Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

Abstract

Hybrid camouflage variation
Snowshoe hares molt from a brown coat to a white coat in winter. In some populations, however, where winter snow is less extensive, hares molt from a brown coat to a brown coat. Jones et al. show that regulation of the pigmentation gene Agouti is responsible for the winter coat color change. Hybridization with jackrabbits has led to introgression around this gene that facilitates the brown winter morph. Hybridization appears to have provided important adaptive variation to the snowshoe hare.
Science , this issue p. 1355

Full text

EVOLUTIONARY BIOLOGY
Adaptive introgression underlies
polymorphic seasonal camouflage
in snowshoe hares
Matthew R. Jones
1
*, L. Scott Mills
2,3,4
, Paulo Célio Alves
2,5,6
, Colin M. Callahan
1
,
Joel M. Alves
5,7
, Diana J. R. Lafferty
2,4,8
, Francis M. Jiggins
7
, Jeffrey D. Jensen
9,10
,
José Melo-Ferreira
5,6
*, Jeffrey M. Good
1,2
*
Snowshoe hares (Lepus americanus) maintain seasonal camouflage by molting to a white
winter coat,but some hares remain brown during thewinter in regions with low snow cover. We
show that cis-regulatory variation controlling seasonal expression of the Agoutige ne underlies
this adaptive winter camouflage polymorphism. Genetic variation at Agouti clustered by
winter coat color across multiple hare and jackrabbit species, revealing a history of recurrent
interspecific gene flow. Brown winter coats in snowshoe hares likely originated from an
introgressed black-tailed jackrabbit allele that has swept to high frequency in mild winter
environments. These discoveries show that introgression of genetic variants that underlie key
ecological traits can seed past and ongoing adaptation to rapidly changing environments.
Many species undergo reversible changes
in morphology, physiology, and behavior
to cope with the challenges of seasonal
environments. These critical components
of phenotypic plasticity often track the
environment through the photoperiod-dependent
release of hormones (1). However, circannual
rhythms can become desynchronized when abi-
otic conditions change rapidly (2), leading to de-
clines in population fitness (3). The capacity of
species to adapt to rapidly changing environ-
ments will depend in part on the proximate and
ultimate causes of variation underlying seasonal
traits (4,5), which remain poorly understood at
the molecular level (1,2).
At least 21 bird and mammal species undergo
autumn molts from brown to white coats (6–8)
as part of a suite of plastic trait responses to sea-
sonal environments. We used natural variation
in seasonal camouflage of the snowshoe hare
(Lepus americanus)tounderstandthegenetic
basisofthiscriticalseasonaltrait.Autumnmolts
to white winter coats are cued by photoperiod (8)
and generally track seasonal snow cover (7).
Direct estima tes of hare survival have shown
that mismatch between coat color and snow
cover increases predation (3). White winter coats
predominate across the snowshoe hare range,
but some populations molt into brown winter
coats (Fig. 1). In the Pacific Northwest (PNW),
shifts in the probability of white coats coincide
with a gradient in snow cover from warmer
coastal to colder inland environments, consistent
with local selection for seasonal camouflage, with
color morphs co-occurring across a broad poly-
morphic zone (Fig. 1C) (7).
To dissect the genetic basis of polymorphic
seasonal camouflage, we used whole-genome se-
quencesforawinter-whiteharefromMontana
(MT, 33x coverage) (9,10) and a winter-brown
hare from Washington (WA, 22x coverage) and
constructed a reference through iterative map-
ping (11) to the rabbit genome (9,12). We then
sequenced 80 whole exomes (62 Mb, 21 ± 7.6x
coverage per individual) from two regions in the
PNW polymorphic zone (WA, n=26;Oregon,
hereafter OR, n= 26; each region 50% winter-
white), a monomorphic winter-white locality in
MT (n= 14), and a monomorphic winter-brown
locality in British Columbia (BC, n=14;tableS1).
If the polymorphic zone represents admixture
between previously isolated populations, then ge-
netic structure could obscure genotype-phenotype
associations (13). Analysis of 38,694 unlinked
single-nucleotide polymorphisms (SNPs) revealed
geographic structure (Fig. 1C), but genome-wide
genetic differentiation (fixation index, F
ST
) be-
tween winter-brown and winter-white individuals
was ~0 within polymorphic localities (table S2).
