Curriculum Vitae

Dr. Curtis Robert Young, III

Education:
1998 B.S., Biology, University of South Carolina
    Undergraduate Research: Parallel morphological evolution in Fundulus waccamensis of Phelps Lake and Lake Waccamaw
2006 Ph.D., Ecology and Evolution, University of California, Santa Cruz
    Thesis: Population structure, speciation and reticulated evolution in the hydrothermal vent environments of the eastern Pacific and mid-Atlantic
2006-2009 Postdoctoral Research Associate, Harvard University
    Genetic population structure of globally distributed hydrothermal vent mussel endosymbionts
2009-present Postdoctoral Research Associate, MIT
    Computational methods for microbial metagenomics and metatranscriptomics

 

Work Experience:
1998–2000 Research Specialist, University of South Carolina,
Dr. Joe Quattro
2000 Research Specialist, University of South Carolina,
Dr. Jerry Hilbish
2000 Research Technician, Monterey Bay Aquarium Research
Institute (MBARI) Dr. Robert Vrijenhoek
2001 Statistical Consultant, MBARI
2001 Teaching Assistant, University of California, Santa
Cruz
2002 Teaching Assistant, University of California, Santa
Cruz
2002–2006 Graduate Research Assistant, MBARI
2006–2009 Postdoctoral Research Fellow, Harvard University, Colleen Cavanaugh
2009-present Postdoctoral Research Associate, MIT, Ed DeLong

 

Awards & Honors

1997 Howard Hughes undergraduate research fellowship
2000 Summer Institute of Statistical Genetics fellowship
2000 Academic fellowship, UCSC
2001 Academic fellowship, UCSC
2002 Packard Foundation research grant
2004 Summer Institute of Statistical Genetics fellowship
2005 Summer research fellowship, UCSC
2008 USC Office of Research and Health Sciences Research Grant

 

Research interests
 

My research is driven by a combination of empirical
genetic studies, novel statistical analyses, and mathematical modeling, all of which possess one overarching theme: understanding how ecological and evolutionary processes create and maintain biodiversity. My areas of research interest include population genetics, the genetics of speciation, intracellular symbiont evolution, microbial ecology, and population dynamics. Much of my empirical work has been conducted on globally distributed hydrothermal vent taxa and their microbial endosymbionts. My thesis and related work at MBARI included defining the sixth known
hydrothermal vent biogeographic province as well as several population genetic studies of vent
fauna. Much of this work revolves around the identification of species boundaries and the study of hybrid zones at hydrothermal vents.

During my postdoc, I developed a novel pyrosequencing approach for population genetic
studies of microbial symbionts. My work on hydrothermal vent symbionts clarifies the dynamics of genome evolution in intracellular symbionts using two closely related but differentially transmitted symbiont taxa as comparative model systems. Bathymodiolid mussel symbionts are laterally acquired, and as such, both population genetic and phylogenetic analyses suggest high levels of within-host diversity and high rates of recombination. In contrast, vesicomyid symbionts are predominantly vertically transmitted and consequently show low intra-host diversity and lower levels of homologous recombination. I have also been involved in
microbial diversity studies from a variety of niches. My work at MIT involves microbial community analysis in both experimental and observational studies aimed at understanding microbial ecological systems.

My statistical background includes the development of efficient (i.e., Monte Carlo) Bayesian statistical methods to study admixed populations, the application and development of Markov Chain Monte Carlo population genetic algorithms (e.g., hypothesis testing and model adequacy), and posterior simulation-based methods for hypothesis testing in phylogenetics. My mathematical
modeling
experience includes the development of a nonlinear model to study the interaction of hunting policy and reproductive behavior in African game species. The recommendations from this body of work are currently being implemented in the Selous game reserve in Tanzania. I have created several software packages that aid in the analysis of genetic data.

