Aaron Shafer | Trent University
  • People
  • Research
  • Publications
  • Journal Club
  • Popular & Press
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  • Join the Lab!
  • GIT & Genomes
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Aaron Shafer | Trent University

  • People/
  • Research/
  • Publications/
  • Journal Club/
  • Popular & Press/
  • Lab Travels/
  • Join the Lab!/
  • GIT & Genomes/
  • #ShutDownStem/
Pub_cover2.jpg

Aaron Shafer | Trent University

Shafer Lab

Publications

Aaron Shafer | Trent University

  • People/
  • Research/
  • Publications/
  • Journal Club/
  • Popular & Press/
  • Lab Travels/
  • Join the Lab!/
  • GIT & Genomes/
  • #ShutDownStem/
Trent University students in green, other in blue: † denotes undergraduate, * denotes graduate student 

*** GoogleScholar profile here *** All lab papers have preprint links if final article not OA

Book Chapters

  1. Martchenko D*, Prewer E*, Latch EK, Kyle CJ, Shafer ABA (2021) Population genomics of ungulates. In Population Genomics: Wildlife (ed. Hohenlohe P). Springer Publishing, New York. pg 185-209.
  2. Salmona J, Heller R, Lascoux M, Shafer ABA (2019) Inferring demographic history using genomic data. In Population Genomics: Population genomics concepts, strategies, and approaches (ed. Rajora OM). Springer Publishing, New York. pg 511-539.
  3. Shafer ABA, Davis CS, Coltman DW, Stewart REA (2015) Microsatellite assessment of walrus (Odobenus rosmarus rosmarus) stocks in Canada. In: Walrus in the North Atlantic (eds. Kovacs KM, Stewart REA). NAMMCO Scientific Publications, Tromsø, Norway. 15–32.

Preprints

  1. Aleman JA*, Freeland JR, Shafer ABA, Dorken M, (2024) Allopatric speciation in cattails: Genomic landscapes of divergence across Typha spp. suggest long-term balancing selection, introgressions, and the absence of adaptive divergence. BioRxiv doi:10.1101/2024.07.02.601742
  2. Bonar M*, Northrup JM, Shafer ABA (2024) Proximate drivers of migration propensity: a meta-analysis across species. Authorea doi: 10.22541/au.171355881.18519829/v1
  3. Jones CLC*, Shafer ABA, Frost PC (2023) Well-fed or nearly dead? Using quantitative PCR to detect dietary stress in Daphnia pulex. Authorea doi: 10.22541/au.168120190.08600229/v1
  4. Ridings R†, Gabriel A†, Elliott C†, Shafer ABA (2021) Secondary DNA transfer on denim under three different contact scenarios. BioRxiv doi: 10.1101/2021.11.25.470033

