Michael Denton’s new book is out, Evolution: Still A Theory In Crisis.
Denton’s stance is for structuralism and against functionalism, especially as functionalism appears in it’s current form as the modern synthesis or neo-Darwinism (the cumulative selection of small adaptive changes).
Denton argues for the reality of the types, that “there are unique taxon-defining novelties not led up to gradually from some antecedent form” and that the lack of intermediates undermines the Darwinian account of evolution. He also argues that a great deal of organic order appears to be non-adaptive, including “a great number of the taxa-defining Bauplans,” and that this also undermines the Darwinian account of evolution. Evo-devo is also showing us that “Darwinian selection is not the only or even the main factor that determined the shape and main branches of the great tree of life.”
These arguments are first set forth in Chapters 3 through 5 of the book and then defended throughout the subsequent chapters.
Denton provides a list of some of the Type-Defining Homologs:
The Pentadactyl Limb
The Feather
The Insect Body Plan
The Flower
The Amniotic Membrane
It is not just the major taxa which are characterized by unique defining homologs or novelties:
Centipedes
Beetles
Ants
Butterflies
Even individual species are often defined by unique novelties (autapomorphies in cladist terminology).
To head off a lot of irrelevant objections and nonsense from people who can’t be bothered to read the book, Denton accepts common descent and doesn’t appeal to “goddidit” as a better explanation.
- If types exist, what does that mean for Darwinian evolution?
- Does the existence of non-adaptive order undermine Darwinism?
- Does anyone think neo-Darwinism is even relevant to modern evolutionary theory?
Well looky here. Here is an actual gene study on a living fossil:
Doesn’t it seem to bother anyone the living fossil doesn’t have more widely diverged genes between their members? 🙂 The MRCAs are recent.
One thing I should add, the mutation rates are inferred, they are usually not directly measured. The way to do it was actual measurement of living creatures such as was described in the Loewe and Scherer paper.
Again I have trouble understanding your claims because you use terms so carelessly. What does “treated particulately” mean here? Whose entire genome are you talking about? I thought this was about E. coli, in which case it’s quite possible for the entire genome to be under selection. And what species are you talking about whose entire genome is invariant?
Agreed; that’s what a selective sweep is. What point are you making here?
Agreed. At least it has the same genetic signature as a bottleneck.
Explanation of what?
MRCA of what? Of the entire genomes of a species? This is quite unlikely ever to happen with any sexually reproducing species. Let me know if you find any examples. I agree that it would, if it happened, imply an extremely narrow and extended bottleneck (a selective sweep of the whole genome is pretty much ruled out for any sexually reproducing, recombining population).
A test of what hypothesis? You still seem very confused about the connection, or lack thereof, among genomic change, morphological change, speciation, divergence between species, and coalescence within lineages. What is the test? What is the hypothesis? What is the reason for the hypothesis. Again I ask you to confirm that you are trying to test for a worldwide flood and survival on an ark, all such requests for which you have so far ignored.
stcordova,
Yet again you seem to have no clear idea what you are claiming, what the data are, and what they show. It’s impossible to discuss this with you at the current state of your confusion.
An origin of a new species counts as bottle neck. I later defined “recent” as several million years, how about 10 mya. I also said splitting off of individuals to be the origin of a new species counts as a bottle neck. I also said the intra species variation of living fossils would be interesting and went out on a limb that the hypothesis of MRCA for those would also hold.
ABSTRACT
A review of Cycad genes is consistent with a corollary of the Cordova hypothesis that intra specific variation will point to recent origin of extant species even if the species is considered a living fossil.
MATERIALS AND METHODS
A computer attached to the internet was used to argue with others about the idea. A literature search using google was conducted to see if there is confirming evidence of fossil plants consistent with Cordova’s hypothesis.
RESULTS AND DISCUSSION
Cycads were seen as far back as 300 million years ago. There was the supposition that the Cycads of today were the same as those in the era of dinosaurs, the Mesozoic from 272mya to 65mya. That is the MRCA of Cycads was in the Mesozoic or even the Permian 300 million years ago.
