Combining niche modeling & next-generation sequencing of DNA from museum specimens
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Transcript of Combining niche modeling & next-generation sequencing of DNA from museum specimens
Combining niche modeling & next-generation sequencing of DNA from
museum specimens
John McCormackDirector/Curator, Moore Laboratory of
ZoologyAssistant Professor, Biology Department
Occidental College
Misperception of natural history collections as antiquated and
Victorian
Goal of this talk: show how older museum collections can leverage
today’s technologyDr. Edwards pointed out last week how useful museum specimens are for exploring phylogeography and species limitsMy 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
We have incredible new technologies and data sources
Oxford Nanopore MinIon – 40 kB reads
DNA sequencing Remote-sensing satellites
Every vouchered specimen provides a unique opportunity to link phenotype, genotype, and the ecological niche in the pursuit of outstanding questions in evolutionary biology
Mission Statement
The Phenotype: observable characteristicsGenes +
Environment
http://www.nytimes.com/2013/02/05/science/pigeons-a-darwin-favorite-carry-new-clues-to-evolution.htmlhttp://learning.blogs.nytimes.com/2013/02/06/darwins-pigeons-learning-about-evolution-from-bird-traits/
Phenotypes have always been studied, but we are discovering
new ways to unlock the data3D CT scanning Multivariate
statistics
Phylophenomics?
The Genotype: DNA from museum specimens
Frozen tissue collection at the American Museum of Natural History
Fresh frozen tissue “Ancient” DNA
Moore Laboratory of Zoology
Traditional DNA sequencing with ancient DNA is laborious
time
Three times the work for the same fragment!
design internal primers
three PCRs, sequencing rxns
High quality genomic DNA
Somewhat degraded
DNA
Badly degraded
DNA
Repeat this for each locus (Scott showed
why we prefer to have many loci)
New methods and technologies are especially well-suited to
ancient DNASequence capture, target enrichment, in-solution hybridization
Species1 ACTGASpecies2 TGCATSpecies3 CCCTC
24 hours
All fragments can be pooled and sequenced on a next-generation
sequencing machine
12-15 million reads per lane
But what are these
mysterious probe
sequences?
The difference in “throughput” is perhaps over 1,000,000x
Traditional “Sanger”
sequencing
Sequence capture with next-generation sequencing
The Niche: Ecology from Space
Georeferencing
in real time by GPS
retrospectively w/ Google Earth, field
notes, etc.
Remote-sensingsatellites
Weather StationsTemperatur
eRainSeasonality
GreennessLeaf Area
IndexTree CoverCanopy
Height
The Niche: Ecology from Space
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
The Niche: Ecology from SpaceNASA and the Jet Propulsion Lab are releasing new
environmental data layers for every square kilometer of Earth all the time
Canopy Height
Testing for ecological differences among speciesExtract the
environmental data from all the occurrence points
(where it does live)
As well as from many random
points from the range of the species to
represent the suite of habitats that it could live
in Reduce the
variation to a couple axes and
visualize
Niche model
Localities (dots) + enviro. layers +
analysis (Maxent) =
model of where a species lives
species occurs
Where species could occur (but doesn’t
for whatever reason)
Arteaga et al. 2011 EvolutionMcCormack et al. 2010 Evolution
Testing for ecological differences among species
Visualizing species and their
backgrounds together
Are niches different just
because of where they live?
Or are they more similar/different than you might guess based on where they live?
McCormack et al. 2010 Evolution
Remember: the primary data are drawn from museum specimens (and other sources of georeference data)
Moore Laboratory of ZoologyFounded in 1950 by Robert T. Moore, private bird collectorOver 60,000 skins (highest bird to student ratio worldwide)
Most specimens pre-date knowledge about DNA = virtually no tissue collection
Largest Mexican bird collection in the world (larger than both big collection in Mexico City)
Extinct ImperialWoodpeckers
Is use of museum collections really declining?
