Research method
Phylogenetic Analysis
17 studies
Phylogenetic analysis infers evolutionary relationships from aligned sequences, gene trees, or presence/absence of genes across genomes. Depending on the design the output is a gene-family tree, a species tree, a positive-selection scan on orthologs, or a pan-genome graph of core versus accessory genes. A tree is a hypothesis about history, not an experimental measurement of a protein's current function.
Comparative biologists use phylogenies when they need to know whether a gene family expanded, whether a trait is ancestral, or whether the same pathways keep being selected. It answers 'how are these sequences related, and where did novelty arise?' Its main limitation is that sequence classification and selection statistics are not knockout phenotypes, and shared selection can be convergence or ancient shared pressure.
Studies
17
Findings
5
7 supporting · 0 challenging · 0 qualifying citations
Open tensions
2
Currently
What we know
- A multi-kingdom HSP90 survey found 103 genes on 32 genomes (87 functional, 16 pseudogenes). Vertebrates had the largest counts; Archaea nearly lack HSP90. The phylogeny classifies homologs and pseudogenes; it does not mutate each homolog's chaperone clients.
- Plant MYB inventories are also sequence phylogenies: 155 rice and 197 Arabidopsis MYB genes, with R2R3 the largest subclass. Structure and expression were analysed, but classification remains sequence-based rather than a phenotype for every gene.
- Positive-selection scans across bird orthologs, compared with mammals, found immune pathways as recurrent targets. Genes selected in birds were enriched for selection in mammals, especially viral-response genes, and about 14% of genes were selected in all tests. Shared selection could still be convergence rather than one continuous pressure.
- Aspergillus clade genomics and a Listeria pan-genome reassessment use trees and gene-content matrices together. Aspergillus genomes were ~29–36 Mb with 9,113–13,553 genes, about 20% Aspergillaceae-specific, and section Nigri averaged ~1,800 unique genes. Extending L. monocytogenes by 11 strains covering all serotypes showed a highly stable but not closed pan-genome, with accessory genes in hypervariable hotspots and mobile elements as major accessory components.
- Whole-genome papers for extreme physiology use phylogeny as context rather than as the sole result. The painted-turtle genome is a resource for anoxia and freeze-survival in a tetrapod that can freeze nearly solid then thaw with little damage; the wild Medicago ruthenica assembly is compared with cultivated legumes to retain stress-tolerance traits diluted by domestication. Neither map every protective pathway experimentally or deliver a finished cultivar.
Largest unresolved question
These papers do not build the same kind of tree. HSP90 and MYB papers classify gene families; the immune-gene paper scans orthologs for repeated positive selection (~14% selected in all tests); Aspergillus and Listeria papers mix clade phylogeny with pan-genome gene content; turtle and Medicago papers are organismal genomes whose phylogeny is background for physiology or breeding. A student who treats every 'phylogenetic analysis' hit as a species tree will misread the result.
Procedure
How it works
The main stages of the method. Specific protocols and analysis choices vary between studies.
Collect homologous sequences
Genes or genomes are gathered so that comparable units can be scored — amino acids, nucleotides, or presence/absence. What enters the matrix decides whether the later object is a gene-family tree, a species tree, or a pan-genome graph.
Align the sequences
Positions are lined up so that a substitution model can treat them as homologous sites. Alignment error at this step becomes spurious topology later; poorly conserved families are especially vulnerable.
Infer a tree or a gene-content matrix
A substitution model, coalescent, or presence/absence coding produces a topology and branch lengths, or a core-versus-accessory matrix. Family inventories, ortholog selection scans, clade phylogenies, and organismal genomes used as background are not the same kind of tree.
Read expansions, selection, or accessory genes
Gene-family counts, dN/dS scans, and lineage-specific lists are taken off the tree or the matrix. Shared positive selection can still be convergence or ancient pressure, and presence of an accessory gene is not a virulence phenotype.
Treat the tree as a history hypothesis, not a function assay
Phylogenetic analysis answers how these sequences are related and where novelty is inferred to have arisen. It does not mutate a homolog's clients or substitute for a knockout of current function.
Common misconceptions
If a gene sits in an expanded family on the tree, it has been shown to work as a chaperone, transcription factor, or immune effector.
HSP90 counts (87 functional genes, 16 pseudogenes) and MYB counts (155 rice, 197 Arabidopsis) are sequence classifications. Neither paper experimentally mutates every homolog's clients or phenotype.
Shared positive selection on immune genes in birds and mammals means those genes evolved under one identical pathogen pressure.
About 14% of genes were selected in all tests and viral-response genes were enriched, but the authors note shared selection could reflect convergence or ancient shared pressure, and finer tetrapod clades still need scanning.
