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 current and recent investigations include:

(1) Mitochondrial population genomics of marine fishery species, including Atlantic Cod, Harp Seals, and Wolffish,
(2) Molecular systematics & morphological evolution of deer, with emphasis on Neotropical species (Cervidae),
(3) Biogeographic evolution of cods and pollacks (Gadidae),
(4) Behavioural evolution of true seals of the North Atlantic (Phocidae),
(5) Genomic diversity of the founding human population of Newfoundland,
(6) Phylogeography of Newfoundland "Species-at-Risk" of extinction, including Wolffish, Caribou, Ivory Gulls,
      and the occasional "sea monster".

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

    My laboratory has taken a genomic approach to the interrelated problems of evolution and population and systematic biology. The strategy uses a “long-range PCR” and leap-frog DNA sequencing strategy that permits amplification and sequencing of the entire mtDNA genome of related species as a series of ordered, contiguous fragments. Well-resolved, highly-corroborated molecular phylogenies 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.

    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. The method generates up to 20 complete mtDNA genome sequences in a single experiment.

Pope AM, 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, ATDuggan, SMC Flynn, KA Johnstone, AMPope, & 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]

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]

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. 2008],  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}

         Bio2250 - Principles of Genetics
         Bio2900 - Principles of Evolution & Systematics
         Bio4241 - Advanced Genetics
         Bio4900 - Fundamentals of Genetic Biotechnology
         Med6392 - Human Population Genetics