Recent advances in methods to characterize archaic introgression in modern humans

The exchange and subsequent incorporation of genetic material between distinct lineages, known as introgression, has emerged as a crucial concept in understanding human evolutionary history. With the advent of high-throughput sequencing technologies and the publication of the draft Neanderthal genome in 2010, Green and colleagues were able to demonstrate the presence of Neanderthal DNA in present-day Eurasians, a signature of past interbreeding events with archaic humans. This integration of genetic material from extinct human relatives, such as Neanderthals and Denisovans, into the genomes of modern humans due to historical gene flow events is known as archaic introgression. As new methods and data sets uncover a more complex intermingling between our ancestors and archaic humans than previously thought, the relevance of archaic introgression has only increased, opening exciting new avenues for studying human evolution. Here, we review recent methodological advances in the study of archaic introgression. We begin by providing an overview of the genealogical and genomic signatures left behind by introgression events before reviewing recent methods for studying archaic introgression by outlining their conceptual approaches, data requirements, and types of inferences they support. Finally, we provide recommendations for which methods are most appropriate given a research question and data set, discuss outstanding challenges, and suggest future lines of research to advance the study of archaic introgression.