Benjamin Rubin

Benjamin Rubin

Bioinformatician and evolutionary genomicist.

Curriculum Vitae

Contact Information

berubin[at]princeton.edu

Princeton University
Ecology and Evolutionary Biology
Guyot Hall room 106A
Washington Road
Princeton, NJ 08544-1003

Education

Ph.D., Committee on Evolutionary Biology, University of Chicago, June 2015
B.A., Biology, summa cum laude, Cornell University, May 2009

Professional experience

USDA NIFA Postdoctoral Fellow, Prof. Sarah Kocher
  Viral diversity and transmission dynamics in a socially variable clade of wild pollinators
  Lewis-Sigler Institute for Integrative Genomics
  Princeton University, Apr. 2018-

Postdoctoral Research Associate, Prof. Sarah Kocher
  Genomic evolution of social behavior in bees
  Lewis-Sigler Institute for Integrative Genomics
  Princeton University, Aug. 2015-Mar. 2018

Awards & Activities

  • USDA NIFA Postdoctoral Fellowship ($164,331), 2018-2020
  • Field Museum Brown Family Fellowship ($30,000), 2013-2014
  • NSF Doctoral Dissertation Improvement Grant ($20,529), 2013
  • NSF Graduate Research Fellowship ($123,000), 2010-2013
  • Field Museum Pritzker lab student research grant ($2,000 each), Spring 2012, 2014
  • Field Museum MiSeq research grant ($5,000), Spring 2014
  • UChicago Hinds Fund for student research ($1,500 each), Spring 2010, 2011, 2012
  • Explorer’s Club Youth Activity Fund ($1,000), Summer 2008
  • NAS/IUSSI EntSoc meeting travel award, 2013
  • i5k Community Workshop student travel award, May 2012
  • UChicago Biological Sciences Division travel award, Dec. 2010
  • Highest honors for undergraduate thesis, May 2009
  • Member, Entomological Society of America, Since July 2009
  • Member, The Society for the Study of Evolution, Since Jan. 2011

Publications

  1. Rubin BER (2018 preprint) Social insect colony size is correlated with rates of substitution and DNA repair gene evolution. bioRxiv doi: 10.1101/415570.
  2. Rubin BER, Jones BM, Hunt BG, Kocher SD (2019) Rate variation in the evolution of non-coding DNA associated with social evolution in bees. Phil. Trans. R. Soc. B 374: 20180247.
  3. Rubin BER, Kautz S, Wray BD, Moreau CS (2019) Dietary specialization in mutualistic acacia- ants affects relative abundance but not identity of host-associated bacteria. Molecular Ecology 28(4): 900-916. (commentary: Pringle E (2019) Convergence, constraint and the potential for mutualism between ants and gut microbes. Molecular Ecology. 28(4): 699–702.)
  4. Rubin BER, Sanders JG, Turner KM, Pierce NE, Kocher SD (2018) Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts. Royal Society open science 5: 180369.
  5. Kocher SD, Mallarino R, Rubin BER, Yu DW, Hoekstra HE, Pierce NE (2018) The genetic basis of a social polymorphism in halictid bees. Nature Communications 9: 4338.
  6. Moreau CS, Rubin BER (2017) Diversity and persistence of the gut microbiome of the giant Neotropical bullet ant. Integrative & Comparative Biology icx037.
  7. Rubin BER, Moreau CS (2016) Comparative genomics reveals convergent rates of evolution in ant-plant mutualisms. Nature Communications 7: 12679. (commentary: Pennisi E (2016) Peaceful ant-plant partnerships lead to genomic arms races. Science DOI: 10.1126/science.aah7229.)
  8. Sullam KE, Rubin BER, Dalton CM, Kilham SS, Flecker AS, Russell JA (2015) Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies. ISME J 9(7): 1508-1522.
  9. Rubin BER, Sanders JG, Hampton-Marcell J, Owens SM, Gilbert JA, Moreau CS (2014) DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure. MicrobiologyOpen 3(6): 910-921.
  10. Rubin BER, Gibbons SM, Kennedy S, Hampton-Marcell J, Owens S, Gilbert JA (2013) Investigating the impact of storage conditions on microbial community composition in soil samples. PLoS ONE 8: e70460.
  11. Kautz S, Rubin BER, Moreau CS (2013) Bacterial infections across the ants: frequency and prevalence of Wolbachia, Spiroplasma, and Asaia. Psyche 2013: e936341.
  12. Rubin BER, Anderson RM, Kennedy D, Palmer TM, Stanton ML, Lovette IJ (2013) Polygyny in the nest-site limited acacia-ant Crematogaster mimosae. Insectes Sociaux 60: 231-241.
  13. Moreau CS, Wray BD, Czekanski-Moir JE, Rubin BER (2013) DNA preservation: a test of commonly used preservatives for insects. Invertebrate Systematics 27: 81-86.
  14. Kautz S, Rubin BER, Russell JA, Moreau CS (2013) Surveying bacterial diversity in ants: comparing 454 pyrosequencing with traditional methods. Applied and Environmental Microbiology 79: 525-534.
  15. Rubin BER, Ree R, Moreau CS (2012) Inferring phylogenies from RAD sequence data. PLoS ONE 7: e33394.
  16. Rubin BE, Makarewich CA, Talaba AL, Stenzler L, Bogdanowicz SM, Lovette IJ (2009) Isolation and characterization of microsatellite markers from the acacia-ant Crematogaster mimosae. Molecular Ecology Resources 9: 1212-1214.

