Sweepstakes reproductive success via pervasive and recurrent selective sweeps

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Tables

Appendix 7—table 1

	GL1 likelihood					GL2 likelihood
	${\theta }_W$	${\theta }_{\pi }$	$D_T$	$D_F$	nSites	${\theta }_W$	${\theta }_{\pi }$	$D_T$	$D_F$	nSites
Chr01	0.0046	0.0024	−1.64	−5.77	18332422	0.0056	0.0025	−1.84	−6.71	18332093
Chr02	0.0050	0.0020	−1.98	−6.00	15828347	0.0060	0.0022	−2.11	−6.84	15828079
Chr03	0.0053	0.0020	−2.09	−6.22	20202769	0.0063	0.0021	−2.21	−6.98	20202435
Chr04	0.0054	0.0020	−2.08	−6.03	22584280	0.0065	0.0022	−2.19	−6.79	22583924
Chr05	0.0053	0.0020	−2.10	−6.22	15542562	0.0064	0.0021	−2.22	−6.99	15542313
Chr06	0.0052	0.0019	−2.11	−6.33	17720989	0.0062	0.0021	−2.22	−7.09	17720709
Chr07	0.0056	0.0022	−2.01	−5.88	21080002	0.0066	0.0024	−2.13	−6.64	21079620
Chr08	0.0054	0.0020	−2.09	−6.09	18353883	0.0065	0.0022	−2.21	−6.85	18353624
Chr09	0.0053	0.0019	−2.13	−6.42	18195728	0.0063	0.0021	−2.25	−7.16	18195437
Chr10	0.0051	0.0019	−2.09	−6.27	17450729	0.0061	0.0020	−2.21	−7.06	17450432
Chr11	0.0050	0.0018	−2.14	−6.54	20138893	0.0059	0.0019	−2.26	−7.32	20138619
Chr12	0.0043	0.0016	−2.14	−6.32	19448827	0.0053	0.0017	−2.26	−7.18	19448580
Chr13	0.0049	0.0018	−2.14	−6.38	18651575	0.0059	0.0019	−2.26	−7.18	18651311
Chr14	0.0053	0.0019	−2.14	−6.34	20704894	0.0063	0.0020	−2.25	−7.09	20704623
Chr15	0.0054	0.0019	−2.17	−6.41	18100213	0.0064	0.0020	−2.27	−7.15	18099944
Chr16	0.0051	0.0019	−2.09	−6.13	22233178	0.0061	0.0021	−2.21	−6.93	22232862
Chr17	0.0053	0.0020	−2.06	−5.99	11813809	0.0063	0.0022	−2.18	−6.78	11813609
Chr18	0.0053	0.0019	−2.11	−6.23	15931558	0.0063	0.0021	−2.23	−7.01	15931312
Chr19	0.0055	0.0020	−2.10	−6.23	13858302	0.0065	0.0022	−2.21	−6.98	13858066
Chr20	0.0050	0.0018	−2.15	−6.56	16371168	0.0059	0.0019	−2.27	−7.33	16370967
Chr21	0.0052	0.0019	−2.10	−6.29	14440220	0.0062	0.0021	−2.22	−7.07	14440024
Chr22	0.0054	0.0020	−2.08	−6.12	13838440	0.0065	0.0022	−2.19	−6.89	13838214
Chr23	0.0052	0.0020	−2.08	−6.27	14698719	0.0062	0.0021	−2.20	−7.05	14698473
All	0.0052	0.0019	−2.08	−6.22	17631370	0.0062	0.0021	−2.20	−7.00	17631099

