# Diapherotrites
**Diapherotrites** (Candidatus Iainarchaeota) is a candidate phylum of archaea, known almost entirely from genome sequences rather than cultivated organisms, that was proposed in 2013 as one of the founding members of the archaeal superphylum DPANN.[1](https://www.nature.com/articles/nature12352) Its pro-correct name is Candidatus Iainarchaeota, with "Candidatus Diapherotrites" recorded as an inaccurate spelling of that name, and the preferred name at class level is "Candidatus Iainarchaeia" Rinke et al. 2021.[2](https://lpsn.dsmz.de/phylum/diapherotrites) • [5](https://lpsn.dsmz.de/phylum/iainarchaeota) Most DPANN members lack pure-culture representatives, and the phylum's deep phylogenetic position remains contested.[3](https://journals.asm.org/doi/10.1128/mbio.02918-23)
| Key fact | Detail |
|---|---|
| Status | Candidate (Candidatus) phylum; not validly published; pro-correct name Iainarchaeota[2](https://lpsn.dsmz.de/phylum/diapherotrites) |
| Proposed | Rinke et al. 2013, from single-cell amplified genome pMC2A384[1](https://www.nature.com/articles/nature12352) |
| Etymology | Greek *tritos*, "the third": the 3rd HSM (homogeneous set of MAGs) group discovered[2](https://lpsn.dsmz.de/phylum/diapherotrites) |
| Type species | *Candidatus* 'Iainarchaeaum andersonii' (SAG SCGC_AAA011-E11)[4](https://doi.org/10.1038/ismej.2014.141) |
| Genome (type species) | ~1.24 Mb estimated, 88.5% complete, 47% GC, 1202 CDS[4](https://doi.org/10.1038/ismej.2014.141) |
| Sources of genomes | Homestake Mine groundwater seep (South Dakota, USA); marine oxygen-deficient zones[4](https://doi.org/10.1038/ismej.2014.141) • [3](https://journals.asm.org/doi/10.1128/mbio.02918-23) |
| Cultivated representatives | Most DPANN members lack pure-culture representatives[3](https://journals.asm.org/doi/10.1128/mbio.02918-23) |
## What Diapherotrites is
In the LPSN nomenclatural database, Iainarchaeota is listed as a pro-correct name that is not validly published, and "Candidatus Diapherotrites" Rinke et al. 2013 is recorded as an inaccurate spelling of it.[2](https://lpsn.dsmz.de/phylum/diapherotrites) The preferred name at class level is "Candidatus Iainarchaeia" Rinke et al. 2021, also not validly published.[5](https://lpsn.dsmz.de/phylum/iainarchaeota)
The etymology reflects the phylum's origin in genome binning: the name combines the Greek masculine adjective *tritos* ("the third") to denote the third HSM group, a homogeneous set of metagenome-assembled genomes, discovered; the phylum comprises the genus *Iainarchaeum*.[2](https://lpsn.dsmz.de/phylum/diapherotrites)
## Discovery from single-cell genomics and MAGs
Diapherotrites was proposed in 2013 by Patricia Rinke and colleagues based on phylogenetic analysis of the archaeal single-cell amplified genome pMC2A384, alongside the newly proposed phyla [Parvarchaeota](https://www.edgepedia.org/parvarchaeota), Aenigmarchaeota, and Nanohaloarchaeota.[1](https://www.nature.com/articles/nature12352) The same study coined the identifier DPANN for a monophyletic superphylum grouping Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and [Nanohaloarchaea](https://www.edgepedia.org/nanohaloarchaea), predicting small cell and genome size as unifying features.[1](https://www.nature.com/articles/nature12352) The lineage was described through single-cell genomics of nanosized archaea (0.1–0.8 µm) from brackish/freshwater and hydrothermal environments.[6](https://pmc.ncbi.nlm.nih.gov/articles/PMC6349945/)
The three Diapherotrites SAGs analyzed in the follow-up study all came from a groundwater seep on the ceiling of the Homestake Mine drift at a depth of 100 m in Lead, South Dakota, USA.[4](https://doi.org/10.1038/ismej.2014.141) Later, metagenome-assembled genomes (MAGs) extended the phylum's known range: from 962 MAGs binned from the Eastern Tropical North Pacific and [Arabian Sea](https://www.edgepedia.org/arabian-sea) oxygen-deficient zones, 33 were assigned to DPANN, including one Iainarchaeota MAG.[3](https://journals.asm.org/doi/10.1128/mbio.02918-23) Only the groundwater seep and marine oxygen-deficient zones are documented as sources in the available literature; claims about sediment or hypersaline sources are not settled by these studies.
