Outcome Indicator Framework for England's 25 Year Environment Plan: 2021 - Defra, UK

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Outcome Indicator Framework for England's 25 Year Environment Plan: 2021 - Defra, UK
Outcome Indicator Framework for
England's 25 Year Environment
Plan: 2021
This document supports
D6a: Abundance of priority species in England
D6b: Distribution of priority species in England

Technical background document

Date: May 2021

Prepared by: Fiona Burns (RSPB); and Rob Boyd, Rob Cooke and Nick
Isaac (UKCEH)
We are the Department for Environment, Food and Rural Affairs. We’re responsible
for improving and protecting the environment, growing the green economy and
supporting our world-class food, farming and fishing industries.

We work closely with our 33 agencies and arm’s length bodies on our ambition to
make our air purer, our water cleaner, our land greener and our food more
sustainable. Our mission is to restore and enhance the environment for the next
generation, and to leave the environment in a better state than we found it.

© Crown copyright 2020
This information is licensed under the Open Government Licence v3.0. To view this
licence, visit www.nationalarchives.gov.uk/doc/open-government-licence/

This publication is available at www.gov.uk/government/publications

Any enquiries regarding this publication should be sent to us at
25YEPindicators@defra.gov.uk

www.gov.uk/defra
Contents

1. Introduction ............................................................................................................ 4

2. D6a: Abundance of priority species in England ...................................................... 4

   2.2. Species List...................................................................................................... 4

   2.3. Data Sources ................................................................................................... 5

   2.4. Indicator Methods .......................................................................................... 14

   2.5. The D6a Indicator .......................................................................................... 15

3. D6b Distribution of priority species in England ..................................................... 18

   3.1. Species List.................................................................................................... 18

   3.2. Data Sources ................................................................................................. 18

   3.3. Indicator Methods .......................................................................................... 21

   3.4. The D6b Indicator .......................................................................................... 21

4. References ........................................................................................................... 22
D6. Abundance and distribution of
priority species in England
Technical background document, 2021

1. Introduction
In 2018 the government published its 25 year environment plan for England: A
collection of goals for improving the environment in England. A key commitment of
this plan was to develop a set of indicators for monitoring progress towards these
goals, and a framework for these indicators has now been established. The Outcome
Indicator Framework comprises 66 indicators, split into 10 broad themes, spanning a
range of issues from greenhouse gas emissions to the abundance of threatened
species.

This paper presents robust indicators of the status (abundance and distribution) of
priority species in England, with species identified as conservation priorities being
taken as a proxy for threatened species. Despite the relatively high quality and
quantity of both data and analytical methods in the England, it should be recognised
from the outset that any indicator on the status of priority species will be hampered
by short comings in the availability of data.

2. D6a: Abundance of priority species in
England

2.2. Species List
The species considered for inclusion in the England Priority Species Indicator are
those on the S41 list. Species on the S41 list are those on the 2007 UK Biodiversity
Action Plan list that are present in England with the addition of Hen Harrier. There
are a small number of taxa below the species level (i.e., sub-species) on the S41
lists. Such infra-specific taxa were only retained if the associated species was not
included. This led to the removal of three sub-species and reduced the total taxa on
the S41 list from 943 to 940. However, not all species on that list have suitable data
available. The species in D6a are those species for which annual estimates of
abundance are available, derived from national-scale monitoring schemes.
2.3. Data Sources
Robust English population time-series were sought for as many priority species as
possible to produce the England Priority Species Indicator – D6a. The majority of
these data have previously been published and many are used as part of the
England biodiversity indicator set currently; details of these analyses and the rules
for species inclusion into the data sets are given in the following sections. Table 1
summarises the taxonomic coverage and data sources contributing to D6a.

