Conservation Genetics

, Volume 19, Issue 5, pp 1097–1108 | Cite as

Genomic data indicate ubiquitous evolutionary distinctiveness among populations of California metalmark butterflies

  • Julian R. DupuisEmail author
  • Jeffrey C. Oliver
  • Bryan M. T. Brunet
  • Travis Longcore
  • Jana J. Johnson
  • Felix A. H. Sperling
Research Article


Conservation geneticists have argued that evolutionarily significant units (ESUs) must be both genetically distinct and adaptively significant to be recognized for conservation protection. High-throughput DNA approaches can greatly increase the power to identify genetic distinctiveness, even if inferring adaptive significance remains a challenge. Here we present the first genomic evaluation of Lange’s metalmark, Apodemia mormo langei (Lepidoptera: Riodinidae), a U.S. federally endangered subspecies restricted to sand dune habitats in a single National Wildlife Refuge in California. Previous work based on very few genetic markers detected little genetic distinction for Lange’s metalmark. We use several thousand genome-wide single nucleotide polymorphisms to characterize the population structure of the A. mormo complex across California and determine if Lange’s metalmark qualifies as an ESU. We found that Lange’s metalmark is genetically identifiable, but is no more distinct than many other isolated populations across the study area. It remains unclear whether this genetic variation is adaptive, and so conservation efforts would benefit from more ecological characterization to determine conservation priorities.


Evolutionarily significant unit ESU Conservation genetics Genomics Lepidoptera Apodemia mormo langei 



Funding was provided by a National Science and Engineering Research Council Discovery grant (RGPIN 217174) to FAHS. This research was enabled in part by support provided by WestGrid ( and Compute Canada Calcul Canada ( Availability of specimens of A. m. langei was made possible by funding for the captive propagation program from the U.S. Fish and Wildlife Service’s CVPIA Habitat Restoration Program. We thank Soowon Cho, John Eggers, Jerry Powell, and Dan Rubinoff for help collecting specimens, Kevin Muirhead for bioinformatic assistance, and Jim P. Brock for use of the A. m. langei photograph. We also thank Alfred Vogler and two anonymous reviewers for their insightful comments on this manuscript. Data files are available as Online Resources (STRUCTURE input: Online Resource 3, ML input: Online Resource 4, SNAPP input: Online Resource 5) and raw sequence data are available as Sequence Read Archives (National Center for Biotechnology Information) under accession SRP127676 (SRR6427150-SRR6427258, BioProject PRJNA427807). Final figures generated using Inkscape v0.91 (The Inkscape Team 2017).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10592_2018_1081_MOESM1_ESM.xlsx (59 kb)
Online Resource 1 (XLSX 58 KB)
10592_2018_1081_MOESM2_ESM.pdf (1.4 mb)
Online Resource 2 (PDF 1374 KB)
10592_2018_1081_MOESM3_ESM.str (2.5 mb)
Online Resource 3 (STR 2592 KB)
10592_2018_1081_MOESM4_ESM.phy (67.6 mb)
Online Resource 4 (PHY 69222 KB)
10592_2018_1081_MOESM5_ESM.xml (42 kb)
Online Resource 5 (XML 42 KB)


  1. Allendorf FW (2017) Genetics and the conservation of natural populations: allozymes to genomes. Mol Ecol 26:420–430CrossRefPubMedGoogle Scholar
  2. Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11:697–709. CrossRefPubMedGoogle Scholar
  3. Bennett JR et al (2014) Balancing phylogenetic diversity and species numbers in conservation prioritization, using a case study of threatened species in New Zealand. Biol Conserv 174:47–54. CrossRefGoogle Scholar
  4. Bouckaert RR, Heled J (2014) DensiTree 2: seeing trees through the forest. bioRxiv. CrossRefGoogle Scholar
