Razib Khan One-stop-shopping for all of my content

August 25, 2011

The divisibility of human ancestry

The class human or H. sapiens refers to a set of individuals. On the grand scale it’s really not all that clear and distinct. When do “archaic” humans become “modern” humans? Taking into account human variation, what is a “human universal”? A set of organisms are given a name which denotes the reality that they may share common ancestry, and interact behaviorally, and are potential mates. But many of these phenomenon are fuzzy on the margins. Many of the same issues which emerge in the “species concept” debates are rather general up and down the scales of natural complexity. A similar problem crops up when we conflate the history of genes with the history of populations. Such a conflation has value and utility to a first approximation. The story of mitochondrial Eve was actually the history of one particular locus, the mitochondrial genome. But it did tell us quite a bit about the history of the human species, even if in hindsight it looks as if some scientists overinterpreted those findings. One of the major issues I’ve noticed over the past year, with the heightened likelihood of ...

July 18, 2011

Neanderthal-human mating, months later….


Image credit:ICHTO

Recently something popped up into my Google news feed in regards to “Neanderthal-human mating.” If you are a regular reader you know that I’m wild for this particular combination of the “wild thing.” But a quick perusal of the press release told me that this was a paper I had already reviewed when it was published online in January. I even used the results in the paper to confirm Neanderthal admixture in my own family (we’ve all been genotyped). One of my siblings is in fact a hemizygote for the Neanderthal alleles on the locus in question! I guess it shows the power of press releases upon the media. I would offer up the explanation that this just shows that the more respectable press doesn’t want to touch papers which aren’t in print, but that’s not a good explanation when they are willing to hype up stuff which is presented at conferences at even an earlier stage.

A second aspect I noted is that except for Ron Bailey at Reason all the articles which use a color headshot use a ...

June 16, 2011

Massive Neandertal & Denisovan introgression

Update: John Hawks’ lab is working in the same area, and he disagrees with the specific results presented here. Always reminds you to be careful about sexy results presented at conference! (someone should do a study!)

So claimed Peter Parham at a Royal Society meeting last week, Human evolution, migration and history revealed by genetics, immunity and infection. You can actually listen to the talk by pulling down the mp3 file. To get the part about human evolution and introgression, jump to 24 minutes in.

Here is the general sketch: It looks like ~50 percent of the HLA Class I alleles in Europeans derive from Neandertals, ~70-80 percent of HLA Class I alleles in East Asians derive from Denisovans, and that and ~90-95 percent of HLA Class I alleles in Papuans derive from Denisovans. If you recall, ~2.5% of the total genome content of non-Africans seems to be Neandertal, while ~5% of the total genome content of Papuans seems to be Denisovan. The total genome content proportions are rough estimates, there may be some wiggle room in there. But you can see that the HLA allele admixture estimates from these ancient Eurasian lineages is greater by an order ...

January 26, 2011

Neandertal admixture, revisiting results after shaken priors

After 2010′s world-shaking revolutions in our understanding of modern human origins, the admixture of Eurasian hominins with neo-Africans, I assumed there was going to be a revisionist look at results which seemed to point to mixing between different human lineages over the past decade. Dienekes links to a case in point, a new paper in Molecular Biology and Evolution,  An X-linked haplotype of Neandertal origin is present among all non-African populations. The authors revisit a genetic locus where there have been earlier suggestions of hominin admixture dating back 15 years. In particular, they focus on an intronic segment spanning exon 44 of the dystrophin gene, termed dys44. Of the haplotypes in this they suggested one, B006, introgressed from a different genetic background than that of neo-Africans. The map of B006 shows the distribution of the putative “archaic” haplotype from a previous paper cited in the current one from 2003. As you can see there’s a pattern of non-African preponderance of this haplotype. So what’s dystrophin‘s deal? From Wikipedia:

Dystrophin is a rod-shaped cytoplasmic protein, and a vital part of a protein complex that connects the cytoskeleton ...

August 12, 2010

Hybridization is like sex

480px-Olivia_MunnOne of the major issues which has loomed at the heart of biology since The Origin of Species is why species exist, as well as how species come about. Why isn’t there a perfect replicator which performs all the conversion of energy and matter into biomass on this planet? If there is a God the tree of life almost seems to be a testament to his riotous aesthetic sense, with numerous branches which lead to convergences, and a inordinate fascination with variants on the basic morph of beetles. From the outside the outcomes of evolutionary biology look a patent mess, a sprawling expanse of experiments and misfires.

