Alpha Diversity

Alpha Diversity: Explanation and its importance in ecology

Concept of an Ecosystem

The concept of an ecosystem was proposed by Robert Whittaker who was an American psychologist and researcher in the domain of succession and vegetation gradients. According to him, there are three measures of diversity in an ecosystem such as alpha, beta and gamma diversities. Alpha diversity within an ecosystem refers to the number of species. Beta diversity encompasses the comparison of diverse ecosystems in environmental gradients.

For instance, in a mountainous area that is situated within a coastal area. Beta diversity depicts the size in the change of species from one ecosystem to the other. Gamma diversity reflects the total diversity in a region such as geography diversity. It is the total of the Alpha diversity about diverse ecosystems. Now our experts from Assignment Help UK will tell you about the concept of Biodiveristy.

Concept of Biodiversity

Biodiversity is referred to as the various existing within and among the various forms of life on a site, landscape or ecosystem. Biodiversity can be termed as and measured like an attribute consisting of two components such as richness and evenness. Richness refers to the number of groups of genetically are functionally related individuals in the species.

It has been found in most of the surveys conducted on vegetation that richness is depicted in the form of the number of species and it is normally referred to as species richness. Evenness consists of the proportion of species for functional groups that exist on a site. The more is the equal species in proportion to one another, the greater will be the evenness of the site. A site having low evenness reflects that there are a few dominant species located in the site.

Diversity is used for describing variation in diverse forms such as genetic, life form and functional group. Genetic diversity consists of species and varieties. Life from diversity consists of mosses, trees, grasses, and forbs. The functional group consists of evergreen vegetation, deep-rooted plantation, nitrogen-fixing and soil crust. Biodiversity is measured to identify a combination of richness and evenness existing across a species. One of the main reasons for measuring biodiversity is high biodiversity is often considered synonymous with the health of an ecosystem.

Commonly, diverse communities are considered to have enhanced stability, productivity, and resistance to innovation and other types of disturbances. A diverse habitat consisting of a variety of plants have multiple advantages such as follows:

  • Offering foraging ground for a large variety of vertebrate and insect species.
  • Achieving stability that generous from the plants in the community that can survive insect plagues, disease outbreaks or drought such that the site has some protection of its soil and forage during those years.
  • There are plants which contain diverse genetic material that can be used in long term survival and achieving stability of the community.
  • The community will benefit from having a mixture of plants. For example, the condition of the soil improves when there are nitrogen-fixing deep-rooted plants that permeate nutrients up towards the surface from the layers of soil below other plant roots. Some species of plant functions together for achieving effective survival which is referred to as commensalism and thereby more stability is achieved in diverse communities.
  • Plant communities which are healthy and diverse usually have their niches filled and they are theoretically less exposed to invasions by noxious and opportunistic species those had been introduced in the region. Now our experts from Homework Help UK will tell you about this with the help of an Infographic.
3 Perspective of Community diversity

Concept of Alpha Diversity

Alpha diversity (α-diversity) refers to the mean diversity in species in different sites or habitats within a local scale. The terminology was founded by R. H. Whittaker, along with the terminologies of beta diversity (β-diversity) and gamma diversity (γ-diversity). The idea of Whittaker encompassed the concept that the diversity of species in totality within a given landscape that is the gamma diversity can be determined by two diverse concepts.

The mean diversity of species at different sites or habitats within a more local scale which is referred to as alpha diversity. The differentiation existing between the habitats is referred to as beta diversity. The area of the particular landscape and the sites of habitats within it can be of diverse sizes and in diverse situations.

There has been no significant consensus reached for determining the spatial scales that will be adequate to put alpha diversity in a quantifiable form. So, the experts in this discipline have proposed that the definition of alpha diversity need not be tied with a typical spatial scale. It is possible to measure alpha diversity for a dataset which contains subunits of any scale.

These subunits can be of diverse forms such as sampling units that have already been utilized in the field at the time of carrying out the inventory. They can also be grid cells which are delimited only to conduct an analysis. When the results are extrapolated beyond actual observations, it has to be considered that the diversity of the species in the subunits, commonly depicts the underestimation of the diversity of the species in the comparatively larger areas.

Alpha diversity has been defined in a variety of ways by several ecologists. According to Whittaker, the term was used for diversity in species in a single subunit and also to refer to the mean species diversity within a collection of subunits. It is often argued by many people that the definition of alpha diversity as a mean across all the subunits is preferable. This is because this idea agrees more effectively with the idea that was given by Whittaker who said that diversity in the total species contains alpha and beta components.

