How Can Genetic Techniques Inform Management Decisions?
The development of molecular genetic tools to assist management decisions has increased with the emergence of the field of conservation genetics in the early 1990s. Conservation geneticists are concerned with measuring genetic diversity within groups and determining how it is partitioned among groups. These techniques are used to address a number of important wildlife management issues, including the following:
Demographics and Extinction Risk
Molecular markers can be used to detect the presence of a species, estimate census and effective population sizes, determine sex ratios, and measure other key demographic parameters. Detecting the presence of a species is important to determine their geographic distribution and potential range decline. The concept of an effective population size was introduced by Wright181 and in general terms is the number of individuals in an ideal population that would lose genetic diversity through sampling losses at the same rate as the observed population. It is generally smaller than the census size because not all individuals in a population contribute the same number of offspring to the next generation. It is critical to understand how quickly genetic diversity will be lost in a population, which in part is dictated by their effective population size.111 Two important demographic parameters for managing a population are census size and density. Molecular genetic techniques can be used to identify individuals by determining their unique genotype and quantify a population size using traditional mark recapture methods, which also can be used to estimate the density of individuals per area. This technique can be used with non-invasively collected samples and replace the physical marking of individuals using unique markers, such as ear tags. Sex chromosome-specific markers can be used to determine sex ratios and model population dynamics.171
The demographic history of a population can impact its population dynamics and adaptive potential. When the size of a population is severely reduced, it is said to have undergone a bottleneck.111 Similarly, foundingeventsinvolvetheestablishmentofanewpopulationfromasmallnumberofindividuals. Both bottlenecks and founding events result in populations with low genetic diversity and can impact their evolutionary trajectory because genetic information is lost randomly.191 Lost genetic diversity in a population also can lead to inbreeding depression, which occurs when related or genetically similar animals mate and produce offspring. Inbreeding depression can manifest as reduced fitness of quantitative traits such as number of offspring produced or offspring survival rate.1101 All these forces can result in reduced adaptive potential and increased risk of extinction.111
Two well-known examples of the negative effects of inbreeding depression that resulted from a bottleneck occurred in the African cheetah (Acinonyx jubatus)1111 and the Florida panther (Puma concolor coryi))i2l The genetic diversity of African cheetahs was reduced during the Pleistocene because their population size was dramatically reduced over several generations. Their extremely low levels of genetic diversity are manifested in extant populations by their high infant mortality rates and sperm deformities. Due to the genetic similarity among individuals, cheetahs are unable to reject skin grafts from nominally unrelated individuals.1111
The Florida panther endured two bottlenecks, one during the same time as the African cheetah and a second bottleneck during the 19lh and early 20th century as a result of human activities.1111 By the early 1990s, the Florida panther population had declined to an estimated 20 to 25 individuals and had very low levels of genetic diversity. The animals showed many signs of inbreeding depression, including undescended testicles and low sperm quality, all of which suggested that extinction was very likely. Because genetic diversity takes a long time to increase by mutation, the only source of additional alleles (variable forms of a gene) was from a sister subspecies from Texas (P c. stanleyana). Females from this sister group were transported to Florida where they bred with Florida panthers with positive initial results. Genetic diversity and apparent fitness both increased; however, the long-term success of this genetic rescue remains to be demonstrated. Further, because the rescue was effected by introducing alien genes, and the new genomes may swamp those of the original subspecies, philosophical questions remain about precisely what has been conserved.1131
Resolving Taxonomic Status and Determining Relevant Conservation Units
One of the top priorities of a conservation program should be to resolve any existing taxonomic uncertainties. Funding resources and personnel time that can be devoted to a given project are limited, and it is vital to ensure that the species status of a focus organism is well established. If a focal organism is really the same species as another organism that is not of conservation concern, then precious funds and resources will be wasted. This is fundamentally a question of understanding how genetic diversity is distributed among groups. The expectation is that distinct species will have higher levels of genetic diversity between the taxa than within each species because of the homogenizing effect of gene flow.
One example is the dusky seaside sparrow (Ammodramus maritimus nigrescens), which was initially one of nine recognized subspecies.1141 Genetic analyses, however, only supported the designation of two subspecies.115,161 Conversely, if a species is not recognized as a separate entity, then a species could be lost or identified at a point where the number of organisms remaining precludes conserving the species. This was the case with the New Zealand tuatara, a lizard that was once widely distributed throughout New Zealand but became extinct on the mainland before the arrival of European settlers. Initially, it was managed as a single species. More recently, genetic and morphological analyses identified two species, Sphenodon punctatus and S. guntheri,116,171 that are now managed as separate taxa because they do not currently exchange genetic material.
The identification of conservation units is used to determine the fundamental units that will be the focus of management efforts. Relevant conservation units include consideration of species boundaries as described in the preceding text, but it goes further by identifying subgroups that may be on distinct evolutionary trajectories from other populations within the species. One example is the mountain yellow-legged frog (Rana muscosa) that has undergone a rapid decline in recent decades due to predation by an introduced species, the virulent chytrid fungus (Batrachochytrium dendrobatidis), and habitat destruction related to wildfires. Currently, these frogs exist as isolated mountain populations. When once-widespread species are reduced to a collection of isolated populations, it is useful to understand whether these populations have always been isolated (and are therefore potentially adapted to local conditions) or whether they are merely relics of a previously widespread but uniform population. Genetic analyses determined that existing populations have long been isolated from each other, suggesting that they should be managed as separate units,1181 and this will need to be considered when frogs from captive breeding programs are reintroduced to the wild.
