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Chandler J.A.,California Academy of Sciences | Turelli M.,University of California at Davis
Science | Year: 2014

Brucker and Bordenstein (Reports, 9 August 2013, p. 667) claim that adaptive codivergence of gut bacteria with hosts contributes to hybrid lethality. Yet, they provide no evidence for coadaptation of bacteria and Nasonia hosts. Their data on hybrid viability suggest that bacteria contribute to inviability only because intrinsic hybrid dysfunction increases susceptibility to free-living bacteria. Hologenomic speciation remains testable speculation without experimental support.

Roopnarine P.D.,California Academy of Sciences | Angielczyk K.D.,Integrative Research Center
Science | Year: 2015

The fossil record contains exemplars of extreme biodiversity crises. Here, we examined the stability of terrestrial paleocommunities from South Africa during Earth's most severe mass extinction, the Permian-Triassic.We show that stability depended critically on functional diversity and patterns of guild interaction, regardless of species richness. Paleocommunities exhibited less transient instability-relative to model communities with alternative community organization-and significantly greater probabilities of being locally stable during the mass extinction. Functional patterns that have evolved during an ecosystem's history support significantly more stable communities than hypothetical alternatives.

Ghiselin M.T.,California Academy of Sciences
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

Homology is a relation of correspondence between parts of parts of larger wholes. It is used when tracking objects of interest through space and time and in the context of explanatory historical narratives. Homologues can be traced through a genealogical nexus back to a common ancestral precursor. Homology being a transitive relation, homologues remain homologous however much they may come to differ. Analogy is a relationship of correspondence between parts of members of classes having no relationship of common ancestry. Although homology is often treated as an alternative to convergence, the latter is not a kind of correspondence: rather, it is one of a class of processes that also includes divergence and parallelism. These often give rise to misleading appearances (homoplasies). Parallelism can be particularly hard to detect, especially when not accompanied by divergences in some parts of the body. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Williams G.C.,California Academy of Sciences
PLoS ONE | Year: 2011

Recent advances in deep-sea exploration technology coupled with an increase in worldwide biotic surveys, biological research, and underwater photography in shallow water marine regions such as coral reefs, has allowed for a relatively rapid expansion of our knowledge in the global diversity of many groups of marine organisms. This paper is part of the PLoS ONE review collection of WoRMS (the Worldwide Register of Marine Species), on the global diversity of marine species, and treats the pennatulacean octocorals, a group of cnidarians commonly referred to as sea pens or sea feathers. This also includes sea pansies, some sea whips, and various vermiform taxa. Pennatulaceans are a morphologically diverse group with an estimated 200 or more valid species, displaying worldwide geographic and bathymetric distributions from polar seas to the equatorial tropics and from intertidal flats to over 6100 m in depth. The paper treats new discoveries and taxa new to science, and provides greater resolution in geographic and bathymetric distributions data than was previously known, as well as descriptions of life appearances in life and in situ observations at diverse depth. © 2011 Gary C. Williams.

Agency: NSF | Branch: Continuing grant | Program: | Phase: SEDIMENTARY GEO & PALEOBIOLOGY | Award Amount: 179.82K | Year: 2013

Integrating multidisciplinary tools to study Plio-Pleistocene paleoecology of early hominins from the Omo Valley, Ethiopia

Zeresenay Alemseged, California Academy of Sciences

Technical description:
This study aims to address one of the key research questions for understanding the paleobiology of early hominins: what was the role of ecological change on the development of major early human adaptations? The PIs will address this broad question by developing integrative approaches to bring new data to the paleofaunal databases from the hominin-bearing Omo sequence (paleofauna collected by the The International Omo Research Expedition, IORE, 1966-1976). Existing taxonomic abundance data from these large and systematically collected paleofaunal databases will be integrated with new, independent paleoecological data from stable isotopes and ecomorphological features of the paleofaunal community. The stable isotopic composition of tooth enamel from hominins and other primates from this sequence will also be analyzed for the first time.

