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1:	Huang J, Mullapudi N, Lancto CA, Scott M, Abrahamsen MS, Kissinger JC.
	Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol. 2004;5(11):R88. Epub 2004 Oct 19. PMID: 15535864 [PubMed - indexed for MEDLINE]

2:	Patron NJ, Rogers MB, Keeling PJ.
	Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates. Eukaryot Cell. 2004 Oct;3(5):1169-75. PMID: 15470245 [PubMed - indexed for MEDLINE]

3:	Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D.
	A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol. 2004 May;21(5):809-18. Epub 2004 Feb 12. PMID: 14963099 [PubMed - indexed for MEDLINE]

4:	Harper JT, Keeling PJ.
	Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol. 2003 Oct;20(10):1730-5. Epub 2003 Jul 28. PMID: 12885964 [PubMed - indexed for MEDLINE]

5:	Hannaert V, Saavedra E, Duffieux F, Szikora JP, Rigden DJ, Michels PA, Opperdoes FR.
	Plant-like traits associated with metabolism of Trypanosoma parasites. Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1067-71. Epub 2003 Jan 27. PMID: 12552132 [PubMed - indexed for MEDLINE]

6:	Dale C, Plague GR, Wang B, Ochman H, Moran NA.
	Type III secretion systems and the evolution of mutualistic endosymbiosis. Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12397-402. Epub 2002 Sep 4. PMID: 12213957 [PubMed - indexed for MEDLINE] Items 1 - 3 of 3 1: Gerbod D, Edgcomb VP, Noel C, Vanacova S, Wintjens R, Tachezy J, Sogin ML, Viscogliosi E. Phylogenetic relationships of class II fumarase genes from trichomonad species.Mol Biol Evol. 2001 Aug;18(8):1574-84.PMID: 11470849 [PubMed - indexed for MEDLINE] 2: Fast NM, Kissinger JC, Roos DS, Keeling PJ. Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids.Mol Biol Evol. 2001 Mar;18(3):418-26.PMID: 11230543 [PubMed - indexed for MEDLINE] 3: Henze K, Badr A, Wettern M, Cerff R, Martin W. A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution.Proc Natl Acad Sci U S A. 1995 Sep 26;92(20):9122-6.PMID: 7568085 [PubMed - indexed for MEDLINE]

Division of Endosymbiotic Organelles

ScienceWeek: "Like their free-living ancestors, both chloroplasts and mitochondria divide. Organelle division, segregation, and growth are often uncoupled from the cell division cycle, indicating that organelle and cell division are independent processes. Division of mitochondria and chloroplasts is orchestrated by multicomponent protein machines that assemble and drive the constriction and fission of the organellar membranes. Because both organelles are surrounded by inner and outer membranes that differ in composition, their division machines must accomplish the synchronized constriction of both membranes, the subsequent fusion of the four lipid bilayers, the final separation of the two daughter organelles, and possibly the resolution of the fused membranes back into two discrete bilayers."

ScienceWeek

ScienceWeek: "Schimper in 1885 (2) suggested that chloroplasts were derived from symbiotic microorganisms, and Mereschkowsky in 1905 argued more extensively for the development of different
types of chloroplasts from different types of cyanobacteria (3,4). Much later, the role of bacteria in symbiogenesis was championed by Margulis (5). Many scientists have provided the crucial data that convincingly show the close relationship between chloroplasts and cyanobacteria, including similar
ribosomes, RNA polymerases, and other cellular machinery (briefly reviewed in ref.1). Current research suggests that the cyanobacterial/eukaryote symbiosis occurred only once but diverged rapidly to three major lineages: the greens, the reds, and the rather odd lineage called glaucocystophytes. The greens
are the green algal/land-plant group. The reds are the red algae, now producing much of the agarose consumed by molecular biology labs.

References (abridged):
1. Martin, W. , Rujan, T. , Richly, E. , Hansen, A. ,Cornelsen, S. , Lins, T. , Leister, D. , Stoebe, B. , Hasegawa,M. & Penny, D. (2002) Proc. Natl. Acad. Sci. USA 99, 12246-12251.
2. Schimper, A. F. W. (1885) Jahrbüecher füer WissenschaftlicheBotanik 16, 1-247.
3. Mereschkowsky, C. (1905) Biol. Zent. Bl. 25, 593-604.
4. Martin, W. & Kowallik, K. V. (1999) Eur. J. Phycol. 34,287-295.
5. Margulis, L. (1981) Symbiosis in Cell Evolution: Life andIts Environment on the Early Earth (Freeman, San Francisco)."

