Habitat scores

Habitat scores describes the quality within the sample, using a range of published indices and measures. These include indices for species often associated with coarse woody debris, exposed riverine sediments, coastal grazing marsh, calcareous grassland, acid mire, soft sock cliff, seepages and ancient trees (Index of Ecological Continuity). Some of the indices will be well known, e.g. the IEC/RIEC for assessing and comparing deadwood sites, and others, such as the Coastal Grazing Marsh Ditch Invertebrate Conservation Status Score, are less well known. A lot of this information was used to inform the Pantheon Habitat and resources page.

Acid mire fidelity score (Boyce, 2004)

This index uses only the extant invertebrate fauna of acid mires in England. It should be noted that the acid mire fidelity grade assigned to each species refers to its fidelity to the whole range of acid mire habitats.

  • Grade A = acid mire obligates: species that are exclusive inhabitants of acid mires, with almost all of their British records referring to these habitats.
  • Grade B = acid mire specialists: species that are primarily found in seepages and their margins, but which occasionally occur in other situations. Generally in excess of 75% of British records refer to these habitats.
  • Grade C = acid mire preferential: species found in other wetland habitats, but which nonetheless have a strong association with acid mires. Generally in excess of 50% of British records refer to these habitats.

For more information see: Boyce, D.C. (2004) A review of the invertebrate assemblage of acid mires. English Nature Research Report 592.

Calcareous grassland fidelity score (Alexander, 2003)

The following habitat fidelity classes are used:

  • High = species routinely recorded from calcareous grasslands. They may also be recorded to a greater or lesser degree from other open habitats on freely draining soils, but it is likely that they are mainly dependent on calcareous grasslands to sustain viable populations.
  • Moderate = species routinely recorded from calcareous grasslands, but also from semi-natural open habitats on freely-draining soils over all or part of their geographical area of distribution.
  • Low = species frequently recorded in numbers from calcareous grasslands, but predominantly associated with other types of open habitats over all their British area of distribution.

For more information see: Alexander, K.N.A. (2003) A review of the invertebrates associated with lowland calcareous grassland. English Nature Research Report 512.

Coarse woody debris fidelity score (Godfrey, 2003)

The term "coarse woody debris" (CWD) is used to denote the input of fallen trees and other woody matter into watercourses. CWD may consist of entire trees, root boles, trunks, logs, branches and other pieces of wood that can accumulate within river systems, either submerged or partially submerged in the water.

Details are provided of 147 species that are considered to be particularly associated with CWD, including those species that may benefit from changes in structure afforded by log jams and woody debris. The fidelity scores have been based on whether species are obligate or facultative, xylophagous species or non-xylophagous species that utilise CWD. A total of 15 obligate xylophages have been identified along with 3 possible obligate xylophages, 48 facultative xylophages, 33 probable xylophages and 30 non-xylophages. Further checking and tightening-up of the species within these categories is required. The fidelity classes are:

  • Fidelity score a = obligate xylophages
  • Fidelity score b = possible obligate xylophages
  • Fidelity score c = facultative xylophages
  • Fidelity score d = probable xylophages
  • Fidelity score e = non xylophages

For more information see: Godfrey, A. (2003) A review of the invertebrate interest of coarse woody debris in England. English Nature Research Report 513.

Coastal soft cliff fidelity score (Howe, 2002)

Howe (2002) summarised published data on soft cliff invertebrates in Wales and the UK in general to create the index. 105 species have an association with coastal soft cliffs in the UK. These are subdivided into:

  • Grade 1 = species which are restricted to coastal soft cliff in the UK and dependent, for at least some stage of their life cycle, on soft cliff habitats, and include species which have always been restricted to coastal soft cliff and others which were once more widespread but are now confined to this habitat.
  • Grade 2 = species where the majority of populations or the strongest populations occur on coastal soft cliff in the UK but they can also be found in other habitat types where extensive areas of bare ground and pioneer vegetation, or seepages and fen vegetation occur, such as sand dunes, dry sandy heathland, coastal grassland, sand or gravel pits, inland seepages and reed beds.
  • Grade 3 = species which are associated with coastal soft cliff in the UK, at least in some part of their geographic range, but also occur in a wide range of habitat types where the presence of bare ground, pioneer vegetation, seepages or fen vegetation is of fundamental importance for some of their life cycle.

