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This chapter focuses on Allee effects in relation to genetics and evolution. These topics intersect in four different ways. First, genetics creates its own set of Allee effect mechanisms (e.g., via inbreeding depression). Second, there may be genetic differences among members of a population in their susceptibility to ecological Allee effects. Third, Allee effects are considered in the light of evolution — have populations evolved mechanisms to avoid Allee effects, and if so, how is it possible to find anything other than the ‘ghosts of Allee effects past’ in modern populations? Finally, Allee effects themselves may act as a selection pressure, and members of populations subject to Allee effects may thus evolve different characteristics as compared with those bounded only by negative density dependence. The chapter considers all these four issues in turn.

Populations may respond to environmental changes through phenotypic plasticity, adaptation, migration, or suffer demographic declines if they are unable to respond. Climate change is already causing shifts in species ranges, changes in phenotypes, and altered life history traits and interspecific interactions. The capacity for a population to adapt to new conditions is a function of the amount of genetic and phenotypic variation for traits under selection, fecundity, and the rate of environmental change per generation. Several genomic approaches are available for predicting the extent of maladaptation of populations resulting from climate change based on the mismatch between genotypes and new climates. The conservation of populations that are threatened by rapid climate change may in some cases require management tools including assisted gene flow to facilitate adaptation, and greater connectivity of habitats to facilitate range shifts and migration (i.e., gene flow).

The harmful impacts of inbreeding are generally greater in species that naturally outbreed compared to those in inbreeding species, greater in stressful than benign environments, greater for fitness than peripheral traits, and greater for total fitness compared to its individual components. Inbreeding reduces survival and reproduction (i.e., it causes inbreeding depression), and thereby increases the risk of extinction. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Natural selection may remove (purge) the alleles that cause inbreeding depression, especially following inbreeding or population bottlenecks, but it has limited effects in small populations and usually does not completely eliminate inbreeding depression. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies.

Habitual self-fertilization by hermaphroditic individuals is a sexual route by which genetically identical individuals can arise. The phenomenon occurs in various plants and invertebrates but is known in only one vertebrate species: the mangrove killifish. Selfing is an extreme form of inbreeding (even less severe cases of which often result in inbreeding depression), and for this and other reasons constitutive self-fertilization is rare in the biological world. Instead, most selfing species also outcross occasionally, and thus have a mixed mating system. Habitual selfers nevertheless have some special adaptive advantages not shared by their sexual counterparts. This chapter compares population-genetic and ecological features of mangrove killifish with those of analogous plants and invertebrate animals that likewise have mixed-mating systems. Such species probably gain the best of two worlds by capitalizing jointly on the short-term advantages of selfing (fertilization assurance, and the propagation of fit “clonal” genoypes) and also the long-term as well as short-term advantages of outcrossing (genetic health and adaptability).

When dominance is presence, the selection response equations under inbreeding can become rather complex, they require additional variance components beyond the additive-genetic variance. Further, both transient and permanent components of response can arise. This chapter examines the theory of both the covariance of relatives under general inbreeding, as well as the expected selection response under inbreeding. Due to the decrease in the effective recombination rate under selfing, the Bulmer effect can be rather dramatic, as any linkage disequilibrium generated by selection is only weakly removed by recombination. Finally, this chapter also examines the evolutionary forces that interact to determine the selfing rate for a given population.

Inbreeding reduces survival and reproduction (i.e. it causes inbreeding depression), and thereby increases extinction risk. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies. Impacts of inbreeding are generally greater in species that naturally outbreed than those that inbreed, in stressful than benign environments, and for fitness than peripheral traits. Harmful effects accumulate across the life cycle, resulting in devastating effects on total fitness in outbreeding species.Species face ubiquitous environmental change and must adapt or they will go extinct. Genetic diversity is the raw material required for evolutionary adaptation. However, loss of genetic diversity is unavoidable in small isolated populations, diminishing their capacity to evolve in response to environmental changes, and thereby increasing extinction risk.

