I like to study this problem.

Folowing

I enclose an article that defines very well the difference in species diversity and taxonomic distinctness index. : Clarke, K.R. & Warwick, R.M. 1998. A taxonomic distinctness index and its statistical properties. Journal of Applied Ecology 35:523-531.

Thank you for the recommendation Enrique Reynaldo de la Cruz , unfortunately my doubt emerged by reading exactly that paper

Hello Emanuele Giacomuzzo

I assume we understand the technical side of the question in the same way. I will only share my experience about using Taxonomic Distinctness. Of course, there are many indices of this, one I used is Family-to-Species ratio (species richness being equal, more families indicate to more distinctness, less families to less distinctness). I am (or at least was) a routine user of taxonomic diversity indices, but I considered taxonomic distinctnessin just two occasions, and I think typically researchers mostly use the former and only in some special occasions the latter.

In the first case, I wanted to compare plant diversity between two areas, one in a place that did not seen any appreciable geological disturbance for very long time (from the Tertiary), another was strongly influenced by the last Glaciation. As expected, because of longer and uninterrupted evolutionary trajectory, taxonomic distinctness was higher in an undisturbed place.

In the second case I was looking at carabid diversity in a forest and wanted to know whether competitive exclusion occurs more often among less distinct species or not (in other words, at high population densities whether taxonomic distinctness increased with decreasing species richness).

In other works where I looked at plant diversity (over 20 such cases) I always used species richness, Simpson indices, rarefaction-estimated richness, etc.

There is an implied assumption in your question, that taxonomic identities are at least mostly well defined and well understood or at least that the perception of this for a particular taxon is fixed. This is often not the case. How taxa are distinguished, is very much based on the level of familiarity with that taxon and its relatives, by the taxonomist making the initial decisions. Some entities are distinguished by several easily measured or described characters, others by very few. The number of and choice of characters used may or may not be a function of the organisms in question, or of the value of the characters used to make the distinctions. Different sets of characters, used to distinguish organisms from each other, can provide conflicting taxonomic identities. This is true whether using DNA, biochemical factors, or morphological structures for characters, or any combination of them. For example, did the taxonomist take into account flower structure, seed structure, sperm structure, DNA differences, and the level of genetic and epigenetic variation within each potentially different taxa, etc.? Have they chosen the right genes to distinguish the taxa in question? Did they decide some of these characters were more important than others, and only use those that gave the easiest results to follow, without looking closely at discrepancies? What happens when new technology allows us to examine some new feature that had previously been overlooked, or had been too costly to pursue? For example, perhaps telomere length and/or impact of different soils on the same taxon at different stages of development need to be better understood to really know what is the same or different. The frequency of collection, and geographical broadness which provides the taxonomist with material to study, when establishing or reevaluating taxonomic identities, can vary a great deal in quality and quantity, even between closely related taxa. The funding, capabilities, and attention given each taxonomic group also vary.

The ecological indices you ask about are applications of mathematical formulas, intended to correct gaps in knowledge, sample size, or balance some other inequality, for ecological information. Therefore they may each be needed, to give a clearer picture of what's going on, in the same way that different sets of characters can alter concepts of taxonomic limits. It's like looking at an image on a computer screen, where multiple coded scripts have to run to show all the pixels creating a cohesive image. The more of the possible scripts that are run, the clearer the picture is likely to become. This is not a specific answer to your question, but may help in thinking about why different statistical approaches exist for any biological problem. Some people prefer to focus on the best results, or avoid conflicts by sticking to one approach. It is my opinion that is important to cast a broader net and be honest about the discrepancies. Our group efforts will yield better results this way. The lack of meaningful results from one approach, when another is more useful for a particular data set, may mean something significant in itself.

The taxonomy is the identification and description of taxa with the objective of locating them in a system. Biological diversity is by definition the analysis of variability at any scale, be it ecological or biogeographic (to point out the two extremes). The taxonomy is born from the need to identify living beings and find an order that allows to develop in a coherent way the studies in any branch of biology.

In biological diversity, the objective is to establish the state of relations between living beings in a given territory, determine the degree of balance of these relationships and their causes. This with the objective of determining the changes of the biota in each territory. Therefore, the taxonomy is in some way to the biological sciences, all of them, like metrology to physics.