New Cellular Evolution Theory Rejects Darwinian Assumptions

New Cellular Evolution Theory Rejects Darwinian Assumptions: "Cellular evolution, he argues, began in a communal environment in which the loosely organized cells took shape through extensive horizontal gene transfer. Such a transfer previously had been recognized as having a minor role in evolution, but the arrival of microbial genomics, Woese says, is shedding a more accurate light. Horizontal gene transfer, he argues, has the capacity to rework entire genomes. With simple primitive entities this process can 'completely erase an organismal genealogical trace.' "

MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA

Nature Reviews Microbiology - Reviews: "Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent. Transformation involves the release of naked DNA followed by uptake and recombination. Homologous recombination and DNA-repair processes normally limit this to DNA from similar bacteria. However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition.

"
Christopher M. Thomas & Kaare M. Nielsen MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA Nature Reviews Microbiology 3, 711-721 (2005); doi:10.1038/nrmicro1234

A molecular timeline for the origin of photosynthetic eukaryotes.

Entrez PubMed: "The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating algal origin is, however, frustrated by a meager fossil record. We generated a plastid multi-gene phylogeny with Bayesian inference and then used maximum likelihood molecular clock methods to estimate algal divergence times. The plastid tree was used as a surrogate for algal host evolution because of recent phylogenetic evidence supporting the vertical ancestry of the plastid in the red, green, and glaucophyte algae. Nodes in the plastid tree were constrained with six reliable fossil dates and a maximum age of 3,500 MYA based on the earliest known eubacterial fossil. Our analyses support an ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae (i.e., red, green, and glaucophyte algae plus land plants) from the opisthokonts sometime before 1,558 MYA. The split of the red and green algae is calculated to have occurred about 1,500 MYA, and the putative single red algal secondary endosymbiosis that gave rise to the plastid in the cryptophyte, haptophyte, and stramenopile algae (chromists) occurred about 1,300 MYA. These dates, which are consistent with fossil evidence for putative marine algae (i.e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution."

Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D. A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol. 2004 May;21(5):809-18. Epub 2004 Feb 12.

Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families.

Entrez PubMed: "Aphids (superfamily Aphidoidea) contain eubacterial endosymbionts localized within specialized cells (mycetocytes). The endosymbionts are essential for the survival of the aphid hosts. Sequence analyses of the 16S rRNAs from endosymbionts of 11 aphid species from seven tribes and four families have indicated that the endosymbionts are monophyletic. Furthermore, phylogenetic relationships within the symbiont clade parallel the relationships of the corresponding aphid hosts. Our findings suggest that this endocytobiotic association was established in a common ancestor of the four aphid families with subsequent diversification into the present species of aphids and their endosymbionts."

Munson MA, Baumann P, Clark MA, Baumann L, Moran NA, Voegtlin DJ, Campbell BC. Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families. J Bacteriol. 1991 Oct;173(20):6321-4.

Free Full Text Article 1991

A secondary symbiosis in progress?

Entrez PubMed: "Algae have acquired plastids by developing an endosymbiotic relationship with either a cyanobacterium (primary endosymbiosis) or other eukaryotic algae (secondary endosymbiosis). We report a protist, which we tentatively refer to as Hatena, that hosts an endosymbiotic green algal partner but inherits it unevenly. The endosymbiosis causes drastic morphological changes to both the symbiont and the host cell architecture. This type of life cycle, in which endosymbiont integration has only partially converted the host from predator to autotroph, may represent an early stage of plastid acquisition through secondary symbiosis."

Okamoto N, Inouye I. A secondary symbiosis in progress? Science. 2005 Oct 14;310(5746):287.

You can find a good image here, and a concise commentary on the Science article here.

Gene switching in Amoeba proteus caused by endosymbiotic bacteria -- Jeon and Jeon 117 (4): 535 -- Journal of Cell Science

Gene switching in Amoeba proteus caused by endosymbiotic bacteria -- Jeon and Jeon 117 (4): 535 -- Journal of Cell Science: "The xD strain of Amoeba proteus arose from the D strain by spontaneous infection of X-bacteria (Jeon and Lorch, 1967), and xD amoebae are now dependent on their symbionts for survival. Each xD amoeba contains about 42,000 symbionts within symbiosomes, and established xD amoebae die if their symbionts are removed. Newly infected xD amoebae become dependent on X-bacteria within 18 months (about 200 cell generations) (Jeon and Ahn, 1978)...." Jeon TJ, Jeon KW. Gene switching in Amoeba proteus caused by endosymbiotic bacteria. J Cell Sci. 2004 Feb 1;117(Pt 4):535-43. Epub 2004 Jan 6.