The polymorphic zone also showed no evidence of
admixture on the basis of linkage disequilibrium
patterns (fig. S1) or allele sharing with other
populations (table S3) (14). Thus, geographic var-
iation for winter coat color in the PNW likely
reflects primary intergradation across a gradient
in snow cover.
We tested 513,812 SNPs for coat color asso-
ciations across polymorphic populations and
identified a single outlier region on chromosome 4
in perfect association with winter coat color
(P=4.24×10
−10
, dominant association test;
Fig. 2A, fig. S2, and data S1) (12). We then aug-
mented exome data with low-coverage whole-
genome resequencing of polymorphic zone hares
(~20x per color morph). Coat color associations
based on genotype likelihoods (15,173,804 SNPs)
(15) confirmed a single outlier region (fig. S3)
localized to a ~225-kb interval of elevated F
ST
between color morphs. This interval was centered
on the pigmentation gene Agouti and two flank-
ing genes, Ahcy and Eif2s2, neither of which
are known to be directly involved in coat color
(Fig.2B).Winter-brownhareswerehomozygous
(n= 26) for brown-associated alleles (hereafter a),
whereas winter-white hares were either heter-
ozygous (n= 24) or homozygous (n= 2) for the
alternative allele (hereafter A;Fig.2C).Wethen
induced autu mn molts in 18 captive wild-caught
hares (WA, n= 11; MT, n= 7) and found perfect
concordance between Agouti genotypes and winter
coat colors (Fig. 2C and table S4). This experiment
included a heterozygous (Aa) wild-caught winter-
whitefemalefromWAthatgavebirthincaptivity
to both winter-white and winter-brown offspring
(Fig.2D).Therefore,wintercoatcolorsegregatesas
a dominant locus in both wild and captive animals.
The agouti signaling protein (ASIP) antagonizes
the melanocortin-1 receptor (MC1R) in follicular
melanocytes, shifting melanogenesis toward
lighter pheomelanin pigments or inhibiting pig-
ment production (16). MC1R mutations suppress
expression of winter-white coats in dark or blue
color morphs of arctic foxes, suggesting that
ASIP-MC1R interactions are involved in the de-
velopment of seasonal color molts (17). Agouti is
typically expressed as ventral- or hair cycle–specific
isoformsdistinguished by alternative 5′untrans-
lated regions (5′UTRs; Fig. 2B) (18). Both isoforms
have been associated with lighter dorsal pelage
(19,20). We hypothesized that the development
of winter-white coats, which mostly lack pigments
(8), is controlled by isoform-specific up-regulation
of Agouti during the autumn molt. To test this, we
quantified allele-specific expression of both iso-
forms and the tightly linked Ahcy locus in dorsal
skin biopsies from three captive heterozygous
hares (Aa) undergoing brown-to-white molts.
Quantitative polymerase chain reaction (qPCR)
verified expression of Ahcy and the Agouti hair-
cycle isoform, whereas expression of the ventral
isoform was negligible (Fig. 3A and tables S5 and
S6). Targeted pyrosequencing revealed highly
skewed expression toward the white (A) allele of
the Agouti hair-cycle isoform (P< 0.0001, Student’s
ttest), indicative of cis-regulatory variation, whereas
Ahcy showed equal allelic expression (Fig. 3B and
table S7). These data suggest that winter-white
coats develop because of increased expression
of Agouti during the autumn molt, which fits
with our observed dominance relationships and
previous studies on the evolution of lighter pelage
in deer mice (19,20). Our findings directly link
Agouti expression and the evolution of seasonal
RESEARCH
Jones et al., Science 360, 1355–1358 (2018) 22 June 2018 1of4
1
Division of Biological Sciences, University of Montana,
Missoula, MT 59812, USA.
2
Wildlife Biology Program,
University of Montana, Missoula, MT 59812, USA.
3
Office of
Research and Creative Scholarship, University of Montana,
Missoula, MT 59812, USA.
4
Fisheries, Wildlife, and
Conservation Biology Program, Department of Forestry and
Environmental Resources, North Carolina State University,
Raleigh, NC 27695, USA.
