The US FWS uses the surrogate species concept for managing wildlife. It might be helpful for you.

There is no simple answer to this question.  With many Critically Endangered species their habitat is so compromised there is no option but to manage the species, since to restore the habitat is likely to take so long the species would be lost.  It is the experience of most long-term species projects that species conservation helps drive the restoration of ecosystems.

The comparison between species and habitat approaches is largely redundant since species work drives habitat restoration and often the rebuilding of ecosystems.

If you do not manage ecosystems, you will fail to protect the existing target species. Both are complementary approaches at their respective levels; ecosystem level and species level. The protection of many species fail because of not approaching their respective ecosystem in managament and planning. Take care of your house to protect your family..

It depends on the species and its primary threats, there is no universal solution. Many South East Asian species are primarily threatened by poaching ("Empty forest syndrome"), whereas many "reptiles" and amphibians from Madagascar can apparently cope with fairly high levels of collection (e.g. Golden mantella [Mantella aurantiaca]), while the loss of their often small habitat is the primary threat.

Based in our experience with the Endangered Puerto Rican Amazon, both approaches are very important. As H.M. Poulos mentioned, the USFWS is using a surrogate species concept. However as Pfleiderer says "It depends on the species and its primary threat..." In our case the species almost disappeared so early decisions were more endangered species approached. But when you are dealing with the public for example, it is more "palatable" in general when you use the Ecosystem approach, because you are "selling" a whole package, not just the protection of one species but of many natural resources that will benefit many (e.g. water sheds, fisheries, game, air quality, recreation, education, history, etc.) using an umbrella species. As Alcolado says "If you do not manage ecosystems, you will fail to protect the existing target species..." and all other resources.

Again, no obvious answer. Although I agree that both approaches are important, depending on the species, I would be more in favor of supporting sfforts towards an ecosystem (or ladscape) approach, as - at least in countries like the ones in Latin America - one of the more important causes of endangermente or extinction of species has to do with habitat disturbance. With always limited budgets, resources for conservation should be destined toward habitat conservation and connectivity reconstruction.

I am reading the first opinions above. I want to say somethings, related to Tabriz Region (climate of which, near Caspian Sea, is relatively near of Mediterranean climate). I was working many years with "dilemnas": what choices to do in different Mediterranean agrosystems. CAN I INTRODUCE OR NOT AN EXOTIC SPECIES (from other World Regions, such as South Africa or Australia, Chile, Argentina, Pakistan, micro-regions of Black Sea coast (Abkhazia, Russia), and with same climate or a climate more or less near of the Mediterranean one) of Hymenoptera Chalcidoidea, very useful for biological control of of the same pest of olive, citrus, rosaceous (stone trees or seed trees) orchards or the one of South French and Corsican wineyards. If this species, after release in culture, will risks to eliminate (also) an untargeted wild insect (living near culture of  Mediterranean  agrosystem, taxinomically classified near of the targeted insect)? If this exotic species is NOT ENOUGH EFFICIENT BECAUSE IT CANNOT BE ABLE TO SUPPRESS MORE THAN 50% OF INJURIES OF THE TARGETED PEST after relaese (Quantitative conclusion obtained by previously experimenting, under insectary climatic conditions)?  How to do? Each time,"I had in my brain": practicians in agriculture are favourable to diminish injuries of insect pests. Each time, I relaesed the chalcid species even though risk of success was estimated about 50% control (if the exotic species of chalid fly was specific parasitoid). I winned some times: pest injuries were lowering (sometimes up than 50%; for instance 70-80 % by chance). Of course, it was not sufficient for growers. So, I was searching a second useful chalcid species, which should have some luck to acclimate without attacking another untergeted wild species. Under Mediterranean climate, this second-exotic useful-species might obligatory be attacking another development stage of the pest. I obtained very good economical results in olive, citrus, apricot and peach  orchards. I failed in wineyards, almond and apple orchards.