Appendix 7—table 2

	GL1 likelihood					GL2 likelihood
	${\theta }_W$	${\theta }_{\pi }$	$D_T$	$D_F$	nSites	${\theta }_W$	${\theta }_{\pi }$	$D_T$	$D_F$	nSites
Chr01	0.0068	0.0037	−1.51	−5.99	16159362	0.0090	0.0040	−1.84	−7.55	16159148
Chr02	0.0069	0.0030	−1.86	−6.18	14306627	0.0092	0.0034	−2.10	−7.65	14306351
Chr03	0.0073	0.0029	−1.99	−6.38	18283815	0.0096	0.0033	−2.19	−7.76	18283555
Chr04	0.0074	0.0030	−1.97	−6.14	20435443	0.0097	0.0034	−2.17	−7.52	20435122
Chr05	0.0073	0.0029	−2.00	−6.36	13933982	0.0096	0.0032	−2.20	−7.74	13933752
Chr06	0.0072	0.0028	−2.00	−6.46	16048768	0.0094	0.0032	−2.21	−7.84	16048531
Chr07	0.0076	0.0034	−1.83	−6.06	19008270	0.0099	0.0038	−2.05	−7.46	19007926
Chr08	0.0074	0.0030	−1.98	−6.20	16559106	0.0097	0.0033	−2.18	−7.59	16558861
Chr09	0.0073	0.0028	−2.03	−6.59	16381498	0.0096	0.0032	−2.23	−7.93	16381249
Chr10	0.0070	0.0028	−1.98	−6.42	15789838	0.0093	0.0032	−2.19	−7.83	15789584
Chr11	0.0069	0.0026	−2.04	−6.73	18211081	0.0091	0.0029	−2.24	−8.12	18210846
Chr12	0.0061	0.0024	−2.03	−6.52	17597347	0.0082	0.0027	−2.24	−8.07	17597135
Chr13	0.0068	0.0026	−2.04	−6.58	16846892	0.0090	0.0029	−2.24	−8.01	16846697
Chr14	0.0073	0.0028	−2.04	−6.52	18699877	0.0095	0.0031	−2.23	−7.89	18699625
Chr15	0.0074	0.0028	−2.06	−6.54	16349327	0.0097	0.0031	−2.25	−7.86	16349118
Chr16	0.0070	0.0028	−1.98	−6.27	20259494	0.0092	0.0032	−2.19	−7.71	20259231
Chr17	0.0072	0.0030	−1.93	−6.09	10667396	0.0095	0.0033	−2.15	−7.52	10667225
Chr18	0.0072	0.0029	−2.00	−6.39	14305479	0.0095	0.0032	−2.21	−7.79	14305261
Chr19	0.0075	0.0030	−1.98	−6.33	12465223	0.0098	0.0034	−2.18	−7.68	12465024
Chr20	0.0069	0.0026	−2.06	−6.73	14829191	0.0091	0.0029	−2.25	−8.11	14829009
Chr21	0.0071	0.0029	−1.99	−6.43	13014009	0.0094	0.0032	−2.20	−7.83	13013813
Chr22	0.0074	0.0030	−1.97	−6.30	12407034	0.0097	0.0034	−2.17	−7.70	12406815
Chr23	0.0072	0.0029	−1.97	−6.40	13273011	0.0094	0.0032	−2.18	−7.81	13272801
All	0.0071	0.0029	−1.97	−6.37	15905742	0.0094	0.0032	−2.18	−7.78	15905508

Appendix 7—table 3

Age	Age		’48–’52	’63–’67	GM	May
	class	${\overline{l}}_i$	li	li	$b_i\times {10}^6$	$b_i\times {10}^6$
0	1	1.0000	1.0000	1.0000	0.00	0
1	2	0.3396	0.4966	0.2369	0.00	0
2	3	0.1153	0.2466	0.0561	0.00	0
3	4	0.0392	0.1225	0.0133	0.38	0.52
4	5	0.0133	0.0608	0.0032	0.62	0.78
5	6	0.0045	0.0302	0.0007	1.01	1.15
6	7	0.0015	0.0150	0.0002	1.59	1.67
7	8	0.0005	0.0074	0.0000	2.37	2.31
8	9	0.0002	0.0037	0.0000	3.28	3.03
9	10	0.0001	0.0018	0.0000	4.24	3.73
10	11	0.0000	0.0009	0.0000	5.30	4.48
11	12	0.0000	0.0005	0.0000	6.41	5.24
12	13	0.0000	0.0002	0.0000	7.68	6.07
13	14	0.0000	0.0001	0.0000	8.79	6.78
14	15	0.0000	0.0001	0.0000	10.42	7.79
$C$		10.5	7.9	17.6		20.0
$G$		5.1	6.3	4.6		4.6
$C/G$		2.1	1.3	3.8		3.8

