43
1 Appendices Appendix A: Further information on the Maxent Species Distribution Modelling (SDM) procedure Dr Philip McGowan (Director of World Pheasant Association when work was conducted and co-author) and Dr Peter Garson (Chair of IUCN-SSC Galliformes Specialist Group) are Galliformes experts who were consulted for the selection of covariates for niche modelling. Table A.1. Details on the number of Galliformes locality records in each WWF ecoregion of the study site. Key: EHasm = Eastern Himalayan alpine shrub and meadows, EHb = Eastern Himalayan broadleaf forest, EHsc = Eastern Himalayan sub- alpine conifer forest, Hsb = Himalayan sub-tropical broadleaf forest, Hsp = Himalayan sub-tropical pine forest, NEHsc = North-Eastern Himalayan sub-alpine conifer forest, NTt = Northern Triangle temperate forest, NWHasm = North-western Himalayan alpine shrub and meadows, WHasm = Western Himalayan alpine shrub and meadows, WHb = Western Himalayan broadleaf forest and WHsc = Western Himalayan sub- alpine conifer forest. WWF ecoregion Species EHasm EHb EHs c Hs b Hs p NEHsc NT t NWHasm WHasm WHb WHsc Blood pheasant 10 9 27 4 0 3 0 0 0 1 0 Blyth's tragopan 4 17 4 0 0 2 1 0 0 0 0 Buff-throated partridge 1 1 0 0 0 13 0 0 0 0 0 Cheer pheasant 1 0 2 2 12 2 0 0 33 36 146 113 Chestnut- breasted hill partridge 3 10 8 0 1 1 0 0 0 0 0 Chukar 2 0 3 0 24 0 0 9 4 7 6 Common peafowl 0 0 0 10 18 0 0 0 0 5 1 Common quail 0 0 0 3 0 0 0 0 1 2 0 Common hill partridge 3 24 22 1 11 1 0 1 0 4 1 Himalayan monal 19 16 24 3 45 5 0 67 17 58 44 Himalayan quail 0 0 0 0 4 0 0 0 0 0 0 Himalayan snowcock 1 0 2 0 8 0 0 14 7 10 11

ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

  • Upload
    lamdan

  • View
    212

  • Download
    0

Embed Size (px)

Citation preview

Page 1: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

1

Appendices

Appendix A: Further information on the Maxent Species Distribution Modelling (SDM) procedure

Dr Philip McGowan (Director of World Pheasant Association when work was conducted and co-

author) and Dr Peter Garson (Chair of IUCN-SSC Galliformes Specialist Group) are Galliformes

experts who were consulted for the selection of covariates for niche modelling.

Table A.1. Details on the number of Galliformes locality records in each WWF ecoregion of the study site. Key: EHasm = Eastern Himalayan alpine shrub and meadows, EHb = Eastern Himalayan broadleaf forest, EHsc = Eastern Himalayan sub-alpine conifer forest, Hsb = Himalayan sub-tropical broadleaf forest, Hsp = Himalayan sub-tropical pine forest, NEHsc = North-Eastern Himalayan sub-alpine conifer forest, NTt = Northern Triangle temperate forest, NWHasm = North-western Himalayan alpine shrub and meadows, WHasm = Western Himalayan alpine shrub and meadows, WHb = Western Himalayan broadleaf forest and WHsc = Western Himalayan sub-alpine conifer forest.

WWF ecoregion

Species EHasm EHb EHsc Hsb Hsp NEHscNTt NWHasm WHasm WHb WHsc

Blood pheasant 10 9 27 4 0 3 0 0 0 1 0

Blyth's tragopan 4 17 4 0 0 2 1 0 0 0 0Buff-throated partridge 1 1 0 0 0 13 0 0 0 0 0

Cheer pheasant 1 0 2 2 122 0 0 33 36 146 113Chestnut-breasted hill partridge 3 10 8 0 1 1 0 0 0 0 0

Chukar 2 0 3 0 24 0 0 9 4 7 6

Common peafowl 0 0 0 10 18 0 0 0 0 5 1

Common quail 0 0 0 3 0 0 0 0 1 2 0Common hill partridge 3 24 22 1 11 1 0 1 0 4 1

Himalayan monal 19 16 24 3 45 5 0 67 17 58 44

Himalayan quail 0 0 0 0 4 0 0 0 0 0 0Himalayan snowcock 1 0 2 0 8 0 0 14 7 10 11

Kalij pheasant 5 48 15 5 66 2 0 11 5 35 9

Koklass pheasant 2 0 27 0 71 3 0 54 7 68 29

Red junglefowl 1 32 1 9 44 1 1 6 2 8 10Rufous-throated hill partridge 0 33 8 1 11 0 0 0 0 0 0

