Much has changed since we began the first edition of Introduction to Conservation Genetics 10 years ago. The human population has exceeded 6.6 billion, with consequent increased pressure on the natural world. The number of threatened species has increased by 55% to 16306. Over the same time, global climate change has moved from being a somewhat abstract concern to perhaps the pre-eminent global political focus. The impact of climate change is now clearly discernable on the distribution and behaviour of many species. Sea-level increases are impacting on the viability of low-lying nations and the biota they contain. On a smaller scale, three-quarters of species of bears are now considered to be in danger and the Yangtze River dolphin (referred to in the first edition) has become extinct. Further, invasive species are having an ever more important impact on biodiversity, especially with rapidly increasing trade.

While our objectives in preparing this book are fundamentally those that motivated the first edition, accelerating human impacts bring into even sharper focus the need to integrate genetics into the broader conservation effort.

Threatened species have small, or declining populations. Once small, they lose genetic diversity, become inbred (with consequent reduction in reproductive fitness) and accumulate deleterious mutations. Consequently, Section II considers these factors in detail, as they contribute to extinction risk, and provide the essential background material for the genetic management of threatened species in Section III.

Factors reducing population size

Humans are reducing the size and distribution of wild populations through clearing and fragmentation of habitat, over-exploitation, pollution and the impact of introduced species. Of these, habitat loss is currently having the greatest impact, but threats from global climate change loom ever larger.

Loss of genetic diversity

Loss of genetic diversity in small populations reduces the ability to evolve in response to ever-present environmental change. There are four threats to genetic diversity:

• extinction of populations or species

• extinction of alleles due to sampling in small populations

• inbreeding reducing heterozygosity by redistributing genetic diversity among homozygous individuals and populations

• selection favouring one allele at the expense of others, leading to fixation.

Overwhelmingly the major threat to genetic diversity is extinction of alleles in finite populations by genetic drift. All of the adverse genetic effects of population size reduction depend on the effective population size, rather than the census size. The effective population size is reduced by fluctuations in population sizes, high variation in family sizes, and by unequal sex-ratios. Chapter 11 deals with the effects of small population size on genetic diversity and the factors that influence effective population size.

The World Conservation Union (IUCN), the leading international conservation body, recognizes the crucial need to conserve genetic diversity as one of the three fundamental levels of biodiversity. This book provides the conceptual background for understanding the role of genetic factors in extinction and managing to avoid such extinctions.

Conservation genetics encompasses:

• genetic management of small populations to maximize retention of genetic diversity and minimize inbreeding,

• resolution of taxonomic uncertainties and delineation of management units, and

• the use of molecular genetic analyses in forensics and to understand species' biology.

Purpose of the book

We have endeavoured to make this book appealing to a wide readership. However it is primarily directed towards those encountering the discipline for the first time, either through formal coursework or by self-instruction.

Conservation genetics is a relatively young discipline. While it is founded on more than a century of advances in evolutionary genetics, including population and quantitative genetics and plant and animal breeding, it has developed its own unique attributes, specialist journals, etc. In particular, conservation genetics focuses strongly on processes within small and fragmented populations and on practical approaches to minimize deleterious effects within them. It has implications for organizations and individuals with very different immediate concerns. These include zoo staff undertaking captive breeding programs, wildlife and fisheries biologists and ecologists, planners and managers of National Parks, reserves, water catchments and local government natural areas, foresters and farmers.

In Section III we apply the conclusions on evolutionary genetics of populations and the deleterious genetic consequences of population size reduction (from Sections I and II) to the genetic management of threatened populations and species.

Taxonomic uncertainties and management units

A critical first step in conserving a species is to gain a clear understanding of its taxonomy. Is the population of interest a unique species? Does it actually consist of multiple cryptic species? Or is it simply another population of a common species? Without this knowledge endangered species may be denied protection, or resources wasted on populations of common species. The use of genetic techniques to assist in resolving taxonomic uncertainties is described in Chapter 16. To do this we must first define what is meant by a species and consider briefly how speciation occurs. Populations within species may be so distinct that crosses suffer reduced reproductive fitness (outbreeding depression). The chapter concludes by considering means for defining management units within species.

Management of wild populations

The genetic management of wild populations is considered in Chapter 17. Typically wild population management is concerned with increasing population sizes and alleviating the effects of population fragmentation. Species with inadequate gene flow among population fragments will suffer insidious processes of inbreeding depression, loss of genetic diversity and eventually population extinctions, unless gene flow is re-established. Sadly, there continues to be only limited activity in this area. Genetic management of fragmented populations represents the greatest unmet genetic challenge in conservation biology.

Introduction

In this chapter, we set the scene for the rest of the book. It may be helpful to remind readers of the relevance and importance of soil mechanics for all civil engineering construction: everything we construct sits on the ground in some way or other at some stage in its life. Even aircraft land on runways, and cars drive along roads; in each case there is some stiff layer (pavement) between the wheels and the prepared ground underneath. This stiff layer will help to spread the vehicular load but, in the end, this load must still be supported by the ground. Some examples of typical geotechnical design problems are presented in the next sections.

The term soil mechanics refers to the mechanical properties of soils; the term geotechnical engineering refers to the application of those mechanical properties to the design and construction of those parts of civil engineering systems which are concerned with the active or passive use of soils. Soils are the materials that we find in the ground: the term ground engineering is somewhat equivalent to geotechnical engineering. We will talk a little about the nature of soils in Chapter 3.

The term soil means different things to different people. To an agricultural engineer, the soil is the upper layer of the ground which the farmer ploughs and harrows and in which crops are sown.

Introduction

Soil-structure interaction is one of those interface topics which cannot be treated successfully either as a purely structural problem or as a purely geotechnical problem. A holistic approach is required to the modelling – the identification of the essential details of the problem – and to the subsequent analysis. The geotechnical system in this case is the sum of all the geotechnical and structural elements, and the response of the system will certainly depend on some combination of properties of both the soil and the structure. If the ground and the structure are both behaving elastically, then simple configurations lead to exact analyses. While it has to be admitted that the problems that can be analysed are somewhat idealised, there is sufficient realism to demonstrate and support the important messages of soil-structure interaction.

Let us start with a thought experiment that will seem quite remote from soil-structure interaction. Suppose that we have a quarter kilogram (or half pound) packet of butter (unwrapped) on a plate. We also have a penknife or some other knife with a short, stiff blade, and a palette knife with a rather flexible blade. We place the flat side of the blades of the knives on the block of butter in turn and try to make an impression in the surface. The short, stiff blade will penetrate without difficulty (Fig. 9.1a); the palette knife blade will just bend (Fig. 9.1b).