Fennessy J, Bidon T, Reuss F, Kumar V, Elkan P, Nilsson MA, Vamberger M, Fritz U, Janke A. Multi-locus analyses reveal four giraffe species instead of one. Curr Biol. 2016;26:1–7.
Article
CAS
Google Scholar
Bowden R, MacFie TS, Myers S, Hellenthal G, Nerrienet E, Bontrop RE, Freeman C, Donnelly P, Mundy NI. Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population. PLoS Genet. 2012;8:1–10.
Article
CAS
Google Scholar
Redding DW, Mooers AØ. Incorporating evolutionary measures into conservation prioritization. Conserv Biol. 2006;20:1670–8.
Article
PubMed
Google Scholar
Jetz W, Thomas GH, Joy JB, Redding DW, Hartmann K, Mooers AO, Sheffield S. Global distribution and conservation of evolutionary distinctness in birds. Curr Biol. 2014;24:919–30.
Article
CAS
PubMed
Google Scholar
Doyle JM, Katzner TE, Roemer GW, Cain JW, Millsap BA, McIntyre CL, Sonsthagen SA, Fernandez NB, Wheeler M, Bulut Z, Bloom PH, DeWoody JA. Genetic structure and viability selection in the golden eagle (Aquila chrysaetos), a vagile raptor with a Holarctic distribution. Conserv Genet. 2016;17:1307–22.
Article
Google Scholar
Ruegg KC, Anderson EC, Paxton KL, Apkenas V, Lao S, Siegel RB, DeSante DF, Moore F, Smith TB. Mapping migration in a songbird using high-resolution genetic markers. Mol Ecol. 2014;23:5726–39.
Article
PubMed
Google Scholar
Malenfant RM, Coltman DW, Davis CS. Design of a 9K illumina BeadChip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing. Mol Ecol Resour. 2015;15:587–600.
Article
CAS
PubMed
Google Scholar
Zhao S, Zheng P, Dong S, Zhan X, Wu Q, Guo X, Hu Y, He W, Zhang S, Fan W, Zhu L, Li D, Zhang X, Chen Q, Zhang H, Zhang Z, Jin X, Zhang J, Yang H, Wang JJ, Wang JJ, Wei F. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat Genet. 2012;45:67–71.
Article
CAS
PubMed
Google Scholar
Schweizer RM, Robinson J, Harrigan R, Silva P, Galverni M, Musiani M, Green RE, Novembre J, Wayne RK. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves. Mol Ecol. 2016;25:357–79.
Article
CAS
PubMed
Google Scholar
Funk WC, Lovich RE, Hohenlohe PA, Hofman CA, Morrison SA, Sillett TS, Ghalambor CK, Maldonado JE, Rick TC, Day MD, Polato NR, Fitzpatrick SW, Coonan TJ, Crooks KR, Dillon A, Garcelon DK, King JL, Boser CL, Gould N, Andelt WF. Adaptive divergence despite strong genetic drift: Genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Mol Ecol. 2016;25:2176–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Funk WC, McKay JK, Hohenlohe PA, Allendorf FW. Harnessing genomics for delineating conservation units. Trends Ecol Evol. 2012;27:489–96.
Article
PubMed
PubMed Central
Google Scholar
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O’Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, et al. Great ape genetic diversity and population history. Nature. 2013;499:471–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peters JL, Lavretsky P, DaCosta JM, Bielefeld RR, Feddersen JC, Sorenson MD. Population genomic data delineate conservation units in mottled ducks (Anas fulvigula). Biol Conserv. 2016;203:272–81.
Article
Google Scholar
Nesje M, Roed K, Bell D, Lindberg P, Lifjeld J. Microsatellite analysis of population structure and genetic variability in peregrine falcons (Falco peregrinus). Anim Conserv. 2000;3:267–75.
Article
Google Scholar
Nesje M, Roed K, Lifjeld J, Lindberg P, Steens O. Genetic relationships in the peregrine falcon (Falco peregrinus) analysed by microsatellite DNA markers. Mol Ecol. 2000;9:53–60.
