Alpha Diversity Report

This report provides a comprehensive overview of alpha diversity, a key concept in ecology and biodiversity studies. It begins by defining ecosystems and biodiversity, explaining the components of richness and evenness. The report then delves into alpha diversity, contrasting it with beta and gamma diversity, and discussing various methods for measuring it, including species richness, Shannon index, and Simpson index. The importance of considering rare species and the use of estimators like Chao1 are highlighted. The report also addresses rarefaction curves and their limitations in the context of Next-Generation Sequencing (NGS) data. Finally, it emphasizes the significance of alpha diversity as a tool for assessing ecosystem health, monitoring the impact of environmental changes, and informing conservation strategies. The report concludes by summarizing the importance of biodiversity for human well-being, encompassing economic, recreational, ecological, cultural, and scientific values.

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Alpha Diversity
18th July 2019
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.
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
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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.
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.
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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
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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.
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
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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
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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.
Biodiversity Distribution and Alpha Diversity
In understanding biodiversity distribution and its relationship with the environment as it is
connected with the assessment of conservation initiatives all over the world the concept of
biodiversity becomes increasingly important. Various techniques can be used to forecast the
effects of environmental changes and formulate appropriate management strategies. One such
strategy is assessing the biodiversity across a network of local sites which is described using
three elements such as alpha diversity, beta diversity and gamma diversity. Alpha diversity is the
average number of species that exist in each of the specific sites in the study area. Beta diversity
refers to the differences in the species composition between the different sites Gamma diversity
refers to the total number of species in the study area.
In spite of the several insights that are offered by the combination of Alpha Beta and Gamma
diversity how species turnover is described is often limited by the factor that there is no
consideration for more than two sites at one point of time. In respect of more than two sides, the
average beta diversity is used typically which considers the multisite measures that are
developed but there are certain limitations such as difficult is interpretation. This often makes it
difficult for the researchers to identify the major environmental drivers related to species
turnover.
We now come to know about a new technique which combines two of the pre-existing advances
is its diversity and also the generalized dissimilarity modeling. The method makes it possible for
the differences within the contributions of common species versus rare species that are to be
moderate for better understanding the drivers of biodiversity responses towards the
environmental gradients.
Importance of Alpha Diversity as a constituent of Biodiversity
In the end, we can say that biodiversity is extremely important for the survival of human beings
and other living beings for several reasons. Biodiversity has intrinsic value because each species
has a value of its own and the right to exist irrespective of it is known to have some value for the
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humans. According to the biodiversity book published by the Commonwealth Scientific and
Industrial Research Organisation, there are five major interacting values that humans put on
biodiversity that is as follows:
 Economic- biodiversity offers humans with raw materials that are used in consumption
and production.
 Recreation- many of the recreational initiatives depend on the uniqueness of biodiversity
like bird watching, camping, hiking, fishing, etc. It also impacts the tourism industry.
 Ecological life support- biodiversity offers the ecosystems life by supplying oxygen,
clean water, and air, pollination from plants, wastewater treatment, pest control, and
many other services.
 Cultural- a culture of a nation is closely related to biodiversity through an effective
expression of identity that is achieved through aesthetic and spiritual appreciation.
Spiritual beliefs about various species of animals and plants by people around the world
is an important consideration in the discipline of biodiversity.
 Scientific- biodiversity encompasses a substantial collection of ecological data that are
highly systematic and help us significantly in understanding the natural world around us
and how such a world has originated.
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