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Mammalian Macroevolution Muddle

Posted 9 April 2007 by Nick Matzke

Over the past few days I have been reading the various blog commentaries on the recent Nature paper, Bininda-Emonds et al. (2007), "The delayed rise of present-day mammals." The paper (1) constructed a "supertree" for virtually all extant mammal species (4,510 out of 4,554!!), (2) dated the tree using sequences from 66 genes and 30 fossil calibration points, and (3) concluded that placental mammalian orders arose before the K-T impact 65 million years ago, and that mammalian families arose a substantial time after the K-T impact. Doing phylogeny on this scale is a substantial achievement, and the authors deserve the attention they are getting. But I am not sure that everyone commenting on the "Did the K-T event lead to modern mammals?" issue clearly understands the macroevolutionary concepts involved. [1] To illustrate, I will pick a particularly egregious, and therefore clear, example, from an ID blog. An IDist commentator named Bradford challenged the evolutionists as follows:

Where were the environmental pressures associated with: Egg-laying mammals splitting about 166 million years ago, marsupials splitting from placentals 20 million years later, a 50 million years lull, then during the next 20 million years or so the evolution of the extant orders of mammals occurs and then the asteroid hits. Where are the environmental links corresponding to these events?

Bradford seems to think that modern evolutionary theory says that there "should" be some obvious event like the K-T impact to explain "major" events like the divergence of monotremes and marsupials+placentals, the divergence of marsupials from placentals, the divergence of the mammalian orders, the divergence of the mammalian families, etc. But think about it for a second. There is no reason to think that these divergence events were dramatic when they happened. When the lineage that gave rise to the modern monotremes split from the lineage that gave rise to marsupials+placentals, this was very likely just another routine speciation event. Both of the daughter species in all liklihood still laid eggs. All that happened is that, millions of years after the initial split, one of the lineages lost the egg-laying trait. Attributing the later major innovation to the earlier divergence event is to give the divergence event retroactive, after-the-fact significance, significance the divergence event wouldn't have if you were able get in a time machine and go back and watch the species diverge over a few thousand years. In other words, divergence events are not always the same thing as "major innovation" events (probably not even usually). This fact has substantial significance in several other areas once you start to look think about it. Imagine you are a future paleontologist who is spectacularly lucky and find the fossils representing the exact two species that were the progenitors of the monotreme and marsupials+placentals lineages. My question is, would you even know what you found? If you were to use traditional taxonomy to classify the two fossils, you would probably put the two species in the same genus. If you decided to join the 21st century and use cladistics, you would know that the fossils were early mammals and that they had features shared with all living mammals. But these fossils, even though they are from the true ancestral species of monotremes and marsupials+placentals, probably would not have any major distinguishing derived characters that would allow you to place either species specifically in the monotreme or marsupial/placental branch. The distinguishing characters might not evolve for millions years, many species later in each lineage. The upshot: even if you had the exact fossils from the divergence point, you would probably miss this fact, and not date the divergence point until millions of years later. Here's another interesting implication that also seems difficult to "get." Something like the K-T event could be important for the origin of modern (living today) mammal groups, but this fact could be unrecorded in the molecular phylogenies -- all as a result of the completely standard and prosaic process of extinction. For sake of argument let's assume that date is rock solid. Let's also say that the species of this crown group dominate the Big Mean Predator niche that was formerly occupied by certain Big Mean Dinosaurs, and that after the K-T event it really was the case that this group of mammals immediately took over this niche and dominated it for the next 64 million years. If all of this were true, should we expect the molecular clock, even a perfect, inerrant molecular clock, to give us a date of 64 million years for the modern crown group? Not necessarily. Remember that most species that have ever lived are extinct -- 99% or something. This means that any group that has been sitting around and speciating in its niche for 64 million years will have experienced a large number of extinctions, probably 10 times or more extinct species than there are living species. You can only get DNA from living species, so the only way your molecular clock will give you back the date of 64 million years is if the very first diversification event after this niche was occupied -- remember, two very similar species with small differences -- both produced lineages that just happened to survive all the way down to the present day. If one of those two species went extinct immediately, perhaps outcompeted by its sister species, too bad. If both lineages survived for 20 million years, but some minor predatory innovation in one derived group at 44 million years led to a general advantage of the derived group, and the eventual extinction of the other lineage, then too bad, your molecular clock will read 44 million years ago. If hungry Clovis hunters hiked over to North America 12,000 years ago and ate the last representative of one of the two lineages, then too bad, you won't get the 64 million-years-ago date. None of these scenarios, although they all give different molecular dates for the "diversification" of the crown group, would change the fact that the "key evolutionary event" that "produced" the crown group was the occupying an ecological niche left empty by the dinosaurs. Here's the point: the age of a crown group depends at least as much on subsequent extinctions as it does on whatever "key evolutionary events" we might hypothesize were behind the origin of a particular crown group. I'm not sure there is even a strong reason to think that dating the base of a crown group "should" reflect some significant evolutionary event. The timing of the "original diversification" of a crown group depends just as much on evolutionary events millions of years later! If we assume lineage extinction happens "at random" at a coarse level of analysis, then even a pure null model would suggest that the common ancestor our extant, suriving Big Mean Predators would date to some point after the "key evolutionary event" that produced the lineage in the first place. And the problem would probably get worse, the older the "key evolutionary event" was. Now that I have set this up in imaginary terms, we can think of a few examples where the "key evolutionary event" and the "age of crown group" are not the same. E.g., the origin of "birds" with feathers and flight capability was before Archaeopteryx, 150 mya, but the age of the crown group -- the common ancestor of modern birds -- was much later (although looking at a recent paper indicates that the common ancestor of modern birds might date well back into the Cretaceous). The expected "crown group delay" could be estimated fairly simply with modeling based on some simple assumptions about speciation and extinction rates. The problem would presumably be less severe for more speciose groups. I'm sure someone has already done all this work and probably all of these issues are well-understood amongst people who have seriously thought about cladistics and macroevolution. But I haven't seen much of this in the blog commentaries, or even in the original Nature paper. Maybe the law of large numbers ameliorates the problems I raised. Or am I missing something? P.S.: None of this means I am taking a position for or against attributing "the radiation of modern mammal groups" to the K-T event. What I'm trying to point out is that "modern mammal groups" are pretty much arbitrarily defined from the perspective of someone who is following evolution as it progresses through the ages without knowing what random things will happen to be the survivors tens of millions of years later. I was going to complain about the concepts of "family" and "order" as well, but you can pretty much see what I would say by referring to my "Down With Phyla!" posts. Notes (1) The worst error is to miss the fact that Bininda-Emonds et al. acknowledge that the fossil record unambiguously shows that mammals did radiate dramatically just after the K-T event. So it's not as if they're saying nothing happened after a meteor impact wiped out the dinosaurs.[1.1] It's just that [1.2] those fossil mammal groups were not primarily ancestral to modern lineages. (1.1) Dinosaurs, except birds. And yes, there are various debates about the exact relationship between the dinosaur extinction and the impact event. Perhaps dinos were already on their way out and the meteor was just the coup de grace. For the purposes of this post all we need to know is that many things went extinct at 65 million years ago. (1.2) If the dating used in the study is right; one key point to remember is that fossil calibration points can only give minimum ages for divergence events, so if they find older fossils, or even if they don't, the dates could be moved back.

