Supplementary Information for

The genomic history of the indigenous people of the Canary Islands

Supplementary Information Guide

5 Supplementary Note 1: Archaeological background 3

Supplementary Note 2: Endogenous content and enrichment results 9

Shotgun sequencing 9
WISC capture 9
10 MEGA capture 9

Supplementary Note 3: Authentication criteria 11

Supplementary Note 4: Y-chromosome analysis 12

15 Molecular sex identification 12
Y-chromosome haplogroup classification 12

Supplementary Note 5: Ancestry Inference 16

Datasets 16
20 Principal component analysis 16
Global ancestry 19

Supplementary Note 6: f-statistic analyses 21

25 Supplementary Note 7: qpAdm modelling 22

Supplementary Note 8: Heterozygosity, inbreeding and family relationships 25

Family relationship estimations 25
Heterozygosity estimations 25
30 Inbreeding estimations 26

Supplementary Note 9: Effective population size and founder effects 27

Effective population size 27
Founder effects 27
35
Supplementary Note 10: Phenotype analyses 30

Supplementary Note 11: Admixture proportions for the modern Canarian

population 31
40
Supplementary Note 12: IBD analyses 33
1
 Supplementary Note 1: Archaeological background
Angostura (Tenerife)
The archaeological site of Angostura is located in the volcanic caldera of Las Cañadas at El
5 Teide National Park at 2,050 meters above sea level. The site of Angostura is a small cave facing
the Northwest (NW). This cave was accidentally discovered in 1982 and the National Park staff
members recovered several human remains from the site1. Anthropological studies have allowed
archaeologists to identify a minimum number of eight individuals1. Four of them were young
adults, according to the diagnostic traits on their mandible. The preservation of the human
10 remains was relatively poor due to weathering. The bodies probably were wrapped as funerary
shrouds made in leather were present on the site. The human remains were associated with other
materials such as retama and pine branches, and also remains from lizards (from the now-extinct
Gallotia goliath) and fragments from one ceramic vessel1. One individual from Angostura (Ang-
5) was dated between 1318 – 1394 AD (University of Georgia, Athens) by Arnay and
15 colleagues2. In this study, we dated two additional individuals, yielding dates between 1396 –
1447 cal AD (CAN.039) and 1276 – 1389 cal AD (95% probability) (CAN.040).

Antoncojo (La Gomera)

The cave site of Antoncojo is located in the middle slopes of the southern side of La Gomera.
20 These human remains were accidentally found in the late 1970s by local villagers. The Antoncojo
material was firstly studied by the paleontologist Francisco García-Talavera Casañas in the 1980s
(unpublished). The remains consist of several cranial and postcranial remains belonging to one
male individual. The radiocarbon dating of this individual produced a chronology between 774 –
994 cal AD (95% probability) (CAN.027).
25
Arenas-1 (Tenerife)
The Arenas burial site is part of a larger archaeological complex in Buenavista del Norte on
the northwest coast of Tenerife. This site was excavated in the late 1990s3. The Arenas complex
comprises at least three areas that include both burial and domestic sites. Archaeologists
30 recovered remains from a minimum of nineteen individuals in the burial cave of Arenas-14. This
cave is a collective burial site where individuals were deposited through time. Primary and
disturbed primary burials were recorded in the cave due to its continuous funerary use during a
prolonged period. Furthermore, anthropological analyses have indicated a high frequency of
certain non-metric traits which has been interpreted as evidence of consanguineal relationships
35 among the individuals of Arenas-1. The present study includes a tibiae fragment from Arenas-1
that produced a radiocarbon date between 1228 – 1297 cal AD (95% probability) (CAN.041).

Gerían (La Gomera)

Gerían is a burial cave located in the Argaga ravine on the southwestern side of La Gomera.
40 This area is well-known due to the high concentration of archaeological sites from the
indigenous period, including cave dwellings, burial caves, rock art and ceremonial sites. It is
noteworthy that this ravine has evidence of a long-term occupation from the 5th century AD to
the 14th century AD5. The anthropological analysis of the human remains considered in this study
indicated they belong to a female individual. The radiocarbon data obtained from this individual
45 yielded a chronology between 1160 – 1264 cal AD (95% probability) (CAN.031).

Barranco Majona (La Gomera)

2
 This burial site is located in a volcanic tube in the ravine of Barranco Majona in the
northern region of La Gomera. The analysis of the human remains from Barranco Majona
yielded a minimum number of two individuals (one male and one female), both included in this
study. Radiocarbon analysis confirms that both belonged to the indigenous period: 1399 – 1446
5 cal AD (95% probability) (CAN.028) and 1288 – 1396 cal AD (95% probability) (CAN.029).

Cascajo (Tenerife)
Cascajo is a funerary cave in the volcanic caldera of Las Cañadas at the El Teide National
Park. The cave is opened at the northern base of Cascajo Mountain. This burial site is part of a
10 complex consisting of several dwelling caves, one of them with evidence of an extensive
occupation6. The human remains belong to a non-adult individual treated using natural unguents
to preserve its soft tissues. The upper part of the body had a shroud made from goat leather that
maintained its anatomical connection and preserved most of the soft tissue6. The radiocarbon
dates for these remains indicated that this individual lived in the 15th century AD between 1400 –
15 1450 cal AD (95% probability) (CAN.042)7.

Cendro (Gran Canaria)

The site of Cendro is a settlement of artificial caves and stone houses on the Telde ravine's
left side at the eastern side of Gran Canaria. Cendro and the nearby site of Tara are considered
20 the most populated sites of Telde in indigenous times. In fact, this area played a significant role
in the political administration and economy of the indigenous population based on the
information provided by European chronicles8. Cendro has been systematically excavated in
several archaeological seasons since the 1980s. The human remains appeared commingled with
young animal remains and other archaeological items in a collapsed artificial cave. The human
25 remains consist of several perinatal remains found in primary position but also disturbed by
pillage. Some scholars have proposed that the presence of perinatal remains in Cendro could be
related to the practice of infanticide mentioned in some ethnohistorical sources9. However, recent
studies have provided an alternative hypothesis through genetic and anthropological analyses
pointing to high mortality rates and specific burial practices for the perinatal individuals of
30 Cendro10. This previous study included the genetic analysis of four individuals dated between the
11th and 13th centuries cal AD (95% probability) (CAN.049, CAN.050, CAN.051, CAN.052).
This site has also provided additional radiocarbon dates on charred barley seeds between the 10th
and 13th centuries cal AD (95% probability)11.

35 Cuermeja (Gran Canaria)

The Cuermeja site is located in the La Aldea area on the western side of Gran Canaria. La
Aldea is a wide valley connecting the mountainous inland with the island's western coast.
Archaeological evidence highlights that this site was intensively occupied during the indigenous
period. Cuermeja site includes dry-stone dwellings and burials on tumuli and cysts. In this study,
40 we analyze the human remains of a single and primary burial in a cyst excavated in the 1980s by
the archaeologists of El Museo Canario12. The human bones belong to a woman of 17 – 25 years
of age. Radiocarbon dates obtained for this individual are between 1270 – 1316 cal AD (95%
probability) (CAN.020)12.

45 El Agujero (Gran Canaria)

El Agujero is located on the northwestern coast of Gran Canaria. This site consists of dry-
stone dwellings and tumuli sharing the same space. El Agujero site is currently separated into
several areas due to urban development: Bocabarranco, El Agujero and La Guancha. However,
3
 these sites were part of a continuous burial space during the indigenous period. The most
prominent burial is known as the tumulus of La Guancha. This large circular stone monument
contains 42 burial areas, with a clear hierarchic space organization in concentric rings and radial
walls that arrange the graves and cysts around a central burial. Besides the tumulus of La
5 Guancha, there are other minor tumuli, which can be easily recognized by their central turret,
where they buried the individuals, surrounded by one or more stone terraces. Previously
available radiocarbon dates came from the central and smaller tumuli and gave this site a
chronology between the 11th and 15th centuries AD8,13. The individual included in this study was
excavated in one of the small tumuli (tumulus 6) and produced a radiocarbon date between 1313
10 – 1424 cal AD (95% probability) (CAN.008).

El Capricho (Tenerife)
El Capricho is a burial cave on the volcanic caldera of Las Cañadas at the El Teide National
Park. Archaeologists discovered and excavated the site in the 1980s14. El Capricho contained the
15 remains of two individuals placed in parallel on two large wooden planks used as litter. They
rested on a floor conditioned with stones and plant elements. Along with the bodies, there was a
perforated bead, another fragmented bead, leather from the funerary wraps, and vegetable
elements of the litter14. The anthropological analysis indicated the remains belonged to a male
between 44 – 50 years of age and a female between 40 – 50 years of age15. Further
20 anthropological studies on this site include paleoparasitology, paleodiet and taphonomy analyses.
The absolute chronology places the female individual around 428 – 601 cal AD (95%
probability)16–18. In the present study, we include a teeth sample of the male individual, which
produced a radiocarbon date between 1316 – 1437 cal AD (95% probability) (CAN.043).

25 El Hormiguero (Gran Canaria)

This archaeological site is located on the eastern side of the Cabezo small ravine that joins
the Azuaje ravine just before its end at the northern plateau of the island of Gran Canaria. This
area is characterized by impressive burial nuclei such as El Hormiguero, El Cabezo and El
Barranquillo del Cabezo19. These necropolises are collective deposits that take advantage of the
30 natural caves and overlaps of the cliffs that, with small transformations, allowed the indigenous
people to use them as burial deposits that were later closed from the exterior with stone walls.
One of the burial deposits was studied during an archaeological intervention in 2005. The body
placed in this space was an adult male. However, two newborns were also placed on this site
after the first burial. Two individuals from El Hormiguero were radiocarbon dated. One
35 produced a date around 790 – 900 cal AD (95% probability) and the other one around 1170 –
1280 cal AD (95% probability)8,20. In this study, we include four individuals from El Homiguero
necropolis, three dated around the 12th – 16th centuries (CAN.009; CAN.011; CAN.012) and one
around the 3rd to 6th centuries cal AD (CAN.010).

40 El Huriamen (Fuerteventura)
This burial site is located in the volcanic tube of Huriamen on the western side of
Fuerteventura. The Huriamen site was accidentally discovered by local villagers and later
excavated by archaeologists21. Archaeological work on the cave determined the presence of bone
remains from at least three individuals. They were two males and one female placed in primary
45 position. The female was between 30 – 35 years of age, and the one male with a preserved skull
was between 25 and 30 years of age. Human remains were radiocarbon dated around the 11th –
12th centuries AD. One teeth sample from the female individual is included in the present study
with a radiocarbon date between 1041 to 1213 cal AD (95% probability) (CAN.006).
4
 El Portillo (Tenerife)
The site of El Portillo is located in the northern area of the volcanic caldera of Las Cañadas
at the El Teide National Park. This cave was discovered in the mid-20th century by local
5 researchers. The cave was initially closed by big stone blocks at the time of the discovery.
Behind the blocks, they found six big wood boards, partially burnt, placed vertically, closing the
entrance to the funerary space. Behind the logs, it was found the access to the funerary space. In
1980 an archaeological intervention was undertaken. A total of four individuals were found in a
primary position, including two young males, one mature female and one young female.
10 Radiocarbon dates from two of the individuals yielded chronological ranges from 1430 to 1520
cal AD (95% probability) and from 1540 to 1652 cal AD (95% probability)17,22. Two individuals
from El Portillo are included in the present study. One individual was female and was dated
between 1300 – 1418 cal AD (95% probability) (CAN.046), before the European conquest. The
other individual is one of the young males and belonged to a later phase, yielding a date around
15 1444 – 1625 cal AD (95% probability) (CAN.045).

Guayadeque (Gran Canaria)

Guayadeque is a large ravine with several archaeological sites on the southeastern side of
Gran Canaria. This site includes natural and artificial caves used for domestic and funerary
20 purposes by the indigenous people23–26. Burial caves have been surveyed since the 19th century
by local and overseas explorers. Because of that, this area has provided a vast number of human
remains that are conserved in both Canarian and European museums. These sites contained
hundreds of well-preserved individuals buried over a long period, including mummified human
remains27. Radiocarbon dates from Guayadeque range from the 3rd to the 15th century cal AD,
25 yielding the oldest evidence of human presence in Gran Canaria (this study). We included four
individuals from Guayadeque, and radiocarbon dated them between the 3rd to the 9th centuries cal
AD (CAN.014; CAN.017; CAN.018; CAN.013).

Huerto de los Morales (La Palma)

30 The burial site of Huerto de Los Morales is located on the left margin of the Fernando Porto
ravine in Garafía at the northwestern side of La Palma. This site was accidentally discovered in
1988 by locals. The archaeologists found a minimum number of 11 individuals. The Huerto de
Los Morales site stands out because it has a significant number of non-adult individuals from
perinatal to adolescents. In addition, it is worth mentioning the presence of a small clavicle that
35 could belong to an unborn child in the last semester of pregnancy28. A phalanx from El Huerto de
Los Morales is included in the present study. The human remains belong to a female that lived
around 651 – 775 cal AD (95% probability) (CAN.034).

La Fortaleza (Gran Canaria)

40 The site of La Fortaleza is a large archaeological complex located on the southeast of Gran
Canaria. La Fortaleza comprises three main areas: La Fortaleza Grande, La Fortaleza Chica, and
Titana. This region has natural and artificial caves dedicated to domestic and funerary purposes,
well-preserved grain storage areas (silos), rock engravings and numerous surface structures
mainly used as houses. Other circular buildings in the upper part of La Fortaleza Grande have
45 been interpreted as spaces destined for ritual activities. Radiocarbon dates demonstrate this is a
long-term settlement occupied from the 5th to the 13th century AD29. This study includes a female
radiocarbon dated between 432 – 642 cal AD (95% probability) (CAN.019).

5
 Lomo Galeón (Gran Canaria)
Lomo Galeón is a burial site on the southwestern coast of Gran Canaria. It is situated on the
left margin of the ravine just above the Bahía of Santa Águeda. The site comprises several sets of
gravestone cysts excavated in the 1940s and 1980s8. The archaeologists found four individuals,
5 including three men and one woman30. The three men presented auricular exostosis, a condition
related to swimming in cold/temperate waters31. The site has already been dated between 1250 –
1290 cal AD (95% probability) based on the analysis of one of the individuals32,33. The four
individuals from Lomo Galeón are included in the present study, although paleogenomic analysis
point to them as being two males and two females (instead of three males and one female as
10 determined by anthropological analyses). All remains have been consistently dated between the
12th and 14th centuries cal AD (95% probability) (CAN.021, CAN.022, CAN.023, and
CAN.024).

Los Pasitos (La Palma)

15 Los Pasitos is an archaeological complex situated on the eastern side of La Palma
comprising open-air and cave dwellings, rock-art stations, and a burial cave. A disturbed
funerary deposit was recovered by local archaeologists. This site is located nearby significant
archaeological sites such as Roque de Los Guerra and Belmaco. In this study, we include a male
individual from the site of Los Pasitos (CAN.035) radiocarbon dated between 1157 – 1264 cal
20 AD (95% probability).

Montaña Mina (Lanzarote)

The collective burial cave of Montaña Mina is located in the central area of Lanzarote on
the eastern side of a volcano. Montaña Mina was excavated in 1979 and represents the first
25 indigenous burial in Lanzarote to be systematically excavated34. The cave is placed in an area
where significant archaeological sites are located, including La Atalaya, Lomo de San Andrés,
Zonzamas and Fiquinineo. In this study, we include two male individuals from Montaña Mina.
These individuals are radiocarbon dated between 1045 – 1222 cal AD (95% probability)
(CAN.037) and 1162 – 1264 cal AD (95% probability) (CAN.038).
30
Puente de la Calzada (Gran Canaria)
Puente de la Calzada is a burial cave located in the Guiniguada ravine in the central-eastern
area of Gran Canaria. The site was discovered in 1993 and excavated in 2002. The cave
contained seven individuals that were placed in two different periods. The human remains from
35 the later episode were found in a primary position, while those from the earlier burial were
mainly recovered in a secondary position35. We included two individuals from Puente de La
Calzada, one male and one female, with radiocarbon dates between 1265 – 1388 cal AD (95%
probability) (CAN.26), and 1303 – 1410 cal AD (95% probability) (CAN.025), respectively.

