Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories

Abstract

Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.

Archaeology, demography and life history theory together can help us explain past and present population patterns

“…B 376: 20190711 earlier research [42], is that we now have mutually confirming lines of archaeological evidence with sufficient resolution to identify regional population fluctuations across a period of 30 000 years. Moreover, this is in keeping with the genomic record for episodes of Palaeolithic population replacement, though Loog [43] rightly cautions us about the problems involved in using genetic data to inform about changing population sizes. Of course, as we have seen, the ethnographic and simulation studies mentioned above strongly suggest that the real pattern is one of short-term fluctuations around a mean value determined by environmental productivity.…”

A manifesto for palaeodemography in the twenty-first century

“…Conversely, the same population history can give rise to different genetic patterns [56]. As reviewed by Loog in this volume [57], reconstructing past demography using genetic data (both ancient and modern) requires an inferential approach that compares patterns of genetic variation with model expectations from theoretical population genetics. These approaches divide into two broad categories: pattern-based, descriptive approaches, and explicit models.…”

The effect of habitat loss and fragmentation on isolation-by-distance and time

“…Multiple approaches allow today to investigate species response to HL&F, for example i) by reconstructing the natural history of species and their environment (Hewitt, 1996; Barak et al, 2016; Lyman, 2017; Grace et al, 2019), ii) by comparing populations occurring in landscapes with different degree of habitat disturbance (e.g., Lino et al, 2019; Almeida-Rocha et al, 2020) or iii) by performing long-term experiments (e.g., Haddad et al, 2015, 2017). Genetic data are one of the sources of information that are used to reconstruct the natural history of species (i.e., past changes in population size and connectivity) (Nielsen and Beaumont, 2009; Beichman et al, 2018; Mitchell and Rawlence, 2021; Loog, 2021) and, together with data on the history of habitat changes (e.g., paleoenvironmental data), can provide crucial insights on how species have responded to past HL&F (e.g., Teixeira et al, 2021). Consequently, learning about past species response to HL&F, can contribute to build predictions on how species will be affected by present-day HLF.…”

“…Genetic data are one of the sources of information that are used to reconstruct the natural history of species (i.e., past changes in population size and connectivity) (Nielsen and Beaumont, 2009;Beichman et al, 2018;Mitchell and Rawlence, 2021;Loog, 2021) and, together with data on the history of habitat changes (e.g., paleoenvironmental data), can provide crucial insights on how species have responded to past HL&F (e.g., Teixeira et al, 2021). Consequently, learning about past species response to HL&F, can contribute to build predictions on how species will be affected by present-day HLF.…”