  5. Bouckaert R et al (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537. CrossRefPubMedPubMedCentralGoogle Scholar
  6. Bowen BW (1999) What is wrong with ESUs? the gap between evolutionary theory and conservation principles. J Shellfish Res 17:1355–1358Google Scholar
  7. Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol 29:1917–1932. CrossRefPubMedPubMedCentralGoogle Scholar
  8. Carolan MS (2008) The politics in environmental science: the Endangered Species Act and the Preble’s mouse controversy. Environ Politics 17:449–465. CrossRefGoogle Scholar
  9. Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3 (Bethesda) 1:171–182 CrossRefGoogle Scholar
  10. COSEWIC (2012) Guidelines for Recognizing Designatable Units; Committee on the Status of Endangered Wildlife in Canada. Accessed 15 Dec 2017
  11. Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends Ecol Evol 15:290–295CrossRefPubMedGoogle Scholar
  12. Crawford LA, Desjardins S, Keyghobadi N (2011) Fine-scale genetic structure of an endangered population of the Mormon metalmark butterfly (Apodemia mormo) revealed using AFLPs. Conserv Genet 12:991–1001. Scholar
  13. Cullingham CI, Cooke JE, Coltman DW (2014) Cross-species outlier detection reveals different evolutionary pressures between sister species. New Phytol 204:215–229. CrossRefPubMedPubMedCentralGoogle Scholar
  14. DaCosta JM, Sorenson MD (2016) ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: analyses of two avian genera with contrasting histories. Mol Phylogenet Evol 94:122–135. CrossRefPubMedGoogle Scholar
  15. Danecek P et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158. CrossRefPubMedPubMedCentralGoogle Scholar
  16. Davenport K (2004) A concise update of the information provided in The Butterflies of Southern California (1973) by Thomas C Emmel and John F Emmel. Taxon Rep Int Lepidoptera Surv 4:1–23Google Scholar
  17. de Guia APO, Saitoh T (2006) The gap between the concept and definitions in the evolutionarily significant unit: the need to integrate neutral genetic variation and adaptive variation. Ecol Res 22:604–612. CrossRefGoogle Scholar
  18. Donaldson MR, Burnett NJ, Braun DC, Suski CD, Hinch SG, Cooke SJ, Kerr JT (2016) Taxonomic bias and international biodiversity conservation research. Facets 1:105–113. CrossRefGoogle Scholar
  19. Doremus H (2004) The purposes effects and future of the Endangered Species Act’s best available science mandate. Environmental Law 34:397–450Google Scholar
  20. Dupuis JR, Sperling FAH (2016) Speciation, hybridization, and conservation quanderies: what are we protecting anyway? News Lepidopterist Soc 58:202–204Google Scholar
  21. Dupuis JR et al (2017) Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex. Mol Phylogenet Evol 111:158–168. CrossRefPubMedGoogle Scholar
  22. ESA (1973) US Endangered Species Act of 1973 as amended, Pub. L. No. 93–205, 87 Stat. 884 (Dec. 28, 1973). Accessed 15 Dec 2017
  23. 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. CrossRefPubMedPubMedCentralGoogle Scholar
  24. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedPubMedCentralGoogle Scholar
  25. Fraser DJ, Bernatchez L (2001) Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Mol Ecol 10:2741–2752CrossRefPubMedGoogle Scholar
  26. Funk WC, McKay JK, Hohenlohe PA, Allendorf FW (2012) Harnessing genomics for delineating conservation units. Trends Ecol Evol 27:489–496. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Garner BA et al (2016) Genomics in conservation: case studies and bridging the gap between data and application. Trends Ecol Evol 31:81–83. CrossRefPubMedGoogle Scholar
  28. Goudet J (2005) HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Mol Ecol Notes 5:184–186. CrossRefGoogle Scholar
  29. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321. CrossRefPubMedGoogle Scholar