45 Comments

Torbjörn Larsson · 9 April 2007

Where were the environmental pressures
This layman thinks there could also be other problems here. If we assume that there was a rather fast K-T extinction event, it wasn't just a niche disappearing but larger sets of them. So if a Big Mean Predator reappears, some Pretty Big Herbivores probably needs to do so as well before or concurrently. (Which could be further delayed if the findings that some plants also got badly hit stands up.) Btw, assuming diversification isn't totally independent of speciation :-), wasn't there recent papers showing a historically steady speciation rate over time? (Much as the paper you discuss doesn't show order of magnitude difference in mammals IIRC.) If that is true it doesn't seem like changes in environments drive speciation rates as much as extinction rates.

Dan Gaston · 9 April 2007

While I applaud the authors of the Nature paper for their work, I think it is also important to keep in mind that while the picture it paints may be correct, at least in part, there is also significant controversy over the use of Supertrees themselves right now. While taxon sampling here was extremely well distributed over extant mammalian groups there are issues with the molecular clock assumption, calibration methods, etc. While I applaud the authors for their achievement I don't completely buy their conclusions.

harold · 9 April 2007

Torbjorn Larsson -

That's interesting about speciation having a steady rate over time.

I would have guessed that there would exceptions when massive new niches with relatively little extant competition open, or when a new adaptation allows an entire lineage to be more adapted than predecessors. For example, the Cambrian, or when vertebrates first started spending an entire lifecycle on land. But it would have just been a guess.

(In retrospect, though, the idea of a rapid mammalian radiation immediately after the K-T impact might have been a bit naive, since that event was relatively recent in evolutionary time, and all but the smallest mammals may have long generation times compared to, say, the average insect.)

Nick (Matzke) · 9 April 2007

Argh. There was a mammalian radiation right after K-T. See note 1 of the post.

David Stanton · 9 April 2007

Thanks Nick. Another excellent synopsis of a complicated topic. It's not too surprising that speciation rates might be realtively constant for long periods, since genetic diversity doesn't arise overnight. It's also rasonable to suppose that the rate could vary significantly at times due to environmental changes and extinctions. In fact, there is probably a complex interaction of all three factors, plus others, that make the entire picture quite complicated. But that is the way it is. There are never any simple answers. All we can do is document long-term patterns and then try to explain them the best we can, while at the same time recognizing the limitations of our methods.

What must be remembered is that there will always be some who look for the easy answer. These are people who must see purpose, intelligence, foresight and planning in everything. They want simple rules that produce simple patterns. These are the same kind of people who see patterns in the stars and then assume that they have significance for our everyday lives. But evolution is just what happened. Sometimes it can be dirty and sloppy and very hard to reconstruct. That is precisely because there are no simple rules that are always true.

By the way, I think it is great when creationists start arguing over the details of macroevolution. That pretty much means that they can no longer claim that: "there is no evidence for macroevolution."

Frank J · 9 April 2007

You know, you'd have a lot more credibility as non-creationists if you'd drop their nasty habit of claiming that every new bit of information makes all scientific thought prior to that point, in error.... Creationists like to seize upon any snippet of data that might be misconstrued as a problem for evolution theory, and prematurely pronounce evolution dead. Just like you did here, MG. If you have the data against evolution, publish it. If you don't, go to the lab or to the field and report on what you find. But please, don't walk like a creationist, quack like a creationists, lay creationist eggs, and then claim to be apart from creationists.

