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Baja GeoGenomics consortium

 

Earth-life evolution on the Baja peninsula

 

AbstractTechnical

About Us

Baja GeoGenomics consortium

 

The Baja GeoGenomics consortium (BGGc) aims to constrain the how the physical landscape of the Baja California peninsula has changed over the past 6 million years, determine which of these changes have produced evolutionary genomic signals, and test how those signals differ among mammal, reptile, and plant species. The BGGc will host the first-of-its-kind public data repository for evolutionary pseudocongruence research; its mission is to facilitate the advancement of pseudocongruence science and the quantitative integration of large, complex datasets.

Understanding how diverse processes such as tectonic activity, rainfall gradients, and glacially driven climate cycles shape evolution and biodiversity over time.

Opportunities

Graduate Research Opportunities

Geologic Mapping | Petrology | Geochronology   

MSc – California State University, Sacramento

Population & Geo-genomics | Speciation 

PhD – Arizona State University | PhD – University of Arizona

Volcanology, Petrology, Geochronology

A funded graduate assistantship is available to carry out a Master’s thesis (MSc ) research in geologic field studies in central Baja California, Mexico as part of multidisciplinary investigation of the late Tertiary – Quaternary marine and volcanic stratigraphy, part of a NSF-funded study. A team of geologists and biologists from California State University, University of Oregon, Arizona State University, University of Arizona, and the U.S. Geological Survey will collaborate to investigate geologic and environmental causes for a late Tertiary significant and relatively sharp break in the DNA of numerous species between the north and south halves of the Baja California peninsula. See NSF Award Abstract #1925565 for an overview of the entire study.

The research project may focus on a wide range of sedimentary and volcanic features found in the mid-peninsular area. The team will map and date structural, stratigraphic, and volcanic features in the mid-Peninsular region where the divergence occurs; use modern geochronologic methods to constrain the nature and timing of deposition, volcanism, deformation and uplift. The project will likely involve a combination of approaches, including field mapping of sedimentary strata, facies distribution and associated volcanic deposits and eruptive vents. GIS compilation and paleo-landscape reconstructions will be developed.

Interested students should send a letter of introduction, academic resume, and the names of two references, to Brian Hausback (hausback@csus.edu). Students will also complete the application for admission to the CSUS graduate program:

Sacramento State:

Starting date: Winter-Spring 2020.

Earth-life evolution, Geo-genomics, data integration

The Dolby and Kusumi labs at Arizona State University (School of Life Sciences) welcome graduate (PhD) applications to work on a new NSF-funded project that seeks to understand how Earth processes shape genomic evolution and diversification of species. This project includes reference genome assembly, population genomics (low coverage genome data), seasonal differential expression (RNAseq), and ecological niche modeling for at least six mammal, reptile, and plant species. The position will emphasize integration informatics including new analytical techniques for integrating geological and genomic data. The Dolby lab specializes in Earth-life evolution and geo-genomics; the Kusumi lab specializes in comparative and functional genomics as well as development. Research topics are flexible based on student strengths and interests; options include:

  1. using geologic data to constrain evolutionary genomic models;
  2. applying new developments from information theory to quantify population genomic divergence;
  3. standardizing how we quantify landscape change as the work done by physical processes on that landscape.

The student will work as part of the larger Baja GeoGenomics consortium and have exceptional opportunity for broad training with other biology, geology, and physics collaborators to become an integrative interdisciplinary scientist. Students from any STEM background are welcome to apply. Computational or mathematical strengths are desired. An eagerness to work on complex interdisciplinary problems is key along with strong creativity, problem-solving, and communication skills. Must be able to work both independently and part of a large international team. Inquiries for this position are encouraged. If you are interested, please submit a CV and brief summary of interests including how your background would apply to these topics to Greer Dolby. Women and minorities are particularly encouraged to apply. Interested students will need to apply to the ASU School of Life Sciences PhD program between 1-Oct and 15-Dec

Link to project desicription

Data-rich population genomics & speciation

Whole genome sequencing/ assembly/ annotation, population genomic analyses via low-coverage whole genome sequencing, RNA-Seq and extensive field work

University of Arizona | Desert Laboratory on Tumamoc Hill  

A funded graduate assistantship is available to carry out PhD dissertation research in genome sequencing/assembly/annotation and population genomic analyses via low-coverage whole genome sequencing and RNA-Seq. The position is part of a NSF-funded multidisciplinary GeoGenomics investigation that combines geologic and genomic data to test multiple non-mutually exclusive hypotheses in Baja California peninsula (Mexico). The genomic data will be used to test the effects of marine seaways, glacial refugia, and rainfall timing on the biological diversification through signatures on the genomes of desert reptiles, mammals, and plants. The student will work as part of the larger Baja GeoGenomics consortium (https://bajageogenomics.org/) composed by a team of geologists and biologists from University of Oregon, Arizona State University, California State University, and the University of Arizona. Eagerness to work in a multidisciplinary setting and team is essential.

The research project can focus on:

• Generating de-novo genome sequences, assembly and annotation of lizards and rodents • Conducting population genomic analyses to identify genetic variants from low-coverage genome sequencing

• Parametrize Approximate Bayesian Computation models of neutral divergence for multiple species constrained by the geologic evidence

• Perform landscape genomic analyzes to test concordance with niche modeling hypotheses of expansion-contraction from glacial refugia

• Correlate present-day ecological niches with spatial signals of natural selection both from genome sequencing and differential RNA-Seq expression

• Develop novel bioinformatic approaches for simultaneously integrating geologic, genomic and ecological datasets.

Interested candidates should send CV and a brief summary of interests, including how your background would apply to these topics to both Adrian Munguia-Vega (airdrian@email.arizona.edu) and Ben Wilder (bwilder@email.arizona.edu). Selected students will work in collaboration with Dr. Melanie Culver’s Conservation Genetics Lab and the Desert Lab on Tumamoc Hill at University of Arizona.
Options to join either GIDP-Graduate Interdisciplinary Programs (Genetics) or SNRE-School of Natural Resources and Environment (Natural Resources) PhD graduate programs. https://grad.arizona.edu/catalog/programinfo/GENEPHD https://grad.arizona.edu/catalog/programinfo/NTRSPHD Starting date: As soon as Winter-Spring 2020, rolling application cycle

 

November Field Report – Searching for Species and Seaways

The four geologists in our group had been hunting for overlooked evidence of marine sediments at relatively high elevations along the topographic spine of the Baja peninsula for two weeks, starting in the Bahía de los Ángeles area and working our way south to San Ignacio.