Phenotype SNPs from prehistoric Spain

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for new genomes from prehistoric Spain. Nonzero derived allele counts are highlighted. Note that small derived allele counts may be due to DNA damage.

ASIP, rs2424984, Veddoid brown skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	5/5
ATP019	Early Neolithic	5215–5030	4/4
POR002	Copper Age	3335–2944	2/2
ATP016	Copper Age	3261–2916	14/14
ATP12	Copper Age	3010–2879	3/3
ATP002	Copper Age	2899–2678	8/8
ESP005	Bronze Age	2200–1550	3/3

ASIP, rs6058017, Veddoid brown skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	8/8
ATP019	Early Neolithic	5215–5030	2/2
ATP016	Copper Age	3261–2916	11/11
ATP12	Copper Age	3010–2879	1/1
ATP002	Copper Age	2899–2678	5/5
ESP005	Bronze Age	2200–1550	1/1

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/8
ATP019	Early Neolithic	5215–5030	0/7
C40331	Late Neolithic	3760–3637	0/1
POR003	Copper Age	3622–3369	0/2
ATP016	Copper Age	3261–2916	0/17
POR004	Copper Age	3091–2917	0/2
ATP12	Copper Age	3010–2879	0/1
ATP002	Copper Age	2899–2678	0/14
ESP005	Bronze Age	2200–1550	0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/3
ATP019	Early Neolithic	5215–5030	0/1
C40331	Late Neolithic	3760–3637	1/4
POR003	Copper Age	3622–3369	0/1
ATP016	Copper Age	3261–2916	0/20
ATP12	Copper Age	3010–2879	0/4
ATP002	Copper Age	2899–2678	0/16
ESP005	Bronze Age	2200–1550	0/1

KITLG, rs12821256, blond hair

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/2
ATP005	Early Neolithic	5215–5030	0/1
ATP019	Early Neolithic	5215–5030	0/3
POR003	Copper Age	3622–3369	0/1
POR002	Copper Age	3335–2944	0/1
ATP016	Copper Age	3261–2916	0/12
ATP12	Copper Age	3010–2879	0/5
ATP002	Copper Age	2899–2678	0/13
ESP005	Bronze Age	2200–1550	0/3
PIR001	Bronze Age	2200–1550	0/1

KITLG, rs642742, Veddoid brown skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	8/8
ATP019	Early Neolithic	5215–5030	3/3
C40331	Late Neolithic	3760–3637	0/2
POR003	Copper Age	3622–3369	1/1
ATP016	Copper Age	3261–2916	20/20
ATP12	Copper Age	3010–2879	1/5
ATP002	Copper Age	2899–2678	4/12

MC1R, rs1110400, red hair

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/7
ATP019	Early Neolithic	5215–5030	0/2
C40331	Late Neolithic	3760–3637	0/1
POR002	Copper Age	3335–2944	0/2
ATP016	Copper Age	3261–2916	0/19
ATP002	Copper Age	2899–2678	0/13
ESP005	Bronze Age	2200–1550	0/5
PIR001	Bronze Age	2200–1550	0/2

MC1R, rs11547464, red hair

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	1/4
ATP005	Early Neolithic	5215–5030	0/1
ATP019	Early Neolithic	5215–5030	0/3
SAN216	Late Neolithic	3776–3653	0/2
POR002	Copper Age	3335–2944	0/3
ATP016	Copper Age	3261–2916	0/19
ATP002	Copper Age	2899–2678	0/13
ESP005	Bronze Age	2200–1550	0/7
PIR001	Bronze Age	2200–1550	0/1

MC1R, rs1805005, blond hair, fair skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/5
ATP019	Early Neolithic	5215–5030	0/3
C40331	Late Neolithic	3760–3637	0/1
POR002	Copper Age	3335–2944	0/1
ATP016	Copper Age	3261–2916	0/16
ATP12	Copper Age	3010–2879	0/4
ATP002	Copper Age	2899–2678	0/6
ESP005	Bronze Age	2200–1550	0/5

MC1R, rs1805006, red hair, fair skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/7
ATP019	Early Neolithic	5215–5030	0/5
POR002	Copper Age	3335–2944	0/2
ATP016	Copper Age	3261–2916	0/15
ATP12	Copper Age	3010–2879	0/3
ATP002	Copper Age	2899–2678	0/10
ESP005	Bronze Age	2200–1550	0/4

MC1R, rs1805007, red hair, fair skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	2/7
ATP005	Early Neolithic	5215–5030	0/1
ATP019	Early Neolithic	5215–5030	0/3
SAN216	Late Neolithic	3776–3653	0/2
POR002	Copper Age	3335–2944	0/2
ATP016	Copper Age	3261–2916	0/21
ATP002	Copper Age	2899–2678	0/15
ESP005	Bronze Age	2200–1550	0/6
PIR001	Bronze Age	2200–1550	1/2

MC1R, rs1805008, red hair, fair skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/5
ATP019	Early Neolithic	5215–5030	0/1
C40331	Late Neolithic	3760–3637	0/1
POR002	Copper Age	3335–2944	0/1
ATP016	Copper Age	3261–2916	0/20
ATP002	Copper Age	2899–2678	0/10
ESP005	Bronze Age	2200–1550	0/6
PIR001	Bronze Age	2200–1550	0/1