A similar issue has vexed biologists in relation to sex. Why is it that the vast majority of complex organisms take upon themselves the costs of sex? The existence of a non-offspring bearing form within a species reduces the potential natural increase by a factor of two before the game has even begun. Not only that, but the existence of two sexes who must seek each other out expends crucial energy in a Malthusian world (selfing hermaphrodites obviously don’t have this problem, but for highly complex organisms they aren’t so common). Why bother? (I mean in an ultimate, not proximate, sense)

It seems likely that part of the answer to both these questions on the grande scale is that the perfect is the enemy of long term survival. Sexual reproduction confers upon a lineage a genetic variability which may reduce fitness by shifting populations away from the adaptive peak in the short term, but the fitness landscape itself is a constant bubbling flux, and perfectly engineered asexual lineages may all too often fall off the cliff of what was once their mountain top. The only inevitability seems to be that the times change. Similarly, the natural history of life on earth tells us that all greatness comes to an end, and extinction is the lot of life. The universe is an unpredictable place and the mighty invariably fall, as the branches of life’s tree are always pruned by the gardeners red in tooth and claw.

ResearchBlogging.orgBut it is one thing to describe reality in broad verbal brushes. How about a more rigorous empirical and theoretical understanding of how organisms and the genetic material through which they gain immortality play out in the universe? A new paper which uses plant models explores the costs and benefits of admixture between lineages, and how those two dynamics operate in a heterogeneous and homogeneous world. Population admixture, biological invasions and the balance between local adaptation and inbreeding depression:

When previously isolated populations meet and mix, the resulting admixed population can benefit from several genetic advantages, including increased genetic variation, the creation of novel genotypes and the masking of deleterious mutations. These admixture benefits are thought to play an important role in biological invasions. In contrast, populations in their native range often remain differentiated and frequently suffer from inbreeding depression owing to isolation. While the advantages of admixture are evident for introduced populations that experienced recent bottlenecks or that face novel selection pressures, it is less obvious why native range populations do not similarly benefit from admixture. Here we argue that a temporary loss of local adaptation in recent invaders fundamentally alters the fitness consequences of admixture. In native populations, selection against dilution of the locally adapted gene pool inhibits unconstrained admixture and reinforces population isolation, with some level of inbreeding depression as an expected consequence. We show that admixture is selected against despite significant inbreeding depression because the benefits of local adaptation are greater than the cost of inbreeding. In contrast, introduced populations that have not yet established a pattern of local adaptation can freely reap the benefits of admixture. There can be strong selection for admixture because it instantly lifts the inbreeding depression that had built up in isolated parental populations. Recent work in Silene suggests that reduced inbreeding depression associated with post-introduction admixture may contribute to enhanced fitness of invasive populations. We hypothesize that in locally adapted populations, the benefits of local adaptation are balanced against an inbreeding cost that could develop in part owing to the isolating effect of local adaptation itself. The inbreeding cost can be revealed in admixing populations during recent invasions.

First, plants are good models to explore evolutionary genetics. They’re not as constrained as say mammals, or the typical tetrapod, when it comes to barriers to gene flow between distinct taxa. Hybridization is common, and plants can also self-fertilize as well as cross-fertilize, allowing researchers to push the genetic pool in different directions (”selfing” obviously reduces the effective population and is an extreme form of inbreeding, so it’s a good way to purge genetic variation really quickly). In a perfect abstract world of evolution one might imagine Richard Dawkins’ vehicles and replicators as fluid entities which float along a turbid sea of evolutionary genetic parameters, drift, migration, mutation and selection. But reality is constrained to DNA substrate, which have their own parameters such as recombination, modulators such as epigenetics, and numerous ways to express variation through gene regulation. It’s complicated, and stripping the issues down to their pith is easier said that done.

But the broader dynamics here being examined is the generalist-specialist trade-off, which I think is relevant to the two issues I introduced earlier in this post. Specialists are optimized for their own position in the adaptive landscape, but have difficulties when it is perturbed. Generalists always less than maximum fitness in all landscapes, but higher average fitness across them because they can adapt to changes. Specialization is local adaptation of particular lineages, while in the generalist case you can have invasive species in novel environments. They’re obviously facing an adaptive landscape which is at some remove from what any of the introduced genotypes were “optimized” for, so hybridization produces something new for something new.

