Topics — What a work is about. Nucleation holds whatever reading the owner files here, whether or not an Anthology of the SOTA topic could also hold it; instruction for ML practice belongs to the anthology (ADR-048). The words are seeded from the clusters the reading-time triage of 2026-09-25 found, and grow by decision.
Endosymbiosis and reductive evolution — how one organism comes to live inside another and depend on it, and how that ends — reductive genome evolution by drift, deletional bias or adaptive loss (including the Black Queen dependencies of free-living microbes), complementary loss across partners, nested symbioses and symbiont splitting and replacement, endosymbiotic gene transfer, protein import and host control of transmission, organellogenesis and organelle loss, and eukaryogenesis. The ecology of a partnership is ecology (ADR-055).
35 of 2004 LIT documents. Back to the full index.
| # | Title | Summary | Status |
|---|---|---|---|
| LIT-1557 v3 | Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora | Nowack & Grossman (2012). In the amoeba Paulinella chromatophora, whose photosynthetic chromatophores arose about 60 million years ago, three photosystem I subunits encoded by genes transferred to the nucleus are made in the cytoplasm, traffic into the chromatophores, apparently via the Golgi, and assemble there with chromatophore-encoded subunits. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC3325729) and the publisher’s free PDF is at pnas.org/content/pnas/109/14/5340.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1558 v3 | Dominant contribution of Asgard archaea to eukaryogenesis | Tobiasson, Luo, Wolf & Koonin (2026). Hypothesis tests on constrained trees for widespread eukaryotic genes traced to the last eukaryotic common ancestor give Asgard archaea about half of all likelihood weight in the best-resolved families and the lead in nearly every functional system. The alphaproteobacterial contribution is small and centred on the mitochondrion (oxidative phosphorylation, Fe–S cluster assembly, mitochondrial translation). About a third of families point to other bacteria, scattered across functions, which the authors read as piecemeal gene transfer and not further symbioses. A test of stem lengths finds they do not track acquisition time. The authors infer a complex Asgard ancestor that took up the mitochondrion late. | Active — read in full 2026-10-27 (NOTE-1242) from the PubMed Central copy of the version of record (PMC12872458, open access); worth reading as the largest survey so far of where the last eukaryotic common ancestor’s genes came from, finding Asgard archaea the largest single source in nearly every functional system, the alphaproteobacterial share small and mitochondrial, and other bacteria diffuse (THEORY-1104), and for its test of the stem-length method, which it finds does not behave as a clock (THEORY-1101). Read it knowing that “dominant” means about half of likelihood weight among well-resolved families, not a count of genes; that the paper is itself mitochondrion-late; that its denial of further symbioses is read off the diffuseness of the bacterial signal, not shown; and that it rests on sparse, biased genome sampling, as the authors stress. |
| LIT-1559 v3 | Extreme genome reduction in symbiotic bacteria | McCutcheon & Moran (2011 online; 2012 issue). Review of bacterial symbionts with extraordinarily small genomes, from independent lineages: gene sets rivalling some organelles, lacking genes thought essential elsewhere, with fast protein evolution and abundant chaperones. The authors read these as highly degenerate genomes retaining only the most essential functions, many serving the host. | Unavailable — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1560 v3 | Protein import into bacterial endosymbionts and evolving organelles | Sørensen, Stiller, Kröninger & Nowack (2024 online; 2025 issue). Review of the evidence for protein import from host into bacterial endosymbionts, long taken to mark an organelle off from an endosymbiont. Import of hundreds of proteins is established in two systems, the Paulinella chromatophore and the nitroplast, where the imported proteins come mostly from the host’s own genes or from other bacteria, so gene transfer from the endosymbiont is not required. Elsewhere there are one to seven targeted proteins per system. Each system uses its own targeting signal, and the mechanisms are largely unknown. | Active — read in full 2026-10-27 (NOTE-1241) from the PubMed Central copy of the version of record (PMC12176269, open access); worth reading as the system-by-system statement of what is known about host proteins entering bacterial endosymbionts, import at scale in the Paulinella chromatophore and the nitroplast and single proteins elsewhere, for its point that gene transfer from the endosymbiont is not needed for an organelle (THEORY-1100), and for its ordered scenario of effectors, dependence and general import (THEORY-1107). Read it knowing that it is a review whose import-at-scale evidence is two proteomic studies, that most single-protein cases rest on antibody localization, that the scenario is offered as plausible on limited data, and that import mechanisms are almost entirely unknown. |