Tables 2 and 3 provide a summary of the abundance datasets included in the
indicators. They show the analytical methods used to generate the species’ time-
series in each dataset. Although these vary in detail, the underlying method is
similar. These datasets are generated largely from data collected by national
monitoring schemes. In these schemes, data are collected in a robust and consistent
manner and the geographical coverage is good, with statistical approaches used to
correct for biases in coverage. These datasets are ideal for producing population
time-series for widespread species; however, in some cases the sample size is
insufficient to generate time-series for cryptic, rarer or more range-restricted species.
Each scheme has a set of criteria to determine whether time-series can be
generated for each species and if they are sufficiently robust to be included in the
published results of the scheme. Table 4 gives an overview of the quality of the data
derived from each scheme. Further information about each monitoring scheme and
the data analysis and results can be found in the references given at the end of this
paper.

Bird time-series are well documented, and several data sources are available (Table
3). Some bird species are represented in more than one dataset. The order of the
rows in Table 3 shows the hierarchy used, from top to bottom, to ensure that the
most appropriate and robust data for each species was included in the indicator.

The majority of species time-series start around 1970 and the date of the last
available update is 2018. The Rothamsted Insect Survey started in 1968, but to
avoid over representing these time-series in the overall indicator, data were only
used from 1970 onwards, and the time-series were expressed as a proportion of the
1970 value. Some datasets begin later than 1970, for example the butterfly time-
series begin in 1976. However, the indicator method used is robust to the addition of
species groups after the baseline year (see section 4).

Table 4 highlights the robustness of the data obtained from the monitoring schemes,
and Table 5 gives a summary of the relationship between the number of species on
the S41 list and the number of these for which population time-series are available.
Table 1: Taxonomic breakdown of the England Priority Species Indicator D6a

 Group       Survey                                Species From        To

 Birds       England breeding bird indicators      28         1970     2018

             England wintering waterbird           6          1973     2017
             indicator

             Rare breeding bird panel              5          1981     2016

             Seabird monitoring programme          4          1975     2017

             SCARABBS                              1          1994     2018

             TOTAL                                 44         1970     2018

 Butterflies UK Butterfly Monitoring Scheme        21         1976     2018

 Mammals     National Bat Monitoring Programme     5          1998     2018

             Breeding Bird Survey                  1          1998     2018

             TOTAL                                 6          1998     2018

 Moths       Rothamsted Insect Survey              69         1970     2016

             Priority moths – Butterfly            9          1991     2016
             Conservation

             TOTAL                                 78         1970     2016

 TOTAL                                             149
Table 2: Summary of the analysis methods and criteria for species selection for bird datasets

 Monitoring          Time        Data Type      Species selection method                           Analysis method
 Scheme              period

 Seabird             1986-       Unsmoothed Very small colonies and colonies where                 For the majority of species, a
 Monitoring Panel    2018        index      counting error is known, or suspected, to              combination of SMP and census
 (SMP) and                                  exceed 5% are excluded from SMP time-                  data is used. The 2 census
 Seabird                                    series. The accuracy of time-series obtained           estimates are used, with linear
 censuses                                   using the SMP sample was assessed by                   interpolation for the intervening
                                            comparing them with data from 2 complete               years. The SMP time-series is
                                            censuses of all breeding seabirds in the UK. A         anchored to the 2nd census
                                            time-series was rejected as inaccurate where a         estimate and used in all
                                            discrepancy of more than 15% occurred                  subsequent years. For a small
                                            between the SMP estimate and the census                number of species, the census
                                            figure (Thompson et al. 1997).                         data alone is used.

 Time-series used    Various     Unsmoothed                                                        Various, depending on the original
 in England                      index                                                             dataset, all those used are
 breeding bird                                                                                     described below
 indicators

 Statutory           Various     Population     These surveys are designed to be in depth          Linear interpolation was used to
 Conservation                    estimates      surveys for a particular species and so have       estimate annual values for years
 Agency and                      from 2 or      sufficient data to allow population trends to be   between national surveys.
 RSPB Annual                     more           robustly estimated.
 Breeding Bird
Scheme                       national
(SCARABBS)                   surveys

Common Bird        1970-     Unsmoothed                                                     Unsmoothed population time-
Census/Breeding 2018         index                                                          series were generated from a log-
Bird Survey                                                                                 link linear regression with Poisson
(BBS) joint trends                                                                          errors fitted to site x year data
                                                                                            (BTO 2014a).