  30. Hey J, Waples RS, Arnold ML, Butlin RK, Harrison RG (2003) Understanding and confronting species uncertainty in biology and conservation. Trends Ecol Evol 18:597–603. CrossRefGoogle Scholar
  31. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genet 6:13. CrossRefPubMedPubMedCentralGoogle Scholar
  32. Johnson JJ, Longcore T, Clause A, Pratt G, Dunn J, Osborne K (2007) Propogation handbook for Lange’s metalmark butterfly, Apodemia mormo langei, 1st edn. The Urban Wildlands Group, Los AngelesGoogle Scholar
  33. Johnson JJ, Wilson T, Taylor C, Xia Y, Jones J, Osborne K, Longcore T (2016) Captive rearing of Lange’s metalmark butterfly, 2011–2015, report to the United States Fish and Wildlife Service, CVPIA Habitat Restoration Program. Agreement No.: F11AP00168, Los AngelesGoogle Scholar
  34. Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405. CrossRefPubMedGoogle Scholar
  35. Jombart T, Ahmed I (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27:3070–3071. CrossRefPubMedPubMedCentralGoogle Scholar
  36. 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. CrossRefPubMedPubMedCentralGoogle Scholar
  37. Jost LOU (2008) GSTand its relatives do not measure differentiation. Mol Ecol 17:4015–4026. CrossRefPubMedGoogle Scholar
  38. Jost L (2009) D vs. Gst: response to Heller and Siegismund (2009) and Ryman and Leimar (2009). Mol Ecol 18:2088–2091CrossRefGoogle Scholar
  39. Kalinowski ST (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conserv Genet 5:539–543CrossRefGoogle Scholar
  40. Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 15:1179–1191. CrossRefPubMedPubMedCentralGoogle Scholar
  41. Latour B (1987) Science in action: how to follow scientists and engineers through society. Harvard University Press, CambridgeGoogle Scholar
  42. Leaché AD, Banbury BL, Felsenstein J, Nieto-Montes de Oca A, Stamatakis A (2015) Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies. Syst Biol 64:1032–1047. CrossRefPubMedPubMedCentralGoogle Scholar
  43. Lemmon EM, Lemmon AR (2013) High-throughput genomic data in systematics and phylogenetics. Annu Rev Ecol Evol Syst 44:99–121. CrossRefGoogle Scholar
  44. Lischer HE, Excoffier L (2012) PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28:298–299. CrossRefPubMedGoogle Scholar
  45. Luck GW, Daily GC, Ehrlich PR (2003) Population diversity and ecosystem services. Trends Ecol Evol 18:331–336. CrossRefGoogle Scholar
  46. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet 4:981–994. CrossRefPubMedGoogle Scholar
  47. Mace GM (2004) The role of taxonomy in species conservation. Philos Trans R Soc Lond B 359:711–719. CrossRefGoogle Scholar
  48. Mattoni RHT (1990) The endangered El Segundo blue butterfly. J Res Lepidoptera 29:277–304Google Scholar
  49. Mee JA, Bernatchez L, Reist JD, Rogers SM, Taylor EB (2015) Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.). Evol Appl 8:423–441. CrossRefPubMedPubMedCentralGoogle Scholar
  50. Meirmans PG, Van Tienderen PH (2004) genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4:792–794. CrossRefGoogle Scholar
  51. Michalakis Y, Excoffier L (1996) A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142:1061–1064PubMedPubMedCentralGoogle Scholar
  52. Minh BQ, Nguyen MA, von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30:1188–1195. CrossRefPubMedPubMedCentralGoogle Scholar
  53. Moore JS et al (2014) Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci. Mol Ecol 23:5680–5697. CrossRefPubMedGoogle Scholar
  54. Moritz C (1994) Defining “evolutionarily significant units” for conservation. Trends Ecol Evol 9:373–375CrossRefPubMedGoogle Scholar
  55. Moritz C, Lavery S, Slade R (1995) Using allele frequency and phylogeny to define units for conservation and management. In: Nielsen JL, Powers GA (eds) Evolution and the aquatic ecosystem: defining unique units in population conservation. American Fisheries Society, Maryland, pp 249–262Google Scholar
