GUANCHE - Remains from Canary Islands Reveal Close Affinity to Modern NA 2017

[Mediterranea]

The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5^th century BCE [1, 2, 3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6, 7, 8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7^th–11^th centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%–31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.

gun002	Tenerife	XY	0.21	294.7	74,618	H1cf	E1b1b1b1a1 E-M183	951 ± 26	1089.4 ± 65.5	3.63%/2.42%–4.85%
gun005	Gran Canaria	XX	0.47	341.1	140,873	H2a	NA	1082 ± 26	956 ± 61	2.41%/1.56%–3.27%
gun008	Gran Canaria	XX	0.30	690.9	101,216	L3b1a	NA	1116 ± 26	935.5 ± 56.5	1.65%/1.35%–1.95%
gun011	Tenerife	XY	3.93	931.6	370,465	T2c1d2	E1b1b1b1a1 E-M183	1216 ± 27	791.5 ± 96.5	0.53%/0.38%–0.69%
gun012	Tenerife	XY	0.54	214.3	157,104	U6b1a	E1b1b1b1a1 E-M183	1421 ± 28	621 ± 39	5.97%/4.22%–7.73%
gun001	Tenerife	XY	0.016	9.6	NA	U6b1a	NA	NA	NA	NA
gun004	Tenerife	NA	0.004	49.98	NA	J1c3	NA	NA	NA	5.76%/3.57%–7.95%
gun006	Gran Canaria	XY	0.027	12.21	NA	L3b1a	NA	NA	NA	6.60%/1.87%–11.33%
gun007	Gran Canaria	XY	0.003	3.47	NA	L3b1a	NA	NA	NA	NA
gun013	Tenerife	NA	0.005	14.2	NA	U6b1a	NA	NA	NA	13.79%/1.24%–26.34%
gun014	Tenerife	XY	0.008	4.2	NA	U6b	NA	NA	NA	NA

Analysis of Uniparental Genetic Markers

The mitochondrial genome coverage for the eleven Guanche individuals ranges from 3.4× to 931×. The number of SNPs that support each haplotype varies between 38 and 58 and are reported as deviations from the Reconstructed Sapiens Reference Sequence (RSRS) [13] (Table S1). All positions supporting the predicted haplogroup calls and mutations missing for the absolute haplogroup assignment are listed in Table S1. We found six different mitochondrial haplogroups in eleven individuals (Tables 1 and S1). The Guanches analyzed here carried mitochondrial lineages such as J1c3, H2a, U6b, L3b1a, and T2c1d2 that are common across West Eurasia and/or North Africa [14] (Tables 1 and S1) and are consistent with previous studies on ancient Guanche mitochondrial DNA [6, 7]. Two individuals from Tenerife (gun001 and gun012) and one from Gran Canaria (gun013) carried the U6b1a haplotype, which is hypothesized to be endemic to and a founder lineage of the Canary Islands (Tables 1 and S1) [15]. We also found the H1cf haplotype in one individual from Tenerife (gun002), which is defined by a mutation at position 16260T (Table S1). H1-16260 is also considered a founder lineage of the Canary Islands, for two reasons: (1) it is present in all modern Canary populations [15] and rare outside the Canary Islands (found previously in only a single Algerian individual) [7, 16]; and (2) it was found in pre-Hispanic populations from Tenerife [6], La Palma [7], El Hierro [16], and La Gomera [17]. The three males from whom haplogroup-defining Y chromosome SNPs were retrieved carried the E1b1b1b1a1 (E-M183) haplotype (a major sub-clade of the haplogroup E1b1b1b1, defined by the derived M81 marker), which is again consistent with previous analyses of ancient Guanches [8]. This haplogroup is ubiquitous across modern North African populations and particularly common in Berber-speaking populations of North Africa [8, 18]. The derived mutations supporting the Y chromosome haplogroups are listed in Data S1, sheet 1.


Population Genomic Analysis of Autosomal DNA

A principal component analysis (PCA) of the five samples with the highest autosomal genome coverage, performed using genome-wide autosomal SNPs overlapping with Human Origins (HO) data [19, 20], reveals close affinity to modern Northwest African populations such as Tunisians and Algerians, but with a tendency (especially for individuals from Gran Canaria) to occupy a space outside modern Northwest African variation, closer to Europeans (Figures 2 and S2). However, outgroup f₃ statistics [19] suggest that the Guanches share more genetic drift with non-African test populations than with African test populations, including Northwest African populations of Berber origin (Data S1, sheet 2). This observation is inconsistent with the PCA and the uniparental genetic marker data, indicating that the outgroup f₃ statistic may be misleading, possibly due to the complex history of recent sub-Saharan admixture events in North African populations [12, 21] and the sensitivity of the f₃ estimator to such patterns. This issue seems to extend to other statistics based on allele frequency correlations such as the D statistic [19] since D(Outgroup, Guanches; North African, Sardinian/Anatolian farmer) consistently produces highly significant positive values of D (Z > 4), which would imply a closer relationship between Guanches and Sardinians and Anatolian farmers than between Guanches and North African populations (Data S1, sheet 3).