That supposition of deep-time MRCA cycads was in sharp variance to Cordova’s hypothesis. Recent evidence vindicated Cordova’s hypothesis. A google search found this article:
CONCLUSION
Cycad data are consistent with corollary of Cordova’s hypothesis that MRCAs of most species will be indicated to not be more than several million years even if the species are considered living fossils. It had been presumed the cycads of today were in the era of dinosaurs and there was the possibility the MRCA was even in the Permian period 300 million years ago since there exist Cycad fossils in that time frame. However, genetic evidence overturned the possibility of a 300 milliion year old MRCA and is consistent with Cordova’s hypothesis that most MRCAs of species specified by autapomorpies will have MRCAs that are relatively recent ( less that or equal 10 mya). Observations agree with Cordova’s theory.
Sal can celebrate with a few table spoon so Umeshu wine. 🙂
I didn’t think Sal could get any more pathetic in his YEC blithering but fantasizing he wrote a scientific paper that supports his YECkery is a new low.
No it doesn’t. Why would you imagine that it does?
Why would variation of living fossils be interesting? Why are you defining “recent” as 10ma, and why do you make this prediction, whatever it is?
Both you and your main source are confused, though perhaps in somewhat different ways. Cycads are not living fossils. The fact that the divergences between sister species of cycads (which is not the same as the ages of the species themselves) are relatively recent for the most part is irrelevant to the within-species divergence you are supposedly talking about. The phenomenon you see is easily explained if we postulate a high species turnover rate in cycads, i.e. both high extinction and high speciation rates. This has nothing at all to do with divergence within species.
And here you confuse the MRCA (a species) of the entire cycad clade with the hypothetical and probably nonexistent MRCA (an individual) of a given cycad species.
This is all hopelessly confused. None of this has anything to do with your theory. Nobody has claimed anything like the strawman you set up as your alternative hypothesis (current cycad species in the Permian). And I ask again why you have advanced your hypothesis. What leads you to your conjecture?
Now it’s just a matter of those pesky three orders of magnitude, plus another couple for the history of the lineage.
The readers may wonder why I went out on a limb. Simple!
When I did blast queries some years back, and saw the result of the closest hits, the hits were always close, usually 100% of sequencing experiments in diverse geographical regions. The INTRA-species variation was next to absent. I suspected this could be the case when I looked at the Dayhoff diagrams, but I really really saw it when doing BLAST queries of NIH NCBI data and saw the listings of sequencing experiments. I simply put two and two together — the MRCAs must be recent.
I saw it in the BLAST queries as far back as I can remember, even before the Cycad study. The results don’t surprise me. Not one iota.
The cycad study calibrated their molecular clocks with supposed 55 million year old fossils. Of course, they’ll get a date with those orders of magnitude. The clocking methods are flawed, the method that Loewe and Scherer reported on is superior because it uses experimental data rather than speculative methods.
The cycad studied falsified some ideas. What other problems are lurking?
One paper by the PI is below. I’m not a phylogenist, so I don’t understand most of the terminology, but I could see enough of the calibration methods that would lead to 10 mya dates.
http://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-015-0347-8
Would they be willing to drop the fossil calibration and do a real calibration? They might be horrified at the results just as the horrified researcher that were reported by Loewe and Scherer.
Mass extinctions? You mean bottleneck processes. Gee, I don’t think I’m getting enough credit. I said:
The paper mentions the neogene (23 million years ago) and the word Crown Group:
I disagree with your characterization. You’re just mincing words and not giving a charitable reading.
I searched for conclusions just like the cycad paper, and lo and behold it was there. It doesn’t surprise me such a paper came out. I suspected it years ago when doing BLAST queries on the gene banks.
The paper demonstrates what I was trying to say, the exact wording doesn’t matter as much as the fact the data confirm what I suspected.
This opens to the door of the research I suggested for recent origin of species for every extant species.
Whether you view me as being wrong doesn’t matter. I didn’t show up here to convince anyone, but I wanted to formulate my ideas more cogently through the process of interaction. In the process, I found a data point I was looking for in the Cycad data. It confirms a suspicion I’ve long held but couldn’t quite articulate.
How about research into the ACTUAL origin of every extant species? You make it clear that your conclusions don’t follow the evidence, but that your evidence follows your conclusions.
The reason I gave a 10mya figure was I seemed to recall the E. Coli was given that birth date, this despite the fact it only has 20% conservation! How do they calibrate their clocks? So I said, Ok 10mya is the only figure I have, I’ll go with it, we’ll see if it holds. There may be a calibration issue, but if other studies are calibrated the way it was for the E. Coli clock, we might see that figure emerge again.
