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 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.
My laboratory includes an ABI automated DNA sequencer, which facilitates rapid collection of data on population-sized samples. Commercial DNA identification and forensic services are offered through Terra Nova Genomics, Inc.,
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]
Bio2250
-
Principles of Genetics
Bio2900 -
Principles of
Evolution & Systematics
Bio4241 -
Advanced
Genetics
Bio4900
- Fundamentals of Genetic Biotechnology
Med6392 - Human
Population
Genetics