The biological diversity is based on three fundamental pillars: alpha, beta and gamma. Interestingly, the best-known indices of biological diversity are those corresponding to alpha diversity. These study the equilibrium relations between the living components of a given territory (community, landscape, biome, etc.). But most of the time, beta diversity is ignored, that is, the degree of relationship between a set of territories (the amount and form in which taxa share), and most ignore that the patterns that determine that diversity Beta depending on the individual combinations is the gamma diversity.

When we study the genesis of taxonomy, we discover that this science arises from the need to order the supposed chaos in the associative identification of living beings. But the need arose from very ancient in all civilizations and biological diversity was born from ecology. Linne uses the conceptions of Greek philosophy, but the Mayans, the Chinese, the Hindus had theirs. Whittaker, father of biological diversity, part of his studies in the plant communities of a mountain and deepening, found that the relationships there were much more complex and difficult to interpret than he had thought

It is easy to understand that biological diversity is a science with its own paradigms, where taxonomy provides the system that allows it to develop. Therefore, they have absolutely nothing to do with each other

In response to Dr. Almirall's comments. Thank you for your insight on alpha, beta and gamma taxonomy. However, I disagree with your statement that taxonomy and ecology have absolutely nothing to do with each other . You state they are like the science of measurement relative to physics. That is partially true. However, though there has been some change in how measurements are made, measurement to physics is is still a linear relationship. Taxonomic identities, like ecosystem distinctions, exist at different levels and are based on webs of factors. Which taxa ecologists choose to study is affected by taxonomic stability for those taxa and the set of taxa sampled and their intrinsic taxonomic stability, can create noise in statistical analyses. Many ecologists choose to look only at taxonomically stable species, to avoid problems. However, in doing so, they may remove the most responsive species for looking at differences in processes in and among ecosystems. If resources allow, it seems important to sample several mixtures of taxa to compare ecosystems, and to look at some less stable species as well, that may be responding to changes in their surroundings. In choosing a less taxonomically stable species, it is important to know that the taxonomic instability is intrinsic to the species, not to how well it was studied. Even when this is not possible, it is important to increase the number of statistical approaches to the data available to see what happens, and to run subsets of the data in hand. Taxonomic stability is not the only thing that will cause noise in statistical analyses for ecology studies, though it sure can contribute. True taxonomic stability is also difficult to be sure of. Ecologists have been upset before, by taxonomic changes to species they have already done studies with.

irst, there is no alpha, beta and gamma taxonomy, but alpha beta and gamma diversity. The instability of ecosystems, something that falls in the field of ecology depends on a set of factors, and the instability or behavior of taxa is only one of them. I can talk about the instability of the soils, the relief, the geology, the climate, even the meteorological variability. In such cases, taxonomic instability can often be a valuable indicator. For example, in Cuba, the degree of biological aridity of a territory can be estimated (never determined) if we rely on the neo-tropical evolutionary centers to which the taxa can be associated. Undoubtedly many of the processes that occur in an ecosystem can be interpreted and therefore expressed with the support of the taxonomy. But the vast majority of these processes go beyond taxonomy, and therefore the role of taxa is to characterize them and even evaluate them, not to define their internal order.

Something like the concept of the black box. We take the living beings present in a territory, we put them in a black box, and depending on what we obtain at the exit and according to our previously designed and defined objectives, we make the inferences, although without knowing the interactions and the role that corresponds to each of the thousands of factors involved, many of them abiotic. The closest I know to the analysis of black boxes are the mathematical models, and until now I do not know any precise enough to give acceptable results for the precision of any work. It is for this reason that for any process it is necessary to apply a set of models.

Many years ago it was left behind to think that the ecosystem is a mega organism. To the extreme that the French classification system has been forgotten. The ecosystem is an independent system of the living beings that compose it. However, the latter remain the best tool to measure many of its parameters, as well as to study and characterize its dynamics. What functions do units have to measure space-volume-mass and time in physics?

It is not totally true that ecology uses only the most stable species. For example, to determine the sensitivity of an ecosystem to a certain variable, species sensitive to the variations of that variable are used. Humidity, temperature, etc. With such species the effects are amplified and impacts are much easier to study.

Here I must say that there are many unstable natural systems in the universe, not just ecosystems. The students of geodesy in our planet already found sensible changes in the dimensions of the Earth by years 60 of the last century. The causes were in the development of the megalopolis.

