Learning the lessons of the Land: part II

This series of commentaries (beginning yesterday) was inspired by the latest issue of the Land Institute's Land Report, that describes efforts to use modern science to develop sustainable crops that can conserve resources yet feed large numbers of people.  We were motivated by the thought that not only is this important work, but it should inform our ideas about human--and evolutionary--genetics.

Van Gogh, Farmhouse in a Wheat Field, public domain

In our previous post we introduced the idea of molecular breeding, a genomewide association study (or GWAS)-like approach that experimental breeders in agriculture are taking to speed up and focus their efforts to breed desired traits into agricultural plants.  Here, we want to continue that discussion, to relate the findings made in agricultural genetics to what is being promised for GWAS-like based personalized genomic medicine.

Essential personalized medicine means predicting your eventual disease-related phenotypes from your inherited genotype (and here, we'll extend that beyond just DNA sequence, to epigenetic aspects of DNA modification, assuming that will eventually be identifiable from appropriate cells).

If breeders had been finding that once seed with desired traits had been identified, genome-spanning genetic markers (polymorphic sites along the genome) pointed to a small number of locations with big effects, then we would quickly be able to find, and perhaps use the actual genes diagnostically.  This seems to be true for some plants with small genomes, for traits that seem to be due to the action of variants in one or only a few genes.  This is just what we find for the 'simple' human diseases, or the subset of complex diseases that segregates in families in a way that follows Mendel's principles of inheritance.  There are many examples.

But for many traits, including most complex, delayed onset, life-style related, common disorders that are the main target of the GWAS-ification of medicine in the Collins era of NIH funding, what is being found is quite different.  Mapping is finding hundreds of genes, almost all of which have either very small individual effects, or if larger effects, that are so rare that they are of minimal public health importance (even if very important to those who carry the dangerous allele).  For these, the question is what to do with the countless, variable regions of the genome that make up the bulk of the inherited risk.

This is the same situation as faced in the agricultural breeding arena, for many of the traits, like water- or drought- or pest-tolerance, nutrient yield, or other characteristics desired for large scale farming.  The traits are genomically complex. Even with large samples and controlled and uniform conditions--very unlike the human biomedical situation--it is not practicable or practical to try to improve the trait by individual gene identification.  Nor is it likely that introducing single exotic transgenes will do the trick (as many agribusinesses are acknowledging).

Instead, molecular breeding takes advantage of the plant's own natural variation to select those variants that do what is desired simply by choosing the plants that transmit those variants, and without attempting to engineer or even to identify what they are.  We do not know how reliable the prediction of phenotype from genotype in these circumstances typically is, but the idea is if that you keep selecting plants with the desired regions of the genome that mapping identifies, and breeding them for example with strains that you like for other reasons, you can reduce reliance on individual prediction because eventually every individual will be alike, for the traits you were interested in.

Once that is the case, regardless of the genes or regulatory regions that are involved, you have your desired plants, at least under the conditions of nutrients, climate, and so on, in which the strain was developed.

Clearly this experience is relevant for human genetics, and for evolutionary genetics of the same traits, a topic to which we will turn in our final post in this series.....

"and I want no other fame": The tale of the butterfly novelist--Vladimir Nabokov

Lolita may be a story for adults only, but Vladimir Nabokov told another story that can be enjoyed by all.  It appears to be an amateur's triumph, based on a correct guess that was before its time.  No definitive data could have been assembled to tell the tale while Nabokov was alive.  But thanks to the very regular, clocklike way that DNA accumulates variation among descendants over time, the guess seems to have been confirmed with current methods.

Polyommatous blue, by Lilly M.,
Wikimedia Commons

The immediate story is told by Carl Zimmer in the NY Times, but is based on a paper just published in the Proceedings of the Royal Society.  If Lolita was about a man in pursuit of a (too-)young person he obsessively adores, the story of the Polyommatous blue butterflies is one of a man chasing a group of old species that he obsessively adores.

It has long been widely known that Nabokov was a persistent, knowledgeable, dedicated if technically amateur butterfly enthusiast.   It was also long known that he did extensive work on the structures and relationships of the species that came years ago to be known as 'Nabokov blues'.  You can read about this, with maps and illustrations, in a fine book by Kurt Johnson and Steve Coates, Nabokov's Blues: The Scientific Odyssey of a Literary Genius, Zoland Books, 1999.  Johnson is a lepidopterist, expert in these butterflies.

