Monitoring of allis shad and smelt in Tamar Estuaries – EC18234 – MBA and EA MONITORING OF ALLIS SHAD AND SMELT IN TAMAR ESTUARIES EC18234 A report from: The Marine Biological Association of the United Kingdom and the Environment Agency. To: Trudy Russell Address: Natural England, Polwhele, Truro, Cornwall TR4 9AD Email: [email protected] Phone: 0300 060 0354 Authors: Stephen P. Cotterell (MBA) and Robert J. Hillman (EA) 1 Monitoring of allis shad and smelt in Tamar Estuaries – EC18234 – MBA and EA Recommended citation: Cotterell S.P. & Hillman R.J. (2016). Monitoring of allis shad and smelt in the Tamar Estuary – EC18234. Natural England Evidence Project Report RP02463, York. MONITORING OF ALLIS SHAD AND SMELT IN TAMAR ESTUARIES – EC18234 Executive summary In April 2015, the Marine Biology Association (MBA) and Environment Agency (EA) were commissioned by Natural England (NE) to investigate the distribution of allis shad (Alosa alosa) and smelt (Osmerus eperlanus), protected as features in the Plymouth Sound and Estuaries Special Area for Conservation (SAC) and Tamar Estuary Sites Marine Conservation Zone (MCZ) respectively. Allis shad are rare in the UK and populations are declining in Europe. The only confirmed spawning sites for allis shad are in the Tamar Estuary. This site is also an important area for spawning populations of smelt. The UK smelt population is depleted and protecting estuaries used by the species is important because they can become locally extinct from isolated estuaries and will not return. The main threats to Allis shad and smelt include pollution, over-exploitation, habitat destruction/degradation and barriers to migration. Natural England is responsible for reporting to government on the condition of these species. Prior to this study allis shad and smelt populations were poorly researched within the site. In spring/summer 2015 the EA surveyed the spawning distribution of allis shad in the upper Tamar Estuary and River and the upper Lynher Estuary and River. The EA monitored the allis shad adult spawning migration at Gunnislake Fish Trap and Gunnislake Fish Counter cameras. In August 2015 a boat-towed plankton net survey was undertaken by MBA/EA in the upper Tamar estuary from Gunnislake to Cotehele to look for allis shad and smelt larvae. No young shad were found though smelt were present between Okeltor Boathouse, upstream of Calstock and Cotehele. Allis shad eggs were not found in the Lynher River or Estuary or in the River Tamar; allis shad eggs were only found at one spawning site in the upper Tamar Estuary at Cottage Run. Allis shad eggs were present from late May until early July 2015 and none were recorded migrating upstream at Gunnislake Weir in 2015, suggesting that all spawning occurred at one site downstream of the weir. Low flows at Gunnislake Weir in 2015 (due in part to a leaking sluice gate in a bypass channel) are thought to have deterred upstream allis shad migration. The EA collated all existing allis shad records from the Tamar and Lynher Rivers and Estuaries held in their archive. Records were provided to NE from adult allis shad caught at 2 Monitoring of allis shad and smelt in Tamar Estuaries – EC18234 – MBA and EA Gunnislake Fish Trap, seen on Gunnislake Fish Counter cameras, caught by anglers and salmon netsmen, sightings, records of carcasses found and the distribution of spawning sites from egg surveys. A review was also undertaken by the EA of previous allis shad spawning migrations on the Tamar. An analysis was undertaken of the environmental conditions associated with the adult run at Gunnislake Weir and the environmental conditions associated with spawning records, based upon egg surveys in the River Tamar and estuary. The estimated size of the allis shad run into the River Tamar at Gunnislake Weir is presented as are observations on the allis shad spawning run, including size measurements, sex-ratio, estimated age and spawning history of individuals on the spawning migration. The EA undertook egg surveys between February and April 2016 to monitor the smelt spawning distribution and timing of the spawning run in the upper Tamar and Lynher Estuaries. A pair of fyke nets was used by the EA at Impham Meadow in the upper Tamar Estuary, to determine the timing of the smelt spawning run and describe the makeup of the smelt spawning migration. Smelt eggs were not recorded on the Lynher. Very small numbers of live smelt eggs were recorded in the Upper Tamar Estuary below Cottage Run Weir between mid-March and early April 2016. However, the number of eggs found did not suggest that smelt had spawned in great numbers if at all at Cottage Run; it is possible that the small number of smelt eggs found were deposited by the tide. The reasons for an apparent