Genomic landscape of human diversity across Madagascar

Abstract

Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.

Grass Functional Traits Differentiate Forest and Savanna in the Madagascar Central Highlands

“…As such, woodlands of the central highlands have been historically and persistently classified as degraded forests (Koechlin et al, 1974;White, 1983;Faramalala, 1995) and managed as such through suppression of fire (Kull, 2002). Recent studies however support early origins of these extensive grasslands with their numerous endemic grass, forb, and animal species that evolved locally millions of years before human colonization (Bond et al, 2008;Vorontsova et al, 2016;Hackel et al, 2018), which occurred only a few 1,000 years before present (Pierron et al, 2017). Grassland, woodland and forest co-occur in the central highlands of Madagascar with changes in vegetation types occurring over small scales, often just meters where there are no discernible differences in climate and soils.…”

A new late Pleistocene subfossil site (Tsaramody, Sambaina basin, central Madagascar) with implications for the chronology of habitat and megafaunal community change on Madagascar's Central Highlands

“…The island's subfossil (Late Pleistocene and Holocene) record has contributed greatly to our understanding of Madagascar's recent ecological evolution, and aided interpretations of recent environmental change; this record includes large‐bodied lemurs, elephant birds, pygmy hippos, crocodyliforms, turtles, bats, carnivorans, rodents and the aardvark‐like Plesiorycteropus (Burney et al ., ; Godfrey et al ., , ; Gommery et al ., ; Goodman & Muldoon, ; Goodman et al ., ; Samonds, ). The arrival of humans, the timing of which is still under debate (Anderson et al ., ; Dewar et al ., ; Godfrey et al ., ; Hansford et al ., ; Pierron et al ., ), nevertheless pre‐dated the decline and extinction of many of them, including the island's large (> 10 kg) native animals; the megafaunal crash did not occur until sometime during the past two millennia (Burney et al ., ; Crowley, ; Godfrey et al ., ). Megafaunal extinction is widely believed to have been induced by humans, either directly (via hunting) or indirectly (via landscape transformation), aided by Late Pleistocene and Holocene climatic change (e.g.…”

Human Migration and the Spread of the Nematode ParasiteWuchereria bancrofti

“…In our study, we did not have samples from Madagascar so can only correlate the divergence time between African populations with that of other migration events. The timing of divergence between African populations of Wb (1.4 -2.5 kya) does coincide with admixture among the Malagasy and Bantu speaking people of Africa (1.8 kya) [Pierron et al, 2014, Pierron et al, 2017 and it is possible that this admixture event spread Wb to continental Africa and subsequently throughout all of Africa.…”