Trinity College Dublin; The Broad Institute
Trinity College Dublin
Favourite thing to do in my job: Smell freshly-burned collagen from ten-thousand year old goat bone
I'm a geneticist in Dublin who has just finished my PhD, looking at the history of domestic goat using ancient DNA.
I’m an Irish 26 year old who did my college undergraduate degree in Trinity College Dublin, followed by my PhD project which I just finished. I’m from the countryside in Meath, but have mostly been living in Dublin for the past eight years. I currently live with my boyfriend near the centre of the city. We spend an awful lot of our time talking about economics, politics, dachshunds, history, music, film, and television – occasionally even biology and genetics!
In my spare time I read a lot – for Christmas I received The Guns of August, the first three Uplift books, and In The First Circle. I play a lot of board games and card games (hopelessly addicted to Magic) with friends and used to be President of the TCD Gamers Society. I listen to far too many podcasts. I go to the cinema as much as I can, which isn’t frequent.
I extract DNA from ancient goat bones and use their genomic information to study the 10,000 year history of their domestication.
The genome is an incredibly rich source of information, which we can exploit to study past events such as population size changes or migration, and also the effects of selection and evolution. This is particularly true when we look at the genomes of many individuals simultaneously – a field called population genetics. Most population geneticists study present-day genomes to infer past events, but sometimes older events are hidden by more recent ones. To get around this, some researchers focus instead on genomes extracted from ancient materials (bone, hair, teeth, clothing, even chewing gum), which can reveal processes which were otherwise unknown to us. An example of this was discussed in the second lecture. A tiny finger bone from Denisova Cave in the Altai Mountains of Russia revealed a sister group of humans, called the Denisovans, which were closely related to the Neanderthals. Denisovans contributed to the modern human gene pool, but their ancestry is mostly found in people from southeast Asia and Papua New Guinea.
My research uses a similar idea, but rather than focusing on humans, I investigate a species with which we also have a close relationship: the goat. Humans have been managing and domesticating goat for the past ten thousand years, which has had a substantial effect on their biology (e.g. how they look and behave), which is based on changes to their genomes. By sequencing genomes from goats throughout these ten thousand years, we can try to determine how these change occurred, such as which genes appeared to have changed earliest. My work has shown that a gene involved in coat colour – the KIT gene – was affected by selection by about 8,000 years ago, suggesting that early farmers may have valued different coat colours.
Ancient goat genomes can also tell us something about how humans from the same time. For example, I found that all modern European goats have ancestry from ancient wild goat from Turkey. This means that ancient farmers were likely restocking their herds with local wild goat, as the practice of goat herding spread from southwest Asia into Europe. Something else I discovered that the managed goat at the beginning of farming (the “Neolithic” or New Stone Age) in the Levant (Syria, Lebanon, Israel, and Jordan) were very different from those in Copper, Bronze, and Iron Ages. These later goats looked much more like Neolithic goat from more eastern regions such as Iran. An explanation for this is that people begin moving and trading more in these time periods, and this resulted in goats similar to those from Neolithic Iran being brought into the Levant. Exactly how and from where this happened, I’m not sure, but it’s something I want to continue studying.
If the Lectures made you realize that there is a lot to our history and evolution you may not have known, then my research might do that same. We’ve only been farming for ten thousand years – no time at all in our evolutionary history – but that has had a profound effect on our societies, our diet, our culture, and our animal partners. Where we have gone, they’ve gone with us; when our populations have grown, livestock has too. Our histories have been intertwined for ten millennia, and ancient genomes can help recover this shared past.
My Typical Day
If I'm working in our ancient laboratory, I will be wearing protective clothing to prevent contamination as I drill animal bones and extract DNA for sequencing. Other days, I work mostly on my computer, processing sequencing information and comparing ancient goats to modern ones.
If the day is an “Ancient DNA” day, I head downstairs to the basement of our building where our ancient DNA laboratory is found. As contamination from modern DNA is a problem in ancient DNA research, I have to be sure I have not gone to our lab upstairs, and have to wear freshly-washed clothes that have also not been in our lab upstairs. There is so little DNA in most ancient bone samples that even a small amount of contamination would have a huge effect on our work, so we try to avoid this at all costs.
We have to wear special clothing in our ancient DNA laboratory, that reduces the chance that we contaminate the ancient samples. This means hair nets, face masks, a boiler-suit and two layers of gloves. In the ancient DNA laboratory, the first thing we do is give everything a quick clean with a mixture of bleach and water – we are very paranoid about contamination, so cleaning is something we spend a lot of time doing! Bleach is a powerful oxidative agent, which means it interacts with and changes any DNA in the lab environment (and anything else it runs into contact with), reducing the chance that there is contamination in the environment.
If I am sampling a bone, my typical work would be as follows: first I document and photograph the bones that our archaeologist collaborators have sent us. Then the bones are “UV-ed” – put underneath a UV light for 30 minutes, which removes DNA contamination on the surface of the bones. After all the bones have been UVed, I place each into its own bag, and then start sampling one by one. I take one bone and place it into a hood that has a strong extractor fan. Then I remove surface layer of bone and dirt with a small drill bit, and UV the bone one last time. Now, it’s drilling time! I use a small saw and cut into the densest part of the bone. Using tweezers (no touching allowed) I transfer this to a shaker and turn it on for 30-60 seconds. This reduces the bone to a fine powder, which I weigh (we typically used 0.15g of powder) and store in a test tube. Then I wash everything with bleach, and start on the next sample. This entire process may take about 30-40 minutes a bone. From there, I will eventually extract DNA from the bone powder and sequence the sample, to see if there is any DNA preserved and which species it is.
If I’m not working in the ancient DNA lab, I will be at my desk in the lab upstairs. Here, I work mostly with computers. I use tools for handling biological data (“bioinfomatics”), mostly looking at the genomes of the ancient goat that we have sequenced (“genomics”). This involves a lot of managing files, computer space, and long chains of computer tasks (the boring stuff), but also fun work such as looking at how ancient goat relate to each other and also modern goat.
My favourite CHRISTMAS LECTURE memory is:
This was my first year watching the lectures, but I would have to say when Alice showed just how small an amount of time humans have been around - it's very easy to forget that farming is *only* about 11,000 years old, cities ~4,500 years old, and humans as we know them ~200,000 years old - a sliver of geological time!
How would you describe yourself in 3 words?
Tasteless, Curious, Impatient
What's the best thing you've done in your career?
Getting my goat research published in an academic journal.
What or who inspired you to follow your career?
Honestly I have only ever followed what interested me, rather any person or book etc. Biology, genetics, and then the genetics of ancient animals are fascinating, so that is why I have made it my career.
What was your favourite subject at school?
A tie between History and Biology.
What did you want to be after you left school?
A grown-up (I still don't know the answer to this).
Were you ever in trouble at school?
Once I got detention for *honestly* forgetting my Math homework...the embarrassment.
Who is your favourite singer or band?
Impossible to answer. Three of my current favourite: Devo, Talking Heads, Villagers.
What is the most fun thing you've done?
Exploring Japan for two-and-a-half-weeks this September.
Tell us a joke.
Repetition is a form of comedy. Repetition is a form of comedy.