Annex A
Title of project:
Contract to identify whether persistent areas of
harbour porpoise and bottlenose dolphin are
supported by available evidence
Date for return of tenders:
26 February 2013
Contract Reference No:
C13-0241-0634
Address for tender
submission:
1 electronic copy to be sent to
TenderResponse@jncc.gov.uk
PLEASE DO NOT SEND TENDERS DIRECTLY TO
RICHARD FERRIS, DORA IANTOSCA OR GORDON
GREEN VIA THEIR PERSONAL EMAIL ADDRESSES,
AS THIS WILL INVALIDATE YOUR TENDER
Tender responses must be less than 10 MB in size.
On receipt of your tender, you will receive an automated
e-mail to confirm receipt by JNCC Support Co. If you do
not receive this automated email, please contact, in the
following order:
- Sue Wenlock (00 44 1733 866880)
- Rick Amos (00 44 1733 866877)
- Carl Cilenti (00 44 1733 866878)
Eunice Pinn
Marine Mammal Advisor
Joint Nature Conservation Committee, Inverdee House,
Baxter Street, Aberdeen, AB11 9QA
Tel: +44 (0) 1224 266580
Email: eunice.pinn@jncc.gov.uk
Contacts for technical
information relating to this
project specification:
Contact for any queries
regarding the tendering
procedure:
Dora Iantosca or Gordon Green
Finance Team
Joint Nature Conservation Committee
Email: Dora.Iantosca@jncc.gov.uk or
Gordon.green@jncc.gov.uk
Tel: 01733 866894 or 01733 866860
Proposed start-date:
25 March 2013
Proposed end-date:
25 September 2013
1. Summary of work
This contract will aim to identify whether discrete and persistent areas of relatively high
harbour porpoise and bottlenose dolphin density exist in the UK marine area. The results of
the research under this contract will be used by JNCC in the further development of the UK’s
Natura 2000 network.
Article 4 of the 1992 Directive on the Conservation of natural habitats and of wild flora and
fauna (92/43/EEC) (the ‘Habitats Directive’), in describing the requirements for Special Areas
of Conservation (SACs) to be proposed for Annex II species (i.e. harbour porpoise
Phocoena phocoena and bottlenose dolphin Tursiops truncatus), states that, “for aquatic
species which range over wide areas, such sites will be proposed only where there is a
clearly identifiable area representing the physical and biological factors essential to their life
and reproduction”. The UK Government is fully implementing this Directive and, as part of
this implementation, JNCC and the Statutory Nature Conservation Bodies (SNCBs) provide
advice on suitable areas that may qualify as SACs. JNCC provide advice on UK offshore
waters (i.e. from 12 to 200 nautical miles from the coast and the UK Continental Shelf as set
out in Orders made under Section 1(7) of the Continental Shelf Act 1964), and each of the
country conservation agencies provides advice from the coast out to the 12 nautical mile
territorial seas limit.
The UK has identified 10 SACs which list the presence of bottlenose dolphins (3 of which list
the species as a qualifying feature, i.e. grade A to C) and 27 SACs for harbour porpoise (1 of
which lists the species as a qualifying feature). The large number of Annex I habitat sites
with harbour porpoise listed as a non-qualifying feature reflects this species widespread
distribution and the fact that its presence on pre-existing sites has not to date been found to
be significantly different from neighbouring areas. In other words, it has been difficult to
clearly identify sites for harbour porpoise and offshore bottlenose dolphin. The work
proposed here will build on the work undertaken to date through the Joint Cetacean Protocol
(JCP).
The Joint Cetacean Protocol (JCP) has been developed as a mechanism for bringing
together the many disparate datasets on cetacean abundance and distribution at the NW
European Atlantic scale (see http://jncc.defra.gov.uk/page-5657). Effort-related cetacean
sightings data from all major UK-lead data sources have been included e.g. the Small
Cetaceans in the European Atlantic and North Sea (SCANS) and Cetacean Offshore
Distribution and Abundance in the Offshore Atlantic (CODA) surveys, the European Seabirds
at Sea (ESAS) surveys, SeaWatch Foundation (SWF), the Atlantic Research Coalition
(ARC) and other non-governmental organisations, as well as industry (e.g. in relation to
potential renewable energy installations in UK waters). These data, collected between 1979
and 2010, represent the largest NW European cetacean sightings resource ever collated.
