General Discussion on the Nature and Methods of Cladistics

[Eddie (Edward Robinson)]

Following up on suggestions by people here, I have started reading website material on cladistics. At this point I do not want to debate anything about cladistics but only to understand exactly how it differs from the older analysis of evolutionary relationships.

Here is a statement from the site http://palaeos.com/systematics/cladistics/index.html:

“Contrary to popular belief, cladistics does not describe the actual evolutionary path of life. That is, it is not concerned with or describe the evolution of later organisms from common ancestors in the way that, say, Darwin or more recently Richard Dawkins do, and what the Evolutionary systematics of Romer and Simpson also describes. It simply provides a means of determining in which way (i.e. the branching order) living organisms are related to each other. Cladograms, in other words, are not evolutionary trees.”

Preliminary questions for the people here who have knowledge of cladistics:

1 – Is the above statement correct?

2-- If so, should it be amplified or qualified in any way, to avoid misunderstanding?

3-- If not, where is it incorrect, and why?

At this point I am just gathering reactions. Depending on the answers, I may want to present other passages from other sources, and ask parallel questions. I am busy with other work now, and may not be able to respond to replies for some time, but I can still read the replies of others and learn from them in the meantime.

[John_Harshman]

@Eddie

1 – Is the above statement correct?

Sort of, but not in the way you think.

@Eddie

If so, should it be amplified or qualified in any way, to avoid misunderstanding?

Yes, I imagine. I’ve already offered you a better source, Tree Thinking. Random web sites are not a substitute.

The term “evolutionary tree” is specific; it refers to a tree in which the internal nodes are real taxa rather than hypothetical ancestors as in a cladogram. Cladistics eschews such things because we don’t and can’t have the data to make such assignments except in a few special cases. I’m not sure that Darwin or Dawkins (who isn’t even a systematist) ever made evolutionary trees, and I would like to know of an example. But it used to be common in paleontology, most often as a linear series of hypothesized ancestors and descendants. Think of the “horse series”, for example.

@Eddie

If not, where is it incorrect, and why?

Well, it seems to make the claim that cladograms only deal with extant species, which is an odd claim coming from a paleontology site.

Again, Tree Thinking is probably your best bet. For nuts and bolts, Joe Felsenstein’s Inferring Phylogenies.

[Paul_King]

I think it is adequately clarified by the preceding statement.

Cladistics is based not on morphological similarity (as in the Linnaean system and more recently phenetics) or on ancestor and descent relationship (as in Evolutionary systematics) but in sister-group relationships between related taxa.

Cladistics does not identify any species as an ancestor of any other. It identifies groups which share a common ancestor.

[T_aquaticus]

@John_Harshman

I’m not sure that Darwin or Dawkins (who isn’t even a systematist) ever made evolutionary trees, and I would like to know of an example.

For Darwin, two possible examples come to mind:

A.

B.

I request the reader to turn to the diagram illustrating the action, as formerly explained, of these several principles; and he will see that the inevitable result is, that the modified descendants proceeding from one progenitor become broken up into groups subordinate to groups. In the diagram each letter on the uppermost line may represent a genus including several species; and the whole of the genera along this upper line form together one class, for all are descended from one ancient parent, and, consequently, have inherited something in common. But the three genera on the left hand have, on this same principle, much in common, and form a subfamily, distinct from that containing the next two genera on the right hand, which diverged from a common parent at the fifth stage of descent. These five genera have also much in common, though less than when grouped in subfamilies; and they form a family distinct from that containing the three genera still further to the right hand, which diverged at an earlier period. And all these genera, descended from (A), form an order distinct from the genera descended from (I). So that we here have many species descended from a single progenitor grouped into genera; and the genera into subfamilies, families and orders, all under one great class. The grand fact of the natural subordination of organic beings in groups under groups, which, from its familiarity, does not always sufficiently strike us, is in my judgment thus explained. No doubt organic beings, like all other objects, can be classed in many ways, either artificially by single characters, or more naturally by a number of characters. We know, for instance, that minerals and the elemental substances can be thus arranged. In this case there is of course no relation to genealogical succession, and no cause can at present be assigned for their falling into groups. But with organic beings the case is different, and the view above given accords with their natural arrangement in group under group; and no other explanation has ever been attempted.

