Soares, A. E. R. | Search bioRxiv

bioRxiv2025

Revisiting the African mtDNA Landscape: A Continental Update from Complete Mitochondrial Genomes

AbstractAfrica harbors the richest diversity of mitochondrial DNA lineages, reflecting its central role in human evolutionary history. Early studies of mtDNA variation provided the first genetic evidence for the African origin of modern humans. With complete mitochondrial genome sequencing, we can now reconstruct maternal lineages with high resolution, yet large parts of the continent remain underrepresented. Using a newly developed long-range sequencing assay, we generated 1,288 complete mitochondrial genomes from 14 countries across sub-Saharan Africa, focusing on previously understudied regions. We combined these with over 3,600 publicly available African mitogenomes to produce a comprehensive dataset and updated overview of maternal genetic diversity across the continent. We contextualized this diversity with autosomal structure and information on major human expansions, integrating archaeological and linguistic evidence. Our analyses reveal a demographic expansion of Niger-Congo speakers around 17 thousand years ago (kya), followed by a second expansion associated with Bantuspeaking groups around 6 kya. We identify haplogroup L3e as a key marker of this early Bantu expansion, tracking its spread across sub-Saharan Africa. Distinct demographic signatures also emerge for different geographic sub-branches of Bantu speakers. These findings highlight the power of mitochondrial DNA to trace maternal ancestry and demographic history in Africa, while also acknowledging its limitations for phylogeographic reconstruction.

evolutionary biology↗

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↗

bioRxiv2017

Natural selection shaped the rise and fall of passenger pigeon genomic diversity

The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. While theory predicts that large populations will be more genetically diverse and respond more efficiently to selection, passenger pigeon genetic diversity was surprisingly low. To investigate this we analysed 41 mitochondrial and 4 nuclear genomes from passenger pigeons, and 2 genomes from band-tailed pigeons, passenger pigeons closest living relatives. We find that passenger pigeons large population size allowed for faster adaptive evolution and removal of harmful mutations, but that this drove a huge loss in neutral genetic diversity. These results demonstrate how great an impact selection can have on a vertebrate genome, and invalidate previous results that suggested population instability contributed to this species surprisingly rapid extinction.

genomics↗