Prezewalski Horse

In honor of Endangered Species Day, the National Academy of Sciences features Professor Elizabeth Thompson on their Facebook page as a guest publisher to write a few remarks regarding her research in genetics and her involvement in Conservation Biology, as follows:

Despite the many challenges facing the endangered species of our world, this is also an exciting time to be involved in the science of Conservation Biology and studies of biodiversity. Genomics is providing non-invasive tools to study populations in their natural habitat, to understand the genetic structure of these populations, and assist in maintaining genetic diversity within them.

We receive our DNA as copies of parts of the DNA in our two parents and in turn copy some of that DNA to our offspring. The exact combinations that form the genome of each living organism are truly unique. However, parts of our genomes are shared. In any species, individuals have common ancestors, and a single segment of DNA in such an ancestor may be copied over repeated transmissions to the current individuals. This shared genome, or gene identity by descent (IBD), underlies the genetic trait similarities we see in relatives.

The process of meiosis, in which DNA is copied to a sperm or egg cell, is highly random. The survival of genome, and hence of genetic diversity within a species, depends not only on which individuals survive and reproduce, but also on the DNA copied in meiosis. At any single location in the genome, Mendel’s First Law tells us that there is a 50-50 chance that an individual transmits their paternal [maternal] DNA. More importantly, DNA is copied in large segments: for smaller chromosomes, there is close to a 50% chance that an intact parental chromosome will be transmitted. In this sense, genomes are short. Remote relatives have high probability of not sharing any genome IBD directly from common ancestors, but, if they do, the DNA segments shared will be millions of base pairs long. This complicates, but also make fascinating, questions of the survival of genetic diversity in small populations.

The consequences of these theoretical processes are exciting, but far more exciting both as a statistician and as a scientist, is to make inferences from genetic data on current individuals. Genetic and genomic technologies have changed out of all recognition over the last 35 years. Initially, there were few genetic markers that would work to analyze diversity in a remnant species, even where there was a related species for which markers had been developed. For the “Prezewalski Horse” there was the wealth of markers from the race-horse world, but for the “California Condor” the closest available were markers developed for chickens! Nonetheless, we were able not only to clear up many uncertainties in the recorded pedigree of the “Przewalski Horse,” but also to infer broad patterns of relatedness among the small number of surviving adult California Condors. For both species, the founding population is no more than 12 individuals. Even 12 individuals, when not already closely related, can harbor substantial genetic diversity, but without decisions informed by genetic analysis much will be lost to the re-established populations now numbering many hundreds.

A huge technological advance has been the ability to type DNA markers from hair or from feces, rather than requiring blood samples. This has transformed genetic studies from being limited to captive or closely managed populations, to populations that can be studied in the wild. New genomic technologies provide a wealth of markers across the genome, and even for small populations of quite differentiated species, DNA markers are robust enough to be useful. Previously, with few genetic data, a specification of pedigree relationships among individuals was important to inform genetic analysis, again limiting studies to closely managed populations. Now, the segments of DNA shared IBD by current individuals can be detected without the need for any knowledge of pedigree ancestry. Indeed, genetic studies have moved from considering the IBD expected under specified relationships to IBD realized in the actual descent of DNA. Due to the randomness of meiosis, the realized descent can differ quite markedly from its expectation, and it is realized descent that underlies genetic similarities and diversity among individuals.

This in turn opens up new lines of genetic analysis; a known pedigree can be used to detect departures from Mendelian expectations. Although the randomness of DNA inheritance accounts for much of the variation among individuals and loss of genetic diversity, selection also operates in all populations. In any managed population, selection may be imposed, intentionally or unintentionally. With informative genetic markers across the genome, we have the potential to detect specific regions of the genome that are under selection. These may include selection for or against introgressed genome segments from hybridization with closely related species, or regions that harbor genes responsible for inbreeding depression.

However, conservation is much broader than only genetic analyses, and finally, on this Endangered Species Day, I call on all of us to honor and recognize those who work in biological and ecosystem conservation around the world. They are on the front lines in the fight to save the endangered species of our planet, and many work in difficult and sometimes dangerous places.