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1. Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation

   https://doi.org/10.1073/pnas.1817678116  

   Scheinfeldt, Laura B. ; Soi, Sameer ; Lambert, Charla ; Ko, Wen-Ya ; Coulibaly, Aoua ; Ranciaro, Alessia ; Thompson, Simon ; Hirbo, Jibril ; Beggs, William ; Ibrahim, Muntaser ; et al ( February 2019 , Proceedings of the National Academy of Sciences)

   Anatomically modern humans arose in Africa ∼300,000 years ago, but the demographic and adaptive histories of African populations are not well-characterized. Here, we have generated a genome-wide dataset from 840 Africans, residing in western, eastern, southern, and northern Africa, belonging to 50 ethnicities, and speaking languages belonging to four language families. In addition to agriculturalists and pastoralists, our study includes 16 populations that practice, or until recently have practiced, a hunting-gathering (HG) lifestyle. We observe that genetic structure in Africa is broadly correlated not only with geography, but to a lesser extent, with linguistic affiliation and subsistence strategy. Four East African HG (EHG) populations that are geographically distant from each other show evidence of common ancestry: the Hadza and Sandawe in Tanzania, who speak languages with clicks classified as Khoisan; the Dahalo in Kenya, whose language has remnant clicks; and the Sabue in Ethiopia, who speak an unclassified language. Additionally, we observed common ancestry between central African rainforest HGs and southern African San, the latter of whom speak languages with clicks classified as Khoisan. With the exception of the EHG, central African rainforest HGs, and San, other HG groups in Africa appear genetically similar to neighboring agriculturalist or pastoralist populations. We additionally demonstrate that infectious disease, immune response, and diet have played important roles in the adaptive landscape of African history. However, while the broad biological processes involved in recent human adaptation in Africa are often consistent across populations, the specific loci affected by selective pressures more often vary across populations.

    

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2. South-to-north migration preceded the advent of intensive farming in the Maya region

   https://doi.org/10.1038/s41467-022-29158-y  

   Kennett, Douglas J. ; Lipson, Mark ; Prufer, Keith M. ; Mora-Marín, David ; George, Richard J. ; Rohland, Nadin ; Robinson, Mark ; Trask, Willa R. ; Edgar, Heather H. ; Hill, Ethan C. ; et al ( December 2022 , Nature Communications)

   Abstract The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region. 

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3. Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History

   https://doi.org/10.1093/molbev/msz271  

   Sprengelmeyer, Quentin D ; Mansourian, Suzan ; Lange, Jeremy D ; Matute, Daniel R ; Cooper, Brandon S ; Jirle, Erling V ; Stensmyr, Marcus C ; Pool, John E ; Larracuente, Amanda ( November 2019 , Molecular Biology and Evolution)

   Abstract A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that could reflect its precommensal niche. Here, we document the collection of 288 D. melanogaster individuals from multiple African wilderness areas in Zambia, Zimbabwe, and Namibia. The presence of D. melanogaster in these remote woodland environments is consistent with an ancestral range in southern-central Africa, as opposed to equatorial regions. After sequencing the genomes of 17 wilderness-collected flies collected from Kafue National Park in Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these genomes with existing data, we probed the history of this species’ geographic expansion. Demographic estimates indicated that expansion from southern-central Africa began ∼10,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,400 years ago. This improved model of demographic history will provide an important resource for future evolutionary and genomic studies of this key model organism. Our findings add context to the history of D. melanogaster, while opening the door for future studies on the biological basis of adaptation to human environments. 

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4. Historical genomes elucidate European settlement and the African diaspora in Delaware

   https://doi.org/10.1016/j.cub.2023.04.069  

   Fleskes, Raquel E. ; Owsley, Douglas W. ; Bruwelheide, Karin S. ; Barca, Kathryn G. ; Griffith, Daniel R. ; Cabana, Graciela S. ; Schurr, Theodore G. ( June 2023 , Current Biology)

   The 17th-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid- Atlantic region of the United States.1 The demographic features of these initial colonial migrations are not uni- formly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.2 European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African- descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.3,4 To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery’s Rest archaeological site (circa 1675–1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individ- uals of European maternal descent, buried 15–20 feet from a northern group of three individuals of African maternal descent.5 Autosomal results further illuminate genomic similarities to Northwestern European refer- ence populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17th and early 18th century North America. 

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5. The genomic prehistory of the Indigenous peoples of Uruguay

   https://doi.org/10.1093/pnasnexus/pgac047  

   Lindo, John ; De La Rosa, Rosseirys ; Santos, Andre L. C. d. ; Sans, Mónica ; DeGiorgio, Michael ; Figueiro, Gonzalo ; Nelson, ed., Karen E. ( April 2022 , PNAS Nexus)

   The prehistory of the people of Uruguay is greatly complicated by the dramatic and severe effects of European contact, as with most of the Americas. After the series of military campaigns that exterminated the last remnants of nomadic peoples, Uruguayan official history masked and diluted the former Indigenous ethnic diversity into the narrative of a singular people that all but died out. Here, we present the first whole genome sequences of the Indigenous people of the region before the arrival of Europeans, from an archaeological site in eastern Uruguay that dates from 2,000 years before present. We find a surprising connection to ancient individuals from Panama and eastern Brazil, but not to modern Amazonians. This result may be indicative of a migration route into South America that may have occurred along the Atlantic coast. We also find a distinct ancestry previously undetected in South America. Though this work begins to piece together some of the demographic nuance of the region, the sequencing of ancient individuals from across Uruguay is needed to better understand the ancient prehistory and genetic diversity that existed before European contact, thereby helping to rebuild the history of the Indigenous population of what is now Uruguay.

    

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