MLZ georeference data first made available
Our research at the Moore Lab
Every vouchered specimen provides a unique opportunity to link phenotype, genotype, and the ecological niche in the pursuit of outstanding questions in evolutionary biology
Mission Statement
Mexico is topographically complex
What is the role of mountains in species diversification?
Describing the basic units of biodiversity
Our research focus
Madhvi VenkatramanUndergraduate
Unicolored JaysAphelocoma unicolor
Whitney TsaiLaboratory Technician
Wood-quailDendrortyx
Fiona GowenMaster’s Student
Western Scrub-JayAphelocoma californica
Field Work
CollectionsWork
Molecular Work
Why is it important to make a one-to-one link between phenotype and genetics?
Mexican Jay Aphelocoma wollweberi
Transvolcanic Jay Aphelocoma ultramarina
In mitochondrial DNA, the two species are divergent with no evidence for gene
flow
McCormack et al. Molecular Ecology 2008
Why is it important to make a one-to-one link between phenotype and genetics?
Mexican Jay Aphelocoma wollweberi
Transvolcanic Jay Aphelocoma ultramarina
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?
McCormack & Venkatraman submitted ms.
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.
Why is it important to make a one-to-one link between phenotype and genetics?
Mexican Jay Aphelocoma wollweberi
Transvolcanic Jay Aphelocoma ultramarina
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.
McCormack & Venkatraman submitted ms.
Why is it important to make a one-to-one link between phenotype and genetics?
Mexican Jay Aphelocoma wollweberi
Transvolcanic Jay Aphelocoma ultramarina
Also, the fact that Transvolcanic Jays were recognized as different
species was due to research linking
phenotypes and genotypes of museum specimens
McCormack et al. Molecular Ecology 2008
Genotype
Why is it important to make a one-to-one link between phenotype and genetics?
Mexican Jay Aphelocoma wollweberi
Transvolcanic Jay Aphelocoma ultramarina
Also, the fact that Transvolcanic Jays were recognized as different
species was due to research linking
phenotypes and genotypes of museum specimens
MJs
TJs
UJs
McCormack et al. Molecular Ecology 2008
Phenotype
Spearfishing vs. trawling for DNA
Traditional “Sanger”
sequencing
Sequence capture with next-generation sequencing
New methods and technologies are especially well-suited to
ancient DNASequence capture, target enrichment, in-solution hybridization
What are these mystery probes designed from?
Somewhat conserved so they work on a broad swath of speciesNot so conserved that there is no
variation to build phylogenies with
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
Brant FairclothUCLA
UCEs found in mammals… and birds
Found over 5,000 UCE regions shared between birds and lizards.
Faircloth et al. 2012 Syst Biol
And all amniotes!
Core UCE is conserved (anchor) & variation found in the flanks
Freq
uenc
y va
riant
bas
es
Distance from core UCE
Faircloth et al. 2012 Syst Biol
All fragments can be pooled and sequenced on a next-generation
sequencing machine
Illumina HiSeq or MiSeq
For very rapid divergences,
randomness in gene histories needs to be
accounted for(Edwards Lecture)
Applications of UCEsEvolutionary origin of turtles
Sunbittern + tropicbirds?
shorebird + hoatzin???
McCormack et al. 2013 PLoS OneBird phylogeny from 1,500 loci
UCE sequence capture of ancient DNA from museum skins
Would revolutionize older museum collections that pre-date knowledge about DNA
(like the Moore Lab)
Unicolored JaysAphelocoma unicolor
TissueIndiv1: 1147 UCE lociIndiv2: 1347
Recent Toe Pad - 1990
Indiv1: 273 Indiv2: 323 Indiv3: 199 Indiv4: 563
TissueIndiv1: 528 Indiv2: 612
Old Toe Pad - 1940as high as 151
SummaryExciting new technologies are available to mine genetic and ecological information from museum specimens
Sequence capture using conserved probe sets are promising for “ancient” DNA from study skins
Ecological data from satellites allow for construction and comparison of species niches
These advances promise to make older natural history collections increasingly relevant to modern research