Genetic monitoring
Genetic monitoring is the use of molecular markers
Genetic marker
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify cells, individuals or species. It can be described as a variation that can be observed...

 to (i) identify individuals, species or populations, or (ii) to quantify changes in population genetic metrics (such as effective population size
Effective population size
In population genetics, the concept of effective population size Ne was introduced by the American geneticist Sewall Wright, who wrote two landmark papers on it...

, genetic diversity
Genetic diversity
Genetic diversity, the level of biodiversity, refers to the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary....

 and population size) over time. Genetic monitoring can thus be used to detect changes in species abundance and/or diversity, and has become an important tool in both conservation
Conservation management system
A conservation management system is a procedure for maintaining a species or habitat in a particular state. It is a means whereby humankind secures wildlife in a favourable condition for contemplation, education or research, in perpetuity. It is an important topic in cultural ecology, where...

 and livestock
Livestock refers to one or more domesticated animals raised in an agricultural setting to produce commodities such as food, fiber and labor. The term "livestock" as used in this article does not include poultry or farmed fish; however the inclusion of these, especially poultry, within the meaning...

 management. The types of molecular markers used to monitor populations are most commonly mitochondrial, microsatellites or single-nucleotide polymorphisms (SNPs), while earlier studies also used allozyme
Variant forms of an enzyme that are coded by different alleles at the same locus are called allozymes. These are opposed to isozymes, which are enzymes that perform the same function, but which are coded by genes located at different loci....

 data. Species gene diversity is also recognized as an important biodiversity
Biodiversity is the degree of variation of life forms within a given ecosystem, biome, or an entire planet. Biodiversity is a measure of the health of ecosystems. Biodiversity is in part a function of climate. In terrestrial habitats, tropical regions are typically rich whereas polar regions...

 metric for implementation of the Convention on Biological Diversity
Convention on Biological Diversity
The Convention on Biological Diversity , known informally as the Biodiversity Convention, is an international legally binding treaty...



Types of population changes that can be detected by genetic monitoring include population growth and decline, spread of pathogens, adaptation to environmental change, hybridization, introgression and fragmentation events. Most of these changes are monitored using ‘neutral’ genetic markers (markers for which mutational changes do not change their adaptive fitness
Fitness (biology)
Fitness is a central idea in evolutionary theory. It can be defined either with respect to a genotype or to a phenotype in a given environment...

 within a population). However markers showing adaptive responses to environmental change can be ‘non-neutral’ (e.g. mutational changes affect their relative fitness within a population).

Two broad categories of genetic monitoring have been defined: Category I encompasses the use of genetic markers as identifiers of individuals (Category Ia), populations and species (Category Ib) for traditional population monitoring. Category II represents the use of genetic markers to monitor changes of population genetic parameters, which include estimators of effective population size
Effective population size
In population genetics, the concept of effective population size Ne was introduced by the American geneticist Sewall Wright, who wrote two landmark papers on it...

 (Ne), genetic variation, population inter-mixing, structure and migration.

Estimating abundance and life history parameters – Category Ia

At the individual level, genetic identification can enable estimation of population abundance and population increase rates within the framework of mark-recapture models. The abundance of cryptic or elusive species that are difficult to monitor can be estimated by collecting non-invasive biological samples in the field (e.g. feathers, scat or fur) and using these to identify individuals through microsatellite or single-nucleotide polymorphism (SNP) genotyping. This census of individuals can then be used to estimate population abundance via mark-recapture analysis. For example, this technique has been used to monitor populations of grizzly bear
Grizzly Bear
The grizzly bear , also known as the silvertip bear, the grizzly, or the North American brown bear, is a subspecies of brown bear that generally lives in the uplands of western North America...

, Brush-tailed Rock-wallaby
Brush-tailed Rock-wallaby
The Brush-tailed Rock-wallaby or Small-eared Rock-wallaby is a kind of wallaby, one of several rock-wallabies in the genus Petrogale. It inhabits rock piles and cliff lines along the Great Dividing Range from about 100 km north-west of Brisbane to northern Victoria, in vegetation ranging from...