A 'not closed' pan-genome means Listeria gene content is chaotic and therefore phylogenetically useless.
The pan-genome was highly stable but not closed; accessory genes concentrate in hypervariable hotspots. Presence/absence still informs diagnostics and phylogenetics even though it does not prove each virulence phenotype.
Related
Claim ledger
What the evidence shows
Drawn from 17 studies in this library. Mix labels say which citation roles are present; they are not a strength score. Supports means evidence for a finding; Challenges means evidence against a stated position; Qualifies marks scope.
A multi-kingdom HSP90 survey found 103 genes on 32 genomes (87 functional, 16 pseudogenes). Vertebrates had the largest counts; Archaea nearly lack HSP90. The phylogeny classifies homologs and pseudogenes; it does not mutate each homolog's chaperone clients.
Plant MYB inventories are also sequence phylogenies: 155 rice and 197 Arabidopsis MYB genes, with R2R3 the largest subclass. Structure and expression were analysed, but classification remains sequence-based rather than a phenotype for every gene.
Positive-selection scans across bird orthologs, compared with mammals, found immune pathways as recurrent targets. Genes selected in birds were enriched for selection in mammals, especially viral-response genes, and about 14% of genes were selected in all tests. Shared selection could still be convergence rather than one continuous pressure.
Aspergillus clade genomics and a Listeria pan-genome reassessment use trees and gene-content matrices together. Aspergillus genomes were ~29–36 Mb with 9,113–13,553 genes, about 20% Aspergillaceae-specific, and section Nigri averaged ~1,800 unique genes. Extending L. monocytogenes by 11 strains covering all serotypes showed a highly stable but not closed pan-genome, with accessory genes in hypervariable hotspots and mobile elements as major accessory components.
Study Role Design N Population Outcome Aspergillus genomic diversity Supports Computational / modellingComparative genomics of Aspergillus genomes in MycoCosm Multi-genome Aspergillus comparison (≈29–36 Mb; 9,113–13,553 genes) — genome count not a single primary N in stored summary Aspergillus / Aspergillaceae genomes Genome size, gene content, and clade-specific gene expansions How open is the Listeria pan-genome? Supports Computational / modellingExtended L. monocytogenes complete-genome set covering all serotypes for pan-genome analysis N=16 · 16 completely sequenced chromosomes (extended by 11 strains in this work) Listeria monocytogenes genomes across serotypes Pan-genome stability and accessory-gene hotspot dynamics Whole-genome papers for extreme physiology use phylogeny as context rather than as the sole result. The painted-turtle genome is a resource for anoxia and freeze-survival in a tetrapod that can freeze nearly solid then thaw with little damage; the wild Medicago ruthenica assembly is compared with cultivated legumes to retain stress-tolerance traits diluted by domestication. Neither map every protective pathway experimentally or deliver a finished cultivar.
- What extreme physiologies does the painted turtle genome encode?
- What can a wild Medicago genome teach about stress tolerance?
Study Role Design N Population Outcome What extreme physiologies does the painted turtle genome encode? Supports Computational / modellingGenome assembly and comparative analyses with supporting anoxia RNA-seq N=1 · Chrysemys picta bellii reference genome; RNA-seq from n = 4 turtles per normoxic/anoxic group (16 libraries) Western painted turtle (Chrysemys picta bellii) Genome of a slowly evolving, anoxia- and freeze-tolerant tetrapod providing a model for extreme physiological adaptations What can a wild Medicago genome teach about stress tolerance? Supports Computational / modellingDe novo assembly/annotation of Medicago ruthenica with stress-trait comparisons to cultivated legumes ~914 Mb estimated genome; PacBio/Illumina assembly resource — not a sample-N study Wild Medicago ruthenica Genome features linked to stress tolerance for alfalfa improvement
Debates
Tensions and limits
Some items are genuine disagreements on the same question. Others mark different assays, populations, or outcomes.
These papers do not build the same kind of tree. HSP90 and MYB papers classify gene families; the immune-gene paper scans orthologs for repeated positive selection (~14% selected in all tests); Aspergillus and Listeria papers mix clade phylogeny with pan-genome gene content; turtle and Medicago papers are organismal genomes whose phylogeny is background for physiology or breeding. A student who treats every 'phylogenetic analysis' hit as a species tree will misread the result.
These papers do not build the same kind of tree. HSP90 and MYB papers classify gene families; the immune-gene paper scans orthologs for repeated positive selection (~14% selected in all tests); Aspergillus and Listeria papers mix clade phylogeny with pan-genome gene content; turtle and Medicago papers are organismal genomes whose phylogeny is background for physiology or breeding. A student who treats every 'phylogenetic analysis' hit as a species tree will misread the result.
