Online Resource 2 s1

Online Resource 2

The full set of Kruskal-Wallis tests to show significant and non-significant differences in values of the three measures of genetic diversity and population size categories (a), IUCN Red List categories (b), and studies using all three control region domains (c). Unequal variance t-tests and supporting Wilcoxon rank sum tests to show significant and non-significant differences in mean and median values of genetic diversity between island, mainland and island endemic species (d).

(a)

(b)

(c)

(d)

Alonso JC, Martín CA, Alonso JA, Palacín C, Magaña M, Lieckfeldt, Pitra C (2008) Genetic diversity of the great bustard in Iberia and Morocco: risks from current population fragmentation. Conservation Genetics, 10;379–390

Asai S, Akoshima D, Yamamoto Y, Shigeta Y, Matsue M, Momose H (2008) Current status of the Northern Goshawk Accipiter gentilis in Japan based on mitochondrial DNA. Ornithological Science 7;143–156

Baker AJ, Greenslade AD, Darling LM, Finlay C (2007) High genetic diversity in the blue-listed British Columbia population of the purple martin maintained by multiple sources of immigrants. Conservation Genetics 9;495–505.

Bates EM, Deyoung RW, Ballard BM (2009) Genetic Diversity and Population Structure of Reddish Egrets Along the Texas Coast. Waterbirds 32;430–436

Bech N, Boissier J, Drovetski S, Novoa C (2009) Population genetic structure of rock ptarmigan in the “sky islands” of French Pyrenees: implications for conservation. Animal Conservation 12;138–146

Bensch S, Hasselquist, D, (1999) Phylogeographic population structure of great reed warblers: an analysis of mtDNA control region sequences. Biological Journal of the Linnean Society 66;171–185

Brown JW, Coeverden De Groot, PJV, Birt TP, Seutin G, Boag P, Friesen VL (2007) Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus. Molecular Ecology 16;327–343

Bulgin N, Gibbs H, Vickery P (2003) Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus). Molecular Ecology 12;831-844

Cadahía L, Negro JJ, Urios V (2006) Low mitochondrial DNA diversity in the endangered Bonelli’s Eagle (Hieraaetus fasciatus) from SW Europe (Iberia) and NW Africa. Journal of Ornithology 148;99–104

Church A (2011) Mauritius and the rose-ringed parakeet; origin and genetic diversity of the Mauritian population of invasive rose-ringed parakeet. Masters thesis, Durrell Institute of Conservation and Ecology, University of Kent

Cortes-Rodriguez, N. et al., (2008) Geographic variation and genetic structure in the streak-backed oriole: low mitochondrial DNA differentiation reveals recent divergence. Condor 110;729–739

Dong L, Zhang J, Sun Y, Liu Y, Zhang Y, Zheng G (2010) Phylogeographic patterns and conservation units of a vulnerable species, Cabot’s tragopan (Tragopan caboti), endemic to southeast China. Conservation Genetics 11;2231–2242

Duriez O, Sachet JM, Ménoni E, Pidancier N, Miquel C, Taberlet P (2006) Phylogeography of the capercaillie in Eurasia: what is the conservation status in the Pyrenees and Cantabrian Mounts? Conservation Genetics 8;513–526

Eo SH, Wares JP, Carroll JP (2009) Subspecies and units for conservation and management of the northern bobwhite in the eastern United States. Conservation Genetics 11;867–875

Faria PJ, Guedes NMR, Yamashita C, Martuscelli P, Miyaki C (2008) Genetic variation and population structure of the endangered Hyacinth Macaw (Anodorhynchus hyacinthinus): implications for conservation. Biodiversity and Conservation 17;765–779

Haig S, Mullins T (2004) Subspecific relationships and genetic structure in the spotted owl. Conservation Genetics 5;683-705

Hansson B, Hasselquist D, Tarka M, Zehtindjiev P, Bensch S (2008) Postglacial colonisation patterns and the role of isolation and expansion in driving diversification in a passerine bird. PLoS ONE 3;p.e.2794

Hefti-Gautschi B, Pfunder M, Jenni L, Keller V, Ellegren H (2008) Identification of conservation units in the European Mergus merganser based on nuclear and mitochondrial DNA markers. Conservation Genetics 10;87–99

Hendrickson S, Bleiweiss R, Matheus J (2003) Low genetic variability in the geographically widespread andean condor. The Condor 105;1-12

Honnen AC, Hailer F, Kenntner N, Literák I, Dubska L, Zachos FE (2010) Mitochondrial DNA and nuclear microsatellites reveal high diversity and genetic structure in an avian top predator, the white‐tailed sea eagle, in central Europe. Biological Journal of the Linnean Society 99;727–737

Huang Z, Liu NF, Chen YK, Xiao YA (2009) Genetic diversity in peripheral and central populations of Rusty-necklaced Partridge (Alectoris magna) based on mitochondrial and microsatellite DNA. Acta Zoologica Academiae Scientiarum Hungaricae 55;187–197

