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Selection and gene flow define polygenic barriers between incipient butterfly species

https://doi.org/10.1101/2020.04.09.034470

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What this work says

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

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From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

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Interpreting differentiation landscapes in the light of long-term linked selection

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Genotype Imputation with Millions of Reference Samples

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Hybridization Reveals the Evolving Genomic Architecture of Speciation

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The barrier to genetic exchange between hybridising populations

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European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

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Principal components analysis corrects for stratification in genome-wide association studies

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Making sense of genomic islands of differentiation in light of speciation

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Effective population size and patterns of molecular evolution and variation

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Complex modular architecture around a simple toolkit of wing pattern genes

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The genic view of the process of speciation

inferredcites →https://doi.org/10.1073/pnas.0911572107openalex-snapshot

Dissecting comimetic radiations in Heliconius reveals divergent histories of convergent butterflies

inferredcites →https://doi.org/10.1073/pnas.1616755114openalex-snapshot

Population-genomic inference of the strength and timing of selection against gene flow

inferredcites →https://doi.org/10.1073/pnas.1801832115openalex-snapshot

Selection and gene flow shape genomic islands that control floral guides

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What initiates speciation in passion-vine butterflies?

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Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq322openalex-snapshot

MSMS : a coalescent simulation program including recombination, demographic structure and selection at a single locus

inferredcites →https://doi.org/10.1093/gbe/evv203openalex-snapshot

Reticulate Speciation and Barriers to Introgression in theAnopheles gambiaeSpecies Complex

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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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The "hitchhiking effect" revisited.

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Estimation of levels of gene flow from DNA sequence data.

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Testing for Ancient Admixture between Closely Related Populations

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

inferredcites →https://doi.org/10.1093/molbev/msu269openalex-snapshot

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

inferredcites →https://doi.org/10.1093/molbev/msu302openalex-snapshot

Estimation of the Spontaneous Mutation Rate in Heliconius melpomene

inferredcites →https://doi.org/10.1093/molbev/msv011openalex-snapshot

Functional Organization of the Genome May Shape the Species Boundary in the House Mouse

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025953openalex-snapshot

Measures of divergence between populations and the effect of forces that reduce variability

inferredcites →https://doi.org/10.1093/sysbio/syv023openalex-snapshot

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

inferredcites →https://doi.org/10.1098/rspb.2013.2733openalex-snapshot

Sexual selection against natural hybrids may contribute to reinforcement in a house mouse hybrid zone

inferredcites →https://doi.org/10.1098/rstb.2011.0249openalex-snapshot

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

inferredcites →https://doi.org/10.1101/015800openalex-snapshot

Speciation in Heliconius Butterflies: Minimal Contact Followed by Millions of Generations of Hybridisation

inferredcites →https://doi.org/10.1101/gr.159426.113openalex-snapshot

Genome-wide evidence for speciation with gene flow in Heliconius butterflies

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What can hybrid zones tell us about speciation? The case of Heliconius erato and H. himera (Lepidoptera: Nymphalidae)

inferredcites →https://doi.org/10.1111/j.1420-9101.2010.02001.xopenalex-snapshot

Multiple sources of reproductive isolation in a bimodal butterfly hybrid zone

inferredcites →https://doi.org/10.1111/jeb.13047openalex-snapshot

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

inferredcites →https://doi.org/10.1111/jeb.13482openalex-snapshot

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

inferredcites →https://doi.org/10.1111/mec.12796openalex-snapshot

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

inferredcites →https://doi.org/10.1111/mec.12958openalex-snapshot

Testing models of speciation from genome sequences: divergence and asymmetric admixture in I sland S outh‐ E ast A sian S us species during the P lio‐ P leistocene climatic fluctuations

inferredcites →https://doi.org/10.1111/mec.14373openalex-snapshot

Genomics of adaptive divergence with chromosome‐scale heterogeneity in crossover rate

inferredcites →https://doi.org/10.1111/mec.14560openalex-snapshot

Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography

inferredcites →https://doi.org/10.1126/science.1208227openalex-snapshot

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

inferredcites →https://doi.org/10.1126/science.aaw2090openalex-snapshot

Genomic architecture and introgression shape a butterfly radiation

inferredcites →https://doi.org/10.1177/0049124104268644openalex-snapshot

Multimodel Inference

inferredcites →https://doi.org/10.1186/1471-2156-13-27openalex-snapshot

EggLib: processing, analysis and simulation tools for population genetics and genomics

inferredcites →https://doi.org/10.1186/s12862-015-0486-yopenalex-snapshot

Divergence with gene flow across a speciation continuum of Heliconius butterflies

inferredcites →https://doi.org/10.1371/journal.pbio.2000234openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pbio.2006288openalex-snapshot

Recombination rate variation shapes barriers to introgression across butterfly genomes

inferredcites →https://doi.org/10.1371/journal.pbio.3000391openalex-snapshot

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

inferredcites →https://doi.org/10.1371/journal.pbio.3000597openalex-snapshot

Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation

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.1000796openalex-snapshot

Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in Heliconius erato

inferredcites →https://doi.org/10.1371/journal.pgen.1000886openalex-snapshot

Human Population Differentiation Is Strongly Correlated with Local Recombination Rate

inferredcites →https://doi.org/10.1371/journal.pgen.1003090openalex-snapshot

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

inferredcites →https://doi.org/10.1371/journal.pgen.1004410openalex-snapshot

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

inferredcites →https://doi.org/10.1371/journal.pgen.1005397openalex-snapshot

Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1534/genetics.113.149211openalex-snapshot

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

inferredcites →https://doi.org/10.1534/genetics.115.183285openalex-snapshot

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

inferredcites →https://doi.org/10.1534/genetics.115.183814openalex-snapshot

Efficient Strategies for Calculating Blockwise Likelihoods Under the Coalescent

inferredcites →https://doi.org/10.1534/genetics.116.187567openalex-snapshot

Likelihood-Free Inference in High-Dimensional Models

inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot

Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

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.gde.2021.01.010openalex-snapshot

Heliconius butterflies: a window into the evolution and development of diversity

inferred← citeshttps://doi.org/10.1038/s41467-022-32316-xopenalex-snapshot

Repeated genetic adaptation to altitude in two tropical butterflies

inferred← citeshttps://doi.org/10.1093/sysbio/syaa052openalex-snapshot

Defining Species When There is Gene Flow

inferred← citeshttps://doi.org/10.1098/rsos.230354openalex-snapshot

Unexpected colour pattern variation in mimetic frogs: implication for the diversification of warning signals in the genus Ranitomeya

inferred← citeshttps://doi.org/10.1101/2021.11.30.470630openalex-snapshot

Repeated genetic adaptation to high altitude in two tropical butterflies

inferred← citeshttps://doi.org/10.1111/mec.17488openalex-snapshot

Beyond gene flow: (non)‐parallelism of secondary contact in a pair of highly differentiated sibling species

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