5
CIBIO, Centro de Investigação em
Biodiversidade e Recursos Genéticos, InBIO Laboratório
Associado, Universidade do Porto, 4485-661 Vairão,
Portugal.
6
Departamento de Biologia, Faculdade de Ciências
da Universidade do Porto, 4169-007 Porto, Portugal.
7
Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, UK.
8
Department of Biology, Northern
Michigan University, Marquette, MI 49855, USA.
9
School of
Life Sciences, Ecole Polytechnique Fédérale de Lausanne,
1015 Lausanne, Switzerland.
10
School of Life Sciences,
Arizona State University, Tempe, AZ 85281, USA.
*Corresponding author. Email: matthew2.jones@umontana.edu
(M.R.J.); jmeloferreira@cibio.up.pt (J.M.-F.); jeffrey.good@
umontana.edu (J.M.G.)
on June 21, 2018 http://science.sciencemag.org/Downloaded from

camouflage in snowshoe hares and suggest that
cis-regulatory evolution plays an important role
in the origin of seasonal traits.
Comparison of winter-white (MT) and winter-
brown (WA) genomes revealed notably elevated
levels of absolute genetic divergence across Agouti
(Agouti d
XY
= 1.6%; genome-wide d
XY
= 0.41%;
P< 0.0001, randomization test; Fig. 4A and fig.
S4), indicating that the color polymorphism did
not arise from a recent de novo mutation. Alter-
natively, elevated divergence could reflect either
the long-term maintenance of polymorphism
or introgression from another species (21,22).
Six of the 32 species of hares and jackrabbits
(genus Lepus) have winter-white molts, but evo-
lutionary relationships within this rapid radia-
tion are poorly resolved (23). To examine the
origins of winter coat color variants, w e combined
whole-genome sequences of two additional winter-
white snowshoe hares from Pennsylvania and
Utah, two winter-brown black-tailed jackrabbits
(L. californicus) from Nevada, and a previously
sequenced winter-white mountain hare (L. timidus)
from Europe (10). Phylogenetic analyses (24)pre-
dicted a very rare topology at Agouti that clus-
tered individuals by winter coat color (Fig. 4B
and fig. S5). Pairwise divergence between all
winter-brown and winter-white individuals
was significantly elevated across a known cis-
regulatory region of Agouti (25,26)~40-kb
upstream of the transcription start site of the
hair-cycle isoform (P< 0.001, randomization test;
Fig. 4A and fig. S4). Divergence peaked across a
~20-kb interval (d
XY
=2.2to2.4%)thatincluded
a 1033-base insertion on the winter-white haplo-
type and a ~4.3-kb deletion on the winter-brown
haplotype (fig. S4). Additional functional data are
needed to determine if either of these candidate
mutations underlie the observed cis-regulatory
differences in Agouti expression (Fig. 3B).
The elevated interspecific divergence between
color groups suggests that the winter-white and
winter-brown Agouti alleles may have arisen
relatively early in Lepus (21). By contrast, diver-
gence within color groups was strongly reduced
across a larger interval encompassing Agouti
(Fig. 4A and fig. S6), indicating that winter coat
color alleles may have been shared through hy-
bridization. In support of this hypothesis, we
found low, but significant, levels of genome-
wide introgression (27) between snowshoe hares
andbothblack-tailedjackrabbitsandmountain
hares(tableS8).Window-basedanalysesofab-
solute divergence and derived-allele sharing (28)
identified the Agouti interval among the strong es t
genome-wide signatures of introgression in both
winter-brown and winter-white clusters (fig. S7).