Breeding Bird     1995-      Unsmoothed Data from the BBS surveys were only included        Unsmoothed time-series are
Survey (BBS)      2018       index      for species for which the BBS methodology is        estimated using a similar
                                        appropriate, and which are recorded in on at        procedure to the CBC/BBS joint
                                        least 30 BBS squares per year of the survey         trends described (BTO 2014a).
                                        period.

Rare Breeding     Various,   Annual       Species were removed where survey effort          Linear interpolation was used to
Birds Panel       ~1970 -    estimate     was thought insufficient to generate a reliable   estimate any missing data.
(RBBP)            2017                    trend. Additionally, species where individuals
                                          were only infrequently present in the UK (taken
                                          as species where the maximum count was 10
                                          or less and the median was three or less),
                                          were removed.

England           1968-      Unsmoothed Derived from the Wetland Bird Survey (WeBS). As for BBS time-series
Wintering         2017       index      For core species observers record quality of
Waterbird                               visit (visibility, areas missed) and poor-quality
indicator                               site visits are excluded. Only sites with a good
level of coverage are used (≥ 50% of possible
                                               visits undertaken) Further details of analytical
                                               methods are published (BTO 2017; Maclean &
                                               Ausden 2006).

Table 3: Summary of the analysis methods and criteria for species selection for other taxonomic groups

 Group     Dataset and     Time period     Species selection method                  Analysis method
           provider        and Data
                           Type

 Moths     English moth    1968-2016,      Data for 766 moth species were            The Generalised Abundance Index (GAI)
           trends from     TRIM annual     analysed using data from Rothamsted       methodology proposed by Dennis et al. (2006)
           Rothamsted      index.          Insect Survey light trap network          was used to produce English abundance
           Insect Survey                   (Harrower et al. 2019). The 766           trends. This methodology involves estimation
           light trap                      species that were analysed are mostly     of standardised annual flight periods curves for
           network                         macro-moths as the majority of micro-     each species. These flight curves are used to
           (1968 to                        moths had to be excluded due to           estimate the annual total abundance for each
           2016)                           inconsistencies in their recording over   site whilst correcting for gaps in the surveying.
                                           the time period. Of the species           Poisson regression models, with site and year
                                           analysed 423 species produced             explanatory variables, are then fitted to the
                                           reliable trends based on expert           estimated annual total abundance values to
                                           assessment of the underlying data and     determine the abundance trends and also
                                           the analysis results.                     yearly abundance indices. Confidence intervals
                                                                                     were produced by bootstrapping (1,000
                                                                                     samples).
Moths    Butterfly      ~2000-2016.   Expert opinion (Mark Parsons –             Site x year Log-linear Poisson regression
         Conservation   TRIM annual   Butterfly Conservation) was used to        models in TRIM (Pannekoek and van Strien
                        index.        judge whether the number of sites          1996) were used.
                                      monitored was sufficient to represent
                                      the national time-series, given each
                                      species’ distribution.

Bats     National Bat   1997-2018     A power analysis determined that           As BBS time-series (Barlow et al. 2015). In
         Monitoring     Unsmoothed    across all surveys, a sample size of       addition, mixed models are used to investigate
         Programme      index.        30-40 repeat sites (surveyed for more      factors that could influence time-series (e.g.,
         (Bat                         than one year) would give sufficient       bat detector make, temperature). Over
         Conservation                 data to calculate robust species time-     dispersion is a problem for bat detector
         Trust)                       series. This would provide 90% power       surveys, where a single bat repeatedly flying
                                      to detect a decline of 25% over 25         past the observer may give rise to a large
                                      years (0.1 sig. level). Borderline cases   count of bat passes. Based on the results of
                                      are judged based on the quality of the     simulations a binomial model of the proportion
                                      time-series, primarily from the            of observation points on each survey where the
                                      confidence limits (Walsh et al. 2001,      species was observed is used.
                                      Bat Conservation Trust 2013).

