Conservation Genetics

, Volume 19, Issue 3, pp 737–754 | Cite as

Genetic diversity through time and space: diversity and demographic history from natural history specimens and serially sampled contemporary populations of the threatened Gouldian finch (Erythrura gouldiae)

  • Peri E. BoltonEmail author
  • Lee A. Rollins
  • James Brazill-Boast
  • Kimberley L. Maute
  • Sarah Legge
  • Jeremy J. Austin
  • Simon C. Griffith
Research Article


Declines in population size can compromise the viability of populations by reducing the effective population size (Ne), which may result in loss of genetic diversity and inbreeding. Temporal population genetic data can be a powerful tool for testing the presence and severity of reductions in Ne. The Gouldian finch (Erythrura gouldiae) is a flagship for conservation of Australian monsoonal savanna species. This species underwent severe population declines in the twentieth century due to land use changes associated with European colonization. Microsatellite and mitochondrial genetic data from Gouldian finch samples sourced from natural history collections prior to land use changes were compared with contemporary samples to estimate the severity of decline in effective population size and to detect changes in gene flow. These data show that Gouldian finch decline was not as severe as some sources suggest, and that population genetic connectivity has not changed following land use changes in the twentieth century. Multiple estimators of current Ne using genetic data from consecutive years suggest the Gouldian finch Ne is likely between a few hundred and a few thousand individuals, with some estimates within the range considered of conservation concern. This work has identified the need to genetically characterize populations in Queensland, and to understand critical demographic parameters (e.g. lifespan) in the Gouldian finch. Understanding these factors is vital to further improve genetic estimates of population size, key to the formation of appropriate conservation management of this species.


Museum skins Historical biodiversity Estrildidae Biogeography Bottleneck 



We thank all those who have contributed to the collection of blood samples in the field including Gareth Davies, Jo Dessmann, Christophe Dufresnes, Rowena Hamer, Catherine Hamilton, Jan Lewis, Dhanya Pearce, Sarah Pryke, Marjolein Schoe, Nina Svedin, Erica van Rooij, and Hanneke Wiggers in Wyndham. We thank staff of Australian Wildlife Conservancy, in particular Joanne Heathcote, for assistance with fieldwork at Mornington Sanctuary and Northern Territory. Thank you to all the museum staff that contributed to the collection of toe-pads including: Maya Penck at South Australia Museum; Paul Sweet, Thomas Trombone, Joel Cracraft at the American Museum of Natural History; Katie Smith and Karen Roberts at Museum Victoria. Caitlin Morrison extracted DNA from historical toe-pad samples. Thank you to Drew Allen and Dave Nipperess for discussions about rarefaction and comparison of diversity indices, to Nicolas Dussex for help with priors for Approximate Bayesian Computation.


The funding bodies for this work played no role in the conception, design, or interpretation of this work. Financial support for fieldwork at Wyndham was from an Australian Research Council Grant to Sarah Pryke and SCG (DP0881019), Save the Gouldian Fund, and a Macquarie University Research Excellence Scholarship to JB-B. Funding for fieldwork at Northern Territory and Australian Wildlife Conservancy’s Mornington Sanctuary was from Australian Research Council Linkage Grant to Stephen Garnett (LP0668122), supporters of the Australian Wildlife Conservancy, the University of Wollongong, Northern Territory Department of Infrastructure, Planning and Environment, Charles Darwin University, Stuart Leslie Bird Research Fund, and the Professor Allen Keast Award (Birdlife Australia). The Australian Agricultural Company, Australian Department of Defence, Australian Wildlife Conservancy and Jawoyn association allowed KLM access to their land. The genetics work was supported by Australian Research Council grants to SCG and LAR (DP130100418), and an Australian Postgraduate Award to PEB.