— Ed Darrell

MG has not maintained that "evolution is in error" if by that you mean MG infers that descent did not occur. His post addresses mammalian evolution and questions orthodox views about it. Neither is he "claiming that every new bit of information makes all scientific thought prior to that point, in error." Your comments are an absurd overreaction.

— Bradford

You are engaged in a knee-jerk reaction. There is no denial of common descent. And arguing that the conventional view is incomplete is not the same as arguing it is invalid.

— Mike Gene
Fascinating. Bradford and Mike know darn well that, even though they don't deny common descent and explicitly acknowledge mainstream science's ages of events, most of their cheerleaders are YECs. And to maintain that charade they are very careful to "seize upon any snippet of data" to challenge only the "orthodox views" (mainstream science) and never any other "unorthodox views" like YEC or OEC-without-common descent. While Bradford and Mike react with the usual whining about overreacting "Darwinists" they do exactly what Ed accuses them of, and that is trying to have it both ways with "creationism."

Glen Davidson · 9 April 2007

The angiosperms quite famously radiated prior to the Cretaceous extinction, so it's hardly odd that mammals might have as well.

There is experimental evidence showing that new niches opening up do speed up evolution (though speciation hasn't been shown to increase as well, as far as I know), so there was some cause to suppose that mammals might have radiated at the beginning of the Tertiary. However, what that assumption ignores is the fact that many niches probably disappeared along with the occupants of those niches, hence such a broad extinction across trophic levels may not have enhanced mammalian evolution in the way that, say, a disease that wiped out all and only the dinosaurs (minus birds) probably would have.

Let's also not forget that the Cretaceous extinction wasn't the only one affecting the dinosaurs. At the Triassic-Jurassic boundary there was a major extinction, if not one of the Cretaceous-Tertiary proportions. Conceivably mammals sped up evolution because of that extinction, rather than due to the Cretaceous extinction. Certainly it may not have, for it isn't clear that mass extinctions have that effect, I'm just saying don't rule out mass extinctions as causes for radiations, at least if they're more selective than the Cretaceous die-off.

The apparent decline of the dinosaurs during the Cretaceous could have been just the sort of vacating of niches that would help mammals to adaptively radiate, as opposed to the total reduction in diversity noted at the dawning of the Tertiary.

So if angiosperms were known to radiate prior to the mass extinction (with no great jump in evolution in the early Tertiary), why were mammals thought to get a boost from same? I wonder if it isn't due to some sort of exceptionalism in our psyches, as well as the old sense that one group gains at the expense of the other in evolution (often true, but hardly always). We think, there but for the grace of the extinction event..., what matters to us (our evolution) would not have happened. It's a more compelling tale than the most recent one, it just might never have had much going for it, at least with any extinction event which reduced niches as well as organisms occupying those niches.

Glen D
http://tinyurl.com/35s39o

Nick (Matzke) · 9 April 2007

So if angiosperms were known to radiate prior to the mass extinction (with no great jump in evolution in the early Tertiary), why were mammals thought to get a boost from same? I wonder if it isn't due to some sort of exceptionalism in our psyches...[blah blah blah]

AARRRRGGGHHHH!!! Mammalian fossil diversity DOES SPIKE in response to the KT event!! The Nature study doesn't contradict this (and it explicitly cites the papers on the fossil data), because it is dealing with a molecular phylogeny of extant lineage, not a fossil-based phylogeny of all mammals. Either a number of people are missing the basic fossil facts, or I am way, way off-base about something.

fnxtr · 9 April 2007

Nick:

I was going to send this privately but couldn't get the e-mail link to work for me.

Does this steady rate of speciation idea clash with PE, or is it just a matter of degree, or a difference in time scales?

Where would I find research on the limits/freedom of genetic variability? I'm sure it's an ocean of information, I'm hoping you can point me to a friendly beach somewhere I can get my feet wet.

Keeping with the geographical metaphor, I'm wondering about dimensions of plateaus of genetic stability (if there are such things), how wide the plateaus tend to be (diversity in populations) and how long they can last, how the limitations could relate to extinction rates, what events/situations can affect said dimensions... and wondering what other questions dipping a toe in the ocean will generate.

Thanks,
fnxtr

Glen Davidson · 9 April 2007

AARRRRGGGHHHH!!! Mammalian fossil diversity DOES SPIKE in response to the KT event!! The Nature study doesn't contradict this (and it explicitly cites the papers on the fossil data), because it is dealing with a molecular phylogeny of extant lineage, not a fossil-based phylogeny of all mammals. Either a number of people are missing the basic fossil facts, or I am way, way off-base about something.

First of all, did I write "mammalian fossil diversity"? I most certainly didn't. And here is the abstract, with all of the annoying junk that I have to include to properly reference it:

Article Nature 446, 507-512 (29 March 2007) | doi:10.1038/nature05634; Received 26 October 2006; Accepted 31 January 2007 The delayed rise of present-day mammals Olaf R. P. Bininda-Emonds1,11, Marcel Cardillo2,11, Kate E. Jones4, Ross D. E. MacPhee5, Robin M. D. Beck6, Richard Grenyer7, Samantha A. Price8, Rutger A. Vos9, John L. Gittleman10 & Andy Purvis2,3 Lehrstuhl für Tierzucht, Technical University of Munich, 85354 Freising-Weihenstephan, Germany Division of Biology, and, NERC Centre for Population Biology, Imperial College, Silwood Park campus, Ascot SL5 7PY, UK Institute of Zoology, Zoological Society of London, Regents Park, London NW1 4RY, UK Division of Vertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK National Evolutionary Synthesis Center (NESCent), Durham, North Carolina 27705, USA Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Institute of Ecology, University of Georgia, Athens, Georgia 30602, USA Present addresses: Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany (O.R.P.B.-E.); Centre for Macroevolution and Macroecology, School of Botany and Zoology, Australian National University, Canberra 0200, Australia (M.C.). Correspondence to: Olaf R. P. Bininda-Emonds1,11 Correspondence and requests for materials should be addressed to O.R.P.B.-E. (...). Top of page AbstractDid the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals. [Emphases added, and an email address taken out]

