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Don’t throw out the sympatric species with the crater lake water: fine-scale investigation of introgression provides weak support for functional role of secondary gene flow in one of the clearest examples of sympatric speciation

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What this work says

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

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Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

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Incipient sympatric speciation in Midas cichlid fish from the youngest and one of the smallest crater lakes in Nicaragua due to differential use of the benthic and limnetic habitats?

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The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

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The genomics of speciation-with-gene-flow

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Platelet-activating factor.

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Sympatric speciation suggested by monophyly of crater lake cichlids

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Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

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Recombination rate variation in closely related species

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Sympatric speciation in Nicaraguan crater lake cichlid fish

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Speciation through sensory drive in cichlid fish

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Reconstructing Indian population history

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The genomic basis of adaptive evolution in threespine sticklebacks

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Ecological opportunity and sexual selection together predict adaptive radiation

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Genomic divergence in a ring species complex

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Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

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The genomic substrate for adaptive radiation in African cichlid fish

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Evolution of Darwin’s finches and their beaks revealed by genome sequencing

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Ancient hybridization fuels rapid cichlid fish adaptive radiations

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On the unfounded enthusiasm for soft selective sweeps

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Inference of population splits and mixtures from genome-wide allele frequency data

inferredcites →https://doi.org/10.1038/nrg1269openalex-snapshot

Genes and speciation

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Adaptive evolution and explosive speciation: the cichlid fish model

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Genomic signatures of selection at linked sites: unifying the disparity among species

inferredcites →https://doi.org/10.1046/j.1420-9101.2001.00335.xopenalex-snapshot

The genic view of the process of speciation

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Speciation with gene flow on Lord Howe Island

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Previously uncharacterized roles of platelet-activating factor acetylhydrolase 1b complex in mouse spermatogenesis

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Borrowed alleles and convergence in serpentine adaptation

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The effect of selection on a long wavelength-sensitive ( LWS ) opsin gene of Lake Victoria cichlid fishes

inferredcites →https://doi.org/10.1074/jbc.m211836200openalex-snapshot

Targeted Disruption of Intracellular Type I Platelet Activating Factor-acetylhydrolase Catalytic Subunits Causes Severe Impairment in Spermatogenesis

inferredcites →https://doi.org/10.1086/667586openalex-snapshot

Weak Disruptive Selection and Incomplete Phenotypic Divergence in Two Classic Examples of Sympatric Speciation: Cameroon Crater Lake Cichlids

inferredcites →https://doi.org/10.1093/bioinformatics/btv544openalex-snapshot

A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data

inferredcites →https://doi.org/10.1093/bioinformatics/btw411openalex-snapshot

AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology

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/msv223openalex-snapshot

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

inferredcites →https://doi.org/10.1093/molbev/msw286openalex-snapshot

Novel candidate genes underlying extreme trophic specialization in Caribbean pupfishes

inferredcites →https://doi.org/10.1098/rspb.2015.1666openalex-snapshot

Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers

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/10.1098/rstb.2011.0263openalex-snapshot

Genomic divergence during speciation: causes and consequences

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

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

inferredcites →https://doi.org/10.1101/gr.5045006openalex-snapshot

Genomic islands of differentiation between house mouse subspecies

inferredcites →https://doi.org/10.1111/2041-210x.12808openalex-snapshot

Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation

inferredcites →https://doi.org/10.1111/evo.12587openalex-snapshot

A comparative analysis of island floras challenges taxonomy‐based biogeographical models of speciation

inferredcites →https://doi.org/10.1111/evo.12674openalex-snapshot

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

inferredcites →https://doi.org/10.1111/j.0014-3820.2006.tb01857.xopenalex-snapshot

THE CONDITIONS FOR SPECIATION THROUGH INTRASPECIFIC COMPETITION

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05580.xopenalex-snapshot

Widespread yet heterogeneous genomic divergence

inferredcites →https://doi.org/10.1111/j.1439-0426.2012.01985.xopenalex-snapshot

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton

inferredcites →https://doi.org/10.1111/j.1469-7998.1972.tb01722.xopenalex-snapshot