Appendix 7—table 4

Chromosome	$p$ per site	$\mu =p$ per site per year	Number of substitutions per year	Number of years per substitution	Number of sites
Chr01	0.00504	$7.21\times {10}^{-10}$	0.022	45	30875876
Chr02	0.00500	$7.14\times {10}^{-10}$	0.021	49	28732775
Chr03	0.00492	$7.03\times {10}^{-10}$	0.022	46	30954429
Chr04	0.00490	$7.00\times {10}^{-10}$	0.031	33	43798135
Chr05	0.00512	$7.31\times {10}^{-10}$	0.018	54	25300426
Chr06	0.00508	$7.25\times {10}^{-10}$	0.020	50	27762770
Chr07	0.00511	$7.29\times {10}^{-10}$	0.025	40	34137969
Chr08	0.00497	$7.11\times {10}^{-10}$	0.021	47	29710654
Chr09	0.00518	$7.40\times {10}^{-10}$	0.020	51	26487948
Chr10	0.00513	$7.33\times {10}^{-10}$	0.020	50	27234273
Chr11	0.00505	$7.22\times {10}^{-10}$	0.022	45	30713045
Chr12	0.00495	$7.08\times {10}^{-10}$	0.022	46	30948897
Chr13	0.00523	$7.47\times {10}^{-10}$	0.022	46	28829685
Chr14	0.00508	$7.26\times {10}^{-10}$	0.021	47	29586942
Chr15	0.00499	$7.13\times {10}^{-10}$	0.020	49	28657694
Chr16	0.00498	$7.12\times {10}^{-10}$	0.025	40	34794352
Chr17	0.00502	$7.16\times {10}^{-10}$	0.016	64	21723002
Chr18	0.00513	$7.33\times {10}^{-10}$	0.018	55	24902675
Chr19	0.00529	$7.56\times {10}^{-10}$	0.017	60	22015597
Chr20	0.00506	$7.23\times {10}^{-10}$	0.018	56	24843429
Chr21	0.00521	$7.45\times {10}^{-10}$	0.017	60	22358821
Chr22	0.00516	$7.37\times {10}^{-10}$	0.018	57	23744039
Chr23	0.00529	$7.56\times {10}^{-10}$	0.019	52	25242006
Average	0.00508	$7.26\times {10}^{-10}$	0.021	49	28406758
Genome	0.00507	$7.25\times {10}^{-10}$	0.474	2	653355439

Appendix 7—table 5

Term	Description
High fecundity	The ability of organisms (e.g. broadcast spawners) to produce huge numbers of offspring, or on the order of the population size
Sweepstakes reproduction	High variance and high skew in the distribution of number of offspring, where most of the time individuals produce small (relative to the population size) number of offspring, but occasionally a few individuals contribute the bulk of the offspring forming a new generation of reproducing individuals
Random sweepstakes	A chance matching of reproduction in a highly fecund population with favorable environmental conditions; random sweepstakes is one example of a mechanism turning high fecundity into sweepstakes reproduction
Selective sweepstakes	A mechanism turning high fecundity into sweepstakes reproduction, in which juveniles pass through selective filters during their development, resulting in highly skewed offspring distribution
Moran model	A population model of genetic reproduction, in which a single random individual produces one offspring replacing another individual that perishes to keep the population size constant
Genealogy	The ancestral relations of a sample of gene copies (see Appendix 6—figure 21)
Coalescent	A probabilistic model of the random ancestral relations of a hypothetical sample of gene copies
Multiple-merger coalescent	A coalescent process in which a random number of ancestral lineages merges each time (see Appendix 6—figure 21)
$\mathrm{\Xi }$-Beta $(2-\alpha ,\alpha )$-coalescent	A multiple-merger coalescent derived from a model of random sweepstakes
Durrett–Schweinsberg model	A model of recurrent selective sweeps of a new beneficial mutation each time approximating selective sweepstakes
Durrett–Schweinsberg coalescent	A coalescent model for the genealogy at a single site linked to a site experiencing beneficial mutation; during a sweep some lineages of the neutral site may escape a sweep through recombination (see Appendix 6—figure 21)

Appendix 7—table 6

Parameter	ABC prior
${\displaystyle \alpha }$ for the Beta ($2-\alpha ,\alpha$)-coalescent	Uniform between 1.01 and 1.99
${\displaystyle \beta }$, the growth rate for the Beta ($2-\alpha ,\alpha$)-coalescent with population growth	Improper, uniform prior on the whole positive half-line
$c$ for the single-locus DS model	Improper, uniform prior on the whole positive half-line
$c$ for the DS model with recombination	Uniform between 10 and 25 (to force consistency with the posterior in the single-locus analysis)
$\gamma /s$, the ratio of the recombination rate and the selection coefficient, in the DS model with recombination	Uniform between 0 and 10,000
θ, the mutation rate in the DS model with recombination	Uniform between 0 and 10,000
Fraction of whole-chromosome sweeps in the DS model with recombination	Uniform between 0 and 1

