Wednesday, March 28, 2007

Evolution of Mammals

 
A paper in this week's issue of Nature presents a nice summary of recent work on mammalian evolution. Bininda-Emonds et al. (2007) have combined a lot of data from various studies in order to construct a supertree of mammalian evolution. The study incorporates fossil data with molecular sequence data to arrive at estimates of divergence times for 4,510 species of mammal out of a total of 4,554 extant species (99% complete).

This is a study of macroevolution. The authors are addressing questions about the mode, tempo, and pattern of speciation over a period of more than 150 million years. The main questions are when did mammals diversify and did it have anything to do with the mass extinction event at the Cretaceous/Tertiary (K/T) boundary. This is the event that resulted from an asteroid impact 65 million years ago.

The results are presented in the form of a large phylogenetic tree showing the major groups of mammals. The first split in the mammalian tree occurred 166 million years (My) ago when monotremes such as platypus and echidnas (black) split off from the other mammals. Marsupials such as opposums, kangaroos, and koalas (orange) separated from placental mammals 148 My ago.

Within the placental mammals, all of the extant orders appeared by 75 My ago. This includes the clades labelled on the outside of the circle plus other. For a compete list and a description of the species, see the NCBI Taxonomy website [Eutheria].


All of these orders were established at least 10 Myr before the mass extinction event (dashed circle on the circular tree). This is one of the main conclusions of the meta-analysis. The most significant diversification of mammals takes place well before the extinction of non-avian dinosaurs.

The other conclusion is that subsequent radiations at the level of families were not significant until after 50 Myr ago. This period of diversification lasted until about 10 Myr ago. There is no evidence to suggest that the radiations within each order were synchronous, ruling out global climate change as a mechanism.

Furthermore, the data clearly shows no connection between the mass extinction event at the K/T boundary (65 Myr ago) and subsequent radiations of mammalian groups. This effectively rules puts an end to the long held belief that mammals diversified after the devastation in order to fill up the niches left by dinosaurs. This is not the first paper to refute that belief but it may be the final nail in the coffin.

This summary serves as a warning to those who continue to associate evolution with environmental change. At this level of analysis there does not seem to be a connection between rates of speciation and climate change. This is most obvious with respect to the asteroid impact of 65 My ago. While it led to mass extinction, it did not lead to increases in the rate of evolution of the survivors. The branching pattern of cladogenesis in the figure is hardly affected by the cataclysm.

Similarly, there are no other speciation events that correlate with known climate change over the past 150 million years, including recent ice ages. There is growing recognition among evolutionary biologists that rates of speciation cannot be attributed to large-scale environmental change. (The data has not prevented speculation. Many reports on this paper attempt to manufacture some correlation between global environmental change and speciation. The old idea of a link between them is too entrenched to give up so easily.)

There's an interesting sidebar to this story. The paper clearly states the two main conclusions,
... the pivotal macroevolutionary events for extant mammalian lineages occur either well before the boundary (significant decrease in diversification rate at approximately 85 Myr ago, after establishment and initial radiations of the placental superorders and major orders at approximately 93 Myr ago) or well afterwards, from the Early Eocene onwards (when net diversification began to accelerate)....

Therefore, the demise of the non-avian dinosaurs, and the K/T mass extinction event in general, do not seem to have had a substantial direct impact on the evolutionary dynamics of the extant mammalian lineages.
However, in the title of the paper, The delayed rise of present-day mammals, the authors focus attention on the second conclusion at the expense of the first. Some of the press releases picked up on this emphasis, leading to the false impression that mammalian evolution is more recent than scientists thought [Did the Dino Die-Off Make Room for Mammals?] while others got it right [Mammals not such late developers, after all].