You talk about the linearity of physical units. In principle we must take into account that physical systems of metrology were created by man. Even, I have the opinion that the most perfect, the decimal metric, was thought from the system of Linnaeus, which evidently departed from the Socratic teachings, that is, from the understanding of the systems that existed in ancient Greece. Had it been the Mayans, who also have their basal system for the ordering of living beings, it would have been thought of in another way.

But to my taste, in 2000 a Spaniard, in a little known work, found that in a set of taxonomic groups it was possible to express a taxonomic level in function of another by means of exponential equations. Without going into details that would lengthen this, I can tell you that this shows that taxonomic systems, like man-made systems, are nothing more than inclusive hierarchical sets, whose levels can be expressed in terms of each other.

Thank you for your correction Dr. Almirall on alpha, beta, gamma diversity, not taxonomy. My apology on that. However, please consider that it is highly unlikely that the same equation would always apply to the nesting of taxonomic levels for different sets of taxa. For the same specimens, one taxonomist's genus/spp. is an earlier taxonomist's genus/sections and a later taxonomist may decide to split off a new genus for a portion of the species formerly in the original genus. Individual variation in expression can result in errors in separating taxa as well, and these misinterpretations can stand for years. Taxonomic concepts are human constructs, including those for soils and geology, however, botanical taxonomy is based on living, adapting entities, which have variation within individuals, and through time as well as space. Can you share the 2000 reference? It sounds like an interesting paper. I'm wondering which taxa and which taxonomic levels worked for the equation and whether the exact same equation worked with multiple sets of nested taxa. As for the black box, that works with stable taxonomic identities, however if you rely on them, you are more likely to ignore highly ecologically responsive taxa. Ideally, stable responsive taxa should be used. However, stabilizing such taxonomic identities may also mean simplifying the characters used for separating them and/or accepting a higher level of variablility among related taxa and within individuals for a larger number of characters, than for other less responsive taxa, at least until new characters can be practically added to the mix. A black box approach can work with individuals, but then you have the problem of replicating results and comparing results to those of others.

Martín-Piera, F. (2000): Estimaciones prácticas de biodiversidad utilizando táxones de alto rango en insectos. En Hacia un proyecto CYTED para el Inventario y Estimación de la Diversidad Entomológica en Iberoamérica: PriBES 2000 (F. Martín-Piera, J. J. Morrone & A. Melic, Eds.). m3m-Monografías Tercer Milenio, vol. 1, Sociedad Entomológica Aragonesa (SEA), Zaragoza, pp. 36-54.

Dear colleague Miriam

The reference I am sending you is of the article in which Martin-Piera found in some insects the possibility of expressing the richness of species according to the wealth of families, using for it an equation of the type x = a ** b * x. I also add an article that we wrote some time ago about how that type of equation fits the Cuban endemic flora.

The use of higher level taxa, it seems, will be very useful to apply classical methods in the analysis of biological diversity on a continental scale. At the level of species that is not possible because it is prevented by Buffon's law. The only analysis of biological diversity at a continental level was done by Gentry in the rainforests of all the continents where that biome is present. To achieve this, I use wealth in families, and how the wealth of each family is pondered.

This had previously been done to study the Russian prairies by Tolmachov

https://www.researchgate.net/publication/318760929_My_Village_Biodiversity_Documentation_of_Western_Ghats_Biodiversity_through_Network_of_Students_and_Teachers

https://www.researchgate.net/publication/331076568_Global_Warming_Mitigation_Through_Carbon_Sequestrations_in_the_Central_Western_Ghats/stats

https://www.researchgate.net/publication/323180165_Salient_Ecological_Sensitive_Regions_of_Central_Western_Ghats_India

https://www.researchgate.net/publication/332331409_Sustainable_Management_of_Bannerghatta_National_Park_India_with_the_Insights_in_Land_Cover_Dynamics

https://www.researchgate.net/publication/301609558_Geospatial_analysis_of_forest_fragmentation_in_Uttara_Kannada_District_India

Higher value of taxonomic distinctness in a area, indicates the establishment of different genera with greater taxonomic diversity and wide range of ecological condition with large ecological niche. But taxonomic distinctness does not differentiate distinctly the system under putative disturbances, which might be due to higher species assemblage and that lower value of distinctness are not exactly result of extreme disturbance factors .