40 Punta Azul (El Hierro)

Punta Azul is a burial site located in a volcanic tube at the cliff of the southwestern coast of
El Hierro. The site of Punta Azul is part of a large sepulchral area composed of dispersed natural
caves that worked as collective burials. Among them, we can find some of the most important
indigenous burial places, such as Montaña de La Lajura, Cueva de la Ballena or Letime36,37. The
45 site was discovered in 1947 by the archaeologists Álvarez Delgado and Diego Cuscoy. They
identified six individuals in a primary position and other human remains in a secondary/disturbed
position. They only recovered those elements that were considered relevant at the time. The
recovered materials included five complete and five fragmented skulls, 18 mandibles, ten
6
 femurs, a piece of fur from a mortuary shroud, a lithic instrument, and a goat horn39. This site
was re-excavated in 1994. They found an intensively disturbed burial where human remains were
totally disarticulated in a secondary/disturbed position. More than 6,000 bone specimens were
collected, including bones, bone fragments and teeth40. Some studies on the Punta Azul site have
5 been focused on performing paleopathological41–45, paleodietary and paleo-nutritional studies46–
48
, as well as the establishment of discriminant functions for the tibia49, and the analysis of the
particular characteristics of this population and its comparison with other contexts44,50,51.Two
radiocarbon dates have already been obtained for two individuals from Punta Azul: 1022 – 1159
cal AD (95% probability) and 1040 – 1214 cal AD (95% probability)36. Four individuals from
10 Punta Azul are included in the present study. Two are male and two are female (CAN.001,
CAN.002, CAN.003, and CAN.004). Radiocarbon dates were obtained for these individuals
yielding a chronology between the 13th and 15th centuries cal AD.

Salitre (Tenerife)
15 Salitre is a burial site located in a volcanic crevice on the northern side of Montaña Rajada
at the volcanic caldera of Las Cañadas (El Teide National Park). The site has been known since
the 19th century, but archaeological fieldwork was not performed until 1945. Human remains and
fragments of leather shrouds and clothes were recovered from this site39. The bodies were in
supine decubitus over a two-layered bed mostly made of stone and vegetables. There is evidence
20 of planks and forks used to make floorboards and even shelf systems that could hold standing
bodies39,52. The human remains show excellent preservation due to the natural presence of natron
or salitre in the cave's walls. There is an ongoing debate on the minimum number of individuals
buried here, ranging from 50 to 300. Archaeological excavations have identified a dozen
individuals, male and female, and from all age groups, including children between four and
25 seven years of age17,53. There are two already available radiocarbon dates for this site: 1045 –
1282 cal AD (95% probability) and 1517 – 1656 cal AD (95% probability)2. This study includes
one male radiocarbon dated around 1024 – 1155 cal AD (95% probability) (CAN.048).

Salto Casimiro (La Palma)

30 The burial site of Salto de Casimiro is located in the Hermosilla ravine in the central western
area of La Palma. The site was accidentally discovered in the 1970s during road construction.
Unfortunately, these road works destroyed a significant part of the necropolis. However, an
archaeological intervention was performed in the preserved area of the site (Nuria Álvarez
Rodríguez, personal communication). We included a sample from one female radiocarbon dated
35 between 579 to 652 cal AD (95% probability) (CAN.052).

7
 Supplementary Note 2: Endogenous content and enrichment results
Individuals with high endogenous DNA content (>10%) and post-capture libraries were
sequenced to saturation on an Illumina NextSeq 500 platform (paired-end reads, 2 x 75 bp and 2
5 x 42 bp). Mapping and filtering were performed as in54. Briefly, reads were trimmed and
adapters removed using AdapterRemoval version 1.5.455, with a minimum insert size of 30 bp
and a minimum base quality of 20. Paired-end reads were then merged with a minimum overlap
length of 11 bp. Trimmed merged reads were then mapped to the human reference genome
(GRCh37) using BWA version 0.7.1256. For libraries sequenced using the 2 x 42 bp paired-end
10 method, unmerged reads up to 141 bp were also kept for analysis, replicating the same insert size
as 2 x 75 bp paired-end merged reads. For libraries sequenced using the 2 x 42 bp paired-end
method, we also used the clipOverlap function from bamUtil v.1.0.14 to trim overlaps smaller
than 11 bp on paired-end reads57. The mapping was performed using “bwa -aln” with the seed
option (-l) disabled. After mapping, we removed reads with a mapping quality lower than 30,
15 duplicated reads and reads with alternative mapping coordinates. All filtering was performed
using SAMtools version 0.1.1958. Bam files from different runs were merged per individual
using SAMtools merge.
The amount of endogenous DNA for shotgun and capture libraries was calculated by
dividing the number of reads after filtering by the total number of trimmed reads. To normalize
20 results, a subset of 2 million raw reads was used for comparison between individuals. All figures
were produced using R version 3.659 and the package ggplot260.

2.1. Shotgun sequencing

25 Endogenous DNA content was highly variable between and within archaeological sites.
DNA conservation was relatively good for some of the indigenous individuals, with six
individuals from four different archaeological sites showing rates above 30% (Supplementary
Data 1; Supplementary Fig. 1). Overall, endogenous DNA in the shotgun libraries accounted for
10.7 ± 3.8% of the total (median = 4.6%, IQR = 1.5% – 17.7%). Complexity of the libraries was
30 also good, with an average duplicate rate of 0.66 ± 0.12% (Supplementary Data 1;
Supplementary Fig. 2).

2.2. WISC capture

35 WISC capture was applied to 23 shotgun libraries. WISC performance was extremely
variable between individuals, with enrichment values ranging from 0.20X to 29.36X
(Supplementary Fig. 3; Supplementary Data 1). In general, WISC results were modest, with a
mean enrichment value of 6.8 ± 2.9X (median = 3.5X, IQR = 2.2X – 8.7X) and an important
decrease of the libraries complexity (Supplementary Fig. 4). The average duplicate rate increase
40 was 57.3 ± 41.8X (median = 29.0X, IQR = 9.5X – 66.3X), with values ranging between 3.9X
and 492.7X.

2.3. MEGA capture

45 Ancient DNA libraries were also captured for SNPs contained in the Illumina Multiethnic
Genotyping Array (MEGA) array. MEGA capture produces a relatively good increase of
coverage on the targeted SNPs (Supplementary Data 1), with an average increase of intersected
8
 MEGA array SNPs of 81.2 ± 18.5X (median = 60.0X, IQR = 42.1X – 94.6X). Enrichment values
ranged from 22.5X in individual CAN.017 to 226X in individual CAN.026. As observed with
WISC, the decrease of the libraries’ complexity was high. The average duplicate rate increase
was 48.94 ± 24.36X (median = 29.59X, IQR = 16.82X – 53.94X), with values ranging between
5 9.44X and 444.72X.

9
 Supplementary Note 3: Authentication criteria
Authenticity of the data was assessed with MapDamage version 2.0.261,62 to identify the
presence of damage associated with cytosine deamination and fragmentation, and with
5 ContamMix version 1.0-1063 and Schmutzi64 to calculate contamination rates. For contamination
analysis, we used the mtDNA bam files filtered using the same pipeline as for nuclear DNA (see
Supplementary Note 2), and with 3 bp trimmed at both ends to avoid damage interfering with
contamination estimations. Simultaneously, we assessed for the autosomal contamination using
the non-pseudoautosomic X-chromosomal data on male individuals. For that purpose, we used
10 ANGSD65 on X-chromosome polymorphic sites using reads with a base quality >20 and
mapping quality >30.
Post-mortem damage patterns were as expected for ancient DNA. Deamination at the 3’
ends of reads ranged between 6.12% and 44.14%, with an average value of 18.14 ± 2.68%
(Supplementary Data 1; Supplementary Fig. 5). Average insert size was 60.99 ± 3.51 bp, with
15 values ranging between 39.18 and 85.79 bp (Supplementary Data 1; Supplementary Fig. 6).
As published before for most of the individuals of these dataset66, contamination rates are
low accounting for an average value of 1.95% ± 0.54% estimated with ContamMix and 1.52% ±
0.16% with Schmutzi (Supplementary Fig. 7). Most of the human remains also show low levels
of autosomal contamination, except for five males who display 6.1% to 15.2% of contaminated
20 reads (Supplementary Data 1). However, as ANGSD contamination estimations on ancient low
coverage (<0.1X) data are problematic, we decided to keep the three individuals with autosomal
contamination levels >5% and <0.1X for further analysis. Also, as the previously published
gun002 and CAN.027 have contamination estimations of 6% and 8.2%, respectively, and their
mtDNA contamination estimations are very low, we decided to keep them but considering their
25 status.

10
 Supplementary Note 4: Y-chromosome analysis

4.1. Molecular sex identification

5
The molecular sex of the individuals was identified using the ry estimate67 and results were
plotted using the R programming language (version 3.6)59 and the package ggplot260. As
observed before54, we needed to filter pseudo-autosomal and repetitive regions prior to ry
calculation to accurately assess the molecular sex of captured individuals (Supplementary Fig.
10 8). Including previously published genomes from68,71, 21 individuals are females and 28 are
males (Supplementary Data 1, Supplementary Fig. 8).

4.2. Y-chromosome haplogroup classification

15 Male individuals were subjected to Y-chromosome analysis as in54. First, we performed a

SNP calling based on the ISOGG Y-DNA Haplogroup tree 2019-2020 database (v.15.73) using
samtools mpileup, filtering out bases with BASEQ < 30. The resulting variants were classified in
two groups based on the putative presence of DNA damage (C à T or G à A) and were
visually classified among the main haplogroups following the Y-chromosome phylogenetic
20 tree69. Additionally, individuals were classified using pathPhynder’s “best path” method70. All
figures were produced using R v. 3.659 and the R packages ggplot260 and ggtree70.
Including previously published genomes from68,71, a total of 28 ancient individuals from the
Canary Islands were identified as males. Their geographic adscription is as follows: El Hierro (n
= 2), Gran Canaria (n = 12), La Gomera (n = 2), La Palma (n = 1), Lanzarote (n = 2) and
25 Tenerife (n = 9). No males were observed for Fuerteventura; therefore, no information is
available regarding Y-chromosome lineages present in the ancient population of this island.
Overall, the most frequent Y-chromosome haplogroup in the indigenous population of the
Canary Islands is E-M183 (57.1%), followed by T-M184 (21.4%), E-M33 (10.7%) and R-M269
(7.1%). Finally, E-M78 was observed at a frequency of 3.6% (Supplementary Fig. 9;
30 Supplementary Data 2).
Initially, information on the Y-chromosome composition of the indigenous population was
obtained using classical methodologies based on PCR36,72. Although E-M183 was not genotyped,
a SNP for the E-M81 branch was included. As E-M81(xE-M183) is extremely infrequent73 we
can consider all E-M81 males to belong to the E-M183 sublineage. In the 2009 study72, E-M183
35 (E-M81) was also the most common Y-chromosome lineage, although in that case the frequency
was estimated to be 26.7%. The frequency for E-M33 (10.7%) was also estimated to be lower
when using PCR methods (3.3%). On the other hand, the frequency of E-M78 was higher in the
previous study (23.3%) than in this NGS analysis (3.6%). Moreover, haplogroups I-M170, J-
M267 and P-M45* were observed by Fregel et al.72 but not in the present study. Additionally, in
40 the 2017 Y-chromosome analysis of the Punta Azul site in El Hierro36, both E-M183 and E-
M269 were found at a frequency of 43.8%, and E-M33 at 6.3%. One possibility for the
differences in haplogroup frequencies could be that the multiplex-PCR method used in the 2009
and 2017 studies produced incorrect results due to contamination and/or PCR artifacts. However,
for those individuals genotyped using both multiplex-PCR and NGS techniques (Punta Azul site:
45 CAN.001 and CAN.002; Guayadeque site: CAN.013 and CAN.018) results were consistent
using both methodologies, indicating that contamination or PCR errors were not prevalent when
using the PCR approach. Another possibility can be that these differences could be caused by the
11
 fact that sample sizes for the Y-chromosome are still low and also that most of the people
analyzed in the 2009 and 2017 studies came from the Guayadeque site in Gran Canaria and the
Punta Azul site in El Hierro, respectively, instead of being a miscellaneous individuals from the
entire archipelago. From the mtDNA point of view, it is evident that the populations of the
5 different islands were not homogenous. For that reason, we must consider that the same scenario
could be observed for the Y-chromosome. Future paleogenomic efforts would be needed to
characterize the Y-chromosome composition of the Canary Islands at an insular level.

4.2.1. Phylogeographic analysis of Y-chromosome haplogroups

10
4.2.1.1. Haplogroup E-M183

As explained before, most males belonged to the E-M183 haplogroup. Concretely, there are
two of them from El Hormiguero (Gran Canaria) and one male from each of the archaeological
15 sites of Punta Azul (El Hierro), Puente de la Calzada (Gran Canaria), Antoncojo (La Gomera),
Barranco Majona (La Gomera), Los Pasitos (La Palma), Arenas (Tenerife), El Cascajo
(Tenerife), El Capricho (Tenerife), El Portillo (Tenerife) and El Salitre (Tenerife) that belong to
E-M183 haplogroup (Supplementary Fig. 9; Supplementary Data 2). Also, three
decontextualized Tenerife individuals from68 belong to this lineage. This haplogroup has not
20 been observed on the island of Lanzarote but given its small sample size (n=2), a larger sample
size would be needed to characterize the Y-chromosome composition of this population.
Given that North Africa is its most probable origin, a high frequency of E-M183 in the
indigenous population of the Canary Islands is expected. This lineage, derived from E-M81, is
the most common haplogroup in modern North African populations and considered to be
25 autochthonous in this region74,75. Actually, a lineage ancestral to E-M81 has been observed in
early Neolithic people from Morocco dated 7,000 BP54. The highest frequencies of E-M81 are
observed today in Western Sahara (76.9%), Morocco (62.1%) and certain populations in Algeria
(82.1%)73. This study has estimated a TMRCA (time to most recent common ancestor) of only
2,000 - 3,000 years for E-M183, placing the origin of this lineage around the time the Canary
30 Islands were colonized. Solé-Morata et al. 201773 also observed a rapid radiation for E-M183
and identified five different branches within E-M183. We tested our individuals to determine if
they belonged to the basal E-M183* lineage or to some of the sister branches proposed by73. Our
results indicate that all of them belong to E-M183*, which is expected given that its coalescence
date coincides with the time estimated for the human colonization of the Canary Islands.
35 Males belonging to the E-M183 cluster were also assigned to the same haplogroup when
analyzed using pathPhynder (E1b1b1b1a1), except for CAN.023 (Lomo Galeón) and CAN.025
(Puente de la Calzada) from Gran Canaria. According to pathPhynder, CAN.023 belonged to the
ancestral E-M310 haplogroup (E1b1b1b1), and CAN.025 could not be resolved further than the
E haplogroup, probably due to the low coverage of these individuals (<0.1X). Interestingly, E-
40 M183 individuals are placed in the phylogeny near to Mozabite people. Along with them,
indigenous individuals are placed near to Puerto Rican and Iberian individuals, who could be
descendants of Canarian migrants.

4.2.1.2. Haplogroup E-M33

45
Three males from the eastern islands belong to haplogroup E-M33 (Supplementary Fig. 9;
Supplementary Fig. 10; Supplementary Data 2): one from the site of Lomo Galeón (Gran
Canaria) and two from the site of Montaña Mina (Lanzarote). E-M33 is considered to be a sub-
12
 Saharan lineage whose highest frequencies (~50-60%) have been observed in South and Central
Africa74,75. E-M33 is also present in current populations in North Africa, reaching its peak in
West Sahara (9.0%); however no complete sequenced E-M33 Y chromosome is available from
this region. Considering E-M33 is a lineage of sub-Saharan origin, the presence of E-M33 in the
5 indigenous population of the Canary Islands confirms the impact of sub-Saharan migrations into
North Africa prior to ~2,000 years ago. This result is consistent with sub-Saharan mtDNA
lineages such as L1 or L2 observed in the Canarian native people66. It is worth mentioning that
for the two Canarian individuals (CAN.037 and CAN.038) a fraction of the SNPs covered in the
branch leading to E-M33 are ancestral. For CAN.037, only two of the three SNPs covered are
10 derived (67%). For CAN.038, a larger number of SNPs were covered, with 9 out of 15 being
derived (60%). Most of the E-M33 males included by69 in the complete Y-chromosome
phylogeny were of sub-Saharan African origin, mainly from Gambia. The results obtained for
the Canarian indigenous males indicate that they belong to a different sublineage of E-M33 than
that previously observed.
15 When analyzed using pathPhynder, all the individuals were placed within the E-M33
haplogroup. Furthermore, CAN.022 could be assigned to the E1a1 descendant lineage defined by
the marker M44, next to a Mandenka individual.