Article
CAS
PubMed
Google Scholar
Brown J, van Coeverden de Groot PJ, Birt TP, Seutin G, Boag P, Friesen V. 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. Mol Ecol. 2007;16:327–43.
Article
CAS
PubMed
Google Scholar
Jacobsen F, Nesje M, Bachmann L, Lifjeld JT. Significant genetic admixture after reintroduction of peregrine falcon (Falco peregrinus) in Southern Scandinavia. Conserv Genet. 2008;9:581–91.
Article
Google Scholar
Lifjeld JT, Bjornstad G, Steen OF, Nesje M. Reduced genetic variation in Norwegian peregrine falcons Falco peregrinus indicated by minisatellite DNA fingerprinting. Ibis. 2002;144:E19–26.
Article
Google Scholar
Oyler-McCance SJ, Oh KP, Langin KM, Aldridge CL. A field ornithologist’s guide to genomics: Practical considerations for ecology and conservation. Auk. 2016;133:626–48.
Article
Google Scholar
Steenhof K. Prairie falcon (Falco mexicanus). Birds of North America Online. The Cornell Lab of Ornithology; 2013. https://birdsna.org/Species-Account/bna/species/prafal. Accessed 2 Aug 2017
Sibley D. The Sibley Guide to Birds. 2nd ed. New York: Scott & Nix, Inc; 2014.
Google Scholar
Crossley R, Ligouri J, Sullivan B. The Crossley ID Guide: Raptors. Princeton: Princeton University Press; 2013.
Google Scholar
Steenhof K, Kochert MN. Dietary responses of three raptor species to changing prey densitites in a natural environment. J Anim Ecol. 1988;57:37–48.
Article
Google Scholar
Duerr AE, Miller TA, Cornell Duerr KL, Lanzone MJ, Fesnock A, Katzner TE. Landscape-scale distribution and density of raptor populations wintering in anthropogenic-dominated desert landscapes. Biodivers Conserv. 2015;24:2365–81.
Article
Google Scholar
Berry M, Bock C, Haire S. Abundance of diurnal raptors on open space grasslands in an urbanized landscape. Condor. 1998;100:601–8.
Article
Google Scholar
Pandolfino E, Herzog M, Hooper S, Smith Z. Winter habitat associations of diurnal raptors in California’s Central Valley. West Birds. 2011;42:62–84.
Google Scholar
Steenhof K, Carpenter LB, Kochert MN, Lehman RN. Long-term prairie falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions. Condor. 1999;101:28–41.
Article
Google Scholar
Smallwood KS, Thelander C. Bird mortality in the Altamont Pass Wind Resource Area, California. J Wildl Manag. 2008;72:215–23.
Article
Google Scholar
Hoffman S, Smith J. Population trends of migratory raptors in Western North America, 1977-2001. Condor. 2003;105:397–419.
Article
Google Scholar
Paprocki N, Heath JA, Novak SJ. Regional distribution shifts help explain local changes in wintering raptor abundance: Implications for interpreting population trends. PLoS One. 2014;9
McMahon BJ, Teeling EC, Höglund J. How and why should we implement genomics into conservation? Evol Appl. 2014:1–9.
Frankham R. Stress and adaptation in conservation genetics. J Evol Biol. 2005;18:750–5.
Article
CAS
PubMed
Google Scholar
Markert JA, Champlin DM, Gutjahr-Gobell R, Grear JS, Kuhn A, McGreevy TJ, Roth A, Bagley MJ, Nacci DE. Population genetic diversity and fitness in multiple environments. BMC Evol Biol. 2010;10:205.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cade T. Falcons of the World. London: Collins; 1982.
Google Scholar
Kleinschmidt O. Der Formenkreis Hierofalco und die Stellung des ungarischen Wurgfalken in demselben. Aquila. 1901;8:1–48.