Satyr tragopan 12 14 80 3 13 1 0 0 2 4 1

Sclater's monal 21 9 0 0 0 5 0 0 0 0 0

Snow partridge 4 0 2 0 0 0 0 5 5 3 0Temminck's tragopan 2 7 2 0 0 3 0 0 0 0 0

Page 2: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

2

WWF ecoregion

Species EHasm EHb EHsc Hsb Hsp NEHscNTt NWHasm WHasm WHb WHsc

Tibetan eared pheasant 0 0 0 0 0 8 0 0 0 0 0

Tibetan tragopan 1 0 0 0 0 5 0 0 1 0 0

Tibetan snowcock 9 0 0 0 0 4 0 1 6 0 0

Western tragopan 0 0 0 0 21 0 0 99 9 100 110

Page 3: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

3

Table A.2. Details of model AICc values based on choice of regularisation multiplier (beta). The regularisation parameter modifies the smoothness of the response curves that are generated for each species distribution model, which can affect both model complexity and the ability of the model to project to different time periods and region. Asterisks (*) indicate the final model used.

Common name Latin nameNumber locality records

Number model parameters

Beta AICc

Blood pheasant Ithaginis cruentus

56 7 1 1,356

56 7 0.5* 1,353

56 6 2 1,361

56 5 5 1,384

Blyth’s tragopan Tragopan blythii

36 4 1 901

36 4 0.5* 899

36 4 2 906

36 1 5 905

Buff-throated partridge Tetraophasis szechenyii

15 4 1 359

15 4 0.5 356

15 2 2* 356

15 1 5 361

Cheer pheasant Catreus wallichi

463 28 1 11,097

463 26 0.5* 11,075

463 25 2 11,129

463 22 5 11,270

Chestnut-breasted hill partridge

Arborophila mandelli

27 4 1* 656

27 5 0.5 656

27 4 2 664

27 2 5 683

Chukar Alectoris chukar

77 6 1 2,080

77 8 0.5* 2,077

77 3 2 2,097

77 3 5 2,098

Common peafowl Pavo cristatus

65 9 1 1,667

65 10 0.5* 1,666

65 9 2 1,677

65 5 5 1,685

Common quail Coturnix coturnix

12 2 1 342

12 2 0.5* 339

12 2 2 351

12 0 5 346

Common hill partridge  Arborophila torqueola

68 5 1 1,710

68 5 0.5* 1,708

68 4 2 1,711

68 3 5 1,719

Page 4: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

4

Common name Latin nameNumber locality records

Number model parameters

Beta AICc

Himlalayan monal Lophophorus impejanus

303 36 1* 7,789

314 38 0.5 8,257

314 36 2 8,250

314 25 5 8,278

Himalayan snowcock Tetraogallus himalayensis

62 6 1 1,574

62 7 0.5* 1,569

62 4 2 1,582

62 4 5 1,596

Kalij pheasant Lophura leucomenalos

202 28 1* 5,186

202 28 0.5 5,186

202 27 2 5,198

202 17 5 5,219

Koklass pheasant Pucrasia macrolopha

275 29 1* 7,132

275 29 0.5 7,132

275 29 2 7,142

275 20 5 7,187

Red junglefowl Gallus gallus

116 22 1 2,968

116 28 0.5* 2,963

116 10 2 2,985

116 7 5 2,999

Rufous-throated hill partridge

Arborophila rufogularis

53 14 1 1,183

53 16 0.5* 1,180

53 11 2 1,191

53 8 5 1,217

Satyr tragopan Tragopan satyra

132 13 1 3,147

132 17 0.5* 3,134

132 13 2 3,138

132 10 5 3,173

Sclater’s monal Lophophorus sclateri

37 6 1 933

37 6 0.5* 930

37 7 2 941

37 5 5 957

Snow partridge Lerwa lerwa

19 9 1 499

19 13 0.5 548

19 7 2 491

19 4 5* 491

Tibetan eared pheasant Crossoptilon harmani

52 6 1 1,314

52 8 0.5* 1,306

52 6 2 1,314

52 6 5 1,331

Page 5: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

5

Common name Latin nameNumber locality records

Number model parameters

Beta AICc

Tibetan partridge Perdix hodgsoniae

33 4 1* 894

33 5 0.5 899

33 4 2 898

33 4 5 916

Tibetan snowcock Tetraogallus tibetanus

98 8 1 2,677

98 9 0.5* 2,669

98 8 2 2,671

98 7 5 2,678

Temminck’s tragopan Tragopan temminckii

16 5 1 413

16 5 0.5* 406

16 2 2 414

16 1 5 417

Western tragopan Tragopan melanocephalus

350 22 1* 8,384

350 22 0.5 8,384

350 15 2 8,385

350 12 5 8,468

Table A.3. Details of Maxent models including Area Under Curve (AUC) and standard deviation of SDM results. In unbiased data, a high AUC indicates that sites with high predicted suitability values tend to be areas of known presence and locations with lower model prediction values tend to be areas where the species is not known to be present (absent or a random point). An AUC score of 0.5 means that the model is as good as a random guess. The smaller the standard deviation, the more precise the model’s predictions are. Site delimitation method codes: SS = study site only, ON = occupied or neighbouring ecoregions and ER = Himalayan ecoregions only. Feature function codes: l = linear, q = quadratic and p = product.