The JCP project has been conducted in three phases to date. In summary, Phase I (Paxton
& Thomas, 2010) aimed to standardise and combine a representative sample of JCP
datasets, from the Irish sea, and use modelling approaches to predict density and detect
spatial and temporal trends in derived abundance estimates. A power analysis of the
modelled density data showed that declines of 0.3 to 2.2% per year, over a 6 year reporting
period, could be detected for harbour porpoise, bottlenose dolphin and short-beaked
common dolphin. However, this is only likely to be possible in data rich areas, such as the
Irish Sea and for more commonly occurring cetacean species. Phase II (Paxton et al., 2011)
enabled further development and a more detailed analysis of Irish Sea data, with a
geographic extension to include data from parts of the west coast of Scotland. The west
coast geographic extension allowed modelling methods to be tested in a region with a
convoluted coastline, developing methods that were more applicable for using on the entire
geographical range of the JCP dataset. The Phase III analysis produced species specific
density surface, geo-referenced, data that faithfully reflected the spatial patterns of the input
data; however, the estimated densities were higher than those previously published for
similar areas (e.g. by SCANS-II and CODA). In some cases, these were considerably higher
and also possibly unrealistic, particularly for species that tend to occur in large aggregations.
The JCP Steering Group have, therefore, agreed to a re-run of the analysis to address the
issues. The draft report for this reanalysis has now been submitted and is undergoing peer
review prior to publication.
The proposed project will require statistical analysis of the JCP data resource in order to
identify whether discrete and persistent areas of relatively high harbour porpoise and
bottlenose dolphin density exist in UK waters. Currently that data set comprises 38 data
sources with data from at least 542 distinct survey platforms (ships and aircraft) representing
over 1.05 million km of effort covering a 17 year period from 1994-2010 in a 1.09 million km2
prediction region from 48° N to c. 64° N and from the continental shelf edge west of Ireland
to the Kattegat in the east.
2. The Joint Nature Conservation Committee
The Joint Nature Conservation Committee (JNCC) is the statutory adviser to Government on
UK and international nature conservation. Its work contributes to maintaining and enriching
biological diversity, conserving geological features and sustaining natural systems. JNCC
delivers the UK and international responsibilities of the four country nature conservation
agencies – Northern Ireland Environment Agency (NIEA), the Countryside Council for Wales
(CCW) (to become Natural Resources Wales (NRW) in April 2013), Natural England (NE)
and Scottish Natural Heritage (SNH). Collectively, with JNCC, these are referred to as the
Statutory Nature Conservation bodies (SNCBs). For general information on JNCC, refer to
www.jncc.defra.gov.uk.
The JNCC Support Company is made up of specialist support staff to the JNCC and is
responsible for undertaking national and international conservation work on behalf of the four
country nature conservation agencies; NIEA, CCW, NE and SNH. As such, JNCC is
managing the work proposed here on behalf of the other SNCBs.
3. Background to project
Under Article 4 of the EU Habitats Directive there is a requirement, where certain conditions
are met, to protect bottlenose dolphins and harbour porpoises through the designation of
Special Areas of Conservation (SACs) as part of the Natura 2000 network. The sites are
graded A (15% to 100% of national population) to D (non-significant presence). The UK has
a number of sites graded D for both species (26 for harbour porpoises and 7 for bottlenose
dolphins). Three sites are graded C or above for bottlenose dolphins (Moray Firth [Scotland],
Cardigan Bay [Wales] and the Lleyn Peninsula and the Sarnau [Wales]) and one site graded
C for harbour porpoise (Skerries & Causeway [Northern Ireland]).
Initially, the UK interpreted the EU Habitats Directive as applying to territorial waters out to
12 nautical miles. However, since 1999, the UK Government has accepted that it should
apply to marine waters out to 200 nautical miles of the territorial baselines of Member States
and to seabed areas claimed under continental shelf extensions. Consequently, the UK
Government introduced full implementing legislation for the marine area in 2007 through an
amendment of the Habitats Regulations for England and Wales and the introduction of new
Offshore Marine Regulations. These were further amended in 2010. Similar implementing
legislation is also been introduced in Northern Ireland and Scotland. This new legislation
requires the designation of offshore SACs for harbour porpoise and bottlenose dolphins if
the criteria described above are met.