Journal Articles

  1. Cossette M-L*, Stewart DT, Shafer ABA (2024) Comparative genomics of the world’s smallest mammals reveals links to echolocation, metabolism, and body size plasticity. Genome Biology & Evolution (BioRxiv doi: 10.1101/2024.04.28.591546)
  2. Cars B†, Kessler C*, Hoffman E, Côté SD, Koelsch D, Shafer ABA (2024) Island demographics and trait associations in white-tailed deer. Heredity doi: 10.1038/s41437-024-00685-2 (BioRxiv doi: 10.1101/2023.08.01.551454)
  3. Young K*, White KS, Shafer ABA (2024) Unravelling the complex biogeographic and anthropogenic history of Alaska’s mountain goats. Journal of Mammalogy (BioRxiv doi: 10.1101/2023.08.07.552341)
  4. Czajka N*, Northrup JM, Jones M, Shafer ABA (2024) Epigenetic clocks, sex markers, and age-class diagnostics in three harvested large mammals. Molecular Ecology Resources e13956
  5. Kessler C*, Shafer ABA (2024) Genomic analyses capture the human-induced demographic collapse and recovery in a wide-ranging cervid. Molecular Biology & Evolution 41:msae038
  6. McKnight E†, Shafer ABA, Frost PC (2024) Quantifying the effect of water quality on eDNA degradation using microcosm and bioassay experiments. Environmental DNA 6:e530
  7. Aleman JA*, Dorken M, Shafer ABA , Patel T, Volkova P, Freeland JR (2024) Development of genomic resources for cattails (Typha), a globally important macrophyte genus. Freshwater Biology 69:74–83
  8. Haghani A, Li CZ, Lu AT, Robeck TR, Belov K, Breeze CE, Brooke RT, Clarke S, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Gladyshev VN, Gorbunova V, Goya RG, Hogan AN, Hogg CJ, Hore TA, Kiaris H, Kordowitzki P, Takahashi JS, Acosta-Rodríguez VA, Niehrs C, Wallingford MC, Poganik JR, Zhang B, Shindyapina AV, Lee SG, Shafer ABA, Cossette M-L*, [+160 authors], Horvath S, Mammalian Methylation Consortium (2023) Methylation networks underlying mammalian traits. Science 381:602-603 (BioRxiv doi: 10.1101/2021.03.16.435708)
  9. Martchenko D*, Shafer ABA (2023) Contrasting whole-genome and reduced representation sequencing for population demographic inference: an alpine mammal example. Heredity 131:273–281 (Authorea doi 10.22541/au.164190604.45542461)
  10. Lu A, [+38 authors], Cossette M-L* , [+105 Authors], Shafer ABA , [+40 authors], Horvath S (2023) Universal DNA methylation age across mammalian tissues. Nature Aging 3:1144–1166
  11. Wootton E†, Robert C, Taillon J, Côté SD, Shafer ABA (2023) Genomic health is dependent on longterm population demographic history. Molecular Ecology 32:1943–1954
  12. Jones CLC*, Shafer ABA, Frost PC (2023) Characterizing nutritional phenotypes using experimental nutrigenomics: Is there nutrient-specificity to different dietary stress? Molecular Ecology 32:1073–1086
  13. Kessler C*, Wootton E†, Shafer ABA (2023) Speciation without gene-flow in hybridizing deer. Molecular Ecology 32:1117–1132 (BioRxiv doi: 10.1101/2022.04.20.488928)
  14. Cossette M-L*, Stewart DT, Haghani A, Zoller JA, Shafer ABA, Horvath S (2023) Epigenetics and island-mainland divergence in an insectivorous small mammal. Molecular Ecology 32:152-166 (BioRxiv doi: 10.1101/2022.04.14.488253)
  15. Dedato M*, Robert C, Taillon J, Shafer ABA, Côté SD (2022) Demographic history and conservation genomics of Caribou (Rangifer tarandus) in Québec. Evolutionary Applications 15:2043-2053
  16. Bonar M*, Anderson S*, Anderson Jr. CR, Wittemyer G, Northrup JM, Shafer ABA (2022) Genomic correlates for migratory direction in a free-ranging cervid. Proceedings of the Royal Society B 289:20221969 (BioRxiv doi: 2022.05.26.493590)
  17. Elliott C*, Shafer ABA, Stotesbury T (2022) The crux of time: A meta-analysis of ex vivo whole blood degradation. Frontiers in Analytic Science 2:92857
  18. Young K*, White KS, Lewis TL, Shafer ABA (2022) Quantifying the effects of glacial history and future climate change on a unique population of mountain goats, Alaska. Biological Conservation 272:109632 (BioRxiv doi: 10.1101/2022.01.19.476931)