Terrestri Breeding Bird Unsmoothed    Data from the BBS surveys were only        Unsmoothed time-series are estimated using a
al        Survey (BTO) index          included for species for which the BBS     similar procedure to the CBC/BBS joint trends
Mamma                                 methodology is appropriate, and which      described (BTO 2014a).
ls                                    are recorded in on average 30 BBS
                                      squares per year of the survey period.
Table 4: Assessment of robustness of monitoring schemes (based on a 2013 assessment at a UK scale) – Data quality = Red >
Orange > Blue

 Group      Dataset                                  ~Effort       Survey design                           Field method

 Moths      Rothamsted moth survey (1968-)           80            Consistent, Non-random                  Light trap

 Butterflies Wider countryside butterfly survey      750           Consistent, Random                      Transect
             (2007-)

            UK butterfly monitoring scheme (1976-) 1,000           Consistent, Non- random                 Transect

 Mammals National Dormouse Survey (1993-)            300           Consistent, Known sites                 Nest box search

            Breeding bird survey (1995-)             2,400         Consistent, Random                      Transect

            National Bat monitoring program          1,300         Consistent, Random                      Various, field/ roost
            (1997-)                                                                                        counts

            Mammals on Roads (2001-)                 500           Consistent, Random                      Transect

 Birds      Breeding bird survey (1995-)             3,200         Consistent, Random                      Transect

            Common bird census (1970-2000)           300           Consistent, Non-random                  Territory mapping
Seabird monitoring programme, (1986   Species    Consistent, Non-random or Total          Colony counts
-) seabird censuses (1969, 85, 00)    specific

Wetland bird survey (1970-)           3,000      Consistent, Non-random (or almost        Site counts
                                                 total for some species)

Rare birds breeding panel (1970-)     Species    Some variation over time, all or most    Site counts and
                                      specific   known sites                              individual records

SCARABBS (1974-)                      Species    Consistent, stratified random, bespoke   Various, transects
                                      specific   for species
Table 5: Summary of species included in the Abundance of Priority Species Indicator – D6a

 Higher group      Group                  Species on        Species on S41 with
                                          S41               data

 Vertebrates       Amphibians             4

                   Birds                  49                44

                   Fish                   48

                   Mammals                34                6

                   Reptiles               8

 Invertebrates     Beetles                75

                   Butterflies            23                21

                   Dragonflies            2

                   Hymenoptera            31

                   Moths                  142               78

                   True bugs              10

                   True flies             28

                   Riverflies             7

                   Other insects          4

                   Other Invertebrates    76

 Plants            Vascular plants        149

                   Bryophytes             77

 Chromists         Algae                  15
Fungi              Fungi                  64

                    Lichens                94

 Total                                     940               149

2.4. Indicator Methods
To create the composite index, a hierarchical modelling method for calculating multi-
species indicators within a state-space formulation was used (Freeman et al. 2020). This
method offers some advantages over the more traditional geometric mean method: it is
robust, precise, adaptable to different data types and can cope with the issues often
presented by biological monitoring data, such as varying start dates of datasets, missing
values and zero counts. The resulting index is an estimate of the geometric mean
abundance, set to a value of 100 in the start year (the baseline). Changes subsequent to
this reflect the average change in species abundance; if on average species’ trends
doubled, the indicator would rise to 200, if they halved it would fall to a value of 50. A
smoothing process is used to reduce the impact of between-year fluctuations - such as
those caused by variation in weather - making underlying trends easier to detect. The
smoothing parameter (number of knots) was set to the total number of years divided by
three.

Each species in the indicator was weighted equally. When creating a species indicator
weighting may be used to try to address biases in a dataset, for example, if one taxonomic
group is represented by far more species than another, the latter could be given a higher
weight so that both taxonomic groups contribute equally to the overall indicator.
Complicated weighting can, however, make the meaning and communication of the
indicator less transparent. The main bias on the data is that some taxonomic groups are
not represented at all, which cannot be addressed by weighting. For this reason, and to
ensure clarity of communication, equal weighting was used.