, Bengal tiger
Bengal Tiger
The Bengal tiger is a tiger subspecies native to the Indian subcontinent that in 2010 has been classified as endangered by IUCN...

 and snow leopard
Snow Leopard
The snow leopard is a moderately large cat native to the mountain ranges of South Asia and Central Asia...

. Population growth rates are a product of rates of population recruitment
Birth rate
Crude birth rate is the nativity or childbirths per 1,000 people per year . Another word used interchangeably with "birth rate" is "natality". When the crude birth rate is subtracted from the crude death rate, it reveals the rate of natural increase...

 and survival
Mortality rate
Mortality rate is a measure of the number of deaths in a population, scaled to the size of that population, per unit time...

, and can be estimated through open mark-recapture models. For example, DNA from feathers shed by the Eastern Imperial Eagle
Eastern Imperial Eagle
The Eastern Imperial Eagle is a large species of bird of prey that breeds from southeastern Europe to central Asia. Most populations are migratory and winter in northeastern Africa, and southern and eastern Asia. The Spanish Imperial Eagle, found in Spain and Portugal, was formerly lumped with...

 shows lower cumulative survival over time than seen for other long-lived raptors.

Identifying species – Category Ib

Use of molecular genetic techniques to identify species can be useful for a number of reasons. Species identification in the wild can be used to detect changes in population ranges or site occupancy, rates of hybridization and the emergence and spread of pathogens and invasive species
Invasive species
"Invasive species", or invasive exotics, is a nomenclature term and categorization phrase used for flora and fauna, and for specific restoration-preservation processes in native habitats, with several definitions....

. Changes in population ranges have been investigated for Iberian lynx
Iberian Lynx
The Iberian lynx, Lynx pardinus, is a critically endangered species native to the Iberian Peninsula in Southern Europe. It is one of the most endangered cat species in the world. According to the conservation group SOS Lynx, if this species died out, it would be one of the few feline extinctions...

 and wolverine
The wolverine, pronounced , Gulo gulo , also referred to as glutton, carcajou, skunk bear, or quickhatch, is the largest land-dwelling species of the family Mustelidae . It is a stocky and muscular carnivore, more closely resembling a small bear than other mustelids...

, while monitoring of Westslope cutthroat trout
Westslope cutthroat trout
The westslope cutthroat trout , also known as the blackspotted cutthroat, is a subspecies of the cutthroat trout and is a freshwater fish in the salmon family of order Salmoniformes. The cutthroat is the Montana state fish...

 shows widespread ongoing hybridization with introduced rainbow trout
Rainbow trout
The rainbow trout is a species of salmonid native to tributaries of the Pacific Ocean in Asia and North America. The steelhead is a sea run rainbow trout usually returning to freshwater to spawn after 2 to 3 years at sea. In other words, rainbow trout and steelhead trout are the same species....

  (see cutbow
A Cutbow is a fertile hybrid between a rainbow trout and a cutthroat trout . While cutbow hybrids may occur naturally, most native populations of rainbows and cutthroats were separated by geography or habitat...

) and Canada lynx
Canada Lynx
The Canada lynx or Canadian lynx is a North American mammal of the cat family, Felidae. It is a close relative of the Eurasian Lynx . Some authorities regard both as conspecific. However, in some characteristics the Canada lynx is more like the bobcat than the Eurasian Lynx...

The bobcat is a North American mammal of the cat family Felidae, appearing during the Irvingtonian stage of around 1.8 million years ago . With twelve recognized subspecies, it ranges from southern Canada to northern Mexico, including most of the continental United States...

 hybrids have been detected at the southern periphery of the current population range for lynx. The emergence and spread of pathogens can be tracked using diagnostic molecular assays – for example, identifying the spread of West Nile virus
West Nile virus
West Nile virus is a virus of the family Flaviviridae. Part of the Japanese encephalitis antigenic complex of viruses, it is found in both tropical and temperate regions. It mainly infects birds, but is known to infect humans, horses, dogs, cats, bats, chipmunks, skunks, squirrels, domestic...

 among mosquitoes in the eastern US to identify likely geographical origins of infection and identifying gene loci associated with parasite susceptibility in bighorn sheep
Bighorn Sheep
The bighorn sheep is a species of sheep in North America named for its large horns. These horns can weigh up to , while the sheep themselves weigh up to . Recent genetic testing indicates that there are three distinct subspecies of Ovis canadensis, one of which is endangered: Ovis canadensis sierrae...

