Cool new paper by Robert Asher

Cool new paper regarding the fossil record:


Thanks @T.j_Runyon for sharing this.

From the introduction, this seems quite significant:

By ‘well-corroborated’, we mean that one or an extremely small number of mutually consistent topologies, out of an astronomically huge number of possibilities, result from phylogenetic optimality criteria applied to these datasets. Secondly, we measure the phylogenetic impact of fossils, extant taxa and hypothetical ancestors on congruence with this well-corroborated topology of extant taxa.

Would you be able to rephrase this in a way that we laypersons could comprehend its meaning and significance?

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I think Douglas Theobald put it really well in his 29+ Evidences for macroevolutoin article on talk origins:

In science, independent measurements of theoretical values are never exact. When inferring any value (such as a physical constant like the charge of the electron, the mass of the proton, or the speed of light) some error always exists in the measurement, and all independent measurements are incongruent to some extent. Of course, the true value of something is never known for certain in science—all we have are measurements that we hope approximate the true value. Scientifically, then, the important relevant questions are “When comparing two measurements, how much of a discrepancy does it take to be a problem?” and “How close must the measurements be in order to give a strong confirmation?” Scientists answer these questions quantitatively with probability and statistics (Box 1978; Fisher 1990; Wadsworth 1997). To be scientifically rigorous we require statistical significance. Some measurements of a given value match with statistical significance (good), and some do not (bad), even though no measurements match exactly (reality).

So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 1038 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439). Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree, as shown in Figure 1, to better than 38 decimal places. This phenomenal corroboration of universal common descent is referred to as the “twin nested hierarchy”. This term is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.

When two independently determined trees mismatch by some branches, they are called “incongruent”. In general, phylogenetic trees may be very incongruent and still match with an extremely high degree of statistical significance (Hendy et al . 1984; Penny et al . 1982; Penny and Hendy 1986; Steel and Penny 1993). Even for a phylogeny with a small number of organisms, the total number of possible trees is extremely large. For example, there are about a thousand different possible phylogenies for only six organisms; for nine organisms, there are millions of possible phylogenies; for 12 organisms, there are nearly 14 trillion different possible phylogenies (Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). Thus, the probability of finding two similar trees by chance via two independent methods is extremely small in most cases. In fact, two different trees of 16 organisms that mismatch by as many as 10 branches still match with high statistical significance (Hendy et al . 1984, Table 4; Steel and Penny 1993). For more information on the statistical significance of trees that do not match exactly, see “Statistics of Incongruent Phylogenetic Trees”.

The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al . 2002; Penny et al . 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:

“Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al . 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 106.” (Penny and Hendy 1986, p. 414)


Very interesting paper btw, I rarely see any papers that explicitly test the phylogenetic congruence of different data sets. In fact I don’t remember having seen one besides Penny and Hendy 1982.

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They’re talking about assessing “known” phylogenies, “known” because they match lots of different sorts of data, to determine if the fit of morphological data to those phylogenies depends on using fossil taxa in addition to extant ones, as opposed to using extant taxa alone.


Happens all the time. People presenting a new data set frequently examine its congruence with previous data. But that may not get into the title or the abstract.


Its not cool because its poorly thought through. As follows.
First they invoke accepted data conclusions about the timelines of these fossils and thus a deadly presumption is put in.
They are saying the instict is that fossils of these rodents should look more alike to the original one from whence all branches of a tree come. yet a creationist instict would also say that a great diversity , thus fossils, would show a likeness of bodyplans and easily mimic any variety.
One is only looking at a diversity of creatures back in the post flood/pre flood days.
There is absolutely nO reason to see a progression/branching relationship.

Foxes spaghetti boomerang foxtrot poppyseeds Godzilla Sinclair mysterious toothbrush.

I mean since we are just throwing words together…


basically it means that a mammal should be more similar to other mammal than to a reptile in general. but isnt it obvious?

No, it’s not obvious. Why shouldn’t some mammals look outwardly like, say, passerines? Why shouldn’t tits have tits?


No, that’s not what it means at all. It’s not at all clear how what you said is even relevant or a sensible response to Theobald’s article.

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here is what he says:

“In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies”

so in other words he basically saying that similar morphology= similar genetic. or a mammal should be closer to other mammal than to a reptile.

That would be what he’s saying if indeed phylogenetic relationships were determined based on degree of similarity. They are not. If you would actually read some of the text surrounding that figure, it does explain enough about phylogenetic analyses to show you that.



He addresses that exact criticism in “criticisms” which you should have read:


One common objection is the assertion that anatomy is not independent of biochemistry, and thus anatomically similar organisms are likely to be similar biochemically (e.g. in their molecular sequences) simply for functional reasons. According to this argument, then, we should expect phylogenies based on molecular sequences to be similar to phylogenies based on morphology even if organisms are not related by common descent. This argument is very wrong. There is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry. Though this logic may seem quite reasonable initially, all of molecular biology refutes this “common sense” correlation. In general, similar DNA and biochemistry give similar morphology and function, but the converse is not true—similar morphology and function is not necessarily the result of similar DNA or biochemistry. The reason is easily understood once explained; many very different DNA sequences or biochemical structures can result in the same functions and the same morphologies (see predictions 4.1 and 4.2 for a detailed explanation).


ok. lets focus on his criticism:

so basically he is saying that there is no functional reason that the same DNA will code for the same function. right?

Wrong. He’s saying that the same function might not be produced by the same DNA.

If you can’t tell the difference, go away and think about it until you can.

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He’s saying that isn’t required. They don’t have to yield the same trees to perform similar functions.

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right. because different DNA can code for the same function, so there is no need for that DNA to be the same for the same biological system in 2 unrelated species. but he is wrong. we know that even synonymous codons can have a functional effect on biological systems:

You have confused DNA coding for the same function with DNA coding for the same amino acid sequence. Consider octopus eyes vs. vertebrate eyes. Same function, many features of the gross anatomy similar, yet completely different in detail, few homologous proteins, and those few grossly differing in sequence.


That doesn’t explain why different sets of shared similar genes yield similar trees. Also, the fact that a synonymous codon can have a functional consequence doesn’t mean all synonymous codon’s do have functional consequences.
Furthermore, even if there are some functional consequences to non-identical synonymous codons that would explain why some codons are not allowed(and hence why some codon would have to be different, or the same, between two species), that would still not explain why different data sets yield similar trees.

Why should these constraints affect the outcomes of phylogenetic analysis to constrain the trees to be similar? You are still trying to explain sequence-similarity, not tree-similarity.

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