What My Genome Says

Where I Come From

Two independent methods — maximum-likelihood estimation against 1000 Genomes proxies, and principal component analysis with k-nearest neighbours — converge on the same result: predominantly Iberian European ancestry, with a significant Native American component and a meaningful African contribution.

The PCA k-nearest-neighbour result (k=20) places the genome at: PEL 55%, MXL 30%, CLM 15% — consistent with the MLE. In PC1–PC2 space the genome sits equidistant from the European centroid (distance 0.096) and the African centroid (0.097), confirming substantial Iberian ancestry plus an Afro-Colombian contribution. PC3 rises above all European populations, reflecting Native American ancestry.

PCA (PC1–PC2 and PC1–PC3) placing the genome (★) against 2,500+ 1000 Genomes samples. PC2 tracks the European–African axis; PC3 tracks Native American ancestry. The genome sits between the Iberian cluster and the Latino/admixed cluster.

My Father's Line: J-Y6304 — Levantine (Correa Patriline)

The Y chromosome is inherited exclusively from father to son, unchanged except for occasional mutations — tracing the unbroken paternal line: father's father's father, and so on. For Juan, this is the Correa patriline. The Béthencourt / Bettencourt name enters through the maternal grandmother and is not encoded in the Y chromosome.

Direct SNP queries of the WGS (chrY.vcf, avg depth ~20–30×) confirm J-Y6304 definitively: J → J1 (M267) → J1b (L136) → J-Y6304.

M343 (R1b) is ancestral — R1b is ruled out at 29× depth (GQ137). M267 derived confirms J1; Y6304, FGC20310, and Y6308 all derived confirm J-Y6304. The call is unambiguous.

Paternal lineage analysis. M267 derived confirms J1; Y6304, FGC20310, Y6308 all derived confirm J-Y6304. M343 (R1b) ancestral at 29× — Bell Beaker origin excluded. Y chromosome coverage ~20–30× effective depth; 20+ diagnostic SNPs callable.

My Mother's Line: H3/H3g — Ice Age Survivors

Mitochondrial DNA is passed exclusively from mother to child, tracing the maternal line back in an unbroken chain. The mitochondrial genome was sequenced at an average depth of 3,662× — over 100× more coverage than the nuclear genome — giving very high confidence in haplogroup assignment.

My maternal haplogroup is H3/H3g, assigned from the following markers (all confirmed at allele frequency ≥ 95%):

H1 is excluded — the diagnostic 3010 G→A variant is absent. The HVR1 constellation (16111T · 16187T · 16223T · 16290T · 16362C) is documented in H3g and closely related western Iberian H3 branches, confirming the sub-haplogroup assignment.

Maternal lineage analysis. H backbone confirmed at 3,662× depth. H1 excluded by absent 3010 G>A diagnostic. H3 frequency map shows highest concentration in Portugal, Basque Country, Berber North Africa, and the Canary Islands.

H3/H3g is a pre-Bell Beaker European maternal lineage, unbroken for over 10,000 years — a thread of Mesolithic female continuity that survived the Bronze Age steppe expansions that replaced nearly all prior Y-lineages across Western Europe. The maternal line is the oldest layer in this genome.

The Jewish Ancestry: What the Genome Can and Cannot Detect

My family holds a Portuguese certificate of Sephardic Jewish origin (Comunidade Israelita de Lisboa, 2021), documenting descent from Jews expelled from Iberia in 1492–1497 who converted to Christianity and eventually settled in New Granada (modern Colombia).

The genomic picture is nuanced. In PCA space, the genome positions closer to Sephardic Jewish reference samples than to the average Iberian — consistent with Converso ancestry. At the same time, no statistically distinguishable Middle Eastern signal exists above the background of Iberian ancestry. These are not contradictory findings.

The PCA distance analysis confirms: the genome is ~3–4× closer to Iberians (IBS: 0.038) than to HGDP Middle Eastern populations (Druze: 0.147, Palestinian: 0.143, Bedouin: 0.151, Mozabite: 0.138). The Sephardic proximity visible in the PCA reflects shared Iberian ancestry, not a distinct Middle Eastern component.