The point about early diversification is emphasized in the Nature News & Views commentary that's published with the article in the March 29th issue. David Penny and Matthew J. Phillips begin with a summary of the evidence for early evolution,
On page 507 of this issue, Bininda-Emonds and co-authors1 present an evolutionary tree of more than 4,500 mammals, and conclude that more than 40 lineages of modern mammals have survived from the Cretaceous, some 100 million to 85 million years (Myr) ago, to the present. This is paralleled by Brown and colleagues' analyses for birds, just published in Biology Letters: they claim that more than 40 avian lineages have likewise survived from before the extinctions at the Cretaceous/Tertiary (K/T) boundary 65 Myr ago. These numbers of surviving lineages push back the evolutionary history of many mammals and birds much further than earlier estimates based on smaller data sets. But strong claims need strong evidence to support them.
Later on they re-emphasize this point,
But the most challenging aspect of the phylogeny is the inference that more than 40 lineages of living mammals (and of birds, as described by Brown et al. 2007 ) survived from the Cretaceous to the present.
There are some quibbles about the data. Personally, I think the estimates for early divergence are too recent rather than too late . It all depends on the first fixed data point which is the separation of monotremes. This date (166 Myr ago) is a minimum estimate and there's evidence for an older date. The popular report on the Nature website [Disappearing dinos didn't clear the way for us] mentions this possibility. Mark Springer of the University of California, Riverside (USA) is interviewed and the article states,
"This is a reasonable first approximation," he [Springer] says. "Some of the dates and relationships are probably right on, and some are probably going to move around."

For example, says Springer, the team estimates that the deepest split in the mammals' family tree, between the egg-laying monotremes (such as the duck-billed platypus) and the rest happened 166 million years ago. But some molecular analyses suggest it happened more than 200 million years ago; Springer thinks this earlier date is probably closer to the truth. If that fundamental point changes, he notes, other things will have to shift too. "That date influences everything else through the tree," he says.
I suspect he's right and all the dates will move back in time. One wonders whether the late radiation at 50 My will then shift closer to the K/T boundary.

It's clear that more work needs to be done but the significance of this paper is that it assembles a lot of evidence into one place and publicizes a debate that's been smoldering among evolutonary biologists for over adecade.

Bininda-Emonds, O.R.P., Cardillo, M., Jones, K.E., MacPhee, R.D.E., Beck, R.M.D., Grenyer, R., Price, S.A., Vos, R.A., Gittleman, J.L., and Purvis, A. (2007) The delayed rise of present-day mammals. Nature 446: 507-512. [PDF]

Penny, D. and Phillips, M.J. (2007) Evolutionary biology: Mass survivals. Nature News & Views, Nature 446: 501-502. [PDF]

17 comments :

  1. Fabulously summarised!

    It does give me pause and make me wonder, though (doesn't all good science?): if environmental changes, like the K-T impact and past global climate changes, or ecological changes like the extinction of a quite substantial group (i.e., the dinosaurs) didn't affect the diversification trends in mammals, then what did? Those seem like the obvious answers, but since the data shows them to be basically wrong, there must be something else going on.

    Are there any hypotheses floating around that attempt to explain the behaviour of the net diversification rate of the mammalian lineage in light of the observed fact that the K-T extinction wasn't a factor? I'm curious to hear what the competing explanations are.

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  2. You are right that it was not a good idea to fix the age of the root at 166.2 Ma, and that the cladogenesis may well have happened earlier. However, most of the other calibration points are too old because the phylogenetic positions of the fossils in question were misinterpreted. Bininda-Emonds et al. regularly mistook stem-group representatives for crown-group members. For example, the one they took as the oldest rodent is the oldest rodentiamorph, as the paper they cite makes clear -- Rodentia is younger than that, and Rodentiamorpha includes Rodentia plus its closest extinct relatives. For more, please see my comment over at Pharyngula: http://scienceblogs.com/pharyngula/2007/03/dont_blame_the_dinosaurs.php#comments

    This miscalibration pushes most, maybe all, divergence dates too far into the past. I'm sure this more than offsets the effect of the probably too young root.

    Using only minimal ages for the calibration points and no maximal ages may not have been a good idea either. There are rich Late Cretaceous mammal faunas which lack any trace of placentals or marsupials -- in some of those cases I think absence of evidence should be regarded as evidence of absence of a radiation.

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  3. The link I just posted probably didn't work.

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  4. A couple of thoughts here (from a palaeontologist's perspective).