The key criterion as set out in Annex III of the Habitats Directive – ‘Criteria for selecting sites
eligible for identification as Sites of Community Importance and designation as Special
Areas of Conservation’ - is: (a) Size and density of the population of the species present on
the site in relation to the populations present within national territory. The explanatory notes
to the Natura 2000 standard data form suggest the following progressive model to classify
the size of the population in the site relative to the population in the national territory: A:
>15% to 100% of national population B: >2% to 15% of national population C: >0% to 2% of
national population. A fourth category (D) is used in all cases where a population of the
species concerned is present on a site in a non-significant manner. No suggestion is made
on how to classify the site in relation to density though, despite this being listed as one of the
key criteria for identifying sites. Considering abundance without density means that sites
could be designed with harbour porpoises as a qualifying species based entirely on the area
covered by the site. For example, assuming that >0% means > or = to 0.1% of the national
population, it then follows, with a North Sea porpoise population of ca 250,000 individuals
(from SCANS II, 2008), that a site large enough to contain 0.1% (ca 250 individuals) will
meet the size component of this criterion. Therefore sites in the North Sea larger than 450
km2 could potentially be considered for inclusion of harbour porpoise as a qualifying feature
if the density aspect is not taken into account (Pinn, 2008; Mendes et al, 2009).
The size and density criterion has been recognised as difficult to apply to the harbour
porpoise in particular. To address this problem, the European Commission produced
guidance in 2007. This included the results of a workshop held in December 2000. The
workshop concluded that “it is possible to identify areas representing crucial factors for the
life cycle of this species. These areas would be identifiable on the basis of: i. the continuous
or regular presence of the species (although subject to seasonal variations); ii. good
population density (in relation to neighbouring areas); iii. high ratio of young to adults during
certain periods of the year; iv. additionally, other biological elements are characteristic of
these areas, such as very developed social and sexual life.” These guidelines represent the
views of the Commission, but they are not legally binding and are secondary to the
provisions of the Directive. Additionally, the Commission’s guidance provides very little
information on the practical application of these additional criteria, and as such, this has
resulted in the guidance being interpreted and applied differently by each Member State.
The identification of sites with harbour porpoise listed as a qualifying feature continues to be
challenging with only one of the UK’s 27 harbour porpoise sites listing it as a qualifying
species. Conservation efforts have concentrated on threat/impact reduction coupled with
wider surveillance as a mechanism to assess progress and effectiveness of such measures
through which Favourable Conservation Status of this highly mobile species can be
maintained and/or improved.
The UK will continue to search for SACs for harbour porpoises, and this contract is to
undertake a further analysis using the best available data on a UK wide basis.
4. Objectives of work under this contract
This project will interrogate JCP data in order to determine whether there are clearly
identifiable and persistent areas of relatively high harbour porpoise and bottlenose dolphin
density.
The term ‘clearly identifiable’ has been taken to mean that the area can be delineated from
the surrounding (neighbouring) waters by, for example, an elevated abundance on a regular
basis and over a reasonable period of time. The Interagency Marine Mammal Working
Group (MMWG) has agreed that 5 years of data were the minimum requirement to
demonstrate regularity of occurrence over a reasonable period of time (although the 5 years
need not be concurrent; see Pinn, 2008). Given the mobile nature of these species,
particularly harbour porpoise, a reasonably high degree of confidence in the modelled results
is also required.
Models will be fitted to the data, focusing on capturing small-scale spatial, but
relatively long-term temporal, density variations, and will require the following:
1. Initially, areas where there has been insufficient temporal effort (i.e. less than
5 years of data) will need to be identified and mapped (e.g. see Kober et al,
2010). Any persistent areas of high density identified through the modelling
that correspond to areas with insufficient temporal data will not be considered
at this time. Such results should be, however, be reported as they will, be
used to provide an indication of where surveys could potentially be focused in
the future.
2. It is recognised that fitting the model to the entire dataset is too
computationally burdensome. Therefore, for the analysis, the dataset will
need to be divided into a series of subsets. The SNCBs are currently
considering the best subset divisions and will agree this with the successful
contractor.
3. The sightings data will need to be standardised by effort and (relative)
abundance data generated, taking effort into account (see appendix 1 for a
user-friendly guide).
