FST between archaic and present-day samples

Vecchyo, Diego Ortega‐Del; Slatkin, Montgomery

doi:10.1038/s41437-018-0169-8

Cited by 8 publications

(6 citation statements)

References 27 publications

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“…A further assumption of this work, in common with other studies, is of temporal continuity of populations. As shown by Silva et al (2017) and Ortega-Del Vecchyo & Slatkin (2019), this may be a strong assumption, and inferences may be confounded by a history of gene flow or population replacement. These effects can be addressed in future, using more general spatial models.…”

Section: Discussionmentioning

confidence: 99%

Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis

Dai

Lyu

et al. 2022

Preprint

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Innovations in ancient DNA (aDNA) preparation and sequencing technologies have exponentially increased the quality and quantity of aDNA data extracted from ancient biological materials. The additional temporal component from the incoming aDNA data can provide improved power to address fundamental evolutionary questions like characterising selection processes that shape the phenotypes and genotypes of contemporary populations or species. However, utilising aDNA to study past selection processes still involves considerable hurdles such as how to eliminate the confounding effect of genetic interactions in the inference of selection. To circumvent this challenge, in this work we extend the method introduced by He et al. (2022) to infer temporally variable selection from the data on aDNA sequences with the flexibility of modelling linkage and epistasis. Our posterior computation is carried out through a robust adaptive version of the particle marginal Metropolis-Hastings algorithm with a coerced acceptance rate. Moreover, our extension inherits their desirable features like modelling sample uncertainties resulting from the damage and fragmentation of aDNA molecules and reconstructing underlying gamete frequency trajectories of the population. We assess the performance and show the utility of our procedure with an application to ancient horse samples genotyped at the loci encoding base coat colours and pinto coat patterns.

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Section: Discussionmentioning

confidence: 99%

Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis

Dai

Lyu

et al. 2022

Preprint

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“…Several approaches have been developed to model changes in population size or/and connectivity in structured models, although often ignoring the effect of space (e.g., Nielsen and Wakeley 2001; Hey and Nielsen 2004;Gutenkunst et al 2009;Costa and Wilkinson-Herbots 2016;Arredondo et al, 2021). On the other hand, multiple studies have investigated nonequilibrium genetic patterns in homogenous geographically-structured populations (Nagylaki 1974(Nagylaki , 1977Slatkin, 1991;Slatkin, 1993;Duforet-Frebourg and Slatkin, 2016;Ortega-Del Vecchyo and Slatkin, 2019), but to our knowledge not much has been done on non-equilibrium spatial models in varying environments (e.g., habitat contraction).…”

Section: Non-equilibrium Pattern Of Genetic Diversity During Habitat ...mentioning

confidence: 99%

On the genetic consequences of habitat contraction: edge effects and habitat loss

Sgarlata

Maié

Zoeten

et al. 2022

Preprint

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Natural climate change and recent anthropogenic activities have largely contributed to habitat loss and fragmentation across the world, leading to 70% of worldwide remaining forests to be within 1 km of forest edges (Haddad et al., 2015). Ecological studies have shown that edge-effect influences ecological communities, species richness and abundance across many taxa, contributing to worldwide decline in biodiversity. Since edge-effect reduces species abundance and connectivity, it is also expected to negatively influence species genetic variation. In fact, previous theoretical studies had showed that populations closer to the edges of a finite stepping-stone model tends to have shorter coalescence times, and therefore, lower genetic diversity, than central populations. However, predicting the impact of edge effect on local genetic diversity remains challenging in realistic and more complex habitat fragments, where the additive effect of multiple edges is expected to take place. In the present study we explore the genetic consequence of habitat loss at the scale of a habitat fragment (patch-scale), looking at the interplay between patch-size and edge-effect on spatial genetic diversity. We propose a statistical approach to estimate edge-impacted effective population size from habitat cover information and use this measure to predict spatial genetic diversity in both equilibrium and non-equilibrium populations. We address these questions using spatially-explicit simulations and propose a spatially-explicit analytical framework able to model spatio-temporal changes in genetic diversity due to edge-effect and habitat loss.

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“…Thus, contemporary challenges lie within the data analysis, particularly developing new methods that explicitly incorporate spatio‐temporal variation. [ 55 ]…”

Section: Phylogeography and Zooarchaeology Offer Different Insights Omentioning

confidence: 99%

Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies

2020

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Phylogeography and zooarchaeology are largely separate disciplines, yet each interrogates relationships between humans and commensal species. Knowledge gained about human history from studies of four commensal rats (Rattus rattus, R. tanezumi, R. exulans, and R. norvegicus) is outlined, and open questions about their spread alongside humans are identified. Limitations of phylogeographic and zooarchaeological studies are highlighted, then how integration would increase understanding of species' demographic histories and resultant inferences about human societies is discussed. How rat expansions have informed the understanding of human migration, urban settlements, trade networks, and intra-and interspecific competition is reviewed. Since each rat species is associated with different human societies, they identify unique ecological and historical/cultural conditions that influenced their expansion. Finally, priority research areas including nuclear genome based phylogeographies are identified using archaeological evidence to understand R. norvegicus expansion across China, multi-wave colonization of R. rattus across Europe, and competition between R. rattus and R. norvegicus.

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FST between archaic and present-day samples

Cited by 8 publications

References 27 publications

Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis

Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis

On the genetic consequences of habitat contraction: edge effects and habitat loss

Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies

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