BD1454: Appendices to Final Report

BD1454: Appendices to Final Report

Appendix A: Summary of grazing treatment delivery on Experiment 1 and Devon extension sites during 2006-2009. Duration of target sward height (TSH) maintenance (days) prior to plot closure, date of plot closure, and recommendations for the inclusion (Yes) / exclusion (No) of sites from analyses of agronomy and biodiversity data. Asterisks indicate site/years for which most (Yes*) or some (No*) of the data can be included in analyses. Blank entries indicate discontinued sites. Mean TSH duration and the number of sites contributing data are also summarised. Two sites (marked with $) were abandoned during autumn 2008 following persistent breaches of grazing protocols by farmers.

Site
(#=core site) / TSH /
Close
date / Agron / Biodiv / TSH /
Close
date / Agron / Biodiv / TSH / Close
date / Agron / Biodiv / TSH / Close date / Agron / Biodiv

Year

/ 2006 / 2007 / 2008 / 2009

Expt 1 sites

Bragg / 0 / 20/7 / No / No / 0 / 19/7 / No / No / 24 / 30/6 / Yes / Yes / 45 / 12/7 / Yes / Yes
Dadge / 7 / 17/7 / Yes* / Yes* / 64 / 11/7 / Yes / Yes / 8 / 16/7 / Yes / Yes / 87 / 6/7 / Yes / Yes
Foss # / 0 / 5/7 / No / No / 63 / 2/7 / Yes / Yes / 20 / 8/7 / Yes / Yes / 32 / 20/6 / Yes / Yes
Glanville # / 2 / 24/7 / No* / No* / 72 / 12/7 / Yes / Yes / 11 / 4/7 / Yes / Yes / 50 / 15/7 / Yes / Yes
Howlett / 0 / 11/7 / No / No / 57 / 5/7 / Yes / Yes / 21 / 8/7 / Yes / Yes / 24 / 2/7 / Yes / Yes
Lethbridge$ / 1 / 5/8 / No / No / 38 / 19/7 / Yes / Yes / 49 / 22/7 / Yes / Yes*
Luscombe / 0 / 27/7 / No / No / 12 / 16/7 / No / Yes / 0 / - / No / No / 62 / 27/7 / Yes / Yes
Mather / 0 / 17/7 / No / No / 57 / 4/7 / Yes / Yes / 0 / 11/7 / No / No* / 48 / 17/7 / Yes / Yes
Pady # / 0 / 24/7 / No / No / 41 / 24/7 / Yes / Yes / 53 / 28/7 / Yes / Yes / 49 / 17/7 / Yes / Yes
Philp # / 5 / 10/7 / No* / No* / 53 / 17/7 / Yes / Yes / 25 / 5/7 / Yes / Yes / 61 / 13/7 / Yes / Yes
Ponting # / 0 / 7/7 / No / No / 70 / 17/7 / Yes / Yes / 0 / - / No / No / 26 / 14/7 / Yes / Yes
SST # / 6 / 3/7 / No* / No* / 69 / 9/7 / Yes / Yes / 15 / 3/7 / Yes / Yes / 65 / 1/7 / Yes / Yes
Wotton / 0 / 27/7 / No / No / 7 / 18/7 / No / Yes / 5 / 9/7 / No / No* / 55 / 8/7 / No / Yes

Mean TSH / no. sites

/ 1.6 / 1 / 1 / 46.4 / 9 / 11 / 17.8 / 8 / 8 / 50.3 / 11 / 12
Extension sites / TSH / Close
date / Agron / Biodiv / TSH / Close date / Agron / Biodiv
Beauchamp / 0 / 10/7 / No / No / 9 / 2/7 / No / Yes
Drew / 22 / 15/7 / Yes / Yes / 50 / 19/6 / Yes / Yes
Horton / 15 / 16/7 / Yes / Yes / 45 / 15/7 / Yes / Yes
Northmore / 15 / 23/7 / Yes / Yes / 32 / 3/7 / Yes / Yes
Palmer$ / 16 / 23/7 / Yes / Yes*
Pollard / 31 / 4/7 / Yes / Yes / 67 / 28/7 / Yes / Yes
Reddaway / 8 / 23/7 / Yes / Yes / 38 / 26/6 / No / No*
Rogers / 35 / 14/7 / Yes / Yes / 16 / 25/6 / Yes / Yes
Mean TSH / 17.8 / 7 / 7 / 36.7 / 5 / 6

