Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016;17:81–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Armstrong DP, Seddon PJ. Directions in reintroduction biology. Trends Ecol Evol. 2008;23:20–5.
Article
PubMed
Google Scholar
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE. 2008;3:e3376.
Article
PubMed
PubMed Central
Google Scholar
Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genom. 2011;12:1–9.
Article
Google Scholar
Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier (France); 2004.
BirdLife International. Liocichla omeiensis. The IUCN Red List of Threatened Species 2017. Cambridge: BirdLife International; 2017.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Human Genet. 1980;32:314–31.
CAS
Google Scholar
Bruford MW, Wayne RK. Microsatellites and their application to population genetic studies. Curr Opin Genet Dev. 1993;3:939–43.
Article
CAS
PubMed
Google Scholar
Carvajal-Rodriguez A, de Uña-Alvarez J. Assessing significance in high-throughput experiments by sequential goodness of fit and q-value estimation. PLoS ONE. 2011;6:e24700.
Article
CAS
PubMed
PubMed Central
Google Scholar
Castoe TA, Poole AW, de Koning APJ, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD. Rapid microsatellite identification from illumina paired-end genomic sequencing in two birds and a snake. PLoS ONE. 2012;7:e30953.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chapuis M-P, Estoup A. Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol. 2007;24:621–31.
Article
CAS
PubMed
Google Scholar
Chapuis MP, Plantamp C, Streiff R, Blondin L, Piou C. Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations. Mol Ecol. 2015;24:6107–19.
Article
CAS
PubMed
Google Scholar
Collar N, Robson C, de Juana E. Grey-cheeked Liocichla (Liocichla omeiensis). In: del Hoyo J, Elliott A, Sargatal J, Christie DA, de Juana E, editors. Handbook of the birds of the world alive. Barcelona: Lynx Edicions; 2016.
Google Scholar
Dawson DA, Horsburgh GJ, Küpper C, Stewart IRK, Ball AD, Durrant KL, Hansson B, Bacon IDA, Bird S, Klein Á, Krupa AP, Lee JW, Martín-Gálvez D, Simeoni M, Smith G, Spurgin LG, Burke T. New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility—as demonstrated for birds. Mol Ecol Resour. 2010;10:475–94.
Article
CAS
PubMed
Google Scholar
Duncan CJ, Worth JRP, Jordan GJ, Jones RC, Vaillancourt RE. Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia, Nothofagus cunninghamii. Heredity. 2016;116:99–106.
Article
CAS
PubMed
Google Scholar
Excoffier L, Lischer HEL. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010;10:564–7.
Article
PubMed
Google Scholar
Faria J, Pita A, Rivas M, Martins GM, Hawkins SJ, Ribeiro P, Neto AI, Presa P. A multiplex microsatellite tool for conservation genetics of the endemic limpet Patella candei in the Macaronesian archipelagos. Aquat Conserv. 2016;26:775–81.
Article
Google Scholar
Frankham R, Briscoe DA, Ballou JD. Introduction to conservation genetics. Cambridge: Cambridge University Press; 2002.
Book
Google Scholar
Fu Y, Zhang Z. The influence of abnormal low-temperature of spring and summer on the breeding of Omei Shan Liocichla (Liocichla omeiensis). Beijing Norm Univ (Nat Sci). 2011;47:292–5 (in Chinese).
Google Scholar
Fu Y, Dowell SD, Zhang Z. Breeding ecology of the Emei Shan Liocichla (Liocichla omeiensis). Wilson J Ornithol. 2011;123:748–54.
Article
Google Scholar
Gill FB. Ornithology. New York: W.H. Freeman & Company; 2007.
Google Scholar
Gu LY, Liu Y, Wang N, Zhang ZW. A panel of polymorphic microsatellites in the Blue Eared Pheasant (Crossoptilon auritum) developed by cross-species amplification. Chin Birds. 2012;3:103–7.
Article
Google Scholar
Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ. Current trends in microsatellite genotyping. Mol Ecol Resour. 2011;11:591–611.
