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Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares


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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
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Adaptive introgression underlies
polymorphic seasonal camouflage
in snowshoe hares
Matthew R. Jones
*, L. Scott Mills
, Paulo Célio Alves
, Colin M. Callahan
Joel M. Alves
, Diana J. R. Lafferty
, Francis M. Jiggins
, Jeffrey D. Jensen
José Melo-Ferreira
*, Jeffrey M. Good
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 (68)
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
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-
(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
) 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
, 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
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
(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-
to both winter-white and winter-brown offspring
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 cyclespecific
isoformsdistinguished by alternative 5untrans-
lated regions (5UTRs; 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, Students
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
Jones et al., Science 360, 13551358 (2018) 22 June 2018 1of4
Division of Biological Sciences, University of Montana,
Missoula, MT 59812, USA.
Wildlife Biology Program,
University of Montana, Missoula, MT 59812, USA.
Office of
Research and Creative Scholarship, University of Montana,
Missoula, MT 59812, USA.
Fisheries, Wildlife, and
Conservation Biology Program, Department of Forestry and
Environmental Resources, North Carolina State University,
Raleigh, NC 27695, USA.
CIBIO, Centro de Investigação em
Biodiversidade e Recursos Genéticos, InBIO Laboratório
Associado, Universidade do Porto, 4485-661 Vairão,
Departamento de Biologia, Faculdade de Ciências
da Universidade do Porto, 4169-007 Porto, Portugal.
Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, UK.
Department of Biology, Northern
Michigan University, Marquette, MI 49855, USA.
School of
Life Sciences, Ecole Polytechnique Fédérale de Lausanne,
1015 Lausanne, Switzerland.
School of Life Sciences,
Arizona State University, Tempe, AZ 85281, USA.
*Corresponding author. Email:
(M.R.J.); (J.M.-F.); jeffrey.good@ (J.M.G.)
on June 21, 2018 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
= 1.6%; genome-wide d
= 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
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
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, 13551358 (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
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) 5UTRs. Sliding
window averages of F
(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
=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]
on June 21, 2018 from
significantly reduced divergence between spe-
cies (d
= 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
= 0.024, s
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
Despite widespread evidence of hybridization
between animal species, introgression has rarely
been directly linked to ecological adaptation
(3436). 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 Darwins 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.
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Relative expression level
Proportion of white allele
HC isoform
HC isoform
V isoform
equal ratio
Fig. 3. Agouti expression in snowshoe hares during autumn molts. (A) The relative expression level (2DCT,
where DC
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, Studentsttest). Pairs of points represent technical replicates.
tree topologies
Scaled absolute divergence
BGenome-wide tree Local Agouti tree
7 Mb
snowshoe hare
snowshoe hare
jackrabbit mountain hare European rabbit
Observed Agouti
Predicted (selection)
Observed genome-wide
0.00.005 0.015
0.01 1.0
0.2 0.4 0.6 0.8
Observed genome-wide
Observed non-synonymous
Observed Agouti
5.3 5.8 Mb
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
, 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
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
between BC (monomorphic winter-brown) and MT (monomorphic winter-white) hares genome-wide (gray)
and for nonsynonymous SNPs (yellow).The green star indicates F
= 1 at a diagnostic Agouti SNP.
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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;
PORTUGALU.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 Unions 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 ( 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.
Materials and Methods
Figs. S1 to S11
Tables S1 to S9
References (3882)
Data S1
21 November 2017; accepted 1 May 2018
Jones et al., Science 360, 13551358 (2018) 22 June 2018 4of4
on June 21, 2018 from
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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... Discordance due to ILS ultimately depends on effective population sizes across the phylogeny (Pamilo and Nei 1988;Degnan and Rosenberg 2006) and, therefore, should covary with any process that influences local patterns of genetic diversity (e.g., linked negative or positive selection). Likewise, the potential for discordance due to introgression may be influenced by selection against incompatible alleles or, less often, positive selection for beneficial variants (Lewontin and Birch 1966;Jones et al. 2018). These sources of discordance, ILS and introgression, are expected to leave differing signals across the genomes of a sample of species that should allow us to test hypotheses about both the cause and the scale of phylogenetic discordance (Huson et al. 2005;Kulathinal et al. 2009;Green et al. 2010;Vanderpool et al. 2020). ...
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A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.