Species

Site delimitation method

Feature function Beta AUC

Standard deviation

Blood pheasant SS lq 0.5 0.86 0.06

Blyth's tragopan ON lq 0.5 0.82 0.11

Page 6: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

6

Species

Site delimitation method

Feature function Beta AUC

Standard deviation

Buff-throated partridge ER lq 2 0.87 0.21

Cheer pheasant ER lqp 0.5 0.90 0.03Chestnut- breasted hill partridge ON lq 1 0.86 0.08

Chukar ON lq 0.5 0.90 0.04

Common peafowl ON lq 0.5 0.85 0.07

Common quail ON l 2 0.47 0.13

Common hill partridge SS lq 0.5 0.85 0.08

Himalayan monal SS lqp 1 0.80 0.04

Himalayan snowcock ON lq 0.5 0.93 0.04

Kalij phesant SS lqp 1 0.80 0.04

Koklass pheasant ON lqp 1 0.92 0.02

Red junglefowl SS lqp 0.5 0.82 0.05Rufous- throated hill partridge ER lq 0.5 0.94 0.05

Satyr tragopan ER lq 0.5 0.88 0.05

Sclater's monal ON lq 0.5 0.81 0.07

Snow partridge ER lq 5 0.83 0.12

Temminck's tragopan ON lq 0.5 0.78 0.24

Tibetan eared pheasant ON lq 0.5 0.93 0.06

Tibetan partridge ON lq 1 0.80 0.12

Tibetan snowcock ON lq 0.5 0.80 0.12

Western tragopan ON lqp 1 0.95 0.01

Page 7: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

7

Table A.4. Details of predictor variables used in final Maxent models. Key: MAT = Maximum Annual Temperature, MAVT = Maximum Annual Variability in Temperature, MAP = Maximum Annual Precipitation, MAVP = Maximum Annual Variability in Precipitation.

Predictor

Blood pheasant Oct NDVI, Dec NDVI, MAT, MAVT, MAP, MAVP, study site

Blyth’s tragopan Jan NDVI, Feb NDVI, Mar NDVI, Oct NDVI, Dec NDVI, occupied neighbour

Buff-throated partridge Jul NDVI, ecoregions

Cheer pheasant Jan NDVI, Sep NDVI, MAVT, MAVP, elevation, slope, ecoregions

Chestnut-breasted hill partridge Feb NDVI, May NDVI, Oct NDVI, Dec NDVI, MAT, occupied neighbour

Chukar Apr NDVI, MAVT, MAVP, elevation, occupied neighbour

Common peafowl Feb NDVI, March NDVI, Apr NDVI, May NDVI, Jul NDVI, MAVP, slope, occupied neighbour

Common quail Jun NDVI, MAT, occupied neighbour

Common hill partridge Aug NDVI, Oct NDVI, Nov NDVI, Dec NDVI, MAT, MAVT, study site

Himalayan monal Jan NDVI, Feb NDVI, Jun NDVI, Jul NDVI, Aug NDVI, MAT, MAVT, MAVP, elevation, slope, study site

Himalayan snowcock Jun NDVI, MAVP, elevation, slope, occupied neighbour

Kalij pheasant Mar NDVI, Apr NDVI, Jun NDVI, Sep NDVI, Nov NDVI, MAT, MAVT, MAP, MAVP, study site

Koklass pheasant May NDVI, Jun NDVI, Jul NDVI, Aug NDVI, MAT, MAVT, MAVP, elevation, slope, occupied neighbour

Red junglefowl Feb NDVI, Mar NDVI, May NDVI, Jul NDVI, Aug NDVI, Sep NDVI, Oct NDVI, Nov NDVI, MAT, MAP, MAVP, elev, study site

Rufous-throated hill partridge Feb NDVI, Mar NDVI, May NDVI, Jul NDVI, Oct NDVI, Dec NDVI, MAT, MAP, ecoregions

Satyr tragopan Apr NDVI, Jun NDVI, Oct NDVI, MAT, MAVT, elevation, ecoregions

Sclater’s monal Jul NDVI, Dec NDVI, MAT, MAVP, elevation, slope, occupied neighbour

Snow partridge Feb NDVI, Mar NDVI, Apr NDVI, May NDVI, Dec NDVI, MAT, MAVP, elevation, ecoregions

Tibetan eared pheasant Jul NDVI, MAT, MAVT, MAP, MAVP, slope, occupied neighbour

Tibetan partridge Jul NDVI, MAT, MAP, occupied neighbour

Tibetan snowcock Jul NDVI, Oct NDVI, MAT, MAVT, MAVP, occupied neighbour

Temminck’s tragopan Nov NDVI, Dec NDVI, MAT, MAVP, elevation, slope, occupied neighbour