 

Research Experience
  • Hydrothermal vent biology
  • Conservation biology / population dynamics
  • Microbial diversity
  • Symbiont-host coevolution
  • Molecular genetics techniques
  • Pyrosequencing analysis / bioinformatics
  • Metagenomics / metatranscriptomics / proteomics
  • Population genetic / phylogenetic analysis
  • Bayesian statistics
  • Mathematical modeling
  • Computer programming

Teaching Experience
 

Workshop on Markov Chain Monte Carlo Methods in Evolutionary Biology

    Ewha Womens University, Seoul, Korea, 2009
    8 Hour workshop, Course creator / Instructor (with Kristina Fontanez), 59 students
    Coverage: Conditional probability and Bayes’ theorem, statistical distributions, Markov chains, coalescent theory, convergence, tuning, hypothesis testing, R statistical package, Bayesian phylogenetic analysis
  Lecturer, LS190, Harvard University
  Workshop on MCMC convergence applied to population genetic methods
    MBARI, Moss Landing, CA, 2006
    4 Hour workshop, sole instructor, approx. 30 students
    Student level: graduate student through senior research associate
    Coverage: Conditional probability and Bayes’ theorem, statistical distributions, Markov chains, coalescent theory, convergence, tuning, hypothesis testing, R statistical package
  Lecture: “Coalescent Theory,” Population
genetics: Bio 107/207, UCSC: notes
  Teaching assistant, Introductory biology, Bio 20A (2x), UCSC
  Teaching assistant, Evolution: Bio 105, UCSC

Contributed Papers

1998

American society of ichthyology and herpetology conference
Guelph, Canada
Parallel evolution of Fundulus waccamensis
of Phelps Lake and Lake Waccamaw

2001

Second international symposium on hydrothermal vent and seep biology
Brest, France
Gene flow of the deep-sea tubeworm Ridgeia piscesae from
the Juan de Fuca Ridge

2003 Biogeography and biodiversity of chemosynthetic
ecosystems: planning for the future (steering committee)
Southampton Oceanography Centre, UK
Metapopulation structure of Ridgeia piscesae from the Juan de Fuca Ridge
2004

Evolution
University of Colorado, Boulder, CO, USA
Bayesian estimation of cytonuclear covariances

2005

Third international symposium on hydrothermal vent and seep biology
SCRIPPS Institute of Oceanography, La Jolla, CA
One-way gene flow of Ridgeia piscesae between
offset hydrothermal ridges

2008

The 108th General Meeting of the American Society for Microbiology
Boston, MA, USA
Heirarchical population structure of Bathymodiolin
mussel symbionts from hydrothermal vents in two ocean basins

2008

The 108th General Meeting of the American Society for Microbiology
Boston, MA, USA
Pyrosequencing analysis of endosymbiont population
structure: co-occurrence of divergent bacterial symbiont lineages
in a single host clam

2008

Boston Bacterial Meeting
Boston, MA, USA
Pyrosequencing analysis of endosymbiont population
structure: co-occurrence of divergent bacterial symbiont lineages
in a single host clam

2009 The 4th International Symposium on Chemosynthesis-Based Ecosystems
Okinawa, Japan
Bathymodiolin symbiont population structure in two ocean basins: an application of next-generation pyrosequencing to microbial population genetics
2012

ASLO
Salt Lake City, Utah

Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton

Invited Seminars
2004 Center for Discrete Mathematics and Theoretical
Computer Science,
Workshop and working group on reticulated evolution:
Rutgers University, Piscataway, NJ, USA
Bayesian analysis of hybrid populations
2004 Museum of Vertebrate Zoology, UC Berkeley
U.C. Berkeley, Berkeley, CA, USA
Bayesian analysis of hybrid populations: species boundaries
in the hydrothermal vent environment of the eastern Pacific and
mid-Atlanti
c
2006 Neyman Lecture, Statistics Department,
UC Berkeley
U.C. Berkeley, Berkeley, CA, USA
Species boundaries in the hydrothermal vent environment of
the eastern Pacific and mid-Atlantic
2007 Department of Biology, Penn State
Penn State, State College, PA, USA
Gene flow and species boundaries in the hydrothermal vent
environment of the eastern Pacific and mid-Atlantic
2008