They didn't consider diversity at the species level, possibly above (I'm not sure where the cut-off was). So I don't know exactly what "fossil diversity" you mean, what I'm discussing is the diversity changes found in the study at issue in the paper. They didn't find any spikes at all at the K-T boundary, and as I recall (I don't have the issue at hand) they only found one order significantly increasing in diversity apparently in response to the K-T extinction. They indeed say that they "challenge" the hypothesis of "a major, direct influence on" mammal diversification, though this is not said in the abstract in relation to the "fossil record" per se. Glen D http://tinyurl.com/35s39o

fnxtr · 9 April 2007

Fossil data says there was a KT spike in mammalian diversity. Molecular phylogeny says presently-existing groups had diversified before this. Is that what you're trying to say?

Glen Davidson · 9 April 2007

Here's a pretty good summary of the paper by PZ Myers: http://scienceblogs.com/pharyngula/2007/03/dont_blame_the_dinosaurs.php And here's the snarkiness of Nick:

So if angiosperms were known to radiate prior to the mass extinction (with no great jump in evolution in the early Tertiary), why were mammals thought to get a boost from same? I wonder if it isn't due to some sort of exceptionalism in our psyches...[blah blah blah]

Yeah, yeah, you pretend that I was writing about "mammalian fossil diversity" when I was instead discussing the article, then the stupid "[blah, blah, blah]" nonsense from the guy who is shifting goalposts even as the paper is being discussed. Pretty awful reading and writing, I'll say. Instead of dealing with what Bininda-Emonds et al. wrote and what I commented upon, Nick just sneers, changes the subject, and pretends that I don't know that the paper was about genetic-based phylogenies. There's one person who's messing up around here, and it isn't me. True, mammal fossils appeared more diverse after the K-T event, but there are any number of issues of cause and how to pin down the rates of diversification (everyone agrees that diversification proceeded after the K-T event, of course). Then too, if mammals had greatly expanded in numbers (compared to just prior to the extinction event) soon after the K-T boundary, one might see more diversity in the fossils even if there were less diversity of mammals, simply because there were more mammals around to be fossilized at that time. Again:

AARRRRGGGHHHH!!! Mammalian fossil diversity DOES SPIKE in response to the KT event!! The Nature study doesn't contradict this (and it explicitly cites the papers on the fossil data), because it is dealing with a molecular phylogeny of extant lineage, not a fossil-based phylogeny of all mammals. Either a number of people are missing the basic fossil facts, or I am way, way off-base about something.

Yeah, you're way off-base about what was being discussed. So why do you think they turned to the molecular phylogeny anyway? It's in part because there are confounding effects, and also to check the fossil record in general. It takes poor reading comprehension for Nick to suppose I was talking about the "fossil record" when I had stayed on track with what was in the paper, and it takes poor manners for him to snark away like he did. Glen D http://tinyurl.com/35s39o

Nick (Matzke) · 9 April 2007

Glen, those results are all just for mammalian crown groups, i.e. lineages still living today. This says nothing about the question of whether or not mammals in general spiked just after the K-T event. As it turns out, they did. From the paper:

A partial molecular phylogeny emphasizing divergences among placental orders suggested that over 20 lineages with extant descendants (henceforth, 'extant lineages') survived the K/T boundary8. However, the total number of extant lineages that pre-date the extinction event and whether or not they radiated immediately after it remain unknown. The fossil record alone does not provide direct answers to these questions. It does reveal a strong pulse of diversification in stem eutherians immediately after the K/T boundary4, 12, but few of the known Palaeocene taxa can be placed securely within the crown groups of extant orders comprising Placentalia4. The latter only rise to prominence in fossils known from the Early Eocene epoch onwards (approx 50 Myr ago) after a major faunal reorganization4, 13, 14. [...] The supertree therefore contains no evidence that the diversification rate of the extant mammalian lineages increased soon after non-avian dinosaurs went extinct. Although there is strong palaeontological evidence that mammalian diversity, driven by a massively elevated rate of speciation, generally rose rapidly immediately after the K/T boundary4, there is in fact no conflict between the palaeontological and neontological [=living species] interpretations of the known facts. Most diversifications immediately after the K/T boundary were in groups such as multituberculates, plesiadapiforms and 'archaic' ungulates4, as plots of the numbers of genera known in each sub-epoch indicate (Fig. 2c). These groups declined or went extinct early in the Cenozoic era and so are barely, if at all, represented in the phylogeny of living species. The continuing low rates of extant mammalian diversification through this period imply that the dearth of Palaeocene crown-group fossils is a real reflection of the low diversity of those clades. The low rates are also consistent with (but not direct evidence for) the hypothesis that extant lineages were inhibited in some manner by the diversity of the predominantly Palaeocene groups, and only started to diversify with the decline of the latter (Fig. 2c). 4. Alroy, J. New methods for quantifying macroevolutionary patterns and processes. Paleobiology 26, 707---733 (2000) 12. Alroy, J. The fossil record of North American mammals: evidence for a Paleocene evolutionary radiation. Syst. Biol. 48, 107---118 (1999)

(Bolds and italics added. Important distinctions include "extant" groups vs. any groups, crown groups vs. stem groups, etc.) I don't mean to freak out about this, it just seems that a lot of interpretation is going on based on incorrect premises.

