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Hybridization

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Abolishing diversity, one child at a time!

One of the often overlooked historical oddities in the development of the environmental movement in the United States is its past close relationship to what we would today term white supremacy. Though many praise Teddy Roosevelt for his embrace of conservationism and evolutionary theory, he also adhered to the normative racial beliefs of the day, which presumed the superiority of Anglo-Saxon people, and couched that superiority in Darwinian terms. Even less well known is the activism of race theorist Madison Grant, who was as much a conservationist as the intellectual doyen of white supremacy that he is remembered as today (see Defending the Master Race: Conservation, Eugenics, and the Legacy of Madison Grant). In some ways the connection is reasonable and not surprising, in that both are fundamentally conservative preservationist instincts. To preserve the environment and the racial order of the day. The association was clear well into the 20th century, Charles Lindbergh was a prominent eugenicist, but later became an environmentalist, while Garrett Hardin, who originated the term “tragedy of the commons,” opposed high immigration levels and was skeptical of racial diversity.

cover_passing Because of environmentalism’s place within the cultural Left in the United States these corollaries no longer apply. In fact, the Sierra Club and other such organizations tend to be careful to not oppose immigration on environmental grounds any longer because of its racial implications. But, I’ve noticed that many people with an environmental orientation still use what strikes me as quite racialist language in the context of animals. I don’t think it is a problem. Different moral and ethical standards apply to animals. We eat them. We don’t eat humans. But I also think it is funny, as well as somewhat wrong-headed. This came to my attention again because of an article in Nautilus, A Strange New Gene Pool of Animals Is Brewing in the Arctic. There’s a lot of talk about issues like hybrid zones, and pre- and postzygotic isolation (at least implicitly). But this section is just totally confused:

In September, in an inlet some 1,800 miles north of Fargo, North Dakota, where the North American landmass dissolves into the Arctic Ocean, the whales met in the middle. They spent two weeks together, and although not much happened before they turned around, the meeting was historic. The fossil record indicates the last time Pacific and Atlantic bowhead whales came into contact was at least 10,000 years ago.

While it’s tempting to imagine a strange new Arctic teeming with “grolar bears” and “narlugas,” hybridization comes at a cost. Arctic biodiversity will be reduced through gradual consolidation, taking with it a blend of genes that have evolved by natural selection over millennia. “There’s going to be a whole bunch of organisms containing genes that we’re going to lose,” Kelly says. Which genes, exactly, is unclear….

The problem here is that the terms are being mixed up. “Biodiversity” is often applied at the level of species or races, with a diversity index calculated from discrete numbers of population types. If you calculate a diversity index based on Swedish, Nigerians, and Chinese, you start out with three populations and look at their proportions (the more skewed the proportions, the lower the diversity). If you take them all and mix them so they are one random mating population obviously the ecological diversity index is going to go down. But the genetic diversity is not going to down, because genes don’t “mix”. Mixing implies a blending theory of inheritance, what Mendelian genetics overthrew with its understanding of discrete and particulate units of inheritance. The same confusion crops up with the ideas of “disappearing blondes” and “disappearing redheads.” The phenotypes may change in frequency, but the understanding alleles, the genetic variants, remain. From a genetic perspective if you wanted to you could probably pull back out the original populations through selective breeding. Not only does the allelic diversity of the pooled populations not change, but the genotypic diversity increases, because of elevated heterozygosity. Finally, new potential combination genotypes arise from the mixing, so the phenotypic diversity in totality also probably increases (e.g., Brazilians exhibit a wider range of skin color variation than Africans or Europeans).

Of course this is predicated on racial/subspecies level variation and divergence. If the populations are separated long enough then there will be barriers to easy gene flow. This is evident in the modern human-Neandertal event, where the X chromosome seems to have been purified of Neandertal alleles (this is a common tendency with hybridization events). But please note above that the people in the piece are concerned about populations of whales separated for 10,000 years. There are plenty of human populations separated for 10,000, and even 100,000 years. So this isn’t really a terrifying number of generations.

 
• Category: Science • Tags: Hybridization 
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There is a specter haunting the intersection of conservation biology and public policy, the specter of the biological species concept. Coyote-Wolf Hybrids Have Spread Across U.S. East:

Scientists already knew that some coyotes, which have been gradually expanding their range eastward, mated with wolves in the Great Lakes (map) region. The pairings created viable hybrid offspring—identified by their DNA and skulls—that have been found in mid-Atlantic states such as New York and Pennsylvania.

Now, new DNA analysis of coyote poop shows for the first time that some coyotes in the state of Virginia are also part wolf. Scientists think these animals are coyote-wolf hybrids that traveled south from New England along the Appalachian Mountains.

Most of the wolf ancestry in the lower 48 states might be in “coyotes!”

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Genetics, Hybridization 
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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 brunette reconstruction, like the one here which is from the Smithsonian. But the most recent research (dating to 2007) seems to suggest that the Neanderthals may have been highly depigmented. This shouldn’t be too surprising when one considers that they were resident in northern climes for hundreds of thousands of years.