| LIT-1561 v3 | Gene ancestries reveal diverse microbial associations during eukaryogenesis | Bernabeu, Manzano-Morales, Marcet-Houben & Gabaldón (2026). A revised reconstruction of the last eukaryotic common ancestor’s proteome, with thresholds calibrated on the accepted partners, finds two further bacterial donors, Myxococcota (3.92% of the proteome) and Planctomycetota (2.24%), comparable to Alphaproteobacteria (3.99%) and Asgard archaea (3.28%). Stem lengths order the acquisitions as waves, with Planctomycetota before the mitochondrion. About 4.5% of families have viral sisters, mostly giant viruses, some carrying prokaryotic genes. The authors suggest early eukaryotes arose within complex microbial communities through a succession of associations, while conceding their data cannot say whether any donor was a symbiont. | Active — read in full 2026-10-27 (NOTE-1237) from the PubMed Central copy of the version of record (PMC13468126, open access); worth reading as the strongest current case that the last eukaryotic common ancestor received genes from bacterial donors besides the mitochondrial ancestor, Myxococcota and Planctomycetota, in shares comparable to the accepted partners’, and for its ordering of those acquisitions as waves (THEORY-1105). Read it knowing that its thresholds are calibrated on the accepted partners; that its key controls are in a supplement; that the ordering rests on stem lengths as a clock, which Tobiasson et al. dispute; and that the authors say their data cannot tell whether any donor was a symbiont. |
| LIT-1562 v3 | Nitrogen-fixing organelle in a marine alga | Coale et al. (2024). UCYN-A, a streamlined nitrogen-fixing cyanobacterium known as an endosymbiont of a marine alga, is integrated into the alga’s cell architecture and organellar division and imports proteins encoded by the algal genome, so the authors call it an early-stage nitrogen-fixing organelle, the “nitroplast”. | Unavailable — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1563 v3 | Sympatric Speciation in a Bacterial Endosymbiont Results in Two Genomes with the Functionality of One | Van Leuven, Meister, Simon & McCutcheon (2014). In some cicadas of the genus Tettigades, the endosymbiont Hodgkinia has split into two cytologically distinct, metabolically interdependent lineages whose gene loss and retention are almost perfectly complementary, so a three-member symbiosis became four. The authors suggest nonadaptive forces can build organismal complexity. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S009286741401037X/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1564 v3 | Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes | Santana-Molina, Williams, Snel & Spang (2025). The last eukaryotic common ancestor had a complete central carbon metabolism of chimeric origin: six putative Asgard-archaeal enzymes, mainly in cytosolic glycolysis and the pentose phosphate pathway; seventeen alphaproteobacterial ones, mostly mitochondrial and ten in the TCA cycle; and others from various bacteria, with no third dominant donor. Gene loss, horizontal replacement and retargeting have remodelled it since, so that compartment no longer follows origin. The authors read the split as a trace of host–symbiont syntrophy, though the split is what any archaeal-host, bacterial-endosymbiont origin would leave. | Active — read in full 2026-10-27 (NOTE-1239) from the PubMed Central copy of the version of record (PMC11976288, open access); worth reading as a careful, enzyme-by-enzyme history of eukaryotic central carbon metabolism, showing Asgard contributions to cytosolic glycolysis and the pentose phosphate pathway, alphaproteobacterial ones mostly in the mitochondrial TCA cycle, other donors with none dominant, and extensive later replacement and retargeting (THEORY-1109). Read it knowing that it rests on 64 single-gene trees, several weakly supported and all in the supplement; that alphaproteobacterial contributions outnumber Asgard ones 17 to six; and that its support for syntrophy comes from a compartment split that any archaeal-host, bacterial-endosymbiont model predicts, so it does not discriminate syntrophy-first from complexity-first scenarios. |
