MUN logo      Carr Lab, Memorial University of Newfoundland

Research Interests

   I am interested in patterns and processes of molecular phylogeography and evolution within and among species and natural populations of vertebrate animals, and novel genomic biotechnology approaches to these questions. My investigations include:

(1) Mitogenomic Phylogeography of the pre- & post-glacial Nearctic & North Atlantic
(2) Genomic diversity of the founding human population(s) of Newfoundland
(3) Phylogeography of "Species At Risk" of extinction, including the occasional "sea monster"

For further details and other projects, see MSS below, and please contact Steve at scarr@mun.ca.

    My laboratory has taken a mitogenomic approach to the interrelated problems of evolutionary and population genetics and systematic biology. Analyses based on complete maternally-inherited mitochondrial DNA genomes provide well-resolved, highly-corroborated molecular phylogenies within and among species that can generate and test hypotheses about morphological, biogeographic, and behavioral evolution. Phylogeographic analysis [the analysis of genetic relationships in their geographic context] of completely-resolved intraspecific gene trees, based on full-length mtDNA genomes, provides the detailed historical information and necessary statistical power to evaluate vicariance and dispersal phenomena at scales of interest to fisheries managers and population biologists. I have combined this with novel analytical methods, including a Monte Carlo simulation tests of population structure, and a non-parametric Kolmogorov-Smirnoff test of coalescent offsets.

    My lab has developed a new biotechnology, iterative DNA "re-sequencing" on microarrays, which uses a reference DNA sequence to determine homologous sequences in new individuals. Experiments with a human mtDNA chip show that the approach is practical, accurate, and cost-effective. We have developed a multi-species DNA "ArkChip" as a practical method for assessing the genome structure of populations and species of interest to fisheries and Species-at-Risk management The method generates up to 20 complete mtDNA genome sequences in a single experiment. The microarray method also offers opportunities for bioinformatic investigation of factors that influence absolute signal strength, differential signal-to-noise ratios, and confidence in base calling.


Carr Lab Representative Publications:


C Chilaka, SM Carr, N Shalaby, W Banzhaf. Inclusion of 3-gram neural networks for prediction of normalized signal strengths from a DNA-sequencing microarray. Bioinformation, in prep.

CD Wilkerson,
SP Mahoney, &
SM Carr. 2018. Post-glacial recolonization of insular Newfoundland gave rise to an endemic subspecies of woodland caribou, Rangifer tarandus terranovae (Bangs, 1896): evidence from mtDNA haplotypes. Genome, accepted subject to revision.

A Collier & SM Carr. 2018. On the persistence and detection of ancient Beothuk mitochondrial DNA in living First Nations peoples: a review of the data in the context of genealogy. Mitochondrial DNA, accepted subject to revision

LA Lait, HD Marshall, & SM Carr. 2017. Phylogeographic mitogenomics of Atlantic cod (Gadus morhua): variation in and among trans-Atlantic, trans-Laurentian, Northern Cod, and landlocked fjord populations. Genome Biology & Evolution, in press.

C Chilaka, SM Carr, N Shalaby, W Banzhaf. 2017. Use of a neural network to predict normalized signal strengths from a DNA-sequencing microarray. Bioinformation, 13, 313-316. [PDF]

S Royston & SM Carr. 2016b. Conservation genetics of high-arctic gulls at risk. II. Diversity in the mtDNA Control Region of Threatened Ross's Gull (Rhodostethia rosea). Mitochondrial DNA, 27, 3941-3944. [PDF]

S Royston & SM Carr. 2016a. Conservation genetics of high-arctic gulls at risk. I. Conservation genetics of high-arctic gull species at risk. I. Diversity in the mtDNA Control Region of circumpolar populations of the Endangered Ivory Gull (Pagophila eburnea). Mitochondrial DNA, 27, 3995-3999. [PDF]

SM Carr, AT Duggan, GB Stenson, & HD Marshall. 2015. Quantitative phylogenomics of within-specie mitogenome variation: Monte Carlo and non-parametric analysis of phylogeographic structure among discrete transatlantic breeding areas of Harp Seals (Pagophilus groenlandicus). PLoS ONE,10(8): e0134207. doi:10.1371/journal.pone.0134207. [PDF]

SM Carr & WS Davidson. 2015. Panmixia in Greenland Halibut: a response to Roy et al. Canadian Journal of Fisheries and Aquatic Sciences, online. [PDF]


SM Carr, HD Marshall, HT Wareham, & D Craig. 2015. The Big ORF Theory: Algorithmic, computational, and approximation approaches to Open Reading Frames in short- and medium-length dsDNA sequences. Chapter 13, pp. 265-274 in: Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology (Q-N Tran, HR Arabnia, eds.). Elsevier. [PDF]