Broader Significance and Importance:
The results of this research will not only address questions of paleodiets and paleoecology of East African faunas, but may significantly transform our understanding of the the evolution of the mammalian community in the Omo-Turkana Basin of Ethiopia and Kenya from >4 to 1.2 million years ago, which is one of the most significant basins for early human evolutionary studies. This study will also provide direct and fresh data on the diets consumed by at least four hominin species encountered in the Omo sequence, and will better our understanding of when and where hominins first began to significantly consume foods derived from savanna resources. The research will continue international collaborations between US academic institutions and the National Museum of Ethiopia in Addis Ababa, which provides a venue for public outreach and education within Ethiopia and beyond. The data from this project will be incorporated into a database system, and made readily available via several outlets. This proposal will provide graduate training for two graduate students integrating several research communities: geology, geochemistry, paleontology, and paleoanthropology. The research results will be used in a variety of outlets for public outreach.

Agency: NSF | Branch: Continuing grant | Program: | Phase: SYMBIOSIS DEF & SELF RECOG | Award Amount: 82.64K | Year: 2016

Insects live in a world of chemical signals. Chemicals are used as defensive weapons, to signal danger, to mark resources for later foraging or for avoidance, and to identify mates of the correct species and assess their quality. The social insects take this chemically-oriented lifestyle to an extreme. The sophisticated division of labor in social insect colonies requires exquisite regulation of individual behaviors, and chemical pheromones are crucial for organizing work within the colony. Despite these important and diverse roles, we have only a rudimentary understanding of how pheromones originate and evolve. Here, Tsutsui and Fisher will combine genetic manipulations, pheromone analyses, and behavioral tests to clarify how various forces of natural selection shape chemical communication in a social insect. This research will be performed using the invasive Argentine ant (Linepithema humile) as a model system. This ant is a globally widespread invader, is considered one of the 100 worst invasive species in the world, and is a significant agricultural and structural pest. The research of Tsutsui and Fisher is likely to reveal pheromonal and behavioral processes that can be targeted in the development of new control techniques, thus contributing to greater ecological resilience, enhanced food quality and security, and reduced degradation of soil and water by conventional insecticides.

Self/non-self recognition systems have played a central role in many of the major evolutionary transitions. Because components of these recognition systems are often co-opted from existing systems, they can experience conflicting forms of selection after acquiring their new functions. The societies of eusocial insects are an ideal system in which to study the evolutionary trade-offs associated with the evolution of self/non-self recognition systems. In many eusocial insects, cuticular hydrocarbons (CHCs) are used to distinguish colonymates (self) from non-colony members (non-self). However, CHCs have also retained their original function as barriers to desiccation. These two distinct roles of CHCs - as both desiccation barriers and recognition pheromones - are expected to produce different forms of selection, as the optimal molecular proporties for the two functions are quite different. Tsutsui and Fisher will combine functional genomics, chemical ecology, and behavioral ecology to test the overarching hypothesis that evolutionary trade-offs shape the recognition system of social insects. The results of this research will illuminate how genetic and chemical changes lead to changes in individual behavior and, in turn, alter the structure of complex societies.

Agency: NSF | Branch: Standard Grant | Program: | Phase: CROSS-EF ACTIVITIES | Award Amount: 610.64K | Year: 2013

This project will document a suspected peak in marine animal diversity in the Earth?s most diverse marine realm. Investigators from the California Academy of Sciences (CAS), in collaboration with numerous other US and Philippine institutions, will document the kinds of marine organisms in the Coral Triangle of Southeast Asia, focusing on the center of the center of biodiversity, the Verde Island Passage (VIP) of Luzon, Philippines. Researchers will assess the extreme biodiversity across the VIP to determine species distributions, analyze genetic diversity among species, and discover new species, including in the Twilight Zone, accessible through advanced underwater technology that allows exploration at depths below those reached with traditional scuba diving.

The project will establish crucial baseline information on biodiversity at key VIP localities before further impact of global climate change and human development activities. Results will inform regional and global conservation and management policies, and engage the public in protecting coral reef communities integral to oceanic and human health. Data and collections will be preserved and cataloged, and will be available for study into the future.

Agency: NSF | Branch: Standard Grant | Program: | Phase: SEDIMENTARY GEO & PALEOBIOLOGY | Award Amount: 208.86K | Year: 2016

Collaborative Research: Mesozoic Tethyan paleocommunity dynamics: Modelling complexity and stablity during times of biotic escalation and community restructuring

The Mesozoic Era began in the aftermath of Earths largest mass extinction 251 million years ago, ending 66 million years ago with another mass extinction. The current project focuses on ecosystems of an ancient ocean which covered much of western Europe during the Mesozoic and left behind a rich, well-documented fossil record. The groundwork for modern oceans was laid during this time with increasingly complex ecosystems. The relationship between the complexity and stability of ecosystems is, however, poorly understood. The project will examine that relationship by modeling the complex dynamics of Mesozoic marine ecosystems using food webs, which capture the interactions and energy transfer between species in biological communities. Food web reactions to environmental disturbances are informative of ecosystem resilience. Analyzing ancient food webs will be accomplished with a suite of mathematical and computational models.