To illustrate the interspecific variation in trends, bar-charts are published alongside the
indicator. These show the percentage of species showing different trends – strong
increase, increase, no change, decrease, strong decrease – over two time periods (Table
6). The long-term period is that since the start of the indicator (1970 in most cases)
although for species entering into the indicator in subsequent years the period is shorter
(the longest available trend is used, as long as it exceeds that used within the short-term
change measure). The short-term period is the last five years of data (e.g., currently 2013-
18). The five trend class thresholds are based on average annual rates of change over the
assessment period and are derived from the rates of decline used to assign species to the
red and amber lists of Birds of Conservation Concern (Eaton et al. 2009). Asymmetric
percentage change thresholds are used to define these classes as they refer to
proportional change, where a doubling of a species index (an increase of 100%) is
counterbalanced by a halving (a decrease of 50%).

                                                                                    14 of 24
Table 6: Thresholds used to define individual species’ trends

Category            Thresholds                        Threshold–equivalent

Strong increase     Above +2.81% per annum            +100% over 25 years

Increase            Between +1.16% and +2.81%         +33% to + 100% over 25 years
                    p.a.

No change           Between -1.14% and+1.16%          -25% to +33% Over 25 years
                    p.a.

Decrease            Between -2.73% and -1.14%         -50% to -25% over 25 years
                    p.a.

Strong decrease     Below -2.73% p.a.                 -50% over 25 years

2.5. The D6a Indicator
2.5.1 Headline D6a Indicator

The headline abundance indicator was generated by combining 149 priority species’ time-
series (D6a) charting changes in relative species abundance using the multi-species
methods described in the preceding section (Figure 1). The final value is 18, indicating that
the average species abundance in 2018 had declined to just 18% of its value in 1970.

                                                                                    15 of 24
Figure 1: Change in the relative abundance of priority species in England (D6a), 1970-2018

Notes:

1. The line graph shows the trend with its 95% credible interval (shaded area).

2. The bar chart shows the percentage of species within the indicator that have increased,
decreased or shown no change in abundance based on set thresholds of change (Table
6).

3. All species in the priority species indicator are present on Natural Environmental and
Rural Communities Act 2006 – Section 41 (England).

Source: Bat Conservation Trust, British Trust for Ornithology, Butterfly Conservation, UK
Centre for Ecology & Hydrology, Defra, Joint Nature Conservation Committee, People’s
Trust for Endangered Species, Rothamsted Research, Royal Society for the Protection of
Birds.

2.5.2 Assessment of change – headline indicator

The long-term assessment was made by comparing the change and 95% credible
intervals (CI) of the composite indicators between 1970 and 2018. The final value is 18
(95% CI: 17, 19). If the credible interval is entirely below 100 the time series would be
assessed as decreasing, if it was entirely above 100 the indicator would be assessed as
increasing, if the credible interval spanned 100 the indicator would be assessed as no
significant change. Therefore, both the long-term (1970 to 2018) changes are assessed as
decreases.

To assess the short-term trends, the same approach was applied to the most recent 5-
year (2013-2018) period. If the credible interval for the most recent year (2018) is entirely
below the value for 5-years previous (2013) the time-series would be assessed as
decreasing, if it was entirely above the value for 5-years previous the indicator would be
assessed as increasing, if the credible interval spanned the value for 5-years previous the

                                                                                     16 of 24
indicator would be assessed as no significant change. Both the short-term (2013 to 2018)
changes are assessed as decreases.

2.5.3 Change by taxonomic group

The headline indicator (Figure 1) masks variation within and between taxonomic groups.
Figure 2 shows trends for each taxonomic group within D6a. These were generated using
the same methods as the overall indicator.

Figure 2: Change in relative abundance of priority species in England (D6a) by taxonomic
group, 1970-2018

Notes:

1. The line graph shows the trends with their 95% credible intervals (shaded areas) for the
4 taxonomic groups included in the England Priority Species indicator.

2. The bar charts show the percentage of species within the indicator per taxonomic group
that have increased, decreased or shown no change in abundance based on set
thresholds of change (Table 6).

3. All species in the priority species indicator are present on Natural Environmental and
Rural Communities Act 2006 – Section 41 (England).

Source: Bat Conservation Trust, British Trust for Ornithology, Butterfly Conservation, UK
Centre for Ecology & Hydrology, Defra, Joint Nature Conservation Committee, People’s
Trust for Endangered Species, Rothamsted Research, Royal Society for the Protection of
Birds.