Determining Population Structure
An important part of identifying conservation units is testing for population structure, which involves the level of dispersal between geographically distinct areas. When widely distributed populations consist of several distinct genetic subunits, population structure is said to exist. It is also important to understand metapopulation dynamics (periodic local extinction and recolonization events) when they are present. The traditional approach is to group individuals into researcher-determined geographic units and measure the distribution of genetic diversity within and between these groupings.1191 Assignment test and clustering programs like STRUCTURE1201 are being used to determine whether cryptic population structure exists without any a priori groupings of individuals.
The presence of distinct population units has important consequences for wildlife management plans because a widely distributed species with distinct and isolated population segments might have little potential to recolonize habitat after a local population crash. Sometimes the presence of structured populations is indicated by obvious biogeographic barriers or the presence of distinct phenotypes. However, population structure often exists without these telltale signs. Cryptic population structure is rather common in nature, even in large, mobile animals such as the Eurasian lynx (Lynx lynx) in Scandinavia where genetic markers indicate that the species is divided into three distinct genetic units.1211
Captive Breeding Programs
Molecular techniques can be used to inform management decisions during all phases of a captive breeding program. Captive-bred populations ideally should be representative of the genetic diversity found in wild populations. Genetic techniques can be used to define population structure in wild populations to help identify appropriate source populations, confirm the correct species identification for animals included in the captive breeding program, assist initial pairing decisions to ensure that closely related individuals are not mated, help determine appropriate release sites, and monitor the success of reintroduced animals by monitoring their population size and reproductive contributions. Genetic techniques also can be used several years after a captive breeding program is established to reconstruct pedigrees for organisms that live in groups1221 or determine the amount of genetic diversity that a captive population has retained from wild population.123,241
A combination of genetic and morphological analyses were used to discover that the Association of Zoos and Aquarium’s Asiatic lion (Panthera leo persica) captive breeding program included African lion (R leo leo) founders,1251 Asiatic lions have low levels of genetic diversity, so the interbreeding of a closely related subspecies increased their genetic diversity. However, the crossing of two subspecies could reduce adaptations that may have developed in each taxon. The previous example of interbreeding Texas puma with Florida panther may have reduced some of their adaptations to their environment— but if nothing had been done, extinction was the likely outcome.
Managing Invasive Species
Invasive species can have a tremendous negative impact on biodiversity.111 Molecular genetic techniques can be used to identify the source population of an invasive species, monitor potential hybridization with closely related taxa, determine the geographic distribution of an invasive species, and monitor their population dynamics. Genetic techniques also can be used to predict whether an invasive species will have a good chance at becoming established and resisting control agents. Sometimes, invasive species have more genetic diversity than the suspected source populaiton, suggesting that there may have been multiple source populations. The higher amount of genetic diversity created by interbreeding multiple source populations in turn could increase the adaptive potential of the invasive species to resist strong selective pressures, such as herbicides and pesticides.1261
The field of wildlife forensics has used molecular genetic techniques to identify the species of origin of unknown samples, identify the gender of an individual, and determine the geographic location from which an organism was obtained.[26) These techniques have been applied to a wide range of animals that include cetaceans,1271 sharks,128! elephants,1291 and sturgeon.1301 DNA sequence information can be used like grocery store barcodes to match an unknown sample to a database of known samples to determine the species identity. If the population structure of an organism is known, then the most likely geographic source of the organism can be determined by identifying the source population with the most similar genotype to the organism’s genotype of interest, and this information could be used to determine if an animal was taken from a protected population.
Crop and Livestock Management
Genetic diversity is a key aspect of food security. The industrial-scale food production necessary to feed the increasing human population requires a high level of standardization and automation, leading to a focus on a relatively few varieties of crops and animals.1311 While standardization and mass production are important in feeding the world’s population, this strategy is not without risk. When a single variety dominates the food production system in a region, there is a risk of total crop failure when something goes wrong.1321 In low-diversity varieties, all individuals are likely equally vulnerable to diseases or environmental challenges.
A classic manifestation of this risk is the southern U.S. corn blight that occurred in 1970. Commercial corn seeds are produced by crossing different inbred lines of corn. One of these lines was used in seed corn that was widely distributed in the 1960s, which initially contributed to robust and healthy corn crops. However, parasites with short generation times can often out-evolve their relatively long-lived hosts. One such parasite is the fungus Helmithosporium rnaydis, which was a minor agricultural pest until 1970. It is believed that natural mutation created a more virulent form of the fungus which, when combined with the warm, wet summer weather, reduced U.S. corn yields by perhaps 15% that year.133!
Strategies to mitigate these effects in the long term include seed banks and the preservation of heirloom varieties and landraces.1341 Genetic and genomic technologies are useful in mitigating these risks. For example, molecular markers have been used to determine that Iberian landraces of pigs (Sus scrofa domesticus) represent important reservoirs of genetic diversity.1351
The field of genetic ecotoxicology studies the impact of contaminants on an organism’s DNA.1361 Pollutants can increase the mutation rate of DNA and increase the amount of genetic diversity in a population. However, most mutations that affect fitness will be harmful.1261 The genetic diversity of populations from control and contaminated sites can be compared to quantify the impact of a particular contaminant.137,381 Ellegren et al.1391 compared the occurrence of a mutation that causes partial albinism in barn swallows (Hirundo rustica) from a site near the nuclear accident at Chernobyl to barn swallows from uncontaminated sites. They found a higher incidence of partial albinism in barn swallows that bred near Chernobyl compared to their control sites. Quantifying the genetic diversity of a population that was exposed to a pollutant can be used to predict the potential negative impacts of the pollutant on the viability of the population.