Turtles all the way down!

Nature Genetics (2013) doi:10.1038/ng.2615

No time to comment extensively, but check out The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan (open access). The paper and the ScienceDaily press release allude to some phylogenetic confusion as to the relationship of turtles to other reptilian lineages, but my own superficial knowledge of this area left me rather unsurprised by this tree. What am I missing? Though reading the Wikipedia entry it seems that spotty marker coverage has produced a lot of controversy. What’s more striking to me is that so many terrestrial vertebrate lineage seem to have emerged over a relatively short period of time. Though presumably this may simply be an artifact of the reality that most lineages go extinct so we’re only left with relatively deep branching patterns. Someone who knows fossils can chime in.

Against the seriousness of theology

Over at The American Conservative Noah Millman and Rod Dreher are having a discussion over the basic premise that founding texts (e.g., Bible, Koran) and individuals (e.g., Jesus, Muhammad) have a deep influence upon the nature of a religion. Long time readers will be aware that I side much more with Millman on this. In fact I recall that years ago in the comments of Ross Douthat’s old blog at The Atlantic (alas, comments are gone from their archives) I took the more maximalist position that theology and logical coherency are not particularly relevant toward understanding religious phenomena in an exchange with Noah (he made an analogy with law, and I responded that that proved my point about the pliability of religious ideas).

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The end of demic diffusion

German woman, product of Mid-Neolithic?
Source: Siebbi

Yesterday I pointed to a paper which was interesting enough, but didn’t pass the smell test in relation to other evidence we have (at least in my opinion!). A primary concern was the fact that uniparental (male and female lineages) show a peculiar distribution of variation in comparison to autosomal genetic variation (i.e., the vast majority of the genome) in the case of Europe (genome-wide analysis suggest more of Europe’s variation is partitioned north-south, but Y and mtDNA results often imply an east-west split). But a secondary concern I had was that I felt the models were a bit too stylized. In particular following Cavalli-Sforza and Ammerman the authors concluded that demic diffusion better fits their results of genetic variation in Europe (as opposed to continuity of Paleolithic hunter-gatherers). This is likely correct, but these are not the only two models.

A paper out in Nature Communications, using analysis of the phylogenetics of whole ancient mitchondrial genomes, outlines my primary concern when it comes to the models being tested, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans:

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

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Models are great, because rejection is easy

There’s a new paper in PLoS ONE, Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data, which uses a combination of contemporary and ancient (that is, from subfossils) Y and mitochondrial DNA to understand the demographic past of Europe. Recall that the Y traces the direct male lineage, and the mtDNA the direct female lineage. Because they don’t recombine and generate clean converges back to a last common ancestor (there is no reticulation because there is no sex on these loci; they’re inherited from one of the two parents), they’re amenable to a lot of nifty demographic inference generation. In this paper they test specific models, and produce probability distributions of those models. Since it is open access I invite you to read the paper. The problem with these sorts of papers is I have a hard time trusting them until I replicate the results or have a sense of how cranky the software/code is!

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The End of War is not inevitable

I read John Horgan’s a few month ago now, but I haven’t gotten around to saying much about it. Part of the problem is that I don’t know what to think. It’s a small book which manages to wander in many different directions, and the primary focus is Horgan’s mantra that war is not an inevitable fact of the human condition. Since I agree with that proposition much of the argumentation was lost on me.

And yet there is one aspect of the book which was notable: a disputation of the Richard Wrangham’s work in . I’m still quite a fan of Wrangham’s thesis, but over the years I’ve become much more skeptical of one of the primary methods he employs: extrapolation from another ape (in his case, chimpanzees). Similarly, I’m also skeptical of those who claim that we’re more more like bonobos (here’s looking at you Frans de Waal). No, we’re human beings, and our common ancestor with other apes may have been very different from all the descendant lineages. Our cousins are informative and interesting, but we shouldn’t confuse ourselves for our cousins.

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Why atheists can speak in the West

Recently Bill Maher ripped into CSU San Bernadino professor Brian Levin for making the ridiculous equivalence between Christian extremism and Islamic extremism. The problem, which Maher pinpoints, is that Islamic extremism is not that extreme. By this, I mean that Islamic extremism (e.g., Muslim Brotherhood) has much greater broad based support than Christian extremism (e.g., Christian Reconstruction). The difference here is that you’ve heard of the Muslim Brotherhood, while far fewer have heard of Christian Reconstructionists. That’s because the former have democratic support in a populous Muslim country as the ruling party.

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The sex gap

I was recently reading Sexual Behavior in the United States: Results from a National Probability Sample of Men and Women Ages 14–94. At N ~ 6,000 it’s a large sample of American sexual behavior around 2010. There was one descriptive result which I thought was interesting, though not surprising. Before the age of 25 it seems that women are more likely to have sex in a given year than an equivalent age man. After the age of 25 this starts to reverse, and men are more likely to be having sexual intercourse in a given year. The dynamics underlying this phenomenon seem to be easily subject to various speculations, so I’ll leave that to readers. Rather, I offer the graph (data drawn from the paper linked above):

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