Now I found this:
http://www.ncbi.nlm.nih.gov/pubmed/23997230
Gee thanks scientists, you even used the word “recent”. 🙂
stcordova,
I don’t mean to be impolite, but I have no clear idea what you think you’re saying, only that you are very confused on a great many points. This is clearly because you don’t understand what you’re reading and thus don’t know what you’re talking about. I ask you only to consider the possibility that I’m right in this. We could discuss the nature of your confusion, but you seem interested only in doubling down on it.
The word “recent” refers to the hypothesis, not to the ages of the cycads. And once again I should point out that the cycad paper refers to divergences between species, not within them as your hypothesis (if it means anything) actually refers to. You can’t keep conflating all these separate ideas and remain coherent.
I ask again: what is the reason for this hypothesis of yours? What scenario do you think this hypothesis will support if it ever turned out to be true?
I already said it, the lack of intra species divergence! I saw it in BLAST sequences of just about every query I made. Almost no exceptions.
The cycad papers show exactly the problem because they sampled extant species.
How do you interpret this statement to the lay reader:
The word “crown” is used.
From wiki definition of Crown group:
The bold says “most recent common ancestor” as in MRCA.
So does that mean the MRCAs of each of the cycad genera is not more than 12 mya?
So you seem here to be talking about the range of genetic variation between individuals in a single species, is that right?
What problem are you referring to here?
NOW you are apparently NOT talking about the variation within a species, but rather the variation between genera.
I understand your source as saying that if you take two species of cycads in one genus, they have a common ancestor. Take two species of cycads of another genus, and they have a different common ancestor. Take those two common ancestors, and of course THEY had a common ancestor. And THAT branching is estimated to have occurred no more than 12mya.
Now, how does this related to genetic variations within a single species?
Flint,
Note that Sal is using the same term, “common ancestor”, for two quite different things: the population ancestral to two or more species, and the (supposed) individual ancestral to the current population of a single species. But he doesn’t seem to notice that. He’s in his own little world, and nothing anyone says here can penetrate.
Exactly. Or should we say almost near lack of genetic variation.
What does that suggest to you if they look so similar — like — eh — they might share a common ancestor, like — eh — recently? 🙄
They talked about genera, but if the genera aren’t really species, then the species are even more recent. You’ve just strengthened my point.
Looking so similar tells us almost nothing about molecular evolution.
stcordova,
Why do you think intra species divergence would show up on a BLAST? Published genomes tend to be a ‘consensus’ sequence for the entire species (Craig Venter and his dog!). You couldn’t possibly pick up intra species patterns from them.
Sal, despite insisting that you do recognise what MRCA means in a sexual species, you proceed to argue as if you don’t. An MRCA is not the first member of a species, nor (necessarily) a member of a bottlenecked population or the originator of a mutation. It’s just the most recent individual to whom a shared locus can be traced through an assumed series of DNA replications.
It is perfectly reasonable that cycad, horseshoe crab and human species can have MRCAs of the order of a few tens of thousands of years ago (there will be a distribution, depending on the locus). It depends on effective population size, not the designation ‘living fossil’ or residence on an Ark.
There would, I suspect, be a different pattern of MRCA ages for genomes of animals on the Ark vs the rest of the biosphere (some of it, surely, barely troubled by a Flood, even a big one). Rather than wasting their time BLASTing for intra-species divergence, a YEC who buys into phylogenetic methods could profitably look for this bimodal pattern.
I confidently predict they won’t find it (you’d think someone would have noticed!). But anyone can have a go.
stcordova,
What were they horrified about? Basing an estimate on a highly variable 7% region of the genome and ignoring the rest?
Sal,
Your inability to locate variable DNA regions by Blast notwithstanding, there is a rather vast literature on the topic of intraspecific genetic variation. Perhaps you’d like to explore some of it before erroneously concluding that intraspecific divergence does not exist? I would suggest perusing some articles from nearly any issue of the journal Molecular Ecology or essentially any paper on the topic of phylogeography.
Some databases have the alleles, others the sequencing experiments, others the strains.
Yes, we sometimes call the intra specific variants alleles.
Some of the huge databases are at the NIH:
http://www.ncbi.nlm.nih.gov/snp
http://hapmap.ncbi.nlm.nih.gov/whatishapmap.html.en
But even for humans the total variation is around 0.5%
But here is a back of the envelope calculation. Humans are 99.5% or so similar to each other. Humans vs. Chimp are 90% – 95% similar on DNA depending on how we do the comparison. Let’s pick 8% since that’s in between. 8% took 6 milliion years, thus 0.5 (human to human) will take 375,000 years assuming the published clocking rates are correct which I doubt they are. In any case the back of the envelope calculation is within a rough order magnitude with the MRCA figures for humans.