4.2.1.3. Haplogroup R-M269

20
Two indigenous individuals belong to the R-M269 haplogroup (Supplementary Fig. 9;
Supplementary Data 2): one from Punta Azul (El Hierro) and one from Guayadeque (Gran
Canaria). R-M269 is the most common haplogroup in Western Europe, although it is also found
in North Africa in lower frequencies77. When ancient individuals were further classified within
25 R-M269, both showed derived SNPs on the branch clustering R-L11 individuals. Although the
R-L11 lineage is commonly restricted to Western Europe77, it was common in Early Bronze Age
populations from Europe78 and could have reached North Africa with Bronze Age migrations
from this region (as implied by the presence of Bell Beaker pottery79,80). Analysis using
pathPhynder confirmed previous results as both individuals were placed within the R-L11 branch
30 of the R-M269 haplogroup (R1b1a2a1a).

4.2.1.4. Haplogroup T-M184

Six males from our dataset belong to the T-M184 haplogroup (Supplementary Fig. 9;
35 Supplementary Fig. 11; Supplementary Data 2), all of them from different archaeological sites in
Gran Canaria: El Agujero, Cendro, El Hormiguero and Guayadeque. T-M184 originated in the
Near East and began to diversify approximately 25,000 years ago and then dispersed to Europe
and the sub-Saharan Africa81. Today, haplogroup T is widespread, but it is considered to be rare.
As with mtDNA lineages T2 and J266, the presence of the Y-chromosome T-M184
40 haplogroup in the indigenous population of the Canary Islands can be explained by Neolithic
expansions in North Africa, as this haplogroup has been found in early farmers from Europe82. In
fact, this was one of the Neolithic-related lineages directly found in Late Neolithic Moroccan
remains (3,700 - 3,600 BCE) from the Kef el Baroud site54.
When analyzed using pathPhynder, four of the six males were assigned to the same T-M184
45 haplogroup. However, CAN.008 from Guayadeque could not be resolved further than the IJK
haplogroup probably due to the low genome coverage. On the other hand, the Cendro individual
(CAN.049) was assigned to the L208 branch of the T-M184 haplogroup that dispersed all over
western Eurasia after its appearance in the Near East.
13
 4.2.1.5. Haplogroup E-M78

One individual from La Angostura site in Tenerife belongs to the haplogroup E-M78
5 (Supplementary Fig. 9; Supplementary Fig. 12; Supplementary Data 2). This haplogroup is a
widely distributed lineage that most likely originated in northeastern Africa74,83,84 and dispersed
from there approximately 20,300 - 14,800 years ago. For that matter, Upper Paleolithic people
from Morocco dated 15,000 years BP belong to this lineage85. The highest frequencies of the
haplogroup E-M78 are nowadays observed in southern Egypt (50.6%) and Somalia (52.2%)83.
10 Contrary to what happens with E-M81, haplogroup E-M78 shows higher frequencies in eastern
North Africa (25.4%) and decreases towards the West (11.6%). It is worth mentioning that,
according to the data in83 E-M78 is more frequent among Moroccan Arabs (40.0%) than in
northwestern Berber populations (e.g. 3.7% in Asni, 1.5% in Bouhria or 0.0% in Mozabite
Berbers). When analyzed using pathPhynder, this individual could not be resolved further than
15 the parent E-M215 clade. However, our analysis only identified only one read covering the E-
M78 mutation so probably the lack of coverage affected the pathPhynder results.

14
 Supplementary Note 5: Ancestry inference
5.1. Datasets

5 The Canary Islands ancient dataset was first compared to the Human Genome Diversity
Project (HGDP)86, genotyped on Illumina, Inc.’s Multiethnic Genotyping Array (MEGA),
curated as published before54 and including available North African, sub-Saharan African, Near
Eastern and European populations. Our dataset was also compared to the Human Origins panel,
which contains 2,345 present-day humans from 203 populations and 281 ancient individuals
10 genotyped for 594,924 SNPs87. Ancient DNA shotgun data from previously published data was
also integrated into the Human Origins aDNA dataset, including Neolithic and Bronze Age
individuals from Spain88,89, Turkey90, Ireland91, Iran92, and Morocco54, as well as from the
indigenous population of the Canary Islands68,72, the Iberomaurusian site of Taforalt85, ancient
Egypt93 and several archaeological sites from sub-Saharan Africa94,95. We also included
15 published Punic96 and Roman97 individuals as they have been reported to carry North African
ancestry and their comparison with the indigenous people of the Canary Islands could be of
interest for determining historical contacts. Lastly, we filtered the Human Origins dataset in
order to obtain a sub-dataset including both ancient and modern populations from Eurasia
(including North Africa) and sub-Saharan Africa.
20
5.2. Principal component analysis

5.2.1. MEGA-HGDP panel

25 Ancestry of the indigenous people from the Canary Islands was first inferred from PCA
using the MEGA-HGDP reference panel. PCAs were performed both using both LASER98,99
(Supplementary Fig. 13) and the lsqproject option from smartpca100 (Supplementary Fig. 14).
LASER coordinates were calculated as the average of 10 replicates. The first component in this
PCA separates sub-Saharan African from Eurasian populations, while the second one separates
30 European from North African and Middle Eastern populations.
Both the LASER and the lsqproject PCA plot show that the indigenous people of the
Canary Islands are clustered near to Late Neolithic Moroccans and modern North Africans. A
previous study determined that Upper Paleolithic and Early Neolithic people from Morocco
shared the same genetic composition, associated with what is known as the autochthonous
35 Maghrebi component101, while Late Neolithic Moroccans showed admixture with Anatolian
and/or European early farmers54. The indigenous people of the Canary Islands are also placed in
an intermediate position between the ancient North Africans and Sardinians (characterized by
their higher European Neolithic component), and close to Late Neolithic Moroccans as
previously noted64,54,68,102. As expected from the presence of sub-Saharan African mtDNA and
40 Y-chromosome lineages in the indigenous individuals from the Canary Islands66, both the
LASER and lsqproject PCAs indicate that the Canarian natives are closer to sub-Saharan African
populations in PC1 than Late Neolithic Moroccans. However, it could also be due to other
additional migration sources from Eurasia. Also, with our increased sample size, we observe that
the indigenous population is placed more scattered compared to late farmers in Morocco, with
45 some individuals showing a higher affinity for ancient North Africans and other individuals
clustered closer to Sardinians.

15
 MtDNA evidence suggests that eastern and western islands could have a different genetic
composition66, which could account for this variation in the placement of ancient people from the
Canary Islands. To test that hypothesis, we plotted the indigenous people using a different color
code for each island and we observe that western islands are clustered closer to Upper Paleolithic
5 and Early Neolithic North Africans, while eastern islands are placed closer to Sardinians and
other modern European populations (Supplementary Fig. 15). There is only one exception to the
eastern/western distribution: one individual from Tenerife (CAN.039) that is placed within the
eastern islands’ cluster. Some of the archaeological sites from Tenerife we included in this study
belong to the post-contact period. Individual CAN.039 belong to the archaeological site of La
10 Angostura, a site with clear indigenous funerary practices and material culture17. Radiocarbon
dating from this site indicates this burial was used between 1,295 and 1,414 AD17. After
performing RCD on this particular individual, results indicate that CAN.039 was dated between
1,396 – 1,447 cal AD. As contact with European sailors and explorers started in Tenerife in the
13th century, it leaves the possibility of European admixture or that this individual came from a
15 different island.
Although aDNA libraries have been subjected to enrichment techniques, a limitation of our
study is the low coverage of some individuals (Supplementary Data 1), which makes us question
if sample clustering in the PCA can be accurate. The advantage of using LASER is that sequence
data for each reference individual is simulated to match the coverage pattern of each individual.
20 Then a PCA ancestry map is built based on the simulated sequence reads for both the reference
and the ancient individuals. Finally, the ancestry map is projected into the PCA space built based
on the whole reference panel. The stochastic variation introduced by the simulation procedure of
the LASER method can lead to slightly different results in the placement of each individual. For
that reason, our analysis was based on the average of 10 independent replicates. This approach
25 allows us to better place each individual into the PC space, but also, by plotting the result
obtained in 10 replicates, we can test how coverage correlates with uncertainty in the placement
of a particular individual. For that, we compared the replicates of individuals with different
coverage rates in our dataset (Supplementary Fig. 16). Placement in the first component is stable
through replicates, even for individuals with very low coverage (~3%). Coordinate values in PC2
30 fluctuate slightly in low-coverage genomes (~10% of the SNPs covered) and increase in
individuals with lower values (~3%). However, although this phenomenon can account for some
uncertainty on the placement of the individuals in PC2, it is not enough for accounting for the
differentiation between the two clusters of eastern and western Canarian people.

35 5.2.2. Human Origins panel

The indigenous population of the Canary Islands was also compared to other available
modern and ancient populations using the Human Origins panel and the lsqproject option from
smartPCA100. To this end, we compared the Canarian natives to ancient and modern populations
40 from North and sub-Saharan Africa, the Middle East and Eastern, Southern and Western Europe.
In this PCA, the first component separates sub-Saharan African populations from the rest,
while the second component accounts for differentiation within sub-Saharan Africa
(Supplementary Fig. 17). The indigenous people of the Canary Islands cluster with Eurasian
populations, close to modern North Africans and Late Neolithic Moroccans. A better
45 differentiation between Eurasian populations can be observed when PC1 and PC3 are compared
(Supplementary Fig. 18). In this PCA, Late Neolithic North Africans are place between Early
Neolithic Europeans and Upper Paleolithic North Africans. The Canarian natives are also placed
between Prehistoric populations from Europe and North Africa, but in this case, they are
16
 displaced towards European Middle/Late Neolithic and Bronze Age individuals. Again, some
distinction can be observed between eastern and western islands, especially in PC1, creating two
separate clusters with two exceptions. As we observed for the MEGA-HGDP panel, individual
CAN.039 from La Angostura (Tenerife) is placed within the eastern islands cluster. This time,
5 individual CAN.035 from Los Pasitos (La Palma) also shows the same behavior. In this case,
RCD analysis indicated this individual lived around 1,157 – 1,264 cal AD, predating the contact
period with Europeans.
We investigated the relationship between the indigenous people of the Canary Islands and
populations from the Iron Age associated with the Roman expansion in the Mediterranean
10 region. For that, we compared indigenous Canarians with ancient people from Egypt, Iron Age
populations from the Middle East, Sardinia and Western Europe; a Punic individual from Ibiza
and Punic populations from Sardinia; and Roman individuals from the Middle East, Sardinia and
western and southern Europe (Supplementary Fig. 19). As shown before88,97,103,104, from the Iron
Age onwards, populations are characterized by a high mobility. In line with that observation,
15 some Romans from western and southern Europe97, and Punic individuals from Ibiza and
Sardinia 96,103 show genetic affinities with the ancient North African cluster, including the
Canary Islands. Indeed, admixture modeling analyses performed in these individuals confirm the
contribution of a North African component. For example, the Punic individuals from Sardinia
have relatively high levels of North African ancestry (20–35%)103, while individuals from Rome
20 can be modeled with up to 30–50% of a North African contribution97. However, although some
of these individuals have a substantial contribution from this component, they do not overlap
with the indigenous people of the Canary Islands, who show higher affinities with ancient North
Africans (Supplementary Fig. 19).

25 5.3. Global ancestry

For unsupervised clustering analysis, we used the same datasets as for lsqproject PCA, but
pruning for linkage disequilibrium using PLINK v1.90105, with parameters --indep-pairwise 200
25 0.4. In addition, the global ancestry of ancient individuals was determined by unsupervised
30 clustering using ADMIXTURE software v1.3.0106. The analysis was performed in 10 replicates
with different random seeds, and only the highest likelihood replicate for each value of K was
taken into consideration.

5.3.1. MEGA-HGDP panel

35
In Supplementary Fig. 20, we show ADMIXTURE results for the MEGA-HGDP panel with
K=4 ancestral populations. At K=4, the populations are clustered in four groups roughly
corresponding to the four broad geographical areas: sub-Saharan Africa (red), Europe (green),
the Near East (violet) and North Africa (yellow). At K=4, the ancient North African people
40 reproduce the same results observed earlier, with Upper Paleolithic and Early Neolithic
individuals from Morocco composed of 100% of the North African component. However, the
Late Neolithic populations show only part of their genetic composition belonging to this North
African component. Regarding the indigenous population of the Canary Islands, individuals from
the western islands (El Hierro, La Palma, Tenerife and La Gomera) show the same result
45 observed for the Upper Paleolithic and Early Neolithic individuals from Morocco. Meanwhile,
individuals from the eastern islands (Gran Canaria, Lanzarote and Fuerteventura) are explained
as mainly corresponding to North Africa, but with a minor European contribution. This result
correlates with the one observed in PCA and can explain the clustering of eastern and western
17
 individuals of the indigenous people of the Canary Islands, with the first group having a greater
European contribution and the other being more similar to ancient North African people.
However, given the limited amount of modern North African and ancient Eurasian individuals,
the MEGA-HGDP panel is not appropriate to resolve in fine detail the genetic composition of the
5 indigenous people of the Canary Islands.

