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Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi

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What this work says

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

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Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

inferredcites →https://doi.org/10.1002/ajb2.1827openalex-snapshot

Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

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Body shape differences in a pair of closely related Malawi cichlids and their hybrids: Effects of genetic variation, phenotypic plasticity, and transgressive segregation

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Lake Malawi cichlid evolution along a benthic/limnetic axis

inferredcites →https://doi.org/10.1002/jez.b.22006openalex-snapshot

A Small Number of Genes Underlie Male Pigmentation Traits in L ake M alawi Cichlid Fishes

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Comparison of testes structure, spermatogenesis, and spermatocytogenesis in young, aging, and hybrid cichlid fish (Cichlidae, Teleostei)

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Evolution of NADH Dehydrogenase Subunit 2 in East African Cichlid Fish

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Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era

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Morphological disparity in ecologically diverse versus constrained lineages of Lake Malaŵi rock-dwelling cichlids

inferredcites →https://doi.org/10.1007/s11160-009-9128-zopenalex-snapshot

Species concepts, speciation, and taxonomic change in the Lake Malawi mbuna, with special reference to the genus Labeotropheus Ahl 1927 (Perciformes: Cichlidae)

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Functional and Genetic Integration in the Skulls of Lake Malawi Cichlids

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Phylogenetic relationships and evolutionary processes in East African cichlid fishes

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A One-Penny Imputed Genome from Next-Generation Reference Panels

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Fast two-stage phasing of large-scale sequence data

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Gene tree discordance, phylogenetic inference and the multispecies coalescent

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Rapid radiation, ancient incomplete lineage sorting and ancient hybridization in the endemic Lake Tanganyika cichlid tribe Tropheini

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Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit

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The stages of vertebrate evolutionary radiation

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An index of substitution saturation and its application

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Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences

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The genomic substrate for adaptive radiation in African cichlid fish

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ModelFinder: fast model selection for accurate phylogenetic estimates

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Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

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The genomic timeline of cichlid fish diversification across continents

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Phylotranscriptomic consolidation of the jawed vertebrate timetree

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

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Understanding explosive diversification through cichlid fish genomics

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Contrasting signatures of genomic divergence during sympatric speciation

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Selection, hybridization, and the evolution of morphology in the Lake Malaŵi endemic cichlids of the genus Labeotropheus

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

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Phylogeny of a rapidly evolving clade: The cichlid fishes of Lake Malawi, East Africa

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Delimiting Species without Monophyletic Gene Trees

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Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

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The Sequence Alignment/Map format and SAMtools

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BEDTools: a flexible suite of utilities for comparing genomic features

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The variant call format and VCFtools

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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Quartet Inference from SNP Data Under the Coalescent Model

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Unified representation of genetic variants

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PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

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Twelve years of SAMtools and BCFtools

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

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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

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Different Sources of Allelic Variation Drove Repeated Color Pattern Divergence in Cichlid Fishes

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Generic Scan Using AFLP Markers as a Means to Assess the Role of Directional Selection in the Divergence of Sympatric Whitefish Ecotypes

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Application of Phylogenetic Networks in Evolutionary Studies

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Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

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

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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UFBoot2: Improving the Ultrafast Bootstrap Approximation

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A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

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An Approach to the Analysis of Comparative Data When a Phylogeny Is Unavailable or Incomplete

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Gene Trees in Species Trees

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Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish

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Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

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Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

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Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

inferredcites →https://doi.org/10.1093/sysbio/syaa083openalex-snapshot

The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

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The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes

inferredcites →https://doi.org/10.1093/sysbio/syy032openalex-snapshot

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

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Modeling Hybridization Under the Network Multispecies Coalescent

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Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants

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Geographical ancestry of Lake Malawi's cichlid fish diversity

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African cichlid fish: a model system in adaptive radiation research

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Do constructional constraints influence cichlid craniofacial diversification?

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Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

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Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi cichlids

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Coalescent-based phylogenetic inference from genes with unequivocal historical signal suggests a polytomy at the root of the placental mammal tree of life

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Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files

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Irrational exuberance for resolved species trees

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Evolution of a soft‐tissue foraging adaptation in African cichlids: Roles for novelty, convergence, and constraint

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THE SHAPES OF NEUTRAL GENE GENEALOGIES IN TWO SPECIES: PROBABILITIES OF MONOPHYLY, PARAPHYLY, AND POLYPHYLY IN A COALESCENT MODEL

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GENETIC ARCHITECTURE SETS LIMITS ON TRANSGRESSIVE SEGREGATION IN HYBRID CICHLID FISHES

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The zoogeography, ecology and taxonomy of the genus Labeotropheus Ahl, 1927, of Lake Malawi (Pisces: Cichlidae)

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Hybridization and contemporary evolution in an introduced cichlid fish from Lake Malawi National Park

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The genetic mosaic suggests a new role for hitchhiking in ecological speciation

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Divergent selection and heterogeneous genomic divergence