## Phylogenetic placement within DPANN
Diapherotrites' position is one of the less settled questions in archaeal phylogenetics. Two lines of evidence support DPANN monophyly including Diapherotrites: an analysis using 3,242 single gene trees and 31,236 archaeal gene families supported monophyly and placed the archaeal root between DPANN and all other Archaea,[7](https://www.pnas.org/doi/abs/10.1073/pnas.1618463114) and a 2025 phylogenomic analysis of the 11 known DPANN phyla robustly supported monophyly while placing DPANN within Euryarchaeota, descended from probably free-living euryarchaeal-like ancestors.[8](https://preview-www.nature.com/articles/s41564-025-02024-5)
Against this, Williams and colleagues found that Diapherotrites branched basally when analyzed individually, while [Nanoarchaeota](https://www.edgepedia.org/nanoarchaeota), Nanohaloarchaeota, and [Pacearchaeota](https://www.edgepedia.org/pacearchaeota) grouped within Euryarchaeota, raising the possibility that DPANN monophyly is a long-branch-attraction artifact; the strongest evidence against monophyly comes from analyses that place DPANN taxa into the archaeal tree one at a time.[6](https://pmc.ncbi.nlm.nih.gov/articles/PMC6349945/) The same review concluded that phylogenetic resolution of DPANN lineages is sensitive both to taxon sampling and to the methods of analysis used. The two monophyly-supporting studies also disagree with each other on where DPANN sits relative to Euryarchaeota: the 2017 analysis placed the root outside all other Archaea,[7](https://www.pnas.org/doi/abs/10.1073/pnas.1618463114) while the 2025 analysis places DPANN inside Euryarchaeota.[8](https://preview-www.nature.com/articles/s41564-025-02024-5) This disagreement remains unresolved, and GTDB itself flags Iainarchaeota's placement as tentative, requiring additional phylogenomic analyses once more genomes become available.[9](https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-021-00918-8/MediaObjects/41564_2021_918_MOESM1_ESM.pdf)
## Constituent lineages: Iainarchaeia and allied bins
The phylum's type genus is "Candidatus Iainarchaeum" Rinke et al. 2013, and Iainarchaeota is the pro-correct phylum-level name under the [International Code of Nomenclature of Prokaryotes](https://www.edgepedia.org/international-code-of-nomenclature-of-prokaryotes).[5](https://lpsn.dsmz.de/phylum/iainarchaeota) The candidatus-type species is SAG SCGC_AAA011-E11, named *Candidatus* 'Iainarchaeaum andersonii'.[4](https://doi.org/10.1038/ismej.2014.141) At the class level, "Candidatus Iainarchaeia" Rinke et al. 2021 is the preferred name.[5](https://lpsn.dsmz.de/phylum/iainarchaeota) LPSN records only two child taxa in total, none with a validly published name,[5](https://lpsn.dsmz.de/phylum/iainarchaeota) so the phylum's internal diversity beyond the original SAGs and scattered MAGs is not yet well cataloged.