In order to resolve this, we used different statistics to measure genetic similarity between Guanches and modern populations, as well as between different modern North African populations and other populations (Table S2 and Quantification and Statistical Analysis). Both outgroup f₃ statistics and average pairwise differences identify Sardinians as the population sharing the most drift with both modern North Africans and Guanches (Table S2). This is in stark contrast to our expectation that North Africans would cluster with other North Africans. However, it replicates recent findings [21] showing that both ancient and modern Egyptians share more genetic drift with European populations than they do with other North African groups, while still showing evidence of strong genetic affinity to one another in other types of analyses. This behavior might be due to varying degrees of admixture from highly divergent sources (e.g., sub-Saharan populations) into different populations, which can affect the interpretation of f₃ statistics [22]. Therefore, we conclude that these statistics are not suitable to identify the modern population most similar to Guanches in the sense that we intend it for this study (Quantification and Statistical Analysis). In contrast, our extended analyses using F_ST (fixation index) [23, 24] and f₂ [25] identify different North African and Near Eastern populations as most similar to modern North African populations and Guanches, results that are consistent with the PCA and the uniparental genetic analysis (Table S2; Figures 2 and S2). This finding is in agreement with anthropological, archaeological, linguistic [1, 4, 9, 26], and uniparental genetic data [6, 7, 8] and adds to a growing body of new evidence suggesting that some ancient domesticated plants [27] and animals [28] from the Canary Islands originated from North Africa.


The Guanches’ Berber-like affinity is further supported by ADMIXTURE [29] analysis (Figures 3 and S3), where Guanches largely behave like modern Berbers across all values of K. At K = 10, a Northwest African-specific ancestry component makes up the greatest amount of autosomal ancestry in the Guanche and Berber populations in the HO dataset, such as the Mozabite and Saharawi. It is also ubiquitous across other Northwest African populations with Berber ancestry, such as Algerians and Tunisians, consistent with the PCA results. This ancestry component is also represented in present-day Canary Islanders and at a low proportion in some South European populations (Figures 3 and S3). Interestingly, it is also shared by Middle Eastern populations, including some Natufians (Figure 3). Y chromosome E1b1b haplotypes (though not M183 variants) were also common in Natufians (circa 11,000 BCE) and pre-pottery Neolithic male individuals from the Levant (circa 7,000 BCE), suggesting some affinity to North Africans [30].

The results of the ADMIXTURE analysis furthermore show that the Guanches carried early European farmer (EEF)-like ancestry; this ancestry component is widespread (though at varying proportions) in present-day North Africans and Middle Easterners but rare or largely absent in some Berber populations (Figure 3). The EEF component is strongly associated with early Neolithic farmers from Anatolia and Europe (as well as present-day Sardinians), hinting at a possible link between present-day North Africans and the expansion of Neolithic culture through the Mediterranean [31, 32, 33], though it could also reflect post-Neolithic gene flow among Mediterranean groups [34]. The Guanches also appear to have carried varying proportions of Middle Eastern ancestry, best represented by the HO Bedouin_B population.

We also note that one Guanche individual (gun005) carried a greater proportion of hunter-gatherer (HG)-like ancestry than the other individuals, possibly suggesting low-level gene flow from a European source that predates the European conquest. Although our results are overall consistent with an origin from a single ancestral population in North Africa, the possible small-scale introgression from other sources postdating the earliest settling is consistent with archaeological finds of Phoenician-Punic amphora in Buena Vista (Lanzarote) and Roman amphora fragments retrieved from El Bebedero (Lanzarote), indicating that the islands (and local islanders) were in at least sporadic contact with other peoples and cultures prior to the European colonization in the 15^th century CE [5].


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Inferring Phenotypes


Lastly, we obtained phenotypically informative SNPs from the five individuals with the highest genome coverage; however, only individual gun011 yielded high enough coverage to infer genotypes (Table S4). We relied on the HirisPlex and 8-plex prediction systems, which are based on 24 and 8 SNPs respectively, for skin, hair, and eye color prediction [36, 37], as well as 3 SNPs involved in lactose tolerance [38, 39, 40] (Table S4). The results reveal that this individual likely was lactose intolerant and had brown eyes, dark hair, and light or medium skin color. These results are similar for the other individuals where SNP information is available, albeit with lower coverage, suggesting that—at least for this sample of Guanches—the dominating phenotype was lactose intolerant, dark hair, light or medium skin color, and brown eyes (Table S4).


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