Also: Free Full Text articles bold
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Evolution of flagella

Evolution of flagella - Wikipedia, the free encyclopedia: "There are two competing groups of models for the evolutionary origin of the eukaryotic flagellum (referred to as a cilium below to distinguish it from its bacterial counterpart)."

Shaping the mitochondrial proteome.

Entrez PubMed: "Mitochondria are eukaryotic organelles that originated from a single bacterial endosymbiosis some 2 billion years ago. The transition from the ancestral endosymbiont to the modern mitochondrion has been accompanied by major changes in its protein content, the so-called proteome. These changes included complete loss of some bacterial pathways, amelioration of others and gain of completely new complexes of eukaryotic origin such as the ATP/ADP translocase and most of the mitochondrial protein import machinery. This renewal of proteins has been so extensive that only 14-16% of modern mitochondrial proteome has an origin that can be traced back to the bacterial endosymbiont. The rest consists of proteins of diverse origin that were eventually recruited to function in the organelle. This shaping of the proteome content reflects the transformation of mitochondria into a highly specialized organelle that, besides ATP production, comprises a variety of functions within the eukaryotic metabolism. Here we review recent advances in the fields of comparative genomics and proteomics that are throwing light on the origin and evolution of the mitochondrial proteome."

Gabaldon T, Huynen MA. Shaping the mitochondrial proteome. Biochim Biophys Acta. 2004 Dec 6;1659(2-3):212-20.

The apicoplast: a review of the derived plastid of apicomplexan parasites.

Entrez PubMed: "The apicoplast is a plastid organelle, homologous to chloroplasts of plants, that is found in apicomplexan parasites such as the causative agents of Malaria Plasmodium spp. It occurs throughout the Apicomplexa and is an ancient feature of this group acquired by the process of endosymbiosis. Like plant chloroplasts, apicoplasts are semi-autonomous with their own genome and expression machinery. In addition, apicoplasts import numerous proteins encoded by nuclear genes. These nuclear genes largely derive from the endosymbiont through a process of intracellular gene relocation. The exact role of a plastid in parasites is uncertain but early clues indicate synthesis of lipids, heme and isoprenoids as possibilities. The various metabolic processes of the apicoplast are potentially excellent targets for drug therapy."

Waller RF, McFadden GI. The apicoplast: a review of the derived plastid of apicomplexan parasites. Curr Issues Mol Biol. 2005 Jan;7(1):57-79.

Diatom genomics: genetic acquisitions and mergers.

Entrez PubMed: "Diatom algae arose by two-step endosymbiosis. The complete genome of the diatom Thalassiosira pseudonana has now been sequenced, allowing us to reconstruct the remarkable intracellular gene transfers that occurred during this convoluted cellular evolution."

Nisbet RE, Kilian O, McFadden GI. Diatom genomics: genetic acquisitions and mergers. Curr Biol. 2004 Dec 29;14(24):R1048-50.

Possible evolutionary significance of spirochaetes.

Entrez PubMed: "Large symbiotic spirochaetes of the family Pillotaceae (e.g. pillotinas) are found in dry wood and subterranean termites (Hollande & Garagozlou 1967). These morphologically distinctive spirochaetes comprise several genera. Some of them contain microtubules within their protoplasmic cylinders. They demonstrate a variety of relations with their termite and protist hosts. Some are free-living within the lumen of the intestine, some tend to be associated with filamentous and other bacteria, some are found regularly coursing between the numerous undulipodia ( = eukaryotic flagella, cilia, and other (9 + 2) organelles of motility) of hypermastigotes and polymastigotes. Still other smaller termite spirochaetes are regularly attached to protists via specialized attachment sites. Some even form motility symbiosis with their host protists. The analogy between the behaviour of host-associated spirochaetes and the possible steps in the origin of the undulipodia and mitotic system of eukaryotes is discussed briefly."

Margulis L, Chase D, To LP. Possible evolutionary significance of spirochaetes. Proc R Soc Lond B Biol Sci. 1979 Apr 11;204(1155):189-98.

Undulipodia, flagella and cilia.