Western tragopan Jun NDVI, Jul NDVI, MAT, MAVT, MAP, slope, occupied neighbour

Page 8: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

8

Maxent result maps

Figure A.1.a. SDMs for 23/24 species with Himalayan quail shown as point data only (N = 24 maps in total). Polygons = BirdLife shapefile, green dots = point localities and warmer colours = most suitable habitat and cool colours = least suitable habitat. Key: A = Blood pheasant, B = Blyth’s tragopan and C = Buff-throated partridge

Page 9: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

9

Figure A.1.b. SDMs for 23/24 species with Himalayan quail shown as point data only (N = 24 maps in total). Polygons = BirdLife shapefile, green dots = point localities and warmer colours = most suitable habitat and cool colours = least suitable habitat. Key: D = Cheer pheasant, E = Chestnut-breasted hill partridge, F = Chukar and I = common hill partridge.

Page 10: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

10

Figure A.1.c. SDMs for 23/24 species with Himalayan quail shown as point data only (N = 24 maps in total). Polygons = BirdLife shapefile, green dots = point localities and warmer colours = most suitable habitat and cool colours = least suitable habitat. Key: G = Common peafowl and H = Common quail.

Page 11: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

11

Figure A.1.d. SDMs for 23/24 species with Himalayan quail shown as point data only (N = 24 maps in total). Polygons = BirdLife shapefile, green dots = point localities and warmer colours = most suitable habitat and cool colours = least suitable habitat. Key: J = Himalayan snowcock, K = Himalayan monal and L = Himalayan quail.

Page 12: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

12

Figure A.1.e. SDMs for 23/24 species with Himalayan quail shown as point data only (N = 24 maps in total). Polygons = BirdLife shapefile, green dots = point localities and warmer colours = most suitable habitat and cool colours = least suitable habitat. Key: M = Kalij pheasant, N = Koklass pheasant and O = Red junglefowl.

Page 13: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

13

Figure A.1.f. SDMs for 23/24 species with Himalayan quail shown as point data only (N = 24 maps in total). Polygons = BirdLife shapefile, green dots = point localities and warmer colours = most suitable habitat and cool colours = least suitable habitat. Key: P = Rufous-throated hill partridge, Q = Satyr tragopan and R = Sclater’s monal.

Page 14: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

14

Figure A.1.g. SDMs for 23/24 species with Himalayan quail shown as point data only (N = 24 maps in total). Polygons = BirdLife shapefile, green dots = point localities and warmer colours = most suitable habitat and cool colours = least suitable habitat. Key: S = Snow partridge, T = Tibetan partridge and U = Tibetan eared pheasant.

Page 15: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

15

Figure 1. SDMs for 23/24 species with Himalayan quail shown as point data only (N = 24 maps in total). Polygons = BirdLife shapefile, green dots = point localities and warmer colours = most suitable habitat and cool colours = least suitable habitat. Key: V = Tibetan snowcock, W = Temminck’s tragopan and X = Western tragopan.

Page 16: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

16

Appendix B: Calculation of raw Zonation weights and Zonation results

The following section outlines details of species-specific conservation values. We describe how these

values were obtained and re-scaled below.

Confidence in Maxent results. Smoothed response curves (Figure A.2) and maps that

broadly agreed with expert opinion with AUCs greater than 0.5 (better than random) were

scored between 1 (most confident) and 3 (least confident) to reflect our confidence in the

Maxent niche modelling procedure. Examples of poor maps include the Common quail (Fig

A.2. A) and good maps the Western tragopan (Fig A.2. B).

Figure A.2. Examples of ‘good’ (A) and ‘bad’ (B) Maxent receiver operator characteristics. A shows a smooth mean AUC with small standard deviations well above the random prediction line. B shows a jagged mean AUC with large standard deviations below the random prediction line.

Red List. Red List categories were taken from the IUCN Red List (IUCN, 2012) and

converted to numerical scores (Least Concern = 1, Near Threatened = 2, Vulnerable = 3,

Endangered = 4, Critically Endangered = 5). Thus, higher scores corresponded to a higher

global extinction risk.

Phylogenetic distinctiveness (PD). We generated PD scores on a taxonomically complete,

time-calibrated, DNA sequence based Bayesian phylogenetic hypothesis that includes all 291

extant Galliformes taxa (Stein et al 2015). Sixty-two of the 291 in-group taxa were data

deficient (no DNA sequence data), and taxonomic constraints (among species within a genus

or among genera with a family) were used to include the data-deficient taxa. Stein et al (2015)

generated a large posterior distribution of trees to account for the uncertain affinities of data

Page 17: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

17

deficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-

group taxa on 10000 fully resolved tree (Martyn, Kuhn, Mooers, Moulton, & Spillner, 2012)

sampled from the posterior distribution. Fair proportions partitions shared branches according

to the number of descendent taxa, such that a shared branch contributes branch length/number

of descendant taxa to the PD score. For simplicity, the analyses presented here use mean PD

score and included all 24 focal taxa. We conducted additional analyses that excluded two

data-deficient taxa, Chestnut-breasted hill partridge-breasted partridge (Arborophila mandelli)

and Snow partridge (Lerwa lerwa), and the results were qualitatively similar (data not

shown).

