some answers in :

Measuring biological diversity by Magurran

http://www.bio-nica.info/Biblioteca/Magurran2004MeasuringBiological.pdf

This is a simple diversity indices such as Simpson indices of Hill. Shannon is a sensitive index to changes of importance of the rarest species.

There are other indices based on phylogenetic diversity, functional diversity ...

I agree with Alain, We have to had that this index is difficult to interpret - in particular in comparing 2 or more Shannon indices.  

Moreover, some "healthy" ecosystems naturally show a low species diversity, and an increase of diversity could be caused by perturbating factors.

Commonly, higher values of Shannon index could be measured at the ecotone between different habitats, and overall ecosystem diversity could be affected by habitat heterogeneity rather than true ecosystem health...but we should also state what we mean with ecosystem "health".

It is a quite complex issue. In some kind of communities, for example of sessile marine organisms (stony corals, gorgonians and sponges) it is possible to correlate diversity indices (e.g. Shannon's diversity and Pielou's equitability indices) with environmental favorability and stability, but not with community health.. It is due to their comparatively great connectivity to the physical environment.  You can downoload and consult some of my papers about this issue among my ResearchGate  contribuions on sponge, coral and gorgonian communities of Cuba.. 

To monitor ecosystem health you need more specific indicators, than a simple integrative diversity index, Rocco Labadesa clearly states thst some healthy ecosystems can display low divesrsity indices.

AGRRA methodology for coral reefs is an example of a set of specific indicators, and indeed there are other ways, as that used for  the Mesoamerican Coral Reefs..

Dear All,

What do you mean on the health of an ecosystem? I am afraid the state and changes of ecosystems are complex and complicated phenomena. One diversity index generally is not sufficient to characterise these phenomena. The advantage of Shannon –Wiener diversity index is that it was used in many studies and thus one can have a lot of data. Its trouble is that - as many mentioned above – its interpretation is problematical and the density of the dominant species may distort its value.

I note: there were earlier some interesting threads on this matter at RG , I suggest to have a look at them.

I agree with Alain ...it is complex for one type interpretation. 

Dear Shankhadeep Chakraborty,

as pointed by other colleagues, it is important to state what are you calling "ecosystem health". Shannon-Wiener index is a classical index which calculation is based on species identity and/or species abundance. In many cases, this index is not capable to capture ecological differences among species in a community which are often linked with ecosystem functioning/resilience (health?). In this case, functional diversity indexes could be a better approach to describe the ecosystem or you could use a combination of Shannon-Wiener and functional indexes to describe your community/ecosystem.

It is out of my specialties!

The use of more than guide be more logical to describe the state of the environment studied. Shannon guide provides you with the extent of the diversity that exists in the environment so it is impossible to use it alone as a tool for assessment of health of any type of ecosystem?

it's depend of what you study. If it's fauna (or flora) with highly different ecological functions (predator, prey), Shannon is not adapted.

You can look in the Functional Biodiversity Index and use (Rapid biodiversity Index). For exemple, you can look in Laliberte and Legendre or Mouchet and Villeger papers'

Shannon-Weiner species diversity index, and species richness itself, i.e.  the number of different species in an ecosystem, have been for a long time the predominant measure of global biodiversity. This is now changing rapidly (see a recently published paper in Nature) as researchers are realizing that rather than considering the sheer number of species, it is which specific species that are present that is crucial for ecological functions underpinning the provision of ecosystem services and the overall ecosystem functioning..

As the previous responses states, Shannon-Weiner index would not be an appropriate tool to monitor ecosystem health. A time series of the index would probably have more information about ecosystem health, as biodiversity loss in an ecosystem can be an indicator of degradation. Anyway you should take into account what the appropriate timeframe would be, as healthy ecosystems can have cyclic changes in biodiversity.