5.3.2. Human Origins panel

In Supplementary Fig. 21 and Supplementary Fig. 22, we show ADMIXTURE results for
10 the modern and ancient Human Origins panel, respectively, with K values ranging from 2 to 8.
As described before, ADMIXTURE results suggest that both Late Neolithic individuals from
Morocco and the Canarian indigenous population were admixed (Supplementary Fig. 22) with an
ancient Maghrebi component (yellow) and an early Neolithic European component (green)54.
Compared with Late Neolithic Moroccans, the Canary Islands’ indigenous people have a greater
15 contribution from the ancient Maghrebi component. Also, the Canarian natives present a
component that maximizes in European hunter-gatherer and Steppe populations (blue), but is
absent in Late Neolithic Moroccans, which could explain the behavior of the individuals in the
PCA. As the human colonization of the Canary Islands archipelago has been estimated to have
happened between the first-century BC and the second-century AD5,107, additional migration
20 waves are expected to have reached North Africa by that time. Given the presence of Bell-
Beaker pottery in the North African archaeological record79, this steppe component could be
related to the expansion of European Bronze Age populations in North Africa54,102. Also, some
individuals have a component associated with Neolithic Iranians (grey) that is present in ancient
and modern populations from the Near East but also in Bronze Age people from the steppe.
25 Although from a mitochondrial DNA perspective, a sub-Saharan African input in the indigenous
people of the Canary Islands is inferred from the presence of L haplogroups, the unsupervised
clustering analysis only shows a small sub-Saharan contribution (red) in a few individuals, and in
all cases, the observed values are below 5%.
Interestingly, some differences are observed between western and eastern populations. At
30 K=8, individuals from the western islands show a higher proportion of the autochthonous
Maghrebi component and a lower contribution associated with steppe populations when
compared with eastern islands (Fig. 2b). This differentiation can be observed both comparing the
different islands using a ternary plot depicting the main components present on the indigenous
population (Supplementary Fig. 23) and a boxplot showing the contribution mean of each
35 component per island (Supplementary Fig. 24). On the other hand, the contribution of the
European Neolithic and the Near Eastern components are similar in both regions (Supplementary
Fig. 24).
When compared to the current population of the Canary Islands, an increment is observed in
the component likely associated with the Steppe contribution and the Near Eastern component,
40 and a lower autochthonous North African contribution (Fig. 2b). This result is expected giving
the fact that the modern population of the Canary Islands is admixed with the main parental
populations being the indigenous people and European colonizers.
Giving the time of the human colonization of the Canary Islands, it is also interesting to
compare them to modern North Africans, to get an insight of the impact that later migrations had
45 on the region (Fig. 2b). Modern North African people exhibit a lower proportion of the ancient
Maghrebi component when compared to the Canarian natives. As this component is higher in
western North Africa 101, the greatest differences are observed for Egypt and Libya. We also
observe a greater contribution from the Near Eastern and Sub-Saharan African components in
18
 modern North Africans. These differences correlate to additional migration reaching this area in
the last two millennia, including the Arab expansion in the seventh century and the trans-Saharan
migrations.
The high proportion of the Maghrebi component observed in the Canary Islands indigenous
5 people is indicative of their origin being related to Berber populations in North Africa, a
hypothesis that has been supported by extensive archaeological, linguistic, and genetic
analyses66,73,107–122. The inclusion of other historical individuals in the PCA allows us to test
some controverted hypotheses that have been proposed for the origin of the indigenous people
(Supplementary Fig. 19; Supplementary Fig. 23). Based on radiocarbon data obtained from bulk
10 sediment samples in the archaeological site of Buenavista in Lanzarote112, some archaeologists
have proposed chronologies that go as far as the 5th century BCE112–114,121, leading them to
propose a Phoenician origin for the first settlers of the Canary Island112–114,123. However, a recent
review of this data and the application of radiocarbon hygiene criteria have shown that these
older dates for the colonization of the Archipelago are not reliable109. Furthermore, the
15 archaeological record show no clear cultural adscription with Phoenicians. Specifically,
archaeological evidence is composed of small pieces of pottery from non-diagnostic regions and
excavated in a site with a questioned stratigraphy that cannot discard the intrusion of materials
from other periods. For those reasons, scholars have contested the affiliation to this site to the
Phoenician culture115. Regarding an Egyptian origin for the indigenous people of the Canary
20 Islands, although some scholar traditions up to the XIX century proposed a link between Ancient
Egypt and the islands based on the practice of mummification in both regions, archaeologists
promptly disregarded it. However, this association between Egypt and the Canary Islands has
remained in the collective imaginary116. As for the hypothesis on the Roman colonization of the
islands, a few aspects should be taken into consideration. The purple dye workshop in the islet of
25 Lobos is the only site with a clear Roman adscription. However, its archaeological record shows
no interaction between this population and the Canarian indigenous people110,111. In this sense,
absolute radiocarbon dates from this site point to the 1st century BC, previous to the proposed
date of the colonization of the islands (between the 2nd and 5th centuries AD). Also, the materials
found in this site, especially Roman amphoras, provide a relative chronology that situates this
30 settlement in a relatively short period (between 50 and 100 years), showing its limited impact on
the population of the Canarian Archipelago as a whole33,109.
Based on the ADMIXTURE results observed for the indigenous people and the historical
individuals included (ancient Egyptians, Phoenician and Etruscan), the natives of the Canary
Islands have a higher ancient North African component than Egyptians and the Phoenician
35 individual from Ibiza (Supplementary Figures 23 and 24). Also, their percentage of the
autochthonous Maghrebi component is higher than the Etruscan individual with North African
admixture published by97. Egyptian individuals are characterized by having a higher Iran
Neolithic contribution, while the Phoenician and Etruscan individuals have a higher steppe
component than most of the individuals from the Canarian archipelago. Based on those results, it
40 is unlikely that the origin of the natives could be solely related to a single migration event from
these populations.

19
 Supplementary Note 6: f-statistics analyses
We performed the analysis of outgroup f3-statistic using qp3Pop program from
ADMIXTOOLS (https://github.com/DReichLab/AdmixTools), to determine the amount of
5 shared drift between two ancient populations PopA and PopB. For that, we chose an outgroup
population that has not experience any post-divergence gene flow with either PopA or PopB as
the target population (e.g. Jo’hoan North), and calculated the f3-statistic in the form f3(PopA,
PopB; Outgroup). In this way, the result of the f3-statistic will be a positive value proportional to
the length of the shared drift path of populations PopA and PopB with respect to the outgroup.
10 Considering the populations contained in the Human Origins dataset, the indigenous people
of the Canary Islands share more ancestry with Iberian, Aegean and other European Early
Neolithic populations (Supplementary Fig. 25), similarly to the results obtained for Late
Neolithic Morocco54.
PCA and unsupervised clustering results indicate that the eastern islands have a greater
15 contribution from a component related to the Bronze Age expansion in Europe, while western
islands show a higher ancient North African contribution. To test if differences are observed
between islands, we repeated the outgroup f3-statistic calculations at insular level and compared
the amount of shared ancestry with populations of interest. Differences were observed between
the amount of shared ancestry between islands populations with Neolithic and Bronze Age
20 populations from Europe, with the eastern islands producing higher values. Figure S26 shows the
results obtained for Middle Neolithic to Bronze Age populations from Western Europe and Late
Neolithic to Bronze Age populations from the steppe. When compared with Early and Late
Neolithic individuals from North Africa, slightly differences between eastern and western islands
are observed for the Late Neolithic population, but not for the Early Neolithic population.
25 However, outgroup f3-statistics are difficult to compared and do not provide information about
the contribution of different populations, and a more detailed analysis using admixture modeling
is needed.

30

20
 Supplementary Note 7: qpAdm modeling
Admixture modeling was performed using qpAdm from ADMIXTOOLS, following124 and
using the Allen Ancient DNA Resource curated by the Reich Lab at Harvard
5 (https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-
day-and-ancient-dna-data, version 42.4). First, we defined the target as the whole population of
the Canarian archipelago. For the right populations, we chose the same outgroups as in87: Mota,
Ust-Ishim, Kostenki14, GoyetQ116-1, Vestonice16, Malta1, AfontovaGora3, ElMiron,
Villabruna, WHG, EHG, CHG, Iran_N, Natufian, Levant_N and Anatolia_N. For the left
10 populations, we started with the simpler model (one stream of migration) and increased
complexity until reaching statistical significance. With the aim of exploring different admixture
scenarios, we implemented a “rotating” scheme, in which populations are systematically moved
from the set of reference populations to the set of sources.
For the one-stream model, no statistical significance was reached for any of the tested target
15 with any of the possible contributing populations (Supplementary Data 3). However, the one-
stream model with the p-value closer to significance was the one involving one stream of
migration from Morocco_LN. The same result was obtained for the two-stream and three-stream
models, with no populations’ combinations reaching significance. Again, the two models closer
to significance involved the contribution from Morocco_LN (2-stream model: Morocco_LN +
20 Mota; 3-stream model: Morocco_LN + Mota + Russia_EBA Yamnaya). Considering the whole
indigenous population, the simpler admixture models reaching significance involved the
contribution of Morocco_LN, Mota, a source of autochthonous North African ancestry (either
Morocco_IB or Morocco_EN) and a source of steppe ancestry (either Germany_BellBeaker,
Russia_EBA_Yamnaya or Russia_HG_Karelia).
25 The best-fitting model is Morocco_EN (6.9% ± 1.0%), Morocco_LN (73.3% ± 2.2%),
Germany_BellBeaker (13.4% ± 1.8%) and Mota (6.4% ± 1.3%) (Fig. 2c; Supplementary Data 3).
This result indicates that most of the Canarian indigenous people’s ancestry can be linked to Late
Neolithic populations from Morocco. However, a single pulse from this population is not enough
to account for their genetic composition. First of all, ancient Canarians need additional input
30 from the North African Maghrebi component. As proposed earlier54, this result can be explained
considering that the indigenous people originated in a different area of the Maghreb where most
probably the European Neolithic impact was lower. As observed for the mtDNA, additional
pulses of migration from a sub-Saharan African and Eurasian Bronze Age sources are needed to
model the indigenous people of the Canary Islands. Given that the colonization of the Canary
35 Islands occurred long after the Late Neolithic period (~3,000 BCE), most probably around the
first centuries CE, it is expected that additional waves of migration had already reached North
Africa. Regarding the existence of trans-Saharan migrations, genome-wide data from modern
North Africans101 provided evidence of the contribution of sub-Saharan Africans into Morocco
around 1,200 years ago. This date coincided with the rise of the Ghana Empire, which was
40 involved in the trans-Saharan slave trading. However, our results indicate that sub-Saharan
African migrations already reached North Africa by the time of the colonization of the islands
(approx. 2000 BP). When testing modern populations instead of Mota for admixture modeling,
Datog people from Kenia (8.9% ± 1%) and Somali from Tanzania (10.6% ± 1.2%) showed the
highest correlation values as contributors to the indigenous population of the Canary Islands.
45 However, as considering modern and ancient individuals as left populations may introduce bias
in the results124, we consider Mota as the best source population for the sub-Saharan
contribution. In the same vein, the existence of a European Bronze Age component can be

21
 explained by the presence of Bell-Beaker pottery in the North African archaeological record66,102.
It is worth mentioning that models with Iberia_BellBeaker do not reach significance.
Then, we applied the best four 4-stream models to determine differences between a) the two
geographical regions (eastern and western islands), b) each island population (El Hierro, La
5 Palma, La Gomera, Tenerife, Gran Canaria, Fuerteventura and Lanzarote) and c) each individual.
When comparing the eastern and western regions (Supplementary Data 5), we observe that
western islands have a higher contribution of Morocco_EN (8.3% ± 1.1%) than eastern islands
(4.9% ± 1.1%). Also, the Germany_BB contribution is slightly higher in the eastern islands
(16.0% ± 2.0%) than the western islands (11.4% ± 1.9%), while the rest of the components
10 remain relatively stable. If we look at each island by itself, we observe that La Palma has the
highest Morocco_EN contribution (10.1% ± 1.7%), while Lanzarote has the highest
Germany_BB contribution (17.9% ± 3.5%). At an individual level, individuals from the sites of
Guayadeque (CAN.018; 20.2% ± 4.4%) and El Hormiguero (CAN.012; 19.0% ± 3.4%) in Gran
Canaria show the highest Germany_BB proportion (Supplementary Data 6). The lowest values
15 are observed in Antoncojo in La Gomera (CAN.027; 8.10% ± 3.60%) and Punta Azul in El
Hierro (CAN.003; 9.20% ± 3.10%). The opposite occurs for the Morocco_EN contribution:
individuals from the sites of Cendro (CAN.050; 3.4% ± 2.5%) and Guayadeque (CAN.014; 4.0%
± 2.3%) in Gran Canaria show the lowest Morocco_EN proportion (Supplementary Data 6),
while the highest values are found in Salto Casimiro en La Palma (CAN.036; 10.4% ± 1.8%) and
20 a decontextualized individual from Tenerife (gun012; 10.2% ± 2.0%). Interestingly, when
analyzed in combination with radiocarbon data, we observe that the slight differences between
eastern and western regions are observed for the entire period of indigenous occupation
(Supplementary Fig. 27). This result is more clearly seen for the two islands with a larger sample
size: Tenerife and Gran Canaria. When the Morocco_EN contribution is compared with
25 radiocarbon data obtained from the individuals, we observed that values are relatively lower in
Gran Canaria for the entire indigenous occupation period (Supplementary Fig. 28).
Although the presence of a steppe component in the indigenous people of the Canary
Islands can be explained based on a Bronze Age migration to North Africa, it can also be the
result of the impact of Punic or Roman populations in North Africa before the settlement of the
30 archipelago. To test this hypothesis, we repeated the four-stream qpAdm modeling but replacing
German Bell Beakers by available Roman and Punic populations (Supplementary Data 4). The
only working models involved Roman and Punic populations with either a North African or
Middle Eastern admixture. These populations include Roman individuals from England125, a
Punic individual from Ibiza96, and Punic individuals from the Villamar site in Sardinia103. The
35 best-fitting model involves the admixture of Morocco_EN (8.9% ± 1.4%), Morocco_LN (41.3%
± 7.9%), Mota (4.7% ± 1.6%) and Ibiza Punic (45.1% ± 7.3%) (Supplementary Data 4).
However, this result should be taken with caution as data from Punic individual from Ibiza
comes from a low coverage genome (0.47X). Apart from that one, the following best-fitting
model involves the admixture of Morocco_EN (10.7% ± 2.2%), Morocco_LN (20.9% ± 16.6%),
40 Mota (11.2% ± 1.6%) and Sardinia Punic (57.2% ± 13.8%) (Supplementary Data 6). These
results indicate that another explanation for the presence of steppe ancestry in North Africa could
be the admixture of local Berber populations with incoming Punics or Romans. It is worth
mentioning that 5-stream model including both a Bell-Beaker and a Roman/Punic contribution
did not reach significance.
45 One limitation of our study is that sample sizes are low for some islands, for example,
Lanzarote and Fuerteventura with only two individuals. To account for sample size differences,
we compared the qpAdm admixture values obtained at individual level by island (Supplementary

22
 Fig. 29). Mean values for the contribution of Early Neolithic Moroccans to western islands
(8.60% ± 0.57% for El Hierro, 7.67% ± 1.91% for La Gomera and 8.82% ± 1.09% for Tenerife)
was higher than that of those of the eastern island of Gran Canaria (5.54% ± 1.20%). The only
overlapping value between the western and eastern regions is the one calculated from the
5 individual CAN.027 from La Gomera, but never reaching values as low those observed for the
islands of Lanzarote and Fuerteventura. Hence, although some variation is observed within
individuals from the same island, a regional differentiation between eastern and western islands
is confirmed.

10

23
 Supplementary Note 8: Heterozygosity, inbreeding and family
relationships
8.1. Family relationship estimations
5
Family relationships between individuals were estimated using READ software126 based on
the MEGA-HGDP genome-wide data. This method allows us to infer up to second-degree
relationships, including nephew/niece-uncle/aunt, grandparent–grandchild or half-siblings. This
approach is especially appropriate for kinship inferences on ancient DNA data, as it can produce
10 reliable results for individuals with coverage greater than 0.1X. To avoid lack of coverage to
confound the estimations, we excluded CAN.043 from Tenerife and CAN.046 and CAN.039
from Gran Canaria (<0.2X covering the MEGA-HGDP dataset). We only detected two
individuals from Tenerife (CAN.045 and CAN.046) with an average pairwise P0 coinciding with
a second-degree relationship (Supplementary Fig. 30). The rest of the individuals from the
15 islands showed no apparent kinship between them.

8.2. Heterozygosity estimations

Heterozygosity estimates were obtained for each island population and for each
20 archaeological site using popstats127. For this analysis, we used the MEGA-HGDP to increase the
individuals’ coverage and retained only transversions to avoid damage to interfere with results.
Only those archaeological sites with at least two individuals were selected: Punta Azul from El
Hierro; Barranco Majona from La Gomera; El Portillo from Tenerife; El Hormiguero,
Guayadeque, Lomo Galeón, Puente de La Calzada and Cendro from Gran Canaria; and Montaña
25 Mina from Lanzarote. Heterozygosity values were calculated for the Early and Late Neolithic
people from Morocco using the same procedure for comparison, considering that the first one is
population showing signs of isolation and the other one was the result of admixture.
Gran Canaria, Tenerife, and La Palma showed the highest heterozygosity estimations (0.219
± 0.001, 0.218 ± 0.001 and 0.215 ± 0.001, respectively) close to Late Neolithic populations from
30 Morocco (0.213 ± 0.001) (Supplementary Fig. 31). On the other hand, Fuerteventura showed the
lowest heterozygosity estimates (0.184 ± 0.003) followed by Lanzarote and El Hierro (0.193 ±
0.002 and 0.195 ± 0.001, respectively). La Gomera shows intermediate values (0.198 ± 0.001).
However, all of them outgrow values seen for Early Neolithic populations from Morocco (0.157
± 0.001). When sites are compared (Supplementary Fig. 32), Punta Azul from El Hierro has the
35 lowest heterozygosity value (0.196 ± 0.001) as inferred using mtDNA 36,66, while Puente de La
Calzada in Gran Canaria showed the highest (0.260 ± 0.016). Except for Punta Azul, the rest of
archaeological sites are above the pi estimations obtained for Late Neolithic populations from
Morocco (Supplementary Fig. 32). These results confirm previous diversity estimations based on
uniparental markers66 in which islands with more exploitable natural resources (Tenerife, Gran
40 Canaria and La Palma) had more diversity than smaller islands or islands with more limited
resources.
To account for sampling bias, heterozygosity values were estimated for all possible
combinations of two individuals within each island (the lowest sample size, from Fuerteventura
and Lanzarote) and the average value was calculated. To mirror the individuals of Lanzarote and
45 Fuerteventura, we selected for heterozygosity estimations one individual with a low-coverage
genome available and one captured individual. Again, heterozygosity estimations are variable
depending on the individuals involved in the calculation, but mean and median values for the
24
 islands of Tenerife and Gran Canaria are higher than those observed for El Hierro and La
Gomera (Fig. 3a). In order to explore the variation on the heterozygosity estimations, we focused
on the better characterized islands of Tenerife and Gran Canaria (Supplementary Fig. 33).
Variation on the heterozygosity values estimated by pairs of individuals can be explained by low
5 overlap within the two compared individuals, with lower coverages tending to produce lower
heterozygosity estimations, with a moderate correlation between the pi value and coverage
(Tenerife: r=0.449 and p=0.0020; Gran Canaria: r=0.510 and p=0.0078). However, no
combination of two individuals produced values as low as those observed for Lanzarote (pi =
0.193) and Fuervententura (pi = 0.184). Even though these values could be an underestimation of
10 the real values for Lanzarote and Fuerteventura, the results obtained point to a lower
heterozygosity value for these islands, as observed for El Hierro and La Gomera.

