Research

My research focuses primarily on the genomic architecture of ecological divergence and local adaptation. I’m working on projects in a diversity of genera including Anolis lizards, turtles (Trachemys sp.), Heliconius butterflies, and Hawaiian Drosophila.

I’ve also contributed to a number of studies using phylogenomic approaches to investigate core questions in vertebrate systematics. I helped develop a new type of phylogenomic marker that uses target enrichment to capture ultra conserved regions (UCEs) and their variable flanking sequence. I have used these markers to investigate questions in mammalian, reptilian, and avian evolution.

I'm joining the Tishkoff lab in the spring of 2014 and will be working on projects involving local adaptation and demography in African populations.

Areas of specialization

Bioinformatics, evolutionary biology, computational biology, population genomics, phylogenomics, speciation, ultra conserved elements, herpetology and entomology

Education

2013

Postdoctoral Fellow, California Academy of Sciences
Advisors: Durrell Kapan and Brian Simison

2007 – 13

Ph.D. Biology, Boston University 
Advisor: Christopher Schneider 
Dissertation Title: Genomic Analysis of Marco- and Micro-Evolution in the Reptilia

Additional Projects: Mammal, Reptile, and Avian Phylogenomics, with Travis Glenn 
Butterfly Speciation Genomics, with Sean Mullen 

2004 – 07

M.S. Biology, San Diego State University 
Advisor: Tod Reeder 
Thesis: Population structure within the Plateau Striped Whiptail (Aspidoscelis velox complex) a parthenogenetic lizard 

Additional Project: Phylogenetic relationships among Australian skinks of the genusGlaphyromorphus

1997 / 01

B.S. Biology, Union College 
Graduated Cum Laude with Academic and Departmental Honors

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Skills and Techniques

Programming Languages/Frameworks: Python (Modules: Numpy, Scipy, Matplotlib, Biopython, Pysam, Multiprocessing, iPython, MrJob, Pandas, Flask, and Django), MySQL/Sqlite3, Git/Github, Unix/Linux, LSF/SGE/AWS Clusters, Hadoop/MapReduce, also some R, Perl, Html, and CSS

Software: GATK, ABySS, Trinity, Breakdancer, Samtools, VCFtools, Tophat, Cufflinks, Bowtie2, Stampy, GO Elite, Blast/NCBI, MrBayes, Sequencher, Oligo (primer design), Genemapper, GenAlEx, Arlequin

Laboratory: Genomic, RAD-tag, and RNA-seq Illumina library construction, Primer Design, DNA purification, PCR, qPCR (Taqman and Kappa assays), Sanger Sequencing (both ABI3130 and ABI377 genetic analyzers), Microsatellite Genotyping, Bioanalyzer, and constructing cDNA libraries

Miscellaneous Skills: Protein Purification (FPLC), Mammalian Tissue Culture, Ordering and Stocking, Maintaining Laboratory Compliance with Safety Regulations, Training Students and Techs, and Catching lizards

Grants and Scholarships

2012
Grand Challenges Award, Smithsonian Institute Consortia, Next Generation Phylogenetics, MJ Braun, K Wurdack, W Wcislo, J Maldonado, K Helgen, S Brady, M Cummings, TC Glenn, BC Faircloth, RT Brumeld, E Braun, JC McCormack, NG Crawford, N White. $100,000.

2011
Next-generation Sequencing Small Grant. Phylogenetic utility of ultra- conserved elements for the avian tree of life. MJ Braun, ND White, TC Glenn, BC Faircloth, RT Brumeld, EL Braun, JE McCormack, NG Crawford. $10,000
Amazon Education Research Grant (aws.amazon.com), Computational Resources. BC Faircloth, NG Crawford, JE McCormack. $10,000

2010
Amazon Education Research Grant (aws.amazon.com), Computational Resources. NG Crawford, BC Faircloth, TC Glenn. $7,500
Doctoral Dissertation Improvement Grant (NSF). NG Crawford, C Schneider. $15,000

2009
Theodore Roosevelt Memorial Fund (American Museum of Natural History) labwork/fieldwork. $1,500

2005
Theodore Roosevelt Memorial Fund (American Museum of Natural History) labwork/fieldwork. $1,960
Harry E. Hamber Memorial Scholarship, tuition. $1,400

