The shadow effect is a phenomenon seen in genetic studies that use noninvasive genetic data collection methods. It occurs when there are not enough loci and/or loci that have low variance of alleles within the population. As a result, researchers can capture two separate individuals and mistakenly label them as the same individual. This can create a negative bias in the data and portray a population as smaller and less genetically diverse than it is. This is most commonly seen in collection methods that rely on environmental DNA (eDNA) which is collected directly from the environment (such as feces or hair removed from the ground). The accuracy of non-invasive collection data can be increased by increasing the amount of loci being examined during the study.

Background

There are several types of rarefaction methods that can be used to estimate the size of a hard monitor species. The study of population size and density falls under

demography Demography () is the statistical study of human populations: their size, composition (e.g., ethnic group, age), and how they change through the interplay of fertility (births), mortality (deaths), and migration. Demographic analysis examine ...

, the study of populations of any kind of organism. Mark and recapture is a common form of

data collection Data collection or data gathering is the process of gathering and measuring information on targeted variables in an established system, which then enables one to answer relevant questions and evaluate outcomes. Data collection is a research com ...

involving species with large populations. Being able to capture and mark a species in a noninvasive way allows for accurate readings of the population's size, both total and effective over several rounds of recapture. However, for species that are difficult to capture or view directly such as

endangered species An endangered species is a species that is very likely to become extinct in the near future, either worldwide or in a particular political jurisdiction. Endangered species may be at risk due to factors such as habitat loss, poaching, inv ...

, it can be near impossible to use the mark-recapture method to obtain genetic samples. Another method for population size estimation is a

real-time polymerase chain reaction A real-time polymerase chain reaction (real-time PCR, or qPCR when used quantitatively) is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR). It monitors the amplification of a targeted DNA molecule durin ...

(qPCR). qPCR is a molecular approach that measures the amplification of DNA over time rather than just at the end of the reaction. This method is useful because it can rely on eDNA to give an estimate of how abundant a species is in a given habitat. Noninvasive forms of data collection can be achieved through the collection of fur, feces or other fragments of DNA-rich material left behind (eDNA). Once considered costly, modern advancements have allowed for non-invasive data collection to become easier and provide more genetic information about a population. DNA-Barcoding is a method of species identification that uses eDNA to determine the unique genetic makeup of individuals and their species. This method is that it requires a balancing act: Maintaining enough loci markers in the genetic data, and remaining cost-effective. Probability of Identity (PI_AV) is the probability of a randomly selected sample from a population producing the same genotype twice if not enough loci are used during the study. Should loci with little genetic variation or few loci are selected, it is likely that multiple individuals will be identified as too genetically similar, with individuals being excluded from the data set. This creates a negative statistical bias, pushing the results towards a smaller, less genetically diverse mean than is accurate to the population. This is known as the shadow effect.

Applications

The Cabrera vole (''Microtus cabrerae'') is a small, endangered rodent that belongs to the ''

Microtus ''Microtus'' is a genus of voles found in North America, Europe and northern Asia. The genus name refers to the small ears of these animals. They are stout rodents with short ears, legs and tails. They eat green vegetation such as grasses and se ...

'' genus. Existing primarily in Portugal, populations can be difficult to estimate using typical mark-recapture methods due to their small size and ability to quickly disperse over large swaths of prairie land. With the introduction and reduced cost of using environmental DNA (in this case feces) were able to be used in a relatively low cost experiment to estimate the population size of the Cabrera vole in southern Portugal in return for sacrificing demographic (age, sex, health) information.

References

{{Reflist Wikipedia Student Program Genetics

Background

Applications

See also

References