4. Spatio-temporal models will then be fitted to these abundance data for the
appropriate subsets, using similar methods to those employed in the Phase III
analysis (project officer to provide documentation). One difference, however,
will be that a greater focus should be given to capturing small-scale spatial,
but relatively long-term temporal, density variations. Model selection should
be used to identify significant environmental covariates and variance should
be estimated using a parametric bootstrap.
5. The fitted surface should then be examined for persistent areas of high
density between years, using a variety of techniques. An exploration of available
methods for the delineation of such areas should be undertaken and the most
appropriate method used, with a justification provided. Available methods include
alpha hulls (e.g. Pateiro-Lopez & Rodrguez-Casal, 2010), Localize Convex Hulls
(e.g. Getz & Wilmers, 2004), the Local Getis-Ord Gi* statistic (e.g. Kober et al, 2010)
and kernel methods (e.g. Teilmann et al., 2008; Sveegaard et al., 2011).
6. Analysis will be undertaken on the entire sea area for each subset, but
resulting maps will need to be masked to the UK limits. This should allow
boundary effects to be taken into account.
7. The relationship between estimated abundance (including 95% confidence
limits) within these areas and size of area will be examined, to determine if
there are nonlinearities such that a high proportion of overall abundance can
be captured within a relatively small area. Confidence intervals on these
relationships will then be calculated from the parametric bootstrap. The report
should also include information on the variability over time of these areas
(seasonally and inter-annually as appropriate).
These proposed analyses will apply the most robust analytical tools to the most
extensive data source on harbour porpoise and bottlenose dolphin distribution in
waters around the UK to enable the identification of persistent high density areas in a
proactive way. The analyses will also allow the importance and context of any
predefined area to be assessed in a post hoc way.
If applicants want to suggest an alternative analytical approach, they will need to
provide a detailed description of the methodology to be used. A justification outlining
the advantages of their approach over those outlined above will also be required.
The final report may be published as a JNCC report and therefore the contractor will be
required to follow the JNCC report format, details of which will be provided by the project
officer during the project. The report should be supplied in an electronic format using Word.
It should be noted that a project steering group comprising the SNCBs will be developed to
oversee this project.
5. Timescale of contract
This project will commence by 25/03/13. It is anticipated that this work will take 6 months to
complete, with the agreed final report being delivered to the JNCC nominated officer (Eunice
Pinn) by 25/09/2013.
6. Data
Data will be provided by the JNCC Support Company as a MS Access database or in
another format by prior arrangement. They will be supplied solely for the purpose of this
contract and the contractor will be asked to comply with a set of conditions, prohibiting the
use of the data for any other purpose.
Effort-related data from the following survey types will be included: dedicated; platform of
opportunity; and transect (with and without a rigorous distance sampling field protocol).
These data originate from cetacean surveys conducted within NW European waters and
include the following sources: SCANS and SCANS-II; ESAS; Sea Watch; IWDG and ARC.
Data are collected using a variety of survey methods and platforms, and under varying
environmental conditions.
7. Outputs
A fully referenced stand alone report document should be produced on completion of the
work. The report should be no more than 40 pages in length (excluding Appendices) and
should contain the following:
i.
An executive summary of not more than two pages in length and should be written in a
style that is accessible to a non-specialist audience;
ii.
detailed description of the statistical modelling approach used to generate annual
density surfaces for bottlenose dolphin and harbour porpoise;
iii.
Review of methods to delineate areas of high density;
iv.
Interpretation of density surfaces to identify persistent areas of high density over
time;
v.
Identification of potential boundaries for the persistent high density areas, including
density and/or abundance estimates within and without the area (with confidence
intervals).
The structure of the report should be agreed with JNCC’s project officer. The contractor will
be required to provide a draft document for prior approval to ensure the final documents are
in line with expectations. The draft report will be subject to a process of peer review.
Dissemination
The report produced under this contract will be a JNCC product and shall not be published
or disseminated without the permission of JNCC. It may at some point be published on the
JNCC website and all material supplied as part of this contract shall remain copyright of
JNCC. The findings from this contract will also be made available to JNCC, the UK
Conservation Agencies, Defra and the Devolved Administrations.