Supplementary material

10592_2018_1051_MOESM1_ESM.docx (1.5 mb)
Supplementary material 1 (DOCX 1492 KB)


  1. Aktas C (2015) Haplotypes: haplotype inference and statistical analysis of genetic variation. R package version 1.0Google Scholar
  2. Allendorf FW (1986) Genetic drift and the loss of alleles versus heterozygosity. Zoo Biol 5:181–190. CrossRefGoogle Scholar
  3. Antao T, Pérez-Figueroa A, Luikart G (2011) Early detection of population declines: high power of genetic monitoring using effective population size estimators. Evol Appl 4:144–154. PubMedCrossRefGoogle Scholar
  4. Austin JJ, Joseph L, Pedler LP, Black AB (2013) Uncovering cryptic evolutionary diversity in extant and extinct populations of the southern Australian arid zone Western and thick-billed grasswrens (Passeriformes: Maluridae: Amytornis). Conserv Genet 14:1173–1184. CrossRefGoogle Scholar
  5. Baalsrud HT, Sæther B-E, Hagen IJ et al (2014) Effects of population characteristics and structure on estimates of effective population size in a house sparrow metapopulation. Mol Ecol 23:2653–2668. PubMedCrossRefGoogle Scholar
  6. Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48. PubMedCrossRefGoogle Scholar
  7. Bolton PE, West AJ, Cardilini APA et al (2016) Three molecular markers show no evidence of population genetic structure in the Gouldian finch (Erythrura gouldiae). PLoS ONE 11:e0167723. PubMedPubMedCentralCrossRefGoogle Scholar
  8. Bolton PE, Rollins LA, Brazill-Boast J et al (2017) The colour of paternity: extra-pair paternity in the wild Gouldian finch does not appear to be driven by genetic incompatibility between morphs. J Evol Biol 30:174–190. PubMedCrossRefGoogle Scholar
  9. Bonter DN, Bridge ES (2011) Applications of radio frequency identification (RFID) in ornithological research: a review. J Field Ornithol 82:1–10. CrossRefGoogle Scholar
  10. Bouten W, Baaij EW, Shamoun-Baranes J, Camphuysen KCJ (2013) A flexible GPS tracking system for studying bird behaviour at multiple scales. J Ornithol 154:571–580. CrossRefGoogle Scholar
  11. Bowman DMJS., Brown GK, Braby MF et al (2010) Biogeography of the Australian monsoon tropics. J Biogeogr 37:201–216. CrossRefGoogle Scholar
  12. Bristol RM, Tucker R, Dawson DA et al (2013) Comparison of historical bottleneck effects and genetic consequences of re-introduction in a critically endangered island passerine. Mol Ecol 22:4644–4662. PubMedCrossRefGoogle Scholar
  13. Bruniche-Olsen A, Jones ME, Austin JJ et al (2014) Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease. Proc R Soc Lond B Biol Sci 10:20140619. CrossRefGoogle Scholar
  14. Busch JD, Waser PM, DeWoody JA (2007) Recent demographic bottlenecks are not accompanied by a genetic signature in banner-tailed kangaroo rats (Dipodomys spectabilis). Mol Ecol 16:2450–2462. PubMedCrossRefGoogle Scholar
  15. Byrne M, Yeates DK, Joseph L et al (2008) Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota. Mol Ecol 17:4398–4417. PubMedCrossRefGoogle Scholar
  16. Caplins SA, Gilbert KJ, Ciotir C et al (2014) Landscape structure and the genetic effects of a population collapse. Proc R Soc Lond B Biol Sci 281:20141798. CrossRefGoogle Scholar
  17. Catullo RA, Lanfear R, Doughty P, Keogh JS (2014) The biogeographical boundaries of northern Australia: evidence from ecological niche models and a multi-locus phylogeny of Uperoleia toadlets (Anura: Myobatrachidae). J Biogeogr 41:659–672. CrossRefGoogle Scholar
  18. Cornuet J-M, Pudlo P, Veyssier J et al (2014) DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics 30:1187–1189. PubMedCrossRefGoogle Scholar
  19. Crow JF, Kimura M (1970) An introduction to population genetics theory. Harper & Row, New YorkGoogle Scholar
  20. Do C, Waples RS, Peel D et al (2014) NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol Ecol Resour 14:209–214. PubMedCrossRefGoogle Scholar
  21. Dussex N, Rawlence NJ, Robertson BC (2015) Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the Kea (Nestor notabilis). PLoS ONE 10:e0118522. PubMedPubMedCentralCrossRefGoogle Scholar
  22. Earl DA, VonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361. CrossRefGoogle Scholar
  23. Esparza-Salas R (2007) Molecular ecology of the endangered Gouldian Finch Erythrura gouldiae. PhD Thesis. James Cook UniversityGoogle Scholar