They write "Where South American temperate life-forms had come from became a compelling question from the earliest stages of the continent's exploration." Much of their book, which is a readable, popularized narrative, tells of the efforts by Nabokov and others then and since, to understand the taxonomy--species relationships--among the South American blues and their relatives elsewhere. 

The traits of species available to Nabokov and others did not neatly correlate with their locations in the Andes or down into warmer environments.  That meant that some nearby species seemed too different to have had an evolutionarily recent common ancestor.  And, if they did not, and for the group as a whole, where were their origins then?

This issue had arisen out of the work of many naturalists going back at least to the early 1800s.  From an evolutionary point of view a couple of explanations were plausible.  One is polyphenism: species can have very different morphology or behavior depending on the individuals' local environment or genotypes.  And there is mimicry: distantly related species can come to resemble each other by natural selection. But that will only affect the mimicked trait, leaving the species' other traits less similar.  But in any case how did these butterflies get into the Americas?  There were various suggestions.  One possibility that Nabokov entertained was that the species had expanded into the Americas from Asia, by way of the Bering land bridge--that is, into South America from the north, what is now the Arctic.  The North American ancestral species may then have died out, leaving only their South American descendants.

The story in the Times, like news stories tend to do, makes this seem as if Nabokov got this 'blues' story out of the blue, so to speak, and was insistent on this view.  Indeed, Vila et al. in the Proceedings of the Royal Society paper, do the same:

The radiation of Polyommatus blues in the New World was first appreciated by the famous writer Vladimir Nabokov when he was working as curator in the Museum of Comparative Zoology at Harvard in the early 1940s.

And:

Our results show that Nabokov’s inferences based on morphological characters (primarily of the male genitalia) were uncannily correct in delineating not only species relationships but also the historical ordering of these five key events in the evolution of New World blues.

But even brilliant discoveries occur in a context, and people rarely take immovable positions when the evidence is ambiguous. Johnson and Coates go to great lengths to describe the long history of South American biogeography--the distribution of species over space and how it gets that way.  Ideas of species rafting across vast oceans had been suggested, and when continental drift was discovered, land connections between South America and Asia and Africa provided a possible explanation.  But climate change and a northern connection was another possibility.

There's no taking away from Nabokov that he was diligent and insightful, but others were thinking similar kinds of things, about the biogeography of many different species besides butterflies.  As he said in our title quote, he wanted to be known for this work, and properly so.  But at least Johnson and Coates present the history as one of many widely discussed possibilities by many different investigators--including the Northern origin of South American species generally.  Nabakov appears to have weighed different possibilities, and his preferred hunch, given the set of specimens and knowledge available to him, appears to have been right. 

The new paper uses extensive DNA sequence to resolve these tales in detail, data that of course was unavailable in the past.  The authors draw species-relationship trees based on the degree of sequence identity.  The times of splitting among the species were estimated by the number of DNA sequence differences that had arisen.  Many of the branches were  deep--large numbers of sequence variants, suggesting ancient splits, relative to other nearby species in South America.  Since the nearest relations in these instances were in Asia, the American species must more than once--in different expansion waves--have come from Asia.

Paleoclimatology and continental drift, and known climate tolerance patterns in the butterflies made it possible for the butterflies, over many generations, to expand here from Asia and survive in the warmer climes that existed episodically over an estimated period of 10 million years.  DNA analysis can even work when there has been selection for polyphenism or mimicry.  That's because such selection would distort relationships only at the genes involved in those particular traits, but genomewide variation will accumulate in a pattern that corresponds to the species' histories.  Indeed, DNA evidence could provide evidence for it, by showing that though some species looked similar, they really were not very close relatives overall (genomewide).

Here is an application of genetics that is entirely appropriate, that makes it possible to draw convincing inferences, when morphological or behavioral analysis may not.  A tree of descendant genomes accumulates variation probabilistically, so little can be said from observation of just a few nucleotides.  But these erratic patterns even out when thousands of nucleotides are compared, as these authors did.

Even so, let's keep in mind that genetic analysis is not exactly a scientific miracle.  If genes cause traits, then traits will diverge over evolutionary time in ways that generally reflect underlying genetic divergence.  That is why, in effect, Nabokov was indirectly using genomewide genetics to draw his conclusions--he just couldn't see the genes directly.  This is in essence how Darwin did what he did, too, without a good understanding of what inheritance really was.  But what we now have is explicit genetics to replace Nabokov's inferences from aggregate, implicit genetics. And this can get around problems of phenotypes that don't fit the history.

