DOI: 10.5061/dryad.5tb2rbp4v
title: Increasing numbers of harbour seals and grey seals in the Solent

description: Harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus) both
 occur within the UK, but display regional contrasting population trends.
 Whilst grey seals are typically increasing in number, harbour seals have
 shown varying trends in recent decades following repeated pandemics. There
 is a need for monitoring of regional and local populations to understand
 overall trends. This study utilised a 20-year dataset of seal counts from
 two neighbouring harbours in the Solent region of south England.
 Generalised additive models showed a significant increase in the numbers
 of harbour (mean 5.3 to 30.5) and grey seals (mean 0 to 12.0) utilising
 Chichester Harbour. Conversely, in Langstone Harbour there has been a
 slight decrease in the number of harbour seals (mean 5.3 to 4.0).
 Accompanying photographic data from 2016-18 supports the increase in seal
 numbers within Chichester Harbour, with a total of 68 harbour and 8 grey
 seals identified. These data also show evidence of site fidelity of
 harbour seals in this area, with almost a quarter of animals resighted
 within the past three years. Overall, this long-term study indicates an
 increasing number of both harbour and grey seals within the Solent.
 However, more research is required to identify the drivers of this trend.
description: <i>Study
 Area</i> The Solent is
 a sheltered channel system, separated from the English Channel by the Isle
 of Wight and stretching along the coastline of Hampshire and West Sussex
 (Figure 1). It includes numerous estuaries and natural harbours, the
 largest of which are Portsmouth, Langstone, and Chichester Harbours, which
 form a series of connected basins comprised of extensive intertidal mud
 and sand banks. Previous studies have confirmed that harbour seals utilise
 haul-outs in both Chichester and Langstone Harbours, moving between these
 sites via both the sea and a network of tidal channels (Chesworth et al.,
 2010). Grey seals have previously only been reported in a single sighting
 located within Chichester Harbour (Chesworth et al., 2010).
 <i>Data
 Collection</i> Visual surveys
 were undertaken in Chichester Harbour from 1999 to 2012 and 2015 to 2019,
 with surveys in Langstone Harbour from 2009 to 2017 and 2019 (Appendix 1).
 Surveys approximately overlapped with low tide, when the tidal mud flats
 were at their maximum availability for seal haul-outs. However, in some
 cases surveys were limited by poor weather. Pre-2015, data
 was collected on a monthly basis using a combination of boat- and
 land-based surveys and did not include estimates of seal age. Post-2015,
 field protocols at both sites were standardised to ensure the same
 methodology was consistently applied. This included: moving surveys to an
 entirely boat-based platform; conducting surveys concurrently at both
 harbours to remove the chance of individuals being counted twice;
 undertaking surveys at least once a month between May and September to
 capture the harbour seal pupping season (with additional months surveyed
 on an opportunistic basis); and recording the approximate age of
 individuals (adult, sub-adult/juvenile, or pup) where possible. It can be
 challenging to assign an age cohort from observation alone (except for
 newborn pups), especially for harbour seals; despite females having lower
 overall lengths at maturity, they display higher early growth rates than
 males (Hall et al., 2019). Hence sub-adults and juveniles were combined
 into one category. Regardless, age/sex data were not used in the present
 analyses beyond observation of pup numbers. Note that it was not possible
 to collect count data in Langstone Harbour during 2018. Additionally,
 boat-based photo-ID using a digital SLR camera and appropriate zoom lens
 was undertaken in Chichester Harbour from 2016 to 2018. Photo processing
 followed standard protocols (Yochem et al., 1990; Mackey et al. 2007;
 Hastings et al., 2008; Cunningham, et al., 2009; Cordes et al., 2015). In
 brief, photos were sorted by survey and allocated ratings based on their
 quality (i.e., clear focus, good lighting, head visible) for identifying
 pelage markings: Grade 1 (good quality), Grade 2 (sufficient), or Grade 3
 (poor). Only Grade 1 and 2 photos were retained. Four independent
 reviewers manually compared images to identify individual seals based on
 unique pelage markings. ‘New’ individuals were allocated a sequential
 identification number and added to the catalogue. When individuals were
 resighted, the date was noted in a separate spreadsheet. <i>Data
 Analysis</i> Seal count
 data were analysed in R
 (R Core Team, 2019) for each species and site using
 Generalised Additive Models (GAMs, <i>mgcv </i>package, Wood,
 2011) to allow smooth functions to be fitted to temporal covariates (Month
 and Year) based on results from exploratory analyses. Cyclic cubic splines
 were used for Month to ensure there was no discontinuity between January
 and December. To account for overdispersion, GAMs were fitted with a
 Tweedie distribution (Miller et al., 2013). Restricted maximum likelihood
 (REML) was used to minimise over-fitting (Wood, 2011). The best model was
 selected using Akaike’s Information Criterion for small sample sizes
 (AICc; <i>MuMIn</i> package, Barton, 2020). Model assumptions
 were checked by producing standard residual diagnostic plots and an acf
 function was used to check for temporal autocorrelation (Zuur and Ieno,
 2016). See ‘Data Accessibility’ section for a link to code used in these
 analyses.
description: <i>“AllSealCounts.csv”</i> contains counts of harbour and grey seals collected during visual surveys in Chichester and Langstone Harbours, UK. <i>“SolentSeals.html”</i> presents the data exploration and analysis, with an extended example of applying GAMs to harbour seal counts in Chichester Harbour. <em>"SolenSeals.Rmd" </em>presents the RMarkdown code used to prepare SolentSeals.html “<i>SolentSealCatalogue.pdf</i>” contains photographs of all the individual seals recorded in this study, along with their sex (if known) and first sighting date.