  56. Narum SR, Hess JE (2011) Comparison of F(ST) outlier tests for SNP loci under selection. Mol Ecol Resour 11(Suppl 1):184–194 CrossRefPubMedGoogle Scholar
  57. Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA (2013) Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol 22:2841–2847. CrossRefPubMedPubMedCentralGoogle Scholar
  58. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274. CrossRefPubMedGoogle Scholar
  59. Oksanen J et al (2017) vegan: community ecology package. R package version 2.4-4. Accessed 4 Oct 2017
  60. Opler PA, Powell JA (1961) Taxonomic and distributional studies on the Western components of the Apodemia mormo complex (Riodinidae). J Lepidopterists’ Soc 15:145–171Google Scholar
  61. Palsbøll PJ, Berube M, Allendorf FW (2007) Identification of management units using population genetic data. Trends Ecol Evol 22:11–16. CrossRefPubMedGoogle Scholar
  62. Pearse DE (2016) Saving the spandrels? Adaptive genomic variation in conservation and fisheries management. J Fish Biol 89:2697–2716. CrossRefPubMedGoogle Scholar
  63. Pelham JP (2008) A catalogue of the butterflies of the United States and Canada, with a complete bibliography of the descriptive and systematic literature. J Res Lepidoptera 40:1–672Google Scholar
  64. Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:e32253. CrossRefPubMedPubMedCentralGoogle Scholar
  65. Pratt GF, Ballmer GR (1991) Three biotypes of Apodemia mormo (Riodinidae) in the Mojave Desert. J Lepidopterists’ Soc 45:46–57Google Scholar
  66. Pratt GF, Emmel JF, Bernard G (2011) The Buckwheat metalmarks. Am Butterflies Summer/Fall/Winter 2011:4–31Google Scholar
  67. Pritchard JK, Wen X (2004) Documentation for structure software: version 2. University of Chicago Press, ChicagoGoogle Scholar
  68. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  69. Proshek B, Crawford LA, Davis CS, Desjardins S, Henderson AE, Sperling FAH (2013) Apodemia mormo in Canada: population genetic data support prior conservation ranking. J Insect Conserv 17:155–170. CrossRefGoogle Scholar
  70. Proshek B, Dupuis JR, Engberg A, Davenport K, Opler PA, Powell JA, Sperling FA (2015) Genetic evaluation of the evolutionary distinctness of a federally endangered butterfly, Lange’s Metalmark. BMC Evol Biol 15:73. CrossRefPubMedPubMedCentralGoogle Scholar
  71. Puechmaille SJ (2016) The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem. Mol Ecol Resour 16:608–627. CrossRefPubMedGoogle Scholar
  72. R Core Team (2016) R: a language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
  73. Rambaut A, Drummond AJ (2010) FigTree v1.4.2. Institute of Evolutionary Biology, University of Edinburgh. http://www.treebioedacuk/software/figtree. Accessed 10 Jan 2017
  74. Rambaut A, Suchard MA, Xie D, Drummond AJ (2014) Tracer v1.6, available from Accessed 10 Jan 2017
  75. Reveal JL (2007) A new variety of Eriogonum nudum (Polygonaceae) from California. Phytologia 89:287–289Google Scholar
  76. Richmond OMW, Kelly D, Longcore T (2015) Lange’s Metalmark butterfly threat assessment and ranking of potential management alternatives: final report, SacramentoGoogle Scholar
  77. Rokas A, Abbot P (2009) Harnessing genomics for evolutionary insights. Trends Ecol Evol 24:192–200. CrossRefPubMedGoogle Scholar
  78. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228PubMedPubMedCentralGoogle Scholar
  79. Ryder OA (1986) Species conservation and systematics: the dilemma of subspecies. Trends Ecol Evol 1:9–10CrossRefGoogle Scholar
  80. Sboner A, Mu XJ, Greebaum D, Auerbach RK, Gerstein MB (2011) The real cost of sequencing: higher than you think! Genome Biol 12:125CrossRefPubMedPubMedCentralGoogle Scholar
