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Movement of transposable elements contributes to cichlid diversity

https://doi.org/10.1101/2020.02.26.961987

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What this work says

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

inferredcites →https://doi.org/10.1002/bies.200800219openalex-snapshot

Transposable elements: powerful facilitators of evolution

inferredcites →https://doi.org/10.1002/dvg.22940openalex-snapshot

Proximate and ultimate causes of variable visual sensitivities: Insights from cichlid fish radiations

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Selection of Models of DNA Evolution with jModelTest

inferredcites →https://doi.org/10.1007/978-3-642-86659-3openalex-snapshot

Evolution by Gene Duplication

inferredcites →https://doi.org/10.1007/s00239-018-9847-7openalex-snapshot

Transposable Elements Activity is Positively Related to Rate of Speciation in Mammals

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Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

inferredcites →https://doi.org/10.1016/j.cub.2005.08.010openalex-snapshot

Mix and Match Color Vision: Tuning Spectral Sensitivity by Differential Opsin Gene Expression in Lake Malawi Cichlids

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Repeated colonization and hybridization in Lake Malawi cichlids

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Beyond speciation genes: an overview of genome stability in evolution and speciation

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Silencing of Transposable Elements by piRNAs in Drosophila : An Evolutionary Perspective

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Hybridization and adaptive radiation

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Magic traits in speciation: ‘magic’ but not rare?

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Transcriptional co-regulation of evolutionarily conserved microRNA/cone opsin gene pairs: Implications for photoreceptor subtype specification

inferredcites →https://doi.org/10.1017/cbo9780511844164.008openalex-snapshot

Mating and parental care

inferredcites →https://doi.org/10.1017/s095252381200003xopenalex-snapshot

Evolutionary tinkering with visual photoreception

inferredcites →https://doi.org/10.1038/nature07285openalex-snapshot

Speciation through sensory drive in cichlid fish

inferredcites →https://doi.org/10.1038/nature13726openalex-snapshot

The genomic substrate for adaptive radiation in African cichlid fish

inferredcites →https://doi.org/10.1038/nbt.1754openalex-snapshot

Integrative genomics viewer

inferredcites →https://doi.org/10.1038/ncomms14363openalex-snapshot

Ancient hybridization fuels rapid cichlid fish adaptive radiations

inferredcites →https://doi.org/10.1038/ncomms4629openalex-snapshot

Wnt signalling underlies the evolution of new phenotypes and craniofacial variability in Lake Malawi cichlids

inferredcites →https://doi.org/10.1038/ncomms6149openalex-snapshot

The evolution of cichlid fish egg-spots is linked with a cis-regulatory change

inferredcites →https://doi.org/10.1038/nmeth.2109openalex-snapshot

jModelTest 2: more models, new heuristics and parallel computing

inferredcites →https://doi.org/10.1038/nrg1316openalex-snapshot

Adaptive evolution and explosive speciation: the cichlid fish model

inferredcites →https://doi.org/10.1038/s41559-018-0717-xopenalex-snapshot

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

inferredcites →https://doi.org/10.1038/sj.hdy.6800635openalex-snapshot

Genome evolution and biodiversity in teleost fish

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Speciation via introgressive hybridization in East African cichlids?

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Speciation in rapidly diverging systems: lessons from Lake Malawi

inferredcites →https://doi.org/10.1046/j.1365-294x.2003.01905.xopenalex-snapshot

Hybrid origin of a cichlid population in Lake Malawi: implications for genetic variation and species diversity

inferredcites →https://doi.org/10.1073/pnas.0405302102openalex-snapshot

Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi

inferredcites →https://doi.org/10.1073/pnas.0502127102openalex-snapshot

On the origin of Lake Malawi cichlid species: A population genetic analysis of divergence

