral reef organisms to cope with changing environmental conditions, specifically ocean warming and acidification. Dr. Albright uses a combination of laboratory and field experimentation to understand how changing environmental conditions impact the organisms that live in and on reefs and what this means for the ecosystems as a whole.

Learn more about Dr. Albright's work.

Potential projects include:

  1. Population genetics analysis of coral communities of Palau.
  2. Microstructural analysis of coral skeletons using scanning electron microscopy.
Rayna Camille Bell

Rayna Bell studies the ecology and evolution of amphibians and reptiles with an emphasis on island biogeography, hybrid zones and coloration phenotypes. Much of her work in based on a group of diverse and colorful frogs, the hyperoliid reed frogs, which are found throughout sub-Saharan Africa, Madagascar, and the Gulf of Guinea islands. More recently, Rayna has started studying the diversity and evolution of the frog visual system, a research direction that stems from her interests in understanding the ecology and evolution of coloration in frogs.

Additional information on Dr. Bell’s research can be found at: http://www.raynacbell.com.

Potential projects include:

  1. Molecular evolution of vision related genes across the frog tree of life
  2. Phylogeography and island biogeography of Central African tree frogs
  3. Courtship behavior in the Riggenbach’s reed frog
Shannon N. Bennett

sbennett@calacademy.org

Dr. Bennett joined the Academy in 2011 as the first-ever curator of Microbiology, with a special focus on viruses that cause diseases in humans and other animals. Her research focuses on the

evolutionary and ecological origins of emerging infectious disease-causing viruses. Her lab integrates a combination of molecular biology, epidemiology, field work, bioinformatics, virology, and cell culture methods to understand the diversity of viruses in natural systems and how this diversity is shaped and impacts disease potential. We focus specifically on fast-evolving RNA viruses such as dengue, Zika, and chikungunya as well as their predecessors, to identify important factors affecting virus disease dynamics including the role of biodiversity and the perturbation of natural landscapes in driving disease emergence.

Learn more about Dr. Bennett’s research.

Potential projects include, but are not limited to:

  1. Metagenomic analysis of mosquito-borne viruses and other micro-organisms.
  2. Identifying the phylogenetic structure and molecular drivers of diversification in RNA viruses such as dengue, Zika, and chikungunya viruses.
  3. Exploring the biodiversity of Hantaviruses across small mammal populations.
Pim Bongaerts

pbongaerts@calacademy.org

Pim Bongaerts studies the biodiversity and evolution of scleractinian corals on tropical coral reefs. He has a particular interest in mesophotic coral ecosystems (MCEs): light-dependent coral communities that occur at depths beyond regular diving limits (~30-150 m). Although these communities can occupy areas equivalent to that of shallow reefs, they remain largely undocumented and their biodiversity remains poorly understood. Due to their environmentally induced morphological variability and lack of informative genetic markers, scleractinian corals have been notoriously difficult in traditional systematics. Dr Bongaerts’ research focuses on next-generation sequencing and bioinformatics to overcome and assist with some of these challenges, while simultaneously studying the processes leading to adaptation and diversification on tropical coral reefs.

Additional information on Dr. Bongaerts’ research can be found at:

Potential projects include:

  1. Developing a field-based identification assay for a cryptic species complex: mining genome-wide sequencing data to design a diagnostic CAPS marker.
  2. Molecular and morphological phylogeny of the genus Leptoseris: from marker design to a phylogeny, complemented with scanning electron microscopy.
  3. Alignment-free phylogenomics: exploring the use of genomic (k-mer) signatures for coral species identification and delineation (requires intermediate programming skills).
Todd Braje