Google Scholar
Nittinger F, Haring E, Pinsker W, Wink M, Gamauf A. Out of Africa? Phylogenetic relationships between Falco biarmkus and the other Hierofalcons (Aves: Falconidae). J Zool Syst Evol Res. 2005;43:321–31.
Article
Google Scholar
Helbig AJ, Seibold I, Bednarek W, Gaucher P, Ristow D, Scharlau W, Schmidl D, Wink M. 1994. Phylogenetic relationships among Falcon species (genus Falco) according to DNA sequence variation of the cytochrome b gene. In: Meyburg B-U, Chancellor RC, editors. Raptor Conservation Today. Berlin: World Working Group Birds of Prey and Pica Press; 1994. p. 593-599.
Wink M, Sauer-Gurth H, Ellis D, Kenward R. Phylogenetic relationships in the Hierofalco complex (Saker-, Gyr-, Lanner-, Laggar Falcon). In: Raptors Worldwide; 2004. p. 499–504.
Google Scholar
Wink M, Sauer-Gurth H. Phylogenetic relationships in diurnal raptors based on nucleotide sequences of mitochondrial and nuclear marker genes. In: Raptors Worldwide; 2004. p. 483–98.
Google Scholar
Sambrook J, Russell D. Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2001.
Google Scholar
Bolger A, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One. 2013;8:e85024.
Article
PubMed
PubMed Central
CAS
Google Scholar
Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella K V., Altshuler D, Gabriel S, DePristo MA. From fastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline. In Current Protocols in Bioinformatics; 2013(SUPL.43); 1–33.
Google Scholar
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Voskoboynik A, Neff NF, Sahoo D, Newman AM, Pushkarev D, Koh W, Passarelli B, Fan HC, Mantalas GL, Palmeri KJ, Ishizuka KJ, Gissi C, Griggio F, Ben-shlomo R, Corey DM, Penland L, White RA, Weissman IL, Quake SR. The genome sequence of the colonial chordate, Botryllus schlosseri. elife. 2013;2:e00569.
Article
PubMed
PubMed Central
Google Scholar
Mccoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetititve transposable elements. PLoS One. 2014;9:e106689.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin A, Sirotkin A, Vyahhi N, Tesler G, Alekseyev M, Pevzner P. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J Comput Biol. 2012;19:455–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009;19:1117–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parra G, Bradnam K, Ning Z, Keane T, Korf I. Assessing the gene space in draft genomes. Nucleic Acids Res. 2009;37:298–7.
Article
CAS
Google Scholar
Doyle JM, Katzner TE, Bloom PH, Ji Y, Wijayawardena BK, DeWoody JA. The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos). PLoS One. 2014;9:20–2.
Google Scholar
Smit A, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. Accessed 10 Aug 2015.
Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004;5:59.
Article
PubMed
PubMed Central
Google Scholar
Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003;19(Suppl. 2):ii215–25.
PubMed
Google Scholar
Hahn C, Bachmann L, Chevreux B. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach. Nucleic Acids Res. 2013;41:e129.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69:313–9.
Article
PubMed
Google Scholar
Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9.
Article
CAS
PubMed
Google Scholar
Zhan X, Pan S, Wang J, Dixon A, He J, Muller MG, Ni P, Hu L, Liu Y, Hou H, Chen Y, Xia J, Luo Q, Xu P, Chen Y, Liao S, Cao C, Gao S, Wang Z, Yue Z, Li G, Yin Y, Fox NC, Wang J, Bruford MW. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nat Genet. 2013;45:563–6.
Article
CAS
PubMed
Google Scholar
Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Falin LJ, Grabmueller C, Humphrey J, Kerhornou A, Khobova J, Aranganathan K, Langridge N, Lowy E, Mcdowall MD, Maheswari U, Nuhn M, Ong CK, Overduin B, Paulini M, Pedro H, Perry E, Spudich G, Tapanari E, Walts B, Williams G, Ruiz MT, Stein J, et al. Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res. 2016;44:574–80.
