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Eukaryotes' Closest Relatives?

The authors did ancestral-state reconstructions with several high-level phylogenies, since that is still not very well-settled. In their diagram, they have

LECA -- mito - multi - nopp - closed - sex
  • Discoba (in Excavata) -- mito - ? - ? - ? - sex
  • Metamonada (in Excavata) -- h2some - multi - ? - closed - sex
  • Amorphea / Obazoa / Opimoda -- mito - multi - ? - closed - sex
    • Amoebozoa -- mito - multi - pp - closed - sex
    • Opisthokonta -- mito - multi - nopp - closed - sex
      • Fungi -- mito - multi - nopp - closed - sex
      • Metazoa (animals) --mito - multi - ? - ? - sex
  • Diaphoretickes / Diphoda -- mito - multi - nopp - closed - sex
    • Cryptista (in Hacrobia) -- mito - nomulti - nopp - ? - nosex
    • Haptista (in Hacrobia) -- mito - nomulti - nopp - ? - nosex
    • Archaeplastida -- mito - ? - nopp - ? - sex
      • Glaucophyta -- mito - multi - nopp - open - nosex
      • Rhodophyta (red algae) -- mito - nomulti - nopp - closed - sex
      • Chloroplastida (green algae) -- mito - nomulti - nopp - ? - sex
        • Chlorophyta -- mito - nomulti- nopp - closed - sex
        • Streptophyta (incl. land plants) -- mito - nomulti - nopp - open - sex
    • SAR clade -- mito - multi - nopp - closed - sex
      • Rhizaria -- mito - multi - (pp) - closed - sex
      • SA clade -- mito - multi - nopp - closed - sex
        • Alveolata -- mito - multi - nopp - closed - sex
        • Stramenopiles -- mito - multi - nopp - closed - sex

    With ancestral-state reconstruction, the authors found that the last eukaryotic common ancestor (LECA) was multinucleate, as were all the supergroups but Hacrobia. The LECA also had mitochondria, sex (meiosis-cell-fusion cycle), and closed division. It did not have the authors' restriction of polyploidy, however, meaning that it did ordinary reproduction as a haploid. Ordinary reproduction as a diploid is something that was invented several times, as was open division, and reduction of mitochondria to hydrogenosomes and the like. The LECA did not have plastids, something evident from their scattered distribution.
 
The authors discussed "Conflict and Co-operation in a Syncytial LECA" then "Origins of Flagellated Eukaryotes".

As to cooperation, in a multinucleate cell, one nucleus can fill in for another one if some of its genetic material become damaged or deleted.

The authors conclude that the LECA had a single-nucleus flagellated phase that alternated with a multinuclear phase as a way of distributing itself, and they propose that the eukaryote flagellum is an extension of a bit of cytoskeleton outside of the cell body.
 
Returning to this issue, i've found some more papers on the origin and early history of eukaryotes.

Global patterns and rates of habitat transitions across the eukaryotic tree of life | Nature Ecology & Evolution - transitions between saltwater (marine), freshwater, and soil environments, mainly examining environment microbes. There was very little overlap between marine and non-marine organisms, but there was some between freshwater and soil ones, and some more overlap between illuminated (euphotic) and always-dark (aphotic) marine ones.

Nevertheless, there was plenty of evidence of transitions in both directions.

Among familiar species, land plants originated from some freshwater green algae, and the ancestral animals were marine.
Overall, the predicted ancestral habitats of most major eukaryotic clades match their current preferred habitat: this is, for example, the case for all amoebozoan lineages, radiolarians, dinoflagellates and foraminiferans.
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TSAR (telonemids, stramenopiles, alveolates, rhizarians) is ancestrally marine, and most of these groups are mostly marine. Alveolates are ancestrally non-marine, though some of them, dinoflagellates, are marine.

Amorphea is ancestrally non-marine: Obazoa (animals, fungi) and Amoebozoa. Also Excavata.

The Last Eukaryotic Common Ancestor (LECA) was likely non-marine.

"Furthermore, other key early eukaryotic innovations, such as the origin of the plastid organelles, have been inferred to have occurred around 2 billion years ago in low-salinity habitats."

Fungi seem to be very good at colonizing different salinities, though they are primarily non-marine.
 
