Interactive Phylo Tree of Life - Ptree

Interactive Phylo Tree of Life

Taxonomy

GBIFKingdom-to-species classification for biodiversity observations
COLAccepted species names and synonyms across all life
ITISGovernment reference for connecting records by scientific name

Descent

OTTEvolutionary branching synthesized from many phylogenetic trees
EOLTaxon hierarchy for combining descriptions, media and traits
NCBIOrganisms named and grouped for DNA and protein records

Microbes

GTDBBacteria and archaea grouped by genome-based ancestry
ICTVInternationally ratified names and ranks for viruses
SILVABacteria, archaea and eukaryotes grouped by ribosomal RNA

Specialty

WFOPublished plant names resolved under botanical rules
PBDBFossil taxa organized by geologic age and location

Columns

Tree

Branches

“”

Gram stain[1]

Risk group[1]

Temperature[1]

pH[1]

Breeding frequency[1]

Maturity[1]

Longevity[1]

Development time[1]

Offspring count[1]

Offspring mass[1]

Parental care[1]

Ontogeny[1]

Sex & mating[1]

Reproduction[1]

Shape[1]

Construction[1]

Movement[1]

Migration[1]

Nutrition[1]

Respiration[1]

Organization[1]

Earliest fossil[1]

Setting[1]

Position[1]

Vertical range[1]

Climate[1]

Day cycle[1]

Light sensing[1]

Spread[1]

Use & trade[1]

Conservation[1]

Population trend[1]

Linear extent[1]

Mass[1]

Volume[1]

Niche breadth[1]

Drought resistance[1]

Leaf economymm2mgmgg[1]

Gas exchangeµmolmmolmmolm2·s[1]

Growth form[1]

Persistence[1]

Gram-negativeGram-variableGram-positive
risk group 1risk group 2risk group 3
−65 °C105 °C
014
0.05/yr500/yr
0.1 d60,000 d
0.01 yr15,000 yr
embryo 2,000 djuvenile 2,000 d0.05
0.5300M
10 ng3,000 kg
nonepresentprotectionprovisioningbroodingmaternalpaternalbiparentalcooperative
directlarvalegg-layinglive-bearingaltricialsemiprecocialprecocial
separate sexescombined sexessequentialmixedmonogamousnon-monogamouspolygynouspolyandrouspromiscuous
asexualalternatingsexualsemelparousiteroparousinternalexternalbrood parasitic
elongatedtaperedroundedflatcurvedspiralbranched
softinternalexternalaragonitecalcitephosphaticsiliceousorganic
stationarydriftingfacultativeground-movingclimbingburrowingswimmingflyingmobile
residentirregularpartialmigratoryverticalfreshwateroceanicfresh–salt
photosyntheticchemosyntheticabsorptiveherbivorousomnivorouspredatoryparasiticfilter-feedingdetrital
anaerobiclow oxygenflexibleaerobic
singlegroupcolonialclonalsymbiotic
0.01 Ma4,000 Ma
oceancoastfreshwaterwetlandlandhostbuilt
opensurfaceburiedattachedelevatedinternal
depth 11,000 melevation 9,000 m−500 m
wet tropicalseasonally drymontanearidtropicalsubtropicaltemperatecold
diurnalcrepuscularnocturnalcathemeralmixed
blindsensingorientingimaging
endemicnativemanagedintroducednaturalisedinvasive
foodmedicineornamentmaterialservicewatchedcontrolledrestricted
Least ConcernNear ThreatenedVulnerableEndangeredCritically EndangeredExtinct in the WildExtinctData Deficient
decreasingstableincreasing
root depth 50 mlength 200 m0.5 µm
0.1 pg1,000 t
0.001 µm³1,000 m³
0.22
−15 MPa0 MPa
0.3area/mass 700 mm2mg1nitrogen 80 mgg
0.5efficiency 180 µmolmmol0.4flow 2,000 mmolm2·s
treeshrubsubshrubherbgrassclimbersucculentgeophyte
annualbiennialperennialdeciduoussemi-deciduousevergreen

iNat geomodelMDD ranges

Wikipedia
Interactions
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Sync Tree