I could sense this gap every species I looked at, but the the phylogenists were so obsessed with interspecies phylogenies (which I think is illusory) few ever seemed to bother with MRCAs for an extant species. The few exceptions are the mtDNA studies and something like the cycad studies.
Given that each species has maybe 15% orphan genes that none other has:
I realized there was something amiss in the intra specific variation. It was hardly there compared to the inter specific variation.
Just as Denton asserted, there are autapomophies, but they stand out because of how similar the members of each species are to each other.
The species look like islands with features just sort of poofed into existence. And some of the defining features are not noticeable just by sequence comparisons as Shapiro and Sternberg pointed out, there are functional differences that are discrete:
It’s almost seems taboo in the evolutionary literature to cite evidence that shows the species look like islands, and part of that is the lack of intra specific variation. It’s only recently I’ve finally gotten figures of how similar humans are to each other. Relative to the differences between us and chimps.
stcordova,
So you think humans were genetically homogenous at some point after the human/chimp split, and you are calculating the time to attain 99.5% similarity from that ‘100%’ point, by comparison to the time taken to reach 8% dissimilar between human and chimp? It’s a seriously peculiar version of evolution you attack, Sal.
stcordova,
OK, and where they do, there is variation. Surely – otherwise there’d be no point in curating the data! 😀 You are saying you have BLASTed intra species datasets and found no variation in them?
Not just BLAST but I’ve seen annotated consensus databases that point out the allele positions (I use the word allele loosely, SNP is probably better). But the suspicion started with BLAST searches.
The variation in the annotated consensus sequences for humans looked consistent with the 0.5% claim of variation between each human.
But, I’m not that good with gene browsing, especially the latest stuff. That’s why I decided I had to take evening classes at the NIH so they can set me straight. As a bonus I won’t be just learning the gene browsers but also the RNA and Protein browsers of RNA sequences (from RNA Seq) and protein DNA interactions (ChiP Seq). Maybe there are even browsers for ChiRP-Seq (Chromatin Isolation by RNA purification).
I even heard about ChIA-PET
https://en.wikipedia.org/wiki/ChIA-PET
not to be confused with:
https://en.wikipedia.org/wiki/Chia_Pet
Is the problem that intraspecific variation is substantially less than inter-specific variation? How could it be otherwise, given gene flow?
Why not, we genetically homogenous now (0.5% divergence), that suggest to me there was a time we were even more homogenous than we are today. Do you have a problem with that ? 🙂
Oh, that’s the other thing, how diverse do you think the interbreeding pool of Chimp, Orang, Human, and Gorilla Ancestors were — you know, the one we keep doing Incomplete Lineage Sorting (ILS) hypotheses on.
http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/evolution-basics-incomplete-lineage-sorting-and-ancestral-population-sizes
If you think my assumption that at some point humans were mostly homogeneous, then what do you have to say about the interbreeding pool the Chimps Human Orang Gorilla (CHOG) pool we all supposedly came out of? How genetically diverse do you think that interbreeding pool was? 🙂
Which is to point out CHOG was more diverse than the more homogenous lineages that proceeded from CHOG, one of them being the line that led to humans.
And there is another problem because one way to resolve the Orphan Gene issue is to assume ancestral groups had all the genes then got deleted in some of the descendant lines.
Well then, Ok, one has to invoke reductive evolution rather than cumulative evolution to resolve the phylogeny, but then we get even more absurd looking ancestors that would need all the genes on the planet in LUCA.
To some extent, the degree of polymorphism found in a species is going to reflect sampling effort. Here’s a recent paper on human intraspecific diversity (focusing on copy number variants) using 236 whole genomes from 125 different populations:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568308/
The authors found about 15,000 copy number variants (totaling about 200 megabases) and about 32 million single nucleotide variants. The SNVs alone represent about 1% of the human genome.
Edit: Here is a relevant paragraph to add:
Sal, you’re 0.5% estimate is looking a little low, yes?
Yes, I do. Your argument is “Because we are x% (a low number) divergent today, I reckon we were even less diverse previously.” Say what? Why not “more” diverse previously? Review the M&M threads.
