ArticleMolecular ecology2015
The aggregate site frequency spectrum for comparative population genomic inference.
Article in Molecular ecology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- The Effects of Post-Divergence Gene Flow on Simultaneous Divergence Time Testing.Molecular ecology resources · 2026Article
- Pleistocene Glaciation Drove Shared Population Coexpansion in Eastern North American Snakes.Molecular ecology · 2025Article
- Pleistocene island connectivity did not enhance dispersal or impact population size change in Galápagos geckos.Proceedings. Biological sciences · 2025Article
- Genomic evidence of an ancient inland temperate rainforest in the Pacific Northwest of North America.Molecular ecology · 2022Article
- The Evolution of Comparative Phylogeography: Putting the Geography (and More) into Comparative Population Genomics.Genome biology and evolution · 2022Review
- Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits.Genome biology · 2021Article
- Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history.Nature communications · 2018Article
- Whole-genome data reveal the complex history of a diverse ecological community.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling.Genome biology and evolution · 2018Article
- Article
- multi-dice: r package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes.Molecular ecology resources · 2017Article
- Strategies for improving approximate Bayesian computation tests for synchronous diversification.BMC evolutionary biology · 2017Article
- Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies.Current zoology · 2016Article
- Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Reticulation, divergence, and the phylogeography-phylogenetics continuum.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Union of phylogeography and landscape genetics.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Inferring responses to climate dynamics from historical demography in neotropical forest lizards.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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Authors and funding
2 authors.
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Abstract
Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, an endeavour that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to perform complex demographic inference at unprecedented resolution across assemblages of nonmodel species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) data sets collected from multiple, co-distributed species for assemblage-level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multispecies demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subsequently couple the aSFS with a hierarchical approximate Bayesian computation (hABC) framework to estimate degree of temporal synchronicity in expansion times across taxa, including an empirical demonstration with a data set consisting of five populations of the threespine stickleback (Gasterosteus aculeatus). Corroborating what is generally understood about the recent postglacial origins of these populations, the joint aSFS/hABC analysis strongly suggests that the stickleback data are most consistent with synchronous expansion after the Last Glacial Maximum (posterior probability = 0.99). The aSFS will have general application for multilevel statistical frameworks to test models involving assemblages and/or communities, and as large-scale SNP data from nonmodel species become routine, the aSFS expands the potential for powerful next-generation comparative population genomic inference.
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