Adaptive Admixture in Soay Sheep 1
1 Introgression and the Fate of Domesticated Genes in a Wild Mammal
This is the peer reviewed version of the following article: Feulner PGD, Gratten J, Kijas JW, Visscher 2 Population PM, Pemberton JM & Slate J (2013) Introgression and the fate of domesticated genes in a wild mammal population. Molecular Ecology 22: 4210–4221, which has been published in final form at 10.1111/mec.12378. This article may be used for non-commercial purposes in accordance with 3 Wiley Terms and Conditions for self-archiving.
4 Philine G.D. Feulner*1,2, Jacob Gratten*1,3, James W. Kijas4, Peter M. Visscher1,5, Josephine
5 M. Pemberton6, Jon Slate1
6 *joint first authors
7
8 1 Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
9 2 Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306 Ploen,
10 Germany
11 3 The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
12 4 Livestock Industries, CSIRO, Brisbane, Australia
13 5 The University of Queensland Diamantina Institute, Brisbane, Queensland, Australia
14 6 Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh,
15 Edinburgh, EH9 3JT, UK
16
17 Keywords: admixture; adaptive introgression; Soay sheep; domesticated alleles; natural
18 selection
19
20 Corresponding author:
21 Philine Feulner
22 Max Planck Institute for Evolutionary Biology
23 August-Thienemann-Str. 2
24 24306 Plön
1
Adaptive Admixture in Soay Sheep 2
25 Germany
26 Tel: +49 (0) 4522 763-228
27 Fax: +49 (0) 4522 763-310
29
2
Adaptive Admixture in Soay Sheep 3
30 Abstract
31 When domesticated species are not reproductively isolated from their wild relatives, the opportunity
32 arises for artificially selected variants to be re-introduced into the wild. However, the evolutionary
33 consequences of introgression of domesticated genes back into the wild are poorly understood. By
34 combining high-throughput genotyping with 25 years of long-term ecological field data we describe
35 the occurrence and consequences of admixture between a primitive sheep breed, the free-living Soay
36 sheep of St Kilda, and more modern breeds. Utilising data from a 50K ovine SNP chip, together with
37 forward simulations of demographic scenarios, we show that admixture occurred between Soay sheep
38 and a more modern breed, consistent with historical accounts, approximately 150 years ago.
39 Haplotype sharing analyses with other breeds revealed that polymorphisms in coat colour and pattern
40 in Soay sheep arose as a result of introgression of genetic variants favoured by artificial selection.
41 Because the haplotypes carrying the causative mutations are known to be under natural selection in
42 free-living Soay sheep, the admixture event created an opportunity to observe the outcome of a
43 ‘natural laboratory’ experiment where ancestral and domesticated genes competed with each other.
44 The haplotype carrying the domesticated light coat colour allele was favoured by natural selection
45 while the haplotype associated with the domesticated self coat pattern allele was associated with
46 decreased survival. Therefore, we demonstrate that introgression of domesticated alleles into wild
47 populations can provide a novel source of variation capable of generating rapid evolutionary changes.
48
49
3
Adaptive Admixture in Soay Sheep 4
50 Introduction
51 Admixture brings together the genomes of divergent populations. The resulting introgression
52 of alleles from one population into another can either hinder local adaptation by slowing
53 down the rate of adaptive evolution, or promote adaptation by providing a substantial source
54 of genetic variation upon which selection can act. Admixture is an important evolutionary
55 force both in the context of hybrid speciation (Baack & Rieseberg 2007) and adaptation to
56 new environments (Mallet 2005; Nolte & Tautz 2010; Rieseberg 2009; Staubach et al. 2012),
57 and is also hypothesised to facilitate invasions to new environments (Ellstrand &
58 Schierenbeck 2000; Keller & Taylor 2010). Admixture between wild species and their
59 domesticated relatives is a well-documented phenomenon e.g. in sunflowers (Kane et al.
60 2009), radish (Snow et al. 2010), bees (Zayed & Whitfield 2008), dogs/gray wolves
61 (Anderson et al. 2009), cats (Lecis et al. 2006), cattle/bison (Halbert & Derr 2007). However,
62 demonstrating the adaptive impact of admixture is challenging because it requires that
63 introgressed genomic loci can be identified and that their frequency and fitness consequences
64 can be quantified and traced over many generations; to date such studies have largely been
65 restricted to experimental populations (Burke & Rieseberg 2003).
66
67 Recent technological advances have provided new opportunities to study admixture on a
68 genome-wide scale, because many thousands of genomic regions can now be genotyped
69 simultaneously; examples include the datasets generated by the Human HapMap Consortium
70 (Gibbs et al. 2003) and similar efforts for other species (Gibbs et al. 2009; Kijas et al. 2012;
71 Rubin et al. 2013). Combining high-throughput genomics methods with long-term ecological
72 data from wild populations promises to improve our understanding of the genome-wide
73 impact of admixture and the evolutionary fate of introgressed alleles in nature.
4
Adaptive Admixture in Soay Sheep 5
74
75 The Soay sheep of the St Kilda archipelago, Scotland are a free-living population that has
76 been the focus of an intensive long-term (almost three decades) field study on the island of
77 Hirta (Clutton-Brock & Pemberton 2004; Coulson et al. 2001). Soay sheep originated during
78 early domestication of sheep and are amongst the most primitive of all surviving breeds
79 (Chessa et al. 2009). They closely resemble the wild ancestors of modern sheep (Figure 1),
80 and have survived on the remote island with which they share their name for up to 4000 years
81 (Figure 2). In the past several hundred years, other breeds are known to have existed on the St
82 Kilda archipelago. The history of sheep on the St Kilda islands is closely tied to that of the
83 human settlers who inhabited the largest island in the group, Hirta, until they and their
84 livestock were evacuated in 1930 (see Figure 2). It is known that the St Kildans kept the Old
85 Scottish Shortwool breed (also known as Dunface) until the late 1800s, and there are
86 anecdotal reports suggesting that Dunface sheep were placed on Soay by the St Kildans
87 (Elwes 1912; see Methods). The Dunface breed was later replaced by Scottish Blackface
88 sheep from ~1870, and has now gone extinct (Elwes 1912). However, the Boreray breed,
89 which survives on the neighbouring island of Boreray, was founded by crossing Dunface
90 sheep with Scottish Blackface Sheep (Morton Boyd 1981). Therefore, Boreray sheep can be
91 regarded as a ‘living museum’ containing Dunface genes.
