Pumapard, leopard-puma hybrids?

Pumapard, 1904

You are probably aware of Panthera hybrids from Napoleon Dynamite. Specifically, Ligers, the largest of all the big cats. But the hybridization of the Panthera species shouldn’t be so shocking. They have diversified only within the last 2 to 4 million years. The lone New World variant (or at least surviving New World variant, recall the extinct American lion), the jaguar, arrived a few million years ago across Beringia. This is not too surprising, as many iconic “American” animals, such as the American bison, made the same journey (Camels went the other direction). But there were already “big cats” in the New World. The puma or cougar. These are not Panthera, and I only recently realized that jaguars were not closely related to this species. Rather, the puma is the ironically largest of the “small cats”.

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Disease: global & historical context

Citation: Corona, Erik, et al. “Analysis of the Genetic Basis of Disease in the Context of Worldwide Human Relationships and Migration.” PLoS Genetics 9.5 (2013): e1003447.

The above figure is from a paper in PLoS GENETICS, Analysis of the Genetic Basis of Disease in the Context of Worldwide Human Relationships and Migration. The authors synthesize two diverse domains of human genomics. First, there are biomedically focused genome-wide association studies and their like which attempt to identify risk alleles for particular diseases. In some cases these risk alleles are very penetrant, in that a particular state predicts with high likelihood a disease phenotype. But in most cases the yield is elevated or decreased risks for highly complex traits such as type 2 diabetes. Second, there is the domain of evolutionary genomics which attempts to reconstruct a phylogenetic and population genetic history so as to frame contemporary patterns of variation in their proper context. How this might be important or of interest is obvious in the case of malaria resistance genes. Alleles conferring resistance have arisen in multiple populations due to parallel environmental pressures. Phylogenetic relationships between these populations should inform your predictions as to the likely similarities of the mutations between the populations. Meanwhile, population genetic theory can give you clues as to the likelihood of multiple adaptations.

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Obesity as morality and health

Normally I don’t post “read the whole thing,” but this really applies in the case of Virginia Hughes’ new piece in Nature, The big fat truth. The ‘counter-intuitive’ finding is that in some age groups the slightly overweight have the lowest mortality rates. This is not totally surprising news, though there has been a long term debate on whether this is an artifact or not. Hughes notes:

If the obesity-paradox studies are correct, the issue then becomes how to convey their nuances. A lot of excess weight, in the form of obesity, is clearly bad for health, and most young people are better off keeping trim. But that may change as they age and develop illnesses.

The key here is that one-size-fits-all public health jeremiads are probably counter-productive in the long term. The question isn’t whether to present nuances, it is how to do it well. It doesn’t seem the status quo is working out so well after all.

How the race, intelligence, and genetics question will semi-resolve within the next 10 years

Prompted by my post Ta-Nehisi Coates reached out to Neil Risch for clarification on the nature (or lack thereof) of human races. All for the good. The interview is wide ranging, and I recommend you check it out. Read the comments too! Very enlightening (take that however you want).

When it comes to this debate I have focused on the issue of population substructure, or race. The reason is simple. Due to Lewontin’s Fallacy it is widely understood among the “well informed general public” that “biology has disproved race.” Actually, this is a disputable assertion. For a non-crank evolutionary biologist who is willing to defend the race concept for humans, see Jerry Coyne. When you move away from the term “race,” then you obtain even more support from biologists for the proposition that population structure matters. For example, a paper in PLoS GENETICS which came out last week: Analysis of the Genetic Basis of Disease in the Context of Worldwide Human Relationships and Migration. In other words, it is useful to understand the genetic relationships of populations, and individual population identity, because traits correlate with population history. Barring total omniscience population history will always probably matter to some extent, because population history influences suites of traits. If nothing in evolutionary biology makes sense except in light of phylogeny, much of human biology is illuminated by phylogeny.

But that doesn’t speak to the real third rail, intelligence. Very few people are offended by the idea of the correlation between lactase persistence and particular populations. Neil Risch says in the interview with Coates:

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A little knowledge is dangerous

Being public on the internet means having to interact with many different sorts. Recently I’ve been having to deal with a heckler on Facebook. The heckler is actually of a particular type. I’m still trying to learn genetics at this point in my life, so I don’t propose to assert that my opinions are beyond dispute. But there is a variety of discussion which is not fruitful.

