What is a plant?
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Sebastian S Cocioba
Jan 11, 2016, 4:14:35 PM1/11/16
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It may sound like a silly question but there are some interesting overlaps and exceptions to most definitions. So guys and gals:
Dennis Oleksyuk
Jan 11, 2016, 4:41:30 PM1/11/16
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Is it even a correct question from the perspective of molecular biology and evolution?
It implies that the tree of life if discrete and its branches don't intersect. Which is not true, right? The evolution is a continuum of changes and DNA get mixed long after species diverge on the tree of life, right?
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Sebastian S Cocioba
Jan 11, 2016, 5:14:48 PM1/11/16
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Exactly. The issue of identity has been on my mind as I delve deeper into my scholarly pursuits. There are plants that do not photosynthesize and ones that are parasitic. There are other organisms in the hot mess that is Protista that are not considered plants, mainly due to unicellularity which is a no-no to botanical taxonomists. Curious question, no?
My research buddy and I have had lengthy discussions and can't seem to agree that the kingdom of Plantae is as efficiently discriminative as people may claim. This genetic continuum makes it difficult to anthropically put things neatly in jars with labels and sort things. Everything is related but is the threshold of relation and non-relation as clearly defined as we would hope? Can we really separate plants from other multicellular organisms as conveniently as we do now?
Its an interesting question and wanted to share and possibly spark a conversation. Any other thoughts?
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John Griessen
Jan 11, 2016, 7:30:16 PM1/11/16
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On 01/11/2016 04:14 PM, Sebastian S Cocioba wrote:
> Its an interesting question and wanted to share and possibly spark a conversation. Any other thoughts?
I've got this nice 1800's book from the early days of science where just being somewhere new was plenty to get your
> Its an interesting question and wanted to share and possibly spark a conversation. Any other thoughts?
name in the books. It has engraved images every few pages that scan beautifully. I wonder if it is in the freepublished scanned
books yet...
Anyway, to me, a plant is doing the magic of photosynthesis, else it's not a plant. One celled or no.
But then, I didn't start thetaxonomy.
Xabier Vázquez Campos
Jan 11, 2016, 9:41:22 PM1/11/16
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The modern taxonomy tries to incorporate the phylogenetic data we have, and so, represent the evolutionary history of life. It's not just based on opinion. But as Dennis says, the taxonomy will never provide a perfect classification, as it is based in the idea of an immutable world, and the evolution is a continuous change that's why when you talk about the evolutionary history of a given species/phyla ... you would often have to use many clade names that do not correspond to any of the taxonomic ranks. And high-rank phylogenetics aren't as easy as resolving the phylogeny within a genus or family.
Dennis, some modern models can build phylogenies with interconnected branches to indicate HGT (Horizontal Gene transfer) events.
Following the proposal of Cavalier-Smith (2002), Plantae would include all that contain chloroplasts derived from a single endosymbiotic event in which the host cell engulfed a Cyanobacteria, and so, the plastids have two membranes. For this reason, Plantae is often referred to as Archaeplastidia, old plastids, to differentiate those taxa that have acquired plastids in a secondary endosymbiotic event, e.g. Euglenozoa.
Based on ITIS, Plantae (kingdom) would include:
https://en.wikipedia.org/wiki/Plant#Current_definitions_of_Plantae
John, oxygenic or anoxygenic photosynthesis? Even if you refer to oxygenic photosynthesis you would include cyanos, which by no means are plants
Dennis, some modern models can build phylogenies with interconnected branches to indicate HGT (Horizontal Gene transfer) events.
Following the proposal of Cavalier-Smith (2002), Plantae would include all that contain chloroplasts derived from a single endosymbiotic event in which the host cell engulfed a Cyanobacteria, and so, the plastids have two membranes. For this reason, Plantae is often referred to as Archaeplastidia, old plastids, to differentiate those taxa that have acquired plastids in a secondary endosymbiotic event, e.g. Euglenozoa.
Based on ITIS, Plantae (kingdom) would include:
- Viridiplantae: green algae, vascular plants, mosses, etc
- Biliphyta
- Glaucophyta
- Rhodophyta (red algae)
https://en.wikipedia.org/wiki/Plant#Current_definitions_of_Plantae
John, oxygenic or anoxygenic photosynthesis? Even if you refer to oxygenic photosynthesis you would include cyanos, which by no means are plants
Sebastian S Cocioba
Jan 12, 2016, 12:04:43 AM1/12/16
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Thanks for the detailed insights, Xavier! Really eye opening thoughts about plastid uptake. There are also non-photosynthetic "plants" that are parasitic and are often in the plantae kingdom. Im a bit embarrassed for not knowing more about the organisms I work with and am grateful there are people out there who study these informatics and taxonomic fields. I knew this thread would be worth starting! Please, if anyone else cares to chime in feel free. Am curious what others on the list think about this seemingly simple topic.
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Xabier Vázquez Campos
Jan 12, 2016, 12:23:07 AM1/12/16
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It isn't much different to the issue with animal parasites, e.g. Nematodes and Platyhelminths, in the sense that the have experience a loss of many usual characteristics of their free-living relatives.
In this paper, authors comment about the gene loss suffered by the plastids in taxa that have evolved towards a non-photosynthetic way of life, including some microalgae
http://www.cell.com/trends/plant-science/fulltext/S1360-1385%2805%2900302-X
In this paper, authors comment about the gene loss suffered by the plastids in taxa that have evolved towards a non-photosynthetic way of life, including some microalgae
http://www.cell.com/trends/plant-science/fulltext/S1360-1385%2805%2900302-X
Tristan Eversole
Jan 12, 2016, 12:44:35 AM1/12/16
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> It implies that the tree of life if discrete and its branches don't intersect. Which is not true, right? The evolution is a continuum of changes and DNA get mixed long after species diverge on the tree of life, right?
