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Photograph of David Carlini

David Carlini Assoc Professor Department of Biology

Additional Positions at AU
Affiliate Faculty, Environmental Science
PhD, Marine Science, Virginia Institute of Marine Science, The College of William and Mary<br/>
MS, Marine Biology, Florida Institute of Technology<br/>
BS, Aquatic Biology, University of California, Santa Barbara

My research interests include 1) the evolution and genetics of natural populations, and 2) the molecular evolution of protein-coding genes. With regard to 1), our research involves comparing surface and cave populations of freshwater amphipod and isopod crustaceans. The cave populations we study are derived from nearby surface populations, so by comparing their genetic attributes (e.g., population structure, nucleotide sequence variation, patterns of gene expression) we can identify the evolutionary changes that occurred during or following the invasion of cave habitats. By comparing multiple independently-derived cave populations and/or species, we can determine whether the same types of genetic changes have taken place independently, or whether each cave population/species harbors its own unique set of mutations. For example, in one pair of amphipod populations, all the individuals from the cave population had a nonsense mutation in a DNA repair gene, ablating their ability to repair UV-induced DNA damage, whereas all surface individuals lacked that mutation and retained repair ability. Since UV light does not penetrate into caves, it seems reasonable to assume that such a mutation could spread in a cave population, but not in a surface population regularly exposed to UV light. However, in a second pair of cave and surface populations of the same species, both populations retained the ability to repair UV-induced DNA damage, indicating that the genes that have been altered in one cave population are not necessarily altered in other cave populations. We employ next-generation sequencing of transcriptomes (RNA-seq) to obtain both sequence and expression data that can be used to address these types of questions.

I am also interested in the functional significance of synonymous mutations which, due to the degeneracy of the genetic code, are changes in the DNA sequences of protein-coding genes that do not result in altering the amino acid sequences of their encoded proteins. However, using both experimental and computational approaches, we have demonstrated that synonymous mutations are not "silent", that is, they do have some impact on biological fitness. Experimental introduction of synonymous mutations in the protein-coding genes of fruit flies (Drosophila melanogaster) and in those of bacteria (Escherichia coli) demonstrated that they can impact the efficiency and accuracy of protein synthesis (translational selection). Furthermore, we have demonstrated that these changes have a measurable impact on biological fitness.
See Also
Biology Department
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Fall 2022

  • BIO-485 Bioinformatics

Spring 2023

  • BIO-356 Genetics With Laboratory

  • BIO-356 Genetics With Laboratory

  • BIO-356 Genetics With Laboratory

  • BIO-356 Genetics With Laboratory

  • BIO-356 Genetics With Laboratory

Scholarly, Creative & Professional Activities

Selected Publications

(† Denotes AU undergraduate student. * Denotes AU graduate student)

  • Fong, DW, Orndorff W, Carlini DB. 2021. Species status evaluation of Lirceus usdagalan, L. culveri, and L. hargeri populations (Isopoda; Asellidae) based on a large scale next-generation sequence data set. Conservation Genetics 22: 661-667.
  • †Ballard A, †Bieniek S, Carlini DB. 2019. The fitness consequences of synonymous mutations in Escherichia coli: Experimental evidence for a pleiotropic effect of translational selection. Gene 694: 111-120.
  • Østbye K, Østbye  E, Lien AM, †Lee LR, Lauritzen SE, Carlini DB. 2018. Morphology and life history in cave and surface populations of Gammarus lacustris. PLoS ONE 13: e0205556.
  • Carlini DB, Fong DW. 2017. The transcriptomes of cave and surface populations of Gammarus minus (Crustacea: Amphipoda) provide evidence for positive selection on cave downregulated transcripts. PLoS ONE 12: e0186173.
  • Carlini DB, †Makowski M. 2015. Codon bias and gene ontology in holometabolous and hemimetabolous insects. Journal of Evolutionary Zoology Part B: Molecular and Developmental Evolution 324: 686–698.
  • Carlini DB, *Satish S, Fong DW. 2013. Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda). BMC Evolutionary Biology (doi:10.1186/1471-2148-13-89).
  • *Aspiras AC, †Prasad R, Fong DW, Carlini DB, Angelini DR. 2012. Parallel reduction in expression of the eye development gene hedgehog in separately derived cave populations of the amphipod Gammarus minus. Journal of Evolutionary Biology 25: 995–1001.
  • *Hutchins B, Fong DW, Carlini DB. 2010. Genetic population structure of the Madison Cave isopod, Antrolana lira (Flabellifera; Cirolanidae) in the Shenandoah Valley of the eastern United States. Journal of Crustacean Biology 30: 312–322.
  • Hense W, *Anderson N, Hutter S, Stephan W, Parsch J, Carlini DB. 2010. Experimentally increased codon bias in the Drosophila Adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity. Genetics 184: 547–555.
  • Carlini DB, †Manning J, †Sullivan PG, Fong DW. 2009. Molecular genetic variation and population structure in morphologically differentiated cave and surface populations of the freshwater amphipod Gammarus minus. Molecular Ecology 18: 1932–1945.

Research Interests

Current projects in my lab include: 1) transcriptome profiling of cave and surface populations of freshwater amphipods (Gammarus minus, Stygobromus tenuis, and Crangonyx shoemaker), with an aim toward identifying and characterizing patterns of variation in differentially regulated genes, 2) use of next-generation sequencing to evaluate the species status of Lirceus usdagalun, a cave-dwelling freshwater isopod on the U.S. endangered species list, 3) comparison of photolyase sequence variation, photolyase gene expression, and UV-tolerance in cave and surface populations of freshwater crustaceans, and 4) honey bee (Apis mellifera) metagenomics.