FeedingEaten byEatsPreyed upon byPreys onKilled byKillsFood stolen bySteals food fromNourished byNourishesTrophically interacts withFarmed byFarms
ParasitesParasitesParasitizesEndoparasitesLives insideEctoparasitesLives onRoot parasitesRoot parasite ofHemiparasitesHemiparasite ofParasitoidsParasitoid ofEndoparasitoidsEndoparasitoid ofEctoparasitoidsEctoparasitoid ofHyperparasitesParasitizes a parasite
Disease and transmissionPathogensInfectsCarried byCarriesReservoir hostsReservoir for
Symbiosis and hostsHosted byHostsSymbiontsMutualistsCommensalsCommensal ofLived on byLives onLived inside byLives insideGuestsGuest ofEctomycorrhizal hostHosts ectomycorrhizaeArbuscular hostHosts arbuscular mycorrhizaeEpiphytesGrows on
Flowers and dispersalFlowers visited byVisits flowers ofPollinated byPollinatesDispersed byDisperses
Habitat and proximityHabitat forLives inHabitat created byCreates habitat forRoost forRoosts inInhabited byInhabitsLives nearLived under byLives underVisited byVisitsCo-roosts withCo-occurs withAdjacent to
Other associationsEggs laid on byLays eggs onEggs laid in byLays eggs inAffected by allelopathyAllelopathic towardEcologically related toInteracts with

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PhotoRange
Common ancestor

Ptree is created by Michael Dayah of Ptable and exists thanks to openly-licensed biodiversity data.

The provided material details frameworks for biodiversity classification, evolutionary descent tracking, microbial grouping, and the quantitative measurement of various biological and environmental parameters, all structured within a conceptual phylogenetic representation. Taxonomy is established through various global reference systems such as GBIF for kingdom-to-species classification, COL for accepted names and synonyms, and ITIS for government record linking by scientific name, while descent is managed by OTTE for evolutionary branching synthesis and EOL for the hierarchy combining descriptions and traits. Furthermore, resources like NCBI group organisms based on DNA and protein records, and SILVA groups bacteria, archaea, and eukaryotes based on ribosomal RNA.

The data structure incorporates a comprehensive set of columns that quantify diverse biological characteristics. These metrics range from developmental and physiological measures such as longevity, development time, offspring counts, mass, volume, and growth forms, to specific environmental factors like temperature, pH, flow rates, vertical range, climate variables, light sensing, and nutritional modes (e.g., photosynthetic versus chemosynthetic). Specific physiological measurements include gas exchange rates, nutrient assimilation efficiency, and material properties such as leaf economics and mass.

The document further elaborates on specific biological processes through detailed interaction matrices. These interactions define complex ecological relationships, including feeding dynamics where organisms are categorized by what they eat, what preys upon, and what they are preyed upon by. Relationships are also defined across pathogenic structures, detailing how organisms infect others, the transmission of diseases, and symbiotic arrangements such as mutualism, commensalism, and parasitism, specifying whether entities live inside or on hosts. Specific ecological associations are mapped, describing how species interact with their habitat, including proximity, coexistence, visitation, pollination, dispersal mechanisms, and the creation of habitats. These interactions further categorize relationships like host-parasite dynamics, where information is tracked regarding the reservoir hosts, endoparasites, ectoparasites, and hyperparasites.

The structure also defines specific traits across different domains, including morphology (shape, construction), movement (migration, climbing, flying), nutritional modes (herbivorous, omnivorous, predatory), environmental response (drought resistance), and spatial organisation (vertical range, linear extent). The data integrates complex metrics such as mass, area/mass ratios, and various rate calculations for flow and exchange. These variables are applied across different taxa, with categories distinguishing between Gram-negative and Gram-positive bacteria and correlating these classifications with risk groups and specific environmental conditions like temperature ranges.

Finally, the text acknowledges the reliance on this structured system by citing Michael Dayah for the creation of Ptree, which utilizes openly licensed biodiversity data to represent the common ancestor and subsequent evolutionary branching.