  24. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620. PubMedCrossRefGoogle Scholar
  25. Evans S, Fidler M (2005) The Gouldian finch. Indruss Productions, BrisbaneGoogle Scholar
  26. Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol 13:853–864. PubMedCrossRefGoogle Scholar
  27. Excoffier LG, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetic analyses under Linux and Windows. Mol Ecol Resour 10:564–567. PubMedCrossRefGoogle Scholar
  28. Fagundes NJR, Ray N, Beaumont M et al (2007) Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci USA 104:17614–17619PubMedPubMedCentralCrossRefGoogle Scholar
  29. Ford J (1987) Hybrid zones in Australian birds. Emu 87:158–178. CrossRefGoogle Scholar
  30. Frankham R (1995) Effective population size/adult population size ratios in wildlife: a review. Genet Res 89:491–503. CrossRefGoogle Scholar
  31. Frankham R (2005) Genetics and extinction. Biol Conserv 126:131–140. CrossRefGoogle Scholar
  32. Frankham R, Bradshaw CJA, Brook BW (2014) Genetics in conservation management: revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biol Conserv 170:56–63. CrossRefGoogle Scholar
  33. Franklin IR (1980) Evolutionary change in small populations. In: Soulé ME, Wilcox BA (eds) Conservation biology: an evolutionary-ecological perspective. Sinauer Associates, Sunderland, pp 135–149Google Scholar
  34. Franklin D (1999) Evidence of disarray amongst granivorous bird assemblages in the savannas of northern Australia, a region of sparse human settlement. Biol Conserv 90:53–68. CrossRefGoogle Scholar
  35. Franklin DC, Burbidge AH, Dostine PL (1999) The harvest of wild birds for aviculture: an historical perspective on finch trapping in the Kimberley with special emphasis on the Gouldian finch. Aust Zool 31:92–109. CrossRefGoogle Scholar
  36. Franklin DC, Whitehead PJ, Pardon G et al (2005) Geographic patterns and correlates of the decline of granivorous birds in northern Australia. Wildl Res 32:399–408. CrossRefGoogle Scholar
  37. Fu Y-X (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925PubMedPubMedCentralGoogle Scholar
  38. Garnett ST, Szabo JK, Dutson G (2011) The action plan for Australian birds 2010. CSIRO Publishing, CollingwodGoogle Scholar
  39. Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10:305–318. PubMedCrossRefGoogle Scholar
  40. Gilbert KJ, Whitlock MC (2015) Evaluating methods for estimating local effective population size with and without migration. Evolution 69:2154–2166. PubMedCrossRefGoogle Scholar
  41. Graham CH, Ferrier S, Huettman F et al (2004) New developments in museum-based informatics and applications in biodiversity analysis. Trends Ecol Evol 19:497–503. PubMedCrossRefGoogle Scholar
  42. Habel JC, Husemann M, Finger A et al (2014) The relevance of time series in molecular ecology and conservation biology. Biol Rev 89:484–492. PubMedCrossRefGoogle Scholar
  43. Hare MP, Nunney L, Schwartz MK et al (2011) Understanding and estimating effective population size for practical application in marine species management. Conserv Biol 25:438–449. PubMedCrossRefGoogle Scholar
  44. Hartmann S, Schaefer HM, Segelbacher G (2014) Genetic depletion at adaptive but not neutral loci in an endangered bird species. Mol Ecol 23:5712–5725. PubMedCrossRefGoogle Scholar
  45. Heslewood MM, Elphinstone MS, Tidemann SC, Baverstock PR (1998) Myoglobin intron variation in the Gouldian finch Erythrura gouldiae assessed by temperature gradient gel electrophoresis. Electrophoresis 19:142–151. PubMedCrossRefGoogle Scholar
  46. Heuman GA (1926) Birds in the Northern Territory and the new finch. Emu 25:134–136CrossRefGoogle Scholar
  47. Hill WG (1981) Estimation of effective population size from data on linkage disequillibrium. Genet Res 38:209–216. CrossRefGoogle Scholar
  48. Hoban SM, Gaggiotti OE, Bertorelle G (2013) The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study. Mol Ecol 22:3444–3450. PubMedCrossRefGoogle Scholar
  49. Hoban S, Arntzen JA, Bruford MW et al (2014) Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion. Evol Appl 7:984–998. PubMedPubMedCentralCrossRefGoogle Scholar
  50. Hoeck PEA, Beaumont MA, James KE et al (2009) Saving Darwin’s muse: evolutionary genetics for the recovery of the Floreana mockingbird. Biol Lett. PubMedPubMedCentralCrossRefGoogle Scholar