Entrez PubMed: "The term flagella is ambiguous. It refers to bacterial structures composed of flagellin protein and to eukaryotic structures composed of microtubule proteins and ATPase (tubulin and dynein). The fact that cilia are nearly identical to eukaryotic flagella and have nothing in common with prokaryotic flagella is not apparent from the terminology. It is proposed that the 30-year old suggestion of Smagina and reiterated by Kuznicki and others, be adopted: that cilia and eukaryotic flagella be called 'undulipodia.' The term flagella ought to be restricted to prokaryotic organelles, bacterial flagella and spirochaete axial filaments: solid structures composed of flagellin which protrude through the plasma membrane and lack intrinsic motility throughout their length. Undulipodia are defined as intrinsically motile intracellular structures showing a 9-fold symmetry in the pattern of arrangement of 24 nm diameter microtubules. They are limited to eukaryotes, members of the protoctist, animal and plant kingdoms."

Margulis L. Undulipodia, flagella and cilia. Biosystems. 1980;12(1-2):105-8.

Cell symbiosis [correction of symbioisis] theory: status and implications for the fossil record.

Entrez PubMed: "Recent geological treatises have presented three alternative models of the origins of eukaryotes as if they merited equal treatment. However, modern biological techniques, especially nucleic acid and protein sequencing, have clearly established the validity of the symbiotic theory of the origin of eukaryotic organelles. The serial endosymbiotic theory in its most extreme form states that three classes of eukaryotic cell organelles (mitochondria, plastids and undulipodia) originated as free-living bacteria (aerobic respirers, phototrophic bacteria and spirochetes respectively) in association with hosts that become the nucleocytoplasm (Thermoplasma-like archaebacterial hosts). Molecular biological information, primarily derived from ribosomal RNA nucleotide sequencing studies leads to the conclusion that the symbiotic origin theory for both mitochondria and plastids has been proven. The probability of an ancestral archaebacterial-Thermoplasma-like host for the nucleocytoplasm has been rendered more likely by discoveries by Dennis Searcy and his colleagues and Carl Woese and his colleagues. The most equivocal postulate of the symbiotic theory, the origin of undulipodia (cilia and other organelles of motility that develop from kinetosomes is under investigation now. The status of these postulates, as well as their implications for the fossil record, is briefly summarized here."

Margulis L, Stolz JF. Cell symbiosis [correction of symbioisis] theory: status and implications for the fossil record. Adv Space Res. 1984;4(12):195-201.

Symbiosis as a mechanism of evolution: status of cell symbiosis theory.

Entrez PubMed: "Several theories for the origin of eukaryotic (nucleated) cells from prokaryotic (bacterial) ancestors have been published: the progenote, the direct filiation and the serial endosymbiotic theory (SET). Compelling evidence for two aspects of the SET is now available suggesting that both mitochondria and plastids originated by symbioses with a third type of microbe, probably a Thermoplasma-like archaebacterium ancestral to the nucleocytoplasm. We conclude that not enough information is available to negate or substantiate another SET hypothesis: that the undulipodia (cilia, eukaryotic flagella) evolved from spirochetes. Recognizing the power of symbiosis to recombine in single individual semes from widely differing partners, we develop the idea that symbiosis has been important in the origin of species and higher taxa. The abrupt origin of novel life forms through the formation of stable symbioses is consistent with certain patterns of evolution (e.g punctuated equilibria) described by some paleontologists."

Margulis L, Bermudes D. Symbiosis as a mechanism of evolution: status of cell symbiosis theory. Symbiosis. 1985;1:101-24.

Early evolution of microtubules and undulipodia.

Entrez PubMed: "A critique of both autogeneous and symbiotic hypotheses for the origin of microtubules and cilia and eukaryotic flagella (undulipodia) is presented. It is proposed that spirochetes provided the ancient eukaryotic cell with microtubules twice; cytoplasmic microtubules originated from phagocytosed spirochetes whereas axopodial tubules of undulipodia were transformed from ectosymbiotic spirochetes. A role in transport for microtubules in spirochetes together with a detailed scenario by which free-living spirochetes attached as ectosymbionts and subsequently differentiated into undulipodia is outlined. A mechanism for the continuity of motility in the form of 'training' of the novel microtubular axoneme by the ancient spirochete motility apparatus is proposed. Transitional states (missing links) are unlikely to have survived. Constraints regarding the nature of the host cell are discussed. A corresponding flowchart of the early evolution of eukaryotes is presented in which plastids and mitochondria are polyphyletic in their origins."