tbraje@calacademy.org

Todd's 15-plus years of archaeological research has been been conducted in island and coastal settings in California, Oregon, Florida, Mexico, and the Solomon Islands. Much of his work focuses on California's Channel Islands and his interests in maritime migrations and adaptations, human-environmental ecodynamics, and historical ecology. His diverse research includes fieldwork at some of the oldest sites along the New World Pacific Coast, occupied by Pleistocene maritime voyagers, and 19th century commercial abalone processing camps, created by Chinese immigrants during the California Gold Rush. His work has been applied in helping to evaluate, manage, and conserve Pacific Coast abalone, mussels, sheephead, fur seals, and a variety of other shellfish, fish, and sea mammals. The student will develop a project using zooarchaeological and archaeometry techniques that applies deep historical perspectives to modern issues of coastal conservation and sustainability. Using shell midden samples from California’ Channel Islands, the student will assist Dr.Braje with a historical ecological analysis of existing collections. Based on the interests of the student and the available collections, the student will develop a project using zooarchaeological and archaeometry techniques that applies deep historical perspectives to modern issues of coastal conservation and sustainability.

Learn more about Dr. Braje’s work.

Potential projects include:

  1. Decoding the deep history of foodweb changes, size fluctuations in prey species, and changes in the biogeography or abundances of keystone marine species.
Lauren Esposito

lesposito@calacademy.org

Lauren Esposito received her PhD in 2011 through the American Museum of Natural History/City University of New York collaborative program, and joined the Academy in 2015. Lauren’s research is focused on the systematics and evolution of arachnids, in particular scorpions. Her research has taken her on expeditions around the world, but much of her focus is on the arachnid communities in the Caribbean, Baja California, and the southwestern USA. Lauren uses a combination of methods including genomics, venomics, morphology, morphometrics and niche modelling to answer questions and test hypotheses about the biogeography, diversification, cryptic speciation, and adaptive radiations of arachnid life. Additionally, Lauren is the co-director of a non-profit organization, Islands & Seas, that is dedicated to promoting research, education outreach, and sustainable development in special places on earth.

Learn more about Dr. Esposito’s research.

Potential projects:

  1. Adapting to a life of salt: using genomics to understand the adaptation and diversification of arthropod communities on post-pleistocene salt flats in western North America.
  2. Biogeography of Caribbean Arthropods: testing biogeographic hypotheses concerning the timing and colonization of the Caribbean using genetic datasets from multiple arthropod groups.
  3. Cryptic Scorpions: Using genetic and morphological information to describe new species of scorpions.
Jack Dumbacher

jdumbacher@calacademy.org

Dr. Dumbacher’s research focuses on describing the diversity in bird and mammal species and understanding the factors that cause species to diversify. Using samples from an array of bird and mammal species, including birds from Papua New Guinea, owls from North America, and sengis (aka “elephant shrews” from Africa), he uses genetic tools to describe biodiversity and to understand evolutionary relationships. Much of this work is calculated to ask conservation- related questions about populations that may need attention in the wild.

Learn more about Dr. Dumbacher’s research and academic interests here and here.

Potential projects include:

  1. Studying genetic and morphological variation in western populations of Barred Owls (Strix varia). The Academy has nearly 280 specimens of Barred Owls collected from Northern California, and these show interesting variation in plumage and other characters that may be the result of selection, drift, and hybridization with Spotted Owls.
  2. Studying the genetic relationships of sengis – especially the genera Petrodromus and Elephantulus, found in Africa. The Academy has samples from multiple species whose relationships are poorly understood, and simple phylogenetic analyses will be helpful in determining their genetic histories and distinctness.
  3. Working on aspects of the genetic evolution of poisonous birds (particularly the evolution of the voltage-gated sodium channel that is the target of the toxin, batrachotoxin, that poisonous pitohui birds carry). Dr. Dumbacher is currently assembling sequence data from the different sodium channel genes to understand how birds have achieved resistance to the toxins that they carry.
Brian Fisher

bfisher@calacademy.org

Dr. Fisher’s research focuses on uncovering the patterns and processes of species formation in ants, specifically in Madagascar, and demonstrating how this knowledge can help us achieve a sustainable future. Fisher’s research is motivated by the urgent need to document the biosphere and “tree of life, especially in tropical systems. Documenting life on earth is one of the first big data project undertaken by scientists. Efforts to digitize these museum collections provide new opportunities to ask questions about how life evolved and is distributed across the planet. AntCat.org and Antweb.org, the largest resources on ant taxonomy and biology, provide an API accessible window into efforts to create a virtual museum of global biodiversity data including types, specimens, images, taxonomic history, and literature. Dr. Fisher is looking for an intern that combines an interest in evolutionary biology and computational and visualization skills to explore, question, visualize and interact with large-volume biodiversity data found in AntCat.org and AntWeb.org.