Hull JM, Anderson R, Bradbury M, Estep JA, Ernest HB (2007) Population structure and genetic diversity in Swainson’s Hawks (Buteo swainsoni): implications for conservation. Conservation Genetics 9;305–316

Idaghdour Y, Broderick D, Korrida A, Chbel F (2004) Mitochondrial control region diversity of the houbara bustard Chlamydotis undulata complex and genetic structure along the Atlantic seaboard of North Africa. Molecular Ecology 13;43–54

Ishtiaq F, Dutta S, Yumnam B, Jhala YV (2011) Low genetic diversity in the endangered great Indian bustard (Ardeotis nigriceps) across India and implications for conservation. Conservation Genetics 12;857–863

Jiang HX, Hou YQ, Qian FW, Chu GZ, Li YX, Wang H, Shan K, Zheng GM (2008) Population genetic divergence and migration pattern of the Saunders's gull Larus saundersi. Acta Zool. Sin, 54;767–776

Jiang P, Ge Y, Lang Q (2007) Genetic structure among wild populations of Elliot's Pheasant Syrmaticus ellioti in China from mitochondrial DNA analyses. Bird Conservation 17;177-185

Johnson JA, Dunn PO (2006) Low Genetic Variation in the Heath Hen Prior to Extinction and Implications for the Conservation of Prairie-Chicken Populations. Conservation Genetics 7;37–48

Johnson JA, Burnham KK, Burnham WA, Mindell DP (2007) Genetic structure among continental and island populations of gyrfalcons. Molecular Ecology 16;3145–3160

Kvist L, Giralt D, Valera F, Hoi H, Kristin A, Darchiashvili G, Lovaszi P (2011) Population decline is accompanied by loss of genetic diversity in the Lesser Grey Shrike Lanius minor. Ibis 153;98-109

Kvist L, Viiri K, Dias P (2004) Glacial history and colonization of Europe by the blue tit Parus caeruleus. Journal of Avian Biology 35;352-359

Lerner HRL, Johnson JA, Lindsay AR, Kiff LF, Mindell DP (2009) It's not too late for the harpy eagle (Harpia harpyja): high levels of genetic diversity and differentiation can fuel conservation programs. PLoS ONE 4; p.e7336.

Lopes IF, Tomasulo-Seccomandi AM, Bryan Jr AL, Brisbin (2011) Genetic status of the wood stork (Mycteria americana) from the southeastern United States and the Brazilian Pantanal as revealed by mitochondrial DNA analysis. Genetics and Molecular Research 10;1910–1922

Lopes IF, Haig SM, Lama SND (2010) Genetic Characterization of Neotropical Jabiru Storks: Insights for Conservation. Waterbirds 33;425–437

Marshall HD, Baker AJ (1997) Structural conservation and variation in the mitochondrial control region of fringilline finches (Fringilla spp.) and the greenfinch (Carduelis chloris). Molecular Biology and Evolution 14;173-184

Marthinsen G, Wennerberg, Soldheim R, Lifjeld JT (2008) No phylogeographic structure in the circumpolar snowy owl (Bubo scandiacus). Conservation Genetics 10;923–933

Martínez-Cruz B, Godoy JA, Negro JJ (2004) Population genetics after fragmentation: the case of the endangered Spanish imperial eagle (Aquila adalberti). Molecular Ecology 13;2243–2255

Martínez-Fresno M, Henriques-Gil N, Arana P (2007) Mitochondrial DNA sequence variability in red-legged partridge, Alectoris rufa, Spanish populations and the origins of genetic contamination from A. chukar. Conservation Genetics 9;1223–1231

Mila B, McCormack JE, Castañeda G, Wayne RK, Smith TB (2007) Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco. Proceedings of the Royal Society B: Biological Sciences 274;2653–2660

Muñoz-Fuentes V, Green AJ, Negro JJ, Sorenson MD (2005) Population structure and loss of genetic diversity in the endangered white-headed duck, Oxyura leucocephala. Conservation Genetics 6;999–1015

Nittinger F, Gamauf A, Pinsker W, Wink M, Haring E (2007) Phylogeography and population structure of the saker falcon (Falco cherrug) and the influence of hybridization: mitochondrial and microsatellite data. Molecular Ecology 16;1497–1517

Oyler-McCance SJ, Ransler FA, Berkman LK, Qwinn TW (2007) A rangewide population genetic study of trumpeter swans. Conservation Genetics 8;1339–1353

Ozaki K, Yamamoto Y, Yamagishi S (2010) Genetic diversity and phylogeny of the endangered Okinawa Rail, Gallirallus okinawae. Genes & genetic systems 85;55–63

Patirana A, Hatch S, Friesen VL (2002) Population differentiation in the red-legged kittiwake (Rissa brevirostris) as revealed by mitochondrial DNA. Conservation Genetics 3;355-340