It is assumed that dominance genetic variance contributes little to the prediction of evolutionary change in polygenic traits. This is based on the assumption that populations are large, panmictic, and randomly mating. However, the ecological contexts of most wild populations studied to date violate one, if not several, of these assumptions, and the widespread occurrence of inbreeding and inbreeding depression of phenotypic traits and fitness suggests dominance genetic effects are ubiquitous. This chapter reviews what genetic dominance represents at the level of a single locus and how this contributes to phenotypic variation and discusses how to estimate dominance variance with emphasis on the complications arising in wild populations and with inbreeding. Next, empirical estimates of dominance variance are reviewed. Since no estimates exist of dominance variance in the wild (except for humans), laboratory and agricultural populations are examined, and it is shown that dominance variance is a major contributor to phenotypic variation and in some cases contributes as much as additive genetic variance. This chapter also discusses how inbreeding and dominance affect predictions of evolutionary change, and ends with a review of some of the empirical questions for which genetic dominance is an important quantity in its own right. In this chapter, it is argued that dominance variance has been ignored for too long, may hamper the ability to predict evolutionary change, can be a major contributor to phenotypic variance, is interesting to study in its own right, and provides many avenues of research to be addressed by empirical study.

Inbreeding and its consequences are the main subject of Chapter 3, beginning with the concepts of identity by descent versus identity by state, the inbreeding coefficient F, genotype frequencies with inbreeding, and calculation of the inbreeding coefficient from pedigrees. Inbreeding and heterosis are discussed along with the effects of inbreeding in humans and other organisms, regular systems of mating (selfing and partial selfing, sib mating), and the utility of recombinant inbred lines. The chapter emphasizes the intimate connection between inbreeding and hierarchical population structure as measured by the F-statistics.

In this chapter, Corey J. A. Bradshaw and Barry W. Brook, discuss measures of biodiversity patterns followed by an overview of experimental design and associated statistical paradigms. Conservation biology is a highly multidisciplinary science employing methods from ecology, Earth systems science, genetics, physiology, veterinary science, medicine, mathematics, climatology, anthropology, psychology, sociology, environmental policy, geography, political science, and resource management. Here we focus primarily on ecological methods and experimental design. It is impossible to census all species in an ecosystem, so many different measures exist to compare biodiversity: these include indices such as species richness, Simpson's diversity, Shannon's index and Brouillin's index. Many variants of these indices exist. The scale of biodiversity patterns is important to consider for biodiversity comparisons: α (local), β (between‐site), and γ (regional or continental) diversity. Often surrogate species ‐ the number, distribution or pattern of species in a particular taxon in a particular area thought to indicate a much wider array of taxa ‐ are required to simplify biodiversity assessments. Many similarity, dissimilarity, clustering, and multivariate techniques are available to compare biodiversity indices among sites. Conservation biology rarely uses completely manipulative experimental designs (although there are exceptions), with mensurative (based on existing environmental gradients) and observational studies dominating. Two main statistical paradigms exist for comparing biodiversity: null hypothesis testing and multiple working hypotheses – the latter paradigm is more consistent with the constraints typical of conservation data and so should be invoked when possible. Bayesian inferential methods generally provide more certainty when prior data exist. Large sample sizes, appropriate replication and randomization are cornerstone concepts in all conservation experiments. Simple relative abundance time series (sequential counts of individuals) can be used to infer more complex ecological mechanisms that permit the estimation of extinction risk, population trends, and intrinsic feedbacks. The risk of a species going extinct or becoming invasive can be predicted using cross‐taxonomic comparisons of life history traits. Population viability analyses are essential tools to estimate extinction risk over defined periods and under particular management interventions. Many methods exist to implement these, including count‐based, demographic, metapopulation, and genetic. Many tools exist to examine how genetics affects extinction risk, of which perhaps the measurement of inbreeding depression, gene flow among populations, and the loss of genetic diversity with habitat degradation are the most important.

Genetic factors affect the extinction probability of populations in a variety of ways. Inbreeding depression can reduce fecundity and survival, and thereby decrease population growth rate and increase extinction probability. Multiple studies have shown that inbreeding depression can negatively impact populations in the wild. Loss of genetic variation in small populations also decreases the capacity of populations to evolve to changing environmental conditions. Population viability analysis is a modeling approach that integrates information on demography, genetics, threats, and management actions to predict population persistence. Genomics will advance incorporation of genetic factors into predicting extinction risk by improving our ability to estimate inbreeding depression and evolutionary potential.