For more information see: Howe, M.A. 2002. A Review of the Coastal Soft Cliff Resource in Wales, with particular reference to its Importance for Invertebrates. CCW Natural Science Report No. 02/5/1.

Exposed riverine sediments fidelity score - Coleoptera (Bates, 2005)

Exposed riverine sediments (ERS) occur within river systems at the juncture of the aquatic and terrestrial, and consist of poorly vegetated alluvial deposits of silts, sands and gravels, which are habitat for a wide range of rare and highly specialised beetles. The fidelity scores used in Pantheon originate from Bates 2005 (see link below) who worked in collaboration with Adrian Fowles, who had developed a previous set of scores.

The criteria for the inclusion as a fidelity 1 or 2 species were designed to include both species fairly fastidiously associated with ERS, and bare ground species for which ERS are very important habitats.Species with fidelity scores of 1 are more closely associated with ERS habitat than species with a fidelity of 2.

  • Fidelity score 1 = species dependent for at least some stage in their life cycle on bare or sparsely vegetated sediments on the banks of rivers. Some of these species may also inhabit exposed lacustrine sediments, particularly where wave action forms banks of sediment on lake shores, as these features are in many ways ecologically similar to riverine shoals.

  • Fidelity score 2 = species strongly associated with exposed riverine sediments for at least some stage of their life cycle, but also occurring in a wider range of habitat types, such as flushes, seepages, pond margins, etc., where the presence of bare sediment is of fundamental importance for some stage of their life cycle.

Species that are commonly found (sometimes in abundance) on ERS, but which are also often found in less open habitats, or in bare ground habitats well away from water, are not included because they could easily reflect the quality of adjoining habitats rather than ERS itself.

For more information see: Bates, A.J. 2005. The ecology and conservation of beetles (Coleoptera) living on exposed riverine sediments. PhD thesis, University of Birmingham.

Exposed riverine sediments fidelity score - Diptera (Drake, Godfrey, Hewitt & Parker, 2007)

The species listed under this fidelity scores have been derived from surveys of the Diptera of sandy exposed riverine sediments (ERS). Species surveyed were allocated to ERS fidelity classes:

  • Fidelity score 1: total fidelity (11 species)
  • Fidelity score 2: strong fidelity (20 species)
  • Fidelity score 3: moderate fidelity (54 species)

The two principal microhabitats sampled during the surveys were bare wet margins and drier, higher deposited material with sparse ruderal vegetation. Other micro-habitats that were sampled were more densely vegetated deposits or the actual river banks, any obvious variations in particle size (sand, pebbles, organic silt), position on large bars (upstream, edge, downstream, by backwater channels), and isolated ponds within the river’s channel.

The fidelity scores were first proposed based on on work in Devon (Bell, D., Sadler, J.P., and Drake, C.M. 2004. The invertebrate fauna of exposed riverine sediments in Devon: a survey report. Unpublished report to The Environment Agency and Devon County Council) and were subsequently expanded based on more extensive sampling of 18 rivers in England, Wales and Scotland (see link below).

For more information see: Drake, C.M., Godfrey, A., Hewitt, S.M., and Parker, J. 2007. Fly Assemblages of Sandy Exposed Riverine Sediment. Buglife.

Grazing marsh ditches: salinity index  (Palmer, Drake & Stewart, 2013)

Brackish grazing marsh systems are naturally poorer in species than freshwater systems, so this difference needs to be taken into account during site evaluation. As many grazing marshes are situated near the coast, their ditches often support invertebrates tolerant of salinity. Salt-tolerant invertebrate species that can be used as indicators of brackish conditions are given a score in this index, based on a scale of 0 (least tolerant of saline conditions) to 2 (dependent on at least mildly saline conditions).

It is important to note that this index is applicable only to ditches in coastal grazing marshes and floodplain grazing marshes near the coast, in England and Wales.

  • Score 0 - Freshwater species tolerant of only mildly brackish water. These are not routinely found more often in brackish than in fresh conditions, or close to the coast rather than inland.
  • Score 1 - Species tolerant of mildly brackish conditions. These are found more in brackish conditions than in completely fresh water, or near the coast more often than inland.
  • Score 2 - Species that are obligately dependent upon mild to moderately brackish conditions. These are absent from completely fresh water except as strays from nearby brackish sites.