  51. Holland SM (2012) Analytic Rarefaction v2.0.
  52. Holmes MW, Hammond TT, Wogan GOU et al (2016) Natural history collections as windows on evolutionary processes. Mol Ecol 25:864–881. PubMedPubMedCentralCrossRefGoogle Scholar
  53. Jackson H, Morgan BJT, Groombridge JJ (2013) How closely do measures of mitochondrial DNA control region diversity reflect recent trajectories of population decline in birds? Conserv Genet 14:1291–1296. CrossRefGoogle Scholar
  54. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806. PubMedCrossRefGoogle Scholar
  55. Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405. PubMedCrossRefGoogle Scholar
  56. Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:94. PubMedPubMedCentralCrossRefGoogle Scholar
  57. Jones O, Wang J (2010) COLONY: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 10:551–555. PubMedCrossRefGoogle Scholar
  58. Jones AT, Ovenden JR, Wang Y-G (2016) Improved confidence intervals for the linkage disequilibrium method for estimating effective population size. Heredity 117:1–7. CrossRefGoogle Scholar
  59. Joseph L, Zeriga T, Adcock GJ, Langmore NE (2011) Phylogeography and taxonomy of the Little Bronze-Cuckoo (Chalcites minutillus) in Australia’s monsoon tropics. Emu 111:113–119. CrossRefGoogle Scholar
  60. Joseph L, Boussès P, Wilke T, Austin JJ (2016) Ancient DNA resolves the subspecific identity of the holotype of the Galah Eolophus roseicapilla, a widespread Australian cockatoo. Emu 720:472–475. CrossRefGoogle Scholar
  61. Kearns AM, Joseph L, Toon A, Cook LG (2014) Australia’s arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima. Nat Commun 5:1–11. CrossRefGoogle Scholar
  62. Larsson JK, Jansman HAH, Segelbacher G et al (2008) Genetic impoverishment of the last black grouse (Tetrao tetrix) population in the Netherlands: detectable only with a reference from the past. Mol Ecol 17:1897–1904. PubMedCrossRefGoogle Scholar
  63. Leberg PL (2002) Estimating allelic richness: effects of sample size and bottlenecks. Mol Ecol 11:2445–2449. PubMedCrossRefGoogle Scholar
  64. Lee AM, Engen S, Sæther B-E et al (2011) The influence of persistent individual differences and age at maturity on effective population size. Proc R Soc London B Biol Sci 278:3303–3312. CrossRefGoogle Scholar
  65. Legge S, Garnett S, Maute K et al (2015) A landscape-scale, applied fire management experiment promotes recovery of a population of the threatened Gouldian Finch, Erythrura gouldiae, in Australia’s Tropical Savannas. PLoS ONE 10:e0137997. PubMedPubMedCentralCrossRefGoogle Scholar
  66. Librado P, Rozas J (2009) DnaSP v5: a Software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452. PubMedCrossRefGoogle Scholar
  67. Luikart G, Ryman N, Tallmon DA et al (2010) Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conserv Genet 11:355–373. CrossRefGoogle Scholar
  68. Mondol S, Bruford MW, Ramakrishnan U (2013) Demographic loss, genetic structure and the conservation implications for Indian tigers. Proc R Soc London B Biol Sci 280:20130496. CrossRefGoogle Scholar
  69. Morris K, Austin JJ, Belov K (2013) Low major histocompatibility complex diversity in the Tasmanian devil predates European settlement and may explain susceptibility to disease epidemics. Biol Lett 9:20120900. PubMedPubMedCentralCrossRefGoogle Scholar
  70. Mourier T, Ho SYW, Gilbert MTP et al (2012) Statistical guidelines for detecting past population shifts using ancient DNA. Mol Biol Evol 29:2241–2251. PubMedCrossRefGoogle Scholar