92
93 In 1932, one hundred and seven Soay sheep were moved from Soay to Hirta (i.e. after the
94 human population and their Scottish Blackface sheep were evacuated). Since then Soay sheep
95 have existed as unmanaged free-living populations on Soay and Hirta and are regarded as a
96 feral breed. While Soays are believed to be more or less unchanged since the bronze age,
97 Dunface were typical of Northern European short-tailed breeds that were improved during the
5
Adaptive Admixture in Soay Sheep 6
98 middle ages (Ryder 1981). Scottish Blackface sheep are a modern breed that gradually
99 replaced the Dunface breed throughout Scotland in the 1800s (Ryder 1981) and is now the
100 most numerous breed in the UK.
101
102 Surprisingly for a small island population, Soay sheep show a high degree of molecular and
103 phenotypic polymorphism. Two of the most striking polymorphisms (Figure 1 top panel) are
104 for coat colour (dark-light) and coat pattern (wild-self type). Gene mapping studies have
105 identified the molecular basis of these polymorphisms in the TYRP1 (Gratten et al. 2007) and
106 ASIP (Gratten et al. 2010) genes, respectively. The two genes are on different chromosomes,
107 segregate independently, and do not have epistatic effects (Gratten et al. 2012); i.e. the
108 polymorphisms and their effects are independent of each other. Subsequent investigation of
109 the relative fitness of TYRP1 revealed positive selection and a microevolutionary increase of
110 the frequency of the TYRP1 T allele, which is associated with light coat colour (Gratten et al.
111 2008). This microevolutionary trend is explained by genetic linkage between the causal
112 mutation underlying the colour polymorphism and quantitative trait loci with antagonistic
113 effects on size and fitness (Gratten et al. 2008). Similarly at ASIP, there was negative viability
114 selection on the self-pattern associated haplotype (Gratten et al. 2012). By employing gene-
115 dropping simulations, it has been shown that microevolutionary trends in the frequency and
116 excess of ASIP heterozygotes cannot be explained by genetic drift alone (Gratten et al. 2012).
117 When the coat colour mutation was identified, an exceptionally high degree of linkage
118 disequilibrium in the genomic region around TYRP1 was noted, and it was suggested that this
119 could be a signature of admixture between Soay sheep and another breed; for further details
120 see (Gratten et al. 2010).
121
6
Adaptive Admixture in Soay Sheep 7
122 In this study we tested whether genetic variation segregating within the contemporary Soay
123 sheep population on Hirta has been enhanced by the introgression of genes from more modern
124 breeds. Having demonstrated evidence of admixture, we then used genomic data and
125 simulations of different historical scenarios to investigate the origins of introduced genetic
126 variation. Admixture with Dunface sheep in the latter half of the 1800s appears to be the most
127 plausible explanation. We next performed an analysis of haplotype sharing between Soay
128 sheep and a global sample of modern breeds to show that the coat colour and pattern
129 polymorphisms found in the contemporary Soay sheep population arose due to introgression
130 of domesticated alleles. Therefore, previous studies of selection at the loci containing the
131 causative genes (Gratten et al. 2012; Gratten et al. 2008) reveal the outcome of a natural
132 experiment spanning approximately 150 years in which domesticated and ancestral alleles
133 carrying different coat colour and pattern variants were in competition with each other. We
134 show that domesticated alleles do not necessarily cause reduced fitness and that they can
135 provide genetic variation that enables microevolution.
136
7
Adaptive Admixture in Soay Sheep 8
137 Materials and Methods
138 Genotype Data
139 Dense, high-throughput genotyping was facilitated by the International Sheep Genomics
140 Consortium’s (ISGC) recent development of the ovine 50K SNP chip, which has been used to
141 describe genetic variation in around 70 sheep breeds (Kijas et al. 2012). Samples of 486 Soay
142 sheep from the Hirta population and 20 Boreray sheep (5 samples from Boreray and 15 from a
143 captive flock in Wales) were genotyped. 48,144 markers gave satisfactory genotype calls in
144 the Soay samples, of which 48,034 markers passed the quality control of the ISGC. We
145 performed additional quality control utilising the PLINK (Purcell et al. 2007) software.
146 Individuals with a call rate less than 90% and markers with a call rate less than 99% were
147 removed. Loci with a significant deviation from Hardy-Weinberg expectations (Wigginton’s
148 exact test (Wigginton et al. 2005), p ≤ 0.001) and a minor allele frequency of less than 5%
149 were excluded, as were loci on the sex chromosomes. This stringent filtering left 29,564
150 markers, which were further pruned to 11,405 markers (such that no marker pairs exceeded an
151 r2 threshold of 0.5; mean pairwise r2 was 0.014 combined across all breeds), for subsequent
152 analysis. To achieve this linkage disequilibrium pruning, based on the variance inflation
153 factor (VIF), was implemented in PLINK (window size 50, step size 5, multiple correlation
154 coefficient 2). Note that the simulated datasets (see below) were designed to recreate the
155 number of markers passing these quality control criteria. In addition genotype data for the
156 same markers were utilised for 56 Scottish Blackface sheep and 45 Red Maasai sheep
157 (serving as a non-European genetically distinct outgroup breed), available through the ISGC.
158 For a comparison with a previous STRUCTURE analysis of a variety of sheep breeds (Kijas
159 et al. 2009), the marker set was reduced to a comparable number of loci (1,660 SNPs) and the
160 analysis was repeated.
8
Adaptive Admixture in Soay Sheep 9
161
162 Admixture Simulations
163 We investigated whether the ISGC SNP chip was capable of detecting admixture events that
164 could have occurred on St Kilda in the mid-late 1800s. Historical accounts suggest that Soay
165 sheep on the island of Soay may have undergone an admixture event with Dunface sheep: “A
166 few rams of the race which preceded the introduction of the Black-faced rams [Dunface
167 sheep] were once introduced into Soay, but they did no good” (Donald Ferguson ground
168 officer on St Kilda) (Elwes 1912). Therefore, we simulated the sheep populations (Soays,
169 Dunface, Borerays and Scottish Blackface) that have inhabited the St Kilda islands and one
170 outgroup (Red Maasai) population to verify that our approach can distinguish clearly
171 separated populations as distinct and non-admixed. We simulated a scenario consistent with
172 the historical report (see Figure 2) plus an alternative scenario in which Soays remained a
173 pure breed well separated from the more modern European breeds that have inhabited St
174 Kilda. Parameters for the simulation were based on long-term field data available for the Soay
175 sheep of Hirta, such as a generation time of four years and a litter size of one.