  19. Elliott C†, Stotesbury T, Shafer ABA (2022) Using total RNA quality metrics for time since deposition estimates in degrading bloodstains. Journal of Forensic Sciences 67:1776–1785 (BioRxiv doi:10.1101/2021.04.28.441847)
  20. Borja Martinez G*, Tapia-Flores D, Shafer ABA, Vázquez-Domínguez E (2022) Highland forest’s environmental complexity drives landscape genomics and connectivity of the rodent Peromyscus melanotis. Landscape Ecology 37:1653–1671
  21. Anderson SJ*, Richard JH, Côté SD, Shafer ABA (2022) Genomic architecture of extreme phenotypes in a wild cervid. BMC Genomics 23:126 (BioRxiv 841528)
  22. Quintero-Galvis JF*, Saenz-Agudelo P, Amico GC, Vazquez S, Shafer ABA, Nespolo RF (2022) Genomic diversity and demographic history of the Dromiciops genus (Marsupilia;Microbiotheriidae). Molecular Phylogenetics and Evolution 168:107405
  23. Martchenko D*, White KS, Shafer ABA (2022) Long-term data reveal effects of climate, road access, and latitude on mountain goat horn size. Journal of Wildlife Management 86:e22195
  24. Widanagama S†, Freeland JR, Xinwei Xu, Shafer ABA (2022) Genome assembly, annotation and comparative analysis of the cattail Typha latifolia. G3: Genes, Genomes, Genetics 12:jkab401
  25. Quintero-Galvis JF*, Saenz-Agudelo P, Celis-Diez JL, Amico GC, Vazquez S, Shafer ABA, Nespolo RF (2021) The Biogeography of Dromiciops in Southern South America: middle Miocene transgressions, speciation and associations with Nothofagus. Molecular Phylogenetics and Evolution 163:107234
  26. Wolf JF*, Kriss K, MacAuley K, Munro K, Patterson B, Shafer ABA (2021) Gut microbiome predicts summer core range size in two divergent ungulates. FEMS Microbiology Ecology 97: fiab048 (BioRxiv 2020.08.04.236638)
  27. Haworth SE*, Nituch L, Northrup JM, Shafer ABA (2021) Characterizing the demographic history and prion protein variation to infer susceptibility to chronic wasting disease in a naïve population of white-tailed deer (Odocoileus virginianus). Evolutionary Applications 14: 1528–1539.
  28. Meröndun JB*, Kierepka EM, Shafer ABA, Murray DL (2021) Spatial population genetics reveals competitive imbalances threatening local apex predator persistence. Biological Conservation 256:109062
  29. Gualdieri R†, Orr A*, Cossette ML†, Shafer ABA, Stotesbury T (2021) Whole bovine blood use in forensic research: sample preparation and storage considerations. Science and Justice 61: 214–220
  30. Shafer ABA (2021) Are we paying-to-play? A quantitative assessment of Canadian open access research in ecology and evolution. FACETS 6: 537–544
  31. Cossette ML†, Stotesbury T, Shafer ABA (2021) Quantifying spectral changes and DNA degradation of bloodstains over time under extreme temperatures. Forensic Science International 318: 110627
  32. Jaiswal S*, Gupta A*, Shafer ABA, Prasoodanan V*, Vijay N, Sharma VK (2021) Genomic insights into the molecular basis of sexual selection in birds. Frontiers in Ecology & Evolution 9:538498
  33. White KS, Levi T, Breen J†, Britt M†, Meröndun JB*, Martchenko D*, Shakeri Y, Porter B, Shafer ABA (2021) Integration of population genetic data and demographic modeling for conservation of a small, peninsular mountain goat population. Journal of Wildlife Management 85:271-282 (BioRxiv 484592)
  34. Jones CLC*, Shafer ABA, Prater C, Kim WD†, Wagner ND, Frost PC (2020) The complexity of co-limitation – Nutrigenomics reveal non-additive interactions of calcium and phosphorus on gene expression in Daphnia pulex. Proceedings of the Royal Society B 287: 20202302
  35. Liu G, Gong M, Shafer ABA, Hu X, Huang Y, Zhang L, Wu Y, Wen W, Huixin L (2020) Population demographic history and adaptability of the vulnerable Lolokou sucker frog. Genetica 148:207-213.
