How animals respond to changing environments

The phenotype of an animal is largely dictated by its genetic code. Its DNA encodes proteins that determine the size of its wings, the shape of its beak, and the color of its feathers. So if the animal is faced with a new situation that its ancestors never encountered, such as a novel virus, is it automatically in trouble? Not necessarily. Although an animal cannot change its DNA, there is flexibility in how the DNA is expressed, i.e. how and when certain proteins are made. We study these molecular responses to environmental change. It’s important to understand these mechanisms to better predict how wild populations will weather the various ways in which humans are altering natural ecosystems world-wide.

Effects of pox infection on Darwin’s finches

We used RNA sequencing to characterize gene expression in vegetarian and medium ground finches These sequences tell us what genes were active in the moment that finches were captured. By comparing gene expression of infected and uninfected finches, we can tell how infection changes the cellular and molecular function in these birds.

We found that infected birds of both species upregulated genes in response to infection. Most of these genes were involved in the innate immune system, suggesting that finches do detect infection and respond by activating their immune defenses. However, we saw significant differences between species. Ground finches had a stronger response to infection than vegetarian finches. These results indicate that Darwin’s finches do have some defenses against avian pox; however some species may be more vulnerable to the disease than others. Read more here.

What is “epigenetics?”

Epigenetics refers to changes to gene expression or function that do not include genetic mutations, i.e. changes to the DNA code. For the past 100 years or so scientists have assumed that any evolution in a population of organisms requires a change in DNA. Recent work, however, finds that structures associated with DNA can change gene expression and thus phenotype. Some of these epigenetic changes are induced by the environment and can even be heritable, which means they are a potential other mechanism of adaptation to environmental conditions.

Rapid urbanization in the Galápagos

The Galápagos Islands have experienced a period of rapid environmental change in recent years due to the increase in tourism and development on the islands. We investigated the effects of urbanization on Santa Cruz on two species of Darwin’s finches: medium ground finches (Geospiza fortis) and small ground finches (G. fuliginosa). We compared DNA methylation in blood and sperm cells of finches living near the biggest city in the Galápagos, Puerta Ayora, to finches that lived in relatively undisturbed habitat about 10km away. We found a number of notable changes between populations: both species had DNA methylation differences between urban and rural populations in both blood and sperm. In addition, in one species, G. fortis, we saw that urban birds were significantly larger in size than rural birds. But in neither species did we see genetic differentiation between urban and rural populations. These results suggest that ground finches are responding to environmental changes around Puerto Ayora and that DNA methylation may be involved.

Epigenetic effects of P. downsi on mockingbirds

Can DNA methylation changes help hosts adapt to a new, virulent parasite? In collaboration with Christina Richard’s Lab at the University of South Florida we investigated the epigenetic effects of the avian vampire fly (Philornis downsi) on Galápagos mockingbirds. Using a new technique called epiGBS, we sequenced the genomes of nestlings and tested whether methylation at those sites differed between parasitized and non-parasitized individuals. We did not detect a consistent effect of parasitism on methylation, which may reflect the variable conditions of our study, and/or the variable effects of parasitism on nestlings.

However, we did see a surprising outcome in a “parallel” experiment we ran using zebra finches. In the Galápagos we use an insecticide called permethrin to eliminate the vampire fly in mockingbird nests. So, we needed to make sure that the permethrin itself didn’t have epigenetic effects, which would confound our results. We exposed zebra finch nestlings in captivity to permethrin and to our surprise, we did see significant effects of the insecticide on nestling methylation. The differentially methylated genes were associated with endocrine function, mirroring known physiological effects of permethrin on vertebrates.

The use of insecticides to combat the vampire fly in the Galápagos is controversial because of concern about their effects on native bird and insect species. Although permethrin is largely considered non-toxic to most mammals and birds (it’s a common ingredient in louse shampoos, and insect repellents used for both pets and humans), there are growing concerns about its effects on hormonal pathways. These laboratory results do suggest that permethrin may affect cellular function in nestling zebra finches. However, there were significant differences in the extent of exposure between captive nestlings in an enclosed space, and Galápagos nestlings in the wild. As a result, permethrin should be used judiciously, but it is still an important tool in combating the spread of the avian vampire fly.