176
177 Using QMsim (Sargolzaei & Schenkel 2009) 49,998 SNPs spread approximately evenly
178 across 26 autosomes with a total genome length of 2990 cM were simulated. The simulation
179 was initiated with a historical population comprising 1000 individuals for 1000 generations,
180 with a litter size of one and proportion of male progeny being 0.5. The Red Maasai population
181 was allowed to evolve independently from the European breeds for 1000 generations. The
182 European breeds evolved together for 300 generations after which they split into three
183 lineages representing the Scottish Blackface, Dunface, and Soay breeds, which evolved
184 independently for another 700 generations. The Boreray breed was created by simulating
9
Adaptive Admixture in Soay Sheep 10
185 admixture between equal numbers of Scottish Blackface and Dunface sheep 25 generations
186 ago. We considered two scenarios for Soay sheep. Under the first, admixture was simulated
187 between Dunface and Soay sheep 32 generations ago (i.e. before the Dunface breed was
188 replaced by Scottish Blackface sheep, according to Ferguson’s account). To recreate
189 conditions close to the historical anecdotes of admixture, we assumed a generation time of
190 four years, as indicated by the long-term field and molecular parentage assignment data
191 available for the Soay population on Hirta, and we assumed admixture proportions of 10%
192 Dunface, 90% pure Soay. Under the second scenario, we modelled independent evolution of
193 Soay sheep until the present day; i.e. without admixture with any other breed.
194
195 Before further analysis the 49,998 simulated loci were quality filtered (as described above;
196 see Genotype Data) resulting in 32,230 SNPs with a minor allelic frequency (MAF) > 0.05,
197 which were further pruned to 11,229 SNPs (mean pairwise r2 of 0.016). To ensure that the
198 simulation results were robust and repeatable they were replicated 50 times using a marker
199 panel similar to the pruned one described above. Because the simulated datasets were filtered
200 using the same criteria as used in the real dataset, the number of SNPs in the real and
201 simulated datasets (or in the different replicates of the simulations) are not identical, but all
202 datasets should have similar power given that they are matched for minor allele frequency and
203 pairwise LD. Again, for a comparison with a previous STRUCTURE analysis of a variety of
204 sheep breeds (Kijas et al. 2009), the marker set was reduced to a comparable number of loci
205 (1,977 SNPs) and the analysis was repeated.
206
207
208 Detecting Admixture
10
Adaptive Admixture in Soay Sheep 11
209 For population clustering of both the simulated and real datasets Structure version 2 (Falush
210 et al. 2003; Pritchard et al. 2000) was used, running the linkage model settings with
211 correlated allele frequencies amongst ancestral clusters. Although a larger number of Soays
212 had been typed (486), it was more computationally efficient to randomly select 75 unrelated
213 individuals for the analysis of the real dataset. The admixture proportion α was calculated
214 separately for each population allowing for asymmetric admixture between populations. For
215 each value of K, from one to six, ten replicated runs were performed using a burnin of 20,000
216 generations and running the chain for 10,000 generations. The best K value was determined as
217 the K value at which the likelihood distribution reached a plateau and the variation between
218 replicated runs did not increase substantially. As an additional support, Delta(K) (Evanno et
219 al. 2005) was inspected. Out of the 10 replicated runs the one with the best likelihood value
220 was plotted using Distruct (Rosenberg 2004). It should be noted that the replicates gave
221 qualitatively similar results.
222
223 Haplotype Sharing
224 To make inference on the origin of the coat colour and pattern polymorphisms we examined
225 whether TYRP1 and ASIP haplotypes in Soay sheep are shared with 73 other domestic breeds,
226 including Borerays and Scottish Blackface sheep, and with wild sheep and ungulate species.
227 The extent of haplotype sharing (HS) between breeds provides information on the time since
228 co-ancestry (vonHoldt et al. 2010). Consequently, if haplotypes associated with particular
229 coat colours or patterns were introduced from Dunface sheep, then those haplotypes should
230 show greater HS between Soays and Boreray sheep (which contain Dunface genes) than
231 between Soays and other breeds (including Scottish Blackface sheep) and other sheep and
232 ungulate species. To calculate the extent of HS between Soays and the other breeds and
11
Adaptive Admixture in Soay Sheep 12
233 species we used high density SNP data (described above) in a total of 3,195 sheep, including
234 486 Soays and between 3 and 120 individuals from each of the additional domestic breeds
235 (Supplementary Table 1). Data were also available for 169 individuals from 19 other wild
236 sheep (such as Mouflon Ovis musimon) and ungulate species (Supplementary Table 1).
237 Genotype data were phased for all individuals using default settings in the fastPHASE
238 software (Scheet & Stephens 2006). Phasing was performed separately for domestic sheep
239 (including Soays) and the other sheep and ungulate species. We defined ‘core’ short-range
240 haplotypes in Soays from the six SNPs spanning and flanking (~1Mb) the genes for coat
241 colour (TYRP1) and coat pattern (ASIP). Seven core haplotypes were present in the TYRP1
242 region and four were present in the ASIP region (Supplementary Table 2). These haplotypes
243 were strongly associated with the TYRP1 and ASIP causal mutations in Soays (Gratten et al.
244 2007; Gratten et al. 2010) and thus although the TYRP1 and ASIP causal mutations were not
245 genotyped by the ISGC, the core haplotypes are likely to tag these variants with high accuracy
246 in domestic sheep (see Supplementary Table 2).
247
248 We calculated the extent of HS using custom scripts written in the R statistical computing
249 language (v2.10.0), as follows: for each core haplotype i identified in Soays, and for each
250 non-Soay breed j, we then extracted all chromosomes containing the core haplotype i from
251 Soays and breed j, with strict filtering out of positions for which phase certainty was <90%.
252 Subsequently, for each pair of Soay and non-Soay chromosomes, we determined the location
253 of the first mismatches at SNPs upstream and downstream of the core haplotype, and from
254 this estimated the length of unbroken HS in base pairs. This procedure was repeated for each
255 pairwise comparison of Soay and non-Soay chromosomes to obtain a mean and standard
256 deviation of HS for each core haplotype i between Soays and breed j. To assess significance
12
Adaptive Admixture in Soay Sheep 13
257 of HS between Soays and other breeds, we compared HS for each core haplotype i and each
258 breed j to the mean HS for that core haplotype between Soays and all other breeds (minus
259 breed j), using t-tests, with degrees of freedom equal to the number of other breeds minus 1.
260 Estimating degrees of freedom in this way ensured that we avoided anti-conservative
261 significance testing due to pseudo-replication caused by some animals being involved in
262 multiple pairwise comparisons.
263
13
Adaptive Admixture in Soay Sheep 14
264 Results
265 Detecting Admixture
266 Genome-wide comparisons of unrelated individuals from the contemporary Soay population
267 from Hirta, to those of Boreray sheep (from Boreray and from a pure flock in Wales), Scottish
268 Blackface sheep and Red Maasai sheep (serving as a non-European genetically distinct
269 outgroup breed) supported four distinct genetic clusters (Figure 3 left panel). However,
270 irrespective of the number of clusters (K=2 to 5, Figure 3 right panel), all Soay individuals
271 exhibited evidence of admixture (Figure 3, for K=4 average proportion of Soay cluster 0.776,
272 SD=0.021, average proportion of presumed introgressed cluster 0.217, SD=0.014). Notably,
273 the introgressed cluster in Soays was also identifiable in Boreray sheep, but was not the same
274 cluster that was shared between Boreray and Scottish Blackface sheep. Because Boreray
275 sheep were formed by crossing Dunface and Scottish Blackface sheep, the analysis is
276 consistent with Soay sheep having undergone admixture with the now extinct Dunface sheep.