Station Biologique de Roscoff
Roscoff, France
Workshop on the Taxonomy and Phylogeny of Vesicomyid and Mytilid
Bivalves
Initiated by ChEss,
a field project of the Census of
Marine Life

Coalescent theory used to investigate the phylogenies of
Vesicomyid and Bathymodiolin symbionts

2008 Max Planck Institute for Marine Microbiology
Bremen, Germany
Speciation, symbiont transmission and genomic evolution in
hydrothermal vent taxa and their symbionts
2009 Monterey Bay Aquarium Research Institute
Moss Landing, CA, USA
Speciation, symbiont transmission and genomic evolution in hydrothermal vent taxa and their symbionts
2009

Harvard University
Cambridge, MA, USA
Population Genetics and Evolution of Deep-Sea Hydrothermal Vent and Cold Seep Symbionts: A Tale of the Microbial Ecological Detective

2009

Korea Polar Research Institute
Incheon, Korea
Population Genetics and Evolution of Deep-Sea Hydrothermal Vent and Cold Seep Symbionts

2009 Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Speciation, symbiont transmission and genomic evolution in hydrothermal vent taxa and their symbionts
2010 College of Earth, Ocean, and Environment, University of Delaware, Lewes Delaware, USA Exploring biodiversity in marine systems
2011 Department of Microbiology, Immunololgy, and Molecular Genetics and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA, Microbial Diversity in the Oceans and Beyond
2011 California Academy of Sciences, San Fransisco, CA, USA, Microbial Diversity in the Oceans and Beyond
2011 Department of Biology, Temple University, USA, Microbial Diversity in the Oceans and Beyond: Using Second Generation Sequencing to Explore Microbial Ecological Systems Biology

Peer-reviewed publications


C. L. Van Dover, S. E. Humphris, D. Fornari, C. M.
Cavanaugh, R. Collier, S. K. Goffredi, J. Hashimoto, M. D. Lilley,
A. L. Reysenbach, T. M. Shank, K. L. Von Damm, A. Banta, R. M. Gallant,
D. Götz, D. Green, J. Hall, T. L. Harmer, L. A. Hurtado, P.
Johnson, Z. P. McKiness, C. Meredith, E. Olson, I. L. Pan, M. Turnipseed,
Y. Won, C. R. Young, R. C. Vrijenhoek 2001. Biogeography and ecological
setting of Indian Ocean hydrothermal vents. Science v. 294,
818-823.
doi: 10.1126/science.1064574
click here to request a reprint (cited: 136)

Y. J. Won, C. R. Young, R. A. Lutz, and R. C. Vrijenhoek.
2003. Dispersal barriers and isolation among deep-sea mussel populations (Mytilidae: Bathymodiolus) from eastern Pacific hydrothermal vents. Molecular
Ecology
v. 12:1, 169-184.

doi:10.1046/j.1365-294X.2003.01726.x
click here to request a reprint (cited: 89)

C. R. Young, T. J. S. Merritt, R. G. Vogt, R. C. Wilkerson and
J. M. Quattro. 2005. Intron retention identifies a malarial vector
within the Anopheles (Nyssorhynchus) albitaris complex (Diptera:
Culicidae). Molecular Phylogenetics and Evolution v. 35,
719-724.
doi: 10.1016/j.ympev.2005.03.009
click here to request a reprint (cited: 14)

Shannon B. Johnson, C. R. Young, William J. Jones,
Anders Warén, and R. C. Vrijenhoek. 2006. Migration, isolation,
and speciation of hydrothermal vent limpets (Gastropoda; Lepetodrilidae)
across the Blanco Transform Fault. Biological Bulletin v.
210, 140-157.
click here to request a reprint (cited: 31)


C. R. Young
*, S. Fujio and R. C. Vrijenhoek. 2008.
Directional dispersal between mid-ocean ridges: deep-ocean circulation
and gene flow in Ridgeia piscesae. Molecular Ecology, v.
17:7, 1718-1731.
doi: 10.1111/j.1365-294X.2008.03609.x
click here to request a reprint (cited: 25)