All populations are finite in size so that genetic drift will occur in all natural and managed populations. Genetic drift causes both changes in allele frequencies and the loss of genetic variation. Loss of heterozygosity and loss of alleles are t^ghe two primary measures of the loss of genetic variation in populations. Matings between related individuals (i.e., inbreeding) is more common in small populations, and this will lead to inbreeding depression in small populations. Understanding the effects of genetic drift is especially important for conservation because loss of genetic variation and inbreeding depression can reduce the probability of population persistence.

Genetic management of fragmented populations is one of the major, largely unaddressed issues in biodiversity conservation. Many species across the planet have fragmented distributions with small isolated populations that are potentially suffering from inbreeding and loss of genetic diversity (genetic erosion), leading to elevated extinction risk. Fortunately, genetic deterioration can usually be remedied by augmenting gene flow (crossing between populations within species), yet this is rarely done, in part because of fears that crossing may be harmful (but it is possible to predict when this will occur). Benefits and risks of genetic problems are sometimes altered in species with diverse mating systems and modes of inheritance. Adequate genetic management depends on appropriate delineation of species. We address management of gene flow between previously isolated populations and genetic management under global climate change.

Avian pollination is thought to be less prevalent and less at risk than avian seed-dispersal. The extent of recently revealed bird pollination that does not conform to the classic ornithophily-nectarivore template suggests this mutualism may be cryptic and more prevalent than considered to date. Widespread anthropogenic disturbance has disproportionately impacted the connections between birds and flowers, so that bird pollination may be systematically under-reported. Evidence suggests that where plants are visited by more than one pollinator guild, the relative effectiveness of birds is high compared to invertebrates. In the absence of replacement, the loss of bird pollinators has resulted in pollination failure, increased inbreeding depression, and decreased plant density. Confirmation of seed limitation in pollen-limited plants serviced by birds provides a precautionary sign of the possible long term effects of bird pollinator loss. The quality of pollination service provided by birds has important consequences for gene flow and offspring survival. Pollen limitation experiments suggest that bird-pollinated plants in New Zealand, the Americas, Southeast Asia, and Africa suffer similar levels of pollen limitation, and are typically more strongly pollen-limited than insect-pollinated plants. Thus, bird-pollination appears to be under-reported, hard to replace and at greater risk of failure than currently assumed.

Genetic management of fragmented populations is one of the major, largely unaddressed issues in biodiversity conservation. Many species across the planet have fragmented distributions with small isolated populations that are potentially suffering from inbreeding and loss of genetic diversity (genetic erosion), leading to elevated extinction risk. Fortunately, genetic deterioration can usually be remedied by gene flow from another population (crossing between populations within species), yet this is rarely done, in part because of fears that crossing may be harmful (but we can predict when this will occur). We address management of gene flow between previously isolated populations and genetic management under global climate change.

The inherent stochastic nature of individual life histories implies that finite populations always carry a risk of going extinct, even if their long-term growth potential is positive. The consequences of demographic stochasticity are explored in this chapter, using individual-based computer simulations and simple discrete- and continuous-state stochastic models (branching processes and diffusion models). Simple examples of population viability analysis (PVA) are presented. Demographic stochasticity on the allele level is genetic drift—which leads to reduced viability and evolutionary potential of small populations via inbreeding depression. The ecological pendant of genetic drift is in the focus of the ‘ecological neutral theory’ of Hubbell. Some conceptual and methodological problems of the neutral theory in the context of species abundance distributions are discussed at the end of the chapter.

This chapter provides an overview of beaver dispersal. There are a number of reasons why beavers have to disperse from their native family. As a relatively long-lived species, beavers produce 3–4 newborns every year. If the young stay with their parents and siblings, the colony would grow huge in a few years and soon outstrip its food resources. More importantly, grown-up offpring must find mates to start reproducing themselves. Mating with close relatives would often result in disastrous genetic defects, a phenomenon called inbreeding depression. This chapter discusses the risks that come with dispersal and explains how natural dispersal differs from translocation and homing. It also considers the age at which beavers usually leave their family, along with the timing, direction, distance, and duration of dispersal.