From Archaeopteryx to avian genomics

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DNA Evolution From Archaeopteryx to Albatross
Scott V. Edwards
HHMI High School Teachers Outreach Program
Museum of Comparative Zoology Harvard
University http//www.oeb.harvard.edu/faculty/edwa
rds
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Charles Darwin (1809 - 1882)
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From Darwin to DNA
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Systematics -- revealing the sequence of ancestry
and descent

• Behavior
• Genomics
• Ecology

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A DNA journey through the evolution of birds

• Archaeopteryx and the dinosaur origins of birds
• Bioinformatics exposes turtles as an unsuspected
  cousin of birds
• Controversies on the time scale of avian
  evolution molecules versus fossils
• Songbirds origins from Gondwana
• Populations interactions of ecology, disease and
  exinction

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Archaeopteryx lithographica

• Discovered in Germany
• in 1865
• Only 7 specimens
• The first bird and
• the oldest feathers

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Feathered dinosaurs from China
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Origin of birds from therapod dinosaursfrom
Prum, R. (2003) Nature 421 323-4
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Libraries of specimens, frozen tissue and DNA -
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Two types of molecular tools forphylogenetic
studies
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Trees tell stories on many scales
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Reptile BAC Libraries to the rescue!
Tuatara
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Kangaroo
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Human
Platypus
Haploid genome size (picograms)
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Alligator
Turtle
Snake
Gila Monster
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Emu
Chicken
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1
0
Mammals
Reptiles
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BAC Libraries and Evolutionary Biologyof the
Reptilia
100 - 200 kb BAC inserts

• Systematics
• Large-scale approaches to the Tree of Life
• Discovery of genomic synapomorphies

BAC vector

• Evo-Devo
• Evolution of sex-determining mechanisms
• Evolution of limb and digit loss
• Evolutionary biology of aging
• Origin of feathers
• Neurobiology bird song
• Trangenesis

robotics
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• Evolutionary Genomics
• Evolution of multigene families (i.e., MHC)
• Genome and chromosome evolution
• Population genetics

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Array into 384-well microtiter plates and nylon
filters
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BAC-end sequencing

• A quick way to survey major features of a genome
• Requires little laboratory preparation once a
  genomic
• library is in place
• Automation is essential

100-200 kb insert
Arrayed BAC library
isolate sequence ends of several
thousand clones using primers in vector
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BAC clone
sequencing read
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Bioinformatics - tapping the genomes
evolutionary language
common DNA words
rare DNA words
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The turtle genome is surprisingly similar to birds
Alligator
Mb 1 million DNA base pairs
2.4Mb
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Turtle
99
2.3Mb
Chicken
88
5.8Mb
Mouse
23.7Mb (Chr7)
75
Human
32.7Mb (Chr22)
Xenopus
2.6Mb
Zebra Fish
14.9Mb
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Charles Sibleys TapestryA DNA hybridization
phylogeny of birds
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Molecular dates for the origin of major bird
groups predate the fossil evidence
From Hedges et al. Nature 381 226-229.
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Antarctic fossil duck places avian roots in
Cretaceous(Clarke et al. Nature (2005) 433
305-308)
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Three lineages of perching birds
oscines (true songbirds)
suboscines
Tyrrani
Corvida
Passerida
1,000
1,000 species
3,000
New World, Eurasia, Holarctic
Australia New Guinea
New Old World Tropics
double fossa of humerus
complex syrinx/ learning capacity
distinctive fore- and hind limb musculature
simple yet functionally diverse foot
distinctive bony palate
sperm morphology
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Gondwanan songbirds at the base of the tree(from
Barker et al. 2001. Proc. R. Soc. Lond., v. 269
295)
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Gondwanan spread of perching birds across the
globe
from Ericson, P. G, et al. (2002). "A Gondwanan
origin of passerine birds supported by DNA
sequences of the endemic New Zealand wrens."
Proceedings of the Royal Society of London
series B 269(1488) 235-41.
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Phylogeny of New World Jays suggests an ancient
origin of cooperative breeding
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Across the Australian outback
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Life in the Outback
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Australia expeditions, 1987 - 2005
1987
1990
1996
1997
2002a
2002b
2005
0
1000
km
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Biogeography of western babblers
Photo by Graeme Chapman
Ancestral migration event
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Combining information from many genes
Brown Treecreeper (eastern) lineages
Black-tailed (western) Treecreeper lineages
Pilbara (far west)
Cape York (far north)
Gene 14
Gene 16
Gene 3
Gene 5
Gene 7





Gene 18
Gene 19
Gene 20
Gene 21
Gene 22






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Treecreeper populations are connected
butvariable in size
Weipa
Douglas Hot Springs
Fitzroy Crossing
Forsayth
Doomadgee
Black-tailed Treecreepers
Longreach
Brown Treecreepers
Newman
Bourke
Sedan
Rotzel, Edwards and Beerli, unpubl. data
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Northern finches diverged recently, within the
Pleistocene
Long-tailed Finch
Black-throated Finch
600,000 years ago
700,000 years ago
maps from Schodde and Mason 1999. The Directory
of Australian Birds Passerines
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Mycoplasma-House Finch History
Courtesy Cornell Lab of Ornithology
-Mycoplasma gallisepticum escaped chickens and
invaded House Finches in the eastern U. S.,
1994 -8 years later, finches are more resistant
to the bacterium and recent strains are
attenuated -Have finches evolved resistance?
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Mycoplasma are obligate parasites and have some
of the smallest genomes of any non-virus
sequenced
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Clone arrays as genomic resources for diverse
species
Collections of plasmid, fosmid or BAC clones
Array into 384 well plates
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Print onto nylon membranes for screening
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Macroarray analysis of expressed sequences in
House Finches
infected bird as tester
infected bird as driver
subtracted cDNA probes
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Identical arrays
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upregulated genes
downregulated genes
cDNAs arrayed and hybridized with subtracted
probe
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Macroarray results
distinct hybridizations - differentially
expressed genes
common hybridizations -- noise
C
A

• identical filters
• (A B, C D)
• Reciprocally
• subtracted probes
• (A vs. B, C vs. D)

D
B
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Sequencing suggests change inexpression for heat
shock and immune system genes
Number of sequenced clones
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Preliminary network of genes induced by infection
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The extinct Ivory-billed Woodpecker?
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Worlds largest collection of Ivory-billed
Woodpeckers at Harvard
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A DNA barcode for the Ivory-billed Woodpecker
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Using genetics to determine the geographic origin
of albatrosses caught in fisheries longline nets
Black-footed albatross
Laysan albatross
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Longline fisheries nets catch more than fish
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Active and extinct colonies of Black-footed
Albatrosses
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Locations and genotypes of samples of bycatch
black-footed albatross taken at sea
Walsh, H. E., and S. V. Edwards. 2005.
Conservation Genetics 6289-295.
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Mitochondrial DNA confirms a predominantly
Hawaiian origin of bycatch black-footed
albatrosses
Japan
Hawaii and bycatch
98 of bycatch albatrosses can be assigned to
breeding colonies in Hawaii