The effects of small population size are of major concern in conservation biology, since endangered species have small and/or declining populations. Small populations suffer from inbreeding and loss of genetic diversity resulting in elevated extinction risks. Consequently, a major objective of genetic management is to minimize inbreeding and loss of genetic diversity.

How is genetics used to minimize extinctions?
Knowledge of genetics aids conservation in the following ways.

Reducing extinction risk by minimizing inbreeding and loss of genetic diversity Many small, threatened populations are inbred and have reduced levels of genetic diversity. Inbreeding reduces fecundity and survival and so directly increases extinction risk. Reduced genetic diversity compromises the ability of populations to evolve to cope with environmental change and reduces their chances of long-term persistence. For example, the endangered Florida panther suffers from genetic problems as evidenced by low genetic diversity, and inbreeding-related defects (poor sperm quality and quantity and morphological abnormalities). To alleviate these effects, individuals from its most closely related sub-species in Texas have been introduced into this population. Captive populations of many endangered species (e.g. golden lion tamarin) are managed to minimize loss of genetic diversity and inbreeding.

Identifying populations of concern Genetic markers can identify populations where genetic issues are likely to affect their prospects of long-term survival. Asiatic lions that exist in the wild only in a small population in the Gir Forest in India have very low levels of genetic diversity. Consequently, they have a severely compromised ability to evolve, as well as being susceptible to demographic and environmental risks. The recently discovered Wollemi pine, an Australian relict species previously known only from fossils, contains no genetic diversity among individuals at several hundred loci, so its extinction risk is extreme; it is susceptible to a common die-back fungus and all individuals that were tested were similarly susceptible.

Resolving population structure Information regarding the extent of gene flow among populations is critical to determine whether a species requires translocation of individuals to prevent inbreeding and loss of genetic diversity. Wild populations of the red-cockaded woodpecker are fragmented and genetically differentiated. Further, levels of genetic diversity are correlated with population sizes. Consequently, part of the management of this species involves translocating individuals into small populations to minimize the risks of inbreeding and loss of genetic diversity.

Resolving taxonomic uncertainties The taxonomic status of many species, especially invertebrates and lower plants, is frequently unknown. Thus, an apparently widespread and low-risk species may, in reality, comprise a complex of distinct taxa, some rare or endangered. Such is the case for the unique New Zealand reptile, the tuatara. Genetic marker studies revealed two distinct species, one of which was being neglected in terms of conservation. Similar studies have shown that Australia is home to well over 100 locally distributed species of velvet worms (Peripatus) rather than the seven widespread morphological species previously recognized. Equally, genetic markers may reveal that populations of common species are attracting undeserved protection and resources. Molecular genetic analyses have shown that the endangered colonial pocket gopher from Georgia is indistinguishable from the common pocket gopher in that region, so that there was no necessity to preserve the colonial pocket gopher. In a related vein, the threatened northern spotted owl, the subject of great controversy in the Pacific Northwest of the USA, is genetically very similar to the non-endangered California spotted owl. This latter case remains controversial and unresolved.

Defining management units within species Populations within species may be sufficiently differentiated that they deserve management as separate units i.e. they are adapted to somewhat different environments. Their hybrids may be at a disadvantage, sometimes even displaying partial reproductive isolation. For example, coho salmon (and many other fish species) display genetic differentiation among geographic populations and evidence of adaptation to different conditions (morphology, swimming ability and age at maturation). Thus, they should be managed as separate populations.

Detecting hybridization Many rare species of plants, salmonid fish and canids are threatened with being 'hybridized out of existence' by crossing with common species. Molecular genetic analyses have shown that the critically endangered Ethiopian wolf (simian jackal) is subject to hybridization with local domestic dogs.

Non-intrusive sampling for genetic analyses Many species are difficult to capture, or become stressed by the process. DNA can be obtained from hair, feathers, sloughed skin, faeces, etc. in non-intrusive sampling, the DNA amplified and genetic studies completed without disturbing the animals. For example, the critically endangered northern hairy-nosed wombat is a nocturnal burrowing marsupial that can only be captured with difficulty. They are stressed by trapping and become trap-shy. Sampling has been achieved by placing adhesive tape across their burrows to capture hair when the animals exit their burrows. DNA from non-invasive sampling can be used to identify individuals, determine mating patterns and population structure, and measure levels of genetic diversity.

Defining sites for reintroduction The northern hairy-nosed wombat exists in a single population of approximately 75 animals at Clermont in Queensland, Australia. DNA samples obtained from museum skins identified an extinct wombat population at Deniliquin in NSW as belonging to this species. Thus, Deniliquin is a potential site for reintroduction. Similarly, information from genotyping DNA from sub-fossil bones has revealed that the endangered Laysan duck previously existed on islands other than its present distribution in the Hawaiian Islands.

Choosing the best populations for reintroduction Island populations are considered as an invaluable genetic resource for re-establishing mainland populations, particularly in Australia and New Zealand. However, the black-footed rock wallaby population on Barrow Island, Australia, a potential source of individuals for reintroductions onto the mainland, has extremely low genetic variation and reduced reproductive rate (presumably due to inbreeding). More endangered mainland populations are genetically healthier and may be a more suitable source of animals for reintroductions to other mainland localities. Alternatively, the pooling of several different island populations of this wallaby should provide a genetically healthy population suitable for reintroduction purposes.

Forensics Consumption of meat from threatened whales has been detected by analysing whale meat in Japan and South Korea. Mitochondrial DNA sequences showed that about 9 percent of the whale meat on sale came from protected species of whales, rather than from the minke whales that can be taken legally. Work is in progress to develop related methods to identify tiger bones in Asian medicines. Many other related forensic applications are deriving from molecular genetics.

Understanding species biology Many aspects of species biology can be determined using molecular genetic analyses. For example, mating patterns and reproduction systems are often difficult to determine in threatened species. Studies using genetic markers established that loggerhead turtle females mate with several males. Mating systems in many plants have been established using genetic makers. Birds are often difficult to sex, resulting in several cases where two birds of the same sex were placed together to breed. Probes for loci on the sex chromosomes are now available so that birds can be sexed without having to resort to surgery. Paternity has been determined in many species, including chimpanzees. Methods to census endangered kit foxes, that are nocturnal and secretive, are being developed, based upon counts of scats (faeces). This is only possible because mitochondrial DNA (mtDNA) can be used to distinguish kit fox scats from those of gray foxes, coyotes, red foxes and domestic dogs in the area. Dispersal and migration patterns are often critical to species' survival prospects. These are difficult to determine directly, but can be inferred using genetic analyses.