Szathmary E. Early evolution of microtubules and undulipodia. Biosystems. 1987;20(2):115-31.

Kingdom Animalia: the zoological malaise from a microbial perspective.

Entrez PubMed: "Pain and cognitive dissonance abounds amongst biologists: the plant-animal, botany-zoology wound has nearly healed and the new gash--revealed by department and budget reorganizations--is 'molecular' vs. 'organismic' biology. Here I contend that resolution of these tensions within zoology requires that an autopoietic-gaian view replace a mechanical-neodarwinian perspective; in the interest of brevity and since many points have been discussed elsewhere, rather than develop detailed arguments I must make staccato statements and refer to a burgeoning literature. The first central concept is that animals, all organisms developing from blastular embryos, evolved from single protist cells that were unable to reproduce their undulipodia. The second points to the usefulness of recognizing the analogy between cyclically established symbioses and meiotic sexuality."

Margulis L. Kingdom Animalia: the zoological malaise from a microbial perspective. Am Zool. 1990;30:861-75.

Search for eukaryotic motility proteins in spirochetes: immunological detection of a tektin-like protein in Spirochaeta halophila.

Entrez PubMed: "The serial endosymbiotic theory (SET) for the spirochete origin of undulipodia (cilia and eukaryotic flagella) predicts that a greater number of axonemal proteins will show homology to spirochete than to other bacterial proteins. To continue testing, the SET proteins associated with eukaryotic motility (tektin, centrin and calmodulin) were sought in Spirochaeta halophila. Western blot immunological detection techniques (for tektin and centrin) and two-dimensional gel analysis (for calmodulin) were used. Tektins are filamentous proteins extending the length of the axoneme in sperm tails and other undulipodia. Whole cell extracts of S. halophila were probed with antibodies made against three sea urchin (Lytechinus pictus) sperm axonemal tektins (tektins A, B, and C). In the spirochetes, one tektin-like protein was detected as a band on Western blots (a C tektin.) An antibody made against Lytechinus pictus sperm tail axonemes, affinity-purified against the C tektin of another sea urchin, Stronglyocentrotus purpuratus, bound to a 30 kDa protein from Spirochaeta halophila. The C tektin epitope was not detected in Escherichia coli. Both the poly- and monoclonal anti-centrin antibodies cross-reacted with multiple proteins in the control alga (Tetraselmis striata) and in the putatively negative control bacterium E. coli. No cross reaction was seen between any anti-centrin antibody and S. halophila. Neither did a two-dimensional gel analysis reveal the presence of calmodulin in these spirochetes or in the two other prokaryotes tested (Spiroplasma citri, Acholeplasma laidlawii). Although neither centrin nor calmodulin were detected, a 30 kDa tektin-like protein apparently is present in these spirochetes."

Barth AL, Stricker JA, Margulis L. Search for eukaryotic motility proteins in spirochetes: immunological detection of a tektin-like protein in Spirochaeta halophila. Biosystems. 1991;24(4):313-9.

On the origin of mitosing cells. 1967

Entrez PubMed: "A theory of the origin of eukaryotic cells ('higher' cells which divide by classical mitosis) is presented. By hypothesis, three fundamental organelles: the mitochondria, the photosynthetic plastids and the (9+2) [9(2)+2] basal bodies [kinetosomes] of flagella [undulipodia] were themselves once free-living (prokaryotic) cells. The evolution of photosynthesis under the anaerobic [anoxic] conditions of the early atmosphere to form anaerobic bacteria, photosynthetic bacteria and eventually blue-green algae (and protoplastids) is described. The subsequent evolution of aerobic metabolism in prokayotes to form aerobic bacteria (protoflagella [undulipodia] and protomitochondria) presumably occurred during the transition to the oxidizing atmosphere. Classical mitosis evolved in protozoan-type cells millions of years after the evolution of photosynthesis. A plausible scheme for the origin of classical mitosis in primitive amoeboflagellates [amoebomastigotes] is presented. During the course of the evolution of mitosis, photosynthetic plastids (themselves derived from prokaryotes) were symbolically acquired by some of these protozoans to form the ['eukaryotic' deleted] algae and the green plants. The cytological, biochemical and paleontological evidence for this theory is presented, along with suggestions for further possible experimental verification. The implications of this scheme for the systematics of the lower [smaller] organisms is discussed."

Sagan L. On the origin of mitosing cells. 1967 J NIH Res. 1993 Mar;5(3):65-72.