  71. Navascués M, Depaulis F, Emerson BC (2010) Combining contemporary and ancient DNA in population genetic and phylogeographical studies. Mol Ecol Resour 10:760–772. PubMedCrossRefGoogle Scholar
  72. Nyström V, Angerbjörn A, Dalén L (2006) Genetic consequences of a demographic bottleneck in the Scandinavian arctic fox. Oikos 114:84–94. CrossRefGoogle Scholar
  73. O’Malley C (2006) National Recovery Plan for the Gouldian Finch (Erythrura gouldiae). WWF-Australia, Sydney and Parks and Wildlife NT. Department of Natural Resources, Environment and the Arts, NT Government, PalmerstonGoogle Scholar
  74. Pacioni C, Hunt H, Allentoft M et al (2015) Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial. Mol Ecol 24:5813–5828. PubMedCrossRefGoogle Scholar
  75. Palstra FP, Fraser DJ (2012) Effective/census population size ratio estimation: a compendium and appraisal. Ecol Evol 2:2357–2365. PubMedPubMedCentralCrossRefGoogle Scholar
  76. Paplinska JZ, Taggart DA, Corrigan T et al (2011) Using DNA from museum specimens to preserve the integrity of evolutionarily significant unit boundaries in threatened species. Biol Conserv 144:290–297. CrossRefGoogle Scholar
  77. Paradis E (2010) Pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26:419–420. PubMedCrossRefGoogle Scholar
  78. Peakall R, Smouse PE (2012) GenAlex 6.5: genetic analysis in excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539. PubMedPubMedCentralCrossRefGoogle Scholar
  79. Pepper M, Hamilton DG, Merkling T et al (2016) Phylogeographic structure across one of the largest intact tropical savannahs: molecular and morphological analysis of Australia’s iconic frilled lizard Chlamydosaurus kingii. Mol Phylogenet Evol 106:217–227. PubMedCrossRefGoogle Scholar
  80. Piry S, Luikart G, Cornuet J (1999) BOTTLENECK: a program for detecting recent effective population size reductions from allele data frequencies. J Hered 90:502–503. CrossRefGoogle Scholar
  81. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  82. Prost S, Anderson CNK (2011) TempNet: a method to display statistical parsimony networks for heterochronous DNA sequence data. Methods Ecol Evol 2:663–667. CrossRefGoogle Scholar
  83. Ramakrishnan U, Hadly EA (2009) Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Mol Ecol 18:1310–1330. PubMedCrossRefGoogle Scholar
  84. Ramakrishnan U, Hadly EA, Mountain JL (2005) Detecting past population bottlenecks using temporal genetic data. Mol Ecol 14:2915–2922. PubMedCrossRefGoogle Scholar
  85. Ramos-Onsins SE, Rozas J (2006) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 23:1642–1642. CrossRefGoogle Scholar
  86. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249. CrossRefGoogle Scholar
  87. Rogers AR, Harpending HC (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569. PubMedCrossRefGoogle Scholar
  88. Rollins LA, Svedin N, Pryke SR, Griffith SC (2012) The role of the ord arid intrusion in the historical and contemporary genetic division of long-tailed finch subspecies in northern Australia. Ecol Evol 2:1208–1219. PubMedPubMedCentralCrossRefGoogle Scholar
  89. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138. CrossRefGoogle Scholar
  90. Ruzzante DE, McCracken GR, Parmelee S et al (2016) Effective number of breeders, effective population size and their relationship with census size in an iteroparous species, Salvelinus fontinalis. Proc R Soc London B Biol Sci 283:20152601. CrossRefGoogle Scholar
  91. Schwartz MK, Luikart G, Waples RS (2007) Genetic monitoring as a promising tool for conservation and management. Trends Ecol Evol 22:25–33. PubMedCrossRefGoogle Scholar
