Carr Lab, Memorial University of Newfoundland
Carr Lab, Memorial University of NewfoundlandResearch 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 .
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]
Bio2250 -
Principles of Genetics
Bio2900 - Principles of
Evolution & Systematics
Bio4241 - Advanced
Genetics
Bio4900
- Fundamentals of Genetic Biotechnology
Med6392 - Human Population
Genetics