inferredcites →https://doi.org/10.1073/pnas.0930235100openalex-snapshot

Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes

inferredcites →https://doi.org/10.1073/pnas.1018456108openalex-snapshot

Craniofacial divergence and ongoing adaptation via the hedgehog pathway

inferredcites →https://doi.org/10.1073/pnas.1417803112openalex-snapshot

Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

inferredcites →https://doi.org/10.1073/pnas.1611028113openalex-snapshot

Environmental change explains cichlid adaptive radiation at Lake Malawi over the past 1.2 million years

inferredcites →https://doi.org/10.1073/pnas.1614272113openalex-snapshot

Environmental context for understanding the iconic adaptive radiation of cichlid fishes in Lake Malawi

inferredcites →https://doi.org/10.1073/pnas.1719798115openalex-snapshot

Genetic and developmental origins of a unique foraging adaptation in a Lake Malawi cichlid genus

inferredcites →https://doi.org/10.1073/pnas.2332665100openalex-snapshot

Divergent selection during speciation of Lake Malawi cichlid fishes inferred from parallel radiations in nuptial coloration

inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

inferredcites →https://doi.org/10.1093/gigascience/giz030openalex-snapshot

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

inferredcites →https://doi.org/10.1093/molbev/msi137openalex-snapshot

Adaptive Molecular Evolution in the Opsin Genes of Rapidly Speciating Cichlid Species

inferredcites →https://doi.org/10.1093/molbev/msj083openalex-snapshot

What Is the Role of Genome Duplication in the Evolution of Complexity and Diversity?

inferredcites →https://doi.org/10.1093/molbev/msl014openalex-snapshot

Evolution of the Cichlid Visual Palette through Ontogenetic Subfunctionalization of the Opsin Gene Arrays

inferredcites →https://doi.org/10.1093/molbev/msq344openalex-snapshot

Reverse Evolution in RH1 for Adaptation of Cichlids to Water Depth in Lake Tanganyika

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

inferredcites →https://doi.org/10.1093/molbev/msu069openalex-snapshot

RNA-seq Reveals Transcriptomic Shock Involving Transposable Elements Reactivation in Hybrids of Young Lake Whitefish Species

inferredcites →https://doi.org/10.1093/molbev/msu172openalex-snapshot

Interspecific Variation in Rx1 Expression Controls Opsin Expression and Causes Visual System Diversity in African Cichlid Fishes

inferredcites →https://doi.org/10.1093/molbev/msz294openalex-snapshot

Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation

inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003940openalex-snapshot

Cone Opsin Genes of African Cichlid Fishes: Tuning Spectral Sensitivity by Differential Gene Expression

inferredcites →https://doi.org/10.1098/rspb.2013.1733openalex-snapshot

Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

inferredcites →https://doi.org/10.1101/gr.4565806openalex-snapshot

An initial map of insertion and deletion (INDEL) variation in the human genome

inferredcites →https://doi.org/10.1111/j.0022-1112.2006.00992.xopenalex-snapshot

Photopigment spectral absorbance of Lake Malaŵi cichlids

inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04532.xopenalex-snapshot

Genomic islands of speciation or genomic islands and speciation?

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05617.xopenalex-snapshot

Molecular ecology and adaptation of visual photopigments in craniates

inferredcites →https://doi.org/10.1111/j.1525-142x.2011.00469.xopenalex-snapshot

New evidence for the role of heterochrony in the repeated evolution of cichlid opsin expression

inferredcites →https://doi.org/10.1111/j.1558-5646.2007.00105.xopenalex-snapshot

THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION

inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00450.xopenalex-snapshot

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

inferredcites →https://doi.org/10.1111/j.1749-4877.2008.00137.xopenalex-snapshot

Cichlid fish visual systems: mechanisms of spectral tuning

inferredcites →https://doi.org/10.1111/mec.13205openalex-snapshot

A genetic demographic analysis of L ake M alawi rock‐dwelling cichlids using spatio‐temporal sampling

inferredcites →https://doi.org/10.1111/mec.14439openalex-snapshot

Abundant recent activity of retrovirus‐like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