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Geography disentangles introgression from ancestral polymorphism in Lake Malawi cichlids

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Comparative rates of lower jaw diversification in cichlid adaptive radiations

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PHENOTYPIC PLASTICITY AND HETEROCHRONY IN CICHLASOMA MANAGUENSE (PISCES, CICHLIDAE) AND THEIR IMPLICATIONS FOR SPECIATION IN CICHLID FISHES

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IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

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THE GENETIC BASIS OF A COMPLEX FUNCTIONAL SYSTEM

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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichlid fishes

inferredcites →https://doi.org/10.1111/mec.13880openalex-snapshot

How plasticity, genetic assimilation and cryptic genetic variation may contribute to adaptive radiations

inferredcites →https://doi.org/10.1111/zsc.12213openalex-snapshot

The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves

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

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

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

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Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes

inferredcites →https://doi.org/10.1146/annurev-ecolsys-110316-022645openalex-snapshot

The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics

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The Evolutionary Genomics of Cichlid Fishes: Explosive Speciation and Adaptation in the Postgenomic Era

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African Cichlid Fishes: Model Systems for Evolutionary Biology

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A Revision of the Pseudotropheus elongatus species group (Teleostei: Cichlidae) With Description of a New Genus and Seven New Species

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Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

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A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

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Assortative mating among Lake Malawi cichlid fish populations is not simply predictable from male nuptial colour

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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

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East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation

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Second-generation PLINK: rising to the challenge of larger and richer datasets

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Bushes in the Tree of Life

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BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

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Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids

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Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

inferredcites →https://doi.org/10.1371/journal.pone.0114798openalex-snapshot

Quantitative Genetic Analyses of Male Color Pattern and Female Mate Choice in a Pair of Cichlid Fishes of Lake Malawi, East Africa

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A New Species of Labeotropheus (Perciformes: Cichlidae) from Southern Lake Malaŵi, Africa

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Evidence of Hybridization between Cynotilapia afra and Pseudotropheus zebra (Teleostei: Cichlidae) Following an Intralacustrine Translocation in Lake Malaŵi

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Novel Jaw Morphology in Hybrids between Pseudotropheus zebra and Labeotropheus fuelleborni (Teleostei: Cichlidae) from Lake Malawi, Africa

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Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

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Haplotype-based variant detection from short-read sequencing

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

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inferred← citeshttps://doi.org/10.1101/2025.09.09.675123openalex-snapshot

Whole genome sequencing reveals the phylogenetic relationship and reticulate evolution of Phrynocephalus lizards in Eurasia

inferred← citeshttps://doi.org/10.1111/1755-0998.70161openalex-snapshot

Combining Annotation Software to Identify Orthologous Genes ( CASIO ) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies

inferred← citeshttps://doi.org/10.1111/aen.70006openalex-snapshot

Species delimitation and molecular dating of southern African Tetramesa (Hymenoptera: Eurytomidae): An understudied microhymenopteran group

inferred← citeshttps://doi.org/10.1111/cla.12570openalex-snapshot

Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

inferred← citeshttps://doi.org/10.1111/mec.17080openalex-snapshot

Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

inferred← citeshttps://doi.org/10.1126/sciadv.adt0973openalex-snapshot

Radiation with reproductive isolation in the near-absence of phylogenetic signal

inferred← citeshttps://doi.org/10.1126/science.adk9688openalex-snapshot

CASTER: Direct species tree inference from whole-genome alignments

inferred← citeshttps://doi.org/10.1186/s12864-025-11563-4openalex-snapshot

Genetic traceability, conservation effectiveness, and selection signatures analysis based on ancestral information: a case study of Beijing-You chicken

inferred← citeshttps://doi.org/10.1186/s12915-023-01579-1openalex-snapshot

The genome of the pygmy right whale illuminates the evolution of rorquals

inferred← citeshttps://doi.org/10.1186/s12915-024-01848-7openalex-snapshot

Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)

inferred← citeshttps://doi.org/10.21248/gups.75018openalex-snapshot

The application of baleen whale genomes in conservation and evolutionary research

inferred← citeshttps://doi.org/10.6084/m9.figshare.25302933openalex-snapshot

Additional file 1 of Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)

inferred← citeshttps://doi.org/10.70675/c1c1cf29zfcf5z4b9fza396zc80a51274661openalex-snapshot

Linking microevolutionary and macroevolutionary processes in the diversification of freshwater mollusks from the East African Rift

inferred← citeshttps://doi.org/10.7554/elife.110607openalex-snapshot

Are interphylum spiralian relationships resolvable?

inferred← citeshttps://doi.org/10.7554/elife.110607.1openalex-snapshot

Are interphylum spiralian relationships resolvable?

inferred← citeshttps://doi.org/10.7554/elife.110607.2openalex-snapshot

Are interphylum spiralian relationships resolvable?

inferred← citeshttps://doi.org/10.7554/elife.110607.3openalex-snapshot

Are interphylum spiralian relationships resolvable?

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