Glen Davidson · 9 April 2007

Here's a pretty good summary of the paper by PZ Myers: http://scienceblogs.com/pharyngula/2007/03/dont_blame_the_dinosaurs.php And here's the snarkiness of Nick:

So if angiosperms were known to radiate prior to the mass extinction (with no great jump in evolution in the early Tertiary), why were mammals thought to get a boost from same? I wonder if it isn't due to some sort of exceptionalism in our psyches...[blah blah blah]

Yeah, yeah, you pretend that I was writing about "mammalian fossil diversity" when I was instead discussing the article, then the stupid "[blah, blah, blah]" nonsense from the guy who is shifting goalposts even as the paper is being discussed. Pretty awful reading and writing, I'll say. Instead of dealing with what Bininda-Emonds et al. wrote and what I commented upon, Nick just sneers, changes the subject, and pretends that I don't know that the paper was about genetic-based phylogenies. There's one person who's messing up around here, and it isn't me. True, mammal fossils appeared more diverse after the K-T event, but there are any number of issues of cause and how to pin down the rates of diversification (everyone agrees that diversification proceeded after the K-T event, of course). Then too, if mammals had greatly expanded in numbers (compared to just prior to the extinction event) soon after the K-T boundary, one might see more diversity in the fossils even if there were less diversity of mammals, simply because there were more mammals around to be fossilized at that time. Another problem with trying to correlate diversity by fossil diversity: The pre-Tertiary levels of mammalian diversity were by all accounts rather lower than those afterwards, even if diversification didn't increase dramatically at or after the K-T boundary. Which means that comparing diversification before and after is not so very easy to do, for the sampling of the sparser earlier record is not likely to give as high resolution in the earlier times than in the later times. Put the two together, the probable greater numbers of total mammals after and the resolution problems in the earlier period, and you have some problems in simply looking at greater diversity after and supposing that the K-T event is what did it. Again:

AARRRRGGGHHHH!!! Mammalian fossil diversity DOES SPIKE in response to the KT event!! The Nature study doesn't contradict this (and it explicitly cites the papers on the fossil data), because it is dealing with a molecular phylogeny of extant lineage, not a fossil-based phylogeny of all mammals. Either a number of people are missing the basic fossil facts, or I am way, way off-base about something.

Yeah, you're way off-base about what was being discussed. So why do you think they turned to the molecular phylogeny anyway? It's in part because there are confounding effects, and also to check the fossil record in general. It takes poor reading comprehension for Nick to suppose I was talking about the "fossil record" when I had stayed on track with what was in the paper, and it takes poor manners for him to snark away like he did. Glen D

Nick (Matzke) · 9 April 2007

Just saw your latest comment:

Yeah, yeah, you pretend that I was writing about "mammalian fossil diversity" when I was instead discussing the article, then the stupid "[blah, blah, blah]" nonsense from the guy who is shifting goalposts even as the paper is being discussed.

There is no evidence that you were aware of the fact that mammalian diversity did spike after the K-T event in your original comment to which I reacted:

So if angiosperms were known to radiate prior to the mass extinction (with no great jump in evolution in the early Tertiary), why were mammals thought to get a boost from same?

As I said in my opening post, the mammal-diversity-didn't-jump-after-KT idea is a common and very bad misunderstanding of the Nature paper. So I jumped on you (and someone else) since it seemed that even some PT commentators weren't getting it. If you do get it now, great.

Nick (Matzke) · 9 April 2007

Nick: I was going to send this privately but couldn't get the e-mail link to work for me. Does this steady rate of speciation idea clash with PE, or is it just a matter of degree, or a difference in time scales?

Punctuated equilibrium is about the rapidity of an individual speciation event, from one species to another closely related species, and how this individual speciation event would look in the fossil record. It is not particularly tied to anything we are discussing today, which is the much more macro issue of global patterns of mammal diversification.

Where would I find research on the limits/freedom of genetic variability? I'm sure it's an ocean of information, I'm hoping you can point me to a friendly beach somewhere I can get my feet wet. Keeping with the geographical metaphor, I'm wondering about dimensions of plateaus of genetic stability (if there are such things), how wide the plateaus tend to be (diversity in populations) and how long they can last, how the limitations could relate to extinction rates, what events/situations can affect said dimensions... and wondering what other questions dipping a toe in the ocean will generate.

There are various opinions on this, but my opinion is that natural selection dominates the other processes, and that "stasis" is not primarily due to genetic constraint, but to niche occupancy. If the niche is stable, once a critter occupies it, it will optimize to match the niche and then pretty much sit there until something changes the situation. The natural-selection-dominates view got some substantial support from this recent paper:

Resolving the Paradox of Stasis: Models with Stabilizing Selection Explain Evolutionary Divergence on All Timescales Suzanne Estes and Stevan J. Arnold The American Naturalist, volume 169 (2007), pages 227---244 We tested the ability of six quantitative genetic models to explain the evolution of phenotypic means using an extensive database compiled by Gingerich. Our approach differs from past efforts in that we use explicit models of evolutionary process, with parameters estimated from contemporary populations, to analyze a large sample of divergence data on many different timescales. We show that one quantitative genetic model yields a good fit to data on phenotypic divergence across timescales ranging from a few generations to 10 million generations. The key feature of this model is a fitness optimum that moves within fixed limits. Conversely, a model of neutral evolution, models with a stationary optimum that undergoes Brownian or white noise motion, a model with a moving optimum, and a peak shift model all fail to account for the data on most or all timescales. We discuss our results within the framework of Simpson's concept of adaptive landscapes and zones. Our analysis suggests that the underlying process causing phenotypic stasis is adaptation to an optimum that moves within an adaptive zone with stable boundaries. We discuss the implication of our results for comparative studies and phylogeny inference based on phenotypic characters.

