/usr/lib/R/site-library/phylobase/nexusfiles/shorebird_underscore.nex is in r-cran-phylobase 0.8.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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[Data from Gavin Thomas]
BEGIN TAXA;
DIMENSIONS NTAX = 71;
TAXLABELS
Catoptrophorus_semipalmatus
Tringa_ochropus
Tringa_stagnatilis
Tringa_flavipes
Tringa_nebularia
Tringa_totanus
Tringa_erythropus
Tringa_melanoleuca
Tringa_glareola
Steganopus_tricolor
Phalaropus_lobatus
Phalaropus_fulicaria
Micropalama_himantopus
Eurynorhynchus_pygmeus
Aphriza_virgata
Calidris_canutus
Calidris_tenuirostris
Calidris_temminckii
Calidris_maritima
Calidris_ptilocnemis
Calidris_mauri
Calidris_alba
Calidris_alpina
Calidris_bairdii
Calidris_minutilla
Calidris_pusilla
Calidris_minuta
Calidris_ruficollis
Calidris_subminuta
Arenaria_interpres
Arenaria_melanocephala
Tringa_hypoleucos
Tringa_macularia
Limnodromus_griseus
Gallinago_gallinago
Coenocorypha_aucklandica
Coenocorypha_pusilla
Limosa_fedoa
Limosa_haemastica
Limosa_limosa
Limosa_lapponica
Bartramia_longicauda
Numenius_tahitiensis
Numenius_phaeopus
Numenius_arquata
Numenius_americanus
Rostratula_benghalensis
Jacana_spinosa
Jacana_jacana
Metopidius_indicus
Actophilornis_africanus
Pedionomus_torquatus
Pluvialis_apricaria
Pluvialis_dominica
Eudromias_morinellus
Charadrius_montanus
Charadrius_vociferus
Charadrius_wilsonia
Charadrius_dubius
Charadrius_hiaticula
Charadrius_melodus
Vanellus_vanellus
Vanellus_lugubris
Vanellus_armatus
Recurvirostra_avosetta
Haematopus_longirostris
Haematopus_fuliginosus
Haematopus_moquini
Haematopus_ostralegus
Haematopus_unicolor
Haematopus_finschi
;
END;
BEGIN CHARACTERS;
TITLE MassClutchSize;
DIMENSIONS NCHAR=4;
FORMAT DATATYPE = CONTINUOUS;
CHARSTATELABELS
1 malemass,
2 femalemass,
3 eggmass,
4 clutchsize;
MATRIX
Actophilornis_africanus 143.2 260.7 8.6 4.00
Aphriza_virgata 186.3 216.3 22.4 4.00
Arenaria_interpres 108.0 113.0 17.9 3.50
Arenaria_melanocephala 113.6 124.2 17.3 4.00
Bartramia_longicauda 151.0 164.0 23.5 3.99
Calidris_alba 52.8 55.4 11.2 3.90
Calidris_alpina 41.0 45.1 10.7 3.90
Calidris_bairdii 39.3 39.7 9.6 4.00
Calidris_canutus 126.0 148.0 19.3 3.70
Calidris_maritima 67.6 76.3 13.3 3.90
Calidris_mauri 28.0 31.0 7.5 3.90
Calidris_minuta 24.0 27.1 6.3 3.80
Calidris_minutilla 20.3 22.2 6.4 3.90
Calidris_ptilocnemis 76.3 83.0 14.2 4.00
Calidris_pusilla 25.0 27.0 6.9 4.00
Calidris_ruficollis 25.7 26.6 8.3 4.00
Calidris_subminuta 29.0 32.0 7.5 4.00
Calidris_temminckii 24.3 27.8 5.8 4.00
Calidris_tenuirostris 156.0 174.0 22.0 4.00
Catoptrophorus_semipalmatus 273.0 301.4 39.5 4.00
Charadrius_dubius 38.3 39.2 7.7 3.90
Charadrius_hiaticula 63.5 64.7 10.9 3.80
Charadrius_melodus 54.9 55.6 9.4 3.30
Charadrius_montanus 102.0 114.0 16.5 3.00
Charadrius_vociferus 92.1 101.0 14.5 4.00
Charadrius_wilsonia 59.0 63.0 12.4 3.00
Coenocorypha_aucklandica 101.2 116.1 23.7 2.00
Coenocorypha_pusilla 75.9 85.4 16.1 2.10
Eudromias_morinellus 100.0 117.0 17.0 2.90
Eurynorhynchus_pygmeus 31.0 34.6 8.0 4.00
Gallinago_gallinago 111.0 128.0 16.5 3.90
Haematopus_finschi 517.0 554.0 44.2 2.33