Mostly not, at least in the eukaryotes. Overall, trees seem to describe reality pretty well.
I can think of a few different things you might be talking about, at least two of which fall under the heading of “reticulate evolution."
1) Horizontal transfer. There are a few well-supported cases of this (e.g. rotifers, tardigrades), but claims for rampant horizontal transfer in the eukaryotes don’t seem to have held up.
2) Hybridization. Occasionally you do have a case where species A interbreeds with species B to produce species C. Note that I mean this in a way that’s distinct from, say, a ring species; the hybridization event could have happened a long time ago, with A, B, and C being reproductively incompatible in the present.
3) Incomplete lineage sorting. This isn’t reticulate evolution, but it falls under the heading of “continuum of changes.” Let me see whether I can explain this.
Suppose that you have some common ancestor Z which undergoes a speciation event, producing species A and B, and then B undergoes its own speciation event, producing species C and D. This yields a tree topology with Z as the node at the first bifurcation, B as the node at the second bifurcation, and A, C, and D as the tips of the tree. For the purposes of the following, assume that Z and B are no longer around, for whatever reason; maybe they’re actual ancestral populations that went extinct following a speciation event, or maybe we’ve just renamed them after their respective speciation events.
The population of Z had some set of alleles, which was inherited by populations A and B. As time goes by, the alleles of A and B diverged from each other, because the two populations were reproductively isolated. This reproductive isolation ensured that any genetic change occurring in A was restricted to A, and any genetic change occurring in B was restricted to B. However, genomes change allele by allele, not all at once, so A ends up with a mixture of alleles which originated after the speciation event— alleles unique to A— and alleles inherited from Z. The same goes for B, and the same process, with all its properties, applies to the speciation event which produces C and D.
The odd consequence of this is that sequencing alleles from A, C, D can produce gene trees (trees of individual alleles) which are incompatible with the actual order of speciation events which generated A, C, and D. For example, you can imagine an allele that originated in Z, was inherited unchanged by A and B, got inherited unchanged from B by D, but changed in species C. If we sequenced A, C, and D and used this gene to construct a phylogeny, it would group A and D together as sharing the same most recent common ancestor, which isn’t what happened. This general phenomenon, in which trees of individual genes conflict with the trees of the species which possess them, is known as incomplete lineage sorting. Of course, as we combine inferences from larger and larger numbers of genes, we come closer and closer to reconstructing the true order of speciation events— the species tree.
This is one of those cases where a picture is worth a thousand words, so here’s a picture: https://frederikleliaert.files.wordpress.com/2014/02/fig2-4.jpg
Unfortunately, the caption is in the actual blog post/article, and I can’t link to it directly: https://frederikleliaert.wordpress.com/green-algae/dna-based-species-delimitation-in-algae/
—T.
Tristan Eversole
Jan 12, 2016, 1:25:14 AM1/12/16
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We actually have a proposed taxonomic system which does away with a nested hierarchy of ranks in favor of naming nodes on trees, known as the PhyloCode. It’s rather contentious, I think. Personally, I find ranks somewhat useful; if you’re encountering named clades for the first time, it’s hard to tell how they’re related to each other. (Can you tell, at a glance, whether Opisthokonta is a subset of Ecdysozoa, or the other way around?) There’s also a lot of names. (I never remember the difference between hominins, hominoids, and hominids.)
The phylogenetic networks program that I know about is SplitsTree: http://www.splitstree.org/
I’m not terribly familiar with phylogenetic network theory, mostly because it seems like you generally don’t need it when you’re dealing with animals.
This is the resource that I’ve previously run into on phylogenetic networks, although there are other (possibly better) things out there: http://phylonetworks.blogspot.com
If you asked me what a plant was, I’d say that it’s an informal classification with no strict meaning in phylogenetic systematics, akin to ‘fish’ or ‘reptile,’ but really you might as well pick Viridiplantae/Chlorophyta or Streptophyta and run with that.
—T.
The phylogenetic networks program that I know about is SplitsTree: http://www.splitstree.org/
I’m not terribly familiar with phylogenetic network theory, mostly because it seems like you generally don’t need it when you’re dealing with animals.
This is the resource that I’ve previously run into on phylogenetic networks, although there are other (possibly better) things out there: http://phylonetworks.blogspot.com
If you asked me what a plant was, I’d say that it’s an informal classification with no strict meaning in phylogenetic systematics, akin to ‘fish’ or ‘reptile,’ but really you might as well pick Viridiplantae/Chlorophyta or Streptophyta and run with that.
—T.
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Xabier Vázquez Campos
Jan 12, 2016, 7:36:06 PM1/12/16
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Tim, that works for Eumetazoa but not for all the members of the kingdom Animalia, i.e. Parazoa. For example the Placozoa don't even have tissues, and much less, organs.
Yuriy
Jan 15, 2016, 3:27:22 AM1/15/16
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what is a messy topic?
Sebastian S Cocioba
Jan 15, 2016, 4:19:50 AM1/15/16
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Thats the whole point. It should be simple but its deeper than green, grounded, and growing. So far the conversations the question generated has been very interesting and brought in voices from various schools of thought. Not trying to troll here, just an honest question to spark a discussion. Plant talk has been low on the list's topic menu so I thought I would try to liven things up with a loaded question. Entertaining and educational would be the ideal goal.
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