. Genetic monitoring of invasive species is of conservation and economic interest, as invasions often affect the ecology and range of native species and may also bring risks of hybridization (e.g. for copepods, barred owl
Barred Owl
The Barred Owl is a large typical owl. It goes by many other names, including eight hooter, rain owl, wood owl, and striped owl, but is probably best known as the hoot owl.-Description:...

 and spotted owl
Spotted Owl
The Spotted Owl, Strix occidentalis, is a species of true owl. It is a resident species of forests in western North America, where it nests in tree holes, old bird of prey nests, or rock crevices. Nests can be between 13 and 66 yards high and usually contain two eggs...

, and Lessepsian rabbitfish
Rabbitfishes or spinefoots are perciform fishes in the family Siganidae. The 28 species are in a single genus, Siganus. In some now obsolete classifications, the species having prominent face stripes—colloquially called foxfaces–are in the genus Lo. Other species like the Masked...

Species identification is also of considerable utility in monitoring fisheries and wildlife trade
Wildlife trade
The international wildlife trade is a serious conservation problem, addressed by the United Nations' Convention of International Trade in Endangered Species of Wild Fauna and Flora CITES, which currently has 175 member countries called Parties. The 15th meeting of the Parties took place in Doha,...

, where conventional visual identification of butchered or flensed products is difficult or impossible. Monitoring of trade and consumption of species of conservation interest can be carried out using molecular amplification and identification of meat or fish obtained from markets. For example genetic market surveys have been used to identify protected species and populations of whale (e.g., North Pacific Minke whale
Minke Whale
Minke whale , or lesser rorqual, is a name given to two species of marine mammal belonging to a clade within the suborder of baleen whales. The minke whale was given its official designation by Lacepède in 1804, who described a dwarf form of Balænoptera acuto-rostrata...

) and dolphin species appearing in the marketplace. Other surveys of market trade have focused on pinnipeds, sea horses and shark
Sharks are a type of fish with a full cartilaginous skeleton and a highly streamlined body. The earliest known sharks date from more than 420 million years ago....

s. Such surveys are used to provide ongoing monitoring of the quantity and movement of fisheries and wildlife products through markets and for detecting poaching
Poaching is the illegal taking of wild plants or animals contrary to local and international conservation and wildlife management laws. Violations of hunting laws and regulations are normally punishable by law and, collectively, such violations are known as poaching.It may be illegal and in...

 or other illegal, unreported or unregulated (IUU) exploitation (e.g. IUU fishing
Illegal, unreported and unregulated fishing
Illegal fishing takes place where vessels operate in violation of the laws of a fishery. This can apply to fisheries that are under the jurisdiction of a coastal state or to high seas fisheries regulated by regional organisations....


Although initial applications focused on species identification and population assessments, market surveys also provide the opportunity for a range of molecular ecology investigations including capture-recapture, assignment tests and population modeling. These developments are potentially relevant to genetic monitoring Category II.

Monitoring population genetic parameters – Category II

Monitoring of population changes through genetic means can be done retrospectively, through analysis of 'historical' DNA
Ancient DNA
Ancient DNA is DNA isolated from ancient specimens. It can be also loosely described as any DNA recovered from biological samples that have not been preserved specifically for later DNA analyses...

 recovered from museum-archived species and comparison with contemporary DNA of that species. It can also be used as a tool for evaluating ongoing changes in the status and persistence of current populations. Genetic measures of relative population change include changes in diversity (e.g. heterozygosity and allelic richness). Monitoring of relative population changes through these metrics has been performed retrospectively for Beringian bison
Members of the genus Bison are large, even-toed ungulates within the subfamily Bovinae. Two extant and four extinct species are recognized...

