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Combining niche modeling & next-generation sequencing of DNA from museum specimens

Combining niche modeling & next-generation sequencing of DNA from museum specimens. John McCormack Director/Curator, Moore Laboratory of Zoology Assistant Professor, Biology Department Occidental College . Misperception of natural history collections as antiquated and Victorian.

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Combining niche modeling & next-generation sequencing of DNA from museum specimens

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  1. Combining niche modeling & next-generation sequencing of DNA from museum specimens John McCormack Director/Curator, Moore Laboratory of Zoology Assistant Professor, Biology Department Occidental College

  2. Misperception of natural history collections as antiquated and Victorian

  3. Goal of this talk: show how older museum collections can leverage today’s technology Dr. Edwards pointed out last week how useful museum specimens are for exploring phylogeography and species limits My goal is to show how research specimens provide links to today’s technologies and data sources Which allow a holistic appraisal of an organism’s phenotype, genotype, and ecological niche

  4. We have incredible new technologies and data sources Remote-sensing satellites DNA sequencing Oxford NanoporeMinIon – 40 kB reads

  5. Mission Statement Every vouchered specimen provides a unique opportunity to link phenotype, genotype, and the ecological niche in the pursuit of outstanding questions in evolutionary biology

  6. The Phenotype: observable characteristics Genes + Environment http://www.nytimes.com/2013/02/05/science/pigeons-a-darwin-favorite-carry-new-clues-to-evolution.html http://learning.blogs.nytimes.com/2013/02/06/darwins-pigeons-learning-about-evolution-from-bird-traits/

  7. Phenotypes have always been studied, but we are discovering new ways to unlock the data 3D CT scanning Multivariate statistics

  8. Phylophenomics?

  9. The Genotype: DNA from museum specimens “Ancient” DNA Fresh frozen tissue Moore Laboratory of Zoology Frozen tissue collection at the American Museum of Natural History

  10. Traditional DNA sequencing with ancient DNA is laborious time High quality genomic DNA design internal primers three PCRs, sequencing rxns Somewhat degraded DNA Three times the work for the same fragment! Repeat this for each locus (Scott showed why we prefer to have many loci) Badly degraded DNA

  11. New methods and technologies are especially well-suited to ancient DNA Species1 ACTGA Species2 TGCAT Species3 CCCTC Sequence capture, target enrichment, in-solution hybridization 24 hours

  12. All fragments can be pooled and sequenced on a next-generation sequencing machine But what are these mysterious probe sequences? 12-15 million reads per lane

  13. The difference in “throughput” is perhaps over 1,000,000x Traditional “Sanger” sequencing Sequence capture with next-generation sequencing

  14. The Niche: Ecology from Space in real time by GPS retrospectively w/ Google Earth, field notes, etc. Georeferencing

  15. The Niche: Ecology from Space Remote-sensingsatellites Greenness Leaf Area Index Tree Cover Canopy Height Weather Stations Temperature Rain Seasonality Museum specimens allow us to tap into these data through the record of an individual of a species occurring at a certain place and time on Earth

  16. The Niche: Ecology from Space NASA and the Jet Propulsion Lab are releasing new environmental data layers for every square kilometer of Earth all the time Canopy Height

  17. Testing for ecological differences among species Extract the environmental data from all the occurrence points (where it does live) Niche model As well as from many random points from the range of the species to represent the suite of habitats that it could live in Localities (dots) + enviro. layers + analysis (Maxent) = model of where a species lives Reduce the variation to a couple axes and visualize

  18. Where species could occur (but doesn’t for whatever reason) species occurs McCormack et al. 2010 Evolution Arteaga et al. 2011 Evolution

  19. Testing for ecological differences among species Are niches different just because of where they live? Visualizing species and their backgrounds together Or are they more similar/different than you might guess based on where they live? Remember: the primary data are drawn from museum specimens (and other sources of georeference data) McCormack et al. 2010 Evolution

  20. Moore Laboratory of Zoology Founded in 1950 by Robert T. Moore, private bird collector Over 60,000 skins (highest bird to student ratio worldwide) Largest Mexican bird collection in the world (larger than both big collection in Mexico City) Most specimens pre-date knowledge about DNA = virtually no tissue collection Extinct Imperial Woodpeckers

  21. Is use of museum collections really declining? MLZ georeference data first made available

  22. Our research at the Moore Lab Mission Statement Every vouchered specimen provides a unique opportunity to link phenotype, genotype, and the ecological niche in the pursuit of outstanding questions in evolutionary biology

  23. Our research focus Mexico is topographically complex Describing the basic units of biodiversity What is the role of mountains in species diversification?

