Publications

  1. Letcher, B. H., J. D. Walker, M. J. O’Donnell, A. R. Whiteley, K. H. Nislow, and J. A. Coombs (2018) Three visualization approaches for communicating and exploring passive integrated transponder tag data. Fisheries 43: 241-248. https://doi.org/10.1002/fsh.10067
  2. Devine, M. T., A. H. Roy, A. R. Whiteley, B. I. Gahagan, M. P. Armstrong, and A. Jordaan (2018) Precision and relative effectiveness of a purse seine for sampling age-0 river herring in lakes. North American Journal of Fisheries Management. DOI:10.1002/nafm.10065
  3. Day, C. C., E. L. Landguth, A. Bearlin, Z. A. Holden, and A. R. Whiteley (2018) