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Genomic Biotech for Environmental Monitoring: Phylogeography & connectivity among marine populations as inferred from complete mtDNA genome sequences Steven.

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Presentation on theme: "Genomic Biotech for Environmental Monitoring: Phylogeography & connectivity among marine populations as inferred from complete mtDNA genome sequences Steven."— Presentation transcript:

1 Genomic Biotech for Environmental Monitoring: Phylogeography & connectivity among marine populations as inferred from complete mtDNA genome sequences Steven M Carr Terra Nova Genomics, Inc. & Dept of Biology, Memorial University of Newfoundland St John's NL, Canada 2 nd International Conference on Oceanography Las Vegas NV, 21 July 2014

2 Two Genomes nucDNA genome 2,850,000,000 bp 20,500 genes mtDNA genome ~17,000 bp 38 genes

3 DNA Sequencing on a Microarray Complete mtDNA genome in one experiment [ SM Carr et al. 2008. Comp Biochem Physiol D 3:1-11 ]

4 Molecular Velcro: Multi-species ArkChip (Three fish, three mammals, one bird: 115,984 bp)

5 Information content of DNA microarrays: 7 species X 80 individuals / spp X 16.5 Kbp @ = 9.2 Mbp

6 Atlantic Cod (Gadus morhua) Newfoundland Caribou (Rangifer tarandus) Harp Seals (Pagophilus groenlandicus) Atlantic Wolffish (Anarhicas lupus)

7 Harp Seal pupping & breeding grounds Gulf Front Greenland Sea White Sea

8 Genomic Phylogeography of Pagophilus 16.5 Kbp @ from 83 Harp seals [ Carr, Duggan, Stenson, & Marshall 2014 PLoS ONE, in review ]

9 White Sea Greenland Sea Ice Front Gulf Front ‘99 Stronger geographic structures require fewer migration events; Compare observed tree versus 10,000 random trees Is the observed tree geographically structured?

10 Are populations geographically structured ? Isolation-by-Distance YES: Trans-Atlantic “Stepping-stone” model requires significantly fewer migration events than random expectation

11 Population expansion wrt Climate Change over 300 Ky Wisconsinan glaciation

12 Testing structure of populations within species Kolmogorov – Smirnov non-parametric test: Are cumulative genetic distance curves significantly offset? YES: Diversity among Greenland Sea Harp Seals is younger than among White Sea seals [  versus  ]

13 Spawning Stocks of Atlantic Cod Are they genetically distinguishable populations ?

14 Family Tree of Atlantic Cod: Northern Cod (2J3KL) vs Trans-Laurentian stocks (4WX5Ze) vs Flemish Cap (3M) vs Norwegian Coastal stocks [ Carr & Marshall 2008 Genetics 180,381 & in progress ] Bay Cod

15 Worst-Case Scenario: Oil Spill impacts Genome Ecosystem

16 Genetic Consequences of Environmental Disruption Loss of connectivity: disruption of gene flow & dispersal Local success & dispersal Gene Flow

17

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