  24. MadhviVenkatraman Undergraduate Unicolored Jays Aphelocoma unicolor

  25. Whitney Tsai Laboratory Technician Wood-quail Dendrortyx

  26. Fiona Gowen Master’s Student Western Scrub-Jay Aphelocoma californica

  27. Field Work Molecular Work Collections Work

  28. Why is it important to make a one-to-one link between phenotype and genetics? In mitochondrial DNA, the two species are divergent with no evidence for gene flow Mexican Jay Aphelocoma wollweberi Transvolcanic Jay Aphelocoma ultramarina McCormack et al. Molecular Ecology 2008

  29. Why is it important to make a one-to-one link between phenotype and genetics? In nuclear DNA, a cline of Transvolcanic markers to the north suggested ancient gene flow Is ancient gene flow detectable in the appearance of the individuals carrying the markers? Mexican Jay Aphelocoma wollweberi Transvolcanic Jay Aphelocoma ultramarina McCormack & Venkatraman submitted ms.

  30. Why is it important to make a one-to-one link between phenotype and genetics? Mexican Jay Aphelocoma wollweberi Transvolcanic Jay Aphelocoma ultramarina McCormack & Venkatraman submitted ms.

  31. Why is it important to make a one-to-one link between phenotype and genetics? We could conclude that ancient gene flow had left no detectable trace in the mtDNA or appearance of Mexican Jays! But only because we could make the one-to-one link between genotype and phenotype. Mexican Jay Aphelocoma wollweberi Transvolcanic Jay Aphelocoma ultramarina McCormack & Venkatraman submitted ms.

  32. Why is it important to make a one-to-one link between phenotype and genetics? Also, the fact that Transvolcanic Jays were recognized as different species was due to research linking phenotypes and genotypes of museum specimens Genotype Mexican Jay Aphelocoma wollweberi Transvolcanic Jay Aphelocoma ultramarina McCormack et al. Molecular Ecology 2008

  33. Why is it important to make a one-to-one link between phenotype and genetics? Also, the fact that Transvolcanic Jays were recognized as different species was due to research linking phenotypes and genotypes of museum specimens Phenotype UJs Mexican Jay Aphelocoma wollweberi MJs TJs Transvolcanic Jay Aphelocoma ultramarina McCormack et al. Molecular Ecology 2008

  34. Spearfishing vs. trawling for DNA Traditional “Sanger” sequencing Sequence capture with next-generation sequencing

  35. New methods and technologies are especially well-suited to ancient DNA What are these mystery probes designed from? Sequence capture, target enrichment, in-solution hybridization Somewhat conserved so they work on a broad swath of species Not so conserved that there is no variation to build phylogenies with

  36. Ultraconserved elements (UCEs) as universal markers for sequence capture phylogenomics and ancient DNA UCEs = stretches of DNA that are remarkably conserved across highly divergent species

  37. UCEs found in mammals… and birds Brant Faircloth UCLA Found over 5,000 UCE regions shared between birds and lizards.

  38. And all amniotes! Faircloth et al. 2012 SystBiol

  39. Core UCE is conserved (anchor) & variation found in the flanks Faircloth et al. 2012 SystBiol Frequency variant bases Distance from core UCE

  40. All fragments can be pooled and sequenced on a next-generation sequencing machine IlluminaHiSeq or MiSeq

  41. For very rapid divergences, randomness in gene histories needs to be accounted for (Edwards Lecture)

  42. Applications of UCEs Evolutionary origin of turtles

  43. McCormack et al. 2013 PLoS One Bird phylogeny from 1,500 loci Sunbittern + tropicbirds? shorebird + hoatzin???

  44. UCE sequence capture of ancient DNA from museum skins Would revolutionize older museum collections that pre-date knowledge about DNA (like the Moore Lab)

  45. Tissue Indiv1: 1147 UCE loci Indiv2: 1347 Unicolored Jays Aphelocoma unicolor Tissue Indiv1: 528 Indiv2: 612 Recent Toe Pad - 1990 Indiv1: 273 Indiv2: 323 Indiv3: 199 Indiv4: 563 Old Toe Pad - 1940 as high as 151

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