... This transition is regulated by seasonal expression of the pigmentation gene Agouti. Specifically, differences in Agouti regulation underlie the loss of pigmentation in hairs that grow after the Autumn molt (30). Although the seasonal changes seen in Snowshoe hares occur throughout the entire body and, as such, do not constitute what we define as a color pattern (see Terms and Definitions), these findings are interesting because they suggest that temporal variation in the transcription of pigmentation genes may be a common mechanism by which melanocyte behavior is modified throughout multiple hair/feather cycles. ...
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Vertebrates exhibit a wide range of color patterns, which play critical roles in mediating intra- and interspecific communication. Because of their diversity and visual accessibility, color patterns offer a unique and fascinating window into the processes underlying biological organization. In this review, we focus on describing many of the general principles governing the formation and evolution of color patterns in different vertebrate groups. We characterize the types of patterns, review the molecular and developmental mechanisms by which they originate, and discuss their role in constraining or facilitating evolutionary change. Lastly, we outline outstanding questions in the field and discuss different approaches that can be used to address them. Overall, we provide a unifying conceptual framework among vertebrate systems that may guide research into naturally evolved mechanisms underlying color pattern formation and evolution. Expected final online publication date for the Annual Review of Genetics, Volume 57 is November 2023. Please see for revised estimates.
... In the past decade, rapidly declining sequencing costs have led to a dramatic expansion in the availability of genomic resequencing datasets in diverse organisms, fueling a wide range of novel insights, including the prevalence of adaptive introgression between species (Huerta-Sánchez et al. 2014;Lamichhaney et al. 2015;Jones et al. 2018), the molecular basis of repeated local adaptation (Jones et al. 2012;Hill et al. 2019;Wooldridge et al. 2022), and the complex demographic histories of humans (Nielsen et al. 2017;Fan et al. 2023) and animals of conservation relevance (Robinson et al. 2018). In parallel, rapidly expanding efforts to generate high quality reference genomes across the Tree of Life (Rhie et al. 2021); (Lewin et al. 2022) are poised to empower population genetic inference across a wide diversity of organisms. ...
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The increasing availability of genomic resequencing datasets and high quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in non-model organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analysis. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with HPC clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing datasets from non-mammalian vertebrates. These variant datasets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public datasets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating rapid use and reuse of large genomic datasets.
... Research of the last decade has demonstrated that introgression is a widespread phenomenon in nature and often of great adaptive significance due to its potential to rapidly introduce combinations of beneficial alleles 38,[64][65][66][67][68][69][70] . There is also a growing body of empirical evidence showing that introgression is highly pervasive in canids 71,72 , with remarkable case studies of species such as coyotes and grey wolves 73 and Tibetan and Himalayan wolves and dogs 14 carrying genetic material introgressed from highly divergent and unidentified lineages. ...
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Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell’s fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.
... Investigation into heterozygosity around admixed loci suggested that backcrossing with wild isolates is ongoing at most admixed loci. Yet, many loci have been retained across all years, despite others being removed, which may represent adaptive introgression, a phenomenon that has been observed in many species, providing novel genetic variation to respond to selection [44][45][46] . ...
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Cultural exchange of fermentation techniques has driven the spread of Saccharomyces cerevisiae across the globe, establishing wild populations in many countries. Despite this, most modern commercial fermentations are inoculated using monocultures, rather than relying on natural populations, potentially impacting wild population diversity. Here we investigate the genomic landscape of 411 wild S. cerevisiae isolated from spontaneous grape fermentations in Australia across multiple locations, years, and grape cultivars. Spontaneous fermentations contained highly recombined mosaic strains that commonly exhibited aneuploidy of chromosomes 1, 3, 6 and 9. Assigning wild genomic windows to putative ancestral origin revealed that few closely related commercial lineages have come to dominate the genetic landscape, contributing most of the genetic variation. Fine-scale phylogenetic analysis of loci not observed in strains of commercial wine origin identified widespread admixture with the Beer2 clade along with three independent admixture events from potentially endemic Oceanic lineages that last shared an ancestor with modern East Asian S. cerevisiae populations. Our results illustrate how commercial use of microbes can affect local microorganism genetic diversity and demonstrates the presence of non-domesticated, non-European derived lineages of S. cerevisiae in Australian ecological niches that are actively admixing.