C. R. Young
, F. J. Stewart, C. M. Cavanaugh. 2008. Lateral symbiont
acquisition in a maternally transmitted chemosynthetic clam endosymbiosis.
Molecular Biology and Evolution, v. 25:4, 673-87.
doi: 10.1093/molbev/msn010
click here to request a reprint (cited: 25)

K. Shea, A. Metaxas, C. R. Young and C. R. Fisher. 2008. Processes and interactions in macrofaunal assemblages at hydrothermal vents: a modeling perspective. In Magma to Microbe: Modeling Hydrothermal Processes at Oceanic Spreading Centers, ed. by R.P. Lowell, J. Seewald, A. Metaxas, and M.R. Perfit, Geophys. Monogr. Ser., v. 178, p. 259-274, American Geophys. Union, Washington, DC. (cited: 5)
proof
F. J. Stewart, C. R. Young, C. M. Cavanaugh. 2009. Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Molecular Biology and Evolution. 26(6):1391-1404
doi:10.1093/molbev/msp049
click here to request a reprint and supplimentary material (cited: 16)

T. M. Caro, C. R. Young, A. E. Cauldwell and D. D.
E. Brown. 2009. Animal breeding systems and big game hunting: models
and application. Biological Conservation v. 142:4, 909-929.
doi:10.1016/j.biocon.2008.12.018
click here to request a reprint (cited: 19)

A. M. Guss, G. Roeselers, I. L. G. Newton, C. R. Young, V. Klepac-Ceraj, S. Lory, and C. M. Cavanaugh. 2011. Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. The ISME Journal, 5, 20-29; doi:10.1038/ismej.2010.88; published online 15 July 2010.
click here to request a reprint (cited: 37)

J. McCarren, J. W. Becker, D. J. Repeta, Y. Shi, C. R. Young, R. Malmstrom, S. W. Chisholm, and E. F. DeLong. 2010. Inaugural Article: Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proceedings of the National Academy of Sciences, doi:10.1073/pnas.1010732107
click here to request a reprint
(cited: 39)

H. Kimura, C. R. Young, A. Martinez, and E. F. DeLong. 2011. Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium. The ISME Journal, 5, 1641-1651; doi:10.1038/ismej.2011.36
click here to request a reprint
(cited: 8)

E. A. Ottesen, R. Marin III, C. Preston, C. R. Young, J. P. Ryan, C. A. Scholin, E. F. DeLong. 2011. Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. The ISME Journal, 5, 1881-1895; doi:10.1038/ismej.2011.70
click here to request a reprint (cited: 9)
T. Danhorn, C. R. Young, E. F. DeLong. 2012. Comparison of large-insert, small-insert, and pyrosequencing libraries for metagenomic analysis. The ISME Journal. advance online publication, April 26, 2012; doi:10.1038/ismej.2012.35
click here to request a reprint (cited: 1)
G. F. Dilly, C. R. Young, W. S. Lane, J. Pangilinan, P. R. Girguis. 2012. Exploring the limits of metazoan thermal tolerance: Thermally induced changes in protein abundance by two hydrothermal vent polychaetes. Proceedings of the Royal Society, B.
click here to request a reprint (cited: 1)
F. J. Stewart, T. Dalsgaard, C. R. Young, B. Thamdrup, N. P. Revsbech, O. Ulloa, D. E. Canfield, and E. F. DeLong. 2012. Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton. PLoS ONE 7(5): e37118. doi:10.1371/journal.pone.0037118.
click here to request a reprint (cited: 0)

E. A. Ottesen, C. R. Young, J. M. Eppley, J. P. Ryan, F. P. Chavez, C. A. Scholin, E. F. DeLong. 2013. Pattern and synchrony of gene expression among sympatric marine microbial populations. PNAS; published ahead of print January 23, 2013, doi:10.1073/pnas.1222099110.
click here to request a reprint (cited: 0)

*Corresponding author.