An interesting aspect of talking to people about genetics is that totally novice intelligent lay people are often very easy to communicate with. Genetics isn’t that hard, and when people want to learn new concepts and have the ability to it can be a great joy. Similarly, the numerous people who know much more genetics are easy to talk to, because they operate on a domain of fluency which makes conversation effortless (obviously this may not be reciprocated on their part in terms of their perception of your lack of knowledge!).

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(pre)Historical genetics still has to be historical

Credit: Albozagros

The genetics and history of Tibet are fascinating to many. To be honest the primary reason here is elevation. The Tibetan plateau has served as a fortress for populations who have adapted biologically and culturally to the extreme conditions. Naturally this means that there has been a fair amount of population genetics on Tibetans, as hypoxia is a side effect of high altitude living which dramatically impacts fitness. I have discussed papers on this topic before. And I will probably talk more about it in the future, considering rumblings at ASHG 2012.

But to understand the character of the effect of natural selection on a population it is often very important to keep in mind the phylogenetic context. By this, I mean that evolutionary processes occur over history, and those historical events shape the course of subsequent of phenomena. Concretely, to understand how the Tibetans came to be adapted to high altitudes one must understand who they are related to, and what their long term history is. There is a paper in Molecular Biology and Evolution which attempts to do just that, Genetic evidence of Paleolithic colonization and Neolithic expansion of modern humans on the Tibetan Plateau:

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The algorithms don’t lie, but people may err

Byzantine Emperor Leo “the Khazar” with his son Constantine IV. Credit: Cplakidas

For the past year or so I’ve been getting queries about what I think about Eran Elhaik’s preprint on the genetic character of European Jews. I found some of the conclusions frankly a little weird, but I assumed that things would be cleaned up for publication. Well, it’s been out for a while now: The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses. But some reporting in The Jewish Daily Forward has brought the author and his detractors a bit into the spotlight. The reason is that as you can tell from the title of the author takes a position on the Khazarian origin model of Ashkenazi Jews (in favor). Here is a non-genetic take over at GeoCurrents, the thrust of which I basically concur with.

In any case, many of the problems with the paper remain. Really it all begins and ends here:

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The eternal Aboriginal

Credit: Kwamikagami

National Geographic has an interesting article up, unoriginally titled Australia’s Aboriginals. There are lots of great data in there, though not much novel for anyone who has tread this territory before. For example, Aboriginals tend to have much lower morbidity and mortality when they are living their “traditional” lifestyle. This isn’t a particular novel or surprising outcome. Rather, it seems like a supercharged version of the same problem which occurs when immigrants move from developing to developed societies, and shift toward massive portions and processed food. This modern regime is even impacting native born segments of America’s population in a negative manner. Interesting and true.

But what concerns me is the background assumption that Aboriginals are timeless and static, arriving ~50,000 years ago from Sundaland, and remaining in a stasis. My issue isn’t normative. And I’m fascinated by the inferences some archaeologists have made about the continuity of specific motifs in Aboriginal art. Additionally, from what I understand the material culture of Aboriginals is especially changeless in relation to other populations in the world. But one thing we know about H. sapiens is that cultural forms of expression are quite protean, especially symbolic aspects which might not preserve too well. Would the Aboriginals of Australia be immune from this? I doubt it.

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Saiga through the bottleneck…and back?

Credit: Tierrascott

In the 1980s I was fascinated by the pictorially oriented books on the wildlife of the world which dated to the 1960s and 1970s. One of the great conservation success stories of that era were the Saiga antelope of Eurasia. In 1920 there were only 1,000-2,0000 Saia left in the world. By the 1960s their numbers were in the millions. And so it was until the 1980s.

But the combination of the collapse of the Soviet Union, for which the Saiga was a notable conservation success, and the rise of the Chinese economy, have resulted in another crisis for the Saiga. Today their number is between 10,000-50,000, in a few fragmented regions. And yet this is still higher than their early 20th century bottleneck! The Saiga clearly have the capacity to recover from dramatic population crashes. The key, to be frank, is to keep the Saiga a viable population as China ascends up Maslow’s hierarchy of needs.