277
278 For the simulated datasets we applied the same Bayesian clustering approach as for the real
279 genotype data (Figure 4). The Soay population without admixture forms a homogenous
280 cluster (average proportion of Soay cluster 0.998, SD=0.003, n = 50 individuals), whereas the
281 Soay population under the admixture scenario shows consistent signals of admixture (average
282 proportion of Soay cluster 0.857, SD=0.021 and of Dunface cluster 0.139, SD=0.019, n = 50
283 individuals). Replication of the simulation approach across 50 independent datasets confirmed
284 its consistency (averages over 50 replicates with 50 individuals each: no admixture scenario:
285 proportion of Soay clustering 0.990, SD=0.003; admixture scenario: proportion of Soay
286 clustering 0.801, SD=0.017, proportion of Dunface clustering 0.192, SD=0.017). In all 50
287 replicates admixture was apparent where it was simulated and absent where it was not (i.e. in
14
Adaptive Admixture in Soay Sheep 15
288 pure Soay populations). Most strikingly, the simulation results very closely match the results
289 of the empirical data, supporting the idea that genetic variation from a relatively modern
290 breed (Dunface sheep) was introduced into the Soay population ~150 years ago, and that the
291 intervening period has witnessed a natural experiment where ancestral (feral) and
292 domesticated (post-Agricultural Revolution) genetic variants have been exposed to natural
293 selection.
294
295 Our results contrast with a previous cluster analysis of a large variety of different sheep
296 breeds showing Soays as a distinct breed (Kijas et al. 2009). Repeating our analysis with a
297 reduced marker set demonstrated that the lower number of markers used in the previous study
298 was not capable of detecting the recent admixture event in Soays (not shown). This was
299 further supported by qualitatively similar results when reducing the markers to 1,977 loci in
300 the simulation approach (Figure 5).
301
302 Haplotype Sharing
303 Having found evidence that admixture occurred between Soay sheep, an ancient unmanaged
304 breed and a more recent (influenced by domestication) breed, we investigated whether the
305 conspicuous coat polymorphisms present in Soay sheep arose through admixture. ‘Core’
306 short-range haplotypes (spanning 6 SNPs and ~1Mb) tagging the causal mutations in Soays
307 (Supplementary Table 2) were widespread in domestic breeds (Table 1, Figures 6a & 7a), but
308 largely absent from other sheep and ungulate species (Figure 6b & 7b). Notably, the
309 exceptions mostly involve haplotypes in populations of Mouflon, which are related to the
310 wild progenitor of domestic sheep. Given that Mouflon are not known to exhibit coat colour
311 or pattern polymorphism, we interpret the presence of light and self haplotypes to be due to
15
Adaptive Admixture in Soay Sheep 16
312 imperfect tagging of the causal mutations at TYRP1 and ASIP, although it is also possible that
313 the causal mutations predate the onset of domestication. Either way, the broad distribution of
314 core haplotypes suggests that the colour and pattern mutations were present in the early stages
315 of domestication of modern sheep, rather than occurring de novo in Soay sheep.
316
317 At TYRP1, there are seven ‘core’ haplotypes in Soay sheep, one of which (T1), is the common
318 dark haplotype, and another (T6) is the common light haplotype. The extent of HS between
319 Soays and Borerays was significantly greater than the overall mean HS (between Soays and
320 all other breeds) for several core haplotypes (Table 1, Figure 6a); most notably for the
321 common light-associated haplotype (T6), as well as several low frequency dark-associated
322 (T2, T5) haplotypes. Indeed, Soay sheep had greater HS with Boreray sheep than with any
323 other breed at these haplotypes. At ASIP, there are four core Soay haplotypes, one of which
324 (A1), is the common wild-type pattern haplotype, and another (A3) is the common self-
325 pattern haplotype. A3 showed significant HS between Soays and Borerays (Table 1, Figure
326 7a), as did a low frequency wild-type haplotype (A2). These results, which involved Boreray
327 sheep from the Isle of Boreray as well as farmed Borerays in Wales, are consistent with recent
328 co-ancestry of the TYRP1 and ASIP regions in Soays and Borerays. Notably, Soays did not
329 exhibit long-range HS with Scottish blackface sheep in these chromosomal regions (Figures
330 6a & 7a), suggesting that HS between Soays and Borerays may be a legacy of a shared history
331 of admixture with the now extinct Dunface breed. The HS analyses are consistent with the
332 idea that the light coat colour and self coat pattern were introduced to Soay sheep by Dunface
333 sheep in the 1800s, and suggest that prior to this time all Soay sheep had the dark wild
334 phenotype (which is still the most common Soay morph) seen in Mouflon (see Figure 1).
335
336
16
Adaptive Admixture in Soay Sheep 17
337 Discussion
338 The Structure analysis of high density SNP data provided clear evidence that Soay sheep have
339 experienced relatively recent admixture with a more modern breed, most likely the now
340 extinct Dunface breed. In simulated datasets, admixture between Dunface and Soay sheep
341 approximately 150 years (32 generations) ago produced patterns remarkably similar to those
342 derived from the real data, whereas simulated scenarios where Soay sheep had remained a
343 pure breed did not..
344
345 The evidence of admixture in Soay sheep seems to conflict with a previous study of
346 population genetic structure across sheep breeds, using a panel of 1,317 SNPs, which revealed
347 that Soay sheep were genetically distinct from all other European breeds and found no
348 evidence of admixture (Kijas et al. 2009). However, it seems probable that the discrepancy
349 was due to 1,317 SNPs being an insufficient number of SNPs to detect an admixture event in
350 Soay sheep that happened more than 30 generations ago. To test whether a lack of power was
351 the reason why previous studies have failed to identify admixture we pruned the simulated
352 datasets to < 2000 SNPs and confirmed that the smaller panel was not sufficiently powerful to
353 detect admixture (Figure 5). Thus, there is no conflict between the findings of this study and
354 the earlier one (Kijas et al. 2009).