SM Carr, HT Wareham & Craig D. 2014. A web application for generation of DNA sequence exemplars with open and closed reading frames in genetics and bioinformatics education. CBE – Life Sciences Education 13, 373-374. [PDF]

SM Carr, D Craig, & HT Wareham. 2014 An algorithmic and computational approach to Open Reading Frames in short dsDNA sequences: Evaluation of “Carr’s Conjecture.” Pp. 37-48 in Proceedings of the 14th International Conference on Bioinformatics & Computational Biology. [H. Arabnia et al., eds.].  [PDF]

SM Carr. 2013. Composite and complementary DNA. Lab Business, Nov / Dec 2013. [PDF]

SM Carr. 2013. "Known Knowns, Known Unknowns, & Unknown Unknowns": Computational Science challenges for analysis of multidimensional DNA matrices in Evolutionary & Population Genomics. Pp. 508-512 in Proceedings of The 13th International Conference on Bioinformatics & Computational Biology (H. Arabnia, ed.]. [PDF]

AM Pope, SM Carr, KN Smith, & HD Marshall. 2011. Mitogenomic and microsatellite variation in descendants of the founder population of Newfoundland: high genetic diversity in an historically isolated population. Genome, 54,110-119. [PDF]

SM Carr, AT Duggan, & HD Marshall. 2009. Iterative DNA sequencing on microarrays: a high-throughput NextGen technology for ecological and evolutionary mitogenomics. Laboratory Focus 13, 8-12. [PDF]

HD Marshall, MW Coulson, & SM Carr. 2008. Near neutrality, rate heterogeneity, and linkage govern mitochondrial genome evolution in Atlantic Cod (Gadus morhua) and other gadine fish. Molecular Biology & Evolution 26, 579-589. [PDF]

SM Carr & HD Marshall. 2008. Phylogeographic analysis of complete mtDNA genomes from Walleye pollock (Gadus chalcogrammus Pallas, 1811) shows an ancient origin of genetic biodiversity. Mitochondrial DNA 19, 490-496. [PDF]

SM Carr & HD Marshall. 2008. Intraspecific phylogeographic genomics from multiple complete mtDNA genomes in Atlantic Cod (Gadus morhua): Origins of the "Codmother," trans-Atlantic vicariance, and mid-glacial population expansion. Genetics 108, 381-389. [PDF]

SM Carr, HD Marshall, AT Duggan, SMC Flynn, KA Johnstone, AM Pope, & CD Wilkerson. 2008. Phylogeographic genomics of mitochondrial DNA: patterns of intraspecific evolution and a multi-species, microarray-based DNA sequencing strategy for biodiversity studies. Comparative Biochemistry and Physiology, D: Genomics and Proteomics 3,1-11. [PDF]

SJ Moore, DJ Buckley, A MacMillan, HD Marshall, L Steele, P Ray, Z Nawaz, M Frecker, SM Carr, E Ives, & PS Parfrey. 2008. The clinical and genetic epidemiology of neuronal ceroid lipofuscinosis in Newfoundland. Clinical Genetics 74, 213-222.  [PDF]

SMC Flynn &SM Carr. 2007. Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip. BMC Genomics 8, 339. [PDF]

KA Johnstone, HD Marshall, & SM Carr. 2007. Biodiversity genomics for Species At Risk: patterns of DNA sequence variation within and among complete mitochondrial DNA genomes of three species of Wolffish (Anarhichas spp.). Canadian Journal of Zoology 85,151-158. [PDF]

HD Marshall, KA Johnstone, & SM Carr. 2006. Species-specific oligonucleotides and multiplex PCR for forensic discrimination of two species of scallops, Placopecten magellanicus and Chlamys islandica. Forensic Science International 167,1-7. [PDF]

MW Coulson, HD Marshall, P Pepin & SM Carr. 2006. Mitochondrial phylogeographic genomics of gadine fish: Implications for taxonomy and biogeographic origins. Genome 49,1115-1130. [PDF]

SM Carr, HD Marshall, KA Johnstone, LM Pynn, and GB Stenson. 2002. How To Tell a Sea Monster: Molecular Discrimination of Large Marine Animals of the North Atlantic. The Biological Bulletin 202,1-5. [PDF]

EA Perry, GB Stenson, SE Bartlett, WS Davidson, & SM Carr. 2000. DNA sequence analysis identifies genetically distinguishable populations of harp seals (Pagophilus groenlandicus) in the northwest and northeast Atlantic. Marine Biology 137, 53- 58. [PDF]

SM Carr, DGS Kivlichan, P Pepin & DC Crutcher. 1999. Molecular phylogeny of gadid fishes: implications for the biogeographic origins of Pacific species. Canadian Journal of Zoology 77,19-26. [PDF]