I like Pedro's answer; both, evidently; maybe I could add that (endangered) plant species may occur in more than one ecosystem (example attached); in-situ species conservation may be more practical in one of the two.

In case of migratory animals using seasonal or diurnal habitats (in my profile: bear; elephant), one of the temporal habitats may be replaced by another (e.g. natural by sown or semi-natural pasture; grassland by crop field).

An interesting case of an alternative man-made ecosystem (rice paddy) for floodplain grassland and vice versa is attached.

Of course all our reasoning assumes we agree on how the ecosystem concept is made spatially explicit for our area of interest; in other words, the scale issue.   

Article Fine resolution distribution modelling of endemics in Majell...

Article Reduced Dependence of Crested Ibis on Winter-Flooded Rice Fi...

I recently completed some research in an ecosystem where they took this approach and the results were not good. Specifically, another threatened species and all and the species infrastructure (BMI) it depended on a prey collapsed. Furthermore, this threatened species will likely disappear as well in this ecosystem. Moreover, it is likely that the species they are managing this aquatic ecosystem for will not do well in the long term because they also rely on BMI as a food resource.

Animals

1. Critically endangered species, close to extinction or extinct in the wild (IUCN categories): vertebrates mainly mammals, reptiles, birds and amphibians when there are not enough specimen to maintain even one population in the nature: method: zoological gardens + gene banks

2. Critically endangered species, endangered species: habitat conservation + protection and monitoring each individuum (mainly mammales, birds)-

3. Endangered species, vulnerable species, near thretened species and species in data deficient categories (according to IUCN): habitat based approach.

4. Critically endangered species or close to extinction species if they are invertebrates: habitat based approach.

Plants:

1. Critically endangered species or close to extinction: habitat based approch +  botanical gardens + gene banks

2. Plants in all other categories: habitat based approach

Ecosystem approaches are often marketed as the ideal in that they conserve the whole system and hence save all of the component species.  However when working with threatened populations the system in which they occur is likely to already be disrupted.  The individual animal species may be challenged in its ability to find sufficient food, or protection against predators, safe breeding sites and an advantage over competitors.  It is when working with these individual species that one can start to identify the problems with the system and start correcting them.  This is why species work is so potent and driving ecosystem restoration. 

Like Johannes Pfleidere, I think it's depend of the context, the animal and the SCALE of your study.

At big scale (country) ecosystem approach would be efficient with fragmentation issue for exemple.

At local scale, species apporach could be efficient with population's sensibilisation or detection of the major local threat (poaching, collection, road, etc.).

With ecosystem approach you could protect many species "in one shoot", with species approach you use the umbrella or flagship species concept (still under strong debate (Possingham et al. 2002; Veríssimo et al. 2013)).

Possingham, H. P., Andelman, S. J., Burgman, M. A., Medellı́n, R. A., Master, L. L., & Keith, D. A., 2002. Limits to the use of threatened species lists. Trends in Ecology & Evolution 17: 503-507.

Veríssimo, D., Fraser, I., Girão, W., Campos, A. A., Smith, R. J., & MacMillan, D. C., 2013. Evaluating conservation flagships and flagship fleets. Conservation Letters, doi: 10.1111/conl.12070

Carl has hit the nail on head with his answers to this question. With endangered species, short-term management usually requires species-based approaches, but longer term conservation success requires an ecosystem approach addressing the needs of that species across its lifetime and that of subsequent generations.

In my opinion, the approach to manage and conserve an endangered species under today's general conditions, is a comprehensive strategy which includes in situ and ex situ activities and exercises both simultaneously and in synergy. Unfortunately, although obvious, in situ and ex situ programmes often proceed on separate trails, too often leaving ex situ as the last resource rather than consider it an 'insurance' to maintain genetically viable population(s). E.g. the Northern White rhino (Ceratotherium simum cottoni)  is virtually extinct, for lack of ex situ population, though habitat is available for possible reintroduction.

As already mentioned in several contributions to this question I also think there is no global answer: both attempts may lead to the wanted effect.