Previous studies demonstrated mitochondrial
DNA introgression from black-tailed jackrabbits,
a western North American prairie-scrub species,
into PNW snowshoe hares and speculated that
hybridization may have contributed to the evo-
lution of brown winter coats in snowshoe hares
(29,30). Consistent with this, winter-brown snow-
shoe hares unambiguously nested within black-
tailed jackrabbit variation at Agouti (Fig. 4B
and fig. S5B), resulting in a 174-kb interval of
Jones et al., Science 360, 1355–1358 (2018) 22 June 2018 2of4
Fig. 1. Winter coat color polymorphism and population structure in snowshoe hares. (A)Alternative
winter color morphs in snowshoe hares. [Photo credit: L. Scott Mills research photo] (B) The modeled
range-wide probability of winter-white coats, adapted from (7). (C) Magnification of region outlined in (B)
shows principle components (PC1, 7.42%, and PC2, 5.27%; coat color represented as brown and white
circles) and population ancestry plots of 38,694 unlinked SNPs derived from 80 exomes sampled from five
localities (colored diamonds) overlaid on the probability of winter-white coats in the PNW.
Fig. 2. The genetic basis of winter coat color polymorphism. (A)ExomeSNPassociations
(–log
10
of Pvalues, assuming dominant minor allele; 513,812 SNPs) for polymorphic zone individuals. Red
points above the dashed line exceed the Bonferroni-corrected threshold of P=0.05.(B) Gene structures
of Itch,Ahcy,Agouti,Eif2s2,andRaly across the associated interval on chromosome 4 (chr 4) and alternative
Agouti transcription start sites (arrows) corresponding to hair-cycle (HC) and ventral (V) 5′UTRs. Sliding
window averages of F
ST
(5 kb with 2.5-kb step) between winter-white and winter-brown individuals with
low-coverage whole genomes (15,173,804 SNPs). (C) Dominance of winter coat color inferred from Agouti
genotypesofwild(ORandWA;Hardy-Weinbergc
2
=1.6,P= 0.21) and captive (WA and MT) hares.
(D) Pedigree and genotypes of a mixed-phenotype family (paternal genotype is unknown but inferred to carry
the aallele). [Photo credit: Diana J. R. Lafferty and Matthew R. Jones]
RESEARCH |REPORT
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significantly reduced divergence between spe-
cies (d
XY
= 0.42 versus 1.2% genome-wide; P<
0.001, randomization test) embedded within a
236-kb interval of significant admixture (pro-
portion of introgression,
^
fhom = 0.71; Fig. 4A).
Strong selection at a locus in the ancestral pop-
ulation can reduce divergence between species
(31), resulting in false inferences of introgres-
sion (28); however, coalescent simulations of
shared polymorphism with and without selec-
tion in the ancestral population indicate that
such shallow divergence is highly unlikely in the
absence of interspecific gene flow (Fig. 4C and
fig. S8). We also detected introgression within
the winter-white Agouti group (figs. S7 and S8).
Resolving the origin and functional relevance of
the winter-white signaturesawaitsfurtherinves-
tigation, given that three other North American
Lepus species undergo some degree of seasonal
coat color change (7).
To link introgression with local adaptation, we
tested for selective sweeps on the basis of allele
frequency skews (32) while controlling for demo-
graphic history (fig. S9 and table S9). We detected
a hard sweep overlapping Agouti in winter-brown
individuals from the polymorphic zone but no
evidence for a sweep in winter-white individuals
(figs. S10 and S11). We estimate that the sweep
of the winter-brown allele in the PNW occurred
3000 to 15,000 years ago, after the retreat of
the Cordilleran ice sheet (33). High inferred se-
lection coefficients (s)ontheintrogressedwinter-
brown Agouti background (s

WA
= 0.024, s

OR
=
0.015; fig. S11C) and fixation of alternative Agouti
alleles between monomorphic winter-brown (BC)
and winter-white (MT) localities (Fig. 4D), despite
high gene flow (table S9), indicate that seasonal
camouflage is maintained under strong local
selection.
Despite widespread evidence of hybridization
between animal species, introgression has rarely
been directly linked to ecological adaptation
(34–36). We have shown that introgression has
shaped locally adaptive seasonal camouflage in
snowshoe hares. Recurrent introgression of coat
color variants could facilitate evolutionary re-
sponses to environmental change within popula-
tions as well as the long-term maintenance of
adaptive variation among species, similar to adapt-
ive polymorphisms of beak morphology across
the radiation of Darwin’s finches (22,34). The
evolution of winter-brown coats in snowshoe
hares may have enabled their persistence in en-
vironments with more ephemeral seasonal snow
after the end of the last glacial maximum. Tem-
perate snow-cover duration is predicted to drama-
tically decrease over the next century under most
models of climate change (37), which may further
intensify directional selection for winter-brown
camouflage (3,6). Thus, the establishment of
this dynamic color polymorphism through in-
trogression is likely to be a critical component of
ongoing adaptation to rapidly changing seasonal
environments (7) in this iconic ecological model.
REFERENCES AND NOTES
1. M. E. Visser, S. P. Caro, K. van Oers, S. V. Schaper, B. Helm,
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 365,3113–3127 (2010).
2. B. Helm et al., Proc. Biol. Sci. 280, 20130016 (2013).
3. M. Zimova, L. S. Mills, J. J. Nowak, Ecol. Lett. 19, 299–307
(2016).
4. W. E. Bradshaw, C. M. Holzapfel, Mol. Ecol. 17, 157–166 (2008).
5. A. A. Hoffmann, C. M. Sgrò, Nature 470, 479–485 (2011).
6. L. S. Mills et al., Proc. Natl. Acad. Sci. U.S.A. 110, 7360–7365
(2013).
7. L. S. Mills et al., Science 359, 1033–1036 (2018).
8. M. Zimova et al., Biol. Rev. Camb. Philos. Soc. 10.1111/brv.12405
(2018).
9. M. Carneiro et al., Science 345, 1074–1079 (2014).
Jones et al., Science 360, 1355–1358 (2018) 22 June 2018 3of4
*
Relative expression level
(2
-ΔC
T
)
Proportion of white allele
Agouti
HC isoform
Agouti
(gDNA)
AhcyAgouti
HC isoform
Agouti
V isoform
AB
0.004
0.0
equal ratio
1.0
0.0
0.5
Fig. 3. Agouti expression in snowshoe hares during autumn molts. (A) The relative expression level (2DCT,
where DC
T
isthedifferenceintheqPCRcyclethresholdrelativetoGapdh, a constitutively expressed control
gene)ofhair-cycle(HC)andventral(V)Agouti isoforms in molting skin of winter-white (Aa) snowshoe
hares. (B) Relative abundance of the winter-white allele in the same skin samples for Agouti hair-cycle
transcripts, Ahcy transcripts, and Agouti genomic DNA (gDNA). The aster isk indicates that white-allele
proportions were significantly increased in Agouti transcripts compared to Ahcy transcripts and Agouti
genomic DNA (P< 0.00001, Student’sttest). Pairs of points represent technical replicates.
tree topologies
Scaled absolute divergence
A
C
BGenome-wide tree Local Agouti tree
WA
MT
PA
UT
PA
UT
MT
winter-brown
winter-white
7 Mb
0.6
0
0.6
0
0.6
0
0.6
0.6
0.02
0
0
0
4
Agouti
winter-white
snowshoe hare
winter-brown
snowshoe hare
black-tailed
jackrabbit mountain hare European rabbit
dXY
00.02
Observed Agouti
Predicted (selection)
Observed genome-wide
MT
MT
MT
Density
0
600
0.00.005 0.015
0.01 1.0
0.2 0.4 0.6 0.8
0
10
D
FST
Density
Observed genome-wide
Observed non-synonymous
Observed Agouti
fhom
^
0
1
5.3 5.8 Mb
dXY
MT=Montana
PA=Pennsylvania
UT=Utah
WA=Washington
Fig. 4. The evolution of winter coat color alleles in hares and jackrabbits. (A) Estimated tree
topologies across the Agouti region [top, see (B)]. Pairwise comparisons of mutation-scaled absolute genetic
divergence in 20-kb sliding windows (dashed line indicates location of candidate insertion-deletion
mutations). Gray rectangles represent 99.8% bootstrap quantiles, and red points are windows with
one-tailed P< 0.001 based on randomization tests. Bottom plot shows a finer scale of absolute divergence in
black (d
XY
, red points with one-tailed P< 0.001) and the fraction of introgression in blue (
^
fhom, dark blue points
with zscore > 4) between black-tailed jackrabbits and the WA winter-brown snowshoe hare. (B)Themost
common genome-wide topology (white) and the local Agouti topology (hatched; rabbit outgroup). Brown-
and gray-shaded regions indicate winter-brown and winter-white groups, respectively. (C) Distributions
of d
XY
between the winter-brown snowshoe hare and black-tailed jackrabbits genome-wide (gray), at Agouti
(green), and under simulations of strong ancestral selection (blue). (D) Distributions of SNP F
ST
values
between BC (monomorphic winter-brown) and MT (monomorphic winter-white) hares genome-wide (gray)
and for nonsynonymous SNPs (yellow).The green star indicates F
ST
= 1 at a diagnostic Agouti SNP.
RESEARCH |REPORT
on June 21, 2018 http://science.sciencemag.org/Downloaded from

10. F. A. Seixas, thesis, University of Porto, Porto, Portugal, and
University of Montpellier, Montpellier, France (2017).
11. B . A. J. Sarve r et al., Genome Biol. Evol. 9,726–739
(2017).
12. Materials and methods are available as supplementary
materials.
13. J. K. Pritchard, M. Stephens, N. A. Rosenberg, P. Donnelly,
Am. J. Hum. Genet. 67, 170–181 (2000).
14. D. Reich et al., Nature 488, 370–374 (2012).
15. T. S. Korneliussen, A. Albrechtsen, R. Nielsen, BMC
Bioinformatics 15, 356 (2014).
16. E. Le Pape et al., Proc. Natl. Acad. Sci. U.S.A. 106, 1802–1807
(2009).
17. D. I. Våge et al., Peptides 26, 1814–1817 (2005).
18. H. Vrieling, D. M. Duhl, S. E. Millar, K. A. Miller, G. S. Barsh,
Proc. Natl. Acad. Sci. U.S.A. 91, 5667–5671 (1994).
19. C. R. Linnen, E. P. Kingsley, J. D. Jensen, H. E. Hoekstra,
Science 325, 1095–1098 (2009).
20. M. Manceau, V. S. Domingues, R. Mallarino, H. E. Hoekstra,
Science 331, 1062–1065 (2011).
21. R. F. Guerrero, M. W. Hahn, Mol. Ecol. 26,5362–5368
(2017).
22. F. Han et al., Genome Res. 27, 1004–1015 (2017).
23. J. Melo-Ferreira et al., Syst. Biol. 61, 367–381 (2012).
24. N. Zamani et al., BMC Genomics 14, 347 (2013).
25. D. M. J. Duhl, H. Vrieling, K. A. Miller, G. L. Wolff, G. S. Barsh,
Nat. Genet. 8,59–65 (1994).
26. C. R. Linnen et al., Science 339, 1312–1316 (2013).
27. E. Y. Durand, N. Patterson, D. Reich, M. Slatkin, Mol. Biol. Evol.
28, 2239–2252 (2011).
28. S. H. Martin, J. W. Davey, C. D. Jiggins, Mol. Biol. Evol. 32,
244–257 (2015).
29. E. Cheng, K. E. Hodges, J. Melo-Ferreira, P. C. Alves, L. S. Mills,
Mol. Ecol. 23, 2929–2942 (2014).
30. J. Melo-Ferreira, F. A. Seixas, E. Cheng, L. S. Mills, P. C. Alves,
Mol. Ecol. 23, 4617–4630 (2014).
31. T. E. Cruickshank , M. W. Hahn, Mol. Ecol. 23, 3133–3157
(2014).
32. P. Pavlidis, D. Živkovic, A. Stamatakis, N. Alachiotis, Mol. Biol.
Evol. 30, 2224–2234 (2013).
33. J. J. Clague, T. S. James, Quat. Sci. Rev. 21,71–87 (2002).
34. S. Lamichhaney et al., Science 352, 470–474 (2016).
35. Y. Song et al., Curr. Biol. 21, 1296–1301 (2011).
36. C. Pardo-Diaz et al., PLOS Genet. 8, e1002752 (2012).
37. G. T. Pederson et al., Science 333, 332–335 (2011).
ACKNOW LEDGMENTS
We thank E. Cheng, K. Garrison, and P. Zevit for assistance with
sample collection. We thank R. Bracewell, T. Brekke, M. Carneiro,
Z. Clare-Salzler, M. Dean, E. Kopania, M. S. Ferreira, N. Herrera,
E. Larson, M. Nachman, B. Payseur, B. Sarver, and members of
the NSF EPSCoR UNVEIL network for helpful discussion.
R. Bracewell, B. Cole, T. Cosart, L. Farelo, E. Larson, S. Laurent,
T. Max, S. Pfeifer, B. Sarver, and K. Zarn provided computational or
laboratory support. A. Kumar assisted with the preparation of
Fig. 1. Sequencing was performed at the University of Montana
Genomics Core (supported by a grant from the M. J. Murdock
Charitable Trust), the CIBIO-InBIO University of Porto New-Gen
sequencing platform, the University of Oregon Genomics and Cell
Characterization Core Facility, the HudsonAlpha Institute for
Biotechnology, and Novogene Technology Co., Ltd. Computational
resources were provided by the University of Montana Genomics
Core and the Vital-IT Center for high-performance computing of
the SIB Swiss Institute of Bioinformatics. Funding: This work
was funded by a National Science Foundation (NSF) Graduate
Research Fellowship (DGE-1313190), a NSF Doctoral Dissertation
Improvement Grant (DEB-1702043), NSF Graduate Research
Opportunities Worldwide, Portuguese Fundação para a Ciência e a
Tecnologia (FCT) project grant “CHANGE”(PTDC/BIA-EVF/1624/
2014, supported by National Funds), NSF EPSCoR (OIA-1736249),
NSF (DEB-1743871), a FCT Investigator Grant (IF/00033/2014,
supported by POPH-QREN funds from ESF and Portuguese
MCTES/FCT), FLAD (Luso-American Development Foundation;
PORTUGAL–U.S. Research Networks Program), the Drollinger-Dial
Foundation, an American Society of Mammalogists Grant-in-Aid
of Research, a Swiss Government Excellence Scholarship, and
European Union’s Seventh Framework Programme (CIBIO
New-Gen sequencing platform; grant agreement 286431).
Author contributions: M.R.J., L.S.M., P.C.A., J.D.J., J.M.-F., and
J.M.G. designed the study. J.M.G. coordinated the study. M.R.J.,
C.M.C., J.M.A., and D.J.R.L. generated data. J.M.A. and F.M.J.
helped develop the exome capture experiments. M.R.J. performed
data analyses under the guidance of J.M.G., J.M.-F., and J.D.J.
M.R.J. and J.M.G. wrote the paper with input from the other
authors. All authors approved the manuscript before submission.
Competing interests: None declared. Data and materials
availability: Original sequence data are available in the Sequence
Read Archive (www.ncbi.nlm.nih.gov/sra) under BioProject
PRJNA420081 (SAMN08146448 to SAMN08146534). Previously
generated whole-genome sequence data of snowshoe hare
(SAMN02782769 and SAMN07526959) and mountain hare
(SAMN07526960) are also available in the Sequence Read Archive.
SUPPLEMENTARY MATERIALS
www.sciencemag.org/content/360/6395/1355/suppl/DC1
Materials and Methods
Figs. S1 to S11
Tables S1 to S9
References (38–82)
Data S1
21 November 2017; accepted 1 May 2018
10.1126/science.aar5273
Jones et al., Science 360, 1355–1358 (2018) 22 June 2018 4of4
RESEARCH |REPORT
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Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares
Jeffrey D. Jensen, José Melo-Ferreira and Jeffrey M. Good
Matthew R. Jones, L. Scott Mills, Paulo Célio Alves, Colin M. Callahan, Joel M. Alves, Diana J. R. Lafferty, Francis M. Jiggins,
DOI: 10.1126/science.aar5273
(6395), 1355-1358.360Science
, this issue p. 1355Science
adaptive variation to the snowshoe hare.
introgression around this gene that facilitates the brown winter morph. Hybridization appears to have provided important
is responsible for the winter coat color change. Hybridization with jackrabbits has led toAgoutipigmentation gene show that regulation of theet al.snow is less extensive, hares molt from a brown coat to a brown coat. Jones
Snowshoe hares molt from a brown coat to a white coat in winter. In some populations, however, where winter
Hybrid camouflage variation
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REFERENCES http://science.sciencemag.org/content/360/6395/1355#BIBL
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