Ancestral State Reconstructions Trace Mitochondria But Not Phagocytosis to the Last Eukaryotic Common Ancestor | Genome Biology and Evolution | Oxford Academic
We employed a novel phylogenomic test that summarizes ASR across trees which reconstructs a last eukaryotic common ancestor that possessed mitochondria, was multinucleated, lacked plastids, and was non-phagotrophic as well as non-phagocytic. This indicates that both phagocytosis and phagotrophy arose subsequent to the origin of mitochondria, consistent with findings from comparative physiology. Furthermore, our ASRs uncovered multiple origins of phagocytosis and of phagotrophy across eukaryotes, indicating that, like wings in animals, these traits are useful but neither ancestral nor homologous across groups. The data indicate that mitochondria preceded the origin of phagocytosis, such that phagocytosis cannot have been the mechanism by which mitochondria were acquired.
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ASR = ancestral state reconstruction
phagocytosis = engulfing food items, like bacteria
phagotrophy = living off food acquired with phagocytosis, as opposed to osmotrophy, soaking it up from one's environment, sometimes digested externally with released enzymes.

The authors analyzed the last two separately.

The authors got around the problem of what is the exact phylogeny by using 1789 phylogenies found with phylogeny algorithms.

The broader significance of these findings is that the origin of mitochondria can be attributed to a fateful case of microbial symbiosis but cannot be attributed to a fateful case of indigestion.
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Microbial predators form a new supergroup of eukaryotes | Nature
Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators—Nebulidia and Nibbleridia—that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys.
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Timing the origin of eukaryotic cellular complexity with ancient duplications | Nature Ecology & Evolution
By relatively timing events using phylogenetic distances, we inferred that duplications in cytoskeletal and membrane-trafficking families were among the earliest events, whereas most other families expanded predominantly after mitochondrial endosymbiosis. Altogether, we infer that the host that engulfed the proto-mitochondrion had some eukaryote-like complexity, which drastically increased upon mitochondrial acquisition. This scenario bridges the signs of complexity observed in Asgard archaeal genomes to the proposed role of mitochondria in triggering eukaryogenesis.
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Mitochondria might have done that by providing more energy, and thus more ability to build a complicated internal structure.

Origin and Early Evolution of the Eukaryotic Cell | Annual Reviews
 
A robustly rooted tree of eukaryotes reveals their excavate ancestry | Nature
Using mitochondrial proteins
Our analyses of a 100 taxon × 93 protein dataset with state-of-the-art phylogenetic models and an extensive evaluation of alternative hypotheses show that the eukaryotic root lies between two multi-supergroup assemblages: ‘Opimoda+’ and ‘Diphoda+’. This position is consistently supported across different models and robustness analyses. Notably, groups containing ‘typical excavates’ are placed on both sides of the root, suggesting the complex features of the ‘excavate’ cell architecture trace back to LECA.
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These taxa:

Amorphea ~ Unikonts ~ Opimoda ~ Scotokaryotes
  • Obazoa
    • Opisthokonts
      • Animals, choanoflagellates
      • Fungi
  • Amoebozoa - amoebas
Bikonta ~ Diphoda
  • Diaphoretickes
    • CAM
      • Archaeplastida - green algae (land plants), red algae
    • TSAR
      • Stramenopiles - diatoms, oomycetes, kelp
      • Alveolata - ciliates, apicomplexans, dinoflagellates
      • Rhizaria - foraminiferans, radiolarians
 
An excavate root for the eukaryote tree of life

The "Excavata" are protists with a feeding groove, thus their name.  Excavata

Allowing for variable rates of evolution poses a problem for phylogeny work: it becomes difficult to find the root of the phylogeny tree. The usual solution is to use an outgroup, some sequence from an organism outside the group that one is studying. This has interesting consequences for eukaryotes as a whole.
Because over half of the universal eukaryotic genes are derived from Bacteria or Archaea (10), the eukaryote tree can potentially be rooted with either archaeal or bacterial homologs. However, these genes are quite different. Universal eukaryotic genes of bacterial ancestry (euBacs) tend to be associated with mitochondria-related functions, while genes of archaeal ancestry (euArcs) tend to be involved in information processing such as replication, transcription, translation and protein modification, sorting, and degradation (10).
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From euBacs, the authors earlier found a tree with Discoba branching off first, with Amorphea and Diaphoretickes then branching off from each other. Discoba is a taxon in "Excavata", and it includes Euglena and trypanosomes. Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models | Systematic Biology | Oxford Academic

So they looked at euArcs in this paper. They found branching order
  • Parabasalia - anaerobic
  • Fornicata - anaerobic
  • Preaxostyla - anaerobic
  • Discoba - ancestrally aerobic, with mitochondria
  • Neokaryotes: Amorphea, Diaphoretickes - ancestrally aerobic, with mitochondria
The first four are in  Excavata
  • Parabasalia - no mitochondria, but instead hydrogenosomes, mitochondrion-like structures that release hydrogen in their energy metabolism without combining it with oxygen.
  • Preaxostyla - some of them have hydrogenosome-like structures.

The authors propose an earlier symbiosis with a gamma- or delta-proteobacterium that released hydrogen, and a later one with an alpha-proteobacterium that became the mitochondrion.

