Using Genetics to Uncover Human History

by McDonnell Boehnen Hulbert & Berghoff LLP
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Human history is often something modern man only sees as through a glass, darkly.  This is particularly the case when that history did not occur in the Mediterranean, the Nile Valley, India, or China, or when there is no written record on which scholars can rely.  Exacerbating the disrupting effects of time on history can be when that history occurs in a region where extensive migration has disrupted whatever temporarily stable civilization happened to have taken root at that place at any particular time.

But humans leave traces of themselves in their history and a variety of such traces have been the source of reconstructions outside conventional sources.  Luigi Cavalli-Sforza began the study of human population genetics as a way to understand this history in 1971 in The Genetics of Human Populations, and later extended these studies to include language and how it influences gene flow between human populations.  More recent efforts to use genetics to reconstruct history include Deep Ancestry: The Landmark DNA Quest to Decipher Our Distant Past by Spencer Wells (National Geographic: 2006), and The Seven Daughters of Eve: The Science that Reveals our Genetic Ancestry by Brian Sykes (Carrol & Graf: 2002).  And even more recently, genetic studies have illuminated the "fine structure" of human populations in England (see "Fine-structure Genetic Mapping of Human Population in Britain").

Two recent reports illustrate how genetics can inform history:  the first, in the American Journal of Human Genetics entitled "Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences"; and a second in the Proceedings of the National Academy of Sciences USA, entitled "Genomic landscape of human diversity across Madagascar."  In the first study, authors* from The Wellcome Trust Sanger Institute, University of Cambridge, University of Zurich, University of Otago, Bournemouth University, Lebanese American University, and Harvard University found evidence of genetic admixture over 5,000 years of a Canaanite population that has persisted in Lebanese populations into the modern era.  This population is interesting for historians in view of the central location of the ancestral home of the Canaanites, the Levant, in the Fertile Crescent that ran from Egypt through Mesopotamia.  The Canaanites also inhabited the Levant during the Bronze Age and provide a critical link between the Neolithic transition from hunter gatherer societies to agriculture.  This group (known to the ancient Greeks as the Phoenicians) is also a link to the great early societies recognized through their historical writings and civilizations (including the Egyptians, Assyrians, Babylonians, Persians, Greeks, and Romans); if the Canaanites had any such texts or other writings they have not survived.  In addition, the type of genetic analyses that have been done for European populations has not been done for descendants of inhabitants of the Levant from this historical period.  This paper uses genetic comparisons between 99 modern day residents of Lebanon (specifically, from Sidon and the Lebanese interior) and ancient DNA (aDNA) from ~3,700 year old genomes from petrous bone of individuals interred in gravesites in Sidon.  For aDNA, these analyses yielded 0.4-2.3-fold genomic DNA coverage and 53-264-fold mitochondrial DNA coverage, and also compared Y chromosome sequences with present-day Lebanese, two Canaanite males and samples from the 1000 Genomes Project.  Over one million single nucleotide polymorphisms (SNPs) were used for comparison.

These results indicated that the Canaanite ancestry was an admixture of local Neolithic populations and migrants from Chalcolithic (Copper Age) Iran.  The authors estimate from these linkage disequilibrium studies that this admixture occurred between 6,600 and 3,550 years ago, a date that is consistent with recorded mass migrations in the region during that time.  Perhaps surprisingly, their results also show that the majority of the present-day Lebanese population has inherited most of their genomic DNA from these Canaanite ancestors.  These researchers also found traces of Eurasian ancestry consistent with conquests by outside populations during the period from 3,750-2,170 years ago, as well as the expansion of Phoenician maritime trade network that extended during historical time to the Iberian Peninsula.

Figure 1


The second paper arose from genetic studies of an Asian/African admixture population on Mozambique.  This group** from the University of Toulouse, INSERM, the University of Bordeaux, University of Indonesia, the Max Plank Institute for Evolutionary Anthropology, Institut genomique, Centre Nacional de Genotypage, University of Melbourne, and the Universite de  la Rochelle, showed geographic stratification between ancestral African (mostly Bantu) and Asian (Austronesean) ancestors.  Cultural, historical, linguistic, ethnographic, archeological, and genetic studies supports the conclusion that Madagascar residents have traits from both populations but the effects of settlement history are termed "contentious" by these authors.  Various competing putative "founder" populations (including Arabic, Indian, Papuan, and/or Jewish populations as well as first settlers found only in legend, under names like "Vazimba," "Kimosy," and "Gola") have been posited as initial settlers.  These researchers report an attempt to illuminate the ancestry of the Malagasy by a study of human genetics.

These results showed common Bantu and Austronesian descent for the population with what the authors termed "limited" paternal contributions from Europe and Middle Eastern populations.  The admixture of African and Austronesian populations occurred "recently" (i.e., over the past millennium) but was gender-biased and heterogeneous, which reflected for these researchers independent colonization by the two groups.  The results also indicated that detectable genetic structure can be imposed on human populations over a relatively brief time (~ a few centuries).

