Abstract
Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these lineages would be closely related and occasionally hybridized with lineages that gave rise to extant species. Hence, it is likely that one can find genetic signatures of these ancient introgression events in present-day genomes, so-called ghost introgression. The increasing availability of high-quality genome assemblies for non-model organisms and the development of more sophisticated methods for detecting introgression will undoubtedly reveal more cases of ghost introgression, indicating that the Tree of Life is even more reticulated than assumed. The presence of ghost introgression has important consequences for the study of numerous evolutionary processes, including adaptation, speciation, and macroevolutionary patterns. In addition, detailed studies of introgressed regions could provide insights into the morphology of the extinct lineage, providing an unexpected link between genomics and the fossil record. Hence, new methods that take into account ghost introgression will need to be developed.
Highlights
GhostbustersA first clue for the presence of ghost introgression comes from analyses of organelles, such as mitochondrial DNA (mtDNA) and plastid DNA (Figure 1a)
Evolution is a continuous trial and error process in which most lineages go hominins: the Neanderthals[5] and the Denisovans.[6]
Evolution by natural selection is a continuous trial and error process in which most lineages are lost without leaving fossil remains
Summary
A first clue for the presence of ghost introgression comes from analyses of organelles, such as mitochondrial DNA (mtDNA) and plastid DNA (Figure 1a). Similar to the study on wild boars, Kuhlwilm and co-workers[16] found exceptionally divergent haplotypes in the bonobo (Pan paniscus) genome To test whether these haplotypes were introduced by introgression with chimpanzees (P. troglodytes) or an extinct primate lineage, they computed the S* statistic, which distinguishes between ancestral shared haplotypes and introgressed haplotypes based on their length.[17] This approach confirmed previous work on introgression between bonobos and chimpanzees,[18] and found outlier regions (in terms of the S* statistic) that could not be traced back to any chimpanzee population, suggesting introgression from an extinct lineage. Deeply divergent haplotypes often provide the first clue for the presence of introgression from an extinct lineage.[8,15] The hypothesis of ghost introgression can be further explored with more sophisticated methods (e.g., S* statistic and hidden Markov models) that pinpoint putatively introgressed regions.[17,19] different demographic models can be compared in a statistical framework to confirm or reject the existence of ghost introgression.[21,22,23,24,25]
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