There is a free PDF on Steve Arnold's website at OSU.

Glen Davidson · 9 April 2007

Glen, those results are all just for mammalian crown groups, i.e. lineages still living today. This says nothing about the question of whether or not mammals in general spiked just after the K-T event. As it turns out, they did.

Okay, so why are you going on telling us what we've already read? The fact is that the picture changes regardless of the pulse of diversification of the stem eutherians. The old picture seems to have been one where mammals simply diversified greatly after the K-T boundary. I know (and knew) that the stem eutherians did undergo a good increase in diversification. Whether that really counts as a "spike" could be questioned, but more importantly, it's not "the mammals" greatly increasing in diversity, it's certain groups of mammals. It may be that these constituted a greater portion of the mammals then than I had realized. Perhaps that is what you are going on about. It would have been better to have pointed this out, if true, rather than to attack as if I didn't know that they were discussing molecular phylogenies instead of fossil evidence. I had not thought of the stem eutherians as being so much more diverse than present-day lineages (I'm not a paleontologist for Chrissake), but if they were, the fact that they pulsed (whether or not they "spiked") would mean that this pulse was overall a strong pulse of mammal diversification. I still think it odd, if true, that extant lineages didn't diversify a good deal more when the stem eutherians did. The issue might yet need some wrinkles ironed out. Glen D http://tinyurl.com/35s39o

fnxtr · 9 April 2007

Thank you.

David Stanton · 9 April 2007

Nick said:

"You can only get DNA from living species, ..."

I just wanted to point out that this isn't strictly true any more. It is now possible to get DNA from fossil specimens and extinct species, there are several examples in the literature. Unfortunately, this is relatively difficult, time-consuming and costly. It is also prone to contamination problems. Still, this type of data has the potential to help address some of the types of problems that Nick discusses here. Now if only we could get some real data from dinosaur DNA. Of course then we would have to worry about the Jurrasic Park scenario.

Glen Davidson · 9 April 2007

There is no evidence that you were aware of the fact that mammalian diversity did spike after the K-T event in your original comment to which I reacted:

Two things: I did know that some lineages known only from fossils jumped in diversity, I didn't know that they were (apparently) the more common groups (perhaps I should have? Why?). And I wasn't sure whether or not the fossil record is considered to be reliable in that respect, as compared to the molecular phylogenies. You seem to be saying that it is. Indeed, the authors appear to be indicating that it's reliable enough in the case of the stem eutherians (I probably didn't read the paper, but only the article based on the paper---and the whole issue didn't seem so very important at that time), but perhaps not of much value for the crown groups.

As I said in my opening post, the mammal-diversity-didn't-jump-after-KT idea is a common and very bad misunderstanding of the Nature paper. So I jumped on you (and someone else) since it seemed that even some PT commentators weren't getting it. If you do get it now, great.

I do get it now, because (I think) I figured out something that you didn't bother to tell me, which is that the stem eutherians were the more diverse and common mammals at the time. Less jumping and more explaining would be helpful. Glen D http://tinyurl.com/35s39o

Nick (Matzke) · 9 April 2007

I apologize for jumping. No caffeine, Monday morning, John Mark Reynolds yammering about truth and honesty to data, etc.

harold · 9 April 2007

A very general point about fossils and DNA...

As we know, there are many examples of species, and even within species lineages, that are quite different morphologically (phenotypically), but still extremely similar by most gross measures of genetic homology. This is especially true when we consider that many forms of life go through extremely different morphologic life cycles. Granted, well-trained paelontologists and physical anthropologists are not "fooled" by such things, but they certainly impact which niche an individual is phenotypically adapted to.

Humans and chimpanzees, for example, and not necessarily even a very dramatic example. I'm sure the plant kingdom could furnish us with all sorts of examples of crazily "opposite-looking" plants that turn out to be very closely related genetically.

This is because, presumably, relatively "small" genetic changes can sometimes have dramatic morphologic effects.

What may happen, is that when new niches open up, there may be a radiation in terms of morphologic adaptations that happens very quickly, but without producing a dramatic "quantitative" difference when all the sequences in the genome are looked at together. Once the lineages are geographically or phenotypically isolated from one another, more grossly measurable genetic differences will gradually accumulate.

Glen Davidson · 9 April 2007

All's good now, and what would we do without the coffee bean's evolution?

Though I suppose coffee's one of those things that IDists would point to, if they could get it together. They're not really all that good at PR, they just have captive audiences.

Glen D
http://tinyurl.com/35s39o

David Stanton · 9 April 2007

Harold, you are correct sir. In fact, here is a reference to use as an example:

Biochemical Systematics and Ecology 30:579-592 (2002)

It shows that many species of sage are quite different morphologically, but at least for some genes they are quite similar genetically. By the way, ancient DNA has been successfully extracted and amplified from some species in this group.