  36. Jamieson A†, Anderson SJ*, Fuller J*, Côté SD, Northrup JM, Shafer ABA (2020) Heritability estimates of antler and body traits in white-tailed deer (Odocoileus virginianus) from genomic-relatedness matrices. Journal of Heredity 111:429-435 (BioRxiv 053165)
  37. Coghlan SA*, Shafer ABA, Freeland JR (2021) Development of an environmental DNA metabarcoding assay to assess aquatic plant communities. Environmental DNA 3:372–387
  38. Stotesbury T, Cossette ML†, Newell-Bell T†, Shafer ABA (2020) An exploratory time since deposition analysis of whole blood inferred using metrics of DNA degradation and visible absorbance spectroscopy. Pure and Applied Geophysics doi: 10.1007/s00024-020-02494-0
  39. Peart CR, Tusso S*, Pophaly SD, Botero-Castro F, Wu C-C, Aurioles D, Baird A, Bickham J, Forcada J, Gelatt TS, Galimberti F, Gemmell N, Hoffman JI, Kovacs KM, Kunnisantra M, Lydersen C, Nyman T, Oliviera LR, Orr AJ, Sanvito S, Trillmich F, Valtonen V, Shafer ABA, Wolf JBW (2020) Determinants of genetic variation across eco-evolutionary scales in pinnipeds. Nature Ecology & Evolution doi 4:1095-1104.
  40. Wolf JF*, Kriss K, MacAuley K, Shafer ABA (2020) Panmictic population genetic structure of Northern British Columbia mountain goats (Oreamnos americanus) has implications for harvest management. Conservation Genetics doi 6:613–623
  41. Martchenko D*, Chikhi R, Shafer ABA (2020) Genome assembly and analysis of the North American mountain goat (Oreamnos americanus) reveals species level responses to extreme environments. G3: Genes, Genomes, Genetics 10:437–442
  42. Haworth SE†, White KS, Côté SD, Shafer ABA (2019) Space, time and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate. FEMS Microbiology Ecology 95:fiz095 (BioRxiv 475459)
  43. Meröndun JB*, Murray DL, Shafer ABA (2019) Genome-scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx. Molecular Ecology 28:3186–3196 (BioRxiv 316711)
  44. Kardos M, Shafer ABA (2018) The peril of gene-targeted conservation. Trends in Ecology & Evolution 33:827–839
  45. Jaiswal S*, Gupta A*, Saxena R, Prasoodanan V*, Sharma AK*, Mittal P*, Roy A, Shafer ABA, Vijay N, Sharma VK (2018) Genome sequence of Peacock reveals the peculiar case of a glittering bird. Frontiers in Genetics 9:392
  46. Stoffel MA*, Humble E*, Acevedo-Whitehouse K, Chilvers L, Dickerson B, Galimberti F, Gemmel N, Goldsworthy SD, Nichols H, Krüger O, Pajimans AJ, Pastor T, Robertson B, Sanvito S, Shafer ABA, Wolf JBW, Hoffman JI (2019) Recent demographic histories and genetic diversity across pinnipeds are shaped by anthropogenic interactions and mediated by ecology and life-history. Nature Communications 9:4836
  47. Britt M†, Haworth SE†, Johnson JB*, Martchenko D*, Shafer ABA (2018) The importance of non-academic coauthors in bridging the conservation genetics gap. Biological Conservation 218:118–123
  48. Sun X*, Cai R*, Jin X, Shafer ABA, Hu X, Yang S, Li Y, Qi L, Liu S (2018). Blood transcriptomics of captive forest musk deer (Moschus berezovskii) and possible associations with the immune response to abscesses. Scientific Reports 8:599
  49. Liu G, Shafer ABA, Hu X, Li L, Gong M, Cui L, Ning Y, Li H, Hu D, Qi L, Tian H, Wang B (2018) Metabarcoding insights into the spatial and temporal dietary patterns of the threatened Asian Great Bustard (Otis tarda dybowskii) with potential implications for divergent migratory strategies. Ecology and Evolution 8: 1736-1756
  50. Hu X, Liu G, Shafer ABA, Wei Y, Zhou J, Lin S, Wu H, Zhou M, Hu D, Liu S. Comparative analysis of the gut microbial communities in forest and alpine musk deer using high-throughput sequencing (2017) Frontiers in Microbiology 8:572
  51. Liu G, Hu X, Shafer ABA, Gong M, Han M, Yu C, Zhou J, Bai J, Meng D, Yu G, Dang D. Genetic structure and population history of wintering Asian great bustard (Otis tarda dybowskii) in China: implications for conservation (2017) Journal of Ornithology 158: 761-772
