REFERENCES
Ali, O. A., O’Rourke, S. M., Amish, S. J., Meek, M. H., Luikart, G., Jeffres, C., & Miller, M. R. (2016). RAD capture (Rapture): flexible and efficient sequence-based genotyping. Genetics202 (2), 389–400.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215 , 403–410.
Andermann, T., Cano, Á., Zizka, A., Bacon, C., & Antonelli, A. (2018). SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments. PeerJ6 , e5175.
Arbetman, M. P., & Premoli, A. C. (2011). Oldies (but goldies!): extracting DNA from cryopreserved allozyme supernatants. Journal of Heredity102 , 764–769.
Ávila-Arcos, M. C., Ho, S. Y., Ishida, Y., Nikolaidis, N., Tsangaras, K., Hönig, K., … & Willerslev, E. (2012). One hundred twenty years of koala retrovirus evolution determined from museum skins. Molecular Biology and Evolution, 30 (2), 299-304.
Axelsson, E., Willerslev, E., Gilbert, M. T. P., & Nielsen, R. (2008). The effect of ancient DNA damage on inferences of demographic histories.Molecular Biology and Evolution , 25 (10), 2181–2187.
Bakker, F. T., Bieker, V. C., & Martin, M. D. (2020). Herbarium Collection-Based Plant Evolutionary Genetics and Genomics. Frontiers in Ecology and Evolution , 8 , https://doi.org/10.3389/fevo.2020.603948
Bi, K., Linderoth, T., Vanderpool, D., Good, J. M., Nielsen, R., & Moritz, C. (2013). Unlocking the vault: next‐generation museum population genomics. Molecular Ecology , 22 (24), 6018–6032.
Bi, K., Linderoth, T., Singhal, S., Vanderpool, D., Patton, J. L., Nielsen, R., … & Good, J. M. (2019). Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PLoS genetics15 , e1008119.
Blaimer, B. B., Lloyd, M. W., Guillory, W. X., & Brady, S. G. (2016). Sequence capture and phylogenetic utility of genomic ultraconserved elements obtained from pinned insect specimens. PloS one11 , e0161531.
Burrell, A. S., Disotell, T. R., & Bergey, C. M. (2015). The use of museum specimens with high-throughput DNA sequencers. Journal of Human Evolution , 79, 35­–44.
Campos, P. F., & Gilbert, T. M. (2012). DNA extraction from formalin-fixed material. In Ancient DNA  (pp. 81–85). Humana Press.
Card, D. C., Perry, B. W., Adams, R. H., Schield, D. R., Young, A. S., Andrew, A. L., … & Rochford, M. R. (2018). Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons. Molecular Ecology27 (23), 4744–4757.
Cariou, M., Duret, L., & Charlat, S. (2016). How and how much does RAD-seq bias genetic diversity estimates? BMC Evolutionary Biology16 , 1-8.
Caruso, N. M., Sears, M. W., Adams, D. C., & Lips, K. R. (2014). Widespread rapid reductions in body size of adult salamanders in response to climate change. Global Change Biology20 (6), 1751-1759.
Cook, S., Dodge, C., Morgan, R., & Sandusky, G. E. (2014). DNA/RNA degradation rate in long term fixed museum specimens. Forensic Medicine and Anatomy Research3 , 1.
Crates, R., Olah, G., Adamski, M., Aitken, N., Banks, S., Ingwersen, D., … & von Takach Dukai, B. (2019). Genomic impact of severe population decline in a nomadic songbird. PloS one14 , e0223953.
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., … & McVean, G. (2011). The variant call format and VCFtools. Bioinformatics27 , 2156-2158.
Danecek, P., & McCarthy, S. A. (2017). BCFtools/csq: haplotype-aware variant consequences. Bioinformatics , 33 (13), 2037–2039.
de Medeiros, B. A., & Farrell, B. D. (2018). Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci. PeerJ6 , e5089.
Derkarabetian, S., Benavides, L. R., & Giribet, G. (2019). Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault. Molecular Ecology Resources19 , 1531–1544.
Dray, S., & Dufour, A. B. (2007). The ade4 package: implementing the duality diagram for ecologists. Journal of Statistical Software22 (4), 1–20.
Eaton, D. A., & Overcast, I. (2020). ipyrad: Interactive assembly and analysis of RADseq datasets. Bioinformatics36 (8), 2592–2594.
Edwards, S. V., Potter, S., Schmitt, C. J., Bragg, J. G., & Moritz, C. (2016). Reticulation, divergence, and the phylogeography–phylogenetics continuum. Proceedings of the National Academy of Sciences113 (29), 8025­–8032.
