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).
6 of 191 CASE documents. Back to the full index.
| # | Title | Summary | Status |
|---|---|---|---|
| CASE-167 v2 | The nitroplast: UCYN-A, a streamlined nitrogen-fixing cyanobacterium in a marine alga, whose division is coupled to the host’s and which imports host-encoded proteins, reclassified as an early-stage organelle in 2024 | Candidatus Atelocyanobacterium thalassa (UCYN-A), a metabolically 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. Coale et al. call it an early-stage organelle, the nitroplast (LIT-1562). Used as the case where the line between endosymbiont and organelle is drawn by stated criteria. | Proposed |
| CASE-168 v2 | Monocercomonoides: a eukaryote that lost its mitochondrion entirely after the organelle’s essential jobs were removed in steps, its Fe–S cluster assembly taken over by a bacterial-type SUF system that its relatives share and its glycine cleavage system lost, and kept canonical eukaryotic complexity | The oxymonad Monocercomonoides lacks all hallmark mitochondrial proteins; its mitochondrial iron–sulfur cluster pathway was replaced by a cytosolic SUF system taken from bacteria, and the loss was secondary (LIT-1567). Its genome otherwise shows canonical eukaryotic complexity (LIT-1574). Used as the negative control: loss of function dissolving an integrated compartment, not deepening dependence on it. | Proposed |
| CASE-171 v3 | Mealybugs, Tremblaya and Moranella: a bacterium inside a bacterium inside an insect, amino-acid pathways patched together from three genomes and genes transferred from other bacteria, and an inner symbiont replaced several times while the transferred genes stayed | In the mealybug Planococcus citri, Moranella lives inside Tremblaya. Essential amino-acid pathways need gene products from both bacteria and the insect (LIT-1565). At least 22 genes the insect acquired from other bacteria, none from Tremblaya, fill symbiont gaps (LIT-1569), and the inner symbiont has been replaced several times across mealybugs while those genes persisted (LIT-1572). Used as the case where function is distributed across nested boundaries and constituent lineages turn over. | Proposed |
| CASE-173 v3 | Aphids and Buchnera: an obligate nutritional symbiosis in which neither partner reproduces alone, and the symbiont’s genome reduced to a seventh of E. coli’s | Buchnera lives in aphid bacteriocytes and is passed from mother to egg. Its 641-kb genome keeps the pathways for the amino acids its host needs and has lost most else (LIT-1596); its genes evolve fast and A+T-biased under Muller’s ratchet (LIT-1573). The record’s reading of Wilson and Barker reports Godfrey-Smith placing the pair as both an organism and a Darwinian individual (NOTE-114). Used as the case of high mutual dependence and high reproductive cohesion reached through reduction, with no gene transfer to the host reported in the works it rests on. | Proposed |
| CASE-174 v2 | Paulinella chromatophora: a photosynthetic organelle in the making, from an endosymbiosis independent of the plastids’, its genome reduced to about a third of its coding capacity, and hundreds of host proteins imported into it, most encoded by the host’s own genes rather than transferred from the symbiont | The amoeba Paulinella chromatophora’s chromatophores descend from a cyanobacterium taken up about 60 million years ago, independently of the plastids. Their genome kept 26% of a free-living relative’s genes and lacks essential pathways (LIT-1621). Genes transferred to the nucleus make proteins that are imported into the chromatophores (LIT-1557), and import is reviewed across systems in LIT-1560. Used as the case where host control emerges by gene transfer and import. | Proposed |
| CASE-177 v2 | Hodgkinia in cicadas: one endosymbiont splitting into two to dozens of interdependent lineages, with near-complementary gene sets, idiosyncratic fragmentation in Magicicada, and hosts transmitting up to six times as many cells to keep every lineage | In some Tettigades cicadas, the endosymbiont Hodgkinia split into two cell lineages with almost perfectly complementary gene sets, the functionality of one (LIT-1563), and it has done so at least six times in the genus (LIT-1586). In Magicicada it fragmented into twenty or more genomic circles per species (LIT-1612, LIT-1602). Hosts compensate by transmitting more cells to each egg (LIT-1590). Used as the case where dependence and the number of parts grow with no new collective function, and the host pays. | Proposed |