Sometimes, especially if you are lucky to work on an empathic species (i.e. Ailuropoda melanoleuca or  Tursiops truncatus etc.) a species-attempted approach will help to protect / restore  a complex habitat - in other situations it will surely be easier to convince people to protect an obviously rich habitat like a tropical reef  than to try to get them to be proud of some rare Holothuria sp. So, if you are looking for the most effective way, you will have to look at these factors and then decide…

Johannes, Attila, Simon and others already have pointed out multidimensional nature of this issue and indeed there is no universal answer to your question. Since they are all mainly focused to the animals, I would like to add just few words for small, though highly important organisms (at least in terrestrial ecosystems and freshwater habitats) - the fungi.

Like the mosses, fungi are predominantly best protected by protection measures aimed to their habitats though some species would require more efforts to gain effective protection. E.g. species that suffer from extinction risks might require the additional care by growing them in pure culture. Furthermore, edible species that are faced extinction or are in higher threat categories should be excluded from picking from natural populations by the legislation regulative. These species should be placed on market only if originate from cultures. The same is true for medicinal fungal species, typically used by traditional medicine. To date, there are quite a number of species that are driven to the verge of the extinction by over-exploitation in natural habitats. And the number is still growing. Of course, there are species that would require other kinds of measures..

Simon, I agree with all of your items. I just wanted to mention fungi in this respect (I am dealing with them for almost 30 years now) and to present just two examples where particular endangered fungal species should be considered in other ways than just managed in the frame of the habitat based approach. I did not want to write in too much details as those that may be interested in more information particularly related to fungi could always contact me.

Since you mentioned burning cycles in some grasslands, some fungi are indeed dependent on regular fires, the others would not at all live in such ecological conditions. There are many issues here that reflect the tremendous diversity of fungal life spectrum/strategies...

In our Red Book of Croatian Fungi (downloadable from my RG profile, sadly it is available to date only in Croatian) you can see a number of ecological groups of fungi with specific needs. Many require special way of management. E.g. grassland species that typically inhabit traditionally managed anthropogenic grasslands (like many species of Hygrocybe, Entoloma, Geoglossaceae and many others) may rapidly decrease and vanish under two types of unfavorable conditions simultaneously over a wide area: by natural process of vegetation succession occurring on abandoned grasslands and on the other hand by eutrophication through usage of artificial fertilizers. The similar situation occur with many fimicolous fungi that will rapidly decrease when traditional stock breeding is replaced by intensive mode where animals are kept indoors. Fungi specific to bogs should be also managed by special measures in wide European areas where climate changed unfavorably to these kind of habitats. Various fungal species that lives there should require specific protective measures that strongly depend on their autecology. A number of ECM fungi would hardly survive if corresponding forest types would be left to grow into virgin forests. Thus parallel ways of management is necessary to keep such species together with the others on the same larger locality in question . Etc etc.

All in all, the mycologists are here to study at least the most vulnerable and endangered species in a certain area to be able to decide upon specific measures in collaboration with the other subjects... What I want to say is that one can define much less number of ecological fungal groups that will embrace fair amount of total species (that are faced with any level of threat) than is the total number of species in question. Many of such groups could be thus satisfactory managed through adequate way of protection of their habitats. However, there will always be a fair number of those that will require special care.

species oriented variables are also part of ecosystem therefore ecosystem base approach for conservation of endangered species will be more appropriate.

This press release possibly of interest: http://www.hindustantimes.com/india-news/only-5-out-of-47-reserves-can-sustain-tiger-population-report/article1-1324207.aspx

Thanks so much for all who attempted to contribute in clarifying of my question.  

Hi, Simon;

I am now dealing with white-headed duck (Oxyura leucocephala) that is a migratory, globally endangered species and inbreed in a wetland where I am monitoring this population. It is well documented that nesting destruction by NATIVE rodents is basically a major threat for species. I am passionate to know whether we have permission to make a meaningful decrease in the rodent’s populations that may effect profoundly the ecosystem function or process and consequently negative effect on other taxa to conserve a migratory but globally species in this ecosystem.