Article
CAS
Google Scholar
Li L, Stoeckert CJ, Roos DS. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
van Dongen S. Graph clustering by flow simulation. TheNetherlands: Ph.D thesis, University of Utrecht; 2000.
Edgar RC, Drive RM, Valley M. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kück P, Meusemann K. FASconCAT: Convenient handling of data matrices. Mol Phylogenet Evol. 2010;56:1115–8.
Article
PubMed
CAS
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cingolani P, Platts A, Wang L, Coon M, Nguyen T, Wang L, Land S, Ruden D, Lu X. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2, iso-3. Fly (Austin). 2012;6:1–13.
Article
CAS
Google Scholar
Thorvaldsdóttir H, Robinson J, Mesirov J. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178–92.
Article
PubMed
CAS
Google Scholar
Robinson J, Thorvaldsdottir H, Winckler W, Guttman M, Lander E, Getz G, Mesirov J. Integrative Genomics Viewer. Nat Biotechnol. 2011;29:24–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Waples R, Gaggiotti O. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol. 2006;15:1419–39.
Article
CAS
PubMed
Google Scholar
Freamo H, O’Reilly P, Berg P, Sigbjorn L, Boulding E. Outlier SNPs show more genetic structure between two Bay of Fundy metapopulations of Atlantic salmon than do neutral SNPs. Mol Ecol Resour. 2011;11:254–67.
Article
PubMed
Google Scholar
Helyar SJ, Bekkevold D, Taylor MI, Ogden R, Limborg MT. Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour. 2011;11:123–36.
Article
PubMed
Google Scholar
Bekkevold D, Helyar SJ, Limborg MT, Nielsen EE, Hemmer-Hansen J, Clausen LA, Carvalho GR. Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring. ICES J Mar Sci. 2015;72:1790–801.
Article
Google Scholar
Longmire J, Maltbie M, Baker R. Use of “lysis buffer” in DNA isolation and its implication for museum collections. Occas Pap Museum Texas Tech Univ. 1997;163:1–4.
Google Scholar
Steenhof K, Fuller MR, Kochert MN, Bates KK. Long-range movements and breeding dispersal of Prairie Falcons from southwest Idaho. Condor. 2005;107:481–96.
Article
Google Scholar
Rudnick JA, Katzner TE, Bragin EA, Rhodes OE, Dewoody JA. Using naturally shed feathers for individual identification, genetic parentage analyses, and population monitoring in an endangered Eastern imperial eagle (Aquila heliaca) population from Kazakhstan. Mol Ecol. 2005;14:2959–67.
Article
CAS
PubMed
Google Scholar
Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics. 2012;28:2537–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Clayton D: snpStats: SnpMatrix and XSnpMatrix classes and methods. 2014.
Google Scholar
Paetkau D, Strobeck C. Microsatellite analysis of genetic variation in black bear populations. Mol Ecol. 1994;3:489–95.
Article
CAS
PubMed
Google Scholar
Fridolfsson A-K, Ellegren HA. simple and universal method for molecular sexing of non-ratite birds. J Avian Biol. 1999;30:116–21.
Article
Google Scholar
Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–59.
CAS
PubMed
PubMed Central
Google Scholar
Earl D, Von Holdt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 2011;4:359–61.
Article
Google Scholar
Anderson EC, Dunham KK. The influence of family groups on inferences made with the program Structure. Mol Ecol Resour. 2008;8:1219–29.
Article
CAS
PubMed
Google Scholar
Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics. 2003;164:1567–87.
CAS
PubMed
PubMed Central
Google Scholar
Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14:2611–20.
Article
CAS
PubMed
Google Scholar
Keenan K, McGinnity P, Cross T, Crozier W, Prodohl P. DiveRsity: An R package for the estimation of population genetics parameters and their associated errors. Methods Ecol Evol. 2013;4:782–8.
Article
Google Scholar
Antao T, Lopes A, Lopes RJ, Beja-pereira A, Luikart G. LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics. 2008;9:323.
Article
PubMed
PubMed Central
CAS
Google Scholar
Foll M, Gaggiotti O. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics. 2008;180:977–93.