DNA is more specific and in the sense of time estimation much more rigorously useful than morphology and behavior.  As in forensic applications of genetics, that match sequences to their owners as in crime investigations, analysis that relies on the clear properties of genomes can tell stories that are as powerful as the compelling novels that Vladimir Nabokov wrote.  And he is justly famed for both!

Barcelona vista

Here are some thoughts about the second stop on our trip, Barcelona. We visited with Jaume Bertranpetit, and I gave a lecture to his group at the University of Pampeu Fabra. The group includes many other fine scientists in a beautiful new building, and we met a few who we had not known before. We had both previously been there as part of the PhD committee of one of Jaume's and his colleague Francesc Calafell's students. It was great to see these long-standing friends.

We were there during the weeklong festival of La Mercè, honoring one of the patron saints of the city, so it's only fitting to include a photo of some of the street theatre we saw. These guys were on flexible poles, swaying to music, an act we'd never seen the likes of before.

Jaume's group is probably the leading light of Spain in genetics, if not all of southern Europe, and has been very productive in front-line human genetics for some time. Our familiarity is with their work on human variation and history, especially of Europe (e.g., the reasons for the distribution of alleles associated with cystic fibrosis). They also do biomedical genetics, and are quite aware of the problems with GWAS and related ideas of how to map and deal with the genetic component of human disease. I talked on that subject, explaining how evolutionary perspectives show why we are finding what we are finding: that many important and common diseases that seem to have substantial heritability are not yielding to large-scale association mapping efforts. One member, Sergi Valverde, is a computational biologist trying to wrestle with the network approach to the problem.

We learned of a paper by Jaume and others in BMC Genomics, that looks at the degree of genetic difference in the 'isolate' populations compared to other 'main' populations. There it's reported that while the isolates do have some genetic differences from the surrounding populations, they are not really as different as their language.

A classic example, though not one reported in this paper but in another unpublished paper by Dr Bertranpetit is the Basques. Their isolation was long argued based on their language (apparently ancient and unrelated to what is spoken by surrounding populations in Spain and France).

This is relevant beyond the long-standing interest in the history of the Basques, about which many classical papers in human genetics from the early to mid 20th century were written, or other individual isolates. After a few traits were found to be at high frequency in religious isolates (like the US Amish and Hutterites, in Finland and in French Canadians), the idea became widespread that the bottleneck in population size would simplify the genetic causal basis of otherwise more complex diseases, making them more mappable in the isolate.

This general isolate or bottleneck effect goes beyond the classical reason, that founder effects (recent founding by a small number of people, plus increased relative degree of inbreeding in the small descendant population) would by chance raise the frequency of some recessive traits to high enough frequency that they could be mapped and understood.

However, in the Basques as elsewhere (as Bertranpetit and colleagues note), the degree of bottleneck and the amount of subsequent gene flow with surrounding populations, the differences are far less than was expected. They are not proving to be the mapping bonanza that was hoped. Given the amount of variation that exists, the amount of population constriction needed to do what was hoped is far more severe than has been the case. Of course, isolates may have some disorders at higher frequency, or some very rare causal genotypes basically not found frequently enough elsewhere to be useful. But overall, isolates were over-sold.

In fact, the relative success in mapping in the Iceland population, which was touted in advance as having great potential largely to their isolate status, has proven to be due mainly to the availability of large genealogies, not isolate status. Even in Finland, where much of the hope for the usefulness of isolates was fueled about 15 years ago, and where the local population history can be reconstructed, there has not been a high yield of new genotypes found to be associated with common disease.

The Basque story shows that one has to be circumspect about ideas that seem plausible but can be accepted too uncritically. The history of the Basques is more interesting as history than as genetics. That's a subject too great to go into but a fine book, The Basque History of the World by Mark Kurlansky provides some good material, as does web searching, etc.

Besides seeing our daughter newly installed as a post-graduate violin student in Barcelona, we had a very fine time visiting with Jaume and others. It is a city worth visiting, and Jaume's is a scientifically vibrant group. In addition to his science, he is an effective politician when it comes to program building and resource acquisition. For the last few years he has been the very successful director of a program to recruit scientists to Catalunya, ICREA, which may still be looking for new people, in case any reader might be interested.

-Ken