Oh Look:
More diverse previously. Cool.
You.Are.Confused.
Yes, especially in asexual species.
If bacteria have been around for over a billion years, should we not see some species of bacteria where the genes are as diverged intraspecifically almost as interspecifically? As far as the E. Coli conservation, the genes that are shared have little intra specific variation, which suggest to me the 80% lack of whole genome conservation is due more to gene loss in each lineage than point mutation, and that’s what the literature suggests.
But if you don’t see it as a problem, I have no problem with that. 🙂
I think the question is interesting whether any one finds it a problem or not. The question is whether the MRCAs of all species will indicate recent dates for each crown group of the extant species. That is an interesting question almost independent of the creation/ID/evolution debate.
ADDENDUM:
The molecular clocks keep getting revised!
Dang it. See that! I wasn’t imagining things, the other guys see it too! Up to 99.9% similarity. Told you I saw it!
Also again, when we do intra specific comparisons, we get better clock rates, just like Loewe and Scherer found. This research can’t be stopped because it has relevance to epidemiology.
The traditional clocks were off by a factor of as much as 175.
No because the copy variants may be a small fraction of the population.
Suppose we look at strech of DNA that is 20 bases:
Jane: variant in position 20
John: variant in position 19
Harry: variant in position 18
….
Martha: variant in position 1
So we have variation in all 20 positions, but we don’t say there is 100% variation in that 20 nt strand! That is the problem in the way you characterized your statistics.
The figure of 99.5% similarity:
stcordova,
It ‘suggests’ no such thing. The extent of our homogeneity could be higher, lower or the same as now, in some ancestral population. You can’t simply assume we were 100% identical at some point in the past and work out when that was from the divergence time with chimps. That would be silly.
stcordova,
Yeesh. There is no gene flow in asexual species (barring occasional HGT). One thing that keeps a sexual population hovering closer to a mean, but allows separated populations to diverge, is sex itself. ie, a sexual population would be expected to be less diverse than a combined set consisting of two non-interbreeding lines.
stcordova,
‘Species’ does not translate well into the prokaryote world. There is no natural separation of ‘intraspecific’ vs ‘interspecific’ variation. But we’d certainly expect more variation between any two lineages, the longer the lineages have been diverging. Which is exactly what we find. Hardly the biggest problem for evolutionary theory to account for.
stcordova,
They used a hypervariable region, just 7% of the mitochondrial genome. It gives crap clock rates – although it can be useful for fine-scale phylogeny, precisely because it is hypervariable.
stcordova,
As has already been pointed out, a taxonomic MRCA is not the same as a gene locus MRCA.
A) MRCAs for monomorphic loci are likely to be in the tens to hundreds of thousands of years ago range, for typical eukaryote populations.
B) MRCAs for taxonomic levels of species and above can be any distance back to the origin of life, 3.8 billion years ago, depending on the rank you look at.
The two statements are not incompatible.
stcordova,
You think this pool consisted of interbreeding chimps, humans, orangs and gorillas, or something very like? 😀 I’d say the diversity of ‘CHOG’ would likely be of the order of any typical interbreeding eukaryotic population, personally. Depends on its effective size, mainly. Most of the differences came later.
You apparently don’t understand the argument.
In light of what you say, why are E. Coli not so diverged? Could it be it arose recently? How about all those other asexual species that don’t look so diverged INTRA specifically?
What if we find that lack of INTRA specific diversity to be ubiquitous — that means the MRCAs of most asexual species are recent in geological time. Exactly my hypothesis. You’ve just strengthened my argument.
I think you are criticizing an argument I’m not making. I hope that clarifies what the claim is: asexual species are not as diverged as would be expected if the MRCAs were far back in geological time.
I just provided evidence that the E. Coli’s are similar.
The mainstream view of E. Coli split based on a supposed common ancestor of Salmonella and E. Coli:
https://en.wikipedia.org/wiki/Escherichia_coli#cite_note-pmid9866203-38
But what does the E. Coli MRCA data indicate based on the strains we actually have vs. phylogenetic speculations?
I predict if anyone has the guts to try (and the microbiologists and epidemiologists would be the most interested in real phylogenies vs. speculated ones), they’ll see E. Coli MRCA is more recent than the supposed split of E. Coli.
What happened with evolutionists being surprised with Cycads will be seen with E. Coli. Maybe people know, they just don’t want to come out and say it.
