Lecture Notes: BIOL B242 Conservation Genetics

Kanchon Dasmahapatra ([email protected])

“Conservation genetics is the application of genetics to preserve species as dynamic entities capable of coping with environmental change.” (Frankham et al. 2002).

Conservation genetics is a large and rapidly growing field of conservation biology. It covers a wide range of topics: inbreeding depression, loss of genetic diversity, reduced gene flow, genetic drift, accumulation of deleterious alleles, genetic adaptation to captivity, resolution of taxonomic uncertainties, definition of management units, forensic application, understanding species biology and outbreeding depression.

A whole lecture course could be devoted to the topic of conservation genetics, but we only have a single lecture. Therefore, we will only be able to touch a few of these topics. We will look at two major areas that can be roughly described as:

1. Inbreeding, bottlenecks and loss of genetic diversity 2. Taxonomic uses of genetics in conservation

The theory behind these topics is very important and you have covered some of it in previous lectures. However, instead of peering too closely at the theory, we will explore these themes by means of a number of practical examples that will serve to highlight the importance and the problems of applying genetics to conservation.

But before we explore these areas we should consider whether genetics is actually important in conservation. As conservation biology seeks to prevent extinctions, this boils down to the question of whether or not genetic factors are important in causing extinctions. In the 1980s there was much debate about this question (but as whole lecture courses are nowadays devoted to conservation genetics, surely genetics must have some importance). Since then, empirical and theoretical evidence has mounted establishing a role for genetics in conservation. In this lecture we will examine some of this evidence.

However, there is no denying that human and environmental factors are by far the most important factors causing extinctions. The bulk of extinctions are a result of habitat degradation and over-exploitation brought about by human action. Environmental factors such as catastrophes, disease epidemics and competition from other species are also important.

Inbreeding, bottlenecks and loss of genetic diversity

Inbreeding is the mating of individuals that are related by descent. Offspring resulting from such matings often show reduced fitness compared to non-inbred individuals, a phenomenon known as inbreeding depression. This reduced fitness is thought to arise mainly as a result of deleterious recessive alleles coming into homozygous combination in inbred individuals. Although the harmful effects of inbreeding have been known for some time (Darwin documented evidence for it), most examples come from laboratory experiments. There are very few good examples of inbreeding depression in wild populations primarily because it is difficult to know how inbred a wild individual is.

Is inbreeding depression of concern in organisms of conservation interest? Incestuous matings are unlikely to arise in large populations, however, when populations become very small, incestuous matings are unavoidable and inbreeding depression may occur. Due to space limitations, small population sizes are often unavoidable in zoos and the first good evidence for inbreeding depression in organisms of conservation interest came from captive breeding programs. Probably the best example of inbreeding depression in a wild population is that of the Mandarte Island song sparrow.

While an inbred individual has a low heterozygosity (as measured using molecular markers such as allozymes or microsatellites), a population with a low heterozygosity (or genetic diversity) is not necessarily a sign of inbreeding. This is because genetic drift in a small population can cause the loss of alleles resulting in low heterozygosity in the absence of incestuous matings. High heterozygosity is not strictly the same as high genetic diversity. But a population with a high genetic diversity has lots of alleles and will generally have a high heterozygosity.

A population remaining at size NE for t generations will lose heterozygosity according to:

Ht = H0(1-1/2NE)

(where Ht = heterozygosity after t generations; H0 = initial heterozygosity; NE = effective population size) an equation that you have previously met in the “Inbreeding and neutral evolution” lecture. Something to notice in this equation is the use of NE. NE, the effective population size is often much smaller than the actual population size.

It is usually assumed that a population with a lower genetic diversity will be less fit compared to a population with a higher genetic diversity. This is because a population with a low genetic diversity is in theory less adaptable to environmental changes. For example, a population with a low genetic diversity may lack alleles that confer resistance to particular diseases and therefore be susceptible to the disease in question. The assumption that population with a low genetic diversity is less fit has given rise to the idea of an “extinction vortex”. But evidence for the lowered fitness of populations with low genetic diversity is equivocal. E.g. Glanville fritillary, wolf, Florida panther, cheetah.

Taxonomic uses of genetics in conservation

Taxonomy is important for determining what is out there to be conserved. While some groups of organisms, such as birds and mammals, have received much attention in this respect, the relationships between taxa in other groups, especially “primitive” ones like many invertebrates and bacteria are less well known.