Invited Talks

  • Rubin BER. Social behavior in bees influences the abundance of microbial symbionts. Animal-Microbe Symbioses Gordon Research Conference, Mt. Snow, Vt., June 2019.
  • Rubin BER. The evolution of cooperation and how it shapes the genomes of social insects and their symbionts. Lester Newman Seminar, Portland State University, Apr. 2018.
  • Rubin BER. The evolution of cooperation and how it shapes the genomes of social insects and their symbionts. Department of Botany Seminar, University of Wyoming, Feb. 2018.
  • Rubin BER. The evolution of cooperation and how it shapes the genomes of social insects and their symbionts. Biological Sciences Seminar, The George Washington University, Jan. 2018.
  • Rubin BER. Comparative genomics in halictid bees reveals the genetic underpinnings of social evolution. USDA Agricultural Research Service Webinar, Sept. 2017.
  • Rubin BER. Life history’s influence on genome evolution in social insects and their endosymbionts. EEB Seminar Series, Yale University, Mar. 2017.
  • Rubin BER, Kocher SD. Comparative genomics of bee sociality using 10x linked-read sequencing. 10x Genomics workshop at the International Plant & Animal Genome meeting, Jan. 2017.
  • Rubin BER, The impact of social evolution on the genomes of bees and their endosymbionts. High Throughput Sequencing User Group Seminar, Princeton University, Feb. 2016.
  • Rubin BER, Nascent bacterial endosymbionts compete for sweat bee hosts. EvoGroup Seminar, Princeton University, Dec. 2016.
  • Rubin BER, Plant-ant mutualism alters genome evolution but not symbiotic bacterial communities. Icahn Lab Seminar, Princeton University, Dec. 2015.
  • Rubin BER, The impact of mutualism on genome evolution in plant-ants and their endosymbionts. Molecular Evolution in Social Insects symposium at the Entomological Society of America conference, Nov. 2015.
  • Rubin BER, Convergent selection and rates of evolution in mutualistic plant-ants. Academia Sinica, Oct. 2014.
  • Rubin BER, Convergent selection and rates of evolution in mutualistic plant-ants. Okinawa Institute of Science and Technology, Oct. 2014.
  • Rubin BER, Genome evolution in mutualistic plant-ants. Ecology and Macroevolution seminar, EAWAG, Swiss Institute for Aquatic Science, May 2013.

