Table 4. Key messages from semi-structured interviews.

Theme	Key message	Example quotations
Topic 1: Main features of habitat quality
1.a) Combination of features	Habitat quality is viewed in terms of vegetation composition, but also more holistically as the result of a combination of features, including habitat structure and physical attributes such as water table dynamics.	“Species composition would be the most obvious one, both in terms of species that are there and species that aren’t, relative proportions of those species… And broadly, the impacts of land management …” I4 Heaths, Wetlands, Grasslands
1.b) Habitat structure	Structural and functional aspects of habitats, such as water quality and quantity, surface topography, and management impacts, are highly important for wetlands in the assessment of habitat quality, but may also be of increasing importance in the future for other habitats.	“…it comes back to the functionality of the habitat. If the habitat isn’t functioning and in three dimensional way, just a two dimensional approach to looking at it, then you will end up where you just have species disappearing, because you’re not taking into account the dynamism of that habitat” I2 Wetlands
1.c) Vegetation composition and structure	Vegetation, both in terms of composition and structure, is the dominant factor in habitat quality assessment for grasslands and heathlands. Species assemblages are typically more important for habitat quality assessment than individual species, although both can act as a proxy for environmental conditions.	“The [vegetation] structure is one of the important things. …So we don’t want to see the whole site very homogeneous looking, mature or degenerate, but a diversity of the stages.” I13 Heaths; “If it's unique …that adds to your conservation value.” I8 Grasslands; “Generally [we’re] not looking for specific species, looking more for diversity of a certain level.” I1 Grasslands
1.d) Geographical and temporal variability	Habitat quality assessment may need to reflect geographical differences in condition–whether caused naturally or by historical anthropogenic causes–as well as the temporally dynamic changes that may occur in a habitat.	“There would obviously be altitudinal, geographical, bio-geographical differences as well.” I4 Heaths, Wetlands, Grasslands; “It will have to quite flexible within that to take into account local variation … the way we look is not flexible enough, it’s too rigid, it’s not dynamic–habitats are dynamic.” I2 Wetlands
1.e) Ecosystem services	Ecosystem services, such as water and climate regulation, have the potential be included as an additional factor to biodiversity conservation objectives in habitat quality assessments.	“If you’re faced with choices…I would prefer that that total resource had the capacity to deliver a number of key services, of which biodiversity is not necessarily the most important. If I’m looking at individual sites then the biodiversity is important in that it is part of the value of that site to society. But I wouldn’t expect all bog or peatlands to have that.” I3 Wetlands
1.f) Applicability and practicality	The Common Standards Monitoring guidance acts as the key framework for much of the habitat quality assessment; however, tailoring of CSM indicator-species lists has improved local applicability and practicality for use by local monitoring officers.	“When the JNCC Common Standards were published we wrote our own …translation of it, just added a bit more flesh to the bones really, and perhaps made it a little bit less generic.” I6 Wetlands
Topic 2: Value of individual species
2.a) Structural and functional species	Species that are structurally or functionally important have particular value, especially in wetland habitats. They may have increasing relevance to other habitats in the face of climate change.	“We see Sphagnum as a priority for the accumulation of peat, basically.” I11b Wetlands; “So a priority for us is that with climate warming we’re trying to get bogs to function naturally so they are then more resilient to warming” I11b Wetlands
2.b) Scarce species	Scarce species provide added value to a habitat, and can be important for site designation. However, they are not usually a dominant criterion for assessing habitat quality, in part because they do not occur on enough sites to be widely applicable as indicators.	“… we tried to avoid things which were not particularly common or quite rare, because although they might be telling you that where they occur that that’s an absolutely perfect site, because the hydrology of the soils or whatever is right, they are not very useful in terms of an overall assessment of the condition of a site.” I10 Grasslands
2.c) Invasive species	Invasive species, whether native or non-native, are generally considered negative when they out-compete or cause other detrimental impacts to valued native species, rather than being considered negative per se. Feasibility of removal, and whether invasion is a natural part of range expansion, are also taken into consideration.	“…what is wrong about alien species? The thing that’s wrong about them is that they can become invasive and take over from native vegetation. So if they are doing that then that’s bad, but if they are not, they’re just there at very low cover, then from a vegetation point of view I don’t think you’d worry.” I8 Grasslands
2.d) Historical context	The historical context of a habitat or a particular site can influence the management goals with regards to species assemblage, potentially resulting in over-valuing or undervaluing species.	“I can think of heathlands in this area, lowland heathland, where we now have very scarce species, but they could be historically quite widespread…. Things like Viola lactea … those kind of species, which are associated with a certain set of structures within the heathland. So scarce species can be important because they are actually typical.” I5 Heaths
2.e) Comparative values of species	Valuing some species more highly than others has challenges and potential conflicts, for example over which species to conserve.	“The public view of grasslands is not necessarily our view of grasslands.” I1 Grasslands
Topic 3: Plant & lichen indicator-species