355
356 This study goes beyond the relatively straightforward question of whether admixture between
357 Soays and less primitive domesticated populations occured, by examining the fitness
358 consequences at individual loci (know from previous studies) and interpreting these in the
359 light of our new findings. Because the haplotypes tagging the alleles responsible for light coat
360 colour (at TYRP1) and self coat pattern (at ASIP) are largely absent in other wild sheep and
17
Adaptive Admixture in Soay Sheep 18
361 ungulate species, they appear to have arisen and been favoured during the domestication
362 process. Because they appear to have been introduced to free-living Soay sheep around 150
363 years ago, the intervening period can be regarded as a natural experiment in which wild
364 (Soay) and domesticated (Dunface) genetic variants at TYRP1 and ASIP (and presumably
365 elsewhere in the genome) have been in competition. Previously we have shown selection at
366 the loci containing the causative genes (Gratten et al. 2012; Gratten et al. 2008), but we had
367 no knowledge of the origin and age of the causal mutations in Soay sheep. Measuring the
368 fitness of wild and domestic genotypes in the contemporary Soay sheep population provides
369 an unusual opportunity to observe the outcome of this competition, as does tracking allele
370 frequencies in time. Previous analyses of the relative fitness of TYRP1 genotypes revealed
371 that TT (light) and TG (dark) genotypes had higher fitness than the GG (dark) genotype, and
372 that the frequency of the T allele had continued to increase during the period from 1980-2005
373 (Gratten et al. 2008). In other words, the domesticated TYRP1 T allele introduced by
374 admixture has been favoured by natural selection. This is supported by the Structure analysis,
375 which shows that although Dunface ancestry represents approximately 0.22 of the Soay sheep
376 genome, the introduced light coat associated haplotype (T6) is now at frequency 0.54 among
377 the contemporary sampled animals (Gratten et al. 2008), suggesting this domesticated
378 haplotype responded to positive selection in the wild.
379
380 At ASIP the story is slightly more complex. There is evidence for positive selection on this
381 gene in domestic sheep (Kijas et al. 2012). In Soay sheep, in which natural selection is
382 operating, the frequency of the introduced self-associated haplotype (A4) is 0.20 (Gratten et
383 al. 2012), close to the genome-wide average amount of introgression. However, earlier
384 analyses of the fitness of ASIP genotypes show that this locus is also under selection; animals
18
Adaptive Admixture in Soay Sheep 19
385 that are homozygous for the domesticated self-associated allele tend to have decreased
386 survival (selection coefficient, s=0.42) but increased adult reproductive success (s=0.24)
387 (Gratten et al. 2012). Consistent with this pattern, there has been a statistically significant
388 increase in the frequency of heterozygous animals and a decline in the frequency of
389 homozygous self animals over the last two decades (Gratten et al. 2012) (with the frequency
390 of the self allele remaining relatively stable due to it being associated with relatively low
391 juvenile survival but high adult reproductive success). In summary, domesticated genes
392 introduced into wild Soay sheep have persisted for ~150 years, they are not necessarily at a
393 selective disadvantage, and they may actually have undergone quite rapid increases in
394 frequency once exposed to natural selection.
395
396 More generally, there is considerable interest in understanding the origin of adaptively
397 important genetic variation (Barrett & Schluter 2008; Linnen et al. 2009). The usual
398 distinction is between new mutations that have recently arisen in the population, and
399 ‘standing’ genetic variation; i.e. alleles that have persisted for considerable time in a
400 population yet have remained, until that point, selectively neutral. The variation created by
401 admixture is different to both scenarios, since it tends to involve larger genomic regions that
402 can immediately reach intermediate frequencies through demographic events (e.g.
403 anthropogenic introductions). Additionally, the large regions holding combinations of alleles
404 introduced into a population have already been exposed to selection in domestic populations
405 and are therefore proven to be functional (as a block/combination), or at least non-lethal, in
406 the parental population. Therefore, admixture has the potential to facilitate rapid evolutionary
407 change, as evidenced by the presence and maintenance of coat polymorphisms in the Soay
408 sheep population. Given that anthropogenic influence has facilitated admixture between wild
19
Adaptive Admixture in Soay Sheep 20
409 and domestic populations of many species for several millennia, and the process is relatively
410 common across a wide range of taxa, its evolutionary potential deserves wider attention.
411
412
20
Adaptive Admixture in Soay Sheep 21
413 Acknowledgments
414 PFGD was funded by an EU Marie Curie transfer of knowledge grant (MAERO; grant no.
415 42815) awarded to JS. We thank Dario Beraldi for DNA preparation. We thank JG Pilkington
416 and the many Soay sheep project members and volunteers who have collected phenotypic
417 data and genetic samples during the course of the long-term study on St Kilda. We thank the
418 National Trust of Scotland for granting permission to work on St Kilda, and QinetiQ for
419 logistical support. The long-term data collection on St Kilda has been supported by grants
420 from the Natural Environment Research Council (NERC) and the Wellcome Trust to TH
421 Clutton-Brock, BT Grenfell, LEB Kruuk, MJ Crawley and JMP. This study was funded by
422 NERC through its Environmental Genomics (grant no. NER⁄T⁄S⁄2002⁄00189) and Post-
423 Genomics and Proteomics (grant no. NE⁄D000580⁄1) thematic programmes. Access to The
424 University of Sheffield high performance computer, Iceberg, greatly expedited bioinformatics
425 analyses. We thank the associate editor and reviewers for their insightful comments on an
426 earlier version of the manuscript.
427
428 Author Contributions
429 PGDF, JG, PMV, JMP, and JS designed and performed the experiment. JWK and JMP
430 contributed analysis tools. PGDF and JG analysed the data. PGDF, JG and JS wrote the
431 manuscript.
432
433 Data Accessibility
434 Genotype data from the ISGC are available via CISRO data access portal
435 https://data.csiro.au/dap/home?execution=e3s1 (search for: “ISGC SNP”). Plink map files to
436 extract marker sets of high quality (29,564 SNPS), pruned (11,405 SNPs), and around core
21
Adaptive Admixture in Soay Sheep 22
437 regions (OAR2 and OAR13) are placed onto the Dryad Database (doi:10.5061/dryad.p88q8).
438 Scripts used for the creation of the simulated datasets and for the haplotypes sharing analysis
439 are available as well. In addition we uploaded the simulated datasets in plink format.
440
22
Adaptive Admixture in Soay Sheep 23
441 References
442 Anderson TM, vonHoldt BM, Candille SI, et al. (2009) Molecular and evolutionary history of 443 melanism in North American gray wolves. Science 323, 1339-1343. 444 Baack EJ, Rieseberg LH (2007) A genomic view of introgression and hybrid speciation. Curr 445 Opin Genet Dev 17, 513-518. 446 Barrett RDH, Schluter D (2008) Adaptation from standing genetic variation. Trends Ecol 447 Evol 23, 38-44. 448 Burke JM, Rieseberg LH (2003) Fitness effects of transgenic disease resistance in sunflowers. 449 Science 300, 1250-1250. 450 Chessa B, Pereira F, Arnaud F, et al. (2009) Revealing the history of sheep domestication 451 using retrovirus integrations. Science 324, 532-536. 452 Clutton-Brock T, Pemberton JM (2004) Soay sheep Cambridge. 453 Coulson T, Catchpole EA, Albon SD, et al. (2001) Age, sex, density, winter weather, and 454 population crashes in Soay sheep. Science 292, 1528-1531. 455 Ellstrand NC, Schierenbeck KA (2000) Hybridization as a stimulus for the evolution of 456 invasiveness in plants? Proc Natl Acad Sci USA 97, 7043-7050. 457 Elwes H (1912) Notes on the primitive breeds of sheep in Scotland. The Scottish Naturalist 2, 458 25-32. 459 Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using 460 the software structure: a simulation study. Mol Ecol 14, 2611-2620. 461 Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus 462 genotype data: Linked loci and correlated allele frequencies. Genetics 164, 1567-1587. 463 Gibbs R, Taylor J, Van Tassell C, et al. (2009) Genome-wide survey of SNP variation 464 uncovers the genetic structure of cattle breeds. Science 324, 528-532. 465 Gibbs RA, Belmont JW, Hardenbol P, et al. (2003) The International HapMap Project. 466 Nature 426, 789-796. 467 Gratten J, Beraldi D, Lowder BV, et al. (2007) Compelling evidence that a single nucleotide 468 substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living 469 population of Soay sheep. P Roy Soc B-Biol Sci 274, 619-626. 470 Gratten J, Pilkington JG, Brown EA, et al. (2010) The genetic basis of recessive self-colour 471 pattern in a wild sheep population. Heredity 104, 206-214. 472 Gratten J, Pilkington JG, Brown EA, et al. (2012) Selection and microevolution of coat pattern 473 are cryptic in a wild population of sheep. Mol Ecol 21, 2977-2990. 474 Gratten J, Wilson AJ, McRae AF, et al. (2008) A localized negative genetic correlation 475 constrains microevolution of coat color in wild sheep. Science 319, 318-320. 476 Halbert ND, Derr JN (2007) A comprehensive evaluation of cattle introgression into US 477 federal bison herds. J Hered 98, 1-12. 478 Kane NC, King MG, Barker MS, et al. (2009) Comparative genomics and population genetic 479 analyses indicate highly porous genomes and high levels of gene flow between 480 divergent Helianthus species. Evolution 63, 2061–2075. 481 Keller SR, Taylor DR (2010) Genomic admixture increases fitness during a biological 482 invasion. J Evol Biol 23, 1720-1731. 483 Kijas JW, Lenstra JA, Hayes B, et al. (2012) Genome-wide analysis of the world's sheep 484 breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol 485 10, e1001258. 486 Kijas JW, Townley D, Dalrymple BP, et al. (2009) A genome wide survey of SNP variation 487 reveals the genetic structure of sheep breeds. PLoS ONE 4, e4668.
23
Adaptive Admixture in Soay Sheep 24
488 Lecis R, Pierpaoli M, Biro ZS, et al. (2006) Bayesian analyses of admixture in wild and 489 domestic cats (Felis silvestris) using linked microsatellite loci. Mol Ecol 15, 119-131. 490 Linnen CR, Kingsley EP, Jensen JD, Hoekstra HE (2009) On the origin and spread of an 491 adaptive allele in deer mice. Science 325, 1095-1098. 492 Mallet J (2005) Hybridization as an invasion of the genome. Trends Ecol Evol 20, 229-237. 493 Morton Boyd J (1981) The Boreray sheep of St Kilda, outer hebrides, Scotland: The natural 494 history of a feral population. Biol Conserv 20, 215-227. 495 Nolte AW, Tautz D (2010) Understanding the onset of hybrid speciation. Trends Genet 26, 496 54. 497 Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using 498 multilocus genotype data. Genetics 155, 945-959. 499 Purcell S, Neale B, Todd-Brown K, et al. (2007) PLINK: A tool set for whole-genome 500 association and population-based linkage analyses. Am J Hum Gen 81, 559-575. 501 Rieseberg LH (2009) Evolution: Replacing genes and traits through hybridization. Curr Biol 502 19, R119-R122. 503 Rosenberg NA (2004) distruct: a program for the graphical display of population structure. 504 Mol Ecol Notes 4, 137-138. 505 Rubin CJ, Megens HJ, Barrio AM, et al. (2013) Strong signatures of selection in the domestic 506 pig genome. Proc Natl Acad Sci USA 109, 19529-19536. 507 Ryder ML (1981) Sheep and the clearances in the Scottish Highlands: a biologist's view. The 508 Agricultural History Review. 509 Sargolzaei M, Schenkel FS (2009) QMSim: a large-scale genome simulator for livestock. 510 Bioinformatics 25, 680-681. 511 Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population 512 genotype data: applications to inferring missing genotypes and haplotypic phase. Am J 513 Hum Gen 78, 629-644. 514 Snow AA, Culley TM, Campbell LG, et al. (2010) Long-term persistence of crop alleles in 515 weedy populations of wild radish (Raphanus raphanistrum). New Phytol 186, 537- 516 548. 517 Staubach F, Lorenc A, Messer PW, et al. (2012) Genome Patterns of Selection and 518 Introgression of Haplotypes in Natural Populations of the House Mouse (Mus 519 musculus). PLoS Genet 8, e1002891. 520 vonHoldt BM, Pollinger JP, Lohmueller KE, et al. (2010) Genome-wide SNP and haplotype 521 analyses reveal a rich history underlying dog domestication. Nature 464, 898-902. 522 Wigginton JE, Cutler DJ, Abecasis GR (2005) A note on exact tests of Hardy-Weinberg 523 Equilibrium. Am J Hum Gen 76, 887-893. 524 Zayed A, Whitfield CW (2008) A genome-wide signature of positive selection in ancient and 525 recent invasive expansions of the honey bee Apis mellifera. Proc Natl Acad Sci USA 526 105, 3421-3426. 527 528
529
24
Adaptive Admixture in Soay Sheep 25
530 Figures
531 Figure 1: Photographs illustrating the close resemblance between Mouflon (top panel left) and
532 Soay sheep with the dark-wild coat phenotype (top panel right). Soay sheep light and dark
533 coat colours are shown in the middle panel while self and wild coat patterns are shown in the
534 lower panel. Top panel shows male sheep while middle and lower panels show lambs. Soay
535 photos by Arpat Ozgul.