As conservation decisions are very often based around units such as species or subspecies, it is very important that the taxonomic status of a population is correctly assigned. However, these units on which conservation decisions are based may be difficult to define. What is a species? Upon consideration, this seemingly simple question gradually becomes increasingly complex. No universally accepted definition of a species exists. Even the “experts” do not agree, with at least 22 existing definitions. But as you have covered these topics in the “Biodiversity and species” lecture.

In addition to species definition problem, subspecies are often accorded legal protection, leading to the even more intractable question, “What is a subspecies?”. The subspecies concept is even more subjective and controversial than the species concept. The difficulty lying in the fact that there are no sharp boundaries between what represents a species, a subspecies and mere sub- populations. Two subspecies can possibly be viewed as being two populations part of the way towards full speciation.

Sequences of conserved genes, such as sections of the mitochondrial genome, are widely used to determine species and subspecies status. The sequences are used to build phylogenetic trees as described in the “Evolutionary Trees” lecture. When discrimination between more closely related groups (between populations) is required, faster evolving bits of the genome, such as microsatellites, are often used. But how large are genetic distances for “good species”?

Some problems associated with incorrect taxonomic classification are:

- Endangered species may be denied legal protection and conservation resources, e.g. tuatara. - Resources may be wasted on conserving populations of common species or hybrids, e.g. Florida panther, red wolf. - Population augmentation programs transferring organisms between populations thought to be the same species may result in unwanted hybridization. - Populations that could be used to improve the fitness of inbred populations may be overlooked, e.g. Dusky seaside sparrow.

The utility of genetic markers for taxonomic purposes has also been exploited for a number of forensic applications such as the tracking of rare or elusive animals, or the identification of species from bits of tissue. These applications are primarily a result of our ability to amplify tiny amounts of DNA using the polymerase chain reaction. The small amount of DNA contained in hair shed by animals or even faeces (though this is a smelly and messy business) is often sufficient. The tissue samples used in forensic applications are often highly degraded and contain miniscule amounts of DNA. For this reason, mitochondrial genes are often amplified from such tissue samples as more copies of mtDNA are present per cell compared to nuclear DNA.

The Pyrennean brown bear and the hairy-nosed wombat are cases where hair and/or faecal samples have been used for tracking purposes. The identification of protected whale species in commercially sold food items is another example where genetic tools have been used successfully for conservation purposes.

You may now be able to judge whether or not you think genetics is important in conservation biology. But remember that human factors are still by far more important in causing extinctions.

References

* Caro, T. M. and M. K. Laurenson. 1994. Ecological and genetic factors in conservation: a cautionary tale. Science 263:485-486. - a nice counter to the “how inbreeding kills cheetahs” idea. * O’Brien, S. J. 1994. A role for molecular genetics in biological conservation. Proc. Natl. Acad. Sci, USA 91:5748-5755. - a review covering a lot of ground from a personal (and possibly questionable) view Frankham, R., J. D. Ballou, and D. A. Briscoe. 2002. Introduction to Conservation Genetics. Chapter 15 – Resolving taxonomic uncertainties and defining management units. Chapter 17 – Use of molecular genetics in forensic and to understand species biology. - this book covers the many areas of conservation genetics in more detail. Chapters 15 and 17 are particularly relevant to this lecture’s content.

Read the following if you are interested in the details of any of the examples covered in this lecture:

* Ralls, K., K. Brugger and J. D. Ballou. 1979. Inbreeding and juvenile mortality in small populations of ungulates. Science. 206:1101-1103. Keller, L. F. et al 1994. Selection against inbred song sparrows during a natural population bottleneck. Nature 372: 356-357. * Saccheri, I. et al 1998. Inbreeding and extinction in a butterfly metapopulation. Nature 392:491-494. * Vila, C. et al. 2003. Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proc. R. Soc. London B 270:91-97. Daugherty, C. M., A. Cree, J. M. Hay and M. B. Thompson. 1990. Neglected taxonomy and continuing extinctions of tuatara (Sphenodon). Nature 347: 177-179. Baker, C. S., Cipriano F. and S. R. Palumbi. 1996. Molecular genetic identification of whale and dolphin products from commercial markets in Korea and Japan. Mol. Ecol. 5: 671-685. Wayne, R. K. and S. M. Jenks. 1991. Mitochondrial DNA analysis implying extensive hybridization of the endangered red wolf Canis rufus. Nature 351:565-568.

* Available online