Ewart, K. M., Johnson, R. N., Ogden, R., Joseph, L., Frankham, G. J., & Lo, N. (2019). Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species. Molecular Ecology Resources19 , 1578–1592.
Faircloth, B. C. (2016). PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics , 32 (5), 786-788.
Gautier, M., Gharbi, K., Cezard, T., Foucaud, J., Kerdelhué, C., Pudlo, P., … & Estoup, A. (2013). The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Molecular Ecology22 (11), 3165-3178.
Gauthier, J., Pajkovic, M., Neuenschwander, S., Kaila, L., Schmid, S., Orlando, L., & Alvarez, N. (2020). Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland.Molecular Ecology Resources , 20 , 1191–1205.
Heindler, F. M., Christiansen, H., Frédérich, B., Dettaï, A., Lepoint, G., Maes, G. E., … & Volckaert, F. A. (2018). Historical DNA metabarcoding of the prey and microbiome of trematomid fishes using museum samples. Frontiers in Ecology and Evolution6 , 151.
Hedin, M., Derkarabetian, S., Ramírez, M. J., Vink, C., & Bond, J. E. (2018). Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution. Scientific Reports8 (1), 1-7.
Heller, R., Nursyifa, C., Erill, G. G., Salmona, J., Chikhi, J., Meisner, J., Sand Korneliussen, T., Albrechtsen, A. (2021). A reference‐free approach to analyze RADseq data using standard Next Generation Sequencing toolkits. 10.1111/1755-0998.13324
Hime, P. M., Briggler, J. T., Reece, J. S., & Weisrock, D. W. (2019). Genomic data reveal conserved female heterogamety in giant salamanders with gigantic nuclear genomes. G3: Genes, Genomes, Genetics9 (10), 3467-3476.
Hoffberg, S. L., Kieran, T. J., Catchen, J. M., Devault, A., Faircloth, B. C., Mauricio, R., & Glenn, T. C. (2016). RAD cap: sequence capture of dual‐digest RAD seq libraries with identifiable duplicates and reduced missing data. Molecular Ecology Resources16 (5), 1264–1278.
Holmes, M. W., Hammond, T. T., Wogan, G. O., Walsh, R. E., LaBarbera, K., Wommack, E. A., … & Nachman, M. W. (2016). Natural history collections as windows on evolutionary processes. Molecular Ecology25 (4), 864–881.
Hykin, S. M., Bi, K., & McGuire, J. A. (2015). Fixing formalin: a method to recover genomic-scale DNA sequence data from formalin-fixed museum specimens using high-throughput sequencing. PloS One10 , e0141579.
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L., & Orlando, L. (2013). mapDamage2. 0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics29 (13), 1682–1684.
Katoh, K., Asimenos, G., & Toh, H. (2009). Multiple alignment of DNA sequences with MAFFT. In Bioinformatics for DNA sequence analysis  (pp. 49-64). Humana Press.
Krueger, F. (2015). Trim galore. A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, 516, 517.
Lang, P. L., Weiß, C. L., Kersten, S., Latorre, S. M., Nagel, S., Nickel, B., … & Burbano, H. A. (2020). Hybridization ddRADseq‐sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA. Molecular Ecology Resources, 20 , 1228–1247.
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods9 (4), 357.
Lamichhaney, S., Card, D. C., Grayson, P., Tonini, J. F., Bravo, G. A., Näpflin, K., … & Sackton, T. B. (2019). Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution. Philosophical Transactions of the Royal Society B374 (1777), 20180248.
Leavitt, S. D., Keuler, R., Newberry, C. C., Rosentreter, R., & Clair, L. L. S. (2019). Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material. Plant and Fungal Systematics64 (2), 237-247.
Lopez, L., Turner, K. G., Bellis, E. S., & Lasky, J. R. (2020). Genomics of natural history collections for understanding evolution in the wild. Molecular Ecology Resources , 20 , 1153-1160.
Luca, F., Hudson, R. R., Witonsky, D. B., & Di Rienzo, A. (2011). A reduced representation approach to population genetic analyses and applications to human evolution. Genome Research21 (7), 1087-1098.
Lyra, M. L., Lourenço, A. C. C., Pinheiro, P. D., Pezzuti, T. L., Baêta, D., Barlow, A., … & Faivovich, J. (2020). High-throughput DNA sequencing of museum specimens sheds light on the long-missing species of the Bokermannohyla claresignata group (Anura: Hylidae: Cophomantini). Zoological Journal of the Linnean Society ,190 , 1–21.
Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., … & Lopez, R. (2019). The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research , 47 , W636-W641.
