Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

Abstract

Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization. To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure.ABBA-BABA | D statistic | Neanderthal introgression | stepping stone model |

Genome-wide data substantiate Holocene gene flow from India to Australia

“…It has been shown that ancient population structure could produce patterns similar to those generated by admixture (48). However, even if this substructure existed in the ancestral population of the AUA and NGH, to suspect that the gene flow we detect here might be an artifact attributable to this substructure would require the age of this ancestry to be much older, predating the colonization of the Sahul (49).…”

Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia

“…In the recent human lineage, modern humans, Neanderthals, and Denisovans can be considered the daughter lineages of a common parental ancestor. Therefore, expression of shared genetic polymorphisms with Neanderthals and Denisovans in certain extant populations would be the consequence of biogeographical contingency and drift instead of, or in addition to, admixture with other hominins (18,(39)(40)(41). In a similar vein, expression of a plesiomorphic skeletal phenotype in extant and extinct populations has been interpreted as evidence for admixture with, or "assimilation" of, other hominin populations (42).…”

“…The paleontological and archaeological records thus far remain elusive. An important consideration, therefore, is the persistence of population substructure in Africa (18,(38)(39)(40)(41), which has been inferred from the human paleontological record (33,34) and is concordant with climate fluctuations in the continent (28,30).…”

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

“…These results were interpreted as evidence of Neanderthals interbreeding with the ancestors of all non-Africans and subsequently a Denisovan-like population mainly with the ancestors of South East Asians [37]; however, marginal Denisovan admixture has also been reported in continental Asian populations [31,38], further entangling this later admixture scenario. This notwithstanding, the proportions of admixture are probably overestimates if some degree of structure was present among ancient humans in Africa, as already pointed out in [28,[39][40][41]. If this were the case, incomplete lineage sorting and not introgression could explain some genetic similarities between modern non-African humans and Neanderthals, although certainly not all of them.…”