, Galapagos tortoise
Galápagos tortoise
The Galápagos tortoise or Galápagos giant tortoise is the largest living species of tortoise, reaching weights of over and lengths of over . With life spans in the wild of over 100 years, it is one of the longest-lived vertebrates...

, houting
The houting is an extinct species of fish in the Salmonidae family. This species is distinguishable by having a long, pointed snout, an inferior mouth and 38—46 gill rakers. The houting once occurred in Belgium, France, Germany, the Netherlands and England.'Houtings' were said to be surviving in...

, Atlantic salmon
Atlantic salmon
The Atlantic salmon is a species of fish in the family Salmonidae, which is found in the northern Atlantic Ocean and in rivers that flow into the north Atlantic and the north Pacific....

, northern pike
Northern Pike
The northern pike , is a species of carnivorous fish of the genus Esox...

, New Zealand snapper, steelhead trout, Greater Prairie Chicken
Greater Prairie Chicken
The Greater Prairie Chicken or Pinnated Grouse, Tympanuchus cupido, is a large bird in the grouse family. This North American species was once abundant, but has become extremely rare or extinct over much of its range due to habitat loss. There are current efforts to help this species gain the...

, Mauritius kestrel
Mauritius Kestrel
The Mauritius Kestrel is a bird of prey from the family Falconidae endemic to the forests of Mauritius, where it is restricted to the southwestern plateau's forests, cliffs, and ravines.It is the most distinct of the Indian Ocean kestrels...

 and Hector's Dolphin
Hector's Dolphin
Hector's dolphin is the best-known of the four dolphins in the genus Cephalorhynchus and is found only in New Zealand. At about 1.4 m in length, it is one of the smallest cetaceans....

 and is the subject of many ongoing studies, including Danish and Swedish brown trout
Brown trout
The brown trout and the sea trout are fish of the same species....

 populations. Measuring absolute population changes (e.g. effective population size
Effective population size
In population genetics, the concept of effective population size Ne was introduced by the American geneticist Sewall Wright, who wrote two landmark papers on it...

 (Ne)) can be carried out by measuring changes in population allele frequencies (‘Ftemporal’) or levels of linkage disequilibrium
Linkage disequilibrium
In population genetics, linkage disequilibrium is the non-random association of alleles at two or more loci, not necessarily on the same chromosome. It is also referred to as to as gametic phase disequilibrium , or simply gametic disequilibrium...

 over time (‘LDNe’), while changing patterns of gene flow between populations can also be monitored by estimating differences in allele frequencies between populations over time. Subjects of such studies include grizzly bears, cod
Cod is the common name for genus Gadus, belonging to the family Gadidae, and is also used in the common name for various other fishes. Cod is a popular food with a mild flavor, low fat content and a dense, flaky white flesh. Cod livers are processed to make cod liver oil, an important source of...

, red deer
Red Deer
The red deer is one of the largest deer species. Depending on taxonomy, the red deer inhabits most of Europe, the Caucasus Mountains region, Asia Minor, parts of western Asia, and central Asia. It also inhabits the Atlas Mountains region between Morocco and Tunisia in northwestern Africa, being...

, Leopard frog
Leopard frog
Leopard frogs, also called meadow frogs, are the archetypal "grass frogs" of North America, a collection of about 14 species within the true frog genus Rana. They are generally very similar, green with prominent black spotting...

s and Barrel Medic
Medicago truncatula
Medicago truncatula is a small legume native to the Mediterranean region that is used in genomic research. It is a low-growing, clover-like plant 10–60 cm tall with trifoliate leaves. Each leaflet is rounded, 1–2 cm long, often with a dark spot in the center...

Genetic monitoring has also been increasingly used in studies that monitor environmental changes through changes in the frequency of adaptively selected markers. For example the genetically controlled photo-periodic response (hibernating time) of pitcher-plant mosquitos (Wyeomyia smithii
Wyeomyia smithii
Wyeomyia smithii, the pitcher plant mosquito, is an inquiline invertebrate found only in the phytotelma of the purple pitcher plant, Sarracenia purpurea. In this microcommunity of bacteria, rotifers, protozoa, and midges, W...