  81. Scott JA (1986) The butterflies of North America: a natural history and field guide. Stanford University Press, StanfordGoogle Scholar
  82. Shafer AB et al (2015) Genomics and the challenging translation into conservation practice. Trends Ecol Evol 30:78–87. CrossRefPubMedGoogle Scholar
  83. Shafer AB et al (2016) Reply to Garner et al. Trends Ecol Evol 31:83–84. CrossRefPubMedGoogle Scholar
  84. Sonah H et al (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE 8:e54603. CrossRefPubMedPubMedCentralGoogle Scholar
  85. Stajich JE et al (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12:1611–1618CrossRefPubMedPubMedCentralGoogle Scholar
  86. Taylor E, Darveau C-A, Schulte P (2013) Setting conservation priorities in a widespread species: phylogeographic and physiological variation in the lake chub, Couesius plumbeus (Pisces: Cyprinidae). Diversity 5:149–165. CrossRefGoogle Scholar
  87. The Inkscape Team (2017) Inkscape v0.91. Accessed 10 Mar 2017
  88. USFWS (1976) United States Fish and Wildlife Service: determination that six species of butterflies are endangered species. Fed Regist 41:22041–22044Google Scholar
  89. USFWS (1984) United States Fish and Wildlife Service: revised recovery plan for three endangered species endemic to the Antioch Dunes, California (Lange’s metalmark butterfly, Contra Costa Wallflower, and Antioch Dunes Evening Primrose). US Fish and Wildlife Service, PortlandGoogle Scholar
  90. USFWS (2008) United States Fish and Wildlife Service: species account: Lange’s Metalmark butterfly, Apodemia mormo langei Google Scholar
  91. USFWS, NMFS (1996) US Fish and Wildlife Service and National Marine Fisheries Service: policy regarding the recognition of distinct vertebrate population segments under the Endangered Species Act. Fed Regist 61:4721–4725Google Scholar
  92. Vähä JP, Erkinaro J, Niemela E, Primmer CR (2007) Life-history and habitat features influence the within-river genetic structure of Atlantic salmon. Mol Ecol 16:2638–2654. CrossRefPubMedGoogle Scholar
  93. Vogler AP, Desalle R (1994) Diagnosing units of conservation management. Conserv Biol 8:354–363CrossRefGoogle Scholar
  94. Waples RS (1991) Pacific Salmon, Oncorhynchus spp., and the definition of “species” under the Endangered Species Act. Mar Fish Rev 53:11–22Google Scholar
  95. Waples RS (1995) Evolutionary significant units and the conservation of biological diversity under the Endangered Species Act. In: Nielsen JL, Powers GA (eds) Evolution and the aquatic ecosystem: defining unique units in population conservation. American Fisheries Society, Maryland, pp 8–27Google Scholar
  96. Waples RS, Nammack M, Cochrane JF, Hutchings JA (2013) A tale of two acts: endangered species listing practices in Canada and the United States. Bioscience 63:723–734. CrossRefGoogle Scholar
  97. Wick AA, Pruss S, Spence J, Erbilgin N (2014) Microhabitat use in a northern peripheral population of Apodemia mormo: factors beyond the host plant. J Lepidopterists’ Soc 68:54–60. CrossRefGoogle Scholar
  98. Wright S (1943) Isolation by distance. Genetics 28:114–138PubMedPubMedCentralGoogle Scholar
  99. Zhulidov PA et al (2004) Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res 32:e37. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Department of Plant and Environmental Protection ServicesUniversity of Hawai‘i at MānoaHonoluluUSA
  2. 2.Department of Biological SciencesUniversity of AlbertaEdmontonCanada
  3. 3.Office of Digital Innovation and Stewardship, University LibrariesUniversity of ArizonaTucsonUSA
  4. 4.School of Architecture and Spatial Sciences InstituteUniversity of Southern CaliforniaLos AngelesUSA
  5. 5.Department of Biological SciencesMoorpark CollegeMoorparkUSA

Personalised recommendations