... Genomic studies have identified historical or recent admixture in a wide range of species including bears (Cahill et al., 2015(Cahill et al., , 2018Kumar et al., 2017;Pongracz et al., 2017), hares (Jones et al., 2018), jackals (Galov et al., 2015), dolphins (Brown et al., 2014;Gridley et al., 2018), ducks (Stephens et al., 2020) and parrots (Qu et al., 2012). Hybridisation and genetic admixture have been an integral part of evolutionary adaption and speciation, but it also challenges wildlife facing urbanisation, changing climates and habitat fragmentation (Ottenburghs, 2021;vonHoldt & Aardema, 2020 (Allen et al., 2017;Claridge et al., 2014;Crowther et al., 2020). ...
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Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to interspecific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. But there exists a concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here, we apply genome-wide single-nucleotide polymorphism (SNP) genotyping to a set of 402 wild and captive dingoes collected from across Australia and then carry out comparisons to domestic dogs. We then perform ancestry modelling and biogeographic analyses to characterise population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes. Our work challenges previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in south-eastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policymakers to assess and inform dingo management policy and legislation moving forwards.
... This tradeoff occurs because increased connectivity and hybridization can lead to the homogenization of the gene pool and the loss of unique genetic combinations present only in isolated populations (Muhlfeld et al., 2017). On the other hand, introgressive hybridization has the potential to rapidly increase evolutionary innovation through increased standing genetic variation or the introduction of pre-adapted alleles into a population (Rieseberg et al., 2003;Jones et al., 2018;Oziolor et al., 2019). Gene flow can also increase genetic variation and the effective size of a population, which may help to buffer small populations from extinction through increased evolutionary potential (Holt and Gomulkiewicz, 1997). ...
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Although the concept of connectivity is ubiquitous in ecology and evolution, its definition is often inconsistent, particularly in interdisciplinary research. In an ecological context, population connectivity refers to the movement of individuals or species across a landscape. It is measured by locating organisms and tracking their occurrence across space and time. In an evolutionary context, connectivity is typically used to describe levels of current and past gene flow, calculated from the degree of genetic similarity between populations. Both connectivity definitions are useful in their specific contexts, but rarely are these two perspectives combined. Different definitions of connectivity could result in misunderstandings across subdisciplines. Here, we unite ecological and evolutionary perspectives into a single unifying framework by advocating for connectivity to be conceptualized as a generational continuum. Within this framework, connectivity can be subdivided into three timescales: (1) within a generation (e.g., movement), (2) across one parent-offspring generation (e.g., dispersal), and (3) across two or more generations (e.g., gene flow), with each timescale determining the relevant context and dictating whether the connectivity has ecological or evolutionary consequences. Applying our framework to real-world connectivity questions can help to identify sampling limitations associated with a particular methodology, further develop research questions and hypotheses, and investigate eco-evolutionary feedback interactions that span the connectivity continuum. We hope this framework will serve as a foundation for conducting and communicating research across subdisciplines, resulting in a more holistic understanding of connectivity in natural systems.
Species are considered by some to be the most basal and important taxa in nature, and this central role is used to characterize important ecological and evolutionary processes with theoretical and practical consequences in several fields, but especially in biodiversity. Despite its prominence in biology, there is still a great deal of controversy amongst biologists to what species really are, and which attributes best define them. New methods have been proposed to help us solve this problem, which have profited greatly from our increased ability to investigate genetic variation among individuals across populations and lineages. These new methods and data have shown, though, that there is much more complexity on what constitutes a species than previously envisioned. Recent data has shown that several lineages show high levels of introgression, that is, effective gene flow, even amongst some that have separated long ago. Here we focus on the impact that introgression might have on the ability of different lineages to survive, and the consequences on how we define species. Furthermore, we consider which processes might foster, or hinder, introgression among different lineages, especially in a changing environment, and why we believe introgression may be even more pronounced in the Neotropics, because of their inherent landscape complexity.KeywordsEvolutionConservationNatural selectionGene flowHybridization
The conservation of snowshoe hares (Lepus americanus) and their habitat is a major focus in the American West, largely because of their importance to the federally threatened Canada lynx (Lynx canadensis). Understanding the habitat relationships of snowshoe hare populations at the southern periphery of their distribution is particularly important because a warming climate is reducing the mesic forests and persistent snow cover they require. Using fecal pellet density as an index, we examined the factors influencing snowshoe hare relative abundance at 2 study areas in the Southern Rocky Mountains by comparing suites of candidate models containing fine-scale vegetation and topographical covariates. The Birdseye Gulch study area is within an extensive area containing high elevations, mesic forests, and Canada lynx occurrence. The Three Peaks study area consists of an isolated zone of high elevation and mesic forests surrounded by inadequate habitat and is absent of Canada lynx. Mean hare pellet density in Birdseye Gulch was 2.48 pellets ± 0.46 (SE)/m^2 (n = 49) versus 2.24 ± 0.48/m2 (n = 57) at Three Peaks. Models containing fine-scale vegetation variables best explained pellet densities at Birdseye Gulch. Pellet densities at Three Peaks were best explained by topographical variables, with much unexplained variation within all models. The differing trends in these areas may be due to the absence of resident Canada lynx at Three Peaks and differences in topography between the areas. Our results indicate that snowshoe hare populations can persist in the type of isolated habitat that is increasingly common at the southern range periphery; however, the use of vegetation management to conserve habitat in these areas may be less effective because of weaker associations with vegetation structure.