Right away, we can see multiple lines of descent sharing a single node, so that’s problematic. In my estimation, Darwin was trying to convey a general idea instead of specific evolutionary relationships (i.e. evolutionary trees).

[Nesslig20]

@Eddie

Preliminary questions for the people here who have knowledge of cladistics:
1 – Is the above statement correct?
2-- If so, should it be amplified or qualified in any way, to avoid misunderstanding?
3-- If not, where is it incorrect, and why?

1&3
Well, except for the statement that seems to imply that it is only about “living organisms” I don’t see any particularly wrong about it.

2
It should be specified what they mean by “evolutionary tree”. This is the issue of how different types of diagrams are usually named. A ‘dendrogram’ is a general name used to refer to any tree diagram, even if they are not about phylogenetic histories. Here, by ‘evolutionary tree’ they likely only refer to dendrograms that include descriptions of the ancestor/descendant relationships or the amount of evolutionary change between ancestors and descendants. An example of this is a ‘phylogram’ where the branch lengths represents the relative amount of change (longer branches, fast evolution). In a ‘chronogram’ the branch lengths are aligned to a geological time scale such that branch point denote how many years ago different lineages diverged from a common ancestor. Cladograms (that cladistics produces) purely concerns about the branching order, and nothing else in particular. The lenghts of the branches in a cladogram doesn’t mean anything. So, in this sense, a cladogram is not an evolutionary tree since it doesn’t describe the evolution, only relationships.

[John_Harshman]

Yes, but that’s a hypothetical tree. Shouldn’t count.

[swamidass (S. Joshua Swamidass)]

@T_aquaticus

Right away, we can see multiple lines of descent sharing a single node, so that’s problematic.

Why? That isn’t a problem at all.

Also this isn’t an evolutionary tree in the sense @John_Harshman defined, because taxa aren’t assigned to the internal nodes.

[T_aquaticus]

@swamidass

Why? That isn’t a problem at all.

My understanding is that evolutionary relationships should not be represented by more than two lines of descent per node. Am I getting this wrong, and if so, how?

[John_Harshman]

@swamidass

Also this isn’t an evolutionary tree in the sense @John_Harshman defined, because taxa aren’t assigned to the internal nodes.

I refer to the tree from the Origin, not the one from his notebook. And that one has taxa at every node.

Regarding “evolutionary tree” as a technical term. I think Ernst Mayr is responsible. When the cladist wars began, Mayr was a big propagandist for the old ways, and he assigned pejorative and favorable labels to various sides. “Cladism” was one of his pejorative coinages, but it was adopted by his opponents. “Evolutionary systematics” and (I believe) “evolutionary tree” as applied to trees with real ancestors were others, the word “evolutionary” being attached to claim the high ground, and perhaps to assert that cladistics and cladograms weren’t evolutionary. That’s all ancient history, and nobody makes “evolutionary” trees any more.

[Joe_Felsenstein]

@John_Harshman

Again, Tree Thinking is probably your best bet.

Agree. My book is too advanced (and these days new copies are too expensive).

[Rumraket (Mikkel R.)]

@T_aquaticus

My understanding is that evolutionary relationships should not be represented by more than two lines of descent per node. Am I getting this wrong, and if so, how?

Depends what the tree depicts. Imagine a tree of the lineages derived from single cells that undergo many consecutive cell divisions before they perish. In such a tree each node represents an individual and can give rise to many new individuals, which can then go on to do the same.

And you can have many children too.

