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We thank Y. Wang for constructing E. coli CAP and s70 plasmids,
J. Wang for advice on converting the cryo-EM map to a charge
density distribution map, and Y. Yang for his careful and critical
reading of the manuscript. We also thank the staff of the Center for
Structural Biology Facility at Yale University for computational
support. This work was supported by grant GM22778 to T.A.S.
from the NIH. T.A.S. is an investigator of the Howard Hughes
Medical Institute. B.L. performed protein-sample preparations and
complex assembly used in the structure determination, negative-
stain transmission EM analysis, all model building, refinement, and
structural analysis experiments. C.H. and Z. Y. designed the
cryo-EM experiment. C.H. performed cryo-EM grid preparation,
screening and optimization, high-throughput data collection,
image processing, and map generation with input from R.K.H. and
Z. Y. B.L. and T.A.S. designed the experiments. B.L. and T.A.S.
principally wrote the manuscript with input from all. The 3D
cryo-EM density map and the coordinates for the structure of the
class I CAP-TAC have been deposited in the Electron Microscopy
Data Bank and Protein Data Bank under the accession codes
EMD-7059, EMD-7060, and 6B6H, respectively. The authors
declare no competing financial interests.
Figs. S1 to S7
23 June 2017; resubmitted 20 August 2017
Accepted 2 October 2017
Natural selection shaped the rise and
fall of passenger pigeon
Gemma G. R. Murray,1 André E. R. Soares,1*† Ben J. Novak,1,2 Nathan K. Schaefer,3
James A. Cahill,1 Allan J. Baker,4‡ John R. Demboski,5 Andrew Doll,5
Rute R. Da Fonseca,6 Tara L. Fulton,1,7 M. Thomas P. Gilbert,6,8 Peter D. Heintzman,1,9
Brandon Letts,10 George McIntosh,11 Brendan L. O’Connell,3 Mark Peck,5
Marie-Lorraine Pipes,12 Edward S. Rice,3 Kathryn M. Santos,11 A. Gregory Sohrweide,13
Samuel H. Vohr,3 Russell B. Corbett-Detig,3,14 Richard E. Green,3,14 Beth Shapiro1,14§
The extinct passenger pigeon was once the most abundant bird in North America, and
possibly the world. Although theory predicts that large populations will be more genetically
diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this
disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons
and 2 genomes from band-tailed pigeons, which are passenger pigeons’ closest living
relatives. Passenger pigeons’ large population size appears to have allowed for faster
adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral
genetic diversity. These results demonstrate the effect that selection can have on a
vertebrate genome and contradict results that suggested that population instability
contributed to this species’s surprisingly rapid extinction.
The passenger pigeon (Ectopistes migratorius) numbered between 3 billion and 5 billion individuals before its 19th-century decline and eventual extinction (1). Passenger pi- geons were highly mobile and bred in large
social colonies, and their population lacked clear
geographic structure (2). Few vertebrates have
populations this large and cohesive, and the neutral
model of molecular evolution predicts that effec-
tive population size (Ne) and genetic diversity will
increase in proportion to population size (3). Prelim-
inary analyses of passenger pigeon genomes have,
however, revealed surprisingly low genetic diver-
sity (4). This finding has been interpreted within
the framework of the neutral theory of molec-
ular evolution as the result of a history of large
demographic fluctuations (4). However, in large
populations, natural selection may be particularly
important in shaping genetic diversity: Popula-
tion genetic theory predicts that selection will be
more effective in large populations (3), and se-
lection on one locus can cause a loss of diversity
at other loci, particularly those that are closely
linked (5–8). It has been suggested that this could
explain why the genetic diversity of a species is
poorly predicted by its population size (9–11).
We investigated the impact of natural selection
on passenger pigeon genomes through comparative genomic analyses of both passenger pigeons
and band-tailed pigeons (Patagioenas fasciata).
Although ecologically and physiologically similar
to passenger pigeons, band-tailed pigeons have a
present-day population size three orders of mag-
nitude smaller than that of their close relative,
the passenger pigeon (2, 12, 13).
We applied a Bayesian skyline model of ancestral population dynamics to the mitochondrial
genomes of 41 passenger pigeons from across
their former breeding range (Fig. 1A and table S1)
(14). This returned a most recent effective population size (Ne) of 13 million [95% highest posterior
density (HPD) interval: 2 million to 58 million] and
a similar, stable Ne for the previous 20,000 years
(Fig. 1B). Although this Ne is much lower than the
(census) population size (Nc), it is greater than previous estimates from analyses of nuclear genomes
(4) and is likely to be conservative (14).
We compared nucleotide diversity (p) in the
passenger pigeon nuclear genome to p in the band-tailed pigeon nuclear genome. We analyzed four
high-coverage passenger pigeon genome assemblies (two newly sequenced and two from published raw data; table S2) and two high-coverage
band-tailed pigeon genome assemblies. p was
1Department of Ecology and Evolutionary Biology, University
of California, Santa Cruz, CA 95064, USA. 2Revive & Restore,
Sausalito, CA 94965, USA. 3Department of Biomolecular
Engineering, University of California Santa Cruz, Santa Cruz,
CA 95064, USA. 4Department of Natural History, Royal
Ontario Museum, Toronto, ON M5S 2C6, Canada.
5Department of Zoology, Denver Museum of Nature and
Science, Denver, CO 80205, USA. 6Centre for GeoGenetics,
Natural History Museum of Denmark, University of
Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen,
Denmark. 7Environment and Climate Change Canada, 9250-
49th Street, Edmonton, AB T6B 1K5, Canada. 8NTNU
University Museum, 7491 Trondheim, Norway. 9Tromsø
University Museum, Ui T–The Arctic University of Norway,
9037 Tromsø, Norway. 10Department of Biology, The
Pennsylvania State University, University Park, PA 16802,
USA. 11Collections Department, Rochester Museum and
Science Center, Rochester, NY 14607, USA. 12Marie-Lorraine
Pipes, Zooarchaeologist Consultant, Victor, NY 14564, USA.
13A. Gregory Sohrweide D.D.S., Baldwinsville, NY 13027, USA.
14University of California Santa Cruz Genomics Institute, 1156
High Street, Santa Cruz, CA 95064, USA.
*These authors contributed equally to this work. †Present address:
Laboratório Nacional de Computação Científica, Petrópolis, RJ,
§Corresponding author. Email: firstname.lastname@example.org