Appendix 7—table 7

Chromosome	All sites,$L$	Invariant sites,$I$	Segregating sites,$S$	Fixed sites,$F$	Substitutions per year	Years per substitution
Chr01	18350418	17736728	468247	145443	0.042	24
Chr02	15850624	15269222	437440	143962	0.041	24
Chr03	20231166	19467361	592044	171761	0.049	20
Chr04	22623179	21742567	673837	206775	0.059	17
Chr05	15557754	14963290	457852	136612	0.039	26
Chr06	17738562	17090577	506727	141258	0.040	25
Chr07	21107906	20282169	645738	180000	0.051	19
Chr08	18381649	17681336	549023	151290	0.043	23
Chr09	18212083	17528065	533448	150571	0.043	23
Chr10	17472145	16829837	491408	150899	0.043	23
Chr11	20157683	19439102	550466	168115	0.048	21
Chr12	19475709	18838352	465219	172138	0.049	20
Chr13	18669907	18002288	504278	163341	0.047	21
Chr14	20723905	19946397	605101	172407	0.049	20
Chr15	18123369	17435024	538832	149513	0.043	23
Chr16	22268819	21460587	624520	183712	0.052	19
Chr17	11831346	11376461	344921	109964	0.031	32
Chr18	15955850	15348766	461840	145244	0.041	24
Chr19	13869827	13314508	421341	133978	0.038	26
Chr20	16390870	15807585	448550	134735	0.038	26
Chr21	14455156	13911966	414247	128943	0.037	27
Chr22	13854159	13314972	413965	125222	0.036	28
Chr23	14714440	14154540	424496	135403	0.039	26
Mean	17652892	16997465	503197	152230	0.043	23
Genome	406016526	390941701	11573540	3501286	1.000	1

Appendix 7—table 8

Chromosome	All sites,$L$	Invariant sites,$I$	Segregating sites,$S$	Fixed sites,$F$	Substitutions per year	Years per substitution
Chr01	18350189	17645066	561297	143825	0.041	24
Chr02	15850406	15184885	523368	142153	0.041	25
Chr03	20230947	19356488	704986	169473	0.048	21
Chr04	22622912	21614191	804994	203726	0.058	17
Chr05	15557576	14877918	544750	134908	0.039	26
Chr06	17738379	16995520	603445	139414	0.040	25
Chr07	21107635	20164813	765533	177289	0.051	20
Chr08	18381450	17578929	653357	149164	0.043	23
Chr09	18211894	17429901	633282	148712	0.042	24
Chr10	17471932	16736760	586177	148995	0.043	23
Chr11	20157484	19333140	658299	166045	0.047	21
Chr12	19475530	18739806	565949	169775	0.049	21
Chr13	18669720	17904983	603304	161433	0.046	22
Chr14	20723717	19835886	717441	170390	0.049	21
Chr15	18123186	17334782	640824	147580	0.042	24
Chr16	22268589	21341070	746271	181248	0.052	19
Chr17	11831198	11309988	412831	108379	0.031	32
Chr18	15955648	15261569	550677	143402	0.041	24
Chr19	13869662	13237797	499507	132359	0.038	26
Chr20	16390728	15721255	536397	133077	0.038	26
Chr21	14454994	13833280	494317	127397	0.036	27
Chr22	13853971	13237823	492661	123487	0.035	28
Chr23	14714263	14074517	506140	133606	0.038	26
Mean	17652696	16902190	600252	150254	0.043	23
Genome	406012010	388750367	13805807	3455837	0.987	1

Appendix 7—table 9

Chromosome	PCA group	South/south-east					Þistilfjörður
		$O$	$E$	$p$	$X^2$	$P$	$O$	$E$	$p$	$X^2$	$P$
Chr01	AA	7	7.44	0.33	0.06	0.80	31	28.52	0.63	1.60	0.21
Chr01	AB	31	30.11				28	32.96
Chr01	BB	30	30.44				12	9.52
Chr02	CC	41	30.76	0.76	0.69	0.41	36	39.56	0.75	4.99	0.03
Chr02	CD	22	24.47				34	26.87
Chr02	DD	5	3.76				1	4.56
Chr07	EE	48	48.62	0.85	0.33	0.56	42	43.38	0.78	0.92	0.36
Chr07	EF	19	17.76				27	24.23
Chr07	FF	1	1.62				2	3.38
Chr12	GG	62	61.13	0.96	0.14	0.70	62	61.35	0.93	1.38	0.24
Chr12	GH	6	5.74				8	9.30
Chr12	HH	0	0.13				1	0.35

Appendix 7—table 10

Case	Average number of segregating sites	Average$\mathrm{\Pi }$	Average π per seg site
A	8934.5	1257.0	0.14
B	7765.2	872.2	0.11
C	15568.8	2248.7	0.14
D	9896.6	1574.0	0.16
E	13001.8	1426.9	0.11
F	18857.7	3370.9	0.18

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