    Firstly, the KT extinction isn't necessarily entirely explained by an impact. In fact the evidence against impact-induced mass extinctions has only mounted in the last decade or so. For example, Chixculub is now known to be too old to be linked to the KT (so we have a whopping big crater with no extinction) and serious doubts over North American wildfires supposedly linked to the impact have been cast. The geological record is littered with extinctions that don't match up with even minor extinction events. All other casual mechanisms for mass extinctions are more prolonged (climate change, sea level change, volcanic outpourings etc.).

    Secondly, Bininda-Emonds et al's tree includes extant taxa only. The level of coverage is to be applauded, but if you want to talk about diversification rates in deep time to ignore fossils is perilous to say the least. This is beacuse: a) many fossils sit within crown-group Mammalia and hence are extra nodes on the tree (nodes are what we are counting when we say diversification so this is skewing of the data) and b) fossils are the only evidence we have for the timing of divergence events (to use just a few tie-points and then 'fill in' the rest means you can pretty much get whatever result you want).

    I will await the supertree including all known fossil taxa before I accept any hypothesis about diversification rates across a mass extinction boundary.

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  5. For example, Chixculub is now known to be too old to be linked to the KT

    Keller and friends have most likely drilled through a boulder that fell in from the walls of the primordial crater (which was a semicircle in vertical section, tens of km deep -- of course its walls collapsed, and of course the walls were composed of Cretaceous sediment). I don't understand why they didn't even consider this possibility, and I'm not alone in this. Keller et al. also seem to ignore facts like that the spherule layer gets thicker and thicker the closer you get to Chicxulub, and so on.

    The main episode of Deccan volcanism ended 100,000 years before the boundary, and the global average temperature returned back to normal (it had risen by 3 °C due to the CO2 emissions).

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  6. Malacoda says,

    Secondly, Bininda-Emonds et al's tree includes extant taxa only. The level of coverage is to be applauded, but if you want to talk about diversification rates in deep time to ignore fossils is perilous to say the least.

    I agree completely. Nevertheless, there are two solid conclusions from recent data on mammalian diversification. The first it that it began long before the K/T boundary event. The second is that much of the recent diversification (extant species) is not related to known climate changes.

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  7. As very much a non-expert in these matters, it appears to me that an important point is being missed here. In particular, was the dinosaur extinction a necessary requirement for the development of large mammals, including large primates? These findings do not appear to in any way negate a positive answer to this question as there is still no fossil evidence of the existence of such large mammals prior to the KT boundary. All that this paper appears to this non-expert to assert is that diversification trends in mammals started earlier then previously thought (albeit with the mammals still being small) and that the appearance of large mammals occurred later then previously thought.

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  8. Seconding joshua's question and expanding it: If large-scale environmental changes don't alter diversification rates, why would those rates ever change significantly?

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  9. Global Warming is one among many deceptions aimed at securing a final victory for a Religion that has one overriding goal which it is achieving through its control of the “theoretical” science establishment: That goal is the final destruction of all remaining resistance ( in the USA particularly) to the acceptance of billions of years of Evolution as the one true “scientific” factor of how all that exists came to be as it is.
    Once faith in the evolutionary explanation for the origin of all that exists is established in people’s minds, there are two and only two belief systems available that will take hold and color every aspect of every believer’s life: First: They can become atheists, believing in no religion or “god”, but solely in random chance “evolution”. Second: They can accept some New Age “Force” or little g’d or g’ds which have worked with or “used” billions of years of evolution to create all that is, including mankind, (but belief in the God of the Bible Creationism is not an option).

    Both of these belief systems are totally dependent upon billions of years of evolutionism. Neither can exist without those billions of years of “evolution”. Is there a religion that has given the world this belief in those necessary billions of years? Is there another religion that explains the origin of all that exists without any evolution whatsoever? Would not two such religions be implacable enemies with the highest motivation to discredit and ultimately destroy the other?!

    These two Models--a) evolution; b) no evolution--offer mutually exclusive explanations as to what the Truth is about the Origin of all things. Since the Truth about the Origin of all things is unarguably the foundation of all knowledge, it is certain that the entry of the evolution-dependent “Global Warming” Model into the Origins Sweepstakes is quite different from what its propaganda is telling us.