Relative range change. Measures of range change were calculated after Telfer et al. (2002).

The Galliformes point locality data were aggregated into a Behrmann equal area projection

using a grid with cells measuring 48.24 x 48.24 km, approximating to half a decimal degree

resolution. Only point locality data from Himalayan Galliformes species were used to obtain

measures of sampling effort in the Himalayan network of cells. Data were split into pre-

(<1980) and post-1980 (≥1980) or early vs. later time bins to ensure congruence with other

similar analyses conducted using this database (Mace et al., 2010) and to demarcate the rapid

escalation of anthropogenic change starting around the year 1980 (Millennium Ecosystem

Assessment, 2005). To control for change in geographical coverage with time, only cells that

were surveyed for both time periods being compared were included. The number of grid cells

containing one or more records was counted for each species in each time period. Only

species with a minimum of five cells in the early period were included in the analysis to avoid

curvilinearity given that the rarest species have a far greater capacity to expand than decline

(two species were excluded on these grounds; see Table A.5; Telfer et al., 2002). These grid

cells were then expressed as proportions of the total survey area and logit-transformed. A

linear regression model was fitted to the logit-transformed proportions from the earlier and

later periods and weighted to account for heteroscedasticity. Each species’ standardised

residual was then taken to represent an index of its change in geographic range size, relative

to the trend in the whole group. Full details of the method are in Telfer et al. (2002). The

Page 18: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

18

standardised residuals represent relative change only and without calibration of the index it is

difficult to know if the direction of the residuals represents absolute positive or negative

changes. The standardised residuals represent range contractions and expansions relative to

the trend of the group analysed and not absolute changes.

Endemism to the Himalaya. Measures of endemism were calculated from the proportion of

the Greater Himalaya that intersected the focal species’ global range as measured by BirdLife

range maps (BirdLife International and NatureServe, 2011). The endemism measure reflected

the important of the Greater Himalaya as an areal proportion of each species’ total global

range. A continuous scale was used as definitions of endemism area inherently scale

dependent (Laffan & Crisp, 2003) with 1 = endemic and 0 = not endemic.

Re-scaling the raw weight scores. Scores were scaled to be congruent to the Red List

categories (between 1-5) using the general formula x '=( ( x−a ) ( d−c )b−a )+c where mapping

from (a,b) to (c,d). Note: the adjusted weights for the relative range scores were reversed in

polarity as species that have negative raw scores are higher priorities.

Page 19: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

19

Table A.5 Summary of the species used in the analysis with details of species-specific weightings. Note: the adjusted weights for the relative range change scores have been reversed in polarity as species that have negative raw scores are higher priorities. Confidence in Maxent results were assessed by G. Buchanan and J. Dunn.

      Raw weights (adjusted weights)

Common name Latin name

Confidence in Maxent results

Red List

Endemism

Relative Range Change

Phylogenetic distinctiveness

Blood pheasant

Ithaginis cruentus 2 1 0.22

(1.85)-0.80

(3.17) 35.63 (5.00)

Blyth's tragopan

Tragopan blythii 2 3 0.23

(1.89)1.20

(1.20) 10.43 (1.67)

Buff-throated partridge

Tetraophasis szechenyii 3 1 0.21

(1.81) N/A 14.15 (2.16)

Cheer pheasant

Catreus wallechi 1 3 0.74

(3.95)0.67

(1.72) 11.74 (1.84)

Chestnut-breasted hill partridge

Arborophila mandelli 2 1 1.00

(5.00)0.67

(1.72) 8.32 (1.39)

Chukar Alectoris chukar 1 1 0.03

(1.08)-0.59

(2.97) 8.18 (1.37)

Common peafowl Pavo cristatus 1 1 0.12

(1.44)0.82

(1.57) 15.07 (2.28)

Common quail

Coturnix coturnix 3 1 0.04

(1.12)0.68

(1.71) 9.98 (1.61)

Common hill partridge 

Arborophila torqueola 1 1 0.01

(1.00)-0.09

(2.47) 8.11 (1.36)

Himalayan monal

Lophophorus impejanus 2 1 0.58

(3.30)1.40

(1.00) 13.29 (2.04)

Himalayan quail

Ophrysia superciliosa N/A 5 0.78

(4.11) N/A N/A

Himalayan snowcock

Tetraogallus himalayensis 1 1 1.00

(5.00)0.34

(2.05) 10.28 (1.65)

Kalij pheasant

Lophura leucomenalos 2 1 0.33

(2.29)0.62

(1.77) 6.39 (1.13)

Koklass pheasant

Pucrasia macrolopha 1 1 0.10

(1.36)1.19

(1.21) 24.83 (3.57)

Red junglefowl Gallus gallus 2 1 0.05

(1.16)0.71

(1.68) 9.58 (1.55)