1

Appendix B: Comparison of estimated and actual cattle weights. In each year, on the three core sites that had weighing facilities, an experienced agronomist estimated individual cattle live weights at turnout in April, in mid July and in late September. Actual and estimated cattle weight data are presented in Figure B1. The concordance between estimated and actual weights was high (R2 = 90.1% in 2007, 95.0% in 2008 and 94.8% in 2009).

Figure B1: Actual vs. estimated cattle weights. Blue = 2007, Red = 2008, Green = 2009.

Appendix C: Methodology for development of a re-nesting model for annual breeding productivity of skylarks on silage fields

1. Nest recording

GPS grid references were taken at all nests. Photographs were taken of each nest, to help identify subsequent damage from predators or machinery. Nest locations were marked with two small twists of red insulation tape attached to tall grass stems, so that the markers and the nest formed an equilateral triangle with 2m-long sides. This marking technique has been widely used on skylark nests and does not appear to attract the attention of predators.

Nests were visited on three-day intervals. Daily visits were made at the fledging stage (>7 days old) to confirm fledging and permit daily recapture of radiotagged fledglings. Four-day visiting intervals were used for known-age clutches. Full nest records were assembled for all nests, including all the data required by the British Trust for Ornithology Nest Record Scheme, plus additional information specific to this study.

2. Nesting phenology

2.1 Determining first egg dates (FED) for each nesting attempt

First egg dates are normally determined from nest visits coinciding with the laying, hatching or the chick-rearing periods (when chicks are aged from a knowledge of their developmental phenology) in conjunction with a knowledge nesting phenology. Eggs are laid at a rate of one per day, usually overnight and incubation starts when the last egg is laid. The incubation period is 12 days and most chicks leave the nest between 8 and 9 days after hatching. Nest records collected during this study were in agreement with these figures, though a small proportion of nestlings stayed in the nest longer before fledging.

Nests found during incubation and failing before hatching cannot be aged in this way, wasting valuable phenology data from a substantial umber of nests. An egg density model was developed from known-age clutches, to predict hatching dates from egg length, width and weight measurements. The mean of the estimated hatch dates for the whole clutch was used, as skylark eggs are variable in size and shape. Excluding outlier eggs improved the accuracy of estimates, which were typically within one day of known hatch dates. The equation, derived from three years’ data, was:

Days till hatching = (Egg Density-0.4646) / 0.006042

Egg Density = 1000*weight / length / width2

Where, egg weights were measured in grammes and dimensions in millimetres.

Chick development in farmland passerines is frequently impeded by malnutrition, making development–based ageing criteria inaccurate. The accuracy of ageing estimates was improved by collecting a series of biometrics, including weight, tarsal length (folded toes to the end of the tarsus in the tibio-tarsal joint notch), third primary pin (numbered ascendantly) total length and length of opened feather at tip of third primary pin. Third primary pin development was particularly useful for ageing older chicks and fledglings (>7 days old), once the tarsi were fully-grown.

2.2 Replacement intervals

Consecutive pairs of nesting attempts were principally identified from a knowledge of territory distributions and the timing of nest attempts by the pair in question and those of their neighbours. Pairs known to have completed a nesting attempt were observed repeatedly until their new nest was found. It is possible that a short-lived, failed nesting attempt may have been overlooked during some of the longer replacement intervals. We are confident that this was unlikely to have happened in most instances of intervals up to 43 days, but a 66-day interval was dismissed as a probable error. Skylarks were reluctant to start nests in taller (i.e. older) silage crops, so long replacement delays are plausible. Note that overlooking a short-lived, failed nesting attempt would not affect the re-nesting model, as the appropriate number of days would still elapse in the simulation without any chicks fledging. A sample of female skylarks was trapped on the nest and radiotagged to follow them through to their next nesting attempt. This technique was not very effective and resulted in the immediate desertion of two females, so it was quickly abandoned.