Haematopus_fuliginosus 740.3 778.5 69.5 2.00
Haematopus_longirostris 602.3 626.3 49.0 2.50
Haematopus_moquini 668.0 730.0 55.8 1.70
Haematopus_ostralegus 500.0 536.0 46.7 2.80
Haematopus_unicolor 717.0 734.0 48.2 2.40
Jacana_jacana 108.3 142.8 9.7 3.50
Jacana_spinosa 86.9 145.4 8.3 4.00
Limnodromus_griseus 111.0 116.0 17.5 4.10
Limosa_fedoa 320.0 421.0 44.5 4.10
Limosa_haemastica 222.0 289.0 37.5 4.00
Limosa_lapponica 313.0 354.0 37.0 3.72
Limosa_limosa 264.0 315.0 39.0 3.90
Metopidius_indicus 176.2 282.4 11.9 4.00
Micropalama_himantopus 55.8 60.4 11.2 3.90
Numenius_americanus 640.1 758.6 73.0 4.00
Numenius_arquata 662.0 788.0 76.0 3.90
Numenius_phaeopus 368.0 398.0 50.0 3.90
Numenius_tahitiensis 378.0 489.0 54.8 4.00
Pedionomus_torquatus 54.0 72.4 10.0 3.60
Phalaropus_fulicaria 50.8 61.0 7.5 3.80
Phalaropus_lobatus 32.4 37.4 6.3 4.00
Pluvialis_apricaria 175.0 176.0 32.8 3.90
Pluvialis_dominica 145.0 146.0 26.0 4.00
Recurvirostra_avosetta 258.0 288.0 31.7 3.90
Rostratula_benghalensis 146.0 159.0 12.4 4.00
Steganopus_tricolor 50.2 68.1 9.4 4.00
Tringa_erythropus 142.0 161.0 24.5 4.00
Tringa_flavipes 80.0 83.7 17.4 4.00
Tringa_glareola 62.0 73.0 13.5 4.00
Tringa_hypoleucos 45.5 50.0 12.5 3.90
Tringa_macularia 36.9 48.0 9.0 4.00
Tringa_melanoleuca 164.0 176.0 27.9 3.70
Tringa_nebularia 172.0 175.0 30.5 3.90
Tringa_ochropus 75.0 85.0 15.5 3.90
Tringa_stagnatilis 67.1 76.0 14.0 4.00
Tringa_totanus 123.0 135.0 22.3 4.00
Vanellus_armatus 162.0 167.0 16.5 3.10
Vanellus_lugubris 109.5 113.0 13.7 3.00
Vanellus_vanellus 211.0 226.0 25.5 3.90
;
END;
BEGIN CHARACTERS;
TITLE MatingSystem;
DIMENSIONS NCHAR=1;
FORMAT DATATYPE = STANDARD SYMBOLS="0 1 2";
CHARSTATELABELS
1 matingSystem / Monogamous Polygynous Polyandrous;
MATRIX
Actophilornis_africanus 2
Aphriza_virgata 0
Arenaria_interpres 0
Arenaria_melanocephala 0
Bartramia_longicauda 0
Calidris_alba 2
Calidris_alpina 0
Calidris_bairdii 0
Calidris_canutus 0
Calidris_maritima 0
Calidris_mauri 0
Calidris_minuta 2
Calidris_minutilla 0
Calidris_ptilocnemis 0
Calidris_pusilla 0
Calidris_ruficollis 0
Calidris_subminuta 0
Calidris_temminckii 2
Calidris_tenuirostris 0
Catoptrophorus_semipalmatus 0
Charadrius_dubius 0
Charadrius_hiaticula 0
Charadrius_melodus 0
Charadrius_montanus 2
Charadrius_vociferus 0
Charadrius_wilsonia 0
Coenocorypha_aucklandica 1
Coenocorypha_pusilla 0
Eudromias_morinellus 2
Eurynorhynchus_pygmeus 0
Gallinago_gallinago 0
Haematopus_finschi 0
Haematopus_fuliginosus 0
Haematopus_longirostris 0
Haematopus_moquini 0
Haematopus_ostralegus 0
Haematopus_unicolor 0
Jacana_jacana 2
Jacana_spinosa 2
Limnodromus_griseus 0
Limosa_fedoa 0
Limosa_haemastica 0
Limosa_lapponica 0
Limosa_limosa 0
Metopidius_indicus 2
Micropalama_himantopus 0
Numenius_americanus 0
Numenius_arquata 0
Numenius_phaeopus 0
Numenius_tahitiensis 0
Pedionomus_torquatus 2
Phalaropus_fulicaria 2
Phalaropus_lobatus 2
Pluvialis_apricaria 0
Pluvialis_dominica 0
Recurvirostra_avosetta 0
Rostratula_benghalensis 2
Steganopus_tricolor 2
Tringa_erythropus 0
Tringa_flavipes 0
Tringa_glareola 0