| LIT-1565 v3 | An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs | McCutcheon & von Dohlen (2011). In the mealybug Planococcus citri, the gammaproteobacterium Moranella lives inside the betaproteobacterium Tremblaya. Their complete genomes show little overlap in nutrient-production genes, and several essential amino-acid pathways need a patchwork of gene products from Tremblaya, Moranella and possibly the insect. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC3169327) and the publisher’s free PDF is at cell.com/article/S096098221100724X/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1566 v3 | Dated gene duplications elucidate the evolutionary assembly of eukaryotes | Kay et al. (2026). A relaxed molecular clock dates 135 gene duplications on the two eukaryotic stem lineages, inside a species tree that puts the archaeal branch point at 3.05–2.79 billion years ago, the alphaproteobacterial one at 2.37–2.13 and LECA at 1.80–1.67. Taking the onset of duplications in genes from the mitochondrial partner, about 2.2 billion years ago, as the start of endosymbiosis, most host-side duplications (actin and tubulin, vesicle trafficking, nuclear-targeted paralogues) are older and most other bacterial duplications are younger. The authors reject mitochondrion-early scenarios, argue against serial endosymbiosis, and favour a complexified-archaean, late-mitochondrion sequence. The dates are maximum ages for paralogue functions, and the authors cannot order phagocytosis and the mitochondrion. | Active — read in full 2026-10-27 (NOTE-1234) from the PubMed Central copy of the version of record (PMC12872463, CC BY 4.0); worth reading as the first relaxed-clock dating of the duplications on both eukaryotic stem lineages, which puts most host-side duplications (cytoskeleton, trafficking, nuclear targeting) before the onset of duplications in genes from the mitochondrial partner at about 2.2 billion years ago, and most other bacterial duplications after it (THEORY-1099). Read it knowing that each date is a maximum age for its paralogues’ functions and many intervals reach below 2.2 billion years; that equating the onset of symbiont-gene duplication with endosymbiosis is argued, not tested; that the priors let archaeal duplications be older than any alphaproteobacterial one; and that the authors cannot order phagocytosis and the mitochondrion, though the abstract lists phagocytotic machinery among the features that came first. |
| LIT-1567 v3 | A Eukaryote without a Mitochondrial Organelle | Karnkowska et al. (2016). The genome of the oxymonad Monocercomonoides sp. lacks all hallmark mitochondrial proteins; the mitochondrial Fe–S cluster assembly pathway is replaced by a cytosolic SUF system acquired by lateral transfer from bacteria. Phylogeny places the loss as secondary, so the mitochondrion is not absolutely essential to a eukaryotic cell. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S0960982216302639/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1568 v3 | The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss | Morris, Lenski & Zinser (2012). In free-living bacteria such as Prochlorococcus and Pelagibacter, loss of a costly, leaky function whose products are public goods is favoured at the individual level, and proceeds until production just suffices for the community, leaving the losers dependent on co-occurring helpers. Selection, not drift, makes the dependency. The one worked case is Prochlorococcus’s loss of catalase-peroxidase (katG). | Active — read in full 2026-10-27 (NOTE-1212) from the PubMed Central copy of the version of record (PMC3315703, CC BY-NC-SA); worth reading as the selection route to microbial dependency, in which losing a costly, leaky function is favoured until helpers just supply the community (THEORY-1048). Read it knowing that it is an opinion piece with one worked case (katG in Prochlorococcus) whose benefit is computed, not measured; that it is stated for free-living microbes and credits drift for endosymbiont reduction; that its equations assume linear responses; and that its other examples and the “shooting the moon” acceleration are suggestions. |
| LIT-1569 v3 | Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis | Husnik et al. (2013). Tremblaya’s extreme genomic degeneracy likely followed its acquiring Moranella; at least 22 expressed genes transferred to the mealybug genome from diverse bacteria complement missing symbiont genes, none of them from Tremblaya. The three-way symbiosis depends on genes from at least six lineages, a path to intimate endosymbiosis distinct from the organelles’. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S0092867413006466/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1570 v3 | The Evolution of Dependence and Cohesion in Incipient Endosymbioses | Athreya, Czuppon & Gokhale (2025). An adaptive-dynamics model characterizes endosymbiosis by two collective properties, mutual dependence (survival as a collective) and reproductive cohesion (synchronized reproduction). The faster-growing partner becomes fully obligate first, and the other’s dependence then stays, rises or falls with births and deaths inside the collective. Dependence evolves at all only if the collective’s carrying capacity is high enough. Early on, dependence outruns cohesion, but only under the authors’ chosen trait mapping, which their own appendix shows decides the result. | Active — read in full 2026-10-27 (NOTE-1211) from the bioRxiv preprint, version 2 of 2025-05-31 (CC BY-NC 4.0), not the version of record, which was not reached; worth reading as the first model to separate mutual dependence from reproductive cohesion in an incipient endosymbiosis, with logistic growth for host, symbiont and collective, and for its results that the faster-evolving partner becomes obligate first and that the other’s fate turns on births and deaths inside the collective (THEORY-1051). Read it knowing that its headline result, dependence evolving ahead of cohesion, is fixed by the authors’ choice of how traits enter free growth and dissociation and reverses under the opposite choice in their own appendix (THEORY-1050); that nothing is tested against data, as the authors say; and that obligacy is a phenomenological trade-off, not gene loss. |
| LIT-1571 v3 | How do bacterial endosymbionts work with so few genes? | McCutcheon, Garber, Spencer & Warren (2024). An “Unsolved Mystery” essay on how radically reduced, compositionally biased endosymbiont gene sets function and interact with the host cell. Below about 400 kb endosymbionts lose the ability to build their own envelope, and below about 200 kb, the “tipping point”, translation-related genes erode. Host supply of membranes, transport and translation components is proposed, not shown. | Active — read in full 2026-10-27 (NOTE-1213) from the PubMed Central copy of the version of record (PMC11020763, CC BY); worth reading as the current statement of what endosymbionts with the smallest genomes lack, envelope biogenesis below about 400 kb and parts of translation below about 200 kb, and of the host’s presumed role in supplying them (THEORY-1049). Read it knowing that the thresholds come from a hand-picked matrix with draft genomes, that the composition analysis is called preliminary, and that every mechanism of host supply it names is a hypothesis. |
| LIT-1572 v3 | Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis | Husnik & McCutcheon (2016). Host and symbiont genomes from five mealybug species show Tremblaya from a single ancestral infection but the gammaproteobacterial symbionts inside it from multiple replacements by related lineages, while horizontally transferred genes on the host genome stay stable through the turnover. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC5027413), the bioRxiv preprint is at biorxiv.org/content/10.1101/042267v1, and the publisher’s PDF is at pnas.org/content/pnas/113/37/E5416.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1573 v3 | Accelerated evolution and Muller’s rachet in endosymbiotic bacteria | Moran (1996). Endosymbiont lineages, with small populations and no recombination, should accumulate mildly deleterious mutations. 16S rDNA of five independent endosymbiont clades evolves faster than in free-living relatives, and Buchnera coding genes show elevated nonsynonymous change and A+T-rich substitutions: Muller’s ratchet with mutational bias. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds the scanned article (PMC39726), and Europe PMC’s REST service lists its PDF at europepmc.org/articles/PMC39726?pdf=render. This client could not fetch it: both PMC and Europe PMC answered with a Cloudflare challenge page, and Europe PMC has no full-text XML for the scan. |
| LIT-1574 v3 | The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion | Karnkowska et al. (2019). The genome of Monocercomonoides exilis is as complex as other eukaryotes’ and less reduced than some other metamonads’; its nuclear machinery, cytoskeleton, endomembranes and biosynthetic pathways are canonical. The authors find two preadaptations for losing the mitochondrion: the SUF Fe–S system, which replaced the mitochondrial pathway in all examined relatives including some that kept a mitochondrion-related organelle, and the later loss of the glycine cleavage system and SHMT. Mitophagy went with the organelle, and no compensating change was found. | Active — read in full 2026-10-27 (NOTE-1243) from the PubMed Central copy of the version of record (PMC6759080, open access); worth reading as the account of what happened to the rest of a eukaryotic cell when its mitochondrion was lost, which is almost nothing, and of the two preadaptations that emptied the organelle of essential jobs before it went (THEORY-1098). Read it knowing that it is homology searches on a draft genome with most gene lists in supplementary tables, that “no compensating change” is an absence bounded by annotation, that the order of the preadaptations is inferred from relatives, not dated, and that a highly reduced mitosome below microscopic resolution is not excluded. |