One of the MRCAs of one clade that is close to the E. coli MRCA is described here:
Does not one want to come out and say when the E. Coli MRCA existed? Why do the intra specific MRCA not look to agree with the interspecies times of splits?
Maybe the question doesn’t matter to many, that’s OK, but there does seem to be a gap.
ADDENDUM:
That figure was provided by a paper co-authored by Lenski in 2005.
But as pointed out, a 2010 a paper indicated the clocks of 0157:H7 were off by as much as a factor of 175!
Back of the envelope calculation, the split of E. Coli was previously estimated by Lenski as 1.5 to 2 million years ago. Using the revised clock from the more recent paper, and assuming that clock revision applies, 1.5 million/ 175 = 8,571 years ago. 🙂
A 1987 review of Evolution: A Theory in Crisis from Reports of the NCSE. Regarding “molecular equidistance,” either the reviewer, Philip T. Spieth (listed as Assoc. Prof. of Genetics at UC — Berkeley), or Denton’s Shih Tzu has screwed the pooch. I’ll leave it to the pros to say which.
stcordova,
Probably not. But it’s no good leaping from sexual to asexual organisms and back again. They are sufficiently different for the terms ‘interspecific’ and ‘intraspecific’ to have completely different meanings.
E coli go through a tight bottlenecking phase in their life history, and are subject to intense competition. Like Behe’s malaria parasite, their effective population sizes are closer to those of their hosts than their maximal census sizes may suggest. This reduces the amount of variation to be expected.
Naming species is a human thing. Bacteria that we would call ‘E coli‘ could have arisen recently or a long time ago; I have no particular view on the matter, and it does not affect the possibility of evolution if one finds it recent. It’s certainly not Creationists who are going to find that out, and I doubt people will be shy of publishing regardless of ‘Darwinism’.
But lack of variation is not in itself a good indicator of recent origin, because there are numerous well-investigated causes of such patterns, such as those mentioned above.
stcordova,
You have pointed to both 99.9% identity and 20% latitude in support of your argument!
The current strains of E.coli in Lenski’s lab are less than 30 years old.
Therefore the Flood story is true.
Yes, and the reason for that is that you have made neither a coherent claim nor a coherent argument. You are consistently confusing the MRCA of a locus (an individual) with the MRCA of a current population (a population) with the divergence point between two lineages (also a population). This renders your claims impossible to understand.
Agreed to the extent that MRCA is not the founder of the species any more than the MRCA of Noah is no Adam.
But, the lack of variation is still an indication of a recent MRCA whatever the reasons. It is an interesting question in it’s own right independent of the Creation/Evolution/ID controversy.
That said, mirco biologists, epidemiologists, immunologists have a vested interest in the questions related to MRCAs of various microbes. Their work, as seen above, could be yielding recent dates for the MRCAs of microbial species.
And to that end, just found this. I’ve been saying there will be an incongruity between divergence times and the MRCA of the supposed species that split off.
See. Told you guys! The NIH and the rest of the medical community are starting to see the lack of utility of those phylogeneitc estimates. It has no relevance to the real evolution relevant to public health.
To give an idea of the MRCAs being calculated by microbiologists among strains:
Or maybe Salmonealla were evolving quickly to begin with, people are only surprised because they got the erroneous clock calibrations from evolutionary biologists rather than their fellow microbiologists.
Here is another prediction: lab measured clock rates will be faster than those speculated by evolutionary biologists. I can see the problem already creeping up in the literature. To quote Huxley:
stcordova,
If you’re looking at intraspecies divergence as a whole, I can’t imagine why we would consider the average difference between any one individual and the reference genome as the most useful measure. Nevertheless, if we want to look at frequencies of polymorphisms, here is a recent 1000 genomes paper that gives some data on both the differences between a typical individual and the reference genome as well as population level frequencies of particular polymorphisms (SNPs, CNVs, structural rearrangements, etc.):
http://www.nature.com/nature/journal/v526/n7571/full/nature15393.html
It is utterly unclear to me why you find this amount of genetic variation to be anomalously low, especially give our demographic history.
stcordova,
It is polite to provide the citation.
You quoted from Pettengill
Achtman et al responded:
Your comment
is a classic IDIOTrope that betrays a wholly expected lack of understanding about how science works.
So it’s Okay to accuse published authors of outright dishonesty?
This is hardly the first time Sal has accused mainstream scientists of lying.