8.2. Inbreeding estimations

15 The presence of runs of homozygosity (ROHs) was detected using hapROH128 for both the
Human Origins and the MEGA-HGDP datasets. In this method, haplotype information from a
modern DNA panel is used to detect ROHs longer than 4 cM in aDNA genomes with coverage
as low as 0.3X. We screened for the total sum of ROH segments in four length ranges (4 – 8, 8-
12, 12-20 and >20 cM) in individuals with genome coverage higher than 0.3X.
20 First, we focused on short ROH segments of 4 – 8 cM (ROH [4,8]) that accumulate from
parents on 1 – 30 generations ago and are indicative of the population size of the ancestral
mating pool (background relatedness) over approximate the previous half millennium128. ROH
[4,8] is high among the most ancient individuals and then decreases forward in time due to
population expansions (e. g., the Neolithic transition). Most of the Canary Islands indigenous
25 individuals have at least 20 – 60 cM of their genome composed of ROH [4,8] (Fig. 3b;
Supplementary Data 8), which is indicative of relatively small effective population in the past,
probably on the earliest stages of the human settlement.
Second, we tested our individuals having >20 cM ROH (sROH>20cM) segments greater than
50 cM, which is indicative of small and isolated populations128. We identified five ancient
30 individuals exceeding this long ROH threshold: CAN.004 from El Hierro, CAN.005 from
Fuerteventura, CAN.030 from La Gomera, CAN.038 from Lanzarote and CAN.038 from
Tenerife. Interestingly, the four of them with the greatest sROH>20cM and total ROH exceeding
300 cM are from either islands with the smallest areas and/or with poorer resources. This amount
of ROH can be due to sporadic close-kin matings due to small population sizes. Also, all
35 individuals are from the latest stages of the indigenous period of the Canary Islands (from 12th
century onwards) which can be indicative of the effect of isolation in the archipelago population.

25
 Supplementary Note 9: Effective population size and founder effects
9.1. Effective population size

5 Estimates of effective population size (Ne) for insular populations were obtained using
hapROH128 for HGDP-MEGA dataset as it is the one with a better coverage (Fig. 4a).
Considering the whole population of the archipelago, we observe that the Ne was maintained in
412 individuals (95% CI: [371 – 460]), slightly lower than previously reported considering only
ancient genomes from Gran Canaria and Tenerife129. Also, when considering how Ne evolved
10 around the 1,200 year-transect we have sampled, we observe a decreasing Ne pattern over time
when individuals from all the archipelago are included. When the indigenous population of each
island is analyzed separately, we observe that Mahos from Fuerteventura (mean: 75; 95% CI: [56
– 101]) and Lanzarote (mean: 151; 95% CI: [106 – 221]) exhibit the smallest Ne, followed by
Bimbapes from El Hierro (mean: 204; 95% CI: [163 – 263]). People from Gran Canaria had the
15 highest Ne estimations (mean: 460; 95% CI: [366 – 594]), followed by and Beneahoritas from La
Palma (mean: 395; 95% CI: [272 – 599]) and Guanches from Tenerife (mean: 285; 95% CI: [227
– 366]), coinciding with previous heterozygosity estimations. Surprisingly, La Gomera has the
second-largest Ne estimations of all the islands (mean: 429; 95% CI: [292 – 664]). However, we
have to consider that our individuals from La Gomera consist of one individual from an earlier
20 occupation phase of the archipelago (CAN.027; 9th century) and the other ones from a later
period (12th – 14th centuries), while individuals from Fuerteventura, Lanzarote and El Hierro are
all from the late occupation phase (12th century onwards). If inbreeding increased over time, this
difference may affect Ne estimations. When we removed CAN.027 from the analysis, we
obtained a more reduced Ne for indigenous Gomerans (mean: 281; 95% CI: [180 – 473]).
25 As Ne estimations for the islands of Lanzarote and Fuerteventura are calculated from only
one individual, it is possible that the actual Ne values were higher. We have to consider that the
two individuals from Lanzarote and Fuerteventura presented values of sROH>20cM higher than
50, and therefore they should have been excluded from Ne estimations. For the island of El
Hierro, we calculated Ne including individuals with a substantial portion of their genomes in
30 ROHs and as expected, the Ne value was lower than the one calculated before (mean: 147; 95%
CI: [123 – 177]). A similar result is observed when individuals with ROHs are included for La
Gomera and Tenerife (Supplementary Data 9). In order to further explore the effects of the
sample size limitation in Lanzarote and Fuerteventura, we also estimated Ne considering only one
individual as representative of each island population. For that, we selected individuals with
35 similar a genome-wide coverage as the ones from Lanzarote and Fuerteventura (Supplementary
Data 9). We observed that for all the islands, the Ne confidence intervals estimates are
considerably wider than when using the original sample size. As expected, we also observed that
for different individuals of the same island, Ne estimates based on one individual vary depending
on the proportion of his/her genome on ROHs. For all the above, although the inbreeding level
40 observed in the only two available individuals from Lanzarote and Fuerteventura are a testament
of the small Ne of these island populations, estimates for these islands should be reevaluated
when additional paleogenomic data is available.

9.2. Founder effects

45
To evaluate the history of reductions in population size in the indigenous populations of the
Islands, we used ASCEND130. ASCEND relies on the decay of the allele sharing correlation

26
 across individuals in a population to infer the time and intensity of a founder/bottleneck event to
low-coverage genomes. We followed the recommendations from the authors and ran the analysis
for four different datasets from the MEGA-HGDP panel: (1) all indigenous individuals, (2)
individuals divided by their geographical location (eastern –Lanzarote, Fuerteventura and Gran
5 Canaria– and western –Tenerife, La Gomera, El Hierro, La Palma–); and (3) individuals from
each island with at least N≥5 (Gran Canaria and Tenerife). To avoid confounding bias, we
excluded CAN.039 from the analyses due to possible post-conquest admixture, and filtered out
CAN.046 because of the 2nd-degree relatedness with another individual from Tenerife. In order
to inspect if our results were determined by individuals’s coverage, we filtered out genomes with
10 <0.1X and <0.3X of coverage from each dataset. To obtain the time of the bottleneck or founder
events, we considered the average radiocarbon date of each dataset and 28 years per generation.
For all the analyses, the NRMSD estimator was below the recommended cut-off of 0.29 (median
= 0.04).
According to the results, a shared founder effect for all the indigenous people occurred around
15 720 BCE (95% CI: 944 – 440 BCE) coinciding with the 5th to the 10th centuries BCE
(Supplementary Data 10; Supplementary Fig. 34). This reduction in population occurred with a
low-moderate intensity (95% CI: 1.7 – 2.0) (Supplementary Fig. 35) more similar to founder
events seen in continental populations than to island ones130. Among islanders, only Maltese or
Orcadians have shown similar intensities. Moreover, island populations tend to experience more
20 drastic founder events due to lower founder population sizes and/or maintained low population
sizes within the island due to resource limitation. Considering that different islands most
probably experienced bottlenecks of different intensities, this result can be either an artifact or
reflect a common bottleneck that affected the ancestors of the Canarian indigenous people in the
continent, previous to the colonization time.
25 Considering the ancestry differences between eastern and western individuals commented
before, we run the analysis for each geographic location. Western islands would share a
bottleneck event that occurred around the Era change (95% CI: 184 BCE – 208 CE), while
eastern individuals would share an earlier event between the 8th and 2nd centuries BCE (95% CI:
793 BCE – 121 BCE). The intensity of the bottleneck event is similar in both the eastern and
30 western regions (on average 3.1% and 2.7%, respectively) sharing the continental-like
characteristic with the Archipelago’s. However, this analysis can also produce artifactual results
as different islands could have experienced founder effects of different intensities.
If we consider Gran Canaria alone, a possible bottleneck event is estimated between the 4th
century BCE and the 2nd century CE, similar to the eastern’s potential bottleneck in intensity and
35 time range (95% CI: 2.3% – 2.9%). This result is expected because most of the eastern people
are from Gran Canaria. Alternatively, individuals from Tenerife could have experienced a more
drastic event (95% CI: 3.7% – 4.7%) than the western people but in the same period (95% CI:
242 CE – 66 BCE), similar to those seen in present-day islanders130.
When we filtered individuals based on their SNP coverage, we do not see significant
40 differences in the bottleneck events’ dating, except for Gran Canaria and the eastern dataset
(Supplementary Fig. 34). As Gran Canaria is the island from which we have sampled a more
ample territory (all of the individuals from Tenerife are from a very restricted area of the island)
this result may not be due to coverage itself but to sample diversity.
Even though the minimum recommended sample size N≥5, as we see that coverage and
45 sample size does not seem to affect results in islands such as Tenerife, we ran the analysis with
the El Hierro individuals. In fact, although there are four individuals, only one of the genomes is
below 1X of coverage. Using that dataset, we detected that El Hierro individuals shared a
bottleneck event occurring between the 8th and the 12th centuries CE, few generations before the
27
 individuals lived. The intensity of the event is ~12%, considerably greater than the rest of the
events studied before. However, the fact that all of them are from the same archeological site and
close in time could be affecting the results. More genome-wide data from El Hierro will be
needed to determine if this event affected all the island population.
5

28
 Supplementary Note 10: Phenotype analyses
The Canarian indigenous genomes were assessed for phenotypical traits by analyzing the
alleles present at a population level in several loci of interest (Supplementary Table 1). For that,
5 we performed SNP calling using samtools mpileup, filtering out low-quality bases (BASEQ <
30) and low-quality mapped reads (MAPQ < 25). Due to the low coverage of the genomes, we
only considered one random allele for each position for all the variants (pseudo-haploid calling)
and studied the variants present in the indigenous pool with depth > 1.
First, we assessed the five known MCM6 SNPs associated with lactose tolerance
10 (rs4988235G>T, rs41380347A>C, rs41525747G>C, rs145946881C>G, rs869051967A>C) 131.
All indigenous individuals carried the ancestral alleles for all the variants, except for one
individual with two alleles for the rs4988235A variant (Supplementary Table 1). Probably the
most common phenotype in the Canary Islands indigenous people was lactose intolerant as
previously seen68.
15 We also reviewed the bibliography and considered several medical conditions that are
common in present-day Canarians when compared to the Iberian Peninsula, in order to prove if
their associated variants were already presented in the indigenous gene pool (Supplementary
Table 1). The PLCG2 gene has been associated with autoimmune conditions such as asthma in
present-day Canarians, at high frequency when compared with the Iberian founder population,
20 and has been linked to their North African ancestry132. We found that the derived variant
associated with asthma in this gene (rs3852738T) is found in a frequency of 79.2%, so the
indigenous origin proposed by the authors is plausible.

25
Supplementary Table 1. Phenotypically informative SNPs.

allele Effect
Effect
Gene SNP ID Association Reference N allele
Allele A C G T frequency
Carbohydrate metabolism
MCM6 rs4988235 A Lactase persistence Ref. 131 2 0 20 0 11 0.09
MCM6 rs41380347 C Lactase persistence Ref. 131 18 0 0 0 9 0.00
131 0 0 22 0 11 0.00
MCM6 rs41525747 C Lactase persistence Ref.
131 0 26 0 0 13 0.00
MCM6 rs145946881 G Lactase persistence Ref.
131 26 0 0 0 13 0.00
MCM6 rs869051967 C Lactase persistence Ref.

Medical conditions in Canary Islanders

PLCG2 rs3852738 T Asthma Canary Islanders Ref. 132 5 0 0 19 12 0.792

29
 Supplementary Note 11: Admixture proportions for the modern
Canarian population
Admixture analysis using mtDNA determined that the contribution of the indigenous people
5 to the modern Canarian population was 55.9% for the entire archipelago66. When considering the
islands independently and using the total indigenous population for calculations, the native
contribution ranged from 30.7% in Gran Canaria to 71.4% in La Gomera. When using the
indigenous people of each island as parental populations, values ranged from 0% in El Hierro to
55.5% in La Gomera66. The result obtained for El Hierro was interesting, because when the
10 whole indigenous population was used, the native contribution was 36.2%. This result was
explained considering that the island of El Hierro was almost depopulated at the time of the
European conquest and was later repopulated with indigenous populations from other islands and
European colonizers66. This result was important because it highlighted the necessity of
considering each island independently.
15 Regarding the Y-chromosome, previous admixture analysis estimated a contribution of
indigenous males to the modern Canarian population of 5.9 ± 2.9%, using North Africans as a
proxy for the indigenous population133. This result demonstrated that the modern population of
the Canary Islands exhibit a marked sexual asymmetry on the survival of indigenous lineages:
while mtDNA indicates a relatively high indigenous contribution (>50%), Y-chromosomes in the
20 current population are mostly of European origin (>90%). Direct ancient DNA analysis of the Y-
chromosome of the indigenous population produced an estimate of 16.1 ± 4.6% contribution of
native males to the current population73. The presence of indigenous Y-chromosomes can
explain the higher frequency of E-M183 in current and historical Canarian populations (8.3%,
11.9%)73,134 when compared to the Iberian Peninsula (5.2 %)135,136. Using our new dataset, we
25 repeated the Y-chromosome admixture analysis using the mL estimator as in73, considering three
main parental populations: the Canarian indigenous population, and current Iberian and Sub-
Saharan populations. Admixture estimator mL was calculated based on Y-chromosome
haplogroup frequencies using the WLSAdmix program137. For these admixture estimations, we
only included ancient NGS individuals, with the aim of avoiding putative problems derived from
30 analyzing nuclear DNA with PCR and from sample bias due to most of the individuals coming
from the sites of Guayadeque and Punta Azul (see section 4.2). From a Y-chromosome
perspective, most of the lineages present in the current Canary Islands population are of
European origin (95.3%), while the indigenous and sub-Saharan African components accounting
for 4.0% and 0.7%, respectively. Values within islands vary, with no indigenous components
35 being observed in La Gomera and El Hierro, and with the highest values present in Fuerteventura
(12.5%) and Gran Canaria (9.1%). Sub-Saharan African contribution is absent in Fuerteventura,
La Gomera, El Hierro and Tenerife, and low values are observed in the remaining islands.
Because our sample size is still too low at an insular level, the comparison between calculations
performed using the total indigenous people and each insular population could not be carried out.
40 We also performed admixture estimations based on genome-wide data using qpAdm from
ADMIXTOOLS as described for the ancient individuals, and considering the indigenous,
Spanish and Yoruban populations as contributing sources. For that we merged the array data
from the Canary Islands obtained by132 with the Human Origins data, obtaining a total of 55,516
SNPs. For the total modern Canarian population, the admixture model would imply 17.8% ±
45 1.3% of indigenous people, 79.7% ± 1.0% of Spanish and 2.6% ± 0.5% of Yoruban
contributions. To calculate the contribution of each parental population at an individual level, we
used both the global indigenous population and each respective insular indigenous population.
30
 When the global indigenous people are considered, the islands with the highest indigenous
contributions are observed for El Hierro (25.2% ± 1.8%) and Fuerteventura (23.2% ± 1.4%),
while the lowest are observed for La Palma (12.9% ± 1.4%), Gran Canaria (13.4% ± 0.9%) and
Tenerife (14.2% ± 1.1%) (Supplementary Fig. 36). The sub-Saharan contribution is low in all the
5 islands, with the highest value observed in La Gomera (4.0% ± 0.5%) and the lowest in La Palma
(1.1% ± 0.5%) (Supplementary Fig. 36). When insular indigenous populations are considered for
calculations, the contribution of the native people is higher in La Gomera, Lanzarote and
Fuerteventura, although we cannot rule out the possibility that this result could be due to low
sample sizes, as the two islands with the larger numbers of individuals (Tenerife and Gran
10 Canaria) produce similar results in both analyses.
Regarding of the method used for obtaining the admixture proportions for the modern
Canarian population, it is clear the impact that the European colonization had in the indigenous
people. Although the contribution from the mtDNA is more than 50%, this value is lower than
5% when the Y-chromosome is considered. Genome-wide data point to an overall contribution
15 around 17.8% ± 0.8%, similar to the value obtained from68 (16.7% ± 5.0%). As was previously
observed for the mtDNA, the contribution of the indigenous people to current Canarians is
variable between islands. From the Y-chromosome, we observe than the contribution is almost
zero for the smallest islands of El Hierro, La Palma and La Gomera. Higher values are observed
for the larger islands of Gran Canaria (9.1%) and Tenerife (8.2%). It is interesting that the island
20 of Fuerteventura has a contribution of 12% while Lanzarote, with a similar conquest and
colonization history, has a value of 1.2%. As the Y-chromosome composition was most probably
variable within the archipelago as observed for the mtDNA, all these analyses would need to be
repeated when enough Y-chromosome data is available to perform calculations at an insular
level. Regarding genome-wide analyses, it is expected from historical data that the islands that
25 have received more migration since colonial to modern times, are the ones with the lowest
indigenous and the highest European contributions. This includes the two islands with the capital
cities of the provinces of Las Palmas de Gran Canaria and Santa Cruz de Tenerife, but also the
island of La Palma. The island of La Palma and Tenerife had an important arrival of European
populations, mainly Portuguese and Castillians since the beginning of the Modern period.
30 Although the sub-Saharan African contribution is low, this result is also interesting as it
demonstrates the impact of the slave trade in the Canary Islands and the incorporation of freed
enslaved people into the Canarian society as demonstrated by138.