The contractor shall have free access to use of the results of this contract, subject to
appropriate acknowledgement of JNCC in any written or oral use of the work. The contractor
is encouraged to use the results of this contract to publish peer-reviewed papers, following
JNCC’s dissemination of the contract report.
8. Health and safety
The contractor will be required to provide copies of their Health & Safety Policy Statements
where available, or a note regarding such items as lone working, emergency procedures and
accident reporting. The contractor must provide copies of risk assessments for operations
carried out. The contractor must demonstrate immediate reporting of accidents occurring
within the contract that relate to the contract and occurring within the duration of the contract.
9. Tender submission
The tender submission should include the following:

A brief summary of the Contractor’s experience (including reference to published
experience demonstrating use of the various statistical methods outlined above) in
relation to the requirement of this contract;

Proposed methodology for achieving the aims of the contract, including a detailed
work programme and estimate of time required to achieve each element of the
project;

Details of Quality Control procedures;

Details of the Project team, including their roles and experience, an estimate of their
time input into each task, and CVs of all personnel involved in this contract.

Project plan, including milestones and a timeline for delivery of the draft report
allowing for review and revision prior to delivery of the final report on 25/09/13.

Overall quote for the contract, to include:
Daily rates for all members of the Project Team;
Costs and time allocation should be clearly allocated to specific tasks within
this contract;
Costs for attending start-up, interim and final meetings;
VAT if applicable. Please state clearly whether VAT is applicable or not.
Please take note of the following evaluation criteria that will be used to assess all
applications.
10. Evaluation criteria
JNCC are not bound to accept the lowest priced or, indeed, any tender if they are not of
sufficient quality or detail. Having the technical expertise and experience to compete the
work to a high standard, and being able to complete it within the timescale, are of the
essence for this contract.
1. Quality of proposal, (60% of the total for the three assessment categories)
Clarity of proposal (particularly work plan and deliverables)
15
Understanding of, and relevance to, the project
requirements (in particular, the adequacy of outputs and
understanding/experience of any sampling and/or statistical
analyses required)
20
Soundness and logicality of methods
5
Realism and measurability of milestones
5
Identification and proposed solutions to potential
problems/risks
5
Serious weaknesses which threaten success
5
Probability of success
Sub Total
2. Details of contractor (25 % of the three assessment categories)
5
60
Expertise, experience and balance of team
10
Previous experience of using the team/ team members (if
any)
10
Risks if important team members drop out
3
Adequacy of subcontractors (if any)
2
Sub Total
25
3. Cost (15% of the total for the three assessment categories)
Transparency and correctness of presentation
5
Fairness/reasonableness for the level of work and expertise
required
3
Tender
Score
Evaluation criteria
Max Score
Tenders will be evaluated using the following criteria, noting that the higher the score the
more important the criterion:
Appropriateness of ratio of senior to junior staff time
2
Clarity of each team member’s contribution and value added
5
Sub Total
15
11. Payment
Payment will be made on submission of an invoice, and upon satisfactory completion of the
final report for the contract to the agreed standard of the JNCC Project Officer. However, if
the contractor would prefer staged payments, then they will be expected to submit a
schedule of payments according to specified milestones/deliverables. These will be subject
to agreement at the start of the project.
12. Additional contractor requirements
All tenderers are requested to carefully read the Terms and Conditions applying to this
contract.
All costs associated with the production of figures and the final report must be accounted for
within the rates and fees given.
All work must be undertaken on the contractors own premises. The contractor is expected
to supply all necessary equipment, software, licences etc to carry out the obligations
required under this contract.
13. Further information
The JNCC project officer for this work is Eunice Pinn who can be contacted on 01224
266580; email eunice.pinn@jncc.gov.uk
For all other enquires please contact Dora Iantosca, Procurement services on 01733
866894; email dora.iantosca@jncc.gov.uk
14. References
Bravington, M., Borchers, D. & Northridge, S., 2002. Analysis of harbour porpoise sightings
data in relation to area-based conservation. Final Report to JNCC, Project XGLJ02.
EU, 2007. Guidelines for the establishment of the Natura 2000 network in the marine
environment. Application of the habitats and Birds Directives.
Getz, W.M. and Wilmers, C.C., 2004. A local nearest-neighbor convex-hull construction of
home ranges and utilization distributions. ECOGRAPHY 27: 489-505.