Article
PubMed
PubMed Central
Google Scholar
Sveinsdóttir M, Guðmundsdóttir L, Magnússon KP. Complete mitochondrial genome of the gyrfalcon Falco rusticolus (Aves, Falconiformes, Falconidae). Mitochondrial DNA Part A. 2017;28:370–1.
Article
CAS
Google Scholar
Hackett SJ, Kimball RT, Reddy S, Bowie RCK, Braun EL, Braun MJ, Chojnowski JL, Cox WA, Han K, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T. A phylogenomic study of birds reveals their evolutionary history. Science. 2008;320:1763–9.
Article
CAS
PubMed
Google Scholar
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldon T, Capella-Gutierrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346:1320–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Neilsen SC, Stringham SA, Hu H, Willerslev E, MTP G, Yandell M, Zhang G, Wang J. Genomic diversity and evolution of the head crest in the rock pigeon. Science. 2013;339:1063–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Griffiths C. Syringeal morphology and the phylogeny of the Falconidae. Condor. 1994;96:127–40.
Article
Google Scholar
DeWoody JA, Fernandez NB, Brüniche-Olsen A, Antonides JD, Doyle JM, San Miguel P, Westerman R, Vertyankin VV, Godard-Codding CAJ, Bickham JW. Characterization of the gray whale (Eschrichtius robustus) genome and a genotyping array based on single-nucleotide polymorphisms in candidate genes. Biol Bull. 2017;232:186–197.
Valière N, Fumagalli L, Gielly L, Miquel C, Lequette B, Poulle M-L, Weber J-M, Arlettaz R, Taberlet P. Long-distance wolf recolonization of France and Switzerland inferred from non-invasive genetic sampling over a period of 10 years. Anim Conserv. 2003;6:83–92.
Article
Google Scholar
Solberg KH, Bellemain E, Drageset O-M, Taberlet P, Swenson JE. An evaluation of field and non-invasive genetic methods to estimate brown bear (Ursus arctos) population size. Biol Conserv. 2006;128:158–68.
Article
Google Scholar
Dallas JF, Coxon KE, Sykes T, Chanin PRF, Marshall F, Carss DN, Bacon PJ, Piertney SB, Racey PA. Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter Lutra lutra. Mol Ecol. 2003;12:275–82.
Article
CAS
PubMed
Google Scholar
Bulut Z, Bragin E, DeWoody J, Braham M, Katzner T, Doyle J. Use of noninvasive genetics to assess nest and space use by white-tailed eagles. J Raptor Res. 2016;50:351–62.
Article
Google Scholar
Rudnick JA, Katzner TE, Bragin EA, De Woody JA. A non-invasive genetic evaluation of population size, natal philopatry, and roosting behavior of non-breeding eastern imperial eagles (Aquila heliaca) in central Asia. Conserv Genet. 2008;9:667–76.
Article
Google Scholar
DeWoody YD, DeWoody JA. On the estimation of genome-wide heterozygosity using molecular markers. J Hered. 2005;96:85–8.
Article
CAS
PubMed
Google Scholar
Kraus RHS, Van Hooft P, Megens HJ, Tsvey A, Fokin SY, Ydenberg RC, Prins HHT. Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms. Mol Ecol. 2013;22:41–55.
Article
CAS
PubMed
Google Scholar
Calderón L, Campagna L, Wilke T, Lormee H, Eraud C, Dunn JC, Rocha G, Zehtindjiev P, Bakaloudis DE, Metzger B, Cecere JG, Marx M, Quillfeldt P. Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove. BMC Evol Biol. 2016;16:237.
Article
PubMed
PubMed Central
Google Scholar
Burg T, Croxall J. Global relationships amongst black-browed and grey-headed albatrosses: analysis of population structure using mitochondrial DNA and microsatellites. Mol Ecol. 2001;10:2647–60.