SM Carr & DC Crutcher. 1998. Population genetic structure in Atlantic Cod (Gadus morhua) from the North Atlantic and Barents Sea: contrasting or concordant patterns in mtDNA sequence and microsatellite data? Pp. 91-103 In The Implications of Localized Fishery Stocks (I. Hunt von Herbing, I. Kornfield, M. Tupper, and J. Wilson. eds.). Northeast Regional Agricultural Engineering Service, Ithaca, New York.[ PDF]

ML Vis, SM Carr, WR Bowering, & WS Davidson. 1997.Greenland Halibut (Reinhardtius hippoglossoides) in the North Atlantic are genetically homogeneous Canadian Journal of Fisheries & Auatic Sciences 53, 1813-1821. [PDF]

SM Carr & EA Perry. 1997. Intra- and interfamilial systematic relationships of phocid seals as indicated by mitochondrial DNA sequences. Pp. 277-290 in A. E. Dizon et al. (eds). Molecular Genetics of Marine Mammals. Special Publication No.3 of the Society for Marine Mammalogy, Lawrence KS.

EA Perry, SM Carr, SE Bartlett, & WS Davidson. 1995. A phylogenetic perspective on the evolution of reproductive behavior in pagophilic seals of the Northwest Atlantic as indicated by mitochondrial DNA sequences. Journal of Mammalogy 76, 22-31. [ PDF]

SM Carr, SW Ballinger, JN Derr, LH Blankenship, & JW Bickham. 1986. Mitochondrial DNA analysis of hybridization between sympatric white-tailed deer and mule deer in west Texas. Proceedings of the National Academy of Science (USA) 83, 9576-9580 [PDF]

AC Wilson, RL Cann, SM Carr, M George, UB Gyllensten, KM Helm-Bychowski, RG Higuchi, SR Palumbi, EM Prager, RD Sage, & M Stoneking. 1985. Mitochondrial DNA and two perspectives on evolution. Biological Journal of the Linnean Society 26, 375-400 [PDF]






Carr
                lab group, July 2005
Carr Lab, July 2005

Left to Right: Dr. Steve Carr, Dr. Dawn  Marshall [Asst Prof of Biology], Corinne Wilkerson [M.Sc. candidate], Sarah Flynn [B.Sc. (hons.), 2006], Kim Johnstone [B.Sc. (hons), 2005], Stephanie Royston [M.Sc. 2007],  Samantha Cooper [WISE Summer Student]; not shown: Angela Pope [M.Sc., 2007], Ana Duggan [B.Sc. (hons.) 2008] {Front Row: Architeuthis dux, the Newfoundland Giant Squid}

Current & Recent Lab Members:

    Mr Charles Chilaka (MSc, 2012 - 2016): Computational Science for genomic data

    Ms LInda Lait
(PhD, 2011 - 2016): Mitogenomics of Atlantic Cod & Wolffish stocks
  
    Ms Ashley Collier
(
BSc (hons), 2010): Mitochondrial genome variation in First Nations peoples of Newfoundland
  
    Ms Corinne Wilkerson (MSc 2010). Genetic metapopulation structure of caribou in insular Newfoundland.
   
    Ms Amanda Marsh
(
BSc (hons), 2009): Genome evolution of Wolffish

    Ms Ana Duggan
(
BSc (hons), 2008; Research Assistant, 2007-08). Multi-species re-sequencing microarrays

    Ms Sarah Flynn (
BSc (hons), 2006). Inter-species hybridization on DNA microarrays.
   
    Mr Chacha Mwitaa
(
Visiting Scholar, 2005,University of Dar es Salaam). Molecular Systematics of African catfish species flocks in Lake Victoria.

    Ms Stephanie Royston (MSc, 2007 [with Dr. Ian Jones]). Population Structure of Ivory Gulls.


    Ms Kim Johnstone (BSc (hons), 2005; Research Assistant, 2005-06). Genomics of a Species-at-Risk, Atlantic Wolffish.

    Mr Mark Coulson (MSc June 2004). Genomic Systematics of codfish and pollocks.

    Ms Angela Pope (BSc (hons), 2003; MSc, 2007; Research Associate III, Jan 2011 -)
. Mitochondrial genomics of the founder population of Newfoundland.

    Dr JoAnne Flueck-Smith (2002; Visiting Scientist, University of Bariloche, Argentina). Conservation genetics on an endangered Neotropical deer species, the Huemul (Blastocerus).



Courses Taught:

         Bio2250 - Principles of Genetics
         Bio2900 - Principles of Evolution & Systematics
         Bio4241 - Advanced Genetics
         Bio4250 - Evolutionary Genomics
         Bio4270 - History of Biology
         Bio4900 - Fundamentals of Genetic Biotechnology
         Med6392 - Human Population Genetics

 

 All material © 2017 by Steven M. Carr