PCA including Sephardic Jewish reference samples (Behar et al. 2010 dataset). The genome (★ JUAN) clusters in a region intermediate between Iberians and Sephardic Jews — reflecting the deep Iberian ancestry shared between Converso families and Old Christian Iberians after 500 years of admixture.

Euclidean PCA distances from the genome to reference populations. Iberians (IBS) are the closest group. Middle Eastern populations are 3–4× farther. The interpretation panel (right) explains why this does not contradict the certificate.

Educational Attainment Genetics — and the EA/Cognition Gap

Three independent GWAS datasets were used. All three place the educational attainment (EA) score substantially above average. The most rigorous uses Okbay et al. 2022 (Nature Genetics, N~3 million participants):

The most consistent finding across all three studies is the gap between the EA score and the cognitive proxy — roughly 1.0–1.4 standard deviations. Within the Okbay 2022 framework, EA genetic variance decomposes into ~65% cognitive and ~35% non-cognitive components (conscientiousness, persistence, SES-correlated traits). An EA score that substantially exceeds the cognitive proxy implies elevated genetic loading on the non-cognitive component.

The AR CAG repeat (androgen receptor, chrX) adds a functional data point. A hemizygous deletion at this locus estimates ~14 CAG repeats — approximately the 3rd percentile, meaning higher androgen receptor sensitivity than ~97% of the population. Shorter AR CAG repeats confer greater transcriptional activity of the androgen receptor — pleiotropic effects across multiple phenotypes through a single quantitative change in a transcription factor's activation domain.

Four Stories This Genome Tells

Levantine paternal line, Mesolithic maternal line.  The paternal Y (J-Y6304) traces to the Fertile Crescent / Levant — a lineage that arrived in Iberia through Semitic presence (Sephardic Jewish, Phoenician, or Arab) rather than the Bell Beaker steppe expansion. The maternal mtDNA (H3/H3g) traces to the post-glacial Franco-Cantabrian refugium, over 10,000 years ago. These two lineages tell entirely different stories: one a Levantine thread preserved through a Sephardic converso family (Correa), the other an Ice Age survivor from Atlantic Europe.

Sephardic paternal ancestry — independently confirmed.  The Correa patriline carries J-Y6304, a J1b subclade elevated in Sephardic Jewish and Levantine populations. This is genomically independent of the Lisbon community certificate: the Y chromosome itself points to Middle Eastern origin on the paternal side, while the autosomal genome's proximity to Sephardic Jewish reference samples in PCA space adds a third layer of confirmation. The Béthencourt / Bettencourt name enters through the maternal grandmother and is not encoded in the Y chromosome — the two family histories are carried in separate parts of the genome.

A Mestizo genome, predominantly Iberian.  The autosomal genome is ~55–65% European, ~20–30% Native American, ~10–20% African — consistent with an elite Caleño family pattern. The Native American component (~25%) represents the Nasa, Quimbaya, and Zenú peoples of the Cauca Valley. The African component (~12%) carries the history of enslaved people brought to the Cauca Valley's sugar economy from the 16th century onward. The pedigree traces 18 generations back to Toledo, Spain, before 1492 — the Hurtado family held civic positions in the Jewish community there up to the Alhambra Decree.

Non-cognitive genetic architecture.  The persistent EA > cognitive PGS divergence (∆ ≈ +1.0–1.4 SD across three studies) implies elevated genetic loading on the non-cognitive component of educational outcomes — conscientiousness, grit, persistence, socioeconomic pathway facilitation — relative to the g-factor component. The finding is coherent for someone who achieves formal credentials in philosophy and finance while operating outside conventional academic tracks and institutional structures.

Download the Genome — CC0

The full variant call file is released under CC0. No rights reserved, no restrictions. Use it for polygenic scoring, ancestry research, population genetics, or anything else.