Greg Laden · 9 April 2007

Very nice post. You make many points. We are sympatico, to a large extent (am I using that word correctly?) See:

http://gregladen.com/wordpress/?p=594

Rupert Goodwins · 9 April 2007

This should be very fertile ground for ID. It's an area where evolutionary biology is constantly creating new insights, not all of which will pan out. There's a perfect ferment of predictions, tests, new evidence, reinterpretations of old evidence, involving just about every tool in the box.

If ID has _anything_ positive to add - a set of anomalous step-changes in morphology or genetics, a prediction of lineage events that evolutionary biology would not expect, modifications in advance of environmental pressures - then now's the perfect time to make the pitch.

It's very sad that it never does.

R

levi · 9 April 2007

aaaaaaaaaarrrrrrrrggggghhhhhhhh!!!!!!!! fossil spikes, gradual speciation,super bush, no super tree, no over the hedge! what will it be tommorrow? I don't know, I can't keep up. You highly mutated evolutionists can't agree on anything. is abiogenesis part of the super hedge or not? this must too be over my head. this is how smart I am; the three year old that keeps changing his story is of course telling the truth! Go mutations!

levi · 9 April 2007

wow species diverge now in a few thousand years? and yet a chimp is still a chimp. I know it's a cliche that you evos love to make fun of...and yet never answer. go mutations!

Richard Simons · 10 April 2007

I'm sure the plant kingdom could furnish us with all sorts of examples of crazily "opposite-looking" plants that turn out to be very closely related genetically.
Wild Juniperus communis has a wide range of morphologies, from creeping to small tree, yet is considered to be just one species. Euphorbia includes rhizomatous weeds of grainfields (the spurges), large shrubs like Poinsettia, small bushes (crown of thorns) and cactus-like forms. From Wikipaedia, it seems that studies of their relationships using DNA are in progress.

Torbjörn Larsson · 10 April 2007

That's interesting about speciation having a steady rate over time.
Well, I couldn't find the references, which is why I asked. The greatest net diversification rate in the here presented extant record is before the K-T boundary, but then there are fewer species and a greater inaccuracies in ages. (See for example figure with confidence intervals in http://scienceblogs.com/pharyngula/2007/03/dont_blame_the_dinosaurs.php ) But I see I was mistaken, there is an order of magnitude difference in the graph I mentioned. Interesting to see that the extinct lineages meant so much for diversification, according to Nick's references.
The angiosperms quite famously radiated prior to the Cretaceous extinction,
Another mistake of mine then. I distinctly remember about findings of dead plants with the event associated with the K-T boundary, but it could have been temporary individual deaths.

David Stanton · 10 April 2007

Levi wrote:

"aaaaaaaaaarrrrrrrrggggghhhhhhhh!!!!!!!! fossil spikes, gradual speciation,super bush, no super tree, no over the hedge! what will it be tommorrow? I don't know, I can't keep up. You highly mutated evolutionists can't agree on anything. is abiogenesis part of the super hedge or not? this must too be over my head. this is how smart I am; the three year old that keeps changing his story is of course telling the truth! Go mutations!"

I wrote:

"What must be remembered is that there will always be some who look for the easy answer. These are people who must see purpose, intelligence, foresight and planning in everything. They want simple rules that produce simple patterns. These are the same kind of people who see patterns in the stars and then assume that they have significance for our everyday lives. But evolution is just what happened. Sometimes it can be dirty and sloppy and very hard to reconstruct. That is precisely because there are no simple rules that are always true."

Note: my comment was made twelve hours before Levi posted his.

Then Levi wrote:

"wow species diverge now in a few thousand years? and yet a chimp is still a chimp. I know it's a cliche that you evos love to make fun of...and yet never answer. go mutations!"

Levi, you have been answered dozens of times by many different posters. The answer is always the same. Why do you refuse to even acknowledge the responses? Chimps were not the ancestors of humans and even if they were, there is no reason that every chimp would have to change into a human. Humans and chimps shared a common ancestor about 6 - 7 million years ago. Both species have changed considerably since then. If you want to spout nonsense that everyone knows is nonsense, best to do it on creationist sites where "don't ask don't tell" is the norm and no alternative views are allowed. And oh yea, "go mutations!"

Mike · 10 April 2007

Very interesting post, thanks Nick, especially the point about divergence and major changes not necessarily and even not likely being the same event.

Mike · 10 April 2007

In reading elsewhere I cam across John Alroy's site [ http://www.nceas.ucsb.edu/~alroy/ ]. If you go his CV, you'll find a link to his 1999 paper 'The fossil record of North American mammals: Evidence for a Paleocene evolutionary radiation' and on the home page a link to a his 'graph of everything you always wanted to know about mammals but were afraid to ask', which graphically shows why a major diversification of mammals at the KT boundary might not show up in a DNA analysis of extant mammals.

Lenny's Pizza Guy · 10 April 2007

levi:

a chimp is still a chimp.

In addition to all the scientists and other highly-educated folk who have lambasted you, I have specifically taken the time out of my valuable and modestly-lucrative endeavors as pizza delivery entrepreneur to educate you about bonobos, why they are significant, and why they are not "still" just chimps. I thought, as one not-very-highly educated guy (though at least I can find the "Shift" key...) to another, I might have some chance of getting through your cranium where others had been unable to get their drill-bits to bite. Your astonishingly erudite reply? To repeat yourself. I think I'm now entitled to dig down into my old collection of forehead stickers and select an appropriate one for you, levi. (And, no, it's not a faux-leather "501" patch...) Ah, here it is: M - A - R - O - O - Supplying the final letter is left as an exercise for readers--and, in all likelihood, bonobos!--of greater discernemnt than levi.