                                                                                    17 of 24
3. D6b Distribution of priority species in
England

3.1. Species List
As noted above, there are 940 species that are considered priorities for nature
conservation within England. D6a is limited to species for which annual estimates of
abundance are available, however biological records are available for a broader set of
taxa than those that have available abundance data. When analysed with occupancy-
detection models, these records provide evidence on changes in species’ distributions
over time. Species groups with suitable data span a wide range of taxonomic groups
including bryophytes, lichens, insects, freshwater invertebrates, and other invertebrates.
While the species included are characteristic of a broad range of habitat types across
England, there are plans to include more species as additional data become available.

3.2. Data Sources
Biological records are observations of species at a particular location and at a particular
time. Most records are made by volunteer recorders and, whilst these data may be
collected following a specific protocol, the majority of records are opportunistic. As the
intensity of recording varies in both space and time (Isaac et al. 2014), it can be difficult to
extract robust trends in species’ distributions from unstructured data. Fortunately, a range
of methods now exist for extracting signals of change using these data (e.g., Szabo et al.
2010; Hill, 2012; Isaac et al. 2014). Of these methods - occupancy-detection models - are
best-able to produce robust trends in occupancy (Isaac et al. 2014). Occupancy-detection
models comprise two hierarchically coupled sub-models: an occupancy sub-model (i.e.,
presence versus absence), and a detection sub-model (i.e., detection versus non-
detection). Together, these sub-models estimate the conditional probability that a species
is detected when present. One distinctive feature of occupancy-detection models is that
data need not be available for every year-site combination in order to infer a species’
occupancy (van Strien et al. 2013).

Occurrence records were extracted at the 1km grid square scale and with a temporal
precision of one day. Data were collated through the Biological Records Centre and
include data from the following recording schemes: Aquatic Heteroptera Recording
Scheme; Bees, Wasps and Ants Recording Society; British Arachnological Society Spider
Recording Scheme; British Bryological Society; British Lichen Society; British Myriapod
and Isopod Group - Millipede Recording Scheme & Centipede Recording Scheme;
Bruchidae & Chrysomelidae Recording Scheme; Conchological Society of Great Britain
and Ireland; Cranefly Recording Scheme; British Dragonfly Society; Empididae, Hybotidae
& Dolichopodidae Recording Scheme; Fungus Gnat Recording Scheme; Gelechiid
Recording Scheme; Grasshopper Recording Scheme; Ground Beetle Recording Scheme;
Hoverfly Recording Scheme; Lacewings and Allies Recording Scheme; National Moth

                                                                                        18 of 24
Recording Scheme; Riverfly Recording Schemes: Ephemeroptera, Plecoptera and
Trichoptera; Soldierbeetles and Allies Recording Scheme; Soldierflies and Allies
Recording Scheme; Terrestrial Heteroptera Recording Schemes; UK Ladybird Survey;
Weevil and Bark Beetle Recording Scheme.

Data from between 1970 and 2016 were extracted as this represents the core period of
recording for many of the taxonomic groups. However, some datasets do not cover the
whole period. Since the 2018 indicator the Biological Records Centre has received
updates of the scheme data from some taxonomic groups (Table 7). This has enabled the
improvement of model estimates for certain years (particularly 2016). Note that
approximately 50 of the 105 moth species also appear in D6a.

Table 7: Summary of species’ time-series included in the Priority Indicator (D6b). Only
species in taxonomic groups for which the Biological Records Centre receives data are
presented.