In the first figure of the paper you see F3 wild barley descended from two parental lineages, ME and AQ. The left panels show seed output as a function of heterozygosity, and the right panels as a function of ME genome content. Remember that in subsequent generations the descendants of hybrids will vary quite a big in genetics and phenotype as the original alleles re-segregate.

F1.large

The takeaway is that in novel environments genetic variation seems to result in increased fitness. Why? One concept which one has to introduce is heterosis, whereby crosses between homogeneous lineages produce more fitness offspring. One reason this may be is that there is overdominance, where heterozygotes have greater fitness than the homogyzotes. This is the case with sickle-cell malaria disease. Another reason may be that in the original parental lineages there was a higher fraction of alleles which were deleterious in homozygote genotypes. In plain English, inbreeding resulted in genetic drift which cranked up the proportion of alleles implicated in recessively express negative phenotypes. The authors argue though that in the context local adaptation is strong enough to be a barrier against too much gene flow between the parental wild barely lineages, so the deleterious alleles are less likely to be masked. Only in a novel environment when that benefit was removed from the equation could the negative consequences of inbreeding come to the fore in the total calculus.

Figure 2 shows the results of experiments which examine the fitness of white campion, a European species which has been introduced in North America. In the left panel are crosses between native European lineages, with distance between parental lineages on the x-axis. In the right panel you have the same experiment, but with North American variants, which are products of introductions from various regions of Europe. The plants were grown in a “common garden,” to show how all the genotypes performed when environment was controlled.

F2.large

As you can see moderate levels of hybridization entailed a benefit in the European variants, but not the North American variants. Hybridization between variants which were too distant did produce outbreeding depression in the European case, suggesting perhaps that disruption of co-adapted gene complexes resulted in a greater fitness cost than the masking of deleterious alleles due to inbreeding. One can make the inference from these data that the introduced white campion lineages are already hybridized, the barriers to crossing being removed by a disruption of the adaptive landscapes which each native lineages was optimized for.

Here are the authors from the discussion talking about invasions of exotic species:

Provided that multiple introductions from different source populations have occurred, the benefits of admixture become freely available to introduced populations that do not yet show a pattern of local adaptation. Because the benefits are potentially large, admixture may play an important role during early invasions. Native populations often show evidence of inbreeding depression…and one instant reward of admixture in the introduced range is the release of this genetic burden. Such heterosis effects can contribute significantly to the establishment and early success of invasive species…When tested together in a common garden experiment, invaders can show enhanced fitness-related traits compared with populations from their native range…If there is evidence of admixture, the effects of heterosis might be a default explanation for such observations, perhaps providing a null expectation against which other explanations (such as trait evolution) need to be tested.

What have plants to do with life as a whole? I assume much. Plants differ in the details, but compared to other complex multicellular organisms in regards to evolutionary genetics they’re quite liberated. By this, I mean that their modes of reproduction and promiscuity in hybridization make them more of an ideal “frictionless” test case of evolutionary biology and the power of the classical parameters. Perhaps given enough time natural selection would produce the ideal replicator to rule them all, to drive all others to extinction. But that day is not this day. And that day may never come because the universe is far too protean and erratic. Life is varied, on the phenotypic and genotypic level, and the exogenous processes of climate and geology continue to warp and reshape the adaptive landscape. And more subtly, but just as critically, life is always in an endless race with itself, as pathogens co-evolve with their hosts, and predators figure out how to outfox their prey. Life warps its own adaptive landscapes, and the innovation of one branch may lead to extinction of others as well as the proliferation of new branches.

More prosaically and anthropocentrically what does this say about us? Humans are an expansive species, and over the past 500 years different lineages have been hybridizing promiscuously. New genotypes have arisen in altered landscapes, and our pathogens are also riding the high tide of globalization onward and upward. We are ourselves a “natural experiment.”

Image Credit: Olivia Munn by Gage Skidmore

Link hat tip: Dienekes.

Citation: Verhoeven KJ, Macel M, Wolfe LM, & Biere A (2010). Population admixture, biological invasions and the balance between local adaptation and inbreeding depression. Proceedings. Biological sciences / The Royal Society PMID: 20685700

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