31
 Supplementary Note 12: IBD analyses
We imputed the genomes using GLIMPSE v1.0.1139 with the default parameters as
recommended by140. Given that 0.1X coverage is enough to get 80% of imputation accuracy at
5 common variants (minor allele frequency >= 10%), only >0.1X individuals (N=22) were selected
for the imputation step (Supplementary Data 1). We first computed genotype likelihoods for each
genome using the candidate variant sites contained in the 1000 Genomes phase 3, filtering out
for non-biallelic and singleton variants. We split the chromosomes into 2 Mb chunks using 200
Kb of buffer size with GLIMPSE_chunk. Each chunk was then imputed and phased using
10 GLIMPSE_phase and ligated into the same chromosome using GLIMPSE_ligate. The most
likely haplotypes (--solve parameter) were then sampled from the ligated VCFs. We filtered out
the individuals with an average genotype probability (GP) lower than 0.95 and removed variants
with an INFO score <0.5.
To analyze the population structure among ancient Canarians and between them and other
15 ancient European and African populations in finer detail, we identified shared genomic segments
that are identical by descent (IBD). IBD segments are identical haplotypes that two individuals
share when inherited without recombination141. To obtain IBD segments we built a database
using already published genomes from Neolithic to Iron Age Europe, sub-Saharan Africa, the
Near East and Neolithic to Late Neoltithic North Africa54,85,87,88,90,94,95,97,103,142–146. We selected
20 the individuals with an average coverage >0.1X and genotype probability (GP) >0.95, imputed
them and merged with the imputed ones from the Canary Islands. We then recalculated their
INFO score and filtered out variants with an INFO score <0.5. From the resulting VCFs, we
called the IBD segments using IBDseq141 with the default parameters. We converted the IBD
segments from base pair to centimorgan (cM) using the HapMap II haplotype panel as reference.
25 Finally, we carried out genetic clustering of the ancient individuals using hierarchical community
detection on a network of pairwise IBD-sharing similarities, as in140. Briefly, we used igraph147
to build a weighted network of the individuals using the fraction of the genome shared IBD
between pairs as weights, and used this network to perform community detection using the
Leiden algorithm148 implemented in the leidenAlg R package
30 (https://github.com/kharchenkolab/leidenAlg).
We observe that a single genetic cluster for all the African individuals was created
separating them from European people (Supplementary Fig. 37). It is worth mentioning that this
cluster does not contain the Late Neolithic people from Morocco, that are placed with
Chalcolithic and Early Bronze Age individuals from Europe. The African cluster identifies five
35 communities: three for the Canary Islands people and two for the rest of the ancient North
African and sub-Saharan African individuals. Focusing on the Canarian ones (N=22), we observe
that this analysis separates all individuals from the eastern islands from those of the western
ones, except for El Hierro individuals who are placed in a specific cluster (Fig. 4b), as expected
for individuals who share a high fraction of their genome in IBD and consistent with
40 consanguinity due to isolation. When focusing on the western cluster, we observe that, as
expected in isolated insular environments, individuals from the same island share a higher
fraction of their genome in IBD, clustering them together. One of the cluster groups La Gomera
and La Palma individuals separated from the Tenerife individuals, and then each island in their
own cluster. In the case of the eastern islands, the individuals seem to be more difficult to group
45 together than the western ones, as the fraction of the genome shared IBD within pairs is lower.
Although it is possible to group the Fuerteventura and Lanzarote individuals separated from the
ancient Gran Canarians, the difference is not as significant as in the western people. We can

32
 observe that those individuals are more related to CAN.008 (Agujero) and CAN.017
(Guayadeque) than any other individual from Gran Canaria. The other two Gran Canaria clusters
are formed by individuals from potentially the same archaeological site. Individuals CAN.049 to
CAN.051 belong to the Cendro site, while gun005 and gun008 belong to the University of
5 Edinburgh Museum collection and were probably obtained from the same site, although given
the lack of archaeological context, this cannot be demonstrated. Finally, an important result is
that putative migration between eastern and western islands is not observed, as no individual
from either region shares IBD with the other cluster.

33
 40 ● ●

● ● ●
●
endogenous DNA (%)

30

●
● ●
20 ● ●
● ●

●
●
●
●
10 ●

● ●
●
●
● ●
● ● ●
● ● ●
● ● ●
● ● ● ●
●
● ● ● ●
● ●
0
jo

_C ero
a

ue o

_A ja

El icho

ro

en

lo

_C tre
s_ que

Pu Mu ña_ s
s

io

ul
a

iro
na

to
_A rale

ur
á
on

er

in

Pu zad
co

ca

til

Az
ar
nd

La ale
m

rto Gu eri

Lo ale

im
i
rm

si

l
La ost
j

or

Sa
Lo Are
gu
aj

an
n

as

ia

a_
e

M _Pa
o

as
al
ap

e_ ad
G
_P
to

t
_M

G
C

or
M
ur

ng
m

C
C

_C

nt
s_
An

o_
_

ay

te eo_
_F
El
_H
C

or

s
co

ta
El

la
m

lto
_H
El

lo

on
n

El

e_
La

s
ra

Sa
El

_d
r

_d
Ba

en
ue
H

Supplementary Fig. 1. Comparison of endogenous DNA rates between archaeological sites.

Sample sizes for each archaeological site are as follows: Antoncojo (n=1), Barranco Majona
5 (n=2), Cascajo (n=1), Cuermeja (n=1), El Agujero (n=1), El Capricho (n=1), El Cendro (n=4), El
Hormiguero (n=4), El Huriamen (n=1), El Portillo (n=2), Gerián (n=1), Guayadeque (n=4),
Huerto de los Morales (n=1), La Angostura (n=2), La Fortaleza (n=1), Las Arenas (n=1), Lomo
Galeón (n=4), Los Pasitos (n=1), Montaña Mina (n=2), Museo Canario (sample from
Fuerteventura with no archaeological site adscription; n=1), Puente de La Calzada (n=2), Punta
10 Azul (n=3), Salitre (n=1), Salto Casimiro (n=1). The box represents the interquartile range (25 –
75 percentiles), the bold line is the median and the whiskers represent the minimum and
maximum values observed for each archaeological site. Each individual value is shown in violet
dots.

34
 ●
50 ●
●
●

40 ●
● ●
●
endogenous DNA (%)

●
● ●
●
● ●

30
●
●
●

●
● ● ●
● ●
20 ●
● ●
● ●
● ●
●
● ●
● ● ●
● ● ●
● ●
10 ●
● ●
●
●
● ● ●
●
● ●
● ● ●
● ●
●
● ● ●
●
● ●
●
● ● ●
●
● ● ● ●
● ● ● ●
●
● ●
● ●
● ●
●
● ● ● ●
0 ●

on_target MAPQ25 unique duplicates

Supplementary Fig. 2. Endogenous DNA and duplicate rates for all individuals considered
in the study. Results for the 44 individuals considered (40 new, 4 from71). The box represents the
interquartile range (25 – 75 percentiles), the bold line is the median and the whiskers represent
5 the minimum and maximum values observed for each filtering step. Each individual value is
shown in colored dots.

35
 80

60
percentage of reads

pre−capture−endogenous
40 pre−capture−duplicates
post−capture−endogenous
post−capture−duplicates

20

0
01

02

06

13

21

22

23

24

25

27

28

30

31

34

35

37

38

39

40

41

42

45

46
.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0

.0
AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN

AN
C

C
Supplementary Fig. 3. Comparison of % endogenous content in pre-capture and post-
capture sequencing data of libraries captured using WISC.

36
 125

100
●
●

enrichment (X)
75 ● ●

●
●

50 ●
●

●
● ●
●
●
●
25 ●
●
●
●
● ●
●
● ● ● ●
●
●
● ● ●
● ●
●
● ● ●
● ●
● ● ●
● ●
●
● ● ●
●
● ● ●
● ●
● ● ●
●
●
●
0 ●

on_target MAPQ25 unique duplicates

Supplementary Fig. 4. Comparison of WISC performance in all individuals considered in

the study (n=23). Note: outlier duplicate rate value for individual CAN.023 was removed for
clarity. The box represents the interquartile range (25 – 75 percentiles), the bold line is the
5 median and the whiskers represent the minimum and maximum values observed for each
filtering step. Each individual value is shown in colored dots.

37
 0.4
C > T / G > A damage (%)

0.3

0.2

0.1

0.0
−25 −20 −15 −10 −5 (...) 5 10 15 20 25

position

Supplementary Fig. 5. Deamination damage distribution along reads.

38
 range (25 – 75 percentiles), the bold line is the median and the orange diamonds are the mean.
Supplementary Fig. 6. Insert size for all individuals. The box represents the interquartile

CAN.052
CAN.051
The whiskers represent the minimum and maximum values observed for each sample.

CAN.050
CAN.049
CAN.048
CAN.046
CAN.045
CAN.043
CAN.042
CAN.041
CAN.040
CAN.039
CAN.038
CAN.037
CAN.036
CAN.035
CAN.034
CAN.031
CAN.030
CAN.028

39
CAN.027
CAN.026
CAN.025
CAN.024
CAN.023
CAN.022
CAN.021
CAN.020
CAN.019
CAN.018
CAN.017
CAN.014
CAN.013
CAN.012
CAN.011
CAN.010
CAN.009
CAN.008
CAN.006
CAN.005
CAN.004
CAN.003
CAN.002
CAN.001
150

100

50

0
insert size (pb)

5
 CAN.001 ● ●
CAN.002 ● ●
CAN.003 ● ●
CAN.004 ● ●
CAN.005 ● ●
CAN.006 ● ●
CAN.008 ●●
CAN.009 ● ●
CAN.010 ● ●
CAN.011 ● ●
CAN.012 ● ●
CAN.013 ● ●
CAN.014 ● ●
CAN.017 ● ●
CAN.018 ● ●
CAN.019 ● ●
CAN.020 ●●
CAN.021 ● ●
CAN.022 ● ●
CAN.023 ● ●
CAN.024 ● ●
CAN.025 ● ●
CAN.026 ● ●
CAN.027 ● ●
CAN.028 ● ●
CAN.030 ● ●
CAN.031 ● ●
CAN.034 ● ●
CAN.035 ● ●
CAN.036 ●
●
CAN.037 ● ●
CAN.038 ● ●
CAN.039 ● ●
CAN.040 ● ●
CAN.041 ● ●
CAN.042 ● ●
CAN.043 ● ●
CAN.045 ● ●
CAN.046 ● ●
CAN.048 ●
●
● contamMix
CAN.049 ● ● ● schmutzi
CAN.050 ● ●
CAN.051 ● ●
CAN.052 ● ●

0 5 10 15 20
contamination rate (%)

Supplementary Fig. 7. Contamination rates estimated using contamMix and Schmutzi

software. For each of the 44 individuals, dots represent the mean value of the contamination
estimation obtained, while error bars represent their lower and higher values of the 95%
5 confidence interval.

40
 Sex identification
CAN.001 ● ●

CAN.002 ● ●

CAN.003 ● ●

CAN.004 ● ●

CAN.005 ● ●

CAN.006 ● ●

CAN.008 ● ●

CAN.009 ● ●

CAN.010 ● ●

CAN.011 ● ●

CAN.012 ● ●

CAN.013 ● ●

CAN.014 ● ●

CAN.017 ● ●

CAN.018 ● ●

CAN.019 ● ●

CAN.020 ● ●

CAN.021 ● ●

CAN.022 ● ●

CAN.023 ● ●

CAN.024 ● ● type
CAN.025 ● ●
● filtered
CAN.026 ● ●

CAN.027 ● ● ● no_filter
CAN.028 ● ●

CAN.030 ● ●

CAN.031 ● ●

CAN.034 ● ●

CAN.035 ● ●

CAN.036 ● ●

CAN.037 ● ●

CAN.038 ● ●

CAN.039 ● ●

CAN.040 ● ●

CAN.041 ● ●

CAN.042 ● ●

CAN.043 ● ●

CAN.045 ● ●

CAN.046 ● ●

CAN.048 ● ●

CAN.049 ●

CAN.050 ●

CAN.051 ●

CAN.052 ●

0.00 0.05 0.10 0.15

Ry estimate

Supplementary Fig. 8. Molecular sex determination using the ry estimator, comparing

values obtained before and after pseudo-autosomal and repetitive regions filtering. For each
of the 44 individuals, dots represent the mean value of the ry estimate, while error bars represent
5 their lower and upper bound of the 95% confidence interval.

41
 Supplementary Fig. 9. PathPhynder placement of the indigenous individuals within the Y-
chromosome tree based on the 1000 Genomes database. (A) E-M183, (B) E-M33, (C) R-
M269 and (D) T-M184 clades. CAN.008, CAN.025 and CAN.040 have been excluded from the
5 plots as they were assigned outside the sub-haplogroups considered here.

42
 A1 A1a B B1 B2 BT C CT D2 DE E E1 E1a E1b1 E1b1a E1b1b E2 F G H I J J1 J2 K L LT N NO O P Q1a Q1b R R1 R1a R1b R2 T
80

60

type
ancestral
SNPs

40
ancestral_damage
derived
derived_damage

20

Y−chromosome tree branch

Supplementary Fig. 10. Y-chromosome plot for CAN.038 (E-M33).

43
 A1 A1a B B1 B2 BT C CT D2 DE E E1 E1a E1b1 E1b1a E1b1b E2 F G H I J K L LT N O P Q1a Q1b R R1 R1a R1b R1b1 R1b1a R2 T

75

type
50
ancestral
SNPs

ancestral_damage
derived
derived_damage

25

Y−chromosome tree branch

275 276 277 278 279 280 281 282 283 284 285 339

150

100

type
ancestral
SNPs

ancestral_damage
derived
derived_damage

50

Y−chromosome tree branch

Supplementary Fig. 11. Y-chromosome plot for CAN.008 (above). Below is shown the SNPs
covering each of the branches of the T-M184 haplogroup.
5

44
 A1 A1a B BT C CT D2 DE E E1 E1a E1b1 E1b1a E1b1b E1b1b1a1 E1b1b1a1a1 E1b1b1a1a2 E2 F G I J L N O P R1 R2 T
25

20

15
type
ancestral
SNPs

ancestral_damage
derived
derived_damage
10

Y−chromosome tree branch

Supplementary Fig. 12. Y-chromosome plot for CAN.040 (E-M78).