absence of smelt spawning in the upper Tamar Estuary in spring 2016 are unclear. High flows during February 2016 may have resulted in smelt spawning further down the estuary. However, environmental conditions in March and April appeared to be favourable so it is possible that a change in the spawning substrate at Cottage Run since the 1970s has resulted in this site being unsuitable for smelt spawning. A small number of smelt in spawning condition were caught in the fyke net in mid-March 2016, suggesting that smelt were attempting to spawn in the upper Tamar Estuary. Trawling for adult smelt was first undertaken by beam trawling from Morwellham Quay to Pentillie Quay in August 2015 with smelt present from the upper reaches to Cotehele. In November 2015 the sampling covered the same area and smelt were present around Cotehele and Halton Quay (upper). The sampling had to be cancelled in December and in January a comparison between beam trawling and otter trawling suggested the latter probably caught more smelt where it could be operated. Sampling also extended much further down the river at West Mud, but with fewer sites in the upper reaches. The otter trawl sampling in January and February 2016 caught smelt at Halton Quay (lower) and by March 2016 higher numbers of smelt were found around Halton Quay and many of these were in spawning condition. In total 40 fish species were sampled. In summary, the status of the Tamar allis shad population is uncertain but there are several observations that give cause for concern, namely the sharp downturn in the number of allis shad seen migrating upstream via Gunnislake Fish Trap since 2011 and the apparent use of just one spawning site in the upper Tamar Estuary. The status of the Tamar smelt population is less clear as this is the first year of survey for the species and no spawning site was located, however the presence of a range of age classes suggests that in previous years spawning in the site was successful. The report follows the 3 part structure set out in the proposal. 3 Monitoring of allis shad and smelt in Tamar Estuaries – EC18234 – MBA and EA Contents 1 Part 1. Monitoring of allis shad within Plymouth Sound and Estuaries SAC. Juvenile density; the 2015 spawning distribution of allis shad in the Tamar and Lynher estuaries; and 2015 adult run size of allis shad at Gunnislake Weir ............................................................... 13 1.1 Introduction............................................................................................................... 13 1.2 Objectives .................................................................................................................. 13 1.3 Methods .................................................................................................................... 14 1.3.1 Trawling for larvae and juveniles ....................................................................... 14 1.3.2 Kick-sampling for eggs to assess spawning distribution .................................... 16 1.3.3 Review of Gunnislake Fish Pass camera footage to assess adult run size via upstream migration of allis shad into the River Tamar at the tidal limit ........................ 18 1.3.3.1 General method for review of fish counter camera footage ..................... 18 1.3.3.2 Method used to record allis shad on camera footage ............................... 20 1.4 Results ....................................................................................................................... 20 1.4.1 Trawling for larvae and juveniles ....................................................................... 20 1.4.2 Kick-sampling for eggs to assess spawning distribution .................................... 20 1.4.3 Review of Gunnislake Fish Pass camera footage to assess upstream migration of allis shad into the River Tamar .................................................................................... 24 1.5 Discussion .................................................................................................................. 24 1.5.1 Trawling for larvae and juveniles ....................................................................... 24 1.5.2 Adult run and spawning distribution ................................................................. 25 1.5.3 Timing of spawning at Cottage Run ................................................................... 25 1.5.4 Water Quality ..................................................................................................... 27 2 Part 2. Monitoring of smelt within the Tamar Estuary MCZ ........................................... 29 2.1 Introduction..............................................................................................................