536
537 Figure 2: Possible history of sheep breeds on the St Kilda archipelago. Soay sheep have
538 existed on Soay for up to 4000 years. The current Soay sheep study population, on Hirta, was
539 founded in 1932. The St Kildan people occupied Hirta until 1930 and farmed Dunface sheep
540 until the mid 1800s and Scottish Blackface sheep from then until 1930. We hypothesize that
541 admixture took place between Dunface sheep and Soay sheep on Soay, prior to the deliberate
542 introduction of 107 Soay sheep to Hirta in 1932. Breed codes: BOR = Boreray, DNF =
543 Dunface, SBF = Scottish Blackface, SOA = Soay.
544
545 Figure 3: STRUCTURE analysis of the observed genotyping data of 11,405 SNPs. The
546 genetic clustering analysis suggests that there are 4 distinct clusters (left panel). Allocation of
547 individuals to clusters for K = 2-5 (right panel). All values of K suggest that Soay sheep are
548 admixed, each sheep containing approximately 0.20 of a cluster observed in Boreray sheep
549 but not Scottish Blackface sheep. This pattern is consistent with introgression of Dunface
550 alleles. Note the similarity with the simulated admixture scenario in Figure 4. Breed codes as
551 in Figure 2. RMA = Red Maasai
552
25
Adaptive Admixture in Soay Sheep 26
553 Figure 4: Structure outputs at K = 4 for simulated scenarios with (bottom panel) and without
554 (top panel) admixture between Soay and Dunface sheep. Breed codes are as in Figure 2.
555
556 Figure 5: Structure outputs at K = 4 for the simulated admixture scenario using either 11,229
557 (bottom panel) or 1,977 loci (top panel). Breed codes are as in Figure 2.
558
559 Figure 6: Mean and standard deviation of haplotype sharing between Soay sheep and (a) 66
560 HapMap breeds and (b) other sheep and ungulate species for TYRP1 core-region haplotypes
561 in Soay sheep. Most relevant breed/species codes: BOR = Boreray (BOI = Wild Borerays
562 from Boreray, BOW = Farmed Borerays from Wales), SBF= Scottish Blackface, and AMF,
563 EMF, SMF = Mouflon species. More breed/species codes are as in Supplementary Table 1.
564 Breeds/species that shared no core haplotypes with Soay sheep are not shown.
565
566 Figure 7: Mean and standard deviation of haplotype sharing between Soay sheep and (a) 66
567 HapMap breeds and (b) other sheep and ungulate species for ASIP core-region haplotypes in
568 Soay sheep. Most relevant breed/species codes: BOR = Boreray (BOI = Wild Borerays from
569 Boreray, BOW = Farmed Borerays from Wales), SBF= Scottish Blackface, and AMF, EMF,
570 SMF = Mouflon species. More breed/species codes are as in Supplementary Table 1.
571 Breeds/species that shared no core haplotypes with Soay sheep are not shown.
26
Adaptive Admixture in Soay Sheep 27
572 Figure 1
573
27
Adaptive Admixture in Soay Sheep 28
574 Figure 2
575
576
28
Adaptive Admixture in Soay Sheep 29
577 Figure 3
K = 2
K = 3
K = 4*
K = 5
SOA BOR SBF RMA
578
579
29
Adaptive Admixture in Soay Sheep 30
580 Figure 4
e
r
u
t
x
i
m
d
a
o
n
e
r
u
t
x
i
m
d a
581 SOA BOR SBF RMA
582
30
Adaptive Admixture in Soay Sheep 31
583 Figure 5
i
c
o
l
7
7
9
1
i
c
o
l
9
2
2
1 1
584 SOA BOR SBF RMA
585
31
Adaptive Admixture in Soay Sheep 32
586 Figure 6
a)
7 7
6 6
5 5
4 4
3 3
2 2
1 1
0 0
I I I I I I
T L T T L T
S S
P S B S A E S A P S B S A E S A
D U N R U D U N R U
M M M M
W S W S
O H O H
L F L F
F F
B R A B R A
D P S C G G O D P S C G G O
H H
P O H P O H
H M B H M B
B O B O
C C
A A
A C A C
B B B B
A A A B B B B C A A A B B B B C
A B C A B C
B B C B B C
B B
7 7
) ) b
b 6 6
M M
( (
g g
n n i
i 5 5
r r
a a
h h s
s 4 4
e e
p p
y y t
t 3 3
o o
l l
p p
a a h
h 2 2
n n
a a e
e 1 1
M M
0 0
Z L F Z L F
E E
B S X S A A B S X S A A
H N R N R C C C R G H N R N R C C C R G
M M M M
W W
I I
F A T S L F A T S L
E E
S M R A R A E Q S M R A R A E Q
M C U D I O M C U D I O
O P F C O P F C
I I
E E
G G L L G G L L
E E K M E E K M
D G N D G N
C G G M C G G M
C C M C C M
M M
7 7
6 6
5 5
4 4
3 3
2 2
1 1
0 0
Z F Z L Z F Z L
P X A A A A B B S S E X A B S S P X A A A A B B S S E X A B S S
M M I M M I
I I
J J
T E B K T T T E B K T T
S A A B B S A A B B
D R D R
M T M T
M M M M
O U W O U W
W W
O S S S S O S S S S
N Q S S V N Q S S V
N R V N R V
R S R S
R R S S R R S S
R R
Non-Soay breed Non-Soay breed b)
7 )
b 6
M (
Core haplotype
g n
i 5 r
a T1-GGGAGA-Dark
h s
4
e T2-ACAGGA-Dark
p
y t
o 3
l T3-ACGAGA-Dark
p
a h
2 T5-GCAGGA-Dark
n a
e 1 T6-ACGAAC-Light M
0 T7-GGGAAC-Light
I
F F F
G
V
M M M
O
O
A E S B
587 Other species
588
32
7 7
6 6
5 5
4 4
3 3
2 2
1 1
0 0
I I I I
I I
T L T T L T
P S B S A E S S A P S B S A E S S A
D U N R U D U N R U
M M M M
S S
W W
O O
H H
L F L F
F F
B R B R
A A
D P S C G G O H D P S C G G O H
P O H P O H
H M B H M B
B O B O
C C
A A
A C A C
B B B B
A A A B B B B C A A A B B B B C
A B C A B C
B B C B B C
B B
7 7
) ) b
b 6 6
M M
( (
g g
n n i
i 5 5
r r
a a
h h s
s 4 4
e e
p p
y y t
t 3 3
o o
l l
p p
a a h
h 2 2
n n
a a e
e 1 1
M M
0 0
F F
Z L Z L
E B S X S A A E B S X S A A
H N R N R C C C R G H N R N R C C C R G
M M
M M
W W
I I
F S L F S L
A T A T
S M R A R A E E Q S M R A R A E E Q
