Diving into the Past: Identifying Genetic Admixture Between Populations of Bottlenose Dolphins

By Magdalena Phillips (Trinity '23)

April 2022

Introduction to Our Populations

Imagine you’re sitting on a beach in North Carolina, reading a book and soaking up the sun. Suddenly, someone yells “Dolphin!” You whip your head around to spot the dark fins of bottlenose dolphins passing by. You can’t make out much detail, but the animals look sleek and stream-lined.

Now imagine you’re on a boat at the Atlantic, so far from land that it has disappeared behind the horizon. There’s another shout of “Dolphin!” but these bottlenose dolphins look quite different. They are bulkier and have a white peduncle (a region above their tail). Why do these dolphins look so different from the ones who live closer to shore? If you guessed that they've evolved to live in different habitats, you would be exactly right! Each type is adapted to live in different water depths. The "inshore" dolphins hunt for their food in shallow waters, so they dive only for short amounts of time. The “offshore” dolphins are adapted to live in deeper waters beyond the continental shelf. They dive for longer and go further down than their near-shore counterparts.

These two types of dolphins are what my subteam’s research has been focused on. Overall, we want to know whether the offshore dolphins have evolved genetic adaptations to handle the lack of oxygen, called hypoxia, that they experience on their long dives. In order to do this, we can compare the offshore dolphins' DNA to the inshore dolphins' DNA.

My Research Question

In order to compare how each population has evolved to deal with hypoxia, we first need to understand how they have split off from each other. That is what my research has focused on.

Previous researchers collected skin samples from dolphins along the East Coast. If you look at the map on the right, you can see a dot where each sample was taken. The color of each dot shows what population they belong to. You may notice that there are three colors, not the two we expected! When we analyzed their DNA, we found that the inshore type is split into two genetically different populations. We call the red the "inshore" population and the blue the "shelf" population.

Last year’s team also discovered some evidence of admixture between the inshore and shelf populations. What does that mean? In population genetics, "admixture" is gene flow between populations that had previously not been breeding with each other. Overall, my research goal was to investigate the question: has the shelf population undergone admixture with the inshore population at some point in the past?

Admixture Analysis

For my analysis, I used a program called TreeMix. It was developed in 2012 to identify and quantify admixture between populations. Over the last decade, it has been used to study many different animals, including humans, cows, killer whales, and bottlenose dolphins.

The first step of running TreeMix is to create a maximum likelihood tree. This is essentially TreeMix’s best guess at the population history, assuming that there has been no admixture. On the left, you can see the tree for our populations that I created in TreeMix. Overall, the tree matches what we expected based on other studies of Atlantic bottlenose dolphins. Namely, the offshore population was the earliest to split off, while the inshore and shelf populations have split off from each other more recently. Don't worry about the "drift parameter" on the x axis; you can think of it as essentially the passage of time.

However, a phylogenetic tree like the one we made is often too simple to fully capture the intricacies of populations' histories. The real world is much messier! Therefore, the second step of TreeMix is to add one "admixture event" and see if it improves how well the tree fits the DNA from our populations. I ran this step 100 times, as TreeMix doesn’t always give the same output every time. The most common tree is on the left! It was produced 69/100 times. Although this may seem low, in truth the other runs looked very similar. In all 100 cases, TreeMix found that there was an admixture event from the inshore population into the shelf population. What varied was the location of the shelf population on the tree. Some runs said that it was more closely related to the offshore population than to the inshore population.

To confirm these results, I used f3 statistics. These essentially measure how closely the DNA matches between populations. If a population has mixed with another one in the past, you would find more of match between their DNA. When you calculate f3 statistics, the output is something called a Z score. If you have never heard of a Z score before, don’t sweat: it’s essentially telling you how far your data is from what you would expect if there wasn't admixture. If the Z score is below -3, then it's quite far from what you would expect and the population is significantly admixed. When I tested the shelf population, the Z score was -4.13, which is below my significance threshold of -3. We can conclude that the shelf population is significantly admixed with the inshore population!

Conclusions and Next Steps

So, what did we find out? Here’s the TLDR:

Offshore dolphins split off early from the inshore and shelf populations
In the past, the inshore population underwent admixture with the shelf population
An overall better understanding of the history of these dolphins

What’s next?

There are still some caveats with these results, especially with the lack of clarity around the location of the shelf population on the tree. TreeMix is known to have difficulty understanding relationships between closely related populations when there is no outgroup. An "outgroup" is a more distantly related population that you can compare your samples too. Thankfully, we have just finished sequencing another round of samples, which included some pilot whale samples. Going forward, this will give me an outgroup to use. Hopefully we will also be able to discover new populations that will further illuminate the fascinating histories of East Coast bottlenose dolphins!