In my opinion, to have a more accurate determination of the ecosystem health you should use more holistic approach, taking into account the species, the food web structure, the biomass transport, etc. Maybe you find interesting the application of the Information Theory to the ecosystem analysis in the Ecosystem Network Analysis (http://www.cbl.umces.edu/~ulan/ntwk/network.html) by Robert Ulanowicz

It is very important to note, as Robert Ulanowicz stated in another thread here in RG 

(https://www.researchgate.net/post/If_I_obtain_the_Shannon-Weiner_diversity_index_as_285_what_can_I_interpret_from_this_about_the_diversity)

that when Robert MacArthur introduced the Shannon-Weiner index into ecology he was calculating the diversity of *processes* not population counts. What Robert has written is a clear warning to see beyond one's nose and simple counts of species like many, too many unfortunately still do when they address "biodiversity" through for instance the Shannon-Weiner diversity index, that does not reflect the health condition of a community, and look instead at the processes as it was the original intention of MacArthur. There are still many, too many papers of this kind, especially in marine biology, published on biodiversity that bring no contribution to knowledge especially on ecosystem health, but on the contrary, they create confusion, noise and chaos and only serve to increase the impact factor and citations of their authors. I can provide a lot of examples in this respect, and this is a clear example of the current neverending story of misuse of diversity indices.

The short answer to you question is an unequivocal YES! The point being that the index directly measures redundancy of some operational factor that systematically ties into species representation. The measurement is readily obtained with a little work and is flatly the first thing you should enumerate (bar none). Most of the ifs ands and buts have been covered in the above conversation list and it is up to you to interpret what the data so gathered are telling you. Go back and read Claude Shannon's original paper before you do anything else. MacArthur used the index in one ecological context yes, but so what? He did not define an exclusive use-function thereby - how could he? The value of the index in population work is not amenable to precise definition. I discussed this matter with MacArthur in my early years as a population ecologist and we agreed on this point.

What you must do is to somehow track and understand how the index moves, how it varies with time and space in order to comprehend the health of the system under study. Chuck in as many other variables as you have time to count/measure. Stick the whole thing into a spreadsheet (Excel is good), perform whatever interventions, manipulations in respect of the system that you can (or can be observed as they are presented to you) and thereby try to understand what the ecology is (trying) to tell you.

I strongly disagree with the previous intervention. With the rise of easily accessible phylogenetic trees and functional trait databases, just analyzing species richness, in whatever form it takes (Shannons, Simpsons, S,  etc.) seems rather outdated. Rapidly, it seems, functional diversity and phylogenetic diversity, and their associated metrics (e.g. Rao's Q, FDis, and etc.), are now being used to answer more specific questions about ecosystem function, community assembly, trophic networks, ecosystem health and conservation priorities. Species richness, and also the Shannon-Weiner index have been for a long time the predominant measures of global biodiversity that is supposed to be, but it is not directly, the basis for ecosystem functioning and, hence, its health. This is now changing rapidly (see a recently published paper in Nature) as researchers are realizing that rather than considering the sheer number of species, it is which specific species that are present that is crucial for ecological functions underpinning the provision of ecosystem services. 

Can you please provide link to the paper in Nature you are referring to. Thank you.

Thank you Uma, I am sorry I forgot to put the link in the answer, the link of the Nature paper is  http://www.nature.com/nature/journal/v501/n7468/full/nature12529.html) 

I do not fully agree with Giovanni Zurlini answer suggesting  to discard diversity indices. They are  still a representation of the structural complexity (not  health) of a given community. But they could indicate  change in health condition when compared in different moments.. A diminution of a diversity index in time could be indicating an impairment of the community condition. They can be useful to indicate heath particularly when following them along time. An isolate unique value. of a diversity index does not necessarily indicate health condition of the community..

Dear Pedro everyone is free to agree or disagree, however here the question is not on the use of diversity indices for assessing structural diversity, but rather:

Can the Shannon-Weiner species diversity index be a good monitoring tool for assessment of health of any type of ecosystem?

Do you agree on that?

I fully disagree on this, and I don't care of the downvoter. 

I'm agree with Giovanni Zurlini.

If you want understand the "health" of an ecosystem you have to think about "functional". So FDis index is pretty good.

you can look at this paper:

http://adn.biol.umontreal.ca/~numericalecology/Reprints/Laliberte_Legendre_Ecology_2010.pdf

you can use 3-4 index FRic, FDiv,FEve. it's more complex but it's work. In my thesis, I try to create a "simple" index of assessment of healt for an ecosystem. I had to take the trophic position, the mass and other parameter to obtain a good result. I have currently some papers under review that will perhaps help you (or not) in few months. But with FDis and similar index, I think you will obtain what you want (perhaps a little "heavy" to use easily).

Well I guess the particularity of the word "health" has to be structurally defined.