    With that in mind let’s see how and why these billions of years of evolutionism are the real cornerstone of the Global Warming “News”, and then answer the big questions.

    (Note: These are sample quotations that anyone can multiply many times on line.):

    NATIONAL GEOGRAPHIC NEWS: Feb.7, 2007:

    “Today the world faces global warming, but 34 million years ago a distinctly
    chillier menace was sweeping our planet.... Average temperatures around the world
    plunged 15 degrees Fahrenheit....during a span of hundreds of thousands of years...”

    STOPGLOBALWARMINGORG: LEARN MORE:

    “Global warming isn’t opinion. It’s scientific reality...atmospheric greenhouse

    gases have reached levels not seen for millions of years...more carbon dioxide is

    now in the atmosphere than has been in the past 650,000 years....”

    INTERGOVERNMENTAL PANEL ON CLIMATE CHANGE - WIKIPEDIA:

    “...Global atmospheric concentrations of carbon dioxide methane and nitrous

    oxide have increased markedly as a result of human activities since 1750

    and now exceed pre-industrial values over the last 650,000 years....”

    UNDERSTANDING EVOLUTION:

    Your One Stop Source For Information On Evolution

    http://evolution.berkeley.edu/evolibrary/news/060701_warming July 2006:

    “...Increasingly, it seems, global warming shows up on the front page
    of the newspaper--but the evolutionary implications of global warming
    often remain hidden....Global warming is certainly a climatic and
    environmental issue--but it is also an evolutionary one....”
    PHYSORG.COM - SCIENCE: PHYSICS: TECH: NANO: NEWS, Feb. 07, 2007:

    “Study shows largest North American climate change in 65 million years....

    The overwhelming majority of previous climate-change studies on the 400,000

    year transition from the Eocene to the Oligocene epochs, about 33.5 million

    years ago, focus on marine environments....”

    GLOBAL WARMING FAST FACTS, NATIONAL GEOGRAPHIC NEWS 12/6/04

    “...Over the last million years the Earth has fluctuated between colder and
    warmer periods. The shifts have occurred in roughly 100,000 year intervals....
    During the last ice age, approximately 70,000 to 11,500 years ago....

    UNIVERSE TODAY: 6 NEW STORIES 2007/03/24

    "...By analyzing glacial sedimentary rock in Oman, researchers have discovered

    evidence of hot-cold cycles roughly 850-544 million years ago--during

    the period when the earth should have been in a deep freeze....

    For their own reasons the following contrasting comments (and plenty of others!) on the global warming movement are of interest:

    SENATOR JAMES INHOFE (R. OK):

    “Global Warming is the greatest hoax ever perpetrated on the American People.

    SCIENCE DAILY: LONDON, MARCH 6TH (UPI):

    “... Filmmaker Martin Durkin’s documentary ‘The Great Global Warming

    Scandal’...is airing in Britain this week.... Durkin says the greenhouse theory is

    ‘the biggest scam of modern times’.”
    Indeed, one needn’t dig very deep to determine that the now famous Al Gore documentary scaring the bejabbers out of everybody with its doomsday ice-melting, oceans-rising scenario, has as many critics from the world of science and politics and economics as it has supporters. We just aren’t hearing from the critics as much.

    Nor do we hear that “Environmental Activist”, Laurie David (along with her husband, Comedian Larry David from the Seinfeld show) reportedly has “single-handedly forced the debate” by “discovering” and promoting the Gore Documentary...with a book, naturally. The money and prestige stakes in all this are enormous, of course, but “evolution science” is the real beneficiary. It stands to score three big home runs, namely: 1) Resistance to evolutionism in the USA, etc., will be further weakened; 2) Resistance to the Global Warming agenda and environmentalist extremism in the USA, etc., will be dealt a hard blow; 3) Another hard blow will be dealt to Bible Credibility regarding it’s plain teaching of a Creator God who could and did create everything (including mankind in His Image) in six evening and morning days with no evolution necessary.