Rufous- throated hill partridge

Arborophila rufogularis 1.5 1 0.26

(2.01)-0.42

(2.80) 8.28 (1.38)

Satyr tragopan

Tragopan satyra 1 2 1.00

(5.00)0.09

(2.29) 11.45 (1.80)

Sclater's monal

Lophophorus sclateri 2 3 0.55

(3.18)-0.07

(2.45) 13.29 (2.04)

Snow partridge Lerwa lerwa 2 1 0.4 (2.58) -0.21

(2.59) 23.39 (3.38)

Page 20: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

20

      Raw weights (adjusted weights)

Common name Latin name

Confidence in Maxent results

Red List

Endemism

Relative Range Change

Phylogenetic distinctiveness

Temminck's tragopan

Tragopan temmincki 3 1 0.06

(1.20)0.01

(2.37) 10.97 (1.74)

Tibetan eared pheasant

Crossoptilon harmani 1 2 0.62

(3.46)-1.47

(3.83) 5.39 (1.00)

Tibetan partridge

Perdix hodgsoniae 2 1 0.17

(1.65)-2.65

(5.00) 13.37 (2.06)

Tibetan snowcock

Tetraogallus tibetanus 2 1 0.17

(1.65)0.05

(2.33) 12.07 (1.88)

Western tragopan

Tragopan melanocephalus

1 3 0.78 (4.11)

1.20 (4.11)

10.48 (1.67)

Page 21: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

21

Figure A.3 The top two panels show the average Zonation response curves across all species for both A) unconstrained and B) constrained solutions. The bottom two panels show the minimum response curves for the worst off species for both C) unconstrained and D) constrained solutions. Response curve colours correspond to the following Zonation solutions: blue = distribution discounting, red = endemism, green = Red List, purple = phylogenetic distinctiveness and orange = range change. The vertical lines represent 1-proportion of the Himalayan landscape taken up by PAs (i.e. 81.9% of the landscape lost). Comparisons between the proportion of species distributions where the response curves intersect the vertical line (A vs. B and C vs. D) indicate the efficacy of the current PA network in capturing Galliformes distributions. i.e. if PAs were perfectly placed, the proportions of distributions remaining would be equal.

Page 22: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

22

Figure A.4 Zonation result maps (A = basic, B = distribution discounting, C = weighted by Red List, D = weighted by endemism, E = weighted by range change, F = weighted by phylogenetic distinctiveness) for species of Galliformes occurring in the Himalayan region. The warmest colours indicate the most important conservation areas and the coolest colours indicate the least important conservation areas: black = 0-20% (least important areas), dark blue = 20-50%, blue = 50-75%, yellow = 75-90%, pink = 90-95%, dark red = 95-98% and red = 98-100% (most important areas). The top fraction (18.1%) of each solution corresponds to an area of approximately 118,513 km2 out of a total of 654,772 km2, which is equal to the current area taken up by PAs. Note: weighted solutions presented here were weighted after accounting for data uncertainty using distribution discounting.

Page 23: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

23

Appendix C: Further information on the overlap between important areas as identified by different

measures of conservation value

Figure A.5a. Comparison maps for Kappa statistics. Black indicates areas with equal value rasters (0+ 0 or 1+1) whereas red indicates areas with unequal value rasters (0+1). Total no. of cells in area = 687,532. Overlaps are shown for: A = basic x distribution discounting, B = distribution discounting x endemism, C = distribution discounting x Red List, D = distribution discounting x phylogenetic diversity, E = distribution discounting x range changes, F = endemism x range changes

Page 24: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

24

Figure A.5b. Comparison maps for Kappa statistics. Black indicates areas with equal value rasters (0+0 or 1+1) whereas red indicates areas with unequal value rasters (0 and 1). Total no. of cells in area = 687,532. Overlaps are shown for: G = endemism x phylogenetic diversity, H = endemism x range changes, I = Red List x phylogenetic diversity, J = Red List x range changes, K = phylogenetic diversity x range changes.

Page 25: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

25

Table A.6. Table showing details of the protected areas used in the analysis. N = 119. Country codes: PAK = Pakistan, NPL = Nepal, MMR = Myanmar, BTN = Bhutan and IND = India.

