Discussions between researchers about how to picture the history of species

[Jim]

As I understand it, a diagram representing all the research data about the history of gene sequences, besides having lines that look like a tree, would also have some horizontal lines going across between branches, some branches merging back together, and maybe some other features, that some researchers are saying make part of the diagram near the bottom look more like a network than like a tree. Also, instead of having a single vertical line at the bottom, some have two or maybe three vertical lines coming up from a horizontal one.

With all their different ideas about how to draw the diagram and what to call it, I haven’t seen any researchers denying that all the lines of ancestry of all life today go back to two or three kinds of single-celled life that lived billions of years ago.

(edited to add an image)

This might be an artist’s conception of Doolittle’s theory, highlighting and exaggerating some of its features. I’ve never seen more than three trunks coming up from the base, in any theory. I haven’t seen all the details of Doolittle’s theory.

Perspectives on the Phylogenetic Tree – Biology 2e

 

[Brickjectivity]

As I understand it, a diagram representing all the research data about the history of gene sequences, besides having lines that look like a tree, would also have some horizontal lines going across between branches, some branches merging back together, and maybe some other features, that some researchers are saying make part of the diagram near the bottom look more like a network than like a tree. Also, instead of having a single vertical line at the bottom, some have two or maybe three vertical lines coming up from a horizontal one.

With all their different ideas about how to draw the diagram and what to call it, I haven’t seen any researchers denying that all the lines of ancestry of all life today go back to two or three kinds of single-celled life that lived millions of years ago.

Which species have had their dna sequenced? I think that there aren't that many. Maybe that is changing, but it used to take a lot of time and effort. Maybe its becoming more automated? I know that mouse DNA has been recorded as has human DNA, so there is some kind of a map for those two.

Looking about I have found a page that talks about it. Human DNA was first sequenced in 2001 followed by mouse DNA in 2002. They have also sequenced a couple of viruses, chipanzee, a fish, a froggy and a fowl. They probably have some work done on a variety of species. How much I don't know. I'm sure they must have done some work with fruit flies, but those aren't mentioned on the page. No, I'm sure there are many more species than these but not sure which ones.
Timeline: Organisms that have had their genomes sequenced

 

[Brickjectivity]

Are you saying they have sequenced enough species to construct evolutionary trees, or are they guessing?

 

[Heyo]

With all their different ideas about how to draw the diagram and what to call it, I haven’t seen any researchers denying that all the lines of ancestry of all life today go back to two or three kinds of single-celled life that lived billions of years ago.

I haven't seen a single scientific diagram that doesn't have a single line at the bottom. Did you?

 

[Jim]

Which species have had their dna sequenced? I think that there aren't that many. Maybe that is changing, but it used to take a lot of time and effort. Maybe its becoming more automated? I know that mouse DNA has been recorded as has human DNA, so there is some kind of a map for those two.

Looking about I have found a page that talks about it. Human DNA was first sequenced in 2001 followed by mouse DNA in 2002. They have also sequenced a couple of viruses, chipanzee, a fish, a froggy and a fowl. They probably have some work done on a variety of species. How much I don't know. I'm sure they must have done some work with fruit flies, but those aren't mentioned on the page. No, I'm sure there are many more species than these but not sure which ones.
Timeline: Organisms that have had their genomes sequenced

I’ll see what I can find.

 

[Valjean]

As I understand it, a diagram representing all the research data about the history of gene sequences, besides having lines that look like a tree, would also have some horizontal lines going across between branches, some branches merging back together, and maybe some other features, that some researchers are saying make part of the diagram near the bottom look more like a network than like a tree. Also, instead of having a single vertical line at the bottom, some have two or maybe three vertical lines coming up from a horizontal one.

With all their different ideas about how to draw the diagram and what to call it, I haven’t seen any researchers denying that all the lines of ancestry of all life today go back to two or three kinds of single-celled life that lived billions of years ago.

In the old, tree style diagrams, what would a horizontal line between branches represent? I can't picture it.
Branches merging back together? Like different species merging into a single species? Like a crockoduck?

The "network" at the bottom is because primitive bacteria or archaea don't leave much fossil evidence, and they pass genes back and forth so prolifically that a developmental sequence can't be determined.

Do you mean two or three lines coming up from the base to represent several episodes of abiogenesis? Though it may be possible, any evidence of this is long gone. They would be representing conjectural species.