Article
CAS
PubMed
Google Scholar
Hua F, Wang X, Zheng X, Fisher B, Wang L, Zhu J, Tang Y, Douglas WY, Wilcove DS. Opportunities for biodiversity gains under the world’s largest reforestation programme. Nat Commun. 2016;7:12717.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang J, Zhu D, Song X, Chen B, Zeng C, Moermond T, Zhang X, Yue B. High-throughput microsatellite markers discovery for the Sichuan Hill Partridge (Arborophila rufipectus) and assessment of genetic diversity in the Laojunshan population. Biochem Syst Ecol. 2015;60:266–72.
Article
CAS
Google Scholar
Jamieson IG. Founder effects, inbreeding, and loss of genetic diversity in four avian reintroduction programs. Conserv Biol. 2011;25:115–23.
Article
PubMed
Google Scholar
Jarne P, Lagoda PJL. Microsatellites, from molecules to populations and back. Trends Ecol Evol. 1996;11:424–9.
Article
CAS
PubMed
Google Scholar
Keller LF, Waller DM. Inbreeding effects in wild populations. Trends Ecol Evol. 2002;17:230–41.
Article
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.
Article
CAS
PubMed
Google Scholar
Lalitha S. Primer premier 5. Biotech Softw Internet Rep. 2000;1:270–2.
Article
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
Li Y, Korol AB, Fahima T, Beiles A, Nevo E. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol. 2002;11:2453–65.
Article
CAS
PubMed
Google Scholar
Marshall TC, Slate J, Kruuk LEB, Pemberton JM. Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol. 1998;7:639–55.
Article
CAS
PubMed
Google Scholar
McKay BD, Mays HL, Peng Y-W, Kozak KH, Yao C-T, Yuan H-W. Recent range-wide demographic expansion in a Taiwan endemic montane bird, Steere’s Liocichla (Liocichla steerii). BMC Evol Biol. 2010;10:71.
Article
PubMed
PubMed Central
Google Scholar
Meffe GK, Carroll CR. Principles of conservation biology. Sunderland: Sinauer; 1994.
Google Scholar
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 2007;17:240–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nagy S, Poczai P, Cernák I, Gorji AM, Hegedűs G, Taller J. PICcalc: an online program to calculate polymorphic information content for molecular genetic studies. Biochem Genet. 2012;50:670–2.
Article
CAS
PubMed
Google Scholar
Pfender WF, Saha MC, Johnson EA, Slabaugh MB. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet. 2011;122:1467–80.
Article
CAS
PubMed
Google Scholar
Ribon R, Simon JE, Theodoro De Mattos G. Bird extinctions in Atlantic forest fragments of the Viçosa region, southeastern Brazil. Conserv Biol. 2003;17:1827–39.
Article
Google Scholar
Ryman N, Leimar O. Effect of mutation on genetic differentiation among nonequilibrium populations. Evolution. 2008;62:2250–9.
Article
PubMed
Google Scholar
Sudheer PDVN, Mastan SG, Rahman H, Prakash CR, Singh S, Reddy MP. Cross species amplification ability of novel microsatellites isolated from Jatropha curcas and genetic relationship with sister taxa. Mol Biol Rep. 2010;38:1383–8.
Article
PubMed
Google Scholar
Tregenza T, Wedell N. Polyandrous females avoid costs of inbreeding. Nature. 2002;415:71–3.
Article
CAS
PubMed
Google Scholar
Twedt DJ, Wilson RR, Henne-Kerr JL, Grosshuesch DA. Avian response to bottomland hardwood reforestation: the first 10 years. Restor Ecol. 2002;10:645–55.
Article
Google Scholar
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes. 2004;4:535–8.
Article
Google Scholar
Wilson GA, Rannala B. Bayesian inference of recent migration rates using multilocus genotypes. Genetics. 2003;163:1177–91.
PubMed
PubMed Central
Google Scholar
Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review. Mol Ecol. 2002;11:1–16.
Article
CAS
PubMed
Google Scholar
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang L, Zhang ZH, Shen FJ, Hou R, Zhang WP, Liu YL, Tu KY, Yang AL. Identification and characterization of polymorphic microsatellite loci in the red-crowned crane. Genet Mol Res. 2015;14:15169–76.
Article
CAS
PubMed
Google Scholar