Ecological studies on crater lakes in West Cameroon Fishes of Barombi Mbo

inferredcites →https://doi.org/10.1111/j.1469-7998.1973.tb01379.xopenalex-snapshot

Ecological studies on crater lakes in West Cameroon The blood of endemic cichlids in Barombi Mbo in relation to stratification and their feeding habits

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/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.14290openalex-snapshot

Speciation as a sieve for ancestral polymorphism

inferredcites →https://doi.org/10.1126/science.1209202openalex-snapshot

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

inferredcites →https://doi.org/10.1126/science.1252136openalex-snapshot

Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation

inferredcites →https://doi.org/10.1126/science.1253226openalex-snapshot

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

inferredcites →https://doi.org/10.1126/science.aac9927openalex-snapshot

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

inferredcites →https://doi.org/10.1146/annurev.biochem.69.1.419openalex-snapshot

Platelet-Activating Factor and Related Lipid Mediators

inferredcites →https://doi.org/10.1146/annurev.ecolsys.38.091206.095804openalex-snapshot

Sympatric Speciation: Models and Empirical Evidence

inferredcites →https://doi.org/10.1186/1471-2164-14-347openalex-snapshot

Unsupervised genome-wide recognition of local relationship patterns

inferredcites →https://doi.org/10.1186/1742-9994-1-5openalex-snapshot

Reticulate sympatric speciation in Cameroonian crater lake cichlids

inferredcites →https://doi.org/10.1186/2041-1480-4-34openalex-snapshot

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

inferredcites →https://doi.org/10.1371/journal.pbio.0030285openalex-snapshot

Genomic Islands of Speciation in Anopheles gambiae

inferredcites →https://doi.org/10.1371/journal.pbio.0040433openalex-snapshot

Divergent Selection on Opsins Drives Incipient Speciation in Lake Victoria Cichlids

inferredcites →https://doi.org/10.1371/journal.pgen.1002967openalex-snapshot

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

inferredcites →https://doi.org/10.1371/journal.pgen.1006919openalex-snapshot

Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes

inferredcites →https://doi.org/10.1371/journal.pone.0054583openalex-snapshot

Positive Outcomes Influence the Rate and Time to Publication, but Not the Impact Factor of Publications of Clinical Trial Results

inferredcites →https://doi.org/10.1371/journal.pone.0074901openalex-snapshot

Crater Lake Apoyo Revisited - Population Genetics of an Emerging Species Flock

inferredcites →https://doi.org/10.1534/genetics.104.036947openalex-snapshot

Soft Sweeps

inferredcites →https://doi.org/10.1534/genetics.112.145037openalex-snapshot

Ancient Admixture in Human History

inferredcites →https://doi.org/10.1534/genetics.115.174912openalex-snapshot

Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps

inferredcites →https://doi.org/10.1556/select.2.2001.1-2.4openalex-snapshot

Long-term Buildup of Reproductive Isolation Promoted by Disruptive Selection: How Far Does it Go?

What points at this work

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

inferred← citeshttps://doi.org/10.1093/iob/obz018openalex-snapshot

How to Investigate the Origins of Novelty: Insights Gained from Genetic, Behavioral, and Fitness Perspectives

inferred← citeshttps://doi.org/10.1098/rspb.2017.2436openalex-snapshot

Long-distance dispersal over land by fishes: extremely rare ecological events become probable over millennial timescales

inferred← citeshttps://doi.org/10.1101/367623openalex-snapshot

Searching for sympatric speciation in the genomic era

inferred← citeshttps://doi.org/10.1111/mec.14784openalex-snapshot

Speciation in sympatry with ongoing secondary gene flow and a potential olfactory trigger in a radiation of Cameroon cichlids

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