2000
IEF Grant, thesis research. $100
NYSEP Grant, summer stipend. $1,700

1999
Booth - Ferris Grant, summer stipend. $1,700

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Publications

  • Marcus R. Kronforst, Matthew E. B. Hansen, Nicholas G. Crawford, Jason R. Gallant, Rob J. Kulathinal, Durrell D. Kapan, Sean P. Mullen (2013) Hybridization reveals the evolving genomic architecture of speciation. Cell Reports 5:1–12.
  • John E. McCormack, Michael G. Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn, Robb T. Brumfield (2013) A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE 8(1): e54848.
  • Martha M. Muñoz, Nicholas G. Crawford, Thomas J. McGreevy, Rebecca D. Tarvin, Nicholas J. Messana, Liam J. Revell, Rosanne M. Zandvliet, Juanita M. Hopwood, Elbert Mock, André L. Schneider, and Christopher J. Schneider (2013) Divergence in coloration and the evolution of reproductive isolation in the Anolis marmoratus species complex. Molecular Ecology 22(10):2668–2682.
  • John E. McCormack, Michael G. Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn, Robb T. Brumfield (2013) A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE 8(1):e54848.
  • John A. St. John, Edward L. Braun, Sally R. Isberg, Lee G. Miles, Amanda Y. Chong, Jamie Gongora, Pauline Dalzell, Christopher Moran, Taisen Iguchi, Bertrand Bed'Hom, Shane C. Burgess, Amanda M. Cooksey, Todd A. Castoe, Arkhat Abzhanov, Llewellyn D. Densmore, Miryam Venegas-Anya, Matthew J. Greenwold, Roger H. Sawyer, Federico G. Hoffmann, Nicholas G. Crawford, Jennifer C. Drew, Scott V. Edwards, Matthew K. Fujita, Jonathan M. Howard, Brant C. Faircloth, Daniel E. Janes, Shahid Yar Khan, Satomi Kohno, A.P. Jason de Koning, Stacey L. Lance, Fiona M. McCarthy, John E. McCormack, Mark E. Merchant, Daniel G. Peterson, David D. Pollock, Nader Pourmand, Brian J. Raney, Kyria A. Roessler, Jeremy R. Sanford, Carl J. Schmidt, Eric W. Triplett, Tracey D. Tuberville, Erich D. Jarvis, Louis J. Guillette Jr, Travis C. Glenn, Richard E. Green and David A. Ray (2012) Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology 13:415.
  • Kenro Kusumi, Rob J. Kulathinal, Arhat Abzhanov, Stephane Boissinot, Nicholas G. Crawford, Brant C. Faircloth, Travis C. Glenn, Daniel E. Janes, Jonathan B. Losos, Douglas B. Menke, Steven Poe, Thomas J. Sanger, Christopher J. Schneider, Jessica Stapley, Juli Wade, Jeanne Wilson-Rawls (2012) Developing a community-based genetic nomenclature for anole lizards. BMC genomics 12(1):554.
  • Nicholas G. Crawford, Brant C. Faircloth, John E. McCormack, Robb T. Brumfield, Kevin Winker, Travis C. Glenn (2012) More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters 8(5):783-786.
  • Brant C. Faircloth, John E. McCormack, Nicholas G. Crawford, Michael Harvey, Robb T. Brumfield, Travis C. Glenn (2012) Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales. Systematic Biology 61(5):713-715.
  • John E. McCormack, Brant C. Faircloth, Nicholas G. Crawford, Patricia Adair Gowaty, Robb T. Brumfield, Travis C. Glenn (2011) Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis. Genome Research 22(4):746-754.
  • Nicholas G. Crawford (2010) SMOGD: Software for the Measurement of Genetic Diversity. Molecular Ecology Resources 10:556-557. 
  • Nicholas G. Crawford, Jaime Zaldvar-Rae, Cris Hagen, Amanda Schable, Erica Bree Rosenblum, Jeff A. Graves, Tod W. Reeder, Michael G. Ritchie, Travis C. Glenn (2007) Thirteen polymorphic microsatellite DNA loci from whiptails of the genus Aspidoscelis (Teiidae: Squamata) and related cnemidophorine lizards. Molecular Ecology Resources 8:219-223.
  • Nicholas G. Crawford, Cris Hagen, Heather F. Sahli, Elizabeth A. Stacy, Travis C. Glenn (2007) Fifteen polymorphic microsatellite loci from Hawaiian Metrosideros polymorpha (Myrtaceae: Myrtales), a model species for ecology and evolution. Molecular Ecology Resources 8:308-310.
  • Caleb R. Hickman, Maureen B. Peters, Nicholas G. Crawford, Cris Hagen, Travis C. Glenn, Christopher M. Sommers (2008) Development and characterization of microsatellite loci in the American white pelican (Pelecanus erythrorhynchos). Molecular Ecology Resources 8:1439-1441.
  • Nicholas G. Crawford, Maureen B. Peters, Cris Hagen, Travis C. Glenn, Stephen K. Davis, Christopher M. Somers. 2007. Twelve polymorphic microsatellite loci from Spragues pipit, Anthus spragueii (Motacillidae:Passeriformes), a threatened grassland endemic songbird. Molecular Ecology Resources 9:315-317.
  • Olga V. Tsyusko, Tracey D. Tuberville, Maureen B. Peters, Nicholas G. Crawford, Cris Hagen, Steve Weller, Ann Sakai, and Travis C. Glenn (2007) Microsatellite markers isolated from polyploid woodsorrell (Oxalis alpina). Molecular Ecology Notes 7:1284-1286.
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Professional Experience