I agree with the Simon Cropper. Remember that species respond differently to mangement interventions. While in the short term, it may be desirable to find a way to decrease the rodents, the long-term effects of that perspective-based decision could ultimately be to the detriment of the original objective. I'm all for the ecosystem-based approach. Invest more effort in evaluating functional roles as opposed to just numbers and indices. Be weary of quick-fix solutions. Agreeably, it takes time (which is not always on our side) to work through these complex issues. Often, only in hindsight, does the solution seem obvious. I hope you make headway in your research pursuits.

Species ARE part of ecosystem. 

Dr. Simon;

I would appreciate for your very comprehensive explanations. This work are being done in one of international wetland (Ramsar wetland site) named “Gori-gol” which is located in west northern of Iran, East Azerbaijan province and its area is about 120 ha. Every year, this wetland hosts frequently a very small population of white-headed duck near 20 individuals with about 4-6 breeding pairs. As already mentioned, the rodent populations of two species, black and brown rats, are major threat for nests. This fact is documented in some local reports in Persian language based on some frequently and independent observations. As you pointed out other issues such as genetic swamping (it is not probably a fact for this population like other populations specially European ones), using of fertilizers in farmlands which are based in its catchment and subsequent pollution problem i.e. eutrophication, natural predators like Marsh Harrier (Circus aeruginosus), unsustainable use of the meadow grass by local people, etc. are most likely reasons for making an uncertainty to its long-lasting future fate.

Dear Nader

Indeed, you are consdering mangiing  both at species and at ecosystem approach levels, as I proposed in my former answer. For me it is a basic necessary procedrure ,given than in most ecosystems, if not in all, both levels are impinging in species troubles.

It depends on the species, though ecosystem management approach would be ideal. By protecting the ecosystem, the species requirements (resources and mates) are conserved and accessible. It also promotes inter-species interactions, as no species lives in isolation.

Dear Dr. Simon;

Sorry that my acknowledgment takes late. I would appreciate for your valuable and interesting information. Your answer basically covers what I really would to pursue it. Thanks so much for everything.

There is often a mixture of approaches across disciplines. 

One of the primary questions to ask is whether the species decline is due to a biological issue such as low survivability at some stage of the demography; is it because of a lack of a portion of the niche space? (breeding/foraging grounds); is it because of human impacts unsustainable hunting or development?

because it is a wetland species, habitat management may be useful because it would address many of the issues simultaneously and also can partner with actions for protection or management of other species or resources at the same time.

I inserted a good wetland scale resource below.

http://www.nrcs.usda.gov/Internet/FSE_DOCUMENTS/nrcs142p2_016986.pdf

I agree with a lot of what has been said in this thread, regarding this being a multi-faceted question. One thing I am interested in doing is comparing impact assessment tools designed to either protect species (e.g. under the guiding principals of Species at Risk Act) or species habitat/ecosystem (e.g. under the guiding principals of Fisheries Act). When approaching this, I realize it is difficult to compare/evaluate the efficiency of multiple assessment tools when the outputs of said tools differ. I have also found it very difficult to find any insight in the literature. It seems very few have actually compared multiple impact assessment tools used to assess proposed development on species and/or the entire assemblage. Can you provide any suggestions here? Do you know of any techniques, other than a cost-benefit-analysis?

If the goal is to preserve one particular species, the questionis a difficult one. If, however, the goal is to preserve biodiversity, our efforts must focus increasingly at the ecosystem level because of the immense number of species, the majority of which are currently unknown. According to Franklin (1993), an ecosystem approach is the only way to conserve processes and habitats (such as forest canopies, belowground habitats, and hyporheic zones) that, with their constituent species, are poorly known. Continued concern with species i essential, however. Landscape-level issues also need much greater attention. Designing an appropriate system of habitat reserves is one landscape-level concern.

https://www.jstor.org/stable/1941820?seq=1#page_scan_tab_contents