Taxonomic group                  Number of      Number of species      Models
                                 species on     on S41 list with       updated since
                                 S41 list       sufficient data for    Outhwaite et
                                                Priority Indicator     al. (2019)

Ants                             5              3                      YES

Aquatic Bugs                     1              1                      NO

Bees                             17             13                     YES

Bryophytes                       77             9                      NO

Carabids                         13             6                      NO

Centipedes                       1              0                      NO

Craneflies                       5              1                      NO

Dragonflies                      2              1                      YES

Empidid & Dolichopodid           4              3                      NO

Ephemeroptera                    2              1                      NO

Fungus Gnats                     2              0                      NO

Gelechiids                       2              0                      NO

                                                                                   19 of 24
Hoverflies                      5              1                     NO

Ladybirds                       0              0                     NO

Leaf and Seed Beetles           11             4                     NO

Lichens                         86             16                    NO

Millipedes                      3              0                     NO

Molluscs                        7              4                     NO

Moths                           105            93                    NO

Neuropterida                    1              0                     NO

Orthoptera                      3              2                     NO

Plant Bugs                      1              0                     NO

Plecoptera                      1              1                     NO

Shield Bugs                     0              0                     NO

Soldier Beetles                 0              0                     NO

Soldierflies                    5              4                     NO

Spiders                         24             9                     NO

Trichoptera                     3              0                     NO

Wasps                           5              7                     YES

Weevils                         2              2                     NO

Total                           393            181

An occupancy-detection model, following van Strien et al. (2013) and Isaac et al. (2014),
with improvements based on Outhwaite et al. (2018), was applied to all species from those
taxonomic groups for which data were available. For each site-year combination, the
model estimates presence or absence for the species in question given variation in

                                                                                 20 of 24
detection probability: from this the proportion of occupied sites, ‘occupancy’ was estimated
for each year. The models are analysed in a Bayesian framework, meaning that, in
addition to point estimates of occupancy, credible intervals (a measure of uncertainty) can
be generated for each species’ time-series based on multiple iterations (here 999) of
model fitting. A detailed description of the occupancy model can be found in Outhwaite et
al. (2019).

3.3. Indicator Methods
From the occupancy model for each species we extract the proportion of occupied sites
within England. We used only those species with at least 10 records in England and which
passed data availability thresholds (Pocock et al. 2019), to ensure reliable inference.
Although, due to the size of the dataset for moths, model quality tests were unavailable, so
only those moth species with greater than or equal to 10 records in England and greater
than or equal to 50 records across all regions (Outhwaite et al. 2019) were included. Given
these data requirements, 181 species contributed to the Priority Species Indicator - D6b
(Table 7).

To create the composite index, a new hierarchical modelling method for calculating multi-
species indicators within a state-space formulation was used (Freeman et al. 2020), as for
D6a above. The method produces an estimate of the annual geometric mean occupancy
across species. The resulting index is the average of the constituent species’ trends, set to
a value of 100 in the start year (the baseline). Changes subsequent to this reflect the
average change in species abundance; if on average species’ trends doubled, the
indicator would rise to 200, if they halved it would fall to a value of 50. A smoothing
process is used to reduce the impact of between-year fluctuations - such as those caused
by variation in weather - making underlying trends easier to detect. The smoothing
parameter (number of knots) was set to the number of years divided by three.

3.4. The D6b Indicator
3.4.1 Headline D6b Indicator

The headline distribution indicator was generated by combining 181 priority species’ time-
series (D6b) charting changes in the proportion of occupied sites using multi-species
methods (Figure 3).

As for D6a, species were grouped into one of five categories based on both their short-
term (over the most recent five years of data) and long-term (all years) average annual
change in occupancy (Table 6).

                                                                                    21 of 24
Figure 3: Change in the distribution of priority species in England (D6b), 1970-2016

Notes:

1. The line graph shows the trend with its 95% credible interval (shaded area).

2. The bar chart shows the percentage of species within the indicator that have increased,
decreased or shown no change in abundance based on set thresholds of change (Table
6).

3. All species in the priority species indicator are present on Natural Environmental and
Rural Communities Act 2006 – Section 41 (England).

Source: Biological records data collated by a range of national schemes and analysed by
the UK Centre for Ecology & Hydrology.

3.4.2 Assessment of change – headline indicator

The long-term assessment of the composite indicators was made by comparing the
change and 95% credible intervals (CI) between 1970 and 2016. If the credible interval is
entirely below 100 the time series would be assessed as decreasing, if it was entirely
above 100 the indicator would be assessed as increasing, if the credible interval spanned
100 the indicator would be assessed as no significant change. The same approach is also
applied to a short-term period of the last five years of data (e.g., currently 2011-16).

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