Country Name Designated

IUCN category

Status year Area km2

PAK HalejiWildlife Sanctuary IV 1977 2.81

PAK ManshiWildlife Sanctuary IV 1977 22.72

PAK SalkhalaWildlife Sanctuary IV 1982 7.73

PAK KargahWildlife Sanctuary IV 1975 0.66

PAK BajwatWildlife Sanctuary IV 1964 1.12

PAK Chitral Gol National Park II 1984 149.45

NPL Langtang National Park II 1976 1321.74

NPL Sagarmatha National Park II 1976 389.94

NPL Royal Chitwan National Park II 1973 1179.70

NPL Rara National Park II 1976 113.96

NPL Royal Bardia National Park II 1976 909.15

NPLRoyal Suklaphanta

Wildlife Reserve IV 1976 369.45

NPL Koshi TappuWildlife Reserve IV 1976 150.88

NPL Shey-Phoksundo National Park II 1984 3636.40

NPL Khaptad National Park II 1984 233.51

NPL ParsaWildlife Reserve IV 1984 476.51

NPL Shivapuri National Park II 1985 91.08

Page 26: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

26

Country Name Designated

IUCN category

Status year Area km2

NPL Makalu-Barun National Park II 1991 875.06

MMR Khakaborazi National Park II 1996 3732.31

MMR Hukaung ValleyWildlife Sanctuary III 2001 224.35

MMR HponkanraziWildlife Sanctuary III 2001 2132.69

MMR BumhpabumWildlife Sanctuary III 2002 200.09

BTN Jigme Dorji National Park II 1974 4079.90

BTNJigme Singye Wangchuck National Park II 1995 1730.22

BTN KhalingWildlife Sanctuary IV 1974 294.60

BTN Royal Manas National Park II 1966 959.85

BTN Thrumshingla National Park II 1998 784.54

BTN ToorsaStrict Nature Reserve Ia 1993 650.69

BTN SaktengWildlife Sanctuary IV 1993 754.46

BTN PhibsooWildlife Sanctuary IV 1993 236.60

BTN BumdelingWildlife Sanctuary IV 1995 1563.29

IND Khangchendzonga National Park II 1977 735.45

IND Corbett National Park II 1936 318.63

IND Dudhwa National Park II 1977 633.94

Page 27: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

27

Country Name Designated

IUCN category

Status year Area km2

IND Kedarnath Sanctuary IV 1972 451.44

INDGovind Pashu Vihar Sanctuary IV 1955 597.19

IND Katarniyaghat Sanctuary IV 1977 342.20

IND Nanda Devi National Park Ib 1982 141.64

IND Manas Sanctuary IV 1928 0.58

IND Namdapha National Park II 1983 1800.73

IND Itanagar Sanctuary IV 1978 185.31

IND Pakhui Sanctuary IV 1977 855.12

IND Sonai-Rupai Sanctuary IV 1998 0.34

IND Valmiki Sanctuary IV 1978 161.51

IND Dachigam National Park II 1981 332.33

IND Overa Sanctuary IV 1981 31.92

IND Kistwar National Park II 1981 738.01

IND Hokarsar Lake Sanctuary IV 1992 13.72

IND Sechu Tuan Nala Sanctuary IV 1962 284.46

IND Gamgul Siahbehi Sanctuary IV 1962 89.98

IND Tundah Sanctuary IV 1962 106.26

IND Kugti Sanctuary IV 1962 509.91

IND Kalatop-Khajjair Sanctuary IV 1958 60.83

IND Nargu Sanctuary IV 1962 285.54

IND Shikari Devi Sanctuary IV 1962 76.97

Page 28: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

28

Country Name Designated

IUCN category

Status year Area km2

IND Bandli Sanctuary IV 1962 12.84

IND Gobindsagar Sanctuary IV 1962 178.53

IND Naina Devi Sanctuary IV 1982 38.84

IND Majathal Sanctuary IV 1954 23.85

IND Daranghati Sanctuary IV 1962 33.04

IND Shilli Sanctuary IV 1963 2.01

IND Shimla Catchment Sanctuary IV 1958 36.29

IND Talra Sanctuary IV 1962 35.94

IND Darlaghat Sanctuary IV 1962 115.24

IND Raksham Chitkul Sanctuary IV 1962 29.53

IND Lippa Asrang Sanctuary IV 1962 63.20

IND Manali Sanctuary IV 1954 98.50

IND Khokhan Sanctuary IV 1954 17.39

IND Kanawar Sanctuary IV 1954 80.66

IND Chail Sanctuary IV 1976 126.40

IND Tirthan Sanctuary IV 1992 61.61

IND Garumara Sanctuary IV 1984 8.46

IND Chapramari Sanctuary IV 1976 9.56

IND Mahananda Sanctuary IV 1976 160.32

IND Mehao Sanctuary IV 1980 317.56

IND Great Himalayan National Park II 1962 742.55

Page 29: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

29

Country Name Designated

IUCN category

Status year Area km2

IND Valley Of Flowers National Park II 1982 31.66

IND Neora Valley National Park II 1992 92.36

IND Buxa Sanctuary IV 1986 95.47

IND Rupi Bhaba Sanctuary IV 1982 855.28

IND Baltal-Thajwas Sanctuary IV 1987 148.94

IND Overa-Aru Sanctuary IV 1981 454.90

IND Jasrota Sanctuary IV 1987 4.22

