Delser, P. M. | bioRxiv Science

bioRxiv2024

Low-ABC: a robust demographic Inference from low-coverage whole-genome data through ABC

The reconstruction of past demographic histories relies on the pattern of genetic variation shown by the sampled populations; this means that an accurate estimation of genotypes is crucial for a reliable inference of past processes. A commonly adopted approach to reconstruct complex demographic dynamics is the Approximate Bayesian Computation (ABC) framework. It exploits coalescent simulations to generate the expected level of variation under different evolutionary scenarios. Demographic inference is then performed by comparing the simulated data with the genotypes called in the sampled individuals. Low sequencing coverage drastically affects the ability to reliably call genotypes, thus making low-coverage data unsuitable for such powerful inferential approaches. Here, we present Low-ABC, a new ABC approach to infer past population processes using low-coverage whole-genome data. Under this framework, both observed and simulated genetic variation are not directly compared using called genotypes, but rather obtained using genotype likelihoods to consider the uncertainty caused by the low sequencing coverage. We first evaluated the inferential power of this procedure in distinguishing among different demographic models and in inferring model parameters under different experimental conditions, including a wide spectrum of sequencing coverage (1x to 30x), number of individuals, number, and size of genetic loci. We showed that the use of genotype likelihoods integrated into an ABC framework provides a reliable inference of past population dynamics, thus making possible the application of model-based inference also for low-coverage data. We then applied Low-ABC to shed light on the relationship between Mesolithic and Early Neolithic European populations.

genomics↗

bioRxiv2021

Post-glacial expansion dynamics, not refugial isolation, shaped the genetic structure of a migratory bird, the Yellow Warbler (Setophaga petechia)

During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra, and permafrost, leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated populations that persisted in disjunct regions known as refugia. According to this hypothesis, as ice sheets retreated, species recolonised the continent from these glacial refugia, and the mixing of these lineages is responsible for modern patterns of genetic diversity. An alternative hypothesis is that complex genetic patterns could also arise simply from heterogenous post-glacial expansion dynamics, without separate refugia. Both mitochondrial and genomic data from the North American yellow warbler (Setophaga petechia) shows the presence of an eastern and western clade, a pattern often ascribed to the presence of two refugia. However, species distribution modelling (SDM) of the past range of this species fails to identify obvious refugia during the Last Glacial Maximum. Using a climate-informed spatial genetic modelling (CISGeM) framework, which allows us to integrate knowledge of past geographic ranges based on SDM, we reconstructed past population sizes, range expansions, and likely recolonisation dynamics of this species, generating spatially and temporally explicit demographic reconstructions. The model captures the empirical genetic structure despite including only a single, large glacial refugium. The observed contemporary population structure was generated during the expansion dynamics after the glaciation and is due to unbalanced rates of northward advance to the east and west linked to the melting of the icesheets. Thus, modern population structure in this species is consistent with expansion dynamics, and refugial isolation is not required to explain it, highlighting the importance of explicitly testing drivers of geographic structure. Significance statementPatterns of population differentiation in many species have often been attributed to the mixing of isolates from distinct refugia that formed during periods of glaciation, when range fragmentation was likely. By formally bringing together multiple lines of evidence, we demonstrate that the patterns of genetic diversity seen across the range of the yellow warbler (Setophaga petechia) were not the result of multiple isolated refugia. Instead, asymmetric expansion from a single cohesive range generated the observed patterns; the expansions asymmetry was due to the uneven melting of the icesheets over time. Thus, we demonstrate the importance of reconstructing species range dynamics when trying to explain patterns of genetic differentiation.

evolutionary biology↗