McCartney‐Melstad, E., Mount, G. G., & Shaffer, H. B. (2016). Exon capture optimization in amphibians with large genomes. Molecular Ecology Resources16 (5), 1084-1094.
McCormack, J. E., Tsai, W. L., & Faircloth, B. C. (2016). Sequence capture of ultraconserved elements from bird museum specimens. Molecular Ecology Resources16 (5), 1189–1203.
McGaughran, A. (2020). Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time? BMC Genomics, 21 , 1–10.
McGuire, J. A., Cotoras, D. D., O’Connell, B., Lawalata, S. Z., Wang-Claypool, C. Y., Stubbs, A., … & Bi, K. (2018). Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards. PeerJ6 , e4470.
Muletz, C., Caruso, N. M., Fleischer, R. C., McDiarmid, R. W., & Lips, K. R. (2014). Unexpected rarity of the pathogen Batrachochytrium dendrobatidis in Appalachian Plethodon salamanders: 1957–2011. PLoS one9 (8), e103728.
Muletz-Wolz, C. R., Fleischer, R. C., & Lips, K. R. (2019). Fungal disease and temperature alter skin microbiome structure in an experimental salamander system. Molecular Ecology, 28 , 2917-2931.
Newman, C. E., & Austin, C. C. (2016). Sequence capture and next‐generation sequencing of ultraconserved elements in a large‐genome salamander. Molecular Ecology25 (24), 6162–6174.
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution32 (1), 268–274.
Pääbo, S. (1989). Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proceedings of the National Academy of Sciences , 86 (6), 1939–1943.
Paireder, S., Werner, B., Bailer, J., Werther, W., Schmid, E., Patzak, B., & Cichna-Markl, M. (2013). Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues. Analytical Biochemistry432 , 152–160.
Pierson, T. W., Kieran, T. J., Clause, A. G., & Castleberry, N. L. (2020). Preservation-Induced Morphological Change in Salamanders and Failed DNA Extraction from a Decades-Old Museum Specimen: Implications for Plethodon ainsworthiJournal of Herpetology54 , 137–143.
Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS one7 (5), e37135.
Puritz, J. B., Matz, M. V., Toonen, R. J., Weber, J. N., Bolnick, D. I., & Bird, C. E. (2014). Demystifying the RAD fad. Molecular Ecology23 (24), 5937-5942.
Quinlan, A. R., & Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics26 , 841-842.
Rowe, K. C., Singhal, S., Macmanes, M. D., Ayroles, J. F., Morelli, T. L., Rubidge, E. M., … & Moritz, C. C. (2011). Museum genomics: low‐cost and high‐accuracy genetic data from historical specimens. Molecular Ecology Resources11 (6), 1082–1092.
Ruane, S., & Austin, C. C. (2017). Phylogenomics using formalin‐fixed and 100+ year‐old intractable natural history specimens. Molecular Ecology Resources17 , 1003–1008.
Sambrook, J., Russell, D. (2001) Molecular Cloning: A Laboratory Manual, 3rd Edition. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
Sánchez Barreiro, F., Vieira, F. G., Martin, M. D., Haile, J., Gilbert, M. T. P., & Wales, N. (2017). Characterizing restriction enzyme‐associated loci in historic ragweed (Ambrosia artemisiifolia ) voucher specimens using custom‐designed RNA probes. Molecular Ecology Resources17 (2), 209–220.
Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Pääbo, S. (2012). Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PloS one7 (3), e34131.
Schlötterer, C. (2004). The evolution of molecular markers—just a matter of fashion? Nature Reviews Genetics5 (1), 63–69.
Schmid, S., Neuenschwander, S., Pitteloud, C., Heckel, G., Pajkovic, M., Arlettaz, R., & Alvarez, N. (2018). Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics. Ecology and Evolution8 (3), 1480-1495.
Schmitt, C. J., Cook, J. A., Zamudio, K. R., & Edwards, S. V. (2019). Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene. Philosophical Transactions of the Royal Society B374 , 20170387
Shultz, A. J., Adams, B. J., Bell, K. C., Ludt, W. B., Pauly, G. B., & Vendetti, J. E. (2020). Natural history collections are critical resources for contemporary and future studies of urban evolution. Evolutionary Applications , 2020 , 1–15.
Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J., & Birol, I. (2009). ABySS: a parallel assembler for short read sequence data. Genome Research19 (6), 1117-112.
Smith, B. T., Mauck III, W. M., Benz, B. W., & Andersen, M. J. (2020). Uneven missing data skew phylogenomic relationships within the lories and lorikeets. Genome Biology and Evolution12 (7), 1131-1147.