Bibliometric Indices:    
Papers: 17 Cites/paper: 26 h-index: 11
Citations: 469 Papers/author: 3.9 g-index: 16
Cites/year: 35 Authors/paper: 4.3 e-index: 17

(References tabulated using Google Scholar; Bibliometric indices tabulated using PoP software)

Manuscripts in prep./revision

C. R. Young* and P. Towbin. The effects of infanticide, parental care and incidental take on sustainability of hunted populations.

J. A. Maresca, C. R. Young, M. F. Semmelhack, and E. F. DeLong. Replicate sampling changes the apparent transcriptional response of surface-attached bacteria to exogenous autoinducer-2.

Authored software (all programs written in
C)
JADE Jason II annotation database extraction utility. Jason
II is a remotely operated submersible operated by Woods Hole Oceanographic
Institute. This utility extracts sample collection metadata from
the Jason virtual van database and outputs data in Ridge 2000 DMS
format.
MCMCthin Reads IM surface files (MCMC data) and outputs a thinned
MCMC dataset for further analysis.
IM_hypotest Performs the hypothesis tests described in Young, Fujio and Vrijenhoek (2008)
using joint posteriors produced by IM.
migrate_hypotest Performs the hypothesis tests described in Young,
Fujio and Vrijenhoek (2008) using joint posteriors produced by migrate-n.
BayCyde Bayesian cytonuclear disequilibrium: estimates cytonuclear
disequilibrium and fits the immigration model as in Young and Draper.
JAMN Jason II annotation mosaic navigation extraction utility.
This utility extracts navigational metadata from the Jason virtual
van database for use in photo mosaic studies.
MrAICM Computes AIC analogue from posterior simulations.
This program applies the stabilized model discrimination measure
AICM to Bayesian phylogenetic analyses. First described in: C. R. Young, F. J. Stewart, C. M. Cavanaugh. 2008. Lateral symbiont
acquisition in a maternally transmitted chemosynthetic clam endosymbiosis.
Molecular Biology and Evolution, v. 25:4, 673-87. doi: 10.1093/molbev/msn010.
Phoenix A software package for microbial population genetics using 454 pyrosequencing. (Unpublished)

Special Courses, Lectures, or Programs Attended
2000 Summer Institute of Statistical Genetics, NC State
Courses: Population Genetic Data Analysis, Molecular Evolution,
Statistics for Geneticists
2003 Biogeography and biodiversity of chemosynthetic ecosystems:
planning for the future Southampton Oceanography Centre, UK
International steering committee for deep-sea hydrothermal vent
research
2004 Summer Institute of Statistical Genetics, NC State

Courses: Markov Chain Monte Carlo Methods, Coalescent Theory
2004 DIMACS, Workshop/Working group on Reticulated Evolution
Rutgers University, Piscataway, NJ, USA
2008 Workshop on the Taxonomy and Phylogeny of Vesicomyid and Mytilid Bivalves Initiated by ChEss, a field project of the Census of Marine Life.
Station Biologique de Roscoff, Roscoff, France

Research Cruises
2000 9N Cruise to the East Pacific Rise, Richard Lutz
PI, May
R/V Atlantis II, ALVIN
2000 Gorda/Juan de Fuca Ridge, Deborah Stakes PI,
R/V Western Flyer, ROV Tiburon
2000 Monterey Canyon, Jim Barry PI,
R/V Western Flyer, ROV Tiburon
2001 Triple Junction (24S, 25S), Indian Ocean, April-May, Cindy Van Dover, PI