  92. Skoglund P, Sjödin P, Skoglund T et al (2014) Investigating population history using temporal genetic differentiation. Mol Biol Evol 31:2516–2527. PubMedPubMedCentralCrossRefGoogle Scholar
  93. Skroblin A, Lanfear R, Cockburn A, Legge S (2012) Inferring population connectivity across the range of the purple-crowned fairy-wren (Malurus coronatus) from mitochondrial DNA and morphology: implications for conservation management. Aust J Zool 60:199–209. CrossRefGoogle Scholar
  94. Smedley JH (1904) Finches in northern Queensland. Emu 4:68–69. CrossRefGoogle Scholar
  95. Stucky BJ (2012) SeqTrace: a graphical tool for rapidly processing DNA sequencing chromatograms. J Biomol Technol 23:90–93. CrossRefGoogle Scholar
  96. Szpiech ZA, Jakobsson M, Rosenberg NA (2008) ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24:2498–2504. PubMedPubMedCentralCrossRefGoogle Scholar
  97. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedPubMedCentralGoogle Scholar
  98. Tidemann SC (1996) Causes of the decline of the Gouldian Finch Erythrura gouldiae. Bird Conserv Int 6:49–61. CrossRefGoogle Scholar
  99. Tidemann S, Mccartney J, Smith I (1993) Queensland Gouldian finches Erythrura gouldiae and air-sac mite Sternostoma tracheacolum. Sunbird 23:36–40Google Scholar
  100. Toon A, Hughes JM, Joseph L (2010) Multilocus analysis of honeyeaters (Aves: Meliphagidae) highlights spatio-temporal heterogeneity in the influence of biogeographic barriers in the Australian monsoonal zone. Mol Ecol 19:2980–2994. PubMedCrossRefGoogle Scholar
  101. Tovar B (2012) handleFastaDatasets.
  102. Valdiosera CE, García-Garitagoitia JL, Garcia N et al (2008) Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). Proc Natl Acad Sci USA 105:5123–5128. PubMedPubMedCentralCrossRefGoogle Scholar
  103. van Rooij EP, Griffith SC (2011) Breeding ecology of an Australian estrildid, the long-tailed finch (Poephila acuticauda). Emu 111:297–303. CrossRefGoogle Scholar
  104. Wandeler P, Hoeck PE, Keller LF (2007) Back to the future: museum specimens in population genetics. Trends Ecol Evol 22:634–642. PubMedCrossRefGoogle Scholar
  105. Wang J (2009) A new method for estimating effective population sizes from a single sample of multilocus genotypes. Mol Ecol 18:2148–2164. PubMedCrossRefGoogle Scholar
  106. Wang J (2016) A comparison of single-sample estimators of effective population sizes from genetic marker data. Mol Ecol 25:4692–4711. PubMedCrossRefGoogle Scholar
  107. Wang J, Whitlock MC (2003) Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163:429–446PubMedPubMedCentralGoogle Scholar
  108. Wang J, Brekke P, Huchard E et al (2010) Estimation of parameters of inbreeding and genetic drift in populations with overlapping generations. Evolution 64:1704–1718. PubMedCrossRefGoogle Scholar
  109. Wang J, Santiago E, Caballero A (2016) Prediction and estimation of effective population size. Heredity 117:1–14. CrossRefGoogle Scholar
  110. Waples RS (2005) Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Mol Ecol 14:3335–3352. PubMedCrossRefGoogle Scholar
  111. Waples RS (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conserv Genet 7:167–184. CrossRefGoogle Scholar
  112. Waples RS (2010) Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size. Mol Ecol Resour 10:785–796. PubMedCrossRefGoogle Scholar
  113. Waples RS, Antao T (2014) Intermittent breeding and constraints on litter size: consequences for effective population size per generation (Ne) and per reproductive cycle (Nb). Evolution 68:1722–1734. PubMedCrossRefGoogle Scholar
  114. Waples RS, Do C (2010) Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evol Appl 3:244–262. PubMedCrossRefGoogle Scholar
