Ancient RNA: A Whole New World of Possibilities for Paleopathology?

imgres-3I just wrote a piece for BiteSize Bio called Ancient RNA: Does Next Generation Sequencing Offer a New Window into the Past?

In it, I describe an article by Fordyce et al that came out earlier this year in PLoS ONE: Deep Sequencing of RNA from Ancient Maize Kernels. This group of researchers was able to obtain RNA sequences from 700-year-old corn kernels. Neat, right? I was really surprised that this paper didn’t get more attention when it came out. I think it’s basically been taken for granted that studying ancient RNA just isn’t possible, due to RNA’s fragility–so a paper showing that aRNA studies may actually be feasible was pretty exciting in my opinion.

Tom Gilbert, the senior author of the article, told me they have encountered some skepticism regarding the results, because the idea that RNA can’t survive over long periods of time has become so ingrained. Maybe that’s why there hasn’t been more chatter. I thought the paper was pretty thorough, though, in ruling out issues such as contamination. I have to say–I’m a believer so far!

Which leads me to wonder… if you can amplify ancient RNA from ancient corn kernels, is it also possible to do so using other types of samples? Tooth pulp, for example, which should also provide a relatively protected environment? If so, perhaps we could look at infection with RNA viruses (e.g., coronaviruses, influenza, hep C) in times past. Or maybe even gene expression under various conditions. The possibilities seem endless! I’m really curious to see where this line of research goes. Is this just the beginning?

Reconstructing the ancestral microbiome: the American Gut approach

hadza-615I came across the human food project website today. This site is run by the American Gut project folks. You may have heard of their work before: you send them $99 and they send you a home sampling kit. You swab yourself, and they give you a list of the microbes living in your gut. Neat, right? And besides yielding fun information for you, it provides a rich data source for them to analyze (with the goal being to learn more about what Americans are carrying around in their intestines).

I’m waiting for my results to come back from uBiome, a similar service.

Anyway, on the website, I noticed a section entitled Ancestral Microbiome. Exciting! I’ve actually been thinking about how one could go about reconstructing the ancestral microbiome a lot myself lately. Recently, I published a paper entitled Genomics, the origins of agriculture, and our changing microbe-scape in the Yearbook of Physical Anthropology with George Armelagos. One thing we looked at is attempts to learn more about the pre-agricultural microbiome. This is a really tough problem, for several reasons.

One approach would be to use aDNA to characterize microbiomes from ancient remains. The aDNA approach has worked out for some ancient post-agricultural remains (check out Insights from characterizing extinct human gut microbiomes by Tito et al.), but so far nobody has gotten it to work on remains dating prior to the advent of agriculture. Bummer.

Another approach is to study contemporary hunter gatherer groups. This is pretty problematic too, though. First, the very few hunter gatherer groups that are still around have been able to protect their way of life primarily by fending off agriculturalist intruders. This means that they are probably not amenable to being studied by swab-bearing scientists. Second, learning about the hunter gatherer groups around today isn’t necessarily going to tell you all that much about the typical hunter gatherer group living tens of thousands of years ago. The very fact that a hunter gatherer society is still around in a very agriculturalist world suggests that it may be unique in some way. Third, even though some hunter gatherer groups have been able to maintain their traditional subsistence strategies, more or less, it’s possible that they have still been exposed to agriculturalist microbes, which might have altered their microflora.

So how are the Human Food project researchers going about reconstructing the ancestral microbiome? They are studying the Hadza of Tanzania. About 1,000 Hadza live around Lake Eyasi in the northern part of the country, and roughly one-quarter of them live as hunter-gatherers (no crops, no livestock). Not surprisingly, the Hadza are not completely cut off from the world outside their homeland. Contact with agriculturalists stretches back for at least a century. Most Hadza now speak Swahili fluently. Alcohol has become a problem for some, and microbes like TB have been introduced. In the mid 1990s, anthropologist Frank Marlowe found that about 10% of calories that came into Hadza camps was from non-foraged food delivered by missionaries or obtained through trade with agriculturalist neighbors. It’s possible that an increasing stream of money from tourism may result in more calories being obtained from purchased crops nowadays.

It will definitely be interesting to see how the microbiomes of the Hadza differ from those found in other groups in the area. I think this is a project worth doing. But my guess is that there has been a lot of “microbe-creep” between the Hadza and these neighboring groups (and perhaps even foreign tourists). This, along with the other problems I pointed out, would compromise our ability to draw conclusions about the “ancestral” genome. I’m eager to see how this will play out–and curious to hear what other people think.

No ancient DNA in Insects Preserved in Amber

fossil-dominican-amber-insect-stinglees-bee-with-wasp-on-its-head-03151(cp)So the article Absence of Ancient DNA in Sub-Fossil Insect Inclusions Preserved in ‘Anthropocene’ Colombian Copal falls under the killjoy heading for everyone who saw and loved Jurassic Park as a kid. Although the title of the paper sounds complex, what the researchers did was  pretty simple. They took two bees preserved in copal (basically a younger version of amber), one from 10,000 years ago and the other from more recent times (post-world war II). Then they looked for ancient DNA using 454 sequencing. And they found zilch.

They conclude that if you can’t find decent DNA in a 20th century copal sample, it doesn’t seem possible that we will ever be able to obtain DNA from an ancient amber sample. This work is also another nail in the coffin of a series of studies that came out in the early days of ancient DNA research. They claimed to have sequenced ancient DNA from amber-preserved bee, termite, and weevil specimens, sometimes from hundreds of millions of years ago. A number of lines of evidence have now convinced scientists that these exciting findings were just due to contamination.