45
 MEGA−HGDP 823,509 SNPs

150
100
50
0
PC2

−50
−100
−150

Sub−Saharan_Africa Can_ind_people
North_Africa Morocco_EN
−200

Near_East Morocco_LN
Europe Morocco_IB

−500 −400 −300 −200 −100 0 100

PC1

Supplementary Fig. 13. PCA of HGDP-MEGA panel with the indigenous population of the
Canary Islands and other ancient individuals from North Africa projected using LASER.
5

46
 MEGA−HGDP lsqproject

0.05
0.00
PC2

−0.05

Sub−Saharan_Africa Can_ind_people
North_Africa Morocco_EN
−0.10

Near_East Morocco_LN
Europe Morocco_IB

−0.10 −0.05 0.00

PC1

Supplementary Fig. 14. PCA of HGDP-MEGA panel with the indigenous population of the
Canary Islands and other ancient individuals from North Africa projected using lsqproject.

47
 MEGA−HGDP 823,509 SNPs MEGA−HGDP 823,509 SNPs

150

100
100

0
50
0

−100
PC3
PC2

−50
−100

−200
−150

El_Hierro Fuerteventura

−300
La_Palma Lanzarote
La_Gomera Morocco_IB
−200

Tenerife Morocco_EN
Gran_Canaria Morocco_LN

−500 −400 −300 −200 −100 0 100 −200 −150 −100 −50 0 50 100 150

PC1 PC2

Supplementary Fig. 15. PCA of HGDP-MEGA panel with the indigenous population of the
Canary Islands and other ancient individuals from North Africa projected using LASER
(PC1/PC2 left; PC2/PC3 right), where the differentiation between western (green/blue) and
5 eastern islands (red/violet) can be observed.

48
 −100

−100
−80

−80
−60

−60
PC2

PC2
−40

−40
−20

−20
0

0
Middle_East
North_Africa
Europe
AEH004_average CAN.002 (31.1%) Middle_East
North_Africa
Europe
AEH037_average CAN.021 (2.5%)
20

20
Sub−Saharan_Africa AEH004_reps Sub−Saharan_Africa AEH037_reps

100 50 0 −50 −100 100 50 0 −50 −100

PC1 PC1
−100

−100
−80

−80
−60

−60
PC2

PC2
−40

−40
−20

−20
0

Middle_East
North_Africa
Europe
AEH061_average CAN.043 (11.8%) Middle_East
North_Africa
Europe
AEH106_average CAN.036 (79.5%)
20

20

Sub−Saharan_Africa AEH061_reps Sub−Saharan_Africa AEH106_reps

100 50 0 −50 −100 100 50 0 −50 −100

PC1 PC1

Supplementary Fig. 16. Replicates of the HGDP-MEGA PCA for four ancient individuals
of our dataset. Coordinates for the 10 replicates are indicated with grey asterisks and
average value is indicated with a black circle. ID and coverage percentage is indicated for
5 each individual.

49
 Human Origins with Africa

Modern samples
Eastern_Europe Southern_Europe
Middle_East Sub−Saharan_Africa
North_Africa Western_Europe
0.04
0.02 Sardinia

●●
● ●
0.00

●●●
●
●●
●●
●
●
●
●●●
●
●●
●●
●●●
●
●
●●
●
●
●●
●
●
●●
●
●●
●
●
●●
●
●
●
●●
●●●●
●●
●●
●●
●●
●●
●
●
PC2

● ●
−0.02

●
●
−0.04

Ancient samples
Aegean_N Iran_N ● Steppe_EMBA
Anatolia_ChL Kenya_400BP ● Steppe_Eneolithic
Anatolia_N ● Levant_BA ● Steppe_IA
Armenia_ChL Levant_N ● Steppe_MLBA
● Armenia_EBA Malawi_Chencherere_5200BP Switzerland_HG
● Armenia_MLBA Malawi_Fingira_2500BP Tanzania_Luxmanda_3100BP
−0.06

CHG ● Malawi_Fingira_6100BP Tanzania_Pemba_1400BP

Egypt_ancient ● Malawi_Hora_8100BP Tanzania_Pemba_600BP
EHG ● Morocco_EN Tanzania_Zanzibar_1400BP
● Etruscan Morocco_IB WHG
Europe_EN ● Morocco_LN This_study:
● Europe_LNBA Mota El_Hierro
Europe_MNChL Natufian La_Palma
Iberia_EN Phoenician La_Gomera ●
● Iberia_LNBA SA_IronAge Tenerife
−0.08

Iberia_MNChL SA_StoneAge Gran_Canaria

Iran_ChL SHG Fuerteventura ●
Iran_HotuIIIb South_Africa_12000BP Lanzarote
● Iran_LN ● South_Africa_2000BP

−0.02 0.00 0.02 0.04

PC1

Supplementary Fig. 17. PCA of the Human Origins panel with the indigenous population of
the Canary Islands and other ancient and modern individuals from Europe, the Middle
East and Africa (PC1 vs. PC2).
5

50
 Human Origins with Africa Human Origins with Africa

Ancient samples
Aegean_N Iran_N ● Steppe_EMBA
Anatolia_ChL Kenya_400BP ● Steppe_Eneolithic

0.15
Anatolia_N ● Levant_BA ● Steppe_IA
Armenia_ChL Levant_N ● Steppe_MLBA
● Armenia_EBA Malawi_Chencherere_5200BP Switzerland_HG
● Armenia_MLBA Malawi_Fingira_2500BP Tanzania_Luxmanda_3100BP ●
CHG ● Malawi_Fingira_6100BP Tanzania_Pemba_1400BP ●

0.04
Egypt_ancient ● Malawi_Hora_8100BP Tanzania_Pemba_600BP
EHG ● Morocco_EN Tanzania_Zanzibar_1400BP
● Etruscan Morocco_IB WHG ● ●
Europe_EN ● Morocco_LN This_study:
● Europe_LNBA Mota El_Hierro
Europe_MNChL Natufian La_Palma
Iberia_EN Phoenician La_Gomera ●
●
● Iberia_LNBA SA_IronAge Tenerife ●
0.10

Iberia_MNChL SA_StoneAge Gran_Canaria

Iran_ChL SHG Fuerteventura ●

0.02
Iran_HotuIIIb South_Africa_12000BP Lanzarote ●
● Iran_LN ● South_Africa_2000BP ●
●
●
●●
●
●
● ●
● ●●
●●
●

0.00
●
PC3

PC3
0.05

● ●
● ●●
●
● ● ●●●
●●
● ●
●●
●● ●
●
● ●●
● ●●●●
● ●●
●● ● ●●●●●
●

−0.02
● ●●
● ●
●● ● ●●●●
● ●●
●●●●● ● ●
●● ●
●
●
●●●
●●●● ● ●
●
●● ●
●● ●
●●●● ●
●
●●●●
●●● Ancient samples
●
●● ● ●● ●
●●●●
●●
●●
●
● ●●● ● Aegean_N ● Iberia_LNBA ● Steppe_EMBA
●●●● ●●
●
● ●● ●
●
0.00

●●
● ● Anatolia_ChL Iberia_MNChL ● Steppe_Eneolithic
●● ●
●●● ●● Anatolia_N Iran_ChL ● Steppe_IA
● ●● Armenia_ChL Iran_HotuIIIb ● Steppe_MLBA
●●●● ●
●●●● ● ● Armenia_EBA ● Iran_LN Switzerland_HG

−0.04
●
●●● ●● ●
●
●●
●●
●●
● ●●
●●● ● ● Armenia_MLBA Iran_N WHG
●
●
●
●●
●●●
●● ●
●
●●
●●
●●● ●●
●
●
●●● ●
●
●
●●
●●
●
●
●●●● CHG ● Levant_BA This_study:
●
● ●● ●
● Egypt_ancient Levant_N El_Hierro
● EHG ● Morocco_EN La_Palma
● ● Etruscan Morocco_IB La_Gomera
−0.05

Europe_EN ● Morocco_LN Tenerife

● Europe_LNBA Natufian Gran_Canaria

−0.06
Europe_MNChL Phoenician Fuerteventura
Iberia_EN SHG Lanzarote

−0.02 0.00 0.02 0.04 −0.020 −0.015 −0.010 −0.005 0.000 0.005 0.010

PC1 PC1

Supplementary Fig. 18. PCA of the Human Origins panel with the indigenous population of
the Canary Islands and other ancient and modern individuals from Europe, the Middle
East and Africa (PC1 vs. PC3). The right panel shows a close up on the Eurasian populations.
5

51
 0.06
Egypt_ancient West_Europe_Roman
Ibiza_Punic This_study:
Middle_East_IA El_Hierro
Middle_East_Roman La_Palma
Sardinia_IA La_Gomera

0.04
Sardinia_IA_Punic Tenerife
Sardinia_Roman Gran_Canaria
South_Europe_Roman Fuerteventura
0.02
0.00 West_Europe_IA Lanzarote
PC3

−0.02
−0.04
−0.06

−0.005 0.000 0.005 0.010 0.015

PC1

Supplementary Fig. 19. PCA of the Human Origins panel with the indigenous population of
the Canary Islands and other ancient individuals from the Iron Age of Europe and the
Middle East.
5

52
 5
0.0 0.2 0.4 0.6 0.8 1.0
0.0 0.2 0.4 0.6 0.8 1.0

M
or Ba
oc
co M nt
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us
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La ue
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Be
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53
ui
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G
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Ca e
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Pa
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in
ia
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Fu ar
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te e oz
ab
Islands and other ancient individuals from North Africa (lower panel). ve ite
nt
ur
a
of the HGDP-MEGA panel (upper panel) and the indigenous population of the Canary
Supplementary Fig. 20. Unsupervised clustering analysis (K=4) of the modern populations
0.8
0.4
0.0
0.8
0.4
0.0
0.8
0.4
0.0
0.8
0.4
0.0
0.8
0.4
0.0
0.8
0.4
0.0
0.8
0.4
0.0
0.8
0.4
0.0

Supplementary Fig. 21. Unsupervised clustering analysis of the modern populations of the
Human Origins panel including individuals from Europe, the Near East, North African and
Sub-Saharan Africa from K=2 to K=8.

54
 5
0.0 0.4 0.8 0.0 0.4 0.8 0.0 0.4 0.8 0.0 0.4 0.8 0.0 0.4 0.8 0.0 0.4 0.8 0.0 0.4 0.8 0.0 0.4 0.8

WH
Sw G
itz e
rla n S H G
d_H
G

Ana
to li
a_N

Aeg
ean
_N

Eur
ope
_EN

Ib e
ria _
EN
Eur
ope
_M
NC
hL
Ib e
ria _
MN
Ch
L

Islands from K=2 to K=8.

Eur
ope
_LN
BA

Ib e
ria _
S te LN
ppe BA
_En E
e o li H G
th ic

S te
ppe
_EM
BA

S te

55
ppe
_M
LBA

S
A n a te p p e
A rm to lia _ _ IA
en Ch
A rm ia _ C hL
e L
A rm n ia _ E
e n ia BA
_M
LBA
Ira n
_H CHG
o tu
II
Ira n Ib
Ira n _ N
Ira n _ L N
_C
hL
Na
tu fi
an
Lev
a n t_
N
M a K e L e va
la w n y n t_
M a M a i_ C a _ 4 B A
la w la w h _ 0 0
M a i_ F i_ F 5 2 0 B P
la w in g i_ 2 0 B
i_ H ira _ 5 0 0 P
o ra 6 1 0 B P
_81 0B
SA 00B P
_ S to M P
Tan S A n e _ Ao ta
z _ g
T aann ia _ S A Iro n _ A e
T za n L u x S
_12 g
T a n a n z ia _ m a n A _ 20 0 0 B e
z a n a n ia P e m d a _ 0 0 0 P
ia _ _ P e b a 3 1 0 B P
Zan m b _14 0B
z ib a _ 6 0 0 B P
a r_ 0 0 P
M o 1400B P
ro B P
M o c c o _ IB
ro
M o cco _ E
ro N
P h oc c o _ L
Anc e N
ie n E trun ic ia n
t_ E s c
g yp a n
tia n
E l_
H ie
La_ rro
L a _ P a lm
Go a
me
ra
Ten
e rif
e

G ra
n_C
ana
ria
L
Supplementary Fig. 22. Unsupervised clustering analysis of the ancient populations of the

Fue a n za r
rte v o te
e n tu
Human Origins panel as described in Section 5.3.2 and the indigenous people of the Canary

ra
 0
100 ●

10
90

20
80

0.20
● Morocco_LN ●
●● Egypt_ancient

30
●
70
● Phoenician
70 ● Etruscan
● Eastern_islands

40
●
60 60
● Western_islands
● CAN.039 ●

0.15
●●●●

50
●
●
50 ●
●●●●●●
50 ●●● ●●
● ●
● ●
● ● ●●● ●
●

60
●● ●●●
● ●●●●●●● ●
40 40 ●●

triangle.plot$Steppe
●● ● ● ● ● ● ●
● ● ●
●

70
● ●
30 30 ● ●

0.10
● ●● ●
● ●
●
●

80
●
●
20 20 ●
●● ●
● ● ●

90
● ●
● ●
10 10 ● ● ●●

0
0.05
●

10
0 0 ●
●●
●●
10

90

80

70

60

50

40

30

20

10

0
● ●●
●●
0

●
steppe component ●
● ●
●

0.00
●
●● ● ●●

Supplementary Fig. 23. Ternary plot showing the proportion of

0.2
ancestral Maghrebi,
0.4 0.6 0.8

European early farmer and Steppe components on the Canarian indigenous people and
triangle.plot$Maghreb
other ancient populations, based on ADMIXTURE results for K=8.