- HSP90 family across kingdoms
- MYB transcription-factor families in plants
- Why do immune genes keep evolving across tetrapods?
- How open is the Listeria pan-genome?
Study Role Design N Population Outcome HSP90 family across kingdoms Supports Computational / modellingMulti-kingdom survey of HSP90 homologs and phylogeny across sequenced genomes N=32 · 32 genomes yielding 103 HSP90-family genes (87 functional, 16 pseudogenes); phylogeny used 197 sequences Sequenced genomes spanning Archaea, Bacteria, and Eukarya Distribution and evolutionary relationships of the HSP90 gene family MYB transcription-factor families in plants Supports Computational / modellingGenome-wide identification and classification of MYB genes with expression analysis 155 rice and 197 Arabidopsis MYB genes catalogued — gene-family survey, not a sample-N study Rice and Arabidopsis genomes MYB transcription-factor repertoire and subclass distribution Why do immune genes keep evolving across tetrapods? Supports Computational / modellingPositive-selection scans of avian orthologs with comparison to mammalian selection patterns N=39 · 39 bird species; up to 11,231 genes analysed (gene-tree models) Bird genomes (compared with mammal orthologs) Shared positive selection on immune genes across birds and mammals How open is the Listeria pan-genome? Supports Computational / modellingExtended L. monocytogenes complete-genome set covering all serotypes for pan-genome analysis N=16 · 16 completely sequenced chromosomes (extended by 11 strains in this work) Listeria monocytogenes genomes across serotypes Pan-genome stability and accessory-gene hotspot dynamics
PaperFren reads this as a limit on how far one study travels — different assays, populations, or outcomes — not a forced fight between papers.
What 'accessory' or 'lineage-specific' genes imply is itself unsettled. Listeria accessory genes concentrate in hotspots with mobile elements and aid diagnostics, but presence/absence does not prove each virulence phenotype. Aspergillus section Nigri's ~1,800 unique genes are not experimentally validated one by one. Immune-gene sharing of selection between birds and mammals can be convergence or ancient pressure.
What 'accessory' or 'lineage-specific' genes imply is itself unsettled. Listeria accessory genes concentrate in hotspots with mobile elements and aid diagnostics, but presence/absence does not prove each virulence phenotype. Aspergillus section Nigri's ~1,800 unique genes are not experimentally validated one by one. Immune-gene sharing of selection between birds and mammals can be convergence or ancient pressure.
- How open is the Listeria pan-genome?
- Aspergillus genomic diversity
- Why do immune genes keep evolving across tetrapods?
Study Role Design N Population Outcome How open is the Listeria pan-genome? Supports Computational / modellingExtended L. monocytogenes complete-genome set covering all serotypes for pan-genome analysis N=16 · 16 completely sequenced chromosomes (extended by 11 strains in this work) Listeria monocytogenes genomes across serotypes Pan-genome stability and accessory-gene hotspot dynamics Aspergillus genomic diversity Supports Computational / modellingComparative genomics of Aspergillus genomes in MycoCosm Multi-genome Aspergillus comparison (≈29–36 Mb; 9,113–13,553 genes) — genome count not a single primary N in stored summary Aspergillus / Aspergillaceae genomes Genome size, gene content, and clade-specific gene expansions Why do immune genes keep evolving across tetrapods? Supports Computational / modellingPositive-selection scans of avian orthologs with comparison to mammalian selection patterns N=39 · 39 bird species; up to 11,231 genes analysed (gene-tree models) Bird genomes (compared with mammal orthologs) Shared positive selection on immune genes across birds and mammals
PaperFren reads this as a limit on how far one study travels — different assays, populations, or outcomes — not a forced fight between papers.
Timeline
How understanding moved
Study years are when the paper was published. Evidence edits are dated changes to this page's claims. Explanations are when PaperFren added a Discovery — not a claim that the science happened that day.
2026
Concept page published
Phylogenetic Analysis
Change log
What changed
Dated edits to this page's evidence: studies added or removed from a claim, claims added or withdrawn, and new explanations tagged here. Coverage edits are distinct from reviewed research changes and corrections. Dates record PaperFren updates; study publication dates appear in the timeline.
- Coverage updated · Concept page published
Papers
17 studies in this library bear on Phylogenetic Analysis, ordered by citations.
- How many species live on Earth and in the ocean?
A validated taxonomic extrapolation estimates ~8.7 million eukaryotic species on Earth, with most still undescribed.
- What makes Apis cerana’s genome distinctive?
The Asian honey bee genome reveals expanded chemosensory receptors (Ors/Grs/Irs) central to chemical communication and colony life.