| LIT-1585 v2 | Chance and necessity in the evolution of minimal metabolic networks | Pál et al. (2006). Repeatedly simulating successive gene loss on an in silico E. coli metabolic network, with the environment held fixed, gives minimal networks that vary in content by contingency alone but preserve a core metabolism. Simulating each symbiont’s environment predicts the gene content of Buchnera and Wigglesworthia with over 80% accuracy. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1586 v2 | Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas | Łukasik et al. (2018). A single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over four million years, giving complexes of two to six lineages per host. The lineages differ in abundance, size and gene content, and their losses imply extensive sharing of gene products. Together they encode nearly the ancestral gene set. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC5777040) and the publisher’s PDF is at pnas.org/content/pnas/115/2/E226.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1588 v2 | Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes | Timmis, Ayliffe, Huang & Martin (2004). The standard review of endosymbiotic gene transfer: DNA moves from mitochondria and plastids to the nucleus continually and at measurable rates, a minority of transfers become functional nuclear genes whose products are targeted back, and the process has shaped eukaryotic chromosomes. No abstract was seen. The summary is what the review is standardly cited for, and a reading should check it. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1590 v2 | Changes in Endosymbiont Complexity Drive Host-Level Compensatory Adaptations in Cicadas | Campbell et al. (2018). Where Hodgkinia has split into essential lineages of very uneven abundance, rare lineages risk loss at the transmission bottleneck from mother to egg, and a simulation shows the cells needed per egg rising steeply with complexity. Counts in eggs of four cicada species find Sulcia roughly constant and Hodgkinia up to about six times higher in Magicicada septendecim than in a single-lineage species, though only that species differs significantly. Every sampled egg carried every tracked lineage, and the transmission route looks unchanged. The authors read the raised titre as host compensation and a cost of fragmentation, and speculate that it could feed further splitting. | Active — read in full 2026-10-27 (NOTE-1235) from the PubMed Central copy of the version of record (PMC6234865, CC BY 4.0); worth reading as the record’s one documented case of a host compensating for its symbiont’s changes at transmission: cicadas whose Hodgkinia has split into many lineages send more Hodgkinia cells to each egg, not more Sulcia, and every sampled egg carried every tracked lineage (THEORY-1106). Read it knowing that the rise in titre is significant for one species, Magicicada septendecim, of four compared, with five or six eggs each and no phylogenetic control; that the six-lineage species does not differ significantly from single-lineage ones; that lineage presence was tracked by one or two marker genes; and that the order of cause, splitting before titre, is inferred. |
| LIT-1591 v2 | Isolation of an archaeon at the prokaryote–eukaryote interface | Imachi et al. (2020). After 12 years from sampling to culture, an Asgard archaeon related to Lokiarchaeota, Candidatus Prometheoarchaeum syntrophicum MK-D1, was obtained in stable co-culture with a methanogen. It is an anaerobic, extremely slow-growing small coccus that degrades amino acids only in syntrophy, passing hydrogen and formate to partners that can be exchanged, and it has long branching protrusions but no visible internal compartments. From its genome and other Asgard genomes the authors infer that the Asgard ancestor was a partner-dependent amino-acid degrader, and they propose the entangle–engulf–endogenize model of eukaryogenesis as a hypothesis. | Active — read in full 2026-10-27 (NOTE-1238) from the PubMed Central copy of the version of record (PMC7015854, CC BY 4.0); worth reading as the first physiology of an Asgard archaeon, a small, internally simple coccus with branching protrusions that grows only in syntrophy, handing hydrogen and formate to partners that can be exchanged, and for the authors’ inference that the Asgard ancestor was likewise partner-dependent (THEORY-1108). Read it knowing that the organism was grown only in co-culture, never alone; that it is the closest relative of eukaryotes among cultured organisms only; that the ancestral lifestyle is inferred from gene presence in metagenome-assembled genomes; that the entangle–engulf–endogenize model is, in the authors’ words, hypothetical and not definitive; and that the model is not the hydrogen hypothesis, since here the host makes the hydrogen. |