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Pigmentation is an excellent trait to examine patterns of evolutionary change because it is often under natural selection. The genetic architecture of pigmentation in vertebrates also appears to be complex. Yet, most work on pigmentation has focused on a few candidate genes in model species. Benthic-limnetic threespine stickleback ( Gasterosteus aculeautus ) exhibit distinct pigmentation phenotypes, likely an adaptation to occupation of divergent niches. Prior QTL mapping for threespine stickleback pigmentation phenotypes has identified several candidate loci. However—relative to other morphological phenotypes (e.g., spines or lateral plates)—the genetic architecture of threespine stickleback pigmentation remains understudied. Here, we performed QTL mapping for two melanic pigmentation traits (melanophore density and lateral barring) using benthic-limnetic F2 crosses. The two traits mapped to different chromosomes, suggesting a distinct genetic basis. The resulting QTLs were additive, but explained a relatively small fraction of the total variance (~6%). QTLs maps differed by F1 family, suggesting variation in genetic architecture or ability to detect loci of small effect. Functional analysis identified several enriched pathways for candidate loci. Several of the resulting candidate loci for pigmentation, including four loci in enriched pathways ( bco1 , pola1 , sulf1 , and tyms ) have been previously indicated to affect pigmentation in other vertebrates. These findings add to a growing body of evidence suggesting pigmentation is often polygenic.
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Animals that occupy temperate and polar regions have specialized traits that help them survive in harsh, highly seasonal environments. One particularly important adaptation is seasonal coat colour (SCC) moulting. Over 20 species of birds and mammals distributed across the northern hemisphere undergo complete, biannual colour change from brown in the summer to completely white in the winter. But as climate change decreases duration of snow cover, seasonally winter white species (including the snowshoe hare Lepus americanus, Arctic fox Vulpes lagopus and willow ptarmigan Lagopus lagopus) become highly contrasted against dark snowless backgrounds. The negative consequences of camouflage mismatch and adaptive potential is of high interest for conservation. Here we provide the first comprehensive review across birds and mammals of the adaptive value and mechanisms underpinning SCC moulting. We found that across species, the main function of SCC moults is seasonal camouflage against snow, and photoperiod is the main driver of the moult phenology. Next, although many underlying mechanisms remain unclear, mammalian species share similarities in some aspects of hair growth, neuroendocrine control, and the effects of intrinsic and extrinsic factors on moult phenology. The underlying basis of SCC moults in birds is less understood and differs from mammals in several aspects. Lastly, our synthesis suggests that due to limited plasticity in SCC moulting, evolutionary adaptation will be necessary to mediate future camouflage mismatch and a detailed understanding of the SCC moulting will be needed to manage populations effectively under climate change.
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Changing coats with the season Many species of mammals and birds molt from summer brown to winter white coats to facilitate camouflage. Mills et al. mapped global patterns of seasonal coat color change across eight species including hares, weasels, and foxes. They found regions where individuals molt to white, brown, and both white and brown winter coats. Greater proportions of the populations molted to white in higher latitudes. Regions where seasonal coat changes are the most variable (molting to both brown and white) may provide resilience against the warming climate. Science , this issue p. 1033
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Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.
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Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample. Here, we develop a scalable pseudoreference approach to iteratively incorporate sample-specific variation into a genome reference and reduce the effects of systematic mapping bias in downstream analyses. To characterize this framework, we used targeted capture to sequence whole exomes (∼54 Mbp) in 12 lineages (10 species) of mice spanning the Mus radiation. We generated whole exome pseudoreferences for all species and show that this iterative reference-based approach improved basic genomic analyses that depend on mapping accuracy while preserving the associated annotations of the mouse reference genome. We then use these pseudoreferences to resolve evolutionary relationships among these lineages while accounting for phylogenetic discordance across the genome, contributing an important resource for comparative studies in the mouse system. We also describe patterns of genomic introgression among lineages and compare our results to previous studies. Our general approach can be applied to whole or partitioned genomic data and is easily portable to any system with sufficient genomic resources, providing a useful framework for phylogenomic studies in mice and other taxa.