IND Hirapora Sanctuary IV 1987 119.74

IND Limber Sanctuary IV 1987 11.21

IND Lachipora Sanctuary IV 1987 79.57

IND Fambong Lho Sanctuary IV 1984 68.13

IND City Forest National Park II 1992 8.98

IND Gulmarg Sanctuary IV 1987 125.98

IND Askot Musk Deer Sanctuary IV 1986 223.31

IND Mouling National Park II 1986 435.20

IND Sonanadi Sanctuary IV 1987 60.78

IND Sohagibarwa Sanctuary IV 1987 157.39

IND Pong Dam Lake Sanctuary IV 1982 247.71

IND Pin Valley National Park II 1958 849.23

IND Kais Sanctuary IV 1954 12.13

Page 30: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

30

Country Name Designated

IUCN category

Status year Area km2

INDKyongnosla Alpine Sanctuary IV 1977 19.47

IND Shingba Sanctuary IV 1984 39.57

IND Nameri Sanctuary IV 1985 21.32

IND Singalila National Park II 1992 78.09

IND Maenam Sanctuary IV 1987 42.77

IND Binsar Sanctuary IV 1988 45.43

IND Churdhar Sanctuary IV 1985 30.18

IND Tale Valley Sanctuary IV 1995 335.71

IND Dibang Sanctuary IV 1991 766.50

IND Manas National Park II 1990 3.77

IND Valmiki National Park II 1989 334.35

IND Govind National Park II 1990 493.83

IND Sohelwa Sanctuary IV 1988 240.37

IND Gangotri National Park II 1989 214.81

IND Eagle Nest Sanctuary IV 1989 215.35

IND Kamlang Sanctuary IV 1989 780.00

IND Kane Sanctuary IV 1991 54.63

IND Sessa Orchid Sanctuary IV 1989 99.26

INDBarsey Rhododendron Sanctuary IV 1998 137.64

IND Gorumara National Park II 1992 79.13

IND Kibber Sanctuary IV 1992 1279.40

Page 31: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

31

Country Name Designated

IUCN category

Status year Area km2

IND Sainj Sanctuary IV 1994 89.73

IND Sangla Sanctuary IV 1989 648.04

Page 32: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

32

Table A.7. Table showing the number of cells for each unique combination of Zonation solutions (total number of cells = 755,532 across a total area of 654,772 km2). Cell size is 0.009 decimal degrees corresponding to approximately 1 km. Thus, 1 cell ≈ 1 km2. Zonation solution codes: DD = distribution discounting, EN = endemism, PD = phylogenetic distinctiveness, RL = Red List and RRC = relative range change.

DD EN PD RL RRC No. cells

0 0 0 0 0 466,986

0 0 1 0 0 32,584

1 1 0 0 0 2,120

0 1 0 0 0 15,146

0 0 0 0 1 29,519

1 0 1 0 0 16,352

1 1 1 0 0 2,144

0 1 0 0 1 4,422

1 1 0 0 1 5,795

1 0 0 0 1 5,634

0 0 1 0 1 5,230

1 0 1 0 1 14,676

1 1 1 0 1 6,882

0 1 1 0 1 2,274

0 0 0 1 1 1,262

0 1 1 1 1 1,765

1 1 1 1 1 34,257

0 0 1 1 1 377

0 1 0 1 1 4,766

1 1 0 1 1 13,635

1 1 0 1 0 13,056

0 1 1 0 0 5,115

1 0 0 0 0 3,901

1 1 1 1 0 6,538

0 0 0 1 0 29,391

0 1 0 1 0 16,495

0 1 1 1 0 2,342

1 0 1 1 1 3,348

0 0 1 1 0 1,106

1 0 1 1 0 1,762

1 0 0 1 1 2,910

1 0 0 1 0 3,742

Page 33: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

33

Figure A.6 Map showing the existing protected area network in red and potential areas for expansion of the network in blue. Blue areas indicate overlap between five different Zonation solutions and if these areas were formally protected, would conserve multiple facets of conservation value for Galliformes. To aid conservation practitioners and legislators, this map is also provided in .kml format for use with Google Earth in the online version of the Appendix and locality place names and latitude/longitude coordinates are provided in Table A.8.

Page 34: ars.els-cdn.com  · Web viewdeficient taxa. We calculated PD scores (fair proportions; Redding et al., 2008) for all 291 in-group taxa on 10000 fully resolved tree (Martyn, Kuhn,

34

Table A.8 Description and latitude/longitude coordinates of potential target localities for PA expansion.

Locality description Latitude LongitudeNear Tiba Kangri, Nyingchi, China 29°49'60.00''N 94°51'60.00''ENear Daga, Bhutan 27°5'49.021''N 89°52'26.04''ENear North Royal Manas NP, Bhutan 27°1'49.88''N 90°42'54.99''ENear Rohru, Himachal Pradesh, India 31°12'7.20''N 77°45'6.84''ESouth of Dharamsala, Himchal Pradesh, India 32°13'8.55''N 76°19'24.25''ESouth of Wakro, Arunachal Pradesh, India 27°46'57.27''N 96°20'51.57''ENear Gorakhani, Takasindu, Nepal 27°29'24.00''N 86°30'36.00''E