## By the numbers
*Candidatus* 'Iainarchaeaum andersonii' has an estimated genome size of about 1.24 Mb with 88.5% estimated completion.[4](https://doi.org/10.1038/ismej.2014.141) Its genome carries 47% GC content, 1202 protein-coding sequences (782 with function predictions), an average gene length of 822 bp, a single ribosomal RNA operon, roughly 90.4% coding density, 27.6% [overlapping genes](https://www.edgepedia.org/overlapping-gene), 2.16% gene duplication, and 39 tRNAs.[4](https://doi.org/10.1038/ismej.2014.141) The three original SAGs were deposited under [GenBank](https://www.edgepedia.org/genbank) assembly IDs GCA_000402355.1, GCA_000404545.1, and GCA_000404525.1.[4](https://doi.org/10.1038/ismej.2014.141)
A practical reason Diapherotrites is undercounted in surveys: its 16S rRNA genes show multiple mismatches with the majority of archaeal 16S rRNA primers, which could explain the lineage's rarity in amplicon-generated datasets.[4](https://doi.org/10.1038/ismej.2014.141)
## How it compares with other DPANN candidate phyla
DPANN archaea share ultrasmall cell sizes of roughly 0.1–1.5 µm, reduced genomes of about 1.5 Mb, and limited metabolic capacities.[3](https://journals.asm.org/doi/10.1128/mbio.02918-23) Within this group, Iainarchaeota (formerly Diapherotrites) is an exception, reported to carry sufficient anabolic capabilities for a free-living lifestyle despite its small genome.[3](https://journals.asm.org/doi/10.1128/mbio.02918-23) Comparisons of estimated genome sizes place the type species' 1.24 Mb above *Nanoarchaeum equitans* at 0.49 Mb, *Candidatus* Micrarchaeum acidiphilum at about 1 Mb, and *Candidatus* Aenigmarchaeum subterraneum ARMAN-2 at an estimated 0.91 Mb, and close to *Candidatus* Nanosalina J07AB43 at 1.23 Mb.[4](https://doi.org/10.1038/ismej.2014.141) Woesearchaeota and Pacearchaeota joined the superphylum in 2015, and most DPANN members lack pure-culture representatives; *Nanoarchaeum equitans* remains one of the few cultivated members.[3](https://journals.asm.org/doi/10.1128/mbio.02918-23) No Diapherotrites MAGs were recovered from oxygenated surface waters or TARA Oceans surface and deep [chlorophyll maximum](https://www.edgepedia.org/chlorophyll-maximum) assemblies in the oxygen-deficient-zone study.[3](https://journals.asm.org/doi/10.1128/mbio.02918-23)
## References
1. [Insights into the phylogeny and coding potential of microbial dark matter](https://www.nature.com/articles/nature12352)
2. [Phylum: Diapherotrites — LPSN](https://lpsn.dsmz.de/phylum/diapherotrites)
3. [Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential (mBio)](https://journals.asm.org/doi/10.1128/mbio.02918-23)
4. [Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites' (ISME Journal)](https://doi.org/10.1038/ismej.2014.141)
5. [Phylum: Iainarchaeota — LPSN](https://lpsn.dsmz.de/phylum/iainarchaeota)
6. [Genomic diversity, lifestyles and evolutionary origins of DPANN archaea (FEMS Microbiology Reviews)](https://pmc.ncbi.nlm.nih.gov/articles/PMC6349945/)
7. [Integrative modeling of gene and genome evolution roots the archaeal tree of life (PNAS)](https://www.pnas.org/doi/abs/10.1073/pnas.1618463114)
8. [Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors (Nature Microbiology, 2025)](https://preview-www.nature.com/articles/s41564-025-02024-5)
9. [A standardized archaeal taxonomy for the Genome Taxonomy Database — Supplementary Table S17](https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-021-00918-8/MediaObjects/41564_2021_918_MOESM1_ESM.pdf)
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*Topic: Encyclopedia › Life and health › Microorganisms and fungi › Archaea › Archaeal taxonomy and diversity › DPANN superphylum › Other DPANN candidate phyla › Diapherotrites*
*Initially written Sep 17, 2026 · Reviewed: Sep 19, 2026 · Edited: Sep 19, 2026; Oct 11, 2026 · Last review: Sep 19, 2026*
*Copyright 2026 EdgeChat AI, a subsidiary of Biostate AI.*
License: Edgepedia Community License 1.0, https://www.edgepedia.org/edgepedia/license