M C U D I O M C U D I O
F C F C
O P O P
I I
E E
G G L L G G L L
E E K M E E K M
D G N D G N
C G G M C G G M
C C M C C M
M M
7 7
6 6
5 5
4 4
3 3
2 2
1 1
0 0
Z F Z Z F Z
L L
A A B B A A B B
P X A A B S S E X A S S P X A A B S S E X A S S
M M I M M I
I I
J J
T E B K T T T E B K T T
S A A B B S A A B B
D R D R
M M M T M M M T
O U W O U W
W W
O S S S S O S S S S
N Q S S V N Q S S V
N R V N R V
R S R S
R R S S R R S S
R R
Non-Soay breed Non-Soay breed Adaptive Admixture in Soay Sheep 33
589 Figure 7
a) )
) 8 8
b b
M M
( (
g g
n n
i i r
r 6 6
a a
h h
s s
e e p
p 4 4
y y
t t
o o
l l
p p
a a
h h
2 2
n n
a a
e e
M M
0 0
I I I I
I I
L L
T T Z T T Z
P S B S A E S S A E B S P S B S A E S S A E B S
D U N R U H N R N D U N R U H N R N
M M M M M M
S W S W
W W W W
O I O I
H H
L F L F
F F A F F A
B B
A A
D P S C G G O H S M R A D P S C G G O H S M R A
P O H M F C P O H M F C
H M B O P F H M B O P F
B O B O
C C
A A
A C E A C E
B G B G
A A A B B B B C E E A A A B B B B C E E
A B C D E G A B C D E G
B B C C G B B C C G
B C C B C C 8 8
6 6
4 4
2 2
0 0
F Z Z F Z F Z Z F Z
X S A A P X A A A A B B S S E X A B S S X S A A P X A A A A B B S S E X A B S S
R C C C R G R C C C R G
M M M M M M
I I
J J
S L B K T T S L B K T T
T T E T T E
D S A A B B D S A A B B
R A E E Q D R R A E E Q D R
U D I O M M M T U D I O M M M T
C U W C U W
O O
I I
O S S S S O S S S S
G L L N Q S S V G L L N Q S S V
K M N N R V K M N N R V
N R S N R S
G M R R S S G M R R S S
M R M R
M M b) Non-Soay breed
8
)
b
M
(
g
n 6 i
r Core haplotype
a
h
s
e
p 4 A1-AAGGAA-Wild
y
t o
l A2-AAGAGG-Wild
p
a h
2 A3-CGAGAA-Self
n a
e A4-AGAGAA-Self M
0
F F F
M M M
A E S 590 Other species
591
33
)
) 8 8
b b
M M
( (
g g
n n
i i r
r 6 6
a a
h h
s s
e e p
p 4 4
y y
t t
o o
l l
p p
a a
h h
2 2
n n
a a
e e
M M
0 0
I I I I I I
T T Z L T T Z L
S E S E
P S B S A E S A B S P S B S A E S A B S
N N
D U N R U H R N D U N R U H R N
M M M M M M
W S W W W S W W
O H I O H I
L F L F
F F A F F A
B A B A
D P S C G G O M R D P S C G G O M R
H S A H S A
P O H M F C P O H M F C
H M B O P F H M B O P F
B O B O
C C
A A
A C E A C E
B G B G
A A A B B B B C E E A A A B B B B C E E
A B C D E G A B C D E G
B B C C G B B C C G
B C C B C C 8 8
6 6
4 4
2 2
0 0
F Z F Z
Z F Z Z F Z
X S A A P X A A A A B B S S E X A B S S X S A A P X A A A A B B S S E X A B S S
R C C C R G R C C C R G
M M M M M M
I I
J J
T S L T E B K T T T S L T E B K T T
A B B A B B
D S A D S A
R A E E Q D R R A E E Q D R
U D I O M M M T U D I O M M M T
C O U W C O U W
I I
O S S S S O S S S S
G L L N Q S S V G L L N Q S S V
K M N N R V K M N N R V
N R S N R S
G M R R S S G M R R S S
M R M R
M M Adaptive Admixture in Soay Sheep 34
592 Tables
593 Table 1: Extent of haplotype sharing between Soay sheep and other ovine HapMap breeds for
594 TYRP1 and ASIP-region core haplotypes present in Soay sheep. The common Soay haplotypes for
595 each morph are shaded grey. Note that the most common dark and wild haplotypes (T1 and A1)
596 have low haplotype sharing with Boreray sheep and all other breeds, suggesting they are ancestral.
597 In contrast the common light and self haplotypes (T6 and A3) have significant haplotype sharing
598 with Boreray sheep, suggesting a more recent common ancestry.
599
Hap1 Soay sheep HapMap Global HS5 Max HS6 BOR HS8
Freq2 Phenotype3 Breeds4 Mean/SD Mean/Breed7 Mean/SD t (df) P TYRP1 T1 0.366 Dark 63 2.32/0.39 3.04/GAR 2.25/0.20 -0.18 (61) 0.57 T2 0.071 Dark 11 2.93/0.86 4.80/BOR 4.80/0.40 3.52 (9) 3.24 x 10-3 T3 0.006 Dark 35 2.25/0.28 2.90/GAR 2.18/0.04 -0.26 (33) 0.60 T4 0.004 Dark 1 2.69/0.00 2.69/VRS - - - T5 0.003 Dark 20 2.33/0.66 4.11/BOR 4.11/1.20 4.29 (18) 2.21 x 10-4 T6 0.538 Light 14 2.96/0.93 5.67/BOR 5.67/1.15 9.99 (12) 1.80 x 10-7 T7 0.012 Light 18 2.36/0.34 2.59/LAC - - - Total 1.000 66 2.35/0.45 5.67/BOR 4.75/1.74 ASIP A1 0.714 Wild 56 2.19/0.65 3.31/EFW 2.09/0.26 -0.14 (54) 0.56 A2 0.082 Wild 25 2.57/1.42 6.40/BOR 6.40/1.36 6.32 (23) 9.51 x 10-7 A3 0.199 Self 34 2.09/0.80 4.65/GUR 4.31/1.49 3.02 (32) 2.45 x 10-3 A4 0.005 Self 59 1.89/0.42 3.20/ISF 1.88/0.13 -0.02 (57) 0.51 Total 1.000 66 2.18/0.68 6.40/BOR 2.37/1.09 600 1 Core haplotypes are defined in Supplementary Table 2. HaplotypesT1-T7 are from the TYRP1-region ; haplotypes A1- 601 A4 are from the ASIP-region. 602 2 Haplotype frequency in Soay sheep (N=486). 603 3 Phenotypic association of each core haplotype in Soays. 604 4 Number of breeds in the Ovine HapMap project that were found to share each core haplotype identified in Soays 605 5 Mean and standard deviation (SD) of haplotype sharing (HS) with Soays for each core haplotype in all non-Soay 606 breeds. 607 6 Maximum observed mean haplotype sharing with Soays for each core haplotype and the respective breed. 608 7 Breeds and sample sizes in the Ovine HapMap consortium study are defined in Supplementary Table 1. 609 8 Summary of haplotype sharing for each core haplotype between Soays and Boreray (BOR) sheep. The adjusted P- 610 value for significance at α=0.05 is 4.55 x 10-3 based on testing of 11 core haplotypes in Borerays. 611 612
34