You can learn more about Dr. Fisher’s research at Fisherlab.orgIPSIO.org, and Madagascarbio.org.

Potential projects include:

  1. Understanding how ant communities change across elevation and thermal gradients.
  2. Use the curated Antweb images to test the utility of automated image recognition systems for automated taxon identification and how can this tool assist taxonomists endeavors to identify and understand Earth’s rapidly disappearing biological diversity.
  3. Develop tools to extract traits such as color and size from the 200,000 standard images on Antweb and map these traits on the ant tree of life.
Terrence M. Gosliner

tgosliner@calacademy.org

Terry's research on the systematics, phylogenetics and comparative biology of nudibranchs and other sea slugs focuses on the implications of phylogenies in understanding evolution of shell-loss, mimicry, and other comparative aspects of the evolution of these animals. He has studied the diversity of these mollusks along the California coast for more than 40 years. Most recently, this work employs evolutionary studies to develop new strategies for conservation of Philippine reefs in the center of the center of marine biodiversity. He develops key collaborations with research institutions, conservation organizations, and large public exhibits to bring these findings to diverse audiences.

Learn more about Dr. Gosliner's research.

Potential projects:

  1. Systematics of Indo-Pacific nudibranchs.
  2. Descriptions of new species of Philippine nudibranchs using molecular and morphological techniques.
Durrell D. Kapan

dkapan@calacademy.org

Dr. Kapan’s lab at the California Academy of science is currently focused on two related areas of applied science to make an impact on the health of people and the planet. First, he is co-leading a growing collaborative research program to measure the effect of on-the-ground work to restore the resilience of socio-ecological systems concentrating on California forests and second, he has an ongoing research program on ecology, evolution and health related to invasive mosquito vectors (and emerging infections pathogens they transmit—the latter in collaboration with Dr. Shannon Bennett). He also conducts basic research on insect genomics in his lab, including work on Heliconius butterflies and Hawaiian insects including invasive Aedes mosquitoes. Most recently he has been focusing on developing new methods and R-packages to measure gene-sharing between species (introgression) a phenomenon that has applied implications for both conservation and invasive species. Finally, he utilizes citizen science and public outreach to make a positive impact.

Learn more about Dr. Kapan’s research

Potential student projects include:

  1. genomic analysis of insular populations of Aedes mosquito vectors
  2. computational studies of ever growing publicly available genomic data-sets to investigate speciation, gene-flow and hybridization. Study systems in this area could include range from mosquito vectors to warningly-colored butterflies.
  3. analyzing sample return data collected by volunteers from the iNaturalist ‘Mosquitoes in Hawaii Project’ (with over 130 citizen scientists and school students from Hawai'i) to investigate mosquitoes from the Hawaiian Islands. This work builds capacity in the community to respond to pathogen threats such as dengue or Zika virus and serves as a model for similar efforts around the world.
Rebecca Johnson

rjohnson@calacademy.org

Rebecca co-developed and co-manages the current Citizen Science program at the California Academy of Sciences. Her past research primarily focused on the evolutionary history of nudibranchs and the evolution of color pattern in this group. In her current work, she is interested in combining historical museum collections data and current observational data to understand climate and land use change, especially coastal species range shifts. Core to this research is building and facilitating a community of naturalists working together to discover nature, in special places and in their everyday lives. She works with a team of volunteers to discover, document and monitor invertebrates and seaweeds in the intertidal habitats of central California, primarily along the Marin, San Francisco, and San Mateo coasts. Rebecca leads the statewide initiative Snapshot Cal Coast, which mobilizes hundreds of volunteers every year to collectively build a data set of coastal species observations, that is key to understanding species range change. She also leads an Academy initiative to engage San Franciscans in discovering and documenting the City’s biodiversity.