The various definitions of alpha diversity might vary according to the assumption of species diversity. It is often found that various researchers utilize the values that are provided by one or more than one indices of diversity, for instance, species richness that is the degree of richness in many species and it does not consider the degree of a rarity in the individuals but biodiversity can. The Shannon index and the Simpson index are two of the other indices that are used to measure species richness. However, there has been an argument on several occasions that it would be much better to utilize the effective number of species as a system that will be a universal measure of diversity in species.

The measure of Alpha Diversity

The measure makes it possible to weigh the species that are rare and abundant in a variety of ways. This happens just in the manner the diversity indices collectively perform but the meaning of it is more intuitive and convenient to understand. Therefore, it can be said that the effective number of species can be considered as the number of species which are equally abundant and those are required for or obtaining the same mean proportional species abundance like what is observed in respect of the data set of interest. Here all the species might not be equally abundant.

So, we can say that alpha diversity refers to the diversity that exists in a single ecosystem or sample. The simplest measure of alpha diversity is the richness, the number of species or OTUs that are observed within the sample. There are other metrics which consider the abundance of the OTUs or frequencies of the OTUs. This happens to attribute lower weight to a lower abundance of OTUs. The abundance of distribution is possible to be observed by using the octave plot.

Interpretation and estimation of Alpha Diversity

Interpretation is necessary to keep in mind that NGS amplicon sequencing is not effective to measure frequencies for the presence or absence of OTUs effectively. This is the reason behind and unclear and misleading biological meaning of Alpha diversity metrics that are developed for traditional ecology and it is often very difficult to interpret. Estimators of Alpha diversity reveal that there might be some rare species that have not been effectively observed. The purpose of an alpha diversity estimator is to extrapolate from the available observations to the total number of species existing in the community.

One of the most reputed estimators for NGS OTUs is Chao 1. We can understand that estimators cannot be effectively implemented to NGS OTUs has the rare species remain underrepresented by using an abundance threshold where singletons are discarded. Regardless of the number of spurious OTUs, there is an increase at lower abundances. Hence, it is evident that the lower abundance still of the distribution is extremely uncertain and it attempts to extrapolate renders no sense. Now our experts from Do My Assignment UK will tell you abou the refraction in Alpha Diversity.

Rarefaction in Alpha Diversity

Rarefaction is one of the important incidents associated with Alpha diversity to get adequate observations to achieve a successful measurement of an Alpha diversity metric. This is undertaken by drawing a rarefaction curve that depicts the changes in a metric in the form of several observations that keeps on increasing. If the curve converges into horizontal asymptote then it depicts that more observations or more reads will show little or no impact on the metric.

Recording the estimators the asymptote of a rarefaction curve depends based on the lower abundance tail in the distribution. Hence, it is considered to be of dubious value when it is applied to the NGS reads. It is certain for the number of OTUs to increase with an increasing number of reads due to errors even though all the species present in a sample are taken into account. Therefore, it is for certain that the rarefaction cars have to converge into a positive slope.

Now, we come to discuss the units of measurement of Alpha diversity. Alpha diversity metrics use various units at different times. Many a time, the meaning is not obvious and often it is observed that metrics having different units are not possible to be compared with one another. For instance, the Shannon index measures entropy where the unit is expressed in the form of bits of information if the logarithms have base 2.

However, open on many occasions natural logarithms with base e or base 10 are considered. It is interesting to learn that neither of the variants of the Shannon index is related to the number of OTUs. People sometimes do not disclose the variant that is used and this is the reason behind the difficulty in interpreting the numerical values.

Alpha Diversity as a tool of biodiversity measurement

Alpha diversity indicates the diversity that exists within a typical area or ecosystem and it is measured by the number of species or the richness of species within that ecosystem. For instance, if we are involved in monitoring the impact of British farming practices on the diversity of native bird species in a particular area of the country then and we have to compare the diversity of the species within different ecosystems like the undisturbed deciduous wood, a hedgerow bordering a small pasture and arable field of considerable size.

It is possible for us to walk through a transect in which one of the three ecosystems and undertake a counting of the number of bird species that can be observed. In this way, it is possible for us to determine the Alpha diversity in respect of each of the ecosystems.

We should understand that Alpha diversity tool considers abundance tables as inputs. Abundance tables are created in the workbench through the observance of 3 tools such as OTU clustering, Taxonomic Profiling and Build Functional Profile. When OTU clustering and Build Functional Profile are used then the abundance tables that are developed are based on count and the measures of Alpha diversity that are calculated from such tables provide and an absolute number of species.

But, at the time when an abundance table is used that is generated by Taxonomic Profiling Tool then Alpha diversity results do not depict the absolute number of species but the estimates that are convenient in comparative studies that are undertaken for assessing the depth in sequencing or to compare diverse communities. For more infromation you can check with Assignment Writing Service.