Splendiani, A., Fioravanti, T., Giovannotti, M., Olivieri, L., Ruggeri, P., Nisi Cerioni, P., … & Caputo Barucchi, V. (2017). Museum samples could help to reconstruct the original distribution of Salmo trutta complex in Italy. Journal of Fish Biology90 , 2443–2451.
Sørensen, M., Rasmussen, A. R., & Simonsen, K. P. (2016). Enzymatic detection of formalin-fixed museum specimens for DNA analysis and enzymatic maceration of formalin-fixed specimens. In Collection Forum  (Vol. 40, No. 1, pp. 1–6). Department of Psychology, Indiana University, Bloomington, Indiana 47405: The Society for the Experimental Analysis of Behavior.
St Laurent, R. A., Hamilton, C. A., & Kawahara, A. Y. (2018). Museum specimens provide phylogenomic data to resolve relationships of sack‐bearer moths (Lepidoptera, Mimallonoidea, Mimallonidae). Systematic Entomology43 (4), 729-761.
Staats, M., Erkens, R. H., van de Vossenberg, B., Wieringa, J. J., Kraaijeveld, K., Stielow, B., … & Bakker, F. T. (2013). Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens. PloS one , 8 (7), e69189.
Stronen, A. V., Iacolina, L., Pertoldi, C., Kusza, S., Hulva, P., Dykyy, I., … & Faurby, S. (2019). The use of museum skins for genomic analyses of temporal genetic diversity in wild species. Conservation Genetics Resources11 (4), 499-503.
Stuart, B. L., Dugan, K. A., Allard, M. W., & Kearney, M. (2006). Extraction of nuclear DNA from bone of skeletonized and fluid‐preserved museum specimens. Systematics and Biodiversity4 (2), 133-136.
Suchan, T., Pitteloud, C., Gerasimova, N. S., Kostikova, A., Schmid, S., Arrigo, N., … & Alvarez, N. (2016). Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on collection specimens. PloS one , 11 (3), e0151651.
Tin, M. M. Y., Economo, E. P., & Mikheyev, A. S. (2014). Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics. PloS one , 9(5), e96793.
Tingley, M. W., & Beissinger, S. R. (2009). Detecting range shifts from historical species occurrences: new perspectives on old data. Trends in Ecology & Evolution24 (11), 625–633.
Totoiu, C. A., Phillips, J. M., Reese, A. T., Majumdar, S., Girguis, P. R., Raston, C. L., & Weiss, G. A. (2020). Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens. PloS one15 , e0225807.
Tsai, W. L., Schedl, M. E., Maley, J. M., & McCormack, J. E. (2019). More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens. Molecular Ecology Resources , 2019 , 1–8.
Turvey, S. T., Marr, M. M., Barnes, I., Brace, S., Tapley, B., Murphy, R. W., … & Cunningham, A. A. (2019). Historical museum collections clarify the evolutionary history of cryptic species radiation in the world’s largest amphibians. Ecology and Evolution , 9 (18), 10070–10084.
Wall, A. R., Campo, D., & Wetzer, R. (2014). Genetic utility of natural history museum specimens: endangered fairy shrimp (Branchiopoda, Anostraca). ZooKeys , 457 , 1.
Wandeler, P., Hoeck, P. E., & Keller, L. F. (2007). Back to the future: museum specimens in population genetics. Trends in Ecology & Evolution , 22 (12), 634–642.
Wingett, S. W., & Andrews, S. (2018). FastQ Screen: A tool for multi-genome mapping and quality control. F1000Research7 .
Wood, H. M., González, V. L., Lloyd, M., Coddington, J., & Scharff, N. (2018). Next-generation museum genomics: Phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea). Molecular Phylogenetics and Evolution127 , 907-918.
van der Valk, T., Díez-del-Molino, D., Marques-Bonet, T., Guschanski, K., & Dalén, L. (2019). Historical genomes reveal the genomic consequences of recent population decline in eastern gorillas. Current Biology29 (1), 165-170.
Vershinina, A. O., Kapp, J. D., Baryshnikov, G. F., & Shapiro, B. (2019). The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections. Molecular Ecology Resources , 2020 , 1–9.
Yeates, D. K., Zwick, A., & Mikheyev, A. S. (2016). Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world’s biological collections. Current Opinion in Insect Science18 , 83–88.
Yuan, M. L., Wogan, G. O., & Wang, I. J. (2018). Trehalose improves PCR amplification of vertebrate nuclear DNA from historical allozymes. Conservation Genetics Resources10 , 313–315.