But it’s of course much more unlikely that you’ll get a lot of simultaneous speciation events, so applied to populations and species, lineage bifurcations are much more likely.

[Joe_Felsenstein]

Generally the responses to Eddie are good, though of course I can quibble with many of them:

1. “Evolutionary tree” as used by Mayr, and “Cladogram” as used by phylogenetic systematists usually confound two issues: how to make groups in a classification system and how to infer the phylogeny of those species.
2. Best to keep those separate and spend most time on inferring the phylogeny.
3. I sometimes use “evolutionary tree” to explain to people what this “phylo…” thing is.
4. Although Richard Dawkins has hardly spent any time inferring phylogenies, he and his co-author Yan Wong have a big book “The Ancestor’s Tale” that describes what ancestors of ours looked like at various depths in the past, going back in time. They use reasonably well-supported phylogenies inferred by others.
5. Although inferred phylogenies do not have on them estimated phenotypes or genotypes of the organisms that are in the interior of the phylogeny, those can be estimated if you do more numerical and statistical work. Of course neither the phylogenies nor the ancestral states are exactly precisely inferred, because statistics.

[Herman_Mays]

I will second (third? fourth?) the recommendation to read Baum and Smith’s ‘Tree Thinking’. It’s very good. I used it for an introductory systematics course and it worked well. I think people (myself included) often need well constructed, accessible, verbal descriptions before diving into the math.

[swamidass (S. Joshua Swamidass)]

@T_aquaticus

@swamidass

Why? That isn’t a problem at all.

My understanding is that evolutionary relationships should not be represented by more than two lines of descent per node. Am I getting this wrong, and if so, how?

I believe you are getting it wrong.

Some phylogeny programs/algorithms are limited to bifurcating trees. But this is merely a technical limitation idiosyncratic to these methods. In many cases, it is more accurate to have multiple children from a single node.

Very commonly, this is exactly what bayesian analysis of trees creates, because there is not enough data to resolve the branching order of children. In this case, data-driven uncertainty means that more than two children to a node is a better representation of the data. But that also applies absent any data uncertainty. Imagine a single population that represents a species, and then split it into multiple populations, at the same time, each of which evolve into a different species. There is nothing that enforces we must split it into only two populations. There could have been 3, 4, 5 or whatever number of population splits at the same time, and right way to represent it would be a single node with more than 2 children.

[Herman_Mays]

Evolutionary relationships are for taxa.

Phylogenies depict evolutionary relationships.

Tokogenetic relationships are for individuals.

Pedigrees reflect tokogenetic relationships.

There are hard and soft polytomies. Hard polytomies reflect actual simultaneous divergence. Soft polytomies are simply a lack of resolution. Most polytomies are probably soft.

[Roy (30-year veteran)]

@Eddie

2-- If so, should it be amplified or qualified in any way, to avoid misunderstanding?

Definitely. One way to amplify and qualify it would be to add a description of what cladistics does, as well as what it does not do. Perhaps something like this:

What cladistics does do is provide a more precise and verifiable method of creating and testing phylogenetic hypotheses regarding the evolutionary relationships of past and current organisms. In this way, cladistic methodology can even be used to predict properties of yet-to-be discovered organisms.

That would, for example, prevent the false impression that cladistics is only used on extant (current) organisms.

[Roy (30-year veteran)]

@T_aquaticus

My understanding is that evolutionary relationships should not be represented by more than two lines of descent per node. Am I getting this wrong, and if so, how?

While it is standard practice to only include two lines of descent from each node, cladistic analysis can’t always distinguish which of two close branches occurred first. Also, in theory, three or more lines of descent can originate at exactly the same time - I’m thinking of three offspring from the same clutch of an asexual lizard that become widely separated and subsequently evolve in different environments.

[Roy (30-year veteran)]

I’m wondering why, given @Eddie’s frequent negative comments about autodidacts, he’s asking about a definition of cladistics written by a philosopher.