inferredcites →https://doi.org/10.1111/mec.14969openalex-snapshot

Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish

inferredcites →https://doi.org/10.1126/science.1174705openalex-snapshot

Sexual Conflict Resolved by Invasion of a Novel Sex Determiner in Lake Malawi Cichlid Fishes

inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot

A Draft Sequence of the Neandertal Genome

inferredcites →https://doi.org/10.1126/science.432658openalex-snapshot

Intraretinal Distribution of Cone Pigments in Certain Teleost Fishes

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/10.1126/science.aao6809openalex-snapshot

Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish radiations

inferredcites →https://doi.org/10.1146/annurev.genet.34.1.401openalex-snapshot

POLYPLOID INCIDENCE AND EVOLUTION

inferredcites →https://doi.org/10.1146/annurev.genom.9.081307.164228openalex-snapshot

Evolution of Dim-Light and Color Vision Pigments

inferredcites →https://doi.org/10.1159/000113552openalex-snapshot

Interspecific Variation of Photoreceptors in Four Co-Existing Haplochromine Cichlid Fishes

inferredcites →https://doi.org/10.1186/1471-2105-7-474openalex-snapshot

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

inferredcites →https://doi.org/10.1186/1471-2148-12-251openalex-snapshot

Evolution of cichlid vision via trans-regulatory divergence

inferredcites →https://doi.org/10.1186/1471-2148-13-42openalex-snapshot

Genome differentiation in a species pair of coregonine fishes: an extremely rapid speciation driven by stress-activated retrotransposons mediating extensive ribosomal DNA multiplications

inferredcites →https://doi.org/10.1186/1741-7007-6-22openalex-snapshot

Visual sensitivities tuned by heterochronic shifts in opsin gene expression

inferredcites →https://doi.org/10.1186/s12862-020-01629-0openalex-snapshot

Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

inferredcites →https://doi.org/10.1186/s12864-017-3723-5openalex-snapshot

A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions

inferredcites →https://doi.org/10.1186/s12864-018-4714-xopenalex-snapshot

Mobilization of retrotransposons as a cause of chromosomal diversification and rapid speciation: the case for the Antarctic teleost genus Trematomus

inferredcites →https://doi.org/10.1186/s12864-018-5328-zopenalex-snapshot

Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids

inferredcites →https://doi.org/10.1186/s13100-015-0041-9openalex-snapshot

Repbase Update, a database of repetitive elements in eukaryotic genomes

inferredcites →https://doi.org/10.1186/s13100-018-0124-5openalex-snapshot

Transposable elements and gene expression during the evolution of amniotes

inferredcites →https://doi.org/10.13016/m27940x8dopenalex-snapshot

Mechanisms contributing to opsin expression divergence in the visual system of African Cichlids

inferredcites →https://doi.org/10.1371/journal.pbio.1000266openalex-snapshot

The Eyes Have It: Regulatory and Structural Changes Both Underlie Cichlid Visual Pigment Diversity

inferredcites →https://doi.org/10.3390/genes9050254openalex-snapshot

The Role of Transposable Elements in Speciation

inferredcites →https://doi.org/10.3390/genes9100480openalex-snapshot

Unusual Diversity of Sex Chromosomes in African Cichlid Fishes

inferredcites →https://doi.org/10.4061/2011/470875openalex-snapshot

Mating and Parental Care in Lake Tanganyika's Cichlids

inferredcites →https://doi.org/10.5860/choice.39-0311openalex-snapshot

The Cichlid fishes: nature's grand experiment in evolution

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41559-021-01452-wopenalex-snapshot

Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish

inferred← citeshttps://doi.org/10.1111/mec.17574openalex-snapshot

Population Genomics of Adaptive Radiation

inferred← citeshttps://doi.org/10.1146/annurev-animal-061220-023129openalex-snapshot

Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes

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