But, as a matter of experience, I take structural degradation as being almost always synonymous with a slide into decreasing health of a community. In all my years of environmental monitoring I have found that simple H' reduction is the expected mode of response and that index tracks this very well.

Are there some communities that progressively become unhealthy but at the same time exhibit increasing or steady H'? The same number of species registering equally might tend to show this ie as a counter trend as towards Hmax but in practice this does not seem to happen blindly.

Fewer species represented and maybe in greater numbers, say replacement of macro organisms by heaps of bacteria - yes, perhaps, maybe but remember one can always spot this sort of thing at the direct species level (shifts in kinds and abundance) which are measured anyway and besides which I find that H' usually falls off as well.

I hesitate to say H' ALWAYS falls off but I have never never encountered such a thing and I have a truly practical (not to be described as strictly academic but indeed transcending this) global perspective on the matter. Many many ecological communities in many countries.

So, to the crux of the matter, what communities (and under what circumstances) follow a descent into "unhealthiness" with no concurrent reduction in H'?

I think (like other here I hope) it's depend of the context. If you  work on a precise community (carabs, ants, etc.). Simpson, Shannon will be fine (and pretty accurate).

If you are looking for a index that take the complexity of one ecosystem, I think (it's only my opinion), you have to take the functional datas (trophic position for example).

In agricultural landscape, a ecosytem can be "unhealthy" (and yes, I think it's depend of you think about "health") and have a high shannon index. for exemple an ecosystem with 4 herbivorous species (scrounger/parasite/ravageur) and 5 indivuduals for each species will obtain a pretty good Shannon index. But an ecosytem with 15 bugs, 5 spiders, 3 shrews and 1 viper wil have a bad Shannon index. And I think the second ecosystem is more able to sustain a complex diversity with a complex trophic chain. And so, it's more resistant and resilient (there are some papers that discuss the capacity of the resistance according to the functions supported by the species that composes it.

But,... have you not omitted bugs and spiders in the first example (directly above given) as well as artificially constraining species representation to 5? Yes, I agree in principle with the use of an heuristic assemblage for the purposes of illustration but in a concrete "real world" situation one would be usually faced with enumerating many more than 5 species except only in the case of severe degradation, something that I would tag as representing a rather simple and perhaps unhealthy situation. Granted the onset of desertification would result in species reduction in fact right down to almost the vanishing point as one approaches desert-bound salt-domes in the south of Iran. Lack of water combined with the inimical effects of ionic contamination of the salt certainly presses species representation close to the vanishing point as I can attest. But, here is the question - it is still none the less a NATURAL environment. & as one moves outside of the central salt-dome core, things gradually improve. What little rain there is falls on desert that is not contaminated by salt so one sees vegetation appearing. Now the same rain-shower falls on the salt-dome but the salt sucks it up and discharges the water at the base of the dome in super-saline stream(s) sometimes many 100 parts per thousand. I found no life in such streams. No H' at all. But are the communities between this point and on past where rain eventually encourages growth in relatively salt-free sands "unhealthy"? Simple maybe and progressively becoming less so the further they are from the salt-dome proper & so much so that a trend can easily be demonstrated between soil salt content and ecosystem diversity (with distance/salt concentration) from the dome.. What I am asking here is just this: can the concept of "health" be applied along such a gradient? The gradient is stressful in extremeis granted, but there are still plenty of fish and seaweeds in the sea....How may we differentiate between simplification as resulting from a natural stress factor and the simplification we might wish to associate with a community in poor health? What is the operation difference between two such communities. Can the effects beholden to natural (chemical) stress be distinguished from the induction of effects due to a failure to uphold standards of health in a community? Or is it that these two effects owe their presence to some external environmental pressure that is just plain stressful to life as we encounter it? In that case drop the healthy-unhealthy axis because it does not seem to help much in furthering our understanding of ecosystem functioning.

Dear Giovanni.

Maybe I was not enough clear in my explanation. Shannon-Wiener index is not a health index, but a community structure complexity one. I would not use it for community or ecosystem health assessment but existing specific relevant indicators. However what I commented was that  a time series of decreasing Shannon-Wiener Index (or other diversity one)  would be probably indicating a situation of decreasing ecosystem or community heath.