R/V Knorr, ROV JASON
2002 Monterey Canyon, Charlie Paull PI,
R/V Western Flyer, ROV Tiburon
2002 Monterey Canyon, R. C. Vrijenhoek, PI,
R/V Western Flyer, ROV Tiburon
2002 Gorda/Juan de Fuca Ridge, David Clague PI,
R/V Western Flyer, ROV Tiburon
2002 Monterey Canyon, R. C. Vrijenhoek, PI,
R/V Western Flyer, ROV Tiburon
2003 Monterey Canyon, R. C. Vrijenhoek, PI,
R/V Western Flyer, ROV Tiburon
2003 Monterey Canyon, R. C. Vrijenhoek, PI,
R/V Western Flyer, ROV Tiburon
2003 Monterey Canyon, R. C. Vrijenhoek, PI,
R/V Western Flyer, ROV Tiburon
2004 Monterey Canyon, R. C. Vrijenhoek, PI,
R/V Western Flyer, ROV Tiburon
2005 Monterey Canyon, R. C. Vrijenhoek, PI,
R/V Western Flyer, ROV Tiburon
2005 21S-38S, SEPR, R. C. Vrijenhoek, PI,
R/V Atlantis II, ALVIN
2005 Lau-Fiji, R. C. Vrijenhoek, PI,
R/V Melville, JASON II
2005 Monterey Canyon, R. C. Vrijenhoek, PI,
R/V Western Flyer, ROV Tiburon
2006 Lau Basin, C. R. Fisher, PI,
R/V Melville, JASON II
My duties on these cruises included lead scientist
on dives, dive planning, database management, data processing, and
sample archiving. I have spent a total of about 7 months at sea.

Advisors and collaborators
  Dr. Robert Vrijenhoek Montery Bay Aquarium Research Institute (Thesis Advisor)
  Dr. Grant Pogson University of California, Santa Cruz (Thesis Advisor)
  Dr. David Draper University of California, Santa Cruz (Thesis Advisor)
  Dr. Giacomo Bernardi University of California, Santa Cruz (Thesis Advisor)
  Dr. Ed DeLong MIT (Postdoctoral Advisor)
  Dr. Colleen Cavanaugh Harvard University (Postdoctoral Advisor)
  Dr. Peter Girguis Harvard University
  Dr. Yong-jin Won Ewha Woman’s University, Seoul
  Dr. Frank Stewart Massachusetts Institute of Technology
  Dr. Marc Mangle University of California, Santa Cruz
  Dr. Tim Caro University of California, Davis
  Dr. Cory Hauck Los Alamos National Labs
  Dr. Charles Fisher Penn State
  Dr. Kat Shea Penn State
  Dr. Joe Quattro University of South Carolina
  Dr. Jerry Hilbish University of South Carolina

Mentorship / Broader Scientific Impact / Outreach
 

I consider the dissemination of scientific information, both within the scientific community and to the general public, a high priority. At Harvard University, I have mentored two graduate students: F. J. Stewart, currently a postdoctoral associate at MIT, and Kristina Fontanez, currently a 5th year graduate student at Harvard University. I have also mentored one undergraduate student, Kirsten Kester, who recently graduated from Harvard University. Kirsten was recently awarded a Hoopes Prize for her undergraduate thesis under my mentorship. Kirsten’s award was one of only two such prizes awarded in 2009 to students in the Department of Organismic and Evolutionary Biology. Only 24 Hoopes prizes out of a total of 83 prizes awarded university-wide were science-related theses.

At MBARI in 2006, I developed and taught a workshop on MCMC methods in population genetics that was attended by students and senior researchers (~30 participants) from institutions such as MBARI, UCSC, Berkeley and Stanford. I conducted a similar workshop geared towards phylogenetics in Seoul, South Korea (59 participants from 14 institutions). In addition, computer programs that I have written as a service to the general deep-sea community (e.g., JADE and JAMN) are freely available on the web. I routinely give public lectures on deep-sea hydrothermal vent research. For example, I have given lectures at Hammond Elementary School in Columbia, South Carolina. Through such endeavors, I attempt to disseminate my expertise and experience both within and across scientific disciplines and hope to teach and inspire those who are not career scientists, but who want to learn more about ecology, evolution and deep-sea research.

 

Teaching Interests
  • Ecology and Evolution
  • Population Genetics
  • Molecular Evolution
  • Phylogenetics and Speciation
  • Quantitative Methods and Inference in Biology
  • Deep-Sea Biology