Conservation genetics utilizes the tools and concepts of genetics and applies them to problems in conservation biology. For example, molecular genetic techniques, such as protein electrophoresis, and analysis of mitochondrial DNA and highly variable nuclear genes (including DNA fingerprinting), have been important in documenting the extent and pattern of genetic variation in endangered species. We review these techniques and their advantages and disadvantages, and give examples of their application to endan- gered species. For captive animal populations, pedigree analysis has become the basic approach to evaluate breeding priority of particular individuals. Several pedigree analysis techniques are commonly used, but peeling and gene dropping give the most information. We compare these techniques and illustrate their value with applications to the Guam Rail, Przewalski's horse, and other endangered captive animals. The rationale for much conservation genetic interpretation is based in evolutionary genetics. We discuss the avoidance of inbreeding depression and the maintenance of genetic variation-both primary conservation genetic goals-from this perspective. In addition, we suggest aspects of these factors that deserve greater attention in their overall application to conservation planning. Finally, we briefly mention three evolutionary topics-the relationship of heterozygosity and fitness, population bottlenecks, and outbreeding depression-that have implications for conservation genetics. Although simple interpretation in these areas is appealing, we feel that because they are only generally understood and often quite controversial, their application to endangered-species management should be carefully evaluated and moni- tored.

https://www.jstor.org/stable/pdfplus/1941887.pdf

Conservation Genetics: Techniques and Fundamentals.

Gene identity by descent (IBD) is a fundamental concept that underlies genetically mediated similarities among relatives. Gene IBD is traced through ancestral meioses and is defined relative to founders of a pedigree, or to some time point or mutational origin in the coalescent of a set of extant genes in a population. The random process underlying changes in the patterns of IBD across the genome is recombination, so the natural context for defining IBD is the ancestral recombination graph (ARG), which specifies the complete ancestry of a collection of chromosomes. The ARG determines both the sequence of coalescent ancestries across the chromosome and the extant segments of DNA descending unbroken by recombination from their most recent common ancestor (MRCA). DNA segments IBD from a recent common ancestor have high probability of being of the same allelic type. Non-IBD DNA is modeled as of independent allelic type, but the population frame of reference for defining allelic independence can vary. Whether of IBD, allelic similarity, or phenotypic covariance, comparisons may be made to other genomic regions of the same gametes, or to the same genomic regions in other sets of gametes or diploid individuals. In this review, I present IBD as the framework connecting evolutionary and coalescent theory with the analysis of genetic data observed on individuals. I focus on the high variance of the processes that determine IBD, its changes across the genome, and its impact on observable data.

https://www.genetics.org/content/genetics/194/2/301.full.pdf

Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations

SummaryA systematic tabulation is provided of the frequency of different types of inbreeding in the Hadza. Genealogical information was obtained for 931 individuals, alive and dead. Inbreeding was encountered with 165 individuals. There were 49 different types of inbred genealogy. No attempt was made to calculate an average inbreeding coefficient and the reasons for this are given in the text.

The inbreeding coefficients of the Hadza

Summary

A method of calculating inbreeding coefficients is described using a recursive algorithm. This has been programmed in ALGOL 68 and in SNOBOL 4. Advantages and disadvant, ages of this method are discussed, and several examples are given.

On the computation of inbreeding coefficients.

Inbreeding is commonly associated with a lowering of viability and birth weights—a phenomenon known as inbreeding depression. A severe inbreeding depression was encountered in a captive breeding program for Speke's gazelle. Unfortunately, the solution of simply avoiding inbreeding could not be implemented because the entire herd was descended from one import male and three import females. Because of this founder effect, it was impossible to avoid inbreeding. However, laboratory experiments with fruit flies and basic evolutionary theory indicate that animals can rapidly adapt to inbreeding by the selective elimination of the genes responsible for inbreeding depression. These experimental and theoretical results were translated into a breeding program for the Speke's gazelle. The first goal of the breeding program is a demographic goal: increase the total population size as rapidly as possible to the carrying capacity. The other goals all deal with genetic attributes of either parents or offspring: Both parents and offspring should be inbred, and both parents and offspring should have genes from as many different founding ancestors as possible. In this paper, we document that this breeding program does eliminate the inbreeding depression very rapidly, and moreover that the genetic goals of the program aid this elimination exactly as theory predicts. Furthermore, our analysis clearly shows that the gazelles suffered from an inbreeding depression rather than an outcrossing depression. We conclude that inbreeding depressions can be rapidly and effectively reduced by an appropriate breeding program, and hence an inbreeding depression does not constitute an insurmountable barrier to the long-term maintenance of a species in which inbreeding cannot be avoided.

Factors eliminating inbreeding depression in a captive herd of speke's gazelle (Gazella spekei)

An elementary computer algorithm for the calculation of the coefficient of inbreeding

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An elementary computer algorithm for the calculation of the coefficient of inbreeding