) has shifted in response to longer growing seasons for pitcher plants brought on by warmer weather. Experimental wheat
Wheat is a cereal grain, originally from the Levant region of the Near East, but now cultivated worldwide. In 2007 world production of wheat was 607 million tons, making it the third most-produced cereal after maize and rice...

 populations grown in contrasting environments over a period of 12 generations found that changes in flowering time were closely correlated with regulatory changes in one gene, suggesting a pathway for genetic adaptation to changing climate in plants.

Genetic monitoring is also useful in monitoring the ongoing health of small, relocated populations. Good examples of this are found for New Zealand birds, many species of which were greatly impacted by habitat destruction and the appearance of numerous mammalian predators in the last century and have recently become part of relocation programs that transfer a few ‘founder’ individuals to predator-free offshore “ecological” islands
Ecological island
An ecological island is not necessarily an island surrounded by water, but is an area of land, isolated by natural or artificial means from the surrounding land, where a natural micro-habitat exists amidst a larger differing ecosystem....

. E.g. Black robins
Black Robin
The Black Robin or Chatham Island Robin is an endangered bird from the Chatham Islands off the east coast of New Zealand. It is closely related to the New Zealand Robin . It was first described by Walter Buller in 1872. The binomial commemorates the New Zealand botanist Henry H. Travers...

, kakapo
The Kakapo , Strigops habroptila , also called owl parrot, is a species of large, flightless nocturnal parrot endemic to New Zealand...


Status of genetic monitoring in science

In February 2007 an international summit was held at the Institute of the Environment at UCLA, concerning ‘Evolutionary Change in Human Altered Environments: An International Summit to translate Science into Policy’. This led to a special issue of the journal of Molecular Ecology organized around our understanding of genetic effects in three main categories: (i) habitat disturbance and climate change
Climate change
Climate change is a significant and lasting change in the statistical distribution of weather patterns over periods ranging from decades to millions of years. It may be a change in average weather conditions or the distribution of events around that average...

 (ii) exploitation and captive breeding
Captive breeding
Captive breedingis the process of breeding animals in human controlled environments with restricted settings, such as wildlife reserves, zoos and other conservation facilities; sometimes the process is construed to include release of individual organisms to the wild, when there is sufficient...

 (iii) invasive species
Invasive species
"Invasive species", or invasive exotics, is a nomenclature term and categorization phrase used for flora and fauna, and for specific restoration-preservation processes in native habitats, with several definitions....

 and pathogens.

In 2007 a Working Group
Working Group
Working Group can mean:*Working group, an interdisciplinary group of researchers; or*Working Group , kennel club designation for certain purebred dog breeds; or...

 on Genetic Monitoring was launched with joint support from NCEAS and NESCent to further develop the techniques involved and provide general monitoring guidance for policy makers and managers.

Genetic monitoring in natural resource agencies

Many natural resource
Natural resource
Natural resources occur naturally within environments that exist relatively undisturbed by mankind, in a natural form. A natural resource is often characterized by amounts of biodiversity and geodiversity existent in various ecosystems....

 agencies see genetic monitoring as a cost-effective and defensible way to monitor fish and wildlife populations. As such scientists in the U.S. Geological Survey
United States Geological Survey
The United States Geological Survey is a scientific agency of the United States government. The scientists of the USGS study the landscape of the United States, its natural resources, and the natural hazards that threaten it. The organization has four major science disciplines, concerning biology,...

, U.S. Forest Service, National Park Service
National Park Service
The National Park Service is the U.S. federal agency that manages all national parks, many national monuments, and other conservation and historical properties with various title designations...

, and National Marine Fisheries Service
National Marine Fisheries Service
The National Marine Fisheries Service is a United States federal agency. A division of the National Oceanic and Atmospheric Administration and the Department of Commerce, NMFS is responsible for the stewardship and management of the nation's living marine resources and their habitat within the...

have been developing new methods and tools to use genetic monitoring, and applying such tools across broad geographic scales.. Currently the USFWS hosts a website that informs managers as to the best way to use genetic tools for monitoring (see below).

External links

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