Tringa_hypoleucos 0
Tringa_macularia 2
Tringa_melanoleuca 0
Tringa_nebularia 0
Tringa_ochropus 0
Tringa_stagnatilis 0
Tringa_totanus 0
Vanellus_armatus 0
Vanellus_lugubris 0
Vanellus_vanellus 1
;
END;
BEGIN TREES;
TRANSLATE
1 Catoptrophorus_semipalmatus,
2 Tringa_ochropus,
3 Tringa_stagnatilis,
4 Tringa_flavipes,
5 Tringa_nebularia,
6 Tringa_totanus,
7 Tringa_erythropus,
8 Tringa_melanoleuca,
9 Tringa_glareola,
10 Steganopus_tricolor,
11 Phalaropus_lobatus,
12 Phalaropus_fulicaria,
13 Micropalama_himantopus,
14 Eurynorhynchus_pygmeus,
15 Aphriza_virgata,
16 Calidris_canutus,
17 Calidris_tenuirostris,
18 Calidris_temminckii,
19 Calidris_maritima,
20 Calidris_ptilocnemis,
21 Calidris_mauri,
22 Calidris_alba,
23 Calidris_alpina,
24 Calidris_bairdii,
25 Calidris_minutilla,
26 Calidris_pusilla,
27 Calidris_minuta,
28 Calidris_ruficollis,
29 Calidris_subminuta,
30 Arenaria_interpres,
31 Arenaria_melanocephala,
32 Tringa_hypoleucos,
33 Tringa_macularia,
34 Limnodromus_griseus,
35 Gallinago_gallinago,
36 Coenocorypha_aucklandica,
37 Coenocorypha_pusilla,
38 Limosa_fedoa,
39 Limosa_haemastica,
40 Limosa_limosa,
41 Limosa_lapponica,
42 Bartramia_longicauda,
43 Numenius_tahitiensis,
44 Numenius_phaeopus,
45 Numenius_arquata,
46 Numenius_americanus,
47 Rostratula_benghalensis,
48 Jacana_spinosa,
49 Jacana_jacana,
50 Metopidius_indicus,
51 Actophilornis_africanus,
52 Pedionomus_torquatus,
53 Pluvialis_apricaria,
54 Pluvialis_dominica,
55 Eudromias_morinellus,
56 Charadrius_montanus,
57 Charadrius_vociferus,
58 Charadrius_wilsonia,
59 Charadrius_dubius,
60 Charadrius_hiaticula,
61 Charadrius_melodus,
62 Vanellus_vanellus,
63 Vanellus_lugubris,
64 Vanellus_armatus,
65 Recurvirostra_avosetta,
66 Haematopus_longirostris,
67 Haematopus_fuliginosus,
68 Haematopus_moquini,
69 Haematopus_ostralegus,
70 Haematopus_unicolor,
71 Haematopus_finschi
;
TREE * UNTITLED = [&R] ((((((((1:19.701,(2:19.086,((3:13.762,4:13.762,5:13.762,6:13.762,(7:5.324,8:5.324):8.438):3.114,9:16.876):2.21):0.615):2.499,(10:3.42,(11:2.158,12:2.158):1.262):18.78):9.9,((13:17.413,14:17.413,(15:6.019,(16:3.798,17:3.798):2.221):11.394,(18:10.013,((19:2.588,20:2.588):6.989,(21:9.142,(22:8.707,((23:7.836,(24:7.4,(25:6.965,(26:3.483,27:3.483):3.482):0.435):0.436):0.435,(28:2.609,29:2.609):5.662):0.436):0.435):0.435):0.436):7.4):9.287,(30:5.68,31:5.68):21.02):5.4,(32:5.779,33:5.779):26.320999):2.3,(34:23.8,(35:22.8,(36:4.91,37:4.91):17.889999):1):10.6):2.6,(38:11.739,(39:9.303,(40:5.869,41:5.869):3.434):2.436):25.261):13.4,(42:20.299,(43:14.869,(44:10.15,(45:6.404,46:6.404):3.746):4.719):5.43):30.101):13.4,((47:43.3,((48:10.8,49:10.8):21.6,(50:19.845,51:19.845):12.555):10.9):8.8,52:52.099999):11.7):18.072,(((53:8.33,54:8.33):23.437001,((55:26.700001,(56:22.991999,((57:5.548,58:5.548):10.027,(59:12.882,(60:8.793,61:8.793):4.089):2.693):7.417):3.708):3,(62:22.961,63:22.960999,64:22.961):6.739):2.067):1.033,(65:19.1,(66:14.817,(67:12.849,(68:11.072,(69:4.283,70:4.283):6.789,71:11.072):1.777):1.968):4.283):13.7):49.071998);
END;
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