  52. Shafer ABA, Peart C, Tusso S*, Maayan I*, Brelsford A, Wheat C, Wolf JBW (2017) Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference. Methods in Ecology and Evolution 8: 907-917
  53. Shafer ABA, Northrup JM, Wikelski M, Wittemyer G, Wolf JBW (2016) Forecasting ecological genomics: high-tech animal instrumentation meets high-throughput sequencing. PLoS Biology 14:e100235
  54. Shafer ABA, Miller JM, Kardos MD (2016) Cross-species application of SNP chips is not suitable for identifying runs of homozygosity. Journal of Heredity 107: 193-195 (Letter to the editor)
  55. von Rönn JAC*, Shafer ABA, Wolf JBW (2016) Disruptive selection without evolution across a migratory divide. Molecular Ecology 25: 2529-2541
  56. Shafer ABA, Wolf JBW, Alves PC, Bergström L*, Colling G, Dalén L, De Meester L, Ekblom R, Fior S, Hajibabaei M, Hoelzel AR, Hoglund J, Jensen EL*, Krützen M, Norman AJ*, Österling EM, Ouborg NJ, Piccolo J, Primmer CR, Reed FA, Roumet M, Salmona J*, Schwartz MK, Segelbacher G, Thaulow J, Valtonen M*, Vergeer P, Vilà C, Weissensteiner M*, Wheat CW, Zieliński P* (2016) Genomics in conservation: case studies and bridging the gap between data and application - Reply. Trends in Ecology & Evolution 31: 83–84
  57. Cai R*, Shafer ABA, Laguardia A*, Lin Z, Liu S, Hu D (2015) Recombination and selection in the major histocompatibility complex of the endangered forest musk deer (Moschus berezovskii). Scientific Reports 5: 17285
  58. Shafer ABA, Wolf JBW, Alves PC, Bergström L*, Bruford MW, Brannström I*, Colling G, Dalén L, De Meester L, Ekblom R, Fawcett KD*, Fior S, Hajibabaei M, Hill JA, Hoelzel AR, Hoglund J, Jensen EL*, Krause J, Kristensen TN, Krützen M, McKay JK, Norman AJ*, Ogden R, Österling EM, Ouborg NJ, Piccolo J, Popovic D, Primmer CR, Reed FA, Roumet M, Salmona J*, Schenekar T*, Schwartz MK, Segelbacher G, Senn H, Thaulow J, Valtonen M*, Veale A, Vergeer P, Vijay N*, Vilà C, Weissensteiner M*, Wennerström L*, Wheat CW, Zieliński P* (2015) Genomics and the challenging translation into conservation practice. Trends in Ecology & Evolution 30: 78–87
  59. Shafer ABA, Gattepaille LM*, Stewart REA, Wolf JBW (2015) Demographic inferences using short read genomic data in an Approximate Bayesian Computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus. Molecular Ecology 24: 328–345
  60. Northrup JM, Shafer ABA, Anderson Jr. CD, Coltman DW, Wittemyer G (2014) Fine scale genetic correlates to condition and migration in a wild cervid. Evolutionary Applications 7: 937–948
  61. Liu G, Shafer ABA, Wang W, Zimmerman W, Hu D, Chu H, Cao J, Zhao C (2014) Evaluating the reintroduction project of Przewalski’s horse in China using genetic and pedigree data. Biological Conservation 171:288–298
  62. Shafer ABA, Nielsen SE, Northrup JM, Stenhouse GB (2014) Linking genotype, ecotype, and phenotype in an intensively managed large carnivore. Evolutionary Applications 7:301–312
  63. Nielsen SE, Cattet MRL, Boulanger J, Cranston J, McDermid GJ, Shafer ABA, Stenhouse GB (2013) Environmental, biological, and anthropogenic effects on grizzly bear body size: spatial and temporal considerations. BMC Ecology 13:31
  64. Shafer ABA, Wolf JBW (2013) Widespread evidence for incipient ecological speciation: A meta-analysis of isolation-by-ecology. Ecology Letters 16:940–950 (Reviews and Syntheses)
  65. Nielsen SE, Shafer ABA, Boyce MS, Stenhouse GB (2013) Does learning or instinct shape habitat selection? PLoS ONE 8:e53721
  66. Shafer ABA, Northrup JM, White KS, Boyce MS, Côté SD, Coltman DW (2012) Habitat selection predicts genetic relatedness in an alpine ungulate. Ecology 93:1317–1329 (Photo gallery: Bulletin of the Ecological Society of America 93:170–172)
