Re: [DIYbio] What is a plant?

> 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.


> On Jan 11, 2016, at 1:41 PM, Dennis Oleksyuk <mail@dennis-o.com> wrote:
>
> 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?
>
> On Mon, Jan 11, 2016 at 4:14 PM Sebastian S Cocioba <scocioba@gmail.com> wrote:
> It may sound like a silly question but there are some interesting overlaps and exceptions to most definitions. So guys and gals:
>
> What is a plant?
>
> Sebastian S. Cocioba
> CEO & Founder
> New York Botanics, LLC
> Blog: ATinyGreenCell.com
>
>
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