2.3 Duration of the egg-laying season

Annual productivity predictions from re-nesting models are highly sensitive to the assumptions made about the start and end of the egg-laying season. The start and end of the egg-laying season varied considerably between skylark pairs. Normal distributions were used to model start dates and end dates, in order to fit observed peaks near the respective ends of the FED distribution. Known consecutive pairs of nests indicated that there was considerable variation in start and end dates between pairs. Normal distributions were fitted to all FEDs before 1 June and after 15 June, excluding nests that were definitely not first nests or last nests (from consecutive nest pairs). The resulting distributions provided a good fit to the tails of the observed FED distribution. The wide spread of the distributions can result in simulations with only one nesting attempt, but based on our field experience this is likely to be representative of normal skylark behaviour on silage fields. The earliest and latest FED were used to set bounds on the FEDs predicted by this laying season model.

3. Nest survival during silaging operations

Nest survival was measured for each stage in the silaging process: mowing, spreading, windrowing and collection (distinguishing the effects of forage harvesters and mowers from the tractors and trailers used to clear the grass away). Nests were checked immediately before and immediately after each operation, to distinguish failures due to predation or abandonment from those due to the machinery. All nests were checked to see whether they had been run over at each stage, even if the nest contents had survived. Relocating nests after silaging operations was challenging, particularly after mowing and spreading. GPS coordinates only provided approximate locations, accurate to within circa 5m. Metal detectors failed to relocate metal pegs driven into the ground next to nests. The best method was to temporarily stick a twist of red insulation tape to the grass above the nest just before the machinery passed and to watch this marker from close range to see where this went under the machinery. After the operation, the nest would be marked using insulation tape tags, offset from the nest in a triangle pattern.

A high proportion of nests had failed before silaging operations took place. Unlike extant nests, empty nests could be marked more intrusively without risk of attracting predators. Road-marking spray paint cans were used to spray a ring of red or yellow dots centred on the nest but 2m away from it. After mowing, the cut grass swaths could never cover all the spots allowing quick relocation. In 2007 and 2008, dummy clutches of budgerigar eggs were placed in empty nests, to determine whether clutches could survive being run over. Budgerigar eggs are roughly the same width as skylark eggs so the two are comparable when lying on their sides in the nest cup. Budgie eggs are white so they cannot provide representative predation rates for camouflaged skylark clutches. Empty nests only provided information on trafficking rates, but no information on whether nest contents could survive the operations. Budgie clutches greatly increased sample sizes, allowing covariates of silaging event-survival rates to be tested.

4. Post fledging survival

A single chick from each nest was radiotagged before the brood left the nest (fledged). A Biotrack Pip tag was fitted, using a modified Rappole-Tipton harness with a weak link designed to let the tag drop off the bird after use (Rappole & Tipton 1991; Hill et al. 1999). The radiotags were used under an Unconventional Marks License through the British Trust for Ornithology ringing scheme. Full details of the tag design and performance are lodged with the BTO Unconventional Marks Committee and can be provided on request. All chicks were ringed with BTO rings.

The radiotagged chick was relocated daily to confirm that it was still alive and note its location with a GPS. The radiotag aerials on Nestlings and young fledglings occasionally became entangled in dense grass; but daily visits allowed entangled chicks to be released promptly. When a fledgling died, the radiotag was moved on to one of its siblings, if they could be found. Survival rate calculations only used the period when each fledgling carried the radiotag. The behaviour of the fledgling was recorded on each occasion, noting whether it hid, ran or attempted to fly on approach and how far it flew if flushed. This information was used to calculate daily survival rates and determine how long a chick was vulnerable to silaging machinery. Once the chick could no longer be captured by hand, they were only relocated after three-day intervals. Radiotagged fledglings were located before and after each silaging operation to distinguish deaths caused by machinery from those due to predation or starvation. If no signal was detected in the silage field, the area within a radius of several hundred metres was searched, as avian predators tended to carry fledglings away to consume them free of disturbance. Tag batteries nominally lasted 14 days, but in practice, usually lasted at least 20 days. Tags disappearing after 20 days of operation were considered to have run out of battery power and the chicks to have survived till the last sighting.

