Avila-Arcos, M. C. | Search bioRxiv

bioRxiv2017

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

BackgroundAs most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach - in-solution capture-enrichment - retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3,000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC+Y) versus non-enriched (pre-capture) libraries.\n\nResultsWe recovered 17-4,152 times more targeted unique Y-chromosome sequences after capture, where 0.01-6.2% (WGC+Y) and 0.01-23.5% (YCC) of the sequence reads were on-target, compared to 0.0002-0.004% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC+Y) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, WGC+Y yielded greater enrichment than YCC alone. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins.\n\nConclusionsWe present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC+Y enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture for low-complexity libraries, as clonality increases considerably with each round.

genomics↗

bioRxiv2017

Neolithization of North Africa involved the migration of people from both the Levant and Europe

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present the first analysis of individuals genome sequences from early and late Neolithic sites in Morocco, as well as Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans are distinct from any other reported ancient individuals and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. Among ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers ([~]9,000 BCE) and Pre-Pottery Neolithic farmers ([~]6,500 BCE). Although an expansion in Early Neolithic times is also plausible, the high divergence observed in Early Neolithic Moroccans suggests a long-term isolation and an early arrival in North Africa for this population. This scenario is consistent with early Neolithic traditions in North Africa deriving from Epipaleolithic communities who adopted certain innovations from neighbouring populations. Late Neolithic ([~]3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow. Finally, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia [~]5,500 BCE. The cultural and genetic similarities of the Iberian Neolithic cultures with that of North African Neolithic sites further reinforce the model of an Iberian migration into the Maghreb.\n\nSIGNIFICANCE STATEMENTThe acquisition of agricultural techniques during the so-called Neolithic revolution has been one of the major steps forward in human history. Using next-generation sequencing and ancient DNA techniques, we directly test if Neolithization in North Africa occurred through the transmission of ideas or by demic diffusion. We show that Early Neolithic Moroccans are composed of an endemic Maghrebi element still retained in present-day North African populations and distantly related to Epipaleolithic communities from the Levant. However, late Neolithic individuals from North Africa are admixed, with a North African and a European component. Our results support the idea that the Neolithization of North Africa might have involved both the development of Epipaleolithic communities and the migration of people from Europe.

genetics↗