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 have adopted novel genomic 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 (Anarhichas spp.),
(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.

    In cooperation with Newfound Genomics, a local biotechnology company, my lab is developing a new biotechnology, iterative DNA “re-sequencing” on microarrays, which uses a reference DNA sequence to determine homologous sequences in new individuals. The method generates complete mtDNA-genome-sized sequences in a single experiment. 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.

    My laboratory includes an Applied Biosystems automated DNA sequencer, which facilitate rapid collection of data on population-sized samples. This facility has provides a core DNA sequencing service on the MUN campus (“The Helix & Primer”), to facilitate the development of collaborative and contract research work on molecular genetics and genomics. Inquiries are invited at: http://www.mun.ca/biology/scarr/Helix_&_Primer.html   .


Representative Publications:

SM Carr, AT Duggan, and 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, and 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 and 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 and 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, and 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 and 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, and 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, and 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, and 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 and 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 and 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 and 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, and 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, and 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 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. 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}

Current & Recent Lab Members:

    Ms. Ashley Collier (2008 NSERC Summer Student; BSc hons candidate): Mitochondrial genome variation in First Nations peoples of Newfoundland
  
    Ms. Amanda Marsh
(2007-present: BSc hons candidate): Genome evolution of Wolffish

    Ms. Ana Duggan
(2006-present: B.Sc. (hons.) June 2008; Research Assistant I, 2007-2008). Multi-species re-sequencing microarrays

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


    Ms. Stephanie Royston (2004-2008; M.Sc., June 2008 [with Dr. Ian Jones]). Population Structure of Ivory Gulls.


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


    Ms. Corinne Wilkerson (2004-; M.Sc. student). Genetic metapopulation structure of caribou in insular Newfoundland.


    Ms. Angela Pope (B.Sc. (hons), June 2003; M.Sc., Oct 2007)
. 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).


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



Courses Taught:

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

        Information on The Helix & Primer, a DNA sequencing service at Memorial University of Newfoundland


 All material © 2009 by Steven M. Carr