2007 – 2011

Teaching Fellow, Boston University
Introductory Biology, Genetics, Evolution, Animal Behavior

2007

Research Technician, South Carolina, Summer 6 months
supervised by Travis Glenn

2006

South Carolina, Summer, 6 weeks
Microsatellite loci preparation at the Savannah River Ecology Laboratory, supervised by Travis Glenn

2004 – 2005

Graduate Teaching Assistant, SDSU
Introductory Biology and Introductory Zoology

2004

Research Assistant, SDSU
Advisor: Tod Reeder

2002 – 03

Research Associate, Boston Biochem

2001

Research Associate, Pfizer Pharmaceuticals
Research Associate, Harvard Medical School

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Field Experience

2012

Guantanamo Bay, Cuba, Summer, 1 week, collecting lizards 

2009

Guadeloupe, French West Indies, Summer, 5 days, collecting lizards

2007

New Mexico, Summer, 1 week, collecting lizards

2005

New Mexico, Summer, 1 week, collecting lizards
Arizona, Summer, 2 weeks, collecting lizards

2004

Arizona, Summer, 2 weeks, collecting lizards

2001

New York, Summer, 1 week, collecting treefrogs

1999

New York, Summer, 1 week, collecting treefrogs

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Conferences, Meetings, and Talks

2013

UMass Lowell Seminar Series: Invited Speaker 
Presentation Title: From Archosaurs to Anoles: genomic approaches to studying reptile evolution

2012

Union College Seminar Series: Invited Speaker - Union College 
Presentation Title: Genomic approaches to understanding reptile evolution

World Congress of Herpetology, Vancouver. 
Presentation Title: The genetics of colorful pigmentation in Anolis lizards

Evolutionary Genomics Super Group, Broad Institute 
Presentation Title: Ultraconserved elements as phylogenomic markers

MCZ Lunchtime Seminar, Harvard University 
Presentation Title: Thousands of ultraconserved elements in combination with cloud computing and species-tree methods help resolve deep divergences in reptiles, mammals, and birds

2010

The genetics and evolution of animal coloration, Radcliffe Workshop
Presentation Title: Identifying coloration genes when you can’t easily do QTL mapping

2009

Anole Symposium  Harvard University 
Anolis carolinensis: Pigmentation Genetics
Poster Title: Genome scan identifies two loci associated with color polymorphism in Anolis marmoratus

Gordon Conference: Evolutionary & Ecological Functional Genomics - Tilton, New Hampshire. 
Poster Title: Genetics of colorful pigmentation in Anolis lizards

Society for Integrative and Comparative Biology Annual Meeting, Boston Massachusetts
Presentation Title: Evolution of dewlap pigmentation in Anoline lizards

2008

Union College Seminar Series: Invited Speaker - Union College  
Presentation Title: Population structure of the plateau striped whiptail a parthenogenetic species of lizard

2007

Island Biogeography Symposium, Harvard University, Cambridge Massachusetts

2005

American Society of Ichthyologists and Herpetologists 85th Annual Meeting, Tampa, Florida
Presentation Title: Phylogenetic relationships among Australian skinks of the genus Glaphyromorphus

2004

American Society of Ichthyologists and Herpetologists 84th Annual Meeting, Norman, Oklahoma
Evolution Conference, Fort Collins, Colorado

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Society Affiliations

American Society of Ichthyologists and Herpetologists (not presently affiliated)

Society for Comparative and Integrative Biology (not presently affiliated)