Learn more about Dr. Johnson’s research here and here.

Potential projects include:

  1. Comparing historical records to current distribution records of California nudibranchs and other invertebrates.
  2. Phylogeography of marine invertebrates
  3. Phylogeny and phylogeography of terrestrial land snails and slugs
  4. A field guide to local species and creating range maps for intertidal invertebrate species.
Rich Mooi

rmooi@calacademy.org

Rich Mooi received his Master’s and Doctoral degrees from the University of Toronto, Canada, and has been with the Academy since 1990. He studies the systematics, phylogeny, paleontology, and biogeography of echinoderms, particularly sea urchins and sand dollars. His field work has included submersible dives off the Bahamas, paleontology in Alaska, ship-based collecting in Antarctica, and shallow- and deep-water expeditions in the Philippines. His research can be summarized as the study of the origins of evolutionary novelty, for which the Echinodermata constitutes an excellent model system. These studies are culminating in a theory that describes the homologies and evolutionary relationships among major clades throughout the phylum Echinodermata.

Additional information on Dr. Mooi’s research can be found here and here.

Potential projects include:

  1. Origin and evolution of the northeastern Pacific sand dollar fauna (Clypeasteroida: Echinoidea). An examination of both Recent and fossil genera to develop cladistic and morphometric analyses that will examine the origins of this fauna.
  2. Phylogenetics of specific echinoid groups such as heart urchins, sand dollars, and other taxa. Morphometrics, molecular, and morphological analyses can be applied to develop characters for a phylogenetic analysis.
  3. Phylogenetic placement and biogeographic studies of Philippine sea urchins from any of a variety of major groups collected during the expeditions of 2011 and 2014 – 2016.
  4. Origin and evolution of elements of the deep-sea echinoid fauna.
Nathalie Nagalingum

nnagalingum@calacademy.org

Nathalie Nagalingum received her doctoral degree from the University of Melbourne, Australia, is Curator of Botany at the Academy. Her research is focused on understanding the long-term persistence of ferns and cycads—ancient lineages that have survived through multiple episodes of radiation and extinction. To address the history of and processes involved with these episodes, Nathalie has a multi-disciplinary research program that incorporates fossil data, microscopy/morphology, molecular DNA sequencing, big data and patterns of distributions. Nathalie is particularly interested in adopting novel approaches and techniques in her research.

Additional information on Dr. Nagalingum’s research can be found at evolutionofplants.org.

Potential Projects include:

  1. Patterns of evolution of ferns. Generate DNA sequences for inferring phylogenies—what are the morphological and biogeographic patterns of Malaysian ferns?
  2. Resolving the identity of a cycad species. Digitize and mathematically describe leaf shapes (morphometrics)—are there two species or is there simply a morphological variant of one species?
  3. Genomics of the cycad genus Cycas. Using genomic sequence data—do different genome- assembly programs produce different phylogenies?
Luiz A. Rocha

lrocha@calacademy.org

Luiz A. Rocha is the Follett Chair of Ichthyology at the California Academy of Sciences in San Francisco. His major research interests include evolution, conservation, taxonomy, and community ecology of coral reef fishes. He frequently tries to combine these fields, linking ecology to evolution and using molecular tools to answer biogeographic, taxonomic, and conservation questions. The overall objective of this interdisciplinary research is to explain what generates and maintains the extremely high biodiversity in tropical coral reefs and to help sustain it, both shallow and deep. He has spent more than 5,000 hours underwater, and published more than 100 peer-reviewed articles. In addition, his work has been featured in many popular media outlets including the New York Times, Wired, National Geographic, Smithsonian Magazine, among others, and supported ocean conservation efforts across the globe.

Learn more about Dr. Rocha’s research.