Nick (Matzke) · 10 April 2007

What the heck is next to John Alroy's head in that photo?

Mike Traynor · 10 April 2007

Nick,

"What the heck is next to John Alroy's head in that photo?"

I believe it is the abdomen of his very pregnant (and also evidently buff) spouse.

GvlGeologist, FCD · 10 April 2007

What the heck is next to John Alroy's head in that photo?
Um, Nick, I think it may be genetic recombination in action ;^)

levi · 11 April 2007

wow I really have been lambasted, if lambasting means many words that don't have much content other than insulting me. where are these drastic changes? so let me get this straight- common ancestor to chimp to drastic change to a one time new species- more drastic changes Lucy, Java man, Nebraska man, Peking man(all of whom are incredibally credible) to human. However, those species have dissapeared, and the chimp remains the same, and the humans remain the same. Huddle up guys!! From this point on no new species, everyone stay the same, ready break! Again you all will call me dumb but where are these existing changes? Hurry up and say fossil evidence. Are you sure you want to point at the fossil evidence? Hurry up say weve gotten taller! You guys rock! (remember Im the dumb one) Go mutations!

Richard Simons · 11 April 2007

Levi says
so let me get this straight- common ancestor to chimp to drastic change to a one time new species- more drastic changes Lucy, Java man, Nebraska man, Peking man(all of whom are incredibally credible) to human. However, those species have dissapeared, and the chimp remains the same, and the humans remain the same.
You know perfectly well you haven't got it straight.

Science Avenger · 11 April 2007

Levi spewed forth: so let me get this straight- common ancestor to chimp to drastic change to a one time new species- more drastic changes Lucy, Java man, Nebraska man, Peking man(all of whom are incredibally credible) to human.
Nebraska man was the tooth of a pig you ignorant troll.
remember Im the dumb one
Thank you for the reminder, but you supply fresh, incontrovertable evidence of that with every error-filled, sarcasm laden, logically incoherant screed. No one could miss it. Well, except you that is. The underlying presumption of your view of the world is that if you can't grasp something immediately, it must be false, which is sort of the opposite of thinking oneself dumb. However, it certainly guarantees you remaining that way, because it is very difficult to learn much of anything if you so casally dismiss the knowledge (not mere opinions) of those whose intelligence, dedication, and experience in an area so far exceeds your own. So not surprisingly, you seem exactly as clueless today as you did yesterday, and no doubt will be tomorrow. Does that mean you will never change? That's the implication of your "reasoning".

levi · 14 April 2007

a tooth of a pig really? wow I didn't know. maybe it was because science for so long propped it up as the find of it's time. so are you saying those other examples are legitimate? So I give a list of forgeries that we all know are false, and you again insult me, and do nothing to stand up for your evidence. Same as not standing up for forgeries like peppered moths or embryo drawings. hurry insult me tell me again it was a pig tooth and say nothing to stand up for any of these fakes. you would think when someone like me camoes with such inferior knowledge to your own that you could refute me. Call me stupid again, it's been like 15 minutes sinece you have! Go mutations!

Richard Simons · 14 April 2007

Levi:
It is an out and out lie to refer to peppered moth forgeries. The photos of moths glued to the tree trunks were not part of the data. They were to illustrate cryptic coloration.

The tooth identified as 'Nebraska Man' was a mistake that few people believed even before it was corrected. Piltdown man was indeed a forgery - but it was identified as such by evolutionary biologists. Creationists could not have identified it as a forgery as they had no reason to accept or refute anything about it, and certainly could not have checked the age of the material.

Ach! But you know all this anyway.

Tell me, in what way does posting barely-coherent bumptious twaddle give you satisfaction? I have known teenagers and undergraduates with similar attitudes but it's rarely seen in adults.

Science Avenger · 14 April 2007

But I did refute you Levi, inasmuch as your incohrant ramblings can be assigned crisp meaning in the first place. And I didn't call you stupid, I called you clueless, and you again provide fresh evidence. Claiming the moth example of evolution is a forgery because the moths were glued to the tree for an illustration is sort of the lower bound of the "clueless" scale. It is also an excellent example of how creationists will grasp at any argument, no matter how ridiculous, and how oft-refuted it is, that supports their cause.

ben · 14 April 2007

Typical creationist strategy. 1) Enter evolution discussion. 2) Babble like an idiot and show willful ignorance of evolution. 3) Get called idiotic and ignorant because that's how you're acting. 4) Complain that "evolutionists" only hurl insults. 5) Repeat again ad infinitum.

How does doing this refute evolutionary theory or support any alternative to it?

David Stanton · 14 April 2007

Levi wrote:

"However, those species have dissapeared, and the chimp remains the same, and the humans remain the same."

I wrote:

"Humans and chimps shared a common ancestor about 6 - 7 million years ago. Both species have changed considerably since then."

Once again, note that my post was more than a day before Levi posted.

So Levi, got any evidence that chimps and humans haven't changed in 6 - 7 million years, or are you just making stuff up? You need to read and respond to those who answer your "questions" before repeating them over and over and over and over and over again. (By the way, bacteria are still bacteria as well).

Since you are so fond of fraud, maybe you can explain those human footprints next to the dinosaur footprints for us. And oh yea, "go mutations".