Well, bummer. But we’ve still managed to do some pretty impressive things with ancient DNA. We’ve sequenced the Neandertal and Denisovan genomes, for example.Who would have ever believed that was possible ten years ago?

Of dogs and men

a-lot-of-dogs[1]When we cozy up to a dog, or cuddle a cat, or watch a docile cow grazing in a field, it’s easy to forget that the wild ancestors of these animals were not nearly so friendly. Pets and farm animals are so familiar that it’s hard to imagine life without them, but the process of domestication didn’t start until relatively recently in human history. One of the neat things about genetic studies of modern animals is that we are sometimes able to reconstruct their past. In particular, there has been a lot of excitement about potentially revealing the genetic basis for animal domestication. Can a couple of mutations turn a wolf into an affectionate dog? Or does it take a whole slew of genetic changes? Do all domestic animals harbor similar genetic alterations, linked to things like tameness and color? Or does every species become domesticated in its own way? Were most animals domesticated only once? Or does it happen over and over again, in different places, once the idea catches on? Lots of questions about domestication, and the answers are still trickling in.

Recently, a flurry of studies on dog domestication has come out. Over the years, dogs, especially, have gotten a lot of attention from scientists interested in domestication, probably because they love dogs like the rest of us. Although lots of studies have been done, the findings have been a little confusing. And when you consider how tough domestication is to investigate, the ambiguous results start to make sense. Basically, most studies work like this: you get a bunch of dogs and sequence some genes (or genomes, if you are lucky). If dogs from a certain region exhibit a lot of genetic variation, you start to think that maybe this is where they were domesticated. (More variation in one geographic location usually means an animal has a longer history in that spot.) But as it happens, when you do this kind of study, it really matters how you pick and choose your dogs. The more animals that you pick from one location, the more likely you are to find a lot of variation in that region. So if you study a lot of dogs from Asia, you find a lot of variation in Asia, and it seems like dogs must have been domesticated there. If you study a lot of African dogs, then THAT seems like an equally likely site for domestication. On top of that, genetic signatures start to get really murky because domestic dogs sometimes interbreed with wolves. When wolf genes enter a dog population, they introduce new genetic variants–and the greater amount of variation that results can make a dog population look “older” than it really is. I think the latest consensus is that it’s just not clear where dogs were domesticated. It may have happened first in the Middle East or Europe. Or maybe China. There is also a lot of confusion about when dogs were domesticated. Based on studies of nucleotide substitution rates, scientists have hazarded guesses of anywhere from 100,000 YBP (probably way too early) to 15,000 YBP. All of the estimates so far seem to predate agriculture, which began around 10,000 YBP, and both genetic and paleozoological evidence suggests that the dog was probably the first animal domesticated.

OK, so maybe we haven’t had a ton of luck figuring out where or when dogs were domesticated. But that doesn’t mean we can’t learn more about HOW they were domesticated–genetically, that is. Recently, Erik Axelsson, a scientist at Uppsula University in Sweden, and colleagues sequenced the entire genomes of 12 wolves and 60 dogs of various breeds. By comparing the two groups of genomes, they identified 36 genomic regions that appeared to have undergone natural selection in dogs. In other words, under selective pressure to become domesticated, these parts of the dog genome look different from the same parts of the wolf genome. Genes involved in nervous system development seemed to be disproportionately represented among these altered regions of the genome. Since dramatic behavioral changes are some of the first things we think about when comparing wolves and dogs, finding these changes wasn’t terribly surprising. In fact, another study on dog domestication that just came out in Molecular Biology and Evolution concluded that genes expressed in the prefrontal cortex, a region of the brain responsible for complex cognitive behaviors like cooperating with humans during a hunt, evolved rapidly very early in the domestication process. Clearly, our best friend’s brain underwent major changes as we started to spend a lot of time together.

Axelsson’s study also found that genes involved in digestion and food metabolism, including starch digestion, were prominent on the list of dog genes affected by domestication. Since the ability of dogs to thrive in or near human settlements must have involved a big change in their diet (less meat, more starch), this makes sense too. What’s more, another recent whole-genome study on dogs and wolves, carried out by an independent group, identified the same trend: changes in genes involved in starch digestion appeared to be very important for domestication. After finding all these diet-related genetic changes, Axelsson and colleagues suggested that the development of agriculture may have catalyzed the domestication of dogs. This is interesting, since it would put the timing for dog domestication thousands of years later than other genetic studies have estimated. Since dogs being domesticated post-agriculture doesn’t seem compatible with a lot of the other findings, even recent ones, I guess it’s best to take a wait and see approach toward this interpretation.

One of the most exciting things about these recent findings is that they demonstrate that humans and dogs have undergone parallel changes over the course of our shared history. Similar genetic changes to the ones described in dogs have been found in human populations with high-starch diets, for example. And researchers who compiled a relatively comprehensive list of human and dog genes shaped by natural selection identified a substantial amount of overlap. Shared genes mostly fell into two categories: those involved in digestion and those involved in neurological processes. I guess it makes sense. Some people, like anthropologist Peter Wilson, have argued that since the advent of agriculture, we humans have been domesticating ourselves, settling down to live in large communities, eating new things, behaving in new ways. Dogs and people eat a lot of the same things, and we share the same environment. It turns out our genomes reflect our intertwined lives.