Potential projects include:

  1. work on reef fish taxonomic descriptions
  2. population genetics or genomic studies of fishes.
Peter Roopnarine

proopnarine@calacademy.org

Peter Roopnarine received his PhD in Geology from the University of California, Davis, and also holds degrees in Biology and Oceanography. He has been with the Academy since 1999. He studies a variety of topics in paleontology and evolutionary biology, including the dynamics of extinction, modelling ancient and modern ecosystems, and the evolutionary paleoecology of tropical American marine molluscs. Together, these topics focus on developing a theoretical basis for understanding the role of ecological diversity in the evolution and extinction of species.

Learn more about Dr. Roopnarine’s research.

Potential projects include:

  1. Morphometric description and biogeography of a widespread genus of marine bivalves in the tropical western Atlantic, ranging from the Oligocene to the Recent.
  2. Building a food web for the San Francisco Bay and related offshore habitats, including more than 1,300 species, using the Academy's collections and other data.
  3. Examining evolutionary and ecological change in Miocene-Pliocene marine communities of the Dominican Republic using morphometric analysis, quantitative ecological analysis, and multiple species of molluscs.
W. Brian Simison

bsimison@calacademy.org

Brian Simison received his PhD from UC Berkeley in 2000 and joined the Academy in 2007. Brian studies hybridizing systems to understand the processes associated with speciation; what generates, maintains and reduces biodiversity? He and his colleagues use modern comparative genomics tools available through the Academy’s Center for Comparative Genomics to explore these questions. He currently collaborates on three systems, the fresh water turtle genus Trachemys, the coral reef angelfish Centropyge, and the microbiomes associated with spiders.

Learn more about Dr. Simison’s research.

Potential projects include:

  1. Population genomics of Red-eared slider turtles using high throughput sequencing and computational analyses.
  2. Whole genome sequencing and assembly of the angelfish.
  3. Metagenomics of spider communities.
Michelle Trautwein

mtrautwein@calacademy.org

Dr. Michelle Trautwein is an entomologist and evolutionary biologist who specializes on flies, face mites and recovering the tree of life for insects and their relatives. Dr. Trautwein studied studio art and evolutionary biology at the University of Texas at Austin. After an internship studying flies at the Smithsonian in Washington DC, she got her PhD in entomology from North Carolina State University.

More information about Dr. Trautwein’s research can be found at flylogeny.org.

Potential Projects:

  1. Humans host two species of face mites. We know very little about them. By sampling face mites from human hosts from around the world and examining their DNA, we have discovered that there are many distinct lineages of face mites. These mite lineages are genetically structured according to the geographic ancestry of their hosts. We are working to understand how these face mite lineages vary, how their microbiomes differ and how their populations on individual hosts are comprised.
  2. Flies are one of the most species-rich groups of life on the planet. Though there are over 150k described species, fly experts estimate there to be nearly a million undescribed species. Bee flies, or Bombyliidae, are a fascinating group of flies that are flower visitors as adults, but parasitoids of other insects as larvae. At CAS, we have a large, uncharacterized collection of bee flies from Madagascar that includes many undescribed species. We are working to uncover new species of bee flies using morphological and molecular techniques.
Gary Williams

gwilliams@calacademy.org

Gary Williams studies the systematics, evolutionary biology, and biogeography of octocorals, a group of corals found worldwide and at all latitudes, on coral reefs as well as in the deep-sea. His work involves coral communities from various parts of the world from shallow water tropical coral reefs to ocean depths exceeding 6,000 meters (20,000 feet). Octocorals include some of the most beautiful and morphologically diverse animals in the world’s oceans – these are the soft corals, sea fans, and sea pens. They are a group of corals that represent two-thirds of all living coral species and are characterized by having eight feathery tentacles surrounding the mouth of each polyp.

Additional information on Dr. Williams’s research can be found here, here, and here.

Potential projects include:

  1. Molecular phylogenetics of gorgonian and pennatulacean corals from coral reefs of the western Pacific Ocean or the deep-sea of the Eastern Pacific.
  2. Morphological and molecular phylogeny of octocorals using the Academy’s scanning electron microscope and Center for Comparative Genomics.
  3. Using biological illustration to portray morphological diversity in corals of the world.