Subtopic Deep Dive
Teleost Fish Phylogenomics
Research Guide
What is Teleost Fish Phylogenomics?
Teleost fish phylogenomics reconstructs evolutionary relationships of teleost fishes using whole-genome sequences and transcriptomic data following the teleost-specific whole-genome duplication.
Teleosts comprise over 30,000 species, half of all vertebrates, with phylogenomic studies resolving radiations like percomorphs. Key works include Near et al. (2012, 962 citations) on ray-finned fish phylogeny and Hughes et al. (2018, 595 citations) using transcriptomic data. Approximately 10 major papers from 2002-2020 guide the field.
Why It Matters
Accurate teleost phylogenies underpin comparative genomics for adaptation studies, as in Malinsky et al. (2018) revealing gene flow in Malawi cichlid radiations. They inform biodiversity conservation and fisheries management, with Betancur-R et al. (2017, 931 citations) providing a classification for 30,000+ species. Glasauer and Neuhauss (2014, 905 citations) link whole-genome duplication to trait evolution in model teleosts.
Key Research Challenges
Resolving percomorph radiations
Percomorph fishes diversified rapidly ~100 million years ago, causing incomplete lineage sorting in phylogenomic trees. Near et al. (2012) used 77 nuclear loci but noted persistent uncertainties. Hughes et al. (2018) applied 1,105 orthologous genes from transcriptomes to improve resolution.
Accounting for gene flow
Introgression between species complicates tree inference, as shown in Malinsky et al. (2018) for Malawi cichlids with whole-genome data. Hybridization obscures divergence times. Betancur-R et al. (2017) highlight gene flow's role in bony fish classification.
Integrating ancient duplications
Teleost-specific whole-genome duplication creates paralogs that confound orthology. Glasauer and Neuhauss (2014) detail retention patterns post-duplication. Hurley et al. (2006) calibrated timelines but struggled with paralog interference.
Essential Papers
Resolution of ray-finned fish phylogeny and timing of diversification
Thomas J. Near, Ron I. Eytan, Alex Dornburg et al. · 2012 · Proceedings of the National Academy of Sciences · 962 citations
Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genom...
Phylogenetic classification of bony fishes
Ricardo Betancur‐R, E. O. Wiley, Gloria Arratia et al. · 2017 · BMC Evolutionary Biology · 931 citations
Whole-genome duplication in teleost fishes and its evolutionary consequences
Stella M.K. Glasauer, Stephan C. F. Neuhauss · 2014 · Molecular Genetics and Genomics · 905 citations
Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
Lily C. Hughes, Guillermo Ortı́, Yu Huang et al. · 2018 · Proceedings of the National Academy of Sciences · 595 citations
Significance Ray-finned fishes form the largest and most diverse group of vertebrates. Establishing their phylogenetic relationships is a critical step to explaining their diversity. We compiled th...
Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow
Milan Malinsky, Hannes Svardal, Alexandra M. Tyers et al. · 2018 · Nature Ecology & Evolution · 575 citations
Abstract The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individ...
A new time-scale for ray-finned fish evolution
Imogen Hurley, Rachel Lockridge Mueller, Katherine A. Dunn et al. · 2006 · Proceedings of the Royal Society B Biological Sciences · 345 citations
The Actinopterygii (ray-finned fishes) is the largest and most diverse vertebrate group, but little is agreed about the timing of its early evolution. Estimates using mitochondrial genomic data sug...
Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the “ancient fish”
Jun Inoue, Masaki Miya, Katsumi Tsukamoto et al. · 2002 · Molecular Phylogenetics and Evolution · 291 citations
Reading Guide
Foundational Papers
Start with Near et al. (2012, 962 citations) for ray-finned fish backbone, then Glasauer and Neuhauss (2014, 905 citations) on whole-genome duplication, followed by Hurley et al. (2006, 345 citations) for timescales.
Recent Advances
Study Hughes et al. (2018, 595 citations) for transcriptomic advances and Malinsky et al. (2018, 575 citations) for cichlid radiations with gene flow; Betancur-R et al. (2017, 931 citations) for classification.
Core Methods
Phylogenomic inference via multi-species coalescent (ASTRAL in Hughes et al., 2018), ortholog detection post-duplication (Glasauer and Neuhauss, 2014), and divergence dating with fossils (Hurley et al., 2006).
How PapersFlow Helps You Research Teleost Fish Phylogenomics
Discover & Search
Research Agent uses searchPapers and citationGraph to map teleost phylogenomics from Near et al. (2012, 962 citations) as seed, chaining to Hughes et al. (2018) and Betancur-R et al. (2017). exaSearch uncovers percomorph-specific transcriptomic datasets; findSimilarPapers expands to 50+ related works on radiations.
Analyze & Verify
Analysis Agent employs readPaperContent on Hughes et al. (2018) to extract ortholog counts, then runPythonAnalysis with pandas to recompute bootstrap supports from supplementary phylogenies. verifyResponse via CoVe cross-checks divergence times against Near et al. (2012); GRADE assigns A-grade evidence to genome duplication claims in Glasauer and Neuhauss (2014).
Synthesize & Write
Synthesis Agent detects gaps in percomorph resolution between Near et al. (2012) and Malinsky et al. (2018), flagging contradictions in cichlid timelines. Writing Agent uses latexEditText for manuscript drafts, latexSyncCitations to integrate 20+ references, and latexCompile for PDF; exportMermaid visualizes evolutionary trees from Hurley et al. (2006).
Use Cases
"Analyze gene tree discordance in Malawi cichlid phylogenomics"
Research Agent → searchPapers('Malinsky 2018 cichlids') → Analysis Agent → readPaperContent + runPythonAnalysis (pandas on gene flow stats) → statistical output of introgression rates with p-values.
"Draft phylogeny section citing teleost WGD papers"
Synthesis Agent → gap detection (Glasauer 2014 vs Hughes 2018) → Writing Agent → latexEditText + latexSyncCitations + latexCompile → LaTeX section with figure and 15 citations.
"Find code for ray-finned fish ortholog inference"
Research Agent → paperExtractUrls (Hughes 2018) → Code Discovery → paperFindGithubRepo → githubRepoInspect → pipeline code for ASTRAL species tree from transcriptomes.
Automated Workflows
Deep Research workflow compiles systematic review of 50+ teleost papers: searchPapers → citationGraph (Near 2012 hub) → DeepScan 7-steps with CoVe checkpoints verifying radiations. Theorizer generates hypotheses on percomorph gene flow from Malinsky et al. (2018) + Betancur-R et al. (2017), outputting testable predictions with mermaid diagrams.
Frequently Asked Questions
What defines teleost fish phylogenomics?
It reconstructs teleost evolutionary trees using genome-scale data post-teleost-specific whole-genome duplication, resolving radiations like percomorphs (Near et al., 2012; Hughes et al., 2018).
What methods dominate teleost phylogenomics?
Transcriptomic orthologs (1,105 genes in Hughes et al., 2018), whole-genome sequences (Malinsky et al., 2018), and nuclear loci (77 in Near et al., 2012); ASTRAL for species trees handles incomplete lineage sorting.
What are key papers in teleost phylogenomics?
Near et al. (2012, 962 citations) resolves ray-finned phylogeny; Hughes et al. (2018, 595 citations) uses transcriptomes; Betancur-R et al. (2017, 931 citations) classifies bony fishes.
What open problems remain?
Resolving percomorph polytomies, quantifying gene flow impacts (Malinsky et al., 2018), and orthology amid duplications (Glasauer and Neuhauss, 2014) challenge full teleost tree accuracy.
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