5. Daily survival rate calculations

Daily failure rates for nests and fledglings were modelled using standard Mayfield techniques, subdividing the periods of exposure into appropriate phenological stages (Aebischer 1999). A small modification to standard Mayfield analysis practice was necessary to account for a sharp increase in death rates at the time of leaving the nest. The exposure period for nestlings was considered to end when the nestlings reached the last day when they were still in the nest (typically 8 days old). Most chicks left the nest in the following 24-hour period and this period was explicitly included in the early fledgling exposure period (rather than the nestling period). Young fledglings were very vulnerable to cold, wet weather and starvation until they reached 12 days of age.

6. Re-nesting model design

The model simulated the activity of each pair one day at a time throughout a single breeding season. The egg-laying season for each pair was selected at random from the modelled distributions of start and end dates. Clutch sizes were selected at random. Then the model used random numbers between 0 and 1 to randomly choose whether the nest survived each hazard. The hazards presented by silaging operations and the continuous hazards presented by predation, starvation and abandonment were treated differently. Silaging operations were treated as one-off events, when the nest either failed immediately or survived. The model treated each harvest as a two-day process: mowing and spreading on the first day, then windrowing and collecting the silage on the second day. If the nest survived silaging operation on the current day, the daily survival rate was used to determine whether the nest was still extant one day later. The model date counter stepped forward one day in this case, but not for a silaging event. Survival rates differed by date, developmental stage, chick age, cutting height and the day of silaging operations. The model automatically chose the survival rate appropriate to each situation. The numbers of eggs hatching and the numbers of chicks fledging were chosen at random using binomial distributions at the relevant stage in the model. Then the survival of each fledgling was modelled in the same way as a nest, to calculate how many fledglings survived until independence (when they were able to fly away from silaging machinery). After each nest fledged young or failed, the date counter skipped to the FED of the next nest. A replacement interval was chosen at random from the observed distribution. If a low silage cut took place during this interval, the interval was extended by the observed low cutting delay. If the resulting FED was after the end date for the current pair’s egg laying season, the pair was considered to have finished breeding and the model mover on to the next pair.

The model collected cumulative data on productivity for each population of 100 pairs. The productivity summary data was written to a separate text file as one line of data per population. Means and standard deviations were calculated for the productivity per 100 pairs. Differences between scenarios were compared using t-tests. The probability values from these tests are meaningless on their own as all tests can be made to produce significant results by simply increasing the number of simulated populations (Topping & Odderskær, 2004). The t-tests do allow sets of competing scenarios to be compared, to identify which scenarios produce the largest effects on annual productivity.

The re-nesting model was implemented in a Visual Basic for Applications (VBA) module within Microsoft Excel.

7. Sward height measurements

The height of the cutting surface was measured after each cut, as soon as possible after the silage was cleared and before grass growth could resume. Cutting heights on control fields were classified as low if the mean cutting surface height was ≤ 8cm and high if >8cm.

Sward heights were measured weekly on all study fields and plots, throughout the skylark nesting season. Sward height was measured at 20 points, evenly distributed along a “W”-shaped transect, using an HFRO sward stick. Mean sward heights were used to interpolate sward heights on the first egg date of each nest. The height of the stubble from the preceding silage cuts was measured at nests initiated after the first cut. This was the only way to obtain reliable fine-scale information on sward conditions at nest initiation.
Appendix D: Changes in mean sward heights on Experiment 2 sites

Individual graphs show changes in mean sward height on Experiment 2 sites during the four years of the project. In all graphs, blue lines = fertilised control, red = control, green = moderate and yellow = lenient treatments. Confidence intervals are +/- 1 SE. Vertical lines are used to indicate the date grazing commenced (left) and date of plot closure (right) for moderate and lenient treatments.