1. SUPPLEMENTARY METHODS
(a) Missing species and use of surrogates
Twenty-one species were missing from the initial sequence search, these were: Anser brachyrhynchus, Anser fabalis, Burhinus oedicnemus, Calidris temminckii, Carduelis cabaret, Charadrius dubius, Circus macrourus, Circus pygargus, Corvus cornix, Crex crex, Egretta garzetta, Fulica atra, Himantopus himantopus, Ixobrychus minutus, Lanius collurio, Merops apiaster, Oriolus oriolus, Platalea leucorodia, Pluvialis apricaria, Saxicola rubetra and Syrrhaptes paradoxus. However, data for close relatives of three of the missing species were available. I therefore used Ixobrychus sinensis as a surrogate for Ixobrychus minutus, and Merops nubicus as a surrogate for Merops apiaster. There are no congeners of either I. minutus or M. apiaster on the British checklist. I also used Pluvialis dominica as a surrogate for P. apricaria. This is justified because two from a total of four Pluvialis species breed or winter in Britain (P. apricaria and P. squatarola), and previous studies have shown that P. squatarola is most likely to be basal to the remaining three species (Halvorsen et al. 1998).
(b) Outgroup
I used the ostrich Struthio camelus as an outgroup. The ostrich belongs to the Paleognathae, which are reciprocally monophyletic with respect to the Neognathae (Slack et al. 2007), to which all British birds belong.
2. SUPPLEMENTARY RESULTS
Table S1. Median values of phylogenetic diversity lost (PD) and relatedness among species (mean phylogenetic distance – MPD) for British birds of conservation concern. P values are based on comparison with a null distribution (see main text for details).
N / Median observed PD / Median random PD (95% CIs) / P / Median observed MPD / Median random MPD / PAll red list / 32 / 355.20 / 310.23
(241.03-389.09) / ns / 66.33 / 71.89
(65.67-76.97) / <0.1
All amber & red list / 121 / 1386.04 / 1337.27
(1230.14-1449.59) / ns / 72.85 / 71.67
(68.89-74.89) / ns
Green list / 60 / 544.30 / 600.61
(509.54-700.77) / ns / 67.89 / 71.79
(67.53-75.99) / <0.1
HD / 8 / 104.37 / 74.11
(42.85-119.94) / ns / 78.29 / 72.46
(58.18-81.58) / ns
HDrec / 13 / 154.03 / 122.13
(80.75-177.09) / ns / 75.05 / 72.28
(61.46-79.59) / ns
BDr / 6 / 77.52 / 54.61
(29.16-94.96) / ns / 78.42 / 72.75
(54.88-83.15) / ns
BDMr / 16 / 191.89 / 151.68
(104.25-211.94) / ns / 72.27 / 72.18
(62.63-78.75) / ns
BDp / 22 / 223.66 / 210.53
(152.79-276.93) / ns / 61.85 / 71.97
(64.03-77.94) / <0.05
BDMp / 49 / 477.92 / 485.00
(401.72-575.37) / ns / 67.22 / 71.81
(66.97-76.18) / <0.1
BR / 21 / 217.72 / 200.45
(146.30-268.21) / ns / 74.65 / 71.88
(63.79-77.98) / ns
BL / 28 / 331.08 / 270.67
(206.50-344.18) / ns / 64.78 / 71.95
(65.10-77.31) / <0.05
BI / 14 / 129.65 / 131.73
(87.59-188.59) / ns / 69.50 / 72.15
(61.82-79.18) / ns
Small range – 5% / 9 / 143.64 / 83.53
(50.20-132.17) / <0.05 / 67.35 / 72.45
(58.70-80.80) / ns
Small range – 10% / 18 / 234.12 / 170.54
(120.75-233.76) / <0.05 / 67.83 / 72.02
(63.18-78.54) / ns
Small range – 25% / 45 / 485.72 / 442.65
(361.28-531.60) / ns / 71.52 / 71.83
(66.67-76.28) / ns
Small popn. – 5% / 9 / 115.68 / 83.53
(50.20-132.17) / ns / 74.81 / 72.45
(58.70-80.80) / ns
Small popn – 10% / 18 / 210.68 / 170.54
(120.75-233.76) / ns / 76.04 / 72.02
(63.18-78.54) / ns
Small popn – 25% / 45 / 464.77 / 442.65
(361.28-531.60) / ns / 75.11 / 71.83
(66.67-76.28) / ns
BDr restricted / 4 / 47.57 / 35.46
(16.63-70.60) / ns / 79.92 / 72.32
(46.70-86.38) / ns
BDMr restricted / 7 / 101.43 / 63.88
(35.72-106.38) / ns / 67.93 / 72.60
(56.28-82.31) / ns
BDp restricted / 20 / 193.09 / 191.45
(136.63-255.62) / ns / 58.37 / 72.13
(63.74-78.21) / <0.01
BDMp restricted / 40 / 388.72 / 390.11
(315.79-476.23) / ns / 65.62 / 71.79
(66.36-76.43) / <0.05
Abbreviations (Gregory et al. 2002): HD, historical population decline during 1800-1995; HDrec, historical population decline during 1800-1995; BDr, rapid (≥ 50%) contraction of UK breeding range over previous 25 years; BDMr, moderate (25-49%) contraction of UK breeding range over previous 25 years; BDp, rapid (≥ 50%) decline in UK breeding population over previous 25 years; BDMr, moderate (25-49%) decline in UK breeding population over previous 25 years; BR, five-year mean population size of 1-300 breeding pairs in UK; BL, ≥ 50% of UK breeding population in ten or fewer sites, but not rare breeders; BI, ≥ 20% of European breeding population in UK; Small range, species in the fifth percentile (5%), first decile (10%), or first quartile (25%) of range sizes; Small population, species in the fifth percentile (5%), first decile (10%), or first quartile (25%) of population sizes; BDr restricted, BDr with BDp and BDMp species excluded; BDMr restricted, BDMr with BDp and BDMp species excluded; BDp restricted, BDp with BDr and BDMr species excluded; BDMp restricted, BDMp with BDr and BDMr species excluded.
REFERENCES
Gregory, R. D., Wilkinson, N. I., Noble, D. G., Robinson, J. A., Brown, A. F., Hughes, J., Proctor, D., Gibbons, D. W. & Galbraith, C. A. 2002 The population status of birds in the United Kingdom, Channel Islands and Isle of Man: an analysis of conservation concern 2002-2007. British Birds95, 410-448.
Halvorsen, G. A., Byrkjedal, I. & Thompson, D. B. A. 1998 The phylogeny of the tundra plovers. In Tundra Plovers: The Eurasian, Pacific and American Golden Plovers and Grey Plover (ed. I. Byrkjedal & D. B. A. Thompson). London: T & AD Poyser.
Slack, K. E., Delsuc, F., Mclenachan, P. A., Arnason, U. & Penny, D. 2007 Resolving the root of the avian mitogenomic tree by breaking up long branches. Molecular Phylogenetics and Evolution42, 1-13.