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Linked loci and Galapagos finch size Observations of parallel evolution in the finches of the Galapagos, including body and beak size, contributed to Darwin's theories. Lamichhaney et al. carried out whole-genome sequencing of 60 Darwin's finches. These included small, medium, and large ground finches as well as small, medium, and large tree finches. A genomic region containing the HMGA2 gene correlated strongly with beak size across different species. This locus appears to have played a role in beak diversification throughout the radiation of Darwin's finches. Science , this issue p. 470
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Background: Although hybridization is thought to be relatively rare in animals, the raw genetic material introduced via introgression may play an important role in fueling adaptation and adaptive radiation. The butterfly genus Heliconius is an excellent system to study hybridization and introgression but most studies have focused on closely related species such as H. cydno and H. melpomene. Here we characterize genome-wide patterns of introgression between H. besckei, the only species with a red and yellow banded 'postman' wing pattern in the tiger-striped silvaniform clade, and co-mimetic H. melpomene nanna. Results: We find a pronounced signature of putative introgression from H. melpomene into H. besckei in the genomic region upstream of the gene optix, known to control red wing patterning, suggesting adaptive introgression of wing pattern mimicry between these two distantly related species. At least 39 additional genomic regions show signals of introgression as strong or stronger than this mimicry locus. Gene flow has been on-going, with evidence of gene exchange at multiple time points, and bidirectional, moving from the melpomene to the silvaniform clade and vice versa. The history of gene exchange has also been complex, with contributions from multiple silvaniform species in addition to H. besckei. We also detect a signature of ancient introgression of the entire Z chromosome between the silvaniform and melpomene/cydno clades. Conclusions: Our study provides a genome-wide portrait of introgression between distantly related butterfly species. We further propose a comprehensive and efficient workflow for gene flow identification in genomic data sets.
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Anthropogenic climate change has created myriad stressors that threaten to cause local extinctions if wild populations fail to adapt to novel conditions. We studied individual and population-level fitness costs of a climate change-induced stressor: camouflage mismatch in seasonally colour molting species confronting decreasing snow cover duration. Based on field measurements of radiocollared snowshoe hares, we found strong selection on coat colour molt phenology, such that animals mismatched with the colour of their background experienced weekly survival decreases up to 7%. In the absence of adaptive response, we show that these mortality costs would result in strong population-level declines by the end of the century. However, natural selection acting on wide individual variation in molt phenology might enable evolutionary adaptation to camouflage mismatch. We conclude that evolutionary rescue will be critical for hares and other colour molting species to keep up with climate change.
Because they are considered rare, balanced polymorphisms are often discounted as crucial constituents of genome-wide variation in sequence diversity. Despite its perceived rarity, however, long-term balancing selection can elevate genetic diversity and significantly affect observed divergence between species. Here, we discuss how ancestral balanced polymorphisms can be ‘sieved’ by the speciation process, which sorts them unequally across descendant lineages. After speciation, ancestral balancing selection is revealed by genomic regions of high divergence between species. This signature, which resembles that of other evolutionary processes, can potentially confound genomic studies of population divergence and inferences of “islands of speciation”. This article is protected by copyright. All rights reserved.
Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares (Lepus americanus). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to brown summer pelage. Using RNA-sequencing, we tested if patterns of expression were consistent with predictions based on the established phases of the hair growth cycle. We found functionally consistent clustering across skin types, with 766 genes differentially expressed between moult stages. "White" pelage showed more differentially expressed genes that were upregulated relative to other skin types, involved in the transition between late telogen (quiescent stage) and the onset of anagen (proliferative stage). Skin samples from transitional "intermediate" and "brown" pelage were transcriptionally similar and resembled the regressive transition to catagen (regressive stage). We also detected differential expression of several key circadian clock and pigmentation genes, providing important means to dissect the bases of alternate seasonal colour morphs. Our results reveal that pelage colour is a useful biomarker for seasonal change but that there is a consistent lag between the main gene expression waves and change in visible coat colour. These experiments establish that developmental sampling from natural populations of non-model organisms can provide a crucial resource to dissect the genetic basis and evolution of complex seasonally changing traits. This article is protected by copyright. All rights reserved.