Other Presentations

  • Rubin BER, Kocher SD. Social evolution in sweat bees is associated with convergent rate shifts in non-coding sequence. Oral presentation, Evolution Conference, June 2019.
  • Rubin BER. Ant colony size is correlated with genome-wide rates of molecular evolution and constraint on DNA repair. Oral presentation, Entomological Society of America, Nov. 2018.
  • Rubin BER, Kocher SD. Harnessing natural variation to study the evolution of social behavior in bees. Oral presentation, Biology & Genomics of Social Insects at CSHL, May 2018.
  • Rubin BER, Kocher SD. Comparative genomics in halictid bees reveals the genetic underpinnings of social evolution. Oral presentation, Advances in Arthropod Genomics Symposium at the Entomological Society of America, Nov. 2017.
  • Rubin BER, Sanders JS, Kocher SD. Nascent bacterial endosymbionts compete for sweat bee hosts. Oral presentation, International Union for the Study of Social Insects North American Section meeting, Sept. 2016.
  • Rubin BER, Kocher SD. Comparative population genomics in halictid bees provides insights into the evolution of social behavior. Oral presentation, International Congress of Entomology meeting, Sept. 2016.
  • Rubin BER, Moreau CS. Comparative genomics of plant-ants reveals convergent rates of evolution in mutualists. Oral presentation, Biology and Genomics of Social Insects, May 2015.
  • Rubin BER, Moreau CS. Genome-wide rates of molecular evolution are higher in mutualistic plant-nesting ants. Oral presentation, Entomological Society of America, Nov. 2014.
  • Rubin BER, Moreau CS. The genetic basis of mutualism in Pseudomyrmex plant-ants. Oral presentation, International Union for the Study of Social Insects, Aug. 2014.
  • Rubin BER, Moreau CS. Genome-wide rates of molecular evolution are higher in mutualistic plant-nesting ants. Oral presentation, Evolution, June 2014.
  • Rubin BER, Moreau CS. The genome of the big-eyed arboreal ant Pseudomyrmex gracilis. Oral presentation, Entomological Society of America, Nov. 2013.
  • Rubin BER, Moreau CS. The genome of the big-eyed arboreal ant Pseudomyrmex gracilis. Oral presentation, Evolution, June 2013.
  • Rubin BER, Kautz S, Moreau CS. The genome of the arboreal ant Pseudomyrmex gracilis. Poster, Entomological Society of America, Nov. 2012.
  • Rubin BER. Genome evolution in mutualistic plant-ants. Oral presentation, Chicago Area Ant Meeting, Nov. 2012.
  • Rubin BER, Kautz S, Moreau CS. Dietary consequences of plant-ant mutualism. Oral presentation, Entomological Society of America, Nov. 2011.
  • Rubin BER. The evolution of plant-ants: Genomic and dietary consequences of plant-ant mutualistic behavior. Oral presentation, Chicago Area Ant Meeting, Sept. 2011.
  • Rubin BER, Kautz S, Emery VJ, Moreau CS. The evolution of plant-ant mutualism. Oral presentation, Entomological Society of America, Dec. 2010.
  • Rubin BE, Palmer T, Stanton M, Lovette IJ. Polygyny and competition in the acacia-ant Crematogaster mimosae. Poster, Entomological Society of America, Dec. 2009.
  • Rubin BE, Lovette IJ. Colony structure of an African acacia-ant. Poster, International Society for Behavioral Ecology, Aug. 2008.

Teaching Experience

  • TA, Reconstructing the Tree of Life: an Introduction to Systematic and Phylogenetic Biology (Fall 2011)
  • TA, Ecology and Evolution of the Southwest field course (June 2010, 2011, 2015)
  • TA, Public and Private Lives of Insects (Winter 2011, 2015)

Outreach & Service

  • Mentor to eight undergraduate and high school research interns
  • Participant in Field Museum members’ night (2011, 2012, 2013)
  • Field Museum Pritzker Lab Facebook featured scientist (Feb. 2010)
  • UChicago Committee on Evolutionary Biology student spotlight (Feb. 2013)
  • Field Museum collection tours for UChicago undergraduate phylogenetics class (Nov. 2011)
  • and SAIC undergraduate insect biology class (Sept. 2012)
  • Pritzker Lab “Talk to the Scientist Hour” contributor
  • Session moderator for Field Museum REU symposium (Aug. 2014)
  • Reviewer for articles from the journals Nature Ecology & Evolution, ISME J, Systematic Biology, Molecular Ecology, Proceedings B, Ecology and Evolution, Molecular Biology and Evolution, Molecular Ecology Resources, Microbial Ecology, PLoS ONE, mSystems, Florida Entomologist, Axios, Scientific Reports, and Infection, Genetics and Evolution