Andres Aguilar, Ph.D. - US grants

The genetic basis of the speciation process is a difficult issue in evolutionary biology. The proposed project will identify genes related to reproductive isolation and phenotypic differentiation in a highly diverse group of marine fishes, the rockfish (genus Sebastes). Genes that play a role in pigmentation will be targeted. These include genes for gamete recognition and sperm competition. In other species similar genes display signals of natural selection and evolve in a rapid manner. Genes expressed in the gonads and skin of selected rockfish species will be sequenced to generate large sequence databases. This DNA sequence information will be analyzed in a comparative genomic framework to identify genes that are rapidly evolving and subject to selection. Further analysis of genes across a larger set of rockfish species will elucidate the mode and timing of selective events.

Little is known about genes that are important in reproductive isolation in fishes, and this project will generate a suite of candidate genes to study the functional aspects of reproduction in rockfish and other fishes, as well as provide a framework to study speciation in the marine environment. Funding will be used to train undergraduate students from underrepresented groups in genomics and evolutionary analysis.

1204841
Harmon

In many arid and semi-arid regions of the world, including much of Western U.S., water resources management plans are predicated on the assumption that the snow pack holds the majority of the water, gradually melting to replenish the reservoirs as their supplies are metered out to satisfy human water and power demands, and environmental flow mandates. Nowhere is this more evident than in the Sierra Nevada Mountains in California, the remote and sparsely populated mountain range providing the water and power for millions of people. While it is known that this mountain range's steep gradients in elevation, soils and vegetation render it extremely sensitive to climate change, the connection between the underlying hydrologic processes and the water sustainability issues in these regions is not well understood. This project will quantify the effect of a range of documented climate change scenarios on snow melt, runoff, high elevation reservoir operation (hydropower, flood control and recreation) and low elevation multi-purpose reservoir operation (irrigation, flood control, environmental flows and recreation). The San Joaquin River Basin will serve as the prototype for this study, the outcomes of which will be transferrable to other snowpack-controlled river basins. The scientific goal of the proposed project is to connect our emerging process-level understanding of climatic influences on mountain hydrologic processes and resulting changes to the stream response to the ecosystems services sustained by water but dictated by human values and policies. The hypothesis is that changing climate variability in the semi-arid western U.S., and the resulting shift toward an earlier annual runoff in snow-dominated watersheds will create a ripple effect, propagating down the mountain front to force human responses in the form of changes to high elevation hydropower and lowland water supply reservoir operations, and therefore changes to lowland aquatic and riparian ecosystem functions. We will test this hypothesis using current hydrologic process simulation models integrate existing data from the NSF Southern Sierra Critical Zone Observatory, and from state (California Department of Water Resources) and federal agencies (U.S. Bureau of Reclamation, U.S. Fish and Wildlife Service). These simulation models will be driven by archival Global Climate Model (GCM) outputs (temperature, precipitation) for the years 2010 - 2099.

This project will clarify the connection between likely climate change scenarios, stream flows, reservoir storage and releases, and groundwater storage and extractions for snow-dependent river basins. Furthermore, through engagement with key river basin stakeholders, the project will result in practical guidelines to how best to adapt policy to the changing hydrologic conditions in order to sustain water supply, energy and aquatic ecosystem needs in the future. The San Joaquin River basin was selected as the subject of study because it embodies water and sustainability issues in the semi-arid West given (1) its vulnerability to climatic variation due to its reliance on snow pack and a network of reservoirs for hydropower, flood control, and water supply; and (2) its massive lowland river salmon restoration effort, which was initiated in Fall 2009.

Ancient lakes are biodiversity hotspots, home to thousands of unique species with an extraordinary diversity of body forms and functions. With more than 1,500 species found nowhere else on the planet, Lake Baikal is an ideal environment to study the processes that resulted in creation of new species. The Baikal biodiversity hotspot is also a geographical anomaly, because global species diversity normally declines near polar regions. Despite Baikal's renown as the world's oldest, deepest, and largest lake, the evolutionary history of its unique species diversity remains poorly understood. This project examines the evolutionary history of sculpins, a group of primarily bottom-dwelling cold water fishes that colonized Baikal within a relatively short period of the lake's history. Baikal sculpins are uniquely adapted to life in an ancient lake, having evolved multiple open-water and deep-water forms. This project is focused on identifying the molecular basis for such variation, including gene sequences that evolve through generations and gene-expression changes that occur during development. New information gained from this study can be compared to ongoing research on fishes from other ancient lakes, in order to identify unifying processes that explain adaptation in these unique ecosystems.