    This brings us to those big questions growing out of the “billions of years” that are the lifeblood of evolutionism. Followed by their answers, they are:

    Q) What religion and what science are providing those eons of time?

    A) Writing in Kabbala in the 1st century A.D., Pharisee Kabbalist Nechunya ben HaKanna--using a 42 letter name for g’d--determined the age of the universe to be 15.3 billion years. This is the same age that is in today’s textbooks. Other concepts of today’s Pharisaic cosmology (relativity, heliocentricity, Big Bang, expanding universe, superstrings, parallel universes) are found in 13th,16th, 20th century Kabbalist writings.

    Q) Does this Pharisee religion and this Kabbalist "science" have a g’d; or is it atheistic? Or, can it be either so long as it keeps the billions of years of evolution??

    A) As long as the billions of years of evolution are retained, this Religion with its mystic Kabbala writings can accommodate both atheists and any g’d or g’ds or “Force”, etc., just so long as the God of the Biblical six day creation is eliminated.

    Q) What religion and what science is there which explains the creation of everything in six days without any evolution whatsoever?

    A) The Biblical Creation Account of the Christian religion (& some Orthodox Jews) teaches a God who had the power and resources to create everything in a literal evening and morning six day time frame with zero evolution involved...and ALL known science confirms this Account.

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  10. Wow, non sequitur.

    Anyway. Thanks, jackd, for asking the question I meant to ask, had I not been so addle-pated from a long day at work. ;)

    I wonder if you could make an argument that the rates of change are based on internal developments within the genome? E.g., a species happens by pure chance to propagate a mutation that acts as a springboard for multiple future speciation events.

    Or, to take a more heterodox view, maybe there's a factor we can't see like a new parasitic relationship that wasn't preserved in the fossil record. Or maybe a genetic insertion due to viral activity. (There's precedent for the latter in the human genome, isn't there?)

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  11. Larry:

    I like your analysis, and I hope everybody reads it.

    I think, however, that the evidence for a post KT event diversification of mammals is still strong. The fossil evidence for this did not vaporize on publication of this paper, though the paper sure has a lot to say about mammalian diversification in general.

    As for the environmental change - speciation link or lack thereof, I agree with you at this very basic and important level: Claim after claim after claim fails to support the idea. However, I think this is more because of the simplicity of the claim and a lack of understanding of the process. I don't want to rule out environment-speciation links yet, I want to first explain them a different way.

    Here's my post on this, which is in part a direct response to your very excellent post here:

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

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  12. malacoda- just wanted to say that I love your nom de blog. "...ed elli avea del cul fatto trombetta." ;)

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  13. slc asks,

    In particular, was the dinosaur extinction a necessary requirement for the development of large mammals, including large primates? These findings do not appear to in any way negate a positive answer to this question as there is still no fossil evidence of the existence of such large mammals prior to the KT boundary.

    In my opinion the question is loaded with too many assumptions. Why would you even ask it unless you have a concept of evolution that makes certain assumptions about niches and competition between species?

    You are assuming that once a "niche" (whatever that is) is occupied no other species can evolve to occupy that niche. In this case, you are assuming that the large dinosaurs—a subset of all dinosaurs—prevented the evolution of large mammals.

    I don't accept the assumption. I don't know why speciations and radiations occur. What I do know is that many of the standard assumptions need to be challenged.

    The "correct" question, as far as I'm concerned, is the open-ended one and not one that is predicated on an assumption that seems to have no grounding in fact. In other words, there's no evidence that the presence of large dinosaurs prevented the evolution of large mammals so why do you expect scientists to "disprove" this speculation?

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  14. jackd asks,

    Seconding joshua's question and expanding it: If large-scale environmental changes don't alter diversification rates, why would those rates ever change significantly?

    Accident?

    The question goes to the heart of the major controversy in evolution. It's the fight between the adaptionists and the pluralists. The adaptionists tend to believe that most evolutionary change is driven by natural selection.

    In this example, the adaptionists will develop hypotheses about environmental change because they can't conceive of any other way that natural selection could work to create species.