With regard to the interesing Robins's answwer, I think that the identification or definition of a "healthy  ecosystem" is a relative one. I consider as healthy ecosystims those which varies due to natural factor, NOT to direct  human intervention  (pollution, deferestation, overfishing etc) or human induced ones  as for example the ongoing climate change, 

A healthy ecosystem is defined as being ‘stable and sustainable’; maintaining its organization and autonomy over time and its resilience to stress (Costanza, R. 1992: Toward an operational definition of ecosystem health). Assessment of these properties in large-scale systems is made through specific indicators of resilience, organization and vigor (see Mageau, M.T., Costanza, R. and Ulanowicz, R.E. 1995: The development and initial testing of a quantitative assessment of ecosystem health), Shannon-Wiener index is a community structure complexity index that could be used just to estimate the organization complexity but not for the overall assessment of health.

I fully agree. It is just what I tried to mean in my answers.  I only wanted to comment that biological diversity usually decrease when communities or ecosystems are stressed. I was not recommending to use Shannon-Wiener (diversity indices)  as health indicators. It is absurd and practically impossble  to  estimate Shannon.Wiener at the ecosystem level.

Quote: A healthy ecosystem is defined as being ‘stable and sustainable’; maintaining its organization and autonomy over time and its resilience to stress Unquote. This is a fine and laudable statement from an academic standpoint and I agree with it to a certain (limited) extent.

However, in the field,, at any instant in time we are faced with a time-slice - a certain picture thus emerges of distribution and abundance species-wise and from inspection point to inspection point this pattern changes.. There are no stable ecosystems only changing ones the idea of a stable representation is merely a convenient heuristic fiction - all is change - even healthy ecosystems are subject to this constant. So we need some way of measuring this change and some means of determining whether the observed change per time interval is part of the expected background shuffle that might be exhibited in a healthy ecosystem or whether a significant change has taken place such that it might be described as an "unhealthy" movement.

In my mind the protocol is relatively simple. Three successiveiy observed downward shifts in H' over a suitably comprehensive species array usually means the system is in trouble. If such a downtrend occurs over the time exceeding one average segment of reproductive life things are likely pretty grim. If this is also coupled with a relaxation of "organisation" (ie Hmax-H') then the system is really in trouble (the effects of competitive stress relaxing because an external force is knocking-off otherwise successful species etc etc) and so on. 

So, ok, that is the general picture but community-wise, how can we know exactly when an eco-system is about to tip-over? What are the irrefutable markers that may point to the immanence of such an event?

Dear All,

I think it is very useful to express the possibly diverging opinions on the use and interpretation of Shannon-Wiener or Shannon-Weaver but not Shannon-Weiner diversity index. I believe our experiences and the field we research may influence highly our opinions. I am afraid that the easily calculable Shannon-Wiener index (= SWI) was used often unnecessarily when the influencing factors were not considered. I think, not the index is imperfect but many cannot use it as it should be used. The health of an ecosystem is a too complicated notion and also its determination is changeable. I think the use of SWI alone in measuring such complex phenomenon can be restricted. I thank Giovanni, Robin and Pedro their comments helped me to better understand how ecologists consider the interpretation of this very popular index.

I ask the down-voter(s) to take part in the discussion and not anonymously attack the participants.

Thank you all for sharing valuable information.

What about other diversity indices?

Dear all,

I believe H' is a good index to track diversity changes, but this does not directly translate into ecosystem health. For that I prefer the use of indicator species instead of any diversity index, as their meaning is too much scattered and its practical use is limited.

Best!

In New Zealand the use of “indicator species” seems to have taken over completely. For freshwater fish this approach is represented by something called “The Fish Index of Biotic Integrity (Fish IBI) Joy and Henderson 2004. This index can certainly generate a useful metric since it is widely applied but it has several drawbacks the chief of which is formed by an apparent disbelief” in the existence of highly diverse native fish communities ie the discarded 5% (see later).

However, that may be it is also not a “clean” index in that introduced rainbow and brown trout have somehow acceded to the same level of “ecological desirability” as have native species ie brown and rainbow trout are counted-in with native species. However, the truth of the matter is that brown and rainbow trout are rather like clean-living, predatory, but edible forms of Pinus radiatea (a tree species imported from the Monterrey Peninsula and grown in New Zealand for its timber value) now widely considered a “pest” species.