56
 Ancestral Maghrebi component Early European farmer component
1.00

0.6

●
0.75

0.4
●
●

0.50

0.2

0.25

0.0
IB

EN

LN

oe n
an

rro

ia

IB

EN

LN

oe n
an

an

rro

ia

e
rif

rif
er

ur

er

ur
ia

La alm

ot

ia

La alm

ot
ar

ar
o_

o_
ci

sc

ci

sc
ie

ie
o_

o_
pt

pt
ne

ne
o_

ar

o_

ar
om

nt

om

nt
an

an
ni

ni
_H

_H
c

c
ru

ru
_P

_P
gy

gy
ve

ve
nz

nz
c

c
Te

Te
c

c
oc

oc
C

C
_G

_G
oc

oc
oc

oc
Et

Et
_E

_E
te

te
El

El
La

La
La

La
n_

n_
or

or
Ph

Ph
or

or
or

or
er

er
t

t
M

M
ra

ra
en

en
M

M
M

M
Fu

Fu
G

G
ci

ci
An

An
Steppe component Iran Neolithic component
0.20 ●

0.4

0.15
●
0.3

0.10
0.2
●

0.05
0.1

0.00 0.0
B

EN

Eg N
Ph tian

an

rro

ia

EN

Eg N
Ph tian

an

an

rro

ia

e
rif

rif
er

ur

er

ur
a

La alm

ot

La alm

ot
I

I
_L

_L
ar

ar
o_

o_
ci

sc

ci

sc
ie

ie
ne

ne
o_

ar

o_

ar
om

nt

om

nt
yp

yp
an

an
co

ni

co

ni
_H

_H
c

c
ru

ru
_P

_P
ve

ve
nz

nz
Te

Te
cc

cc
oc

oc
oe

oe
C

C
_G

_G
oc

oc
Et

Et
te

te
El

El
La

La
La

La
o

o
n_

n_
or

or
t_

t_
or

or
or

or
er

er
M

M
ra

ra
en

en
M

M
M

M
Fu

Fu
G

G
ci

ci
An

An

Supplementary Fig. 24. Contribution from the ancestral Maghrebi, European early farmer
and the Iran Neolithic and Steppe components on the Canarian indigenous people and
other ancient populations, based on ADMIXTURE results for K=8. Populations include:
5 Morocco_IB (n=5), Morocco_EN (n=4), Morocco_LN (n=3), Phoenician (n=1), Etruscan (n=1),
Ancient_Egyptian (n=3), El Hierro (n=4), La Palma (n=3), La Gomera (n=4), Tenerife (n=11),
Gran Canaria (n=23), Lanzarote (n=2), Fuerteventura (n=2). The box represents the interquartile
range (25 – 75 percentiles), the bold line is the median and the whiskers represent the minimum
and maximum values observed for each population. Outlier values are shown in colored dots.
10

57
 CIP
Iberia_EN ●

Aegean_N ●

Europe_EN ●

Europe_MNChL ●

Iberia_MNChL ●

Anatolia_N ●

Iberia_LNBA ●

Anatolia_ChL ●

Morocco_LN ●

Levant_N ●

Europe_LNBA ●

Etruscan ●

WHG ●

Steppe_MLBA ●

Switzerland_HG ●

Armenia_ChL ●
population

Levant_BA ●

SHG ●

Armenia_EBA ●

Ancient_Egyptian ●

Armenia_MLBA ●

Natufian ●

Phoenician ●

Iran_recent ●

Iran_ChL ●

Steppe_EMBA ●

Steppe_IA ●

CHG ●

Steppe_Eneolithic ●

EHG ●

Iran_LN ●

Iran_HotuIIIb ●

Morocco_EN ●

Iran_N ●

Morocco_IB ●

Ust_Ishim ●

0.20 0.21 0.22 0.23 0.24

f3(aDNA,population;Ju_hoan_North)

Supplementary Fig. 25. Outgroup f3-statistic results for the indigenous population of the
Canary Islands (n = 49). Dots represent the mean of the f3-statistics results and error bars
represent the standard errors.
5

58
 Europe_LNBA Steppe_MLBA

Lanzarote ● Lanzarote ●

Gran_Canaria ● Gran_Canaria ●

Fuerteventura ● Fuerteventura ●
island

island
La_Palma ● La_Palma ●

Tenerife ● La_Gomera ●

La_Gomera ● Tenerife ●

El_Hierro ● El_Hierro ●

0.230 0.235 0.240 0.225 0.230 0.235 0.240

f3(island,Europe_LNBA;Ju_hoan_North) f3(island,Steppe_MLBA;Ju_hoan_North)

Morocco_EN Morocco_LN

La_Gomera ● Gran_Canaria ●

Gran_Canaria ● Fuerteventura ●

Fuerteventura ● Lanzarote ●
island

island

Tenerife ● La_Palma ●

La_Palma ● Tenerife ●

El_Hierro ● La_Gomera ●

Lanzarote ● El_Hierro ●

0.215 0.220 0.225 0.23 0.24 0.25

f3(island,Morocco_EN;Ju_hoan_North) f3(island,Morocco_LN;Ju_hoan_North)

Supplementary Fig. 26. Outgroup f3-statistic results for the islands populations when
5 compared to Europe_LNBA, Steppe_MLBA, Morocco_EN and Morocco_LN. Dots
represent the mean of the f3-statistics and error bars represent the standard errors. Analyses
performed using El Hierro (n=4), La Palma (n=3), La Gomera (n=4), Tenerife (n=11), Gran
Canaria (n=23), Lanzarote (n=2), Fuerteventura (n=2).

59
 0.20
Morocco_EN contribution

0.15

0.10

0.05

0.00

400 800 1200

time (calibrated CE)
1.0
Morocco_LN contribution

0.8

0.6

0.4
400 800 1200
time (calibrated CE)
0.4
Germany_BB contribution

0.3

0.2

0.1

0.0

−0.1
400 800 1200
time (calibrated CE)
0.20

0.15
Mota contribution

0.10

0.05

0.00

−0.05
400 800 1200
time (calibrated CE)

Supplementary Fig. 27. Contributions for the 4-stream model at individual level over time.
Analysis performed using four individuals from El Hierro, three individuals from La Palma; four
individuals from La Gomera, 11 individuals from Tenerife, 23 individuals from Gran Canaria,
5 two individuals from Lanzarote, and two from Fuerteventura. Color code for islands is as in
Supplementary Fig. 15. The squares represent the estimated contribution, while the whiskers
represent its standard error.

60
 0.20
Morocco_EN contribution

0.15

0.10

0.05

0.00

−0.05
400 800 1200
time (calibrated CE)

Supplementary Fig. 28. Contributions for the Morocco_EN component in the 4-stream
model in individuals from Tenerife (N=11; green) and Gran Canaria (N=23; pink) over
time. The squares represent the estimated contribution, while the whiskers represent its standard
5 error.

61
 0.09
Morocco_EN

0.07

0.05
El_Hierro

La_Palma

La_Gomera

Tenerife

Gran_Canaria

Fuerteventura

Lanzarote
island

Supplementary Fig. 29. Contributions for the Morocco_EN component in the qpAdm 4-
stream model for the sub-sampling test in the different islands. Analysis performed using
four individuals from El Hierro, three individuals from La Palma; four individuals from La
5 Gomera, 11 individuals from Tenerife, 23 individuals from Gran Canaria, two individuals from
Lanzarote, and two from Fuerteventura. The box represents the interquartile range (25 – 75
percentiles), the bold line is the median and the red diamonds the mean. The whiskers represent
the minimum and maximum values observed for each population.

62
 5
AverageAverage
pairwisepairwise P0 (± 2SE)
P0 (± 2SE)

0.16 0.16
0.18 0.18
0.20 0.20
0.22 0.22

●
AEH007AEH064
AEH007AEH064
CAN.045 CAN.046

1st
2nd

2nd
●

●
AEH073AEH102
AEH073AEH102
CAN.041 CAN.040
●

AEH007AEH102
AEH007AEH102
CAN.045 CAN.040
degree

1st degree
degree

degree

Identical/Twins

Identical/Twins
●

AEH064AEH073
AEH064AEH073
CAN.046 CAN.041

represent the standard error.

●

AEH007AEH073
AEH007AEH073
CAN.045 CAN.041
●

AEH064AEH102
AEH064AEH102
CAN.046 CAN.040
●

AEH009AEH102
AEH009AEH102
CAN.042 CAN.040
●

AEH063AEH102
AEH063AEH102
CAN.048 CAN.040
●

AEH009AEH073
AEH009AEH073
CAN.042 CAN.041
●

AEH063AEH073
AEH063AEH073
CAN.048 CAN.041

63
Identical/Twins
Identical/Twins
●

AEH007AEH009
AEH007AEH009
CAN.045 CAN.042
●

AEH007AEH063
AEH007AEH063
CAN.045 CAN.048
●

AEH009AEH064
AEH009AEH064
CAN.042 CAN.046
●

AEH063AEH064
AEH063AEH064
CAN.048 CAN.046
●

AEH009AEH063
AEH009AEH063
CAN.042 CAN.048

1st degree
1st degree
Frequency
Frequency

0.0 0.0
0.5 0.5
1.0 1.0
1.5 1.5
2.0 2.0
2.5 2.5
3.0 3.0

2nd degree
2nd degree
0.180

0.180

represents the average pairwise P0 obtained for each pair of individuals, while the error bars
Supplementary Fig. 30. P0 estimations for the indigenous individuals of Tenerife. Each dot
0.195

0.195
Average pairwise P0

Average pairwise P0
0.210

0.210
 0.22 ●
●

0.20
●

● ●
pi

0.18

0.16

Fuerteventura Lanzarote El_Hierro La_Gomera La_Palma Tenerife Gran_Canaria

population

Supplementary Fig. 31. Heterozygosity estimations obtained for all the islands’ populations.
Each dot represents the average pi estimation obtained for each group of individuals, while the
error bars represent the standard errors. The analysis was performed using four individuals from
5 El Hierro, three individuals from La Palma; four individuals from La Gomera, 11 individuals
from Tenerife, 23 individuals from Gran Canaria, two individuals from Lanzarote, and two from
Fuerteventura. The green dotted line represents the pi estimation obtained from Morocco_EN
(N=4; pi = 0.157) and the red dotted line the pi estimation from Morocco_LN (N=3; pi = 0.213).

64
 0.275

●
●
0.250 ●

0.225 ● ●
pi

●
●

0.200
●

0.175

Punta_Azul Barranco_Majona Portillo Lomo_Galeon Montana_Mina El_Cendro Hormiguero Guayadeque Puente_Calzada

population

Supplementary Fig. 32. Heterozygosity estimations obtained for all the archaeological sites
with at least two individuals. Each dot represents the average pi estimation obtained for each
5 group of individuals, while the error bars represent the standard error. The green and red dotted
line represents the same values as in Supplementary Figure 31. Sample size is four for Punta
Azul, Lomo Galeón, El Cendro, El Hormiguero and Guayadeque, while sample size is two for
Barranco Majona, El Portillo, Montaña and Puente de La Calzada.

65
 5
pi pi
a

0.16
0.18
0.20
0.22
0.17
0.19
0.21

●
AEH053_AEH005
●
AEH009_AEH061

●
AEH053_AEH037

●
●

AEH053_AEH038 AEH009_AEH063

●
AEH053_AEH039
●

●
AEH053_AEH040 AEH009_AEH064

●
AEH053_AEH041
●

AEH009_AEH068

●
AEH053_AEH043

●
AEH053_AEH044
●

AEH009_AEH073

●
AEH053_AEH045

●
●

AEH053_AEH046 AEH009_AEH102

●
AEH053_AEH047
●

●
AEH053_AEH048 AEH009_gun002

●
AEH053_AEH050
●

AEH009_gun011

●
AEH053_AEH051

●
●

AEH053_AEH054 AEH009_gun012

●
AEH053_AEH070
●

●
AEH053_AEH172 AEH063_AEH007

●
AEH053_gun005
●

AEH063_AEH061

●
AEH053_gun008

●
AEH053_LLD−0056
●

AEH063_AEH064

●
AEH053_LLD−0057

●
●

AEH053_LLD−0058 AEH063_AEH068

●
AEH053_LLD−0059
●

●
AEH070_AEH005 AEH063_AEH073

66
●
AEH070_AEH037
●

AEH063_AEH102

●
AEH070_AEH038

●
AEH070_AEH039
●

AEH063_gun002

●
AEH070_AEH040

●
●

AEH070_AEH041 AEH063_gun011
●
AEH070_AEH043
Tenerife sub−sampling replicate
●

●
AEH070_AEH044 AEH063_gun012

Gran Canaria sub−sampling replicate

●

AEH070_AEH045
●

gun011_AEH007
●

AEH070_AEH046
●
●

AEH070_AEH047 gun011_AEH061
●

AEH070_AEH048
●

AEH070_AEH050 gun011_AEH064
●

AEH070_AEH051
●

gun011_AEH068
●

AEH070_AEH054
●

AEH070_AEH172
●

gun011_AEH073
●

error. The green and red dotted line represents the same values as in Fig. 3a.
AEH070_gun005
●
●

AEH070_gun008 gun011_AEH102
●

AEH070_LLD−0056
●

AEH070_LLD−0057 gun011_gun002
●

AEH070_LLD−0058
●

gun011_gun012
●

AEH070_LLD−0059

for the islands of Tenerife (a) and Gran Canaria (b). Each dot represents the average pi
SNPs
SNPs

estimation obtained for each sub-sampling replicate, while the error bars represent the standard
2e+05
4e+05
6e+05
2e+05
4e+05
6e+05

Supplementary Fig. 33. Heterozygosity estimations obtained for all sub-sampling replicates
 Archipelago_SB

all
Archipelago

Western_Islands_SB

Western_Islands

geo
Eastern_Islands_SB

Eastern_Islands

Gran_Canaria_rep10

Gran_Canaria_rep9

Gran_Canaria_rep8

Gran_Canaria_rep7

Gran_Canaria_rep6

Gran_Canaria_rep5

Gran_Canaria_rep4

Gran_Canaria_rep3

Gran_Canaria_rep2

Gran_Canaria_rep1

Gran_Canaria_avSB

Gran_Canaria

island
Tenerife_rep10

Tenerife_rep9

Tenerife_rep8

Tenerife_rep7

Tenerife_rep6

Tenerife_rep5

Tenerife_rep4

Tenerife_rep3

Tenerife_rep2

Tenerife_rep1

Tenerife_avSB

Tenerife

El_Hierro

−1600 −1400 −1200 −1000 −800 −600 −400 −200 0 200 400 600 800 1000 1200
Bottleneck inferred time (BCE/CE)

Supplementary Fig. 34. Founder events observed in the indigenous people of the
archipelago, eastern, and western islands; Tenerife, Gran Canaria, and El Hierro. For each
dataset we evaluated the putative effects of the sampling bias (_SB; N=10 in each replicate) and
5 included in the plot mean values of the founder event time period (dots) and their associated
standard error (error bars). For Gran Canaria and Tenerife, we included the average founder
event time for 10 replicates (_rep) with four individuals each and the average time period of the
10 replicates (_avSB). For more information, see Supplementary Note 9.2. The grey tile
represents the time range of the putative archipelago’s founder event, while the blue tile
67
represents the Vandal Minimum period range, and the yellow tile represents the Medieval Warm
Period.

68
 5
Founder intensity (%)

0
5
10
Archipelago

Archipelago_SB

Eastern_Islands

Eastern_Islands_SB

El_Hierro

Gran_Canaria

Gran_Canaria_avSB

Gran_Canaria_rep1

Gran_Canaria_rep10

Gran_Canaria_rep2

Gran_Canaria_rep3

Gran_Canaria_rep4

Gran_Canaria_rep5

Gran_Canaria_rep6

Gran_Canaria_rep7

69
Gran_Canaria_rep8

Gran_Canaria_rep9

Tenerife

Tenerife_avSB

Tenerife_rep1

Tenerife_rep10

Tenerife_rep2

Tenerife_rep3

Tenerife_rep4

Tenerife_rep5

Tenerife_rep6

Tenerife_rep7

Tenerife_rep8

we evaluated the putative effects of the sampling bias (_SB; N=10 in each replicate) and
included in the plot mean values of the founder event intensity (dots) and their associated
Tenerife_rep9

standard error (error bars). For Gran Canaria and Tenerife, we included the average founder
Western_Islands

Supplementary Fig. 35. Intensity observed for each founder event studied. For each dataset
Western_Islands_SB
 event intensity for 10 replicates (_rep) including four individuals each and the average intensity
of the 10 replicates (_avSB). The grey tile represents the intensity range of most island founder
events according to ref. 130, while the dotted line represents the founder intensity of Ashkenazi
Jews (~1.7%).
5

70
 Canarian indigenous people contribution 0.35

0.30

global
0.25
global
insular
0.20

0.15

El_Hierro La_Palma La_Gomera Tenerife Gran_Canaria Fuerteventura Lanzarote

Canarian indigenous people contribution
Spanish contribution

0.8

global
global
insular

0.7

El_Hierro La_Palma La_Gomera Tenerife Gran_Canaria Fuerteventura Lanzarote

Canarian indigenous people contribution
0.05

0.04
Yoruban contribution

0.03
global
0.02 global
insular

0.01

0.00

El_Hierro La_Palma La_Gomera Tenerife Gran_Canaria Fuerteventura Lanzarote

Canarian indigenous people contribution

Supplementary Fig. 36. Admixture estimations based on genome-wide data considering the
global indigenous people (blue) and each insular indigenous population (red). Each dot
represents the average admixture contribution of each population source (Canarian indigenous,
5 Spanish or Yoruban) to each present-day island population, associated to their standard error.
This analysis has been performed using 34 present-day individuals from El Hierro; 35 from La

71
Palma; 78 from La Gomera; 64 from Tenerife; 117 from Gran Canaria; 32 from Fuerteventura
and 56 from Lanzarote.

72
 wtMean
0.2
0.4
0.6

Supplementary Fig. 37. Hierarchical genetic clustering plot of IBD segments detected in the
21_cell

nce
ience

e
9_science

2019_scienc

_science
mente_20

o_2019_scie
science

ce
_science
io_2019_sc

19_scien
tonio_201
io_2019_

nio_2019
im5bp.cle

nio_2019
R81.antonio_

tonio_20
R133.antoni
R131.anton
R1548.an

R1550.antonio_2019_science
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