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Biases in demographic modelling affect our understanding of recent divergence

https://doi.org/10.1101/2020.06.03.128298

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The contribution of ancient admixture to reproductive isolation between European sea bass lineages

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Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations

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Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

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Can one learn history from the allelic spectrum?

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A Darwinian Laboratory of Multiple Contact Zones

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The hitch-hiking effect of a favourable gene

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Fast gapped-read alignment with Bowtie 2

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The origin and remolding of genomic islands of differentiation in the European sea bass

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The genic view of the process of speciation

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Extraordinarily rapid speciation in a marine fish

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Selection and gene flow shape genomic islands that control floral guides

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Genetic Variation and Phenotypic Evolution During Allopatric Speciation

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The variant call format and VCFtools

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Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life

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Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis)

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Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata

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Approximate Bayesian Computation in Population Genetics

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THE AVERAGE NUMBER OF GENERATIONS UNTIL FIXATION OF A MUTANT GENE IN A FINITE POPULATION

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GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data

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From ecology to genetics and back: the tale of two flounder species in the Baltic Sea

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Distortion of allele frequency distributions provides a test for recent population bottlenecks

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Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species

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Computationally Efficient Composite Likelihood Statistics for Demographic Inference

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An ABC Method for Whole-Genome Sequence Data: Inferring Paleolithic and Neolithic Human Expansions

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Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence

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Appropriate Likelihood Ratio Tests and Marginal Distributions for Evolutionary Tree Models with Constraints on Parameters

inferredcites →https://doi.org/10.1098/rstb.2011.0263openalex-snapshot

Genomic divergence during speciation: causes and consequences

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We shall meet again - Genomics of historical admixture in the sea

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The demographic history of Atlantic salmon ( Salmo salar ) across its distribution range reconstructed from approximate Bayesian computations*

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Post-glacial re-colonization of European biota

inferredcites →https://doi.org/10.1111/j.1365-294x.2006.03120.xopenalex-snapshot

Absence of population structure of turbot (Psetta maxima) in the Baltic Sea

inferredcites →https://doi.org/10.1111/j.1365-294x.2008.03715.xopenalex-snapshot

Speciation with gene flow could be common

inferredcites →https://doi.org/10.1111/j.1558-5646.2009.00662.xopenalex-snapshot

LEARNING ABOUT MODES OF SPECIATION BY COMPUTATIONAL APPROACHES

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Model‐based demographic inference of introgression history in European whitefish species pairs'

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Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

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The consequences of not accounting for background selection in demographic inference

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Region‐wide and ecotype‐specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences

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Evolutionary forces shaping genomic islands of population differentiation in humans

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ANGSD: Analysis of Next Generation Sequencing Data

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Descartes’ rule of signs and the identifiability of population demographic models from genomic variation data

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Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

inferredcites →https://doi.org/10.1371/journal.pgen.1000695openalex-snapshot

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

inferredcites →https://doi.org/10.1371/journal.pgen.1003905openalex-snapshot

Robust Demographic Inference from Genomic and SNP Data

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Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

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Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

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Evolution at two time frames: Polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution

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Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

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The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV

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Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis

inferredcites →https://doi.org/10.1534/genetics.114.164350openalex-snapshot

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

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Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

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Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

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Geometry of the Sample Frequency Spectrum and the Perils of Demographic Inference

inferredcites →https://doi.org/10.1534/genetics.118.301336openalex-snapshot

Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data

inferredcites →https://doi.org/10.3389/fmars.2018.00225openalex-snapshot

Platichthys solemdali sp. nov. (Actinopterygii, Pleuronectiformes): A New Flounder Species From the Baltic Sea

inferredcites →https://doi.org/10.7554/elife.36317openalex-snapshot

Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.tree.2020.07.015openalex-snapshot

A Darwinian Laboratory of Multiple Contact Zones

inferred← citeshttps://doi.org/10.1038/s41437-020-00389-3openalex-snapshot

Evolution at two time frames: ancient structural variants involved in post-glacial divergence of the European plaice (Pleuronectes platessa)

inferred← citeshttps://doi.org/10.1038/s41467-021-23096-xopenalex-snapshot

Reply to “Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin”

inferred← citeshttps://doi.org/10.1101/2020.06.12.147322openalex-snapshot

Reproductive barriers as a byproduct of gene network evolution

inferred← citeshttps://doi.org/10.1111/1755-0998.13323openalex-snapshot

DILS: Demographic inferences with linked selection by using ABC

inferred← citeshttps://doi.org/10.1111/eva.13644openalex-snapshot

Exploring coral speciation: Multiple sympatric Stylophora pistillata taxa along a divergence continuum on the Great Barrier Reef

inferred← citeshttps://doi.org/10.1111/jeb.13756openalex-snapshot

Speciation in marine environments: Diving under the surface

inferred← citeshttps://doi.org/10.1111/mec.15695openalex-snapshot

Historical isolation facilitates species radiation by sexual selection: Insights fromChorthippusgrasshoppers

inferred← citeshttps://doi.org/10.17760/d20406231openalex-snapshot

Network thinking applied to modeling biological evolution

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