The argument concerning the valuation of the index (fish IBI) is based on a reference to a (selected) sample-base which is further truncated by dismissing the most diverse records of native fish populations (top 5%) and then creating a mysterious biased weighting-factor dependant on equally apportioned 1/3 intervals of the remainder. Furthermore, all other exotic species that turn up in various samples are then “struck from the register”.

First the exclusion of the top 5% of the samples in respect of their diversity automatically tones-the index down – it caps maximal native ecological expression. Second the use of established samples as the sounding-board for the detection of change, being inherently circular, will not be at all sensitive at the limit and will eventually “wind-down” as time progresses. The introduced species are already saying something about the state of the aquatic environment; in truth they tell the whole story by themselves.

If introduced species succeed because they are able to better partition available trophic levels than native species what is the incurred ecological measurement penalty? The same sun continues to shine over the New Zealand lake and river systems therefore the same ecological carrying capacity exists now as in pre-colonial times. So, counting both native and exotic fish production per unit area/volume, this is surely much the same as it was in the pre-colonial era (excluding artificial injections of nutrients ie farm effluent).

What was happening prior to the invasion of European settlers that differs from now is that there were undoubtedly more native species in a given habitat, or, very much less likely about the same numbers of native species per location but maintaining higher standing populations. This latter scenario is highly unlikely but either way productivity would be much the same then as now. So a more informative index is simply to count the number of native species and form this into a ratio with respect to introduced species.

All introduced species poach energy from native species and that includes both rainbow and brown trout. We may here also use three versions of H'’: that can be calculated on the whole fish population, on native species alone and then on introduced species. Each time this is done there is also an Hmax so that Hmax-H'’ gives a measure of “organisation. Where organisation is high the population is in pretty good shape and where low the reverse is the case.

I agree with Onildo Marini-Filho, but its important to use them altogether to reflect the ecological status.

Shannon's index is a suitable character only for very sensitive groups (lichens, for instance). Many other groups  (Collembola, plants etc.) have the largest values of this index under weak or middle disturbance according to Connell's hypothesis of intermediate disturbance (Connell, J.H., Diversity in Tropical Rainforests and Coral

Reefs, Science, 1978, vol. 199, pp. 1302–1310). Such non-linear relation between diversity and disturbance creates many problems with assessment of health of  ecosystem.

Joe has that hypothesis, yes and there certainly are non-linear responses in H': but there are at least two elements to consider. First, in normal succession H' rises to a maximum and then as species sort themselves out H' gradually settles back to a  level which is characteristic of a climax association. Disturbed communities do not come in one flavour be it "weak", middle or otherwise because it depends on both the input of the disturbing factor(s) and on the developmental state of community succession that is targeted. Not only that but the frequency of the disturbing factor also has to be taken into account because any disturbing instance has the effect of knocking-back later stages of succession and thereby forcing them into earlier stages while still perhaps hanging onto elements belonging to those later stages. The point is that such forcing makes for high diversity intermediate stages - even higher than those which develop through the middle stages of undisturbed succession and, given any time period sufficient to allow succession to re-assert itself the diversity will once again move towards the "stable" climax state ie H' will fall. You can tell where you are at anywhere in this process because Hmax-H' will be very low when you observe the intermediate unstable (moving) states but very high as succession stabilizes towards the climax. H' by itself is equivalent to a measure of organisation (dominance) for a given number of possible states. Succession all the time ushers more such possible states into the message up to the moment all such states have been presented to the possibility of joining into the community, of finding a foot-hold. At a point no more useful footholds appear and then multi-species competition sets in in earnest and a stable climax community emerges characterised by very high Hmax-H', maximum information content for the community as a whole - from beginning to end. Those species thus excluded are sometimes called vagile or opportunistic but this is not a holistic viewpoint imho for they have played their role in providing the "forest giants" their opportunity for success.

yes I can say the Shannon-Weiner species diversity index be a good monitoring tool for assessment of health of any type of ecosystem.but this does not directly translate into ecosystem health. For that I prefer the use of indicator species instead of any diversity index, as their meaning is too much scattered and its practical use is limited. But this does not directly translate into ecosystem health. For that I prefer the use of indicator species instead of any diversity index, as their meaning is too much scattered and its practical use is limited (agree with Onildo Marini-Filho comments)