Eukaryotes probably also had an excavate morphology for much of their early history, and this morphology may have formed the basis for other morphological innovations. However, it is important to note that an excavate morphology is so far unknown for Parabasalia, which were primarily assigned to Excavata based on unrooted trees. Thus, this enigmatic taxon may be a key to understanding eukaryote origins and the nature of LECA and the forces that shaped it.
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lpetrich said:
Ancestral State Reconstructions Trace Mitochondria But Not Phagocytosis to the Last Eukaryotic Common Ancestor | Genome Biology and Evolution | Oxford Academic
We employed a novel phylogenomic test that summarizes ASR across trees which reconstructs a last eukaryotic common ancestor that possessed mitochondria, was multinucleated, lacked plastids, and was non-phagotrophic as well as non-phagocytic. This indicates that both phagocytosis and phagotrophy arose subsequent to the origin of mitochondria, consistent with findings from comparative physiology. Furthermore, our ASRs uncovered multiple origins of phagocytosis and of phagotrophy across eukaryotes, indicating that, like wings in animals, these traits are useful but neither ancestral nor homologous across groups. The data indicate that mitochondria preceded the origin of phagocytosis, such that phagocytosis cannot have been the mechanism by which mitochondria were acquired.
Click to expand...
...
phagocytosis = engulfing food items, like bacteria
...
The broader significance of these findings is that the origin of mitochondria can be attributed to a fateful case of microbial symbiosis but cannot be attributed to a fateful case of indigestion.
Click to expand...
Click to expand...
Their reasoning doesn't make a lot of sense, though. "ASRs uncovered multiple origins of phagocytosis" implies that "the origin of phagocytosis" doesn't refer to any particular time for mitochondria to have preceded. Given that phagocytosis, like wings in animals, is the sort of trait adaptive enough and simple enough to originate multiple times, what's one more? A proto-eukaryote lineage could have evolved phagocytosis, then acquired mitochondria from a fateful case of indigestion, then lost phagocytosis, and then diversified into all the current and extinct eukaryotic clades, some of which subsequently re-evolved phagocytosis.
 
An excavate root for the eukaryote tree of life | Science Advances

 Excavata - excavates are a group of primitive eukaryotes, mostly one-celled with flagella (sing. flagellum, Latin "whip"). Their name is from the feeding groove that many of them have.

It is hard to place them beyond their branching early. For instance The New Tree of Eukaryotes: Trends in Ecology & Evolution has three subgroups of Excavata - Discoba, Metamonada, and Malawimonada - as separate groups, comparable to Opimoda and Diphoda.

Back to my first-mentioned paper. It shows a phylogeny where these groups branch off in sequence:
  • (Acquisition of delta- or gamma-proteobacterium? An early mitochondron?)
  • Parabasalia (Metamonada)
  • Fornicata (Metamonada)
  • Preaxostyla (Metamonada)
  • (Acquisition of alpha-proteobacterium? The ancestor of mitochondria)
  • Discoba
  • Opimoda, Diphoda - their branchings also found in a lot of previous work
So Metamonada is paraphyletic.

This again raises the issue of the origin of mitochondria. Which early eukaryote did some alpha-proteobacterium enter and become a symbiont of?

Some eukaryotes are "amitochondriate", mitochondrion-less, though sometimes with partial mitochondria like hydrogenosomes. Were primary (never had any)? Secondary (lost them)? Or some of both?

Opimoda, Amorphea:
  • Amoebozoa
  • Opisthokonta
    • Holomycota - fungi + some protists
    • Holozoa - animals + some protists
    Diphoda, Diaphoretickes:
    • SAR: Stramenopiles, Alveolata, Rhizaria
    • Archaeplastida: Rhodophyta, Chloroplastida (Chlorophyta, Streptophyta)
 
Evolution and diversification of the nuclear pore complex | Biochemical Society Transactions | Portland Press
The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification.
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Evolution and Natural History of Membrane Trafficking in Eukaryotes: Current Biology - "The membrane-trafficking system is a defining facet of eukaryotic cells. The best-known organelles and major protein families of this system are largely conserved across the vast diversity of eukaryotes, implying both ancient organization and functional unity."

Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode - PubMed - "The apparent relative absence of prokaryotic antecedents for the endomembrane machinery contrasts with the situation for mitochondria, plastids and the nucleus. Overall, the evidence suggests an autogenous origin for the eukaryotic membrane-trafficking machinery."

The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes - PubMed - " Using comparative genomic and phylogenetic approaches, we showed that 24 out of 37 known APC/C subunits, adaptors/co-activators and main targets, were already present in the Last Eukaryotic Common Ancestor (LECA) and were well conserved to a few exceptions in all present-day eukaryotic lineages."
 