Article
CAS
PubMed
Google Scholar
Walsh J, Kovach AI, Babbitt KJ, Brien KMO. Fine-scale population structure and asymmetrical dispersal in an obligate salt-marsh passerine, the Saltmarsh Sparrow (Ammodramus caudacutus). Auk. 2012;129:247–58.
Article
Google Scholar
Ciborowski KL, Levy H, Clucas GV, Rogers AD, Leach AD, Polito MJ, Lynch HJ, Dunn MJ, Hart T. Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc. Ecol Evol. 2016;6:1834–53.
Article
PubMed
PubMed Central
Google Scholar
Ponnikas S, Kvist L, Ollila T. Genetic structure of an endangered raptor at individual and population levels. Conserv Genet. 2013;14:1135–47.
Article
Google Scholar
Steenhof K, Kochert M, Moritsch M. Dispersal and migration of Southwestern Idaho raptors. J F Ornithol. 1984;55:357–68.
Google Scholar
Schmutz J, Fyfe R, Banasch U, Armbruster H. Routes and timing of migration of falcons banded in Canada. Wilson Bull. 1991;103:44–58.
Google Scholar
Lehman RN, Steenhof K, Carpenter LB, Kochert M. Turnover and dispersal of prairie falcons in southwestern Idaho. J Raptor Res. 2000;34:262–9.
Google Scholar
Spieth T. Gene flow and genetic differentiation. Genetics. 1974;78:961–5.
CAS
PubMed
PubMed Central
Google Scholar
Wright S. Evolution in Mendelian Populations. Genetics. 1931;16:97–159.
CAS
PubMed
PubMed Central
Google Scholar
Liu Y, He S, Zeng T, Du X, Shen J, Zhao A, Lu L. Transcriptome analysis of the livers of ducklings hatched normally and with assistance. Asian-Australasian J Anim Sci. 2017;30:773–80.
Article
Google Scholar
Cordeiro CMM, Hincke MT. Quantitative proteomics analysis of eggshell membrane proteins during chick embryonic development. J Proteome. 2016;130:11–25.
Article
CAS
Google Scholar
Elgvin TO, Trier CN, Tørresen OK, Hagen IJ, Lien S, Nederbragt AJ, Ravinet M, Jensen H, Sætre G. The genomic mosaicism of hybrid speciation. Sci Adv. 2017;3:e1602996.
Article
PubMed
PubMed Central
Google Scholar
Trier CN, Hermansen JS, Sætre G, Bailey RI. Evidence for mito-nuclear and sex-linked reproductive barriers between the hybrid Italian Sparrow and its parent species. PLoS Genet. 2014;10:e1004075.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wootton J, Bell DA. metapopulation model of the peregrine falcon in California: Viability and managment strategies. Ecol Appl. 1992;2:307–21.
Article
PubMed
Google Scholar
Wootton J, Bell D. Assessing predictions of population viability analysis: Peregrine falcon populations in California. Ecol Appl. 2014;24:1251–7.
Article
PubMed
Google Scholar
Sonsthagen SA, Williams JC, Drew GS, White CM, Sage GK, Talbot SL. Legacy or colonization? Posteruption establishment of peregrine falcons (Falco peregrinus) on a volcanically active subarctic island. Ecol Evol. 2017;7:107–14.
Article
PubMed
Google Scholar
Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim K-W, Sheng Z, An Y, Searle S, Herrero J, Groenen M, RPM C, et al. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet. 2013;45:776–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Antonides J, Ricklefs R, DeWoody J. The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola). Immunogenetics. 2017;69:175–86.
Article
CAS
PubMed
Google Scholar
Hillier L, Miller W, Birney E, HR WW. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004;432:695–716.
Article
CAS
Google Scholar
Cai Q, Qian X, Lang Y, Luo Y, Xu J, Pan S, Hui Y, Gou C, Cai Y, Hao M, Zhao J, Wang S, Wang Z, Zhang X, He R, Liu J, Luo L, Li Y, Wang J. Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude. Genome Biol. 2013;14:R29.
Article
PubMed
PubMed Central
CAS
Google Scholar