For more information see: Palmer, M., Drake, M. and Stewart, N. (2013) A manual for the survey and evaluation of the aquatic plant and invertebrate assemblages of grazing marsh ditch systems Version 6. Buglife report.

Grazing marsh ditches: status score (Palmer, Drake & Stewart, 2013)

The scoring system used here allocates a score to each species according to its relative rarity, then calculates the average (equivalent to a Species Quality Index or SQI) for a sample. Each of the relevant species is given a Conservation Status score of 1 to 5, as follows:

  • Score 5: *Habitats Directive Annex II and/or IV; WCA Schedule 5; Red List CR, EN, VU (revised assessments); Red List E or V (unrevised lists)
  • Score 4: *Red List Rare (R in unrevised lists), DD or K; Near Threatened
  • Score 3: Nationally Scarce (NS, Nationally Notable Na and Nb)
  • Score 2: Local
  • Score 1: None of the above (common)

* Some of these are UK Biodiversity Action Plan priority species.

Where multiple categories apply to a species, the highest score is used, not the sum of the scores. The Conservation Status Score for a sample is obtained by adding together all the individual species scores, then dividing by the number of taxa recorded. Non-native taxa should not used when calculating this metric, and should be excluded from the sample you upload to Pantheon. Also, if a sample contains fewer than ten invertebrate taxa the SQI should not be calculated.

It is important to note that this score is applicable only to ditches in coastal grazing marshes and floodplain grazing marshes near the coast, in England and Wales.

For more information see: Palmer, M., Drake, M. and Stewart, N. (2013) A manual for the survey and evaluation of the aquatic plant and invertebrate assemblages of grazing marsh ditch systems Version 6. Buglife report.

Index of Ecological Continuity (Original) (Harding & Rose, 1986)

The Index of Ecological Continuity (IEC) original index is based on a listing of the species thought likely to be the remnants of the saproxylic beetle assemblage of Britain’s post-glacial wildwood, and which have survived through a history of wood pasture management systems in certain refugia. The list was published in 1986 and is based on the presence or absence of a select list of beetle species. The original list scores 188 of 695 listed British native saproxylic beetles. The list was revised in 2004 (see below).

The species are graded according to their degree of association with Britain’s remaining areas of old growth – mainly the old wood pastures and historic parklands - and these grades are used as the basis for a scoring system. The total of these scores provides the index. Note that Pantheon displays and uses the Score number (not the Group number) in order to calculate the IEC.

  • Group 1: Species which are known to have occurred in recent times only in areas believed to be ancient woodland, mainly pasture-woodland. Score = 3
  • Group 2: Species which occur mainly in areas believed to be ancient woodland with abundant dead-wood habitats, but which also appear to have been recorded from areas that may not be ancient woodland or for which the locality data are imprecise. Score = 2
  • Group 3: Species which occur widely in wooded land, but which are collectively characteristic of ancient woodland with dead-wood habitats. Score = 1

For more information see: Harding, P.T., and Rose, F. 1986. Pasture-woodlands in Lowland Britain - A review of their importance for wildlife conservation. Institute of Terrestrial Ecology.

Index of Ecological Continuity (Revised) (Alexander, 2004)

The Index of Ecological Continuity (Revised) is based on the listing of the species in the IEC. The list was updated - involving deletions, additions, upgrades and downgrades - to provide a more reliable statement of the range of saproxylic beetles which might be expected on a site with relatively good ecological continuity. The revised list scores 180 of 695 listed British native saproxylic beetles. The scores are the same as those defined in the IEC (Original) (see above).

Both the original and revised IEC scores are returned to maintain audit purposes, so that changes in site score can be related back to individual species assessments.

For more information see: Alexander, K.N.A. 2004. Revision of the Index of Ecological Continuity as used for saproxylic beetles. English Nature Research Report 574.

Seepage fidelity score (Boyce, 2002)

Seepages are very small, flowing waterbodies. They are characterised by generally slow rates of flow, and by being extremely shallow, sometimes no more than a film of water over the substrate. This means that they are most often associated with the uppermost sections of waterbodies, being transitional to streams and rivers as they gather water lower in the catchment. They are also very often derived from springs.