- MYB transcription-factor families in plants
Rice and Arabidopsis encode large MYB families dominated by R2R3 types with distinct expression patterns.
- Aspergillus genomic diversity
Comparative genomics shows Aspergillus species share genome size but harbor large lineage-specific gene sets.
- CRISPR repeats conserve RNA-like structure
CRISPR repeats across microbes form clusters with conserved sequence and predicted RNA secondary structure.
- Was innate immunity already complex in early animals?
Anthozoan cnidarians retain much ancestral metazoan immune/signaling complexity; flies and worms lost many components.
- Selective bacterial BSH shifts host metabolism
Bacteroides bile salt hydrolase BT2086 selectively deconjugates bile acids and alters host metabolism.
- HSP90 family across kingdoms
Comparative genomics maps 103 HSP90-family genes across 32 genomes and deep phylogenetic diversity.
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- What extreme physiologies does the painted turtle genome encode?
The western painted turtle genome informs evolution of extreme anoxia and freeze tolerance in a slowly evolving vertebrate lineage.
- B. dorei rises before T1D autoimmunity
Bacteroides dorei dominates the gut microbiome before autoimmunity in high-risk Finnish children.
- How do Sinocyclocheilus genomes record cave life?
Sinocyclocheilus cavefish genomes reveal troglomorphic adaptations such as eye degeneration and albinism, paralleling and differing from Astyanax.
- Chicken β-defensin gene cluster
Chicken genome encodes 13 β-defensin (Gal) genes in a single innate-immunity cluster.
- How open is the Listeria pan-genome?
Eleven new genomes spanning serotypes show a stable but open pan-genome with nine hypervariable hotspots dominated by mobile elements.
- Immune transcriptome of bacteria-challenged sea bass
Deep RNA-seq of bacteria-challenged Lateolabrax japonicus reveals innate immune genes.
- Why do immune genes keep evolving across tetrapods?
Shared positive selection in birds and mammals concentrates on immune—especially antiviral—genes, implicating pathogens as a consistent selective pressure.
- Pathogenicity factors in Naegleria fowleri
Whole-genome analysis of N. fowleri highlights candidate pathogenicity factors for brain infection.
- What can a wild Medicago genome teach about stress tolerance?
A highly complete Medicago ruthenica genome provides genetic resources for environmental-stress tolerance missing from yield-focused cultivated alfalfa.
Compare studies
Select 2–10 studies. Design and N are labels, not a ranking.
Nothing selected yet.
Questions
What is still open
These papers do not build the same kind of tree. HSP90 and MYB papers classify gene families; the immune-gene paper scans orthologs for repeated positive selection (~14% selected in all tests); Aspergillus and Listeria papers mix clade phylogeny with pan-genome gene content; turtle and Medicago papers are organismal genomes whose phylogeny is background for physiology or breeding. A student who treats every 'phylogenetic analysis' hit as a species tree will misread the result.
What 'accessory' or 'lineage-specific' genes imply is itself unsettled. Listeria accessory genes concentrate in hotspots with mobile elements and aid diagnostics, but presence/absence does not prove each virulence phenotype. Aspergillus section Nigri's ~1,800 unique genes are not experimentally validated one by one. Immune-gene sharing of selection between birds and mammals can be convergence or ancient pressure.
Ask PaperFren about Phylogenetic Analysis
Study this conceptflashcards and short-answer questions
HSP90 phylogeny found 103 genes on 32 genomes, with Archaea nearly lacking the family. What claim does that support, and what experiment is still missing?
It supports a kingdom-level distribution: vertebrates have the largest counts and Archaea almost lack HSP90, with 16 of 103 sequences classed as pseudogenes. It does not show what each functional homolog's chaperone clients are.
Why is 'about 14% of genes selected in all tests' not the same finding as 'immune genes are the only things that evolve'?
The scan found immune pathways as recurrent targets and overlap between bird and mammal selection, especially viral-response genes. Most genes were not selected in all tests; 14% is the shared-selected fraction, not the whole genome.
Aspergillus section Nigri averages ~1,800 unique genes and Listeria accessory genes sit in mobile-element hotspots. How should a diagnostician versus a functional geneticist use those results?
Gene presence/absence and clade-specific content can mark lineages for diagnostics or phylogenetics. Neither result experimentally validates every unique or accessory gene's phenotype, so a functional geneticist still needs infection or knockout assays.
The painted-turtle and Medicago ruthenica genomes are both comparative resources. What physiological or breeding claim is licensed, and what is not?
Turtle sequence is a model for anoxia and freeze-thaw survival in a tetrapod that can freeze nearly solid; M. ruthenica retains stress-tolerance features diluted by domestication and is useful for breeding. Neither paper maps every protective pathway or delivers a commercial cultivar.