Using a "grid-based approach" the researchers performed a high-resolution genetic diversity study that included maternal and paternal lineages as well as genome-wide data from 257 villages and over 2,700 Malagasy individuals.  Maternal inheritance patterns were interrogated using mitochondrial DNA and patterns of paternity assayed using Y chromosomal sequences.  Non-gender specific relationships were assessed through 2.5 million SNPs.  Mitochondrial DNA analyses showed maternal inheritance from either African or East Asian origins (with one unique Madagascar variant termed M23) in roughly equal amounts, with no evidence of maternal gene flow from Europe or the Middle East.  The M23 variant shows evidence of recent (within 900-1500 years) origin.  Y chromosomal sequences, in contrast are much more prevalent from African origins (70.7% Africa:20.7% East Asia); the authors hypothesize that the remainder may reflect Muslim influences, with evidence of but little European ancestry.

Admixture assessments support Southeast Asian (Indonesian) and East African source populations for the Malagasy admixture.  These results provide the frequency of the African component to be ~59%, the Asian component frequency to be ~37%, and the Western European component to have a frequency of about 4% (albeit with considerable variation, e.g., African ancestry can range from  ~26% to almost 93%).  Similar results were obtained when the frequency of chromosomal fragments shared with other populations were compared to the Malagasy population (finding the closest link to Asian populations from south Borneo, and excluding Indian, Somali, and Ethiopian populations, although the analysis was sensitive in one individual to detect French Basque ancestry).  The split with ancestral Asian populations either occurred ~2,500 years ago or by slower divergence between ~2,000-3,000 years ago, while divergence with Bantu populations occurred more recently (~1,500 years ago).

There were also significant differences in geographic distribution between descendants of these ancestral populations.  Maternal African lineages were found predominantly in north Madagascar, with material Asian lineages found in central and southern Madagascar (from mtDNA analyses).  Paternal lineages were generally much lower overall for Asian descendants (~30% in central Madagascar) based on Y chromosome analyses.  Genome-wide analyses showed "highlanders" had predominantly Asian ancestry (~65%) while coastal inhabitants had predominantly (~65%) African ancestry; these results depended greatly on the method of performing the analyses which affected the granularity of the geographic correlates.  Finally, assessing admixture patterns indicated that the genetic results are consistent with single intermixing event (500-900 years ago) for all but one geographic area, which may have seen a first event 28 generations ago and a second one only 4 generations ago.  These researchers also found evidence of at least one population bottleneck, where the number of individuals dropped to a few hundred people about 1,000-800 years ago.

These results are represented pictorially in the paper:

Figure 2


In view of the current political climate, the eloquent opening of the paper deserves attention:

Ancient long-distance voyaging between continents stimulates the imagination, raises questions about the circumstances surrounding such voyages, and reminds us that globalization is not a recent phenomenon.  Moreover, populations which thereby come into contact can exchange genes, goods, ideas and technologies.


* Marc Haber, Claude Doumet-Serhal, Christiana Scheib, Yali Xue, Petr Danecek, Massimo Mezzavilla, Sonia Youhanna, Rui Martiniano, Javier Prado-Martinez, Michał Szpak, Elizabeth Matisoo-Smith, Holger Schutkowski, Richard Mikulski, Pierre Zalloua, Toomas Kivisild, Chris Tyler-Smith

** Denis Pierrona, Margit  Heiskea, Harilanto  Razafindrazakaa, Ignace Rakotob, Nelly Rabetokotanyb, Bodo Ravololomangab, Lucien M.-A. Rakotozafyb,  Mireille  Mialy  Rakotomalalab,  Michel Razafiarivonyb,  Bako Rasoarifetrab,  Miakabola  Andriamampianina Raharijesyb, Lolona Razafindralambob, Ramilisoninab, Fulgence Fanonyb, Sendra Lejamblec, Olivier Thomasc, Ahmed Mohamed  Abdallahc, Christophe Rocherc,, Amal Arachichec, Laure Tonasoa, Veronica Pereda-lotha, Stéphanie Schiavinatoa, Nicolas Brucatoa, Francois-Xavier Ricauta, Pradiptajati Kusumaa,d,e, Herawati  Sudoyod,e, Shengyu Nif, Anne Bolandg, Jean-Francois Deleuzeg, Philippe Beaujardh, Philippe Grangei, Sander Adelaarj, Mark Stonekingf, Jean-Aimé Rakotoarisoab,  Chantal Radimilahy, and Thierry Letelliera

DISCLAIMER: Because of the generality of this update, the information provided herein may not be applicable in all situations and should not be acted upon without specific legal advice based on particular situations.

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