Ecosystem responses to changes in biological complexity and environmental disturbance remain poorly understood. Anthropogenically-driven global biological change is currently resulting in catastrophic losses of biodiversity. To anticipate ecosystem responses and effectively manage resources, we must understand how ecosystems respond to extreme changes; yet there are no precedents in human experience to guide us. The fossil record documents extreme ecosystem changes and this project will provide analogs from the past to enable better forecasts for modern marine ecosystems. This information will be distributed to the public, educators and students through a variety of programs at the California Academy of Sciences.

Agency: NSF | Branch: Continuing grant | Program: | Phase: RSCH EXPER FOR UNDERGRAD SITES | Award Amount: 268.54K | Year: 2014

This REU Site award to the California Academy of Sciences (CAS), located in San Francisco, CA, will support the training of 8 undergraduate students for 8 weeks during the summers of 2014-2018. During the program, students will work with CAS scientists on research projects on biodiversity. Given the abundant resources of the museum, it can support research projects on the systematics, phylogenetics, and biogeography of a diverse range of organisms including extinct human ancestors, spiders, turtles, birds, fish, ants, marine invertebrates, and plants. By conducting an independent research project, students will be trained in a range of research techniques. Depending on the nature of the particular project, students may gain experience with light and scanning electron microscopy, molecular phylogenetics, and/or next-generation sequencing technologies. In addition, students will receive lectures on systematic biology, take educational tours of the facility, and participate in community-building activities. Students will also learn about the ethics of collections-based science, responsible conduct of research in a museum setting, appropriate data collection and archiving, and informed attitudes towards preserving the worlds biodiversity. Furthermore, students will develop oral communication skills through the process of preparing a presentation of their research findings, which are highlighted in a symposium at the end of the program. In conjunction with educators, CAS has developed program assessment tools that provide feedback on every aspect of the program and will also employ the common assessment tool for BIO REU Sites. Interested students are encouraged to contact prospective mentors before applying since shared interests between the mentor and student are a key component of the application process. Letters of recommendation, a statement of interest, and academic performance are also used in the selection process. The program places particular emphasis on attracting students from groups that are under-represented in the sciences.

The CAS REU program hopes to foster in its participants a long-term interest in science by promoting scientific engagement that extends beyond the programs end. Specifically, student participants will be encouraged to present their research at domestic and international scientific conferences.

Students are required to be tracked after the program and must respond to an automatic email sent via the NSF reporting system. More information is available by visiting, or by contacting the PI (Dr. Rich Mooi at

Fossils provide our only direct evidence of past biodiversity and how individual organisms to ecosystems have responded to past and long-term environmental change. This project fills a major gap in the documentation of past environmental change, making available digitized data from the especially rich fossil record of the eastern Pacific marine invertebrate communities of the Cenozoic, the 66 million years that have passed since the extinction of the dinosaurs. Digitization and integration of these data will foster increased accessibility, efficient analysis to understand past change, the identification of factors involved in that change, and enable predictions for how current biodiversity may be impacted by future change. Development of virtual fieldwork experiences will assist stakeholders and educators in understanding how field data and fossil collections are used to infer past ecosystem and environmental conditions.

The data currently exist as a vast collection of fossil specimens and printed materials distributed among multiple natural history collections: this project involves 7 primary institutions, one small collection and one federal institution and will integrate this digitized specimen data with the other two ongoing fossil networks through the web portal iDigPaleo, expanding the resource for fossil invertebrate information by spanning over 500 million years. This wealth of data will provide resources not only to researchers, but will be made available to K-16 educators, government, industry, and the general public. Through the national resource (iDigBio) these data will be integrated with information on modern organisms providing the means to understand important questions on niches, environmental change, transitions in sea levels, etc. Additionally, undergraduate and graduate students will be trained in the modern uses of natural history collections. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program and all data resulting from this award will be available through the national resource (

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