Pavlova A, Zink RM, Rohwer S, Koblik EA, Red'kin YA, Fadeev IV, Nesterov EV (2005) Mitochondrial DNA and plumage evolution in the white wagtail Motacilla alba. Journal of Avian Biology 36;322–336

Phymer J, Gain MG, Austin JE, Johnson DH, Krajewski C (2001) Mitochondrial phylogeography, subspecific taxonomy, and conservation genetics of sandhill cranes (Grus canadensis; Aves: Gruidae). Conservation Genetics 2;203-218

Poyarkov ND, Klenova AV, Kholodova MV (2010) Genetic diversity of swan goose (Anser cygnoides L.) in Russia: analysis of the mitochondrial DNA control region polymorphism. Russian Journal of Genetics 46;493–496

Reding DM, Freed LA, Cann RL, Fleischer RC (2010) Spatial and temporal patterns of genetic diversity in an endangered Hawaiian honeycreeper, the Hawaii Akepa (Loxops coccineus coccineus). Conservation Genetics 11;225–240

Robertson BC, Steeves TE, McBride KP, Goldstien SJ, Williams M, Gemmell NJ (2007) Phylogeography of the New Zealand blue duck (Hymenolaimus malacorhynchos): implications for translocation and species recovery. Conservation Genetics 8;1431–1440

Roques S, Negro JJ (2005) MtDNA genetic diversity and population history of a dwindling raptorial bird, the red kite (Milvus milvus). Biological Conservation 126;41–50

Russello M, Avery ML, Wright, T, (2008) Genetic evidence links invasive monk parakeet populations in the United States to the international pet trade. BMC Evolutionary Biology, 8;217

Santos MH, Lopes IF, Lama SN (2008) Population Genetic Study of Mitochondrial DNA in Roseate Spoonbill (Aves; Platalea ajaja) Breeding Colonies from the Pantanal Wetlands, Brazil. Biochemical Genetics 46;492–505

Shephard JM, Hughes JM, Catterall CP, Oldsen PD (2005) Conservation status of the White-Bellied Sea-Eagle Haliaeetus leucogaster in Australia determined using mtDNA control region sequence data. Conservation Genetics 6;413–429

Solovyeva DV, Pearce JM (2011) Comparative mitochondrial genetics of North American and Eurasian mergansers with an emphasis on the endangered scaly-sided merganser (Mergus squamatus). Conservation Genetics 12;839–844

Swinnerton K, Groombridge JJ, Jones CG, Burn RW, Mungroo, Y (2004) Inbreeding depression and founder diversity among captive and free‐living populations of the endangered pink pigeon Columba mayeri. Animal Conservation 7;353–364

Talbot S, Pearce JM, Pierson BJ, Derksen DV, Scribner KT (2003) Molecular status of the dusky Canada goose (Branta canadensis occidentalis): a genetic assessment of a translocation effort. Conservation Genetics 4;367-381

Uimaniemi L, Orell M, Kvist L, Jokimäki J, Lumme J (2003) Genetic variation of the Siberian tit Parus cinctus populations at the regional level: a mitochondrial sequence analysis. Ecography 26;98–106

Veit ML, Robertson RJ, Hamel PB, Friesen VL (2005) Population genetic structure and dispersal across a fragmented landscape in cerulean warblers (Dendroica cerulea). Conservation Genetics 6;159–174

Wennerberg L, Marthinsen G, Lifjeld JT (2008) Conservation genetics and phylogeography of southern dunlins Calidris alpina schinzii. Journal of Avian Biology 39;423–437

Yang SJ, Lei FM, Qu YH, Yin ZH (2006) Intraspecific phylogeography of the white-rumped snowfinch (Onychostruthus taczanowskii) endemic to the Tibetan Plateau based on mtDNA sequences. Journal of Zoology 268;187–192

Young DL, Allard M (1997) Conservation genetics of the plain pigeon Columba inornata in Puerto Rico and the Dominican Republic. Molecular Ecology 6;877–879

Zan S, Zhou L, Jiang H, Zhang B, Wu Z, Hou Y (2008) Genetic structure of the oriental white stork (Ciconia boyciana): implications for a breeding colony in a non-breeding area. Integrative Zoology 3;235–244

Zhang B, Fang S-G, Xi Y-M (2004) Low genetic diversity in the endangered crested ibis Nipponia nippon and implications for conservation. Bird Conservation International, 14;183-190

Zhang W-W, Zhang Y-M, Qnag Q, Li F (2010) Genetic diversity and population structure of marsh grassbird (Locustella pryeri sinensis) in China. Journal of Forestry Research 21;361–366

Zhou X, Fang W, Chen X (2009) Mitochondrial DNA diversity of the vulnerable Chinese Egret (Egretta eulophotes) from China. Journal of Ornithology 151;409–414

Zink RM, Blackwell-Rago RC (2000) Species limits and recent population history in the curve-billed thrasher. Condor 102;881-886