MC1R, rs1805009, red hair, fair skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/3
ATP019	Early Neolithic	5215–5030	0/4
POR002	Copper Age	3335–2944	0/3
ATP016	Copper Age	3261–2916	0/21
ATP12	Copper Age	3010–2879	0/7
ATP002	Copper Age	2899–2678	0/8
ESP005	Bronze Age	2200–1550	0/4

MCM6, rs182549, ability to digest milk

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/5
ATP019	Early Neolithic	5215–5030	0/5
C40331	Late Neolithic	3760–3637	0/2
POR002	Copper Age	3335–2944	0/2
ATP016	Copper Age	3261–2916	0/15
ATP12	Copper Age	3010–2879	0/4
ATP002	Copper Age	2899–2678	0/6
ESP005	Bronze Age	2200–1550	1/1

MCM6, rs4988235, ability to digest milk

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/4
ATP019	Early Neolithic	5215–5030	0/6
ATP016	Copper Age	3261–2916	0/17
ATP12	Copper Age	3010–2879	0/5
ATP002	Copper Age	2899–2678	0/19
ESP005	Bronze Age	2200–1550	0/3

OCA2, rs1800407, green or hazel eyes

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/4
ATP019	Early Neolithic	5215–5030	0/2
SAN216	Late Neolithic	3776–3653	0/1
POR002	Copper Age	3335–2944	0/1
ATP016	Copper Age	3261–2916	0/13
ATP12	Copper Age	3010–2879	0/6
ATP002	Copper Age	2899–2678	0/12
ESP005	Bronze Age	2200–1550	0/1

OCA2, rs1800414, Mongoloid light skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/2
ATP019	Early Neolithic	5215–5030	0/3
POR002	Copper Age	3335–2944	0/1
ATP016	Copper Age	3261–2916	0/22
ATP12	Copper Age	3010–2879	0/6
ATP002	Copper Age	2899–2678	0/16
ESP005	Bronze Age	2200–1550	0/6
PIR001	Bronze Age	2200–1550	0/1

OCA2/HERC2, rs12913832, blue eyes

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	1/3
ATP019	Early Neolithic	5215–5030	0/3
SAN216	Late Neolithic	3776–3653	0/1
C40331	Late Neolithic	3760–3637	0/1
POR002	Copper Age	3335–2944	0/3
ATP016	Copper Age	3261–2916	0/21
POR004	Copper Age	3091–2917	0/1
ATP12	Copper Age	3010–2879	0/6
ATP002	Copper Age	2899–2678	6/8

SLC24A5, rs1426654, Caucasoid light skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	2/2
ATP019	Early Neolithic	5215–5030	3/3
SAN216	Late Neolithic	3776–3653	1/1
C40331	Late Neolithic	3760–3637	0/3
POR002	Copper Age	3335–2944	1/1
ATP016	Copper Age	3261–2916	18/18
POR004	Copper Age	3091–2917	1/1
ATP12	Copper Age	3010–2879	3/3
ATP002	Copper Age	2899–2678	13/13
ESP005	Bronze Age	2200–1550	3/3

SLC45A2, rs16891982, Caucasoid light skin

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	4/4
POR003	Copper Age	3622–3369	1/1
ATP016	Copper Age	3261–2916	6/13
POR004	Copper Age	3091–2917	0/1
ATP12	Copper Age	3010–2879	0/3
ATP002	Copper Age	2899–2678	0/8
ESP005	Bronze Age	2200–1550	1/4
PIR001	Bronze Age	2200–1550	1/1

TYR, rs1042602, light skin, absence of freckles

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/6
ATP019	Early Neolithic	5215–5030	0/4
SAN216	Late Neolithic	3776–3653	0/1
C40331	Late Neolithic	3760–3637	0/1
POR003	Copper Age	3622–3369	0/1
POR002	Copper Age	3335–2944	0/6
ATP016	Copper Age	3261–2916	0/20
ATP12	Copper Age	3010–2879	0/1
ATP002	Copper Age	2899–2678	4/10
ESP005	Bronze Age	2200–1550	0/1

TYR, rs1393350, blond hair, blue eyes

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	0/6
ATP005	Early Neolithic	5215–5030	0/1
ATP019	Early Neolithic	5215–5030	0/1
C40331	Late Neolithic	3760–3637	1/1
POR002	Copper Age	3335–2944	1/2
ATP016	Copper Age	3261–2916	0/19
POR004	Copper Age	3091–2917	1/1
ATP12	Copper Age	3010–2879	0/3
ATP002	Copper Age	2899–2678	0/15
ESP005	Bronze Age	2200–1550	2/4

TYRP1, rs2733831, light hair and eyes

Sample	Period	Date BC	D/T
MUR	Early Neolithic	5295–5075	1/5
SAN216	Late Neolithic	3776–3653	1/1
POR003	Copper Age	3622–3369	0/1
ATP016	Copper Age	3261–2916	0/18
ATP12	Copper Age	3010–2879	3/3
ATP002	Copper Age	2899–2678	4/9
ESP005	Bronze Age	2200–1550	1/1

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