Archaeogenetics of Southwest Europe

This thesis consists on three chapters that investigate the genetic past of Iberia using
modern and ancient DNA.

The first part offers a snapshot of the current mitochondrial diversity in the
Iberian peninsula based on a newly generated dataset with over one thousand fully
sequenced mitochondrial genomes. The genetic depth and resolution of this dataset
allowed to date the arrival of the vast majority of mitochondrial lineages to Iberia at
the time of the Neolithic. It also made possible to describe patterns in some lineages,
like U6, that were shaped by Medieval and later population movements which were
not considered significant until now.

The second part explores the evolution and transformations of the population in
the east of Iberia from the late Neolithic to the Middle Ages through the genomes of
twenty ancient individuals sequenced to varying depths. The prehistoric individuals
indicate little genomic contribution from local Iberian hunter-gatherers by the end of
the Neolithic and beginning of the Copper Age. I also found evidence for two important
admixture events whose genetic legacy has been lost. The first event is evidence
of genomic influx of ancestry from North African and eastern Mediterranean sources
into the local late Roman population. The second admixture event I detected is heavy
and widespread admixture with North African migrants that settled in the region
during the Islamic period.

The last part focuses on how ancient genomes can be interrogated in a comprehensive
way using modern machine learning techniques to better understand what
ancient individuals looked like. For this purpose I developed an alternative method
using pseudo-phenotypic data to recreate, in an comprehensive way, a polygenic
trait: skin pigmentation. My results confirmed that indigenous European huntergatherers
had darker skin tones than later European populations while also explaining
the different polygenic base of similar phenotypes.