Heterogeneity in effective size across the genome: effects on the inverse instantaneous coalescence rate (IICR) and implications for demographic inference under linked selection

Boitard, Simon; Arredondo, Armando; Chikhi, Lounès; Mazet, Olivier

doi:10.1093/genetics/iyac008

Cited by 17 publications

(27 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We assessed the performance of MSMC2 in the presence of background selection in a S. cerevisiae -like genome by simulating data with the reference gene set and deleterious mutations (see Methods). We found that compared to simulations under a purely neutral scenario (Figure 4A), background selection led to an apparent recent increase in population size despite the real population size being constant (Figure 4B), recapping the results of previous studies (Boitard et al, 2022; Johri et al, 2021). When the real demography is declining, the resulting inferred demography shows a combination of decline followed by a recent expansion.…”

Section: Resultssupporting

confidence: 85%

Section: Resultsmentioning

confidence: 99%

“…Linked selection, and in particular background selection (BgS), was shown to impact demographic inference (Boitard, Arredondo, Chikhi, & Mazet, 2022; Johri et al, 2021). Because the genome of S. cerevisiae is small and has a high density of coding regions, BgS can potentially be strong.…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

The rate of adaptive molecular evolution in wild and domesticatedSaccharomyces cerevisiaepopulations

Raas

Dutheil

2022

Preprint

View full text Add to dashboard Cite

Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilization during the Neolithic period, and the yeast remains of importance in industry and biotechnology giving rise to bona fide domesticated lineages. Here, we conduct a population genomic study of both domesticated and wild lineages of S. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence with S. paradoxus. We fitted models of distribution of fitness effects to population genomic data sets to infer the rate of adaptive non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection to S. cerevisiae protein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. We find that populations with a larger effective population size experience a lower rate of non-adaptive substitutions, as well as a higher rate of adaptive ones, suggesting that, in yeast, adaptive mutations accumulate at a faster rate in large populations. Our analyses revealed the signature of background selection but no Hill-Robertson interference, as recombination was found to mildly impact the efficacy of purifying selection and does not affect the rate of adaptive evolution in yeast. Conversely, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the population's demography. Together, our results provide a detailed characterization of adaptive mutations across S. cerevisiae genomes and populations.

show abstract

Section: Resultssupporting

confidence: 85%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

The rate of adaptive molecular evolution in wild and domesticatedSaccharomyces cerevisiaepopulations

Raas

Dutheil

2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Seychelles' landmass is estimated to have been up to 180 times its present size, and gene flow may have been facilitated by islands in the western Indian Ocean that could have acted as stepping-stones between landmasses during the Pliocene and Pleistocene (Warren et al 2010;Cheke and Hume) This geological signature has been seen in other Seychelles taxa (Groombridge et al 2002;Rocha et al 2013;Labisko et al 2022). However, the large ancestral Ne can also be an artefact of population structure, selection and admixture, all of which are known to introduce biases to coalescent demographic reconstruction (Mazet et al 2016;Johri et al 2021;Boitard et al 2022). For example, if island populations were reproductively separated at some point, PSMC estimates would be inflated as alleles would not coalesce.…”

Section: Demography and Runs Of Homozygositymentioning

confidence: 99%

Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction

Femerling

Oosterhout

Feng

et al. 2022

Preprint

View full text Add to dashboard Cite

High genetic diversity is often a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the IUCN Red List in 2020. By comparing historical, pre-bottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after the demographic recovery. We show that the proportion of severely deleterious mutations has reduced in modern individuals, but mildly deleterious mutations have remained unchanged. Computer simulations suggest that the Seychelles paradise flycatcher avoided extinction and recovered due to its long-term small Ne. This reduced the masked load and made the species more resilient to inbreeding. However, we also show that the chronically small Ne and the severe bottleneck resulted in very low genetic diversity in the modern population. Our simulations show this is likely to reduce the species' adaptive potential when faced with environmental change, thereby compromising its long-term population viability. In light of rapid global rates of population decline, our work highlights the importance of considering genomic erosion and computer modelling in conservation assessments.

show abstract

“…In fact, genetic diversity results from the balance between all the evolutionary processes at play in the species' evolutionary history (see the review of Ellegren & Galtier 2016). Other important factors can strongly impact genetic diversity, including demography and structure, but also linked selection (Boitard et al 2022;Buffalo 2021;Ellegren & Galtier 2016).…”

Section: Recommendationmentioning

confidence: 99%

Reticulated evolution marks the rapid diversification of the Delphinoidae

Fontaine

2022

PCI Evol Biol

View full text Add to dashboard Cite

that introgression has been prevalent in cetacean evolutionary history with instances reported among baleen whales (mysticetes) (Árnason et al. 2018) and among toothed whales (odontocetes), especially in the rapidly diversifying dolphins family of the Delphininae (Guo et al. 2021; Moura et al. 2020).Analysing publicly available whole-genome data from nine cetacean species across three families of Delphinoidae -dolphins, porpoises, and monondontidae -using phylogenomics and demo-genetics approaches, Westbury and colleagues (2022) take a step further in documenting that evolution among these species has been far from a simple bifurcating tree. Instead, their study describes widespread occurrences of introgression among Delphinoidae, drawing a complex picture of reticulated evolutionary history. After describing major topology discordance in phylogenetic gene trees along the genome, the authors use a panel of approaches to disentangle introgression from incomplete lineage sorting (ILS), the two most common causes of tree topology discordances (Hibbins & Hahn 2022). Applying popular tests that separate introgression from ILS, such as the Patterson's D (a.k.a. ABBA-BABA) test (Durand et al. 2011;Green et al. 2010), QuIBL (Edelman et al. 2019), and D-FOIL (Pease & Hahn 2015, the authors report that signals of introgression are present in the genomes of most (if not all) the cetacean species included in their study. However, this picture needs to be nuanced. Most introgression signals seem to echo old introgression events that occurred primarily among ancestors. This is suggested by the differential signals of topology discordance along the genome when considering sliding windows along the genome of varying sizes (50kb, 100kb, and 1Mb), and by patterns of excess derived allele sharing along branches of the species tree, as captured by the f-branch test (Malinsky et al. 2021;Malinsky et al. 2018). The authors further investigated the dynamic of cessation of gene flow (and/or ILS) between species using the F1 hybrid PSMC (or hPSMC) approach (Cahill et al. 2016). By estimating the cross-coalescent rates (CRR) between species pairs with time in light of previously estimated species divergence times (McGowen et al. 2020), the authors report that gene flow (and/or ILS) most likely has stopped by now among most species, but it may have lasted for more than half of the time since the species split from each other. According to the author, this result may reflect the slow process by which reproductive isolation would have evolved between cetacean lineages, and that species isolation was marked by significant introgression events.

show abstract

Heterogeneity in effective size across the genome: effects on the inverse instantaneous coalescence rate (IICR) and implications for demographic inference under linked selection

Cited by 17 publications

References 46 publications

The rate of adaptive molecular evolution in wild and domesticatedSaccharomyces cerevisiaepopulations

The rate of adaptive molecular evolution in wild and domesticatedSaccharomyces cerevisiaepopulations

Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction

Reticulated evolution marks the rapid diversification of the Delphinoidae

Contact Info

Product

Resources

About