3.a) Characteristics of positive indicator-species	Criteria for selecting positive plant and lichen indicators include being distinctive for the habitat, typical for the habitat, or indicating good environmental conditions.	“I suppose we are looking for those particular species which are niche species of that particular habitat” I2 Wetlands; “I mean, basically we tried to select those species that are really indicative in telling you the conditions are right for the maintenance of that grassland…” I10 Grasslands
3.b) Characteristics of negative indicator-species	Negative indicator-species are typically those that out-compete desirable native species, but they also may be those that indicate poor environmental conditions such as heavy grazing and eutrophication. Some species may become negative indicators if they cause ecosystem disbenefits.	“The worst negative indicators are the ones that take up most space. And then species that react to high nutrient levels. . . So it’s species that take up space at the expense of a greater variety of non-competitive things.” I1 Grasslands; “Eriophorum vaginatum is one of these species that transports methane to the atmosphere. So the fact that we know that it’s shunting all this methane up into the atmosphere at the moment is maybe not quite so good.”I3 Wetlands
3.c) Context of indicator-species	The use of species-indicators can be complex and requires flexibility to take into account variation in geographical factors (including scale and altitude), natural habitat variation, and other factors such as past management.	“I think the subshrub depends on where you are, what your soils are, and to a certain extent, past management.” I5 Heaths
Topic 4: Taxa other than plants and lichens
4.a) Importance of other taxa	Plants and lichens are typically considered more useful for the assessment of habitat quality than other taxa. However, other taxa can be an important feature for site designation, in which case the species will typically be monitored by specialists in those taxa rather than as part of routine habitat quality assessment.	“If it’s an SSSI and it’s designated for the habitat and also the birds or invertebrates, then somebody would look at the population trends or there will be some monitoring of other species, but I, or the training I give to the advisors, doesn’t include directly the invertebrates or birds. But they are very important.” I13 Heaths
4.b) Management conflicts	In some cases other taxa require management conditions that are not compatible with high habitat quality; however these different requirements can normally be accommodated, particularly on larger sites.	“Golden plover and blanket bog is probably the classic example … the issue would be some of the sites where golden plover is a feature, as well as the blanket bog, and to manage the blanket bog for the golden plover would effectively render it unfavourable as far as blanket bog condition is concerned.” I9 Wetlands
4.c) Barriers to using other taxa	There are a number of barriers to using other taxa in habitat quality assessment, including limitations in resources, time, skill, knowledge of species’ autecology, and consistency of sightings.	“… you are dependent on the weather conditions when you go out, it’s very much on what we see, so I think all these species they are important but it would be very difficult to record them on a consistent basis”. I1 Grasslands
4.d) Proxy indicators for suitability of other taxa	The quality of a habitat with respect to other taxa may be inferred through using environmental conditions, such as habitat structure and vegetation composition, as a proxy.	“Our role is as habitat specialists. And we look at structure, so we look at the height of vegetation, and we look at the ages of ericoids, and we look at bare ground, so you look at elements of the habitat that invertebrates or reptiles might find useful or interesting. But our colleagues would be expected to pick that up.” I11a Heaths, Wetlands, Grasslands
Topic 5: Species-groups
5.a) Pros and cons of using species-groups	Assessing cover of species-groups can be a useful tool for inferring habitat quality. However, species-groups may not always provide the level of detail necessary, for example for rare subcommunities or as a proxy for environmental conditions.	“…it’s actually quite a useful check that you’ve made your original estimation quite good” I9 Wetlands, Heaths; “…we would definitely be thinking about the amount of Arctostaphylos that there is in those examples of the habitat, rather than just covering dwarf shrubs” I4 Heaths
5.b) Identifying useful species-groups	Cover of species-groups can be useful in habitat quality assessment, such as forbs and grasses for grasslands; dwarf shrubs, graminoids, mosses and lichens for heathlands; and mosses for wetlands, but a group such as ‘graminoids’ can include negative and positive indicator-species.	“You could go just in terms of groups if you don’t want a full list, which will change a lot from site to site, so just looking at ericoids, graminoids, forbs and yeah non vascular species like mosses, that grouping could be useful.” I13 Heaths
Topic 6: Reference communities
6.a) Defining a reference community	There is considerable variation in the examples of each habitat that are seen as high quality, so it would be very difficult to define a reference community.	“…as soon as you start thinking about a reference community, you start thinking, well, there are all these exceptions.” I4 Heaths, Wetlands; “. . .we want a broader view than that, so I don’t quite like NVC held up as an example of what a grassland should be.” I1 Grasslands
6.b) Potential reference community definitions	The NVC tables, or past records where these exist, could be used to define a reference community at site level, or a set of reference communities covering the variation in high-quality habitat.	“I think the NVC is probably the closest you’re going to get to have something that we all agree on that is relatively close to that single reference point, but around it there needs to be that grey area of a little bit of flexibility as well. . .” I2 Wetlands; “If you actually had old records for the site and could go back and compare, that would be very useful…but impractical.” I1 Grasslands