Conservation and Variability of Meiosis Across the Eukaryotes | Annual Reviews - not studied very much across protists, most of eukaryotes' early-branch diversity.

A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis - PubMed
The known phylogenetic distribution of meiosis comprises plants, animals, fungi, and numerous protists. Diplomonads including Giardia intestinalis (syn. G. lamblia) are not known to have a sexual cycle; these protists may be an early-diverging lineage and could represent a premeiotic stage in eukaryotic evolution. We surveyed the ongoing G. intestinalis genome project data and have identified, verified, and analyzed a core set of putative meiotic genes-including five meiosis-specific genes-that are widely present among sexual eukaryotes. The presence of these genes indicates that: (1) Giardia is capable of meiosis and, thus, sexual reproduction, (2) the evolution of meiosis occurred early in eukaryotic evolution, and (3) the conserved meiotic machinery comprises a large set of genes that encode a variety of component proteins, including those involved in meiotic recombination.
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In the paper's family trees, animals are red, fungi in brown, plants in green, and protists in blue.
  • Amorphea
    • Opisthokonta > Metazoa (animals), Fungi
    • Amoebozoa > (Dictyostelia > Dictyostelium), (Conosa > Entamoeba)
  • Diaphoretickes:
    • Archaeplastida (plants)
    • Cryptista > Guillardia
    • SAR > Alveolata > (Apicomplexa > Plasmodium), (Ciliophora > Tetrahymena)
  • Discoba > Euglenozoa > Kinetoplastea > Trypanosoma, Leishmania
  • Metamonada > Fornicata > Diplomonadida > Giardia
Overall phylogeny: Metamonada, (Discoba, (Amorphea. Diaphoretickes))

Or more simply: Giardia, (every other organism studied in this work)

So this paper's conclusion is correct: evidence of meiosis in Giardia means very early evolution of meiosis in eukaryotedom.
 
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An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis - PubMed
We identified homologs of 29 components of the meiotic recombination machinery, as well as the synaptonemal and meiotic sister chromatid cohesion complexes. T. vaginalis has orthologs of 27 of 29 meiotic genes, including eight of nine genes that encode meiosis-specific proteins in model organisms. Although meiosis has not been observed in T. vaginalis, our findings suggest it is either currently sexual or a recent asexual, consistent with observed, albeit unusual, sexual cycles in their distant parabasalid relatives, the hypermastigotes. T. vaginalis may use meiotic gene homologs to mediate homologous recombination and genetic exchange.
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Phylogeny:
Metamonada > Parabasalia > Trichomonas

A great help: Taxonomy browser (root) at NCBI

Also evidence for meiosis early in eukaryotedom. In the phylogeny in "An excavate root for the eukaryote tree of life", Metamonada is paraphyletic, like fish and reptiles, and Parabasalia branched off first, meaning that the ancestral eukaryote had meiosis. The previous result, for Giardia, almost got there.

That leaves Preaxostyla (Anaeromonadea), with Trimastix and the oxymonads. Some oxymonads do meiosis:

Genomics and cell biology of oxymonads | CU Digital Repository - evidence of meiosis
Meiosis and sexual reproduction have been described for Saccinobaculus, Notila and Paranotila by Cleveland (Cleveland 1966, 1950a, 1950b, 1950c). The sexual cycle is the main difference between the genus Notila and Saccinobaculus. All reported sexual cycles in oxymonads involve one step meiosis, in which no chromosome duplication was observed in the meiotic prophase. Following meiosis, the gametes are formed which later fuse and give rise to a diploid cell. For other oxymonads, no sexual cycle has been described, but a recent survey of meiotic genes across the eukaryotic tree of life revealed the presence of the core meiotic machinery in the genome of Monocercomonoides sp. PA203 (Hofstatter and Lahr 2019).
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So they do (XX) -> (X) (X) instead of animal and plant meiosis: (XX) -> (XXXX) -> (XX) (XX) -> (X) (X) (X) (X)

Finally, Conserved meiotic genes point to sex in the choanoflagellates - PubMed
 
Yet more evidence of meiosis being ancestral in eukaryotes: Transcriptomic analyses reveal sexual cues in reproductive life stages of uncultivated Acantharia (Radiolaria) - ScienceDirect
  • Acantharia demonstrate both morphological and genetic evidence of a sexual cycle.
  • Cell division functions are highly expressed in acantharian reproductive stages.
  • Meiosis-related genes are found in acantharian cysts.
  • Nuclear fusion gene family KAR5-GEX1-BMB is enriched in acantharian swarmers.
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Cell nuclear, not atomic nuclear.
 
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