  67. Shafer ABA, Fan CW†, Côté SD, Coltman DW (2012) (Lack of) Genetic diversity in immune genes predates glacial isolation in the North American mountain goat (Oreamnos americanus). Journal of Heredity 103:371–379
  68. Shafer ABA, Corti P, Marin JC, Coltman DW, Davis CS (2012) Development of eight microsatellite loci from the endangered huemul (Hippocamelus bisulcus) and cross-species amplification in six other ungulate species. Conservation Genetics Resources 4:571–573
  69. Shafer ABA, Côté SD, Coltman DW (2011) Hot spots of genetic diversity descended from multiple Pleistocene refugia in an alpine ungulate. Evolution 65:125–138 (Editor’s Choice Article: Science 331:512–513)
  70. Ortego J, Yannic G, Shafer ABA, Mainguy J, Festa-Bianchet M, Coltman DW, Côté SD (2011) Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population. Molecular Ecology 20:1601–1611
  71. Shafer ABA, Poissant J, Côté SD, Coltman DW (2011) Does reduced heterozygosity influence dispersal? A test using spatially structured populations in an alpine ungulate. Biology Letters 7:433–435
  72. Shafer ABA, White KS, Côté SD, Coltman DW (2011) Deciphering translocations from relicts in Baranof Island mountain goats: Is an endemic genetic lineage at risk? Conservation Genetics 12:1261–1268
  73. Corti P, Shafer ABA, Coltman DW, Festa-Bianchet M (2011) Past bottlenecks and current population fragmentation of endangered huemul deer (Hippocamelus bisulcus): implications for preservation of genetic diversity. Conservation Genetics 12:119–128
  74. Mycroft EE†, Shafer ABA, Stewart DT (2011) Cytochrome b sequence variation in water shrews (Sorex palustris). Northeastern Naturalist 18:497–508
  75. Shafer ABA, Cullingham CI, Côté SD, Coltman DW (2010) Of glaciers and refugia: A decade of study sheds new light on the phylogeography of northwestern North America. Molecular Ecology 19:4589–4621 (Invited Review)
  76. Shafer ABA, Hall JC (2010) Placing the mountain goat: a total evidence approach to testing alternative hypotheses. Molecular Phylogenetics and Evolution 55:18–25
  77. Poissant J, Shafer ABA, Mainguy J, Davis CS, Côté SD, Hogg JT, Coltman DW (2009) Genome-wide cross-amplification of domestic sheep microsatellite loci in bighorn sheep and mountain goats. Molecular Ecology Resources 9:1121–1126
  78. Dawe KL, Shafer ABA, Herman TB, Stewart DT (2009) Diffusion of nuclear and mitochondrial genes across a zone of secondary contact in the maritime shrew, Sorex maritimensis: implications for the conservation of a Canadian endemic mammal. Conservation Genetics 10:851–857
  79. Shafer ABA, Williams GR, Shutler D, Rogers REL, Stewart DT (2009) Cophylogeny of Nosema (Microsporidia: Nosematidae) and bees (Hymenoptera: Apidae) suggests both cospeciation and a host-switch. Journal of Parasitology 95:198–203
  80. Shafer ABA, Scott FW, Petersen SD, Rhymer JM, Stewart DT (2008) Following the SINEs: a taxonomic revision of the of the long-tailed shrew complex, Sorex dispar and S. gaspensis. Journal of Mammalogy 89:1421–1427
  81. Williams GR, Shafer ABA, Rogers REL, Shutler D, Stewart DT (2008) First detection of Nosema ceranae, a microsporidian parasite of European honey bees (Apis mellifera), in Canada and central U.S.A. Journal of Invertebrate Pathology 97:189–192
  82. Shafer ABA, Stewart DT (2008) A population crash of the red-backed vole (Myodes gapperi) in Nova Scotia inferred from bycatch of the long-tailed shrew (Sorex dispar). Northeastern Naturalist 15:626–629
  83. Shafer ABA, Stewart DT (2007) Phylogenetic relationships among Nearctic shrews of the genus Sorex (Insectivora, Soricidae) inferred from combined cytochrome b and inter-SINE fingerprint data using Bayesian analysis. Molecular Phylogenetics and Evolution 44:192–203
  84. Shafer ABA, Stewart DT (2006) A disjunct population of Sorex dispar (long-tailed shrew) in Nova Scotia. Northeastern Naturalist 13:603–608