    The pluralists do not claim that these events are due to natural selection. Speciation almost certainly has a significant random genetic drift component. There are large-scale "random" events as well, such as the creation of the Isthmus of Panama and the separation of Australia.

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  15. I completely agree that this is not about large mammals filling large dinosaur niches.

    Also, even though there does seem to be a number of common "niches" that keep coming up again and again in the history of life, niches are not abstractions. Wiping out all the animals in a set of niches does not open the niches they were in, partly because the niches they were in were defined in large part by their very existence. (In my post on this I have an alternative suggestion regarding the "large body" issue)

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  16. “There is no evidence to suggest that the radiations within each order were synchronous, ruling out global climate change as a mechanism.”
    “there are no other speciation events that correlate with known climate change over the past 150 million years, including recent ice ages. There is growing recognition among evolutionary biologists that rates of speciation cannot be attributed to large-scale environmental change.”
    This off-hand dismissal of climate as a stimulant to diversification seems a bit premature. I understood that the Miocene (when the diversification of modern mammal groups is supposed to have really got under way) was a period of major climate change (drying and cooling) leading to spreading grasslands, declining forest cover, expanding ice caps and temperate zones and falling sea levels. The development of what we recognise as a more or less modern flora and fauna at this time seems too much of a coincidence.
    It might not be possible to link a specific evolutionary event to a specific climate event but aren’t we looking at trends here? (Come to think of it, how many such precicely pin-pointable climate events as the Chicxulub impact are there anyway?)
    Does this label me an ‘Adaptationist’? Why does there have to be a ‘fight’ between adaptationists and pluralists? Why can’t it be a bit of both?
    “I don't know why speciations and radiations occur.” Really? But you must have some strong suspicions.
    Sorry, but this line of argument is a spurious method of dismissing others’ observations as idle speculation by disingenuously positing your own ignorance. Shame on you!
    Excellent blog by the way. Nice to see everyone ignoring the conspiracist nut-job.
    Keep it up.

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  17. Steve Law says,

    This off-hand dismissal of climate as a stimulant to diversification seems a bit premature.

    To be specific, it's not a blanket dismissal of the idea that climate change is a cause of radiations. It's a dismissal of the so-called "evidence" that's supposed to support the hypothesis.

    I understood that the Miocene (when the diversification of modern mammal groups is supposed to have really got under way) was a period of major climate change (drying and cooling) leading to spreading grasslands, declining forest cover, expanding ice caps and temperate zones and falling sea levels. The development of what we recognise as a more or less modern flora and fauna at this time seems too much of a coincidence.

    You're talking about climate change that was spread out over tens of millions of years, right? It's hard to see how that could lead to mammalian radiations. Furthermore, if the climate change was so drastic then why didn't other groups also spawn new species during this time?

    It might not be possible to link a specific evolutionary event to a specific climate event but aren’t we looking at trends here?

    Yes, we're looking at trends and correlations. The idea that radiations are stimulated by environmental change needs evidence, otherwise it's just idle speculation.

    That's how science is supposed to work.

    (Come to think of it, how many such precicely pin-pointable climate events as the Chicxulub impact are there anyway?)

    Not many. That's why there's so little evidence in support of the speculation.

    Does this label me an ‘Adaptationist’?

    Yes, because when one bit of evidence is refuted you immediately propose another adaptationist explanation without considering alternative explanations.

    Why does there have to be a ‘fight’ between adaptationists and pluralists? Why can’t it be a bit of both?

    Adaptationists are wedded to adaptationist explanations. Pluralists look at all possible explanations, including those that have nothing to do with adaptation. When you say "why can't it be a bit of both?" you are supporting the pluralist position.

    “I don't know why speciations and radiations occur.” Really? But you must have some strong suspicions.

    Yes, I have some ideas. One of them is that it could be just an accident of history. Another is that mammals are very good generalists and they rapidly spread out to occupy all kinds of environments. This would have happened with, or without, climate change.

    Sorry, but this line of argument is a spurious method of dismissing others’ observations as idle speculation by disingenuously positing your own ignorance. Shame on you!

    Since when is a critical examination of evidence dismissed as an example of ignorance?
     

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