But there are some new tidbits, from researchers in the field of study:

“There is little doubt that this haplotype is present because of mating with our ancestors and Neanderthals,” said Nick Patterson of the Broad Institute of MIT and Harvard University. Patterson did not participate in the latest research. He added, “This is a very nice result, and further analysis may help determine more details.”

David Reich, a Harvard Medical School geneticist, added, “Dr. Labuda and his colleagues were the first to identify a genetic variation in non-Africans that was likely to have come from an archaic population. This was done entirely without the Neanderthal genome sequence, but in light of the Neanderthal sequence, it is now clear that they were absolutely right!”

The modern human/Neanderthal combo likely benefitted our species, enabling it to survive in harsh, cold regions that Neanderthals previously had adapted to.

“Variability is very important for long-term survival of a species,” Labuda concluded. “Every addition to the genome can be enriching.”

Since Nick comments here on occasion I probably should have asked him what he thought of these results back in January, but it goes to show that I’m not thinking like a journalist. Yet.

(Republished from Discover/GNXP by permission of author or representative)
 
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Mr. James Winters at A Replicated Typo pointed me to a short hypothesis paper, Neanderthal-human Hybrids. This paper argues that selective mating of Neandertal males with females of human populations which had left Africa more recently, combined with Haldane’s rule, explains three facts:

- The lack of Neandertal Y chromosomal lineages in modern humans.

- The lack of Neandertal mtDNA lineages in modern humans.

- The probable existence of Neandertal autosomal ancestry in modern humans.

If you don’t know, Haldane’s rule basically suggests that there’s going to be some sort of breakdown in the heterogametic sex. In humans females are homogametic, XX, and males are heterogametic, XY. The breakdown need not be death (or spontaneous abortion). It could be sterility (e.g., some mutation or genetic incompatibility which results in the malfunctioning of the flagella of sperm would do it).

So you have a scenario where only Neandertal males are interbreeding with the intrusive groups from the south. The hybrids from these pairings would then lack Neandertal mtDNA, since mtDNA is passed only from mothers. But the male offspring would have Neandertal Y chromosomes. This is where Haldane’s rule kicks in: these males in their turn would not reproduce. Therefore only the female hybrids would pass on their genes. These females obviously don’t pass on a Y chromosome. And, they would pass on their non-Neandertal mother’s mtDNA.


Obviously this makes logical sense. How plausible do I judge it? That depends on the other options and the probabilities in the moving parts of the model above. My main issue with the idea of Haldane’s rule being operative in Neandertal-non-Neandertal pairings is this: the two lineages had not been separated for very long at all. The authors give ~250,000 years for the most recent common ancestor. Let’s just double that. That still isn’t that big of a divergence. A few years ago I read some stuff on hybridization in mammals. There’s some pretty straightforward reasons having to do with gestation why this is more of an issue in our lineage than birds, for example, where you have instances of viable crosses between species whose last common ancestor lived tens of millions of years in the past. But that doesn’t speak to the issue of Haldane’s rule necessarily. The problems with interfertility tend to crop up on the order of millions of years, not hundreds of thousands.

In any case, what about the alternatives? There could have been some sort of selective bias against mtDNA and Y chromosomal lineages. This can be straightforward biological. Imagine that Neandertal mtDNA is correlated with some diseases with reduce fitness. The authors allude to this sort of issue. But it might be social. Across Latin America there has been wholesale replacement of Amerindian Y chromosomal lineages among mixed-race populations. In fact you have replications across many societies of European Y chromosomal lineages + non-European mtDNA lineages being dominant, with variation in autosomes (e.g., in Mexico the autosome is balanced, in Argentina it is mostly European). There is also the issue that mtDNA and Y chromosomal lineages are subject to more vigorous stochastic dynamics because of smaller effective population sizes than autosomes. Autosomes are a combination of both parental contributions, but the uniparental lineages are passed from only one. Males are a total dead end in regards to the propagation of mtDNA lineages since they do not pass them on, while females naturally do not have a Y chromosome. The Neandertal mtDNA and Y lineages may simply have gone extinct, which is more probable if they were a small minority in the human population ~30,000 years before the present (the probability that a lineage with “fix” and replace all others is proportional to its frequency at time t = 0).

But really the main issue here for me really is the plausibility of hybrid incompatibility between Neandertals and non-Neandertals. This was a common idea a few years ago before the evidence for Neandertal-non-Neandertal admixture, and I’d started to get skeptical of it based on comparisons to other mammals. But now we have more thorough genetic data. To the left is a table from the supplement of Genetic history of an archaic hominin group from Denisova Cave in Siberia. It is showing the time since the last common ancestors between pairs of populations (F = French, the rest of the rows are the same as the columns). I wouldn’t take the dates that seriously. What I want to point out is that the last common ancestor between Neandertals and other human populations isn’t even a multiplicative factor greater than that between Africans and non-Africans. These particular estimates might be wrong in the details of their magnitude, but I think before we assent to the probability of hybrid incompatibilities we need to consider the high likelihood that Neandertals just weren’t nearly as different as we might think, or have thought.

The following video is for entertainment purposes only:

(Republished from Discover/GNXP by permission of author or representative)
 
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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.org But 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

(Republished from Discover/GNXP by permission of author or representative)
 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"