| LIT-1595 v2 | Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry | Pittis & Gabaldón (2016). For 1,078 protein families inferred in the last eukaryotic common ancestor, the branch to the closest prokaryotic relatives, corrected for each family’s rate, is shortest for families of alphaproteobacterial origin and mitochondrial location, longer for other bacterial families, which associate with endomembranes, and longest for archaeal families, which associate with the nucleus. The authors read this as late acquisition of the mitochondrion by a host whose genome already held genes of several bacterial origins, by partners or by transfer. The reading of length as time assumes proportional rates before and after LECA, and the alphaproteobacterial difference from other bacteria is P = 0.044. | Active — read in full 2026-10-27 (NOTE-1240) from the PubMed Central author manuscript (PMC4780264), not the version of record; worth reading as the first proteome-wide test of mitochondrion-early against mitochondrion-late, and for its finding that LECA families sort by origin and cell location (alphaproteobacterial with the mitochondrion, other bacterial with endomembranes, archaeal with the nucleus), with alphaproteobacterial families nearest their prokaryotic relatives (THEORY-1102). Read it knowing that stem length is read as time only under the assumption that rates before and after LECA are proportional; that the alphaproteobacterial difference from other bacteria, on which the chimaeric host turns, is P = 0.044; that stem length also shortens when a closer relative is sampled, as its own Lokiarchaeota control shows; and that it cannot say whether the chimaera came from partners or from gene transfer. |
| LIT-1596 v2 | Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS | Shigenobu et al. (2000). The first complete genome of an obligate insect endosymbiont: Buchnera sp. APS, maternally transmitted in aphid bacteriocytes, has a 640,681-bp chromosome with 583 ORFs and two small plasmids, a subset of E. coli’s gene set reached by loss. It keeps the genes for the amino acids essential to the host and lacks almost all of those for non-essential ones, and uses host-made glutamate and aspartate as precursors, so the two partners’ pathways interlock. It also lacks phospholipid and lipopolysaccharide synthesis, nearly all transcriptional regulators, and recA and uvrABC. The authors infer that it can live only in the bacteriocyte, with membrane lipids perhaps from the host, and compare it to an organelle. All of this is read from gene content. | Active — read in full 2026-10-27 (NOTE-1236) from the publisher’s free PDF of the version of record; worth reading as the first complete genome of an obligate insect endosymbiont, and for its gene-by-gene account of a symbiont that keeps the amino-acid pathways its host lacks, draws precursors from the host, and has lost phospholipid synthesis and nearly all its own regulators (THEORY-1103). Read it knowing that every functional statement is inferred from gene content in one strain, that the host’s dependence is cited from earlier work and maternal transmission stated, neither shown here, and that it names no mechanism of genome reduction: drift and Muller’s ratchet are not in it. |
| LIT-1597 v2 | The hydrogen hypothesis for the first eukaryote | Martin & Müller (1998). Eukaryotes arose from a symbiosis between a strictly hydrogen-dependent, autotrophic archaeal host and a eubacterial symbiont that could respire but produced hydrogen as waste. The host’s dependence on the symbiont’s hydrogen is the selective principle that forged the first eukaryote. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1602 v2 | Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas | Campbell, Łukasik, Simon & McCutcheon (2017). Every Magicicada species harbours Hodgkinia populations of at least twenty genomic circles, 256 in all, with little synteny except between the closest species. Most splitting happened within Magicicada and gives highly variable gene dosages, so Hodgkinia’s degradation has followed different paths in different hosts. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC8879801), the bioRxiv preprint is at biorxiv.org/content/10.1101/199760v1, and the publisher’s free PDF is at cell.com/article/S0960982217313118/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1605 v2 | Host Control of Symbiont Transmission: The Separation of Symbionts Into Germ and Soma | Frank (1996b). A model of hosts that control which symbionts are transmitted, sequestering a germ line of symbionts apart from the somatic ones that serve the host, so as to limit competition among symbiont lineages. No abstract was seen: PubMed’s DOI search returned an unrelated record. The summary is drawn from the title and from what the paper is standardly cited for, and a reading should check it. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1611 v2 | The consequences of genetic drift for bacterial genome complexity | Kuo, Moran & Ochman (2009). Across sequenced bacteria, the genome-wide ratio of replacement to silent substitutions, a measure of how weak purifying selection is, falls strongly as genome size rises. Drift promotes genome reduction in bacteria. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC2720180) and the publisher’s free PDF is at genome.cshlp.org/content/19/8/1450.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1612 v2 | Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia | Campbell et al. (2015). In the long-lived periodical cicada Magicicada tredecim, the Hodgkinia genome has fragmented into many chromosomes or genomes, some in discrete cells, together about 1.1 Mb, nearly ten times the hypothetical single ancestor. The authors tested whether long host life cycles enable the splitting, and compare the result with organelle genome fragmentation. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC4547289), and the publisher’s version is at pnas.org/doi/pdf/10.1073/pnas.1421386112. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1616 v2 | Deletional bias and the evolution of bacterial genomes | Mira, Ochman & Moran (2001). Bacterial genomes stay small and free of nonfunctional DNA because deletions outnumber insertions. In obligate parasites and symbionts, where selection is too weak to maintain genes, genome reduction comes from relaxed selection on gene function, not from selection to lose DNA. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1617 v2 | Host–symbiont conflict over the mixing of symbiotic lineages | Frank (1996a). Symbionts favour dispersal to escape competition with relatives; mixing of symbiont lineages breeds competition and virulence; hosts are favoured to restrict mixing. But a host modifier that reduces mixing spreads only when it is directly associated with reduced virulence, a condition taken from Hoekstra’s work on uniparental inheritance and extended across symbiont life histories. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1621 v2 | Chromatophore Genome Sequence of Paulinella Sheds Light on Acquisition of Photosynthesis by Eukaryotes | Nowack, Melkonian & Glöckner (2008). The chromatophore genome of Paulinella chromatophora, from a primary endosymbiosis independent of and more recent than the plastids’, is 1.02 Mb with 867 protein-coding genes, 26% of a free-living relative’s. Pseudogenes show reduction still under way. It keeps photosynthesis genes and lacks essential amino-acid and cofactor pathways, so the chromatophore depends wholly on its host. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S0960982208002376/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1929 | Three Problems for the Mutual Manipulability Account of Constitutive Relevance in Mechanisms | Leuridan (2012), DOI-10.1093/bjps/axr036. By its abstract, two conceptual problems for Craver’s mutual manipulability account (constitutive relevance threatens to imply causal relevance; parthood as spatiotemporal inclusion meets a counterexample from endosymbiosis) and one methodological one (experimental underdetermination). Unread: no lawful copy reached. The works read with it report that it argues, under Woodward’s interventionism, that constitutive relevance is a form of bidirectional causal relevance. | Unavailable — Sought 2026-11-01 and not reached. The publisher’s copy (OUP, doi 10.1093/bjps/axr036) is paywalled. The one repository copy OpenAlex lists, Ghent University’s Biblio (record 2116239, file 6770914), is marked “restricted” in Biblio’s own metadata and redirected this client to an institutional sign-in, so it is not a free copy. No PhilSci-Archive or PhilArchive deposit was found. Known here only from its abstract and from what the three works read with it say of it (NOTE-1493, NOTE-1490, NOTE-1494). It stays Unavailable until a copy is supplied, not on merit. |
| LIT-2001 v2 | The Major Transitions in Evolution | Maynard Smith & Szathmáry (1995; OUP edition 1997), doi:10.1093/oso/9780198502944.001.0001. Registered unread from the owner’s synthesis of 2026-11-04, which names it as the origin of major evolutionary transitions theory and that theory as the bridge between coexistence, endosymbiosis, game theory and morality. The record has held the theory only through Okasha’s reading of it (LIT-749, NOTE-586). | Unavailable — searched 2026-11-04 for a lawful full text, and none was found, so it is not read and no NOTE is filed. OpenAlex (no email address sent, ADR-008) reports the book closed, with no repository holding a full text. Its only location is Oxford Academic, which is paywalled. The companion Nature article (Szathmáry and Maynard Smith 1995, doi:10.1038/374227a0) is closed as well. A copy the owner supplies returns it to reading. |