The sort of diagram you're going to find in modern scientific literature usually looks more like this: Cladogram - Wikipedia

 

[Jim]

Which species have had their dna sequenced?

I don’t think it requires the whole DNA. Here are some statistics: https://gold.jgi.doe.gov/index

 

[Jim]

Are you saying they have sequenced enough species to construct evolutionary trees, or are they guessing?

It might be more than 300,000

 

[Jim]

I haven't seen a single scientific diagram that doesn't have a single line at the bottom. Did you?

I’ve added an image to the OP.

 

[Jim]

In the old, tree style diagrams, what would a horizontal line between branches represent?

(edited to add something I left out)
Horizontal gene transfer.
(end edit)

Do you mean two or three lines coming up from the base to represent several episodes of abiogenesis?

Archaea, bacteria, and in one theory eukaryotes.

 

[Valjean]

I’ve added an image to the OP.

Excellent article. Thanx.

Good diagram -- I see where you're coming from, now. The quadruple, unlabeled vertical lines from the base and some of the unlabeled horizontal gene transfer lines are conjectural, of course.
The chloroplast and mitochondrial transfers are interesting. I'd always heard them described as endosymbionts, engulfed at some point as free-living organisms. These new theorems are new to me.

Archaea, bacteria, and in one theory eukaryotes.

Got it. Interesting.

 

[sun rise]

Are you saying they have sequenced enough species to construct evolutionary trees, or are they guessing?

We don't have the full record of every species that ever lived but we have enough evidence to draw some conclusions such as all non-Africans have neanderthal DNA which shows that humans and I'm sure animals in general don't care about keeping things simple when an attractive other appears.

 

[Jim]

The quadruple, unlabeled vertical lines from the base and some of the unlabeled horizontal gene transfer lines are conjectural, of course.

I think that diagram is an artist’s conception of Doolittle’s theory. I’ll add a note about that.

 

[Jim]

Are you saying they have sequenced enough species to construct evolutionary trees, or are they guessing?

I think that it’s a kind of fitting process, like curve fitting. It looks for a tree that minimizes the deviations from the data. No single tree that is chosen ever matches the data perfectly. Sometimes different trees are constructed using different gene sequences, then combined into one.

 

[Jim]

The chloroplast and mitochondrial transfers are interesting. I'd always heard them described as endosymbionts, engulfed at some point as free-living organisms.

That might be what those lines represent. That’s how I was reading it. Some horizontal lines represent gene transfer, but maybe not all of them.

 

[LegionOnomaMoi]

Which species have had their dna sequenced?

I’ll see what I can find.

(edited to add something I left out)
Horizontal gene transfer.
(end edit)

Archaea, bacteria, and in one theory eukaryotes.

For HGT data in particular you can always check out HGTree.
Here's an open access article on the database:
HGTree: database of horizontally transferred genes determined by tree reconciliation

 

[Jim]

One way that evolution theories are used is to try to improve the classification systems for plants and animals. Family trees, picturing relationships between species as being like lines of ancestry, seem like a natural way to organize them, and they might have some advantages over other ways, for example maybe not having to revise the system as often. For some time, trees were drawn by comparing parts of the anatomy between species. Now they are drawn by comparing gene sequences or the shapes of proteins.

 

[Valjean]

One way that evolution theories are used is to try to improve the classification systems for plants and animals. Family trees, picturing relationships between species as being like lines of ancestry, seem like a natural way to organize them, and they might have some advantages over other ways, for example maybe not having to revise the system as often. For some time, trees were drawn by comparing parts of the anatomy between species. Now they are drawn by comparing gene sequences or the shapes of proteins.

But both were intended to reflect ancestral relationships. Current DNA analysis is just better at it.

 

[Jim]

I’m putting this here for possible later reference.

Tree of Life: Metaphor, Model, and Heuristic Device

 

[Jim]

I think that different researchers have different personal opinions about whether or not there ever actually was a universal common ancestor, but I don’t think that’s what their discussions between them are really about. It looks to me like their discussions between them are about the best diagram to use to organize information and ideas about all plant and animal species. I see some of them saying that it’s a balance between accuracy and simplicity, and that different models are better for different purposes, and I agree with that. Trying to use their arguments to discredit or defend some beliefs about what the Bible says looks to me like misunderstanding and misusing the research, and defaming the people who do it.