  115. Waples RS, Yokota M (2007) Temporal estimates of effective population size in species with overlapping generations. Genetics 175:219–233. PubMedPubMedCentralCrossRefGoogle Scholar
  116. Waples RS, Do C, Chopelet J (2011) Calculating Ne and Ne/N in age-structured populations: a hybrid Felsenstein-Hill approach. Ecology 92:1513–1522. PubMedCrossRefGoogle Scholar
  117. Waples RS, Luikart G, Faulkner JR, Tallmon DA (2013) Simple life-history traits explain key effective population size ratios across diverse taxa. Proc R Soc London B Biol Sci 280:20131339. CrossRefGoogle Scholar
  118. Waples RS, Antao T, Luikart G (2014) Effects of overlapping generations on linkage disequilibrium estimates of effective population size. Genetics 197:769–780. PubMedPubMedCentralCrossRefGoogle Scholar
  119. Waples RK, Larson WA, Waples RS (2016) Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci. Heredity 117:233–240. PubMedPubMedCentralCrossRefGoogle Scholar
  120. Weber DS, Stewart BS, Garza JC, Lehman N (2000) An empirical genetic assessment of the severity of the northern elephant seal population bottleneck. Curr Biol 10:1287–1290PubMedCrossRefGoogle Scholar
  121. Welch AJ, Wiley AE, James HF et al (2012) Ancient DNA reveals genetic stability despite demographic decline: 3000 years of population history in the endemic hawaiian petrel. Mol Biol Evol 29:3729–3740. PubMedCrossRefGoogle Scholar
  122. Woinarski JCZ, Ash AJ (2002) Responses of vertebrates to pastoralism, military land use and landscape position in an Australian tropical savanna. Austral Ecol 27:311–323. CrossRefGoogle Scholar
  123. Woinarski JCZ, Tidemann S (1992) Survivorship and some population parameters for the endangered Gouldian finch Erythrura gouldiae and two other finch species at two Sites in tropical northern Australia. Emu 92:33–38. CrossRefGoogle Scholar
  124. Woinarski JCZ, Milne DJ, Wanganeen G (2001) Changes in mammal populations in relatively intact landscapes of Kakadu National Park, Northern Territory, Australia. Austral Ecol 26:360–370. CrossRefGoogle Scholar
  125. Woinarski JCZ, Legge S, Fitzsimons JA et al (2011) The disappearing mammal fauna of northern Australia: context, cause, and response. Conserv Lett 4:192–201. CrossRefGoogle Scholar
  126. Woinarski J, Burbidge AA, Harrison P (2014) The action plan for Australian mammals 2012. CSIRO Publishing, MelbourneGoogle Scholar
  127. Zink RM, Barrowclough GF (2008) Mitochondrial DNA under siege in avian phylogeography. Mol Ecol 17:2107–2121. PubMedCrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.Department of Biological SciencesMacquarie UniversitySydneyAustralia
  2. 2.School of Life and Environmental Sciences, Centre for Integrative EcologyDeakin UniversityGeelongAustralia
  3. 3.Institute of Conservation Biology and Environmental ManagementUniversity of WollongongWollongongAustralia
  4. 4.Australian Wildlife ConservancyMornington Wildlife SanctuaryDerbyAustralia
  5. 5.School of Biological Sciences, Australian Centre for Ancient DNAUniversity of AdelaideAdelaideAustralia
  6. 6.National Environmental Science Programme Threatened Species Recovery Hub, Research Institute of Environment and LivelihoodsCharles Darwin UniversityCasuarinaAustralia
  7. 7.Ecosystems and Threatened Species, Regional Operations DivisionNSW Office of Environment and HeritageSydneyAustralia
  8. 8.Biological, Earth & Environmental Sciences, Evolution & Ecology Research CentreUniversity of New South WalesSydneyAustralia

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