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




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.








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.





Also, the fact that Transvolcanic Jays were recognized as different

species was due to research linking

phenotypes and genotypes of museum specimens


Genotype




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


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

Documents

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