Baikal sculpins represent the world's northernmost vertebrate radiation within an ancient lake ecosystem, with at least 33 species estimated to have evolved within the past two million years. Rapid diversification of skeletal morphology and body composition suggests that this clade has undergone ecological release from a stream-living ancestor, but phylogenetic analysis has thus far been limited to a single genetic locus. A genomic inventory of Baikal sculpins will be generated through systematic surveys of all lake habitats and the surrounding watershed. Tributaries to Baikal will also be sampled in the search for a putative ancestral sculpin population. A time-calibrated species tree will be generated from sequence variants at presumed neutral (RADseq) and functional (RNAseq) loci. Gene expression phenotypes will be mapped on the phylogeny to infer relative rates of phenotypic and ecological change. If a putative ancestral population is discovered in the tributaries to Lake Baikal, this system will offer an unprecedented opportunity to understand the genetic factors that predispose certain groups to adaptive radiation.

Understanding the formation of new species in the marine environment has proven to be a challenging task for evolutionary biologists. The potential for high levels of migration and the apparent lack of geographical barriers create a scenario where ecological diversification and life history shifts are likely important in the speciation process. This research program will determine the genomic basis of divergence among closely related species and populations along latitudinal and depth gradients to determine the role of adaptation in the speciation process. Rockfish (Sebastes) are an ideal system to examine these questions as they are a diverse group of temperate fishes inhabiting a wide array of habitats, and they have been subject to numerous phylogenetic studies. This study will build upon a growing set of studies aimed at better understanding the speciation process in the marine environment. Training opportunities will be provided to undergraduate and graduate students at Cal State LA, and data from this project will also serve as a resource for the management of rockfish, many of which are commercially important.


This project will utilize genome scans and de novo genome assemblies to test for speciation histories of rockfish associated with divergence along ecological (depth) or geographic (latitude) gradients. These findings can be used to better understand the role of natural selection on the genome and how this contributes to the diversification of this group. The first aspect of the study will examine the role that ecological adaptation along a depth gradient has played in the formation of new species. The second aspect will contrast these findings with latitudinal divergence among closely related species. Together these results will provide novel insights into the speciation history and genomic divergence for closely related marine species, and provide a framework for understanding the relative roles of selection and genetic drift on generating and maintaining marine diversity.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

With support from the Improving Undergraduate STEM Education: Hispanic-Serving Institutions (HSI Program), this Implementation and Evaluation (Track 2) project aims to engage undergraduate students in field-based activities at two urban institutions: California State University Los Angeles and Mt. San Antonio College. These institutions are located in the greater Los Angeles area, and they serve a commuter-student population. Financial and logistical challenges have made it difficult to augment science courses with field-based activities, despite their documented benefits. The field-based activities will take place in lower-division biology, chemistry and earth science courses and are expected to increase participation and retention of minoritized students in these disciplines. Outcomes from this project should reduce barriers to participation in field-based activities by training instructors in safe field-based practices, and lowering costs associated with field activities. <br/><br/>The set of proposed activities will increase persistence rates across the four majors (Biological Sciences, Chemistry, Geology and Natural Sciences) at the two institutions due to the introduction of engaging field-course experiences that allow students to work in a group setting and connect to environmental issues in their local communities. This work will also increase fieldwork participation rates in the selected majors, which currently have low numbers of minoritized students at both campuses. This is critical to increasing representation, especially Latinx students, in the environmental workforce. Program success will be tracked through pre- and post-course surveys where new field-based activities are implemented. In addition, student and faculty focus groups will be used to assess outcomes at various levels as well as track any related institutional changes. The student population at both participating campuses includes a high proportion of Latinx and other students similarly underrepresented in their participation in STEM fields of study, which should broaden participation in the introductory courses of these majors. This project seeks to increase participation and persistence rates among minoritized students in field-based disciplines in which they are highly underrepresented, which should result in a more diverse workforce and an increase in minority role models for future students. The HSI Program aims to enhance undergraduate STEM education, broaden participation in STEM, and build capacity at HSIs. Achieving these aims, given the diverse nature and context of the HSIs, requires innovative approaches that incentivize institutional and community transformation and promote fundamental research (i) on engaged student learning, (ii) about what it takes to diversify and increase participation in STEM effectively, and (iii) that improves our understanding of how to build institutional capacity at HSIs.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.