Kober, K., Webb, A., Win, I., Lewis, M., O‟Brien, S., Wilson, L.J., Reid, J.B. 2010. An
analysis of the numbers and distribution of seabirds within the British Fishery Limit
aimed at identifying areas that qualify as possible marine SPAs. JNCC report No.
431.
Mendes, S., Tasker, M., Johnston, C., Pinn, E., Reid, J., Goold, J. & Stott, A., 2009.
Reassessment of the criteria for designation of special areas of conservation for
harbour porpoise. JNCC Committee paper JNCC 09 P23. Available at:
http://jncc.defra.gov.uk/pdf/comm09P23-20100728.pdf
Pateiro-Lopez, B. & Rodrguez-Casal, A., 2010. Generalizing the Convex Hull of a Sample:
The R Package alphahull. Journal of Statistical Software, 34, 1-28.
Paxton, C. G. M. & Thomas, L. 2010. Phase I Analysis of the Joint Cetacean Protocol Data.
Report
to
the
JNCC
January
2010.
70
pp.
Available
at:
http://jncc.defra.gov.uk/pdf/JCP_Phase_1_Analysis.pdf
Paxton, C. G. M. Mackenzie, M., Burt, M. L., Rexstad E. & Thomas, L. 2011. Phase II Data
Analysis of Joint Cetacean Protocol Data Resource. Report to the JNCC 2012. 126
pp. Available at: http://jncc.defra.gov.uk/pdf/JCP_Phase_II_report.pdf
Pinn, E.H., 2008. Threshold for designation of special areas of conservation for harbour
porpoise and other highly mobile, wide ranging marine species. JNCC Committee
paper
JNCC
08
P10.
Available
at:
http://jncc.defra.gov.uk/pdf/JNCC_P10Sept08Annex1_amendedFeb09.pdf.
Sveegaard et al. 2011. High-density areas for harbor porpoises (Phocoena phocoena)
identified by satellite tracking. MARINE MAMMAL SCIENCE, 27(1): 230–246.
Teilmann, J., Sveegaard, S., Dietz, R., Petersen, I.K., Berggren, P. & Desportes, G., 2008.
High density areas for harbour porpoises in Danish waters. National Environemntal
Reserach Institute, University of Aarhus. 84pp. NERI Technical Report No. 657.
Available from http://www.dmu.dk/Pub/FR657.pdf
Appendix 1: A user friendly overview of the initial analysis required to generate the
abundance grid (from Paxton et al., 2011)
The sightings data from a variety of boats, bigger ships, aeroplanes and helicopters reflects
what is detected by observers during a known period of search time/distance (“the effort”).
What is seen does not wholly reflect what is out there. More animals are seen if there is
more effort and some sorts of animals are easier to see than others or spend more at the
surface so not all animals are detected and not all animals are at the surface to be detected.
Therefore to produce an index of animals per unit effort (the basic information required to
produce a map), the number of animals seen has to be adjusted for lack of detection. We
can do this by looking at the rate at which detection drops off at a distance from the
observer. We can work this out from the histogram of observed distances to the detected
animals. This tells us how good the observers are at detecting things off the trackline. Also
when two or more observers are observing on the trackline, each acts as a check on the
other ones’ detection abilities and again this can be used to correct for under detection.
Some surveys do not record the observed distances (just whether or not they saw animals)
but in a JCP context, this problem can be overcome by applying the detection probabilities
calculated from surveys where people did record the distances.
Marine mammals are not always at the surface. By knowing how much time the animals
spend on average at the surface and knowing the maximum time they can spend on a single
dive an index of their availability at the surface can be worked out.
Once the above details are known, a detection corrected index of seen animals referenced
in space and time can be made. A statistical model incorporating availability can be fitted to
this index and this allows predictions to be made where there was no coverage by vessels.
These predictions are corrected for underdetection and diving by the marine mammals. The
precision (i.e. how close to the unknown truth) and accuracy (the opposite of bias) of these
predictions depends crucially on the amount of effort in the region under consideration and
because of the nature of the statistical model used, the number of estimated animals. The
statistical properties of the fitted model provide an estimate of the uncertainty in the
estimates which allows in turn an interpretation of how reliable the results actually are i.e.
how close to the unknown reality.
Figure 1: A schematic of the initial analysis of the JCP data resource to generate (relative)
abundance grid