The seepage fidelity scores originate from a review of the invertebrate fauna of seepage systems in England (Boyce 2002). Five main types of seepage habitat have been identified in England: slumping cliff seepages; stable cliff seepages; woodland seepages; acid-neutral seepages; calcareous seepages.

Invertebrates showing a strong fidelity for seepages are categorised as obligates, specialists or generalists:

  • Grade A – seepage obligates: species that are exclusive inhabitants of seepages and their margins, with almost all of their British records referring to these habitats.
  • Grade B – seepage specialists: species that are primarily found in seepages and their margins, but which occasionally occur in other situations. Generally in excess of 75% of British records refer to these habitats.
  • Grade C – seepage associates: species found in and around other types of running and shallow water, but which nonetheless have a strong association with seepages and their margins. Generally in excess of 50% of British records refer to these habitats.

Pantheon presents separate fidelity grades for each of the five seepage habitat types, to highlight links between the species and the different habitat types, but it should be noted that the fidelity grade assigned to each species refers to its fidelity to seepages as a whole, rather than to any individual seepage habitat type. This is because a number of the invertebrates graded are found in more than one of the seepage habitats discussed.

For more information see: Boyce, D.C. 2002. A review of seepage invertebrates in England. English Nature Research Report 452.

Western peat bog indicators - spiders (Scott, Oxford & Selden, 2006)

This lists 71 spiders showing a high measure of naturalness from western peat bog systems, under conditions where good peatland naturalness occurs when their naturalness measure >0.5, the Spider SQI >1.8, and with sampling rules applied. The database returns a count of those matching species from the list in the sample. It is unclear how eastern bogs fare under this measure, and there is currently little overall context for it, so it should be used cautiously.

Pantheon returns a score that is simply the total number of species in a sample that are listed as indicator species.

For more information see: Scott, A.G., Oxford, G.S., Selden, P.A. 2006. Epigeic spiders as ecological indicators of conservation value for peat bogs, Biological Conservation, Vol. 127(4): 420–428.

Wadden Sea Saltmarsh fidelity index

This is a 3 class index tracking the fidelity of saltmarsh invertebrates in a sample. It ranges from Hal-1 for very high fidelity species to Hal-3 which are species which can be found on saltmarshes but also several other wetland habitats. The index is North European Seaboard and is part of the wider Wadden Sea trilateral nature conservation initiative between Denmark, Germany, and the Netherlands. The index is mostly spiders, beetles, and flies. The overlap with the UK fauna is high; saltmarshes on the Atlantic seaboard might experience some additional species drop-off. Its main use might be in tracking the success of coastal re-alignment and fallback schemes, as well as demonstrating inherent value between saltmarshes.

“The Wadden Sea, Germany and Netherlands (N1314) - Extension Denmark and Germany, - Volume Two -ANNEXES. Annex 3 List of endemic salt marsh species. The table below lists 271 endemic species in the saltmarshes of the nominated property. A selection of a bibliography in English language with regard to the endemites is given for further information.”


Conservation Community Index (CCI)

As Chadd & Extence note in their 2004 paper “Unlike other summary expressions of conservation value, the Community Conservation Index (CCI) accounts for community richness in the final analysis, as well as the relative rarity of species present.”

It is thus an important addition to Pantheon’s analytical suite. Aquatic & riparian species are ascribed a Conservation Score, based on their conservation status. It should be noted that at this time, the subsequent revisions of those conservation concern status scores are not reflected in this build of the CCI, nor is the ability to locally tweak CCI scores on a regional basis.

As with many other indices of this sort, the species Conservation Scores are summed, and the total divided by the number of contributing species. This overall figure is then multiplied by the Community Score (CoS) which is derived from a lookup table founded on the rarest taxon’s score present in the community (CSmax). In this build of CCI we have used CSmax rather than the biological monitoring working party (BMWP) metric, as the latter involves calculation of that BMWP index to arrive at a CCI value. Users should be mindful of these issues when deploying the CCI.

Chadd, R. & Extence, C. 2004. The conservation of freshwater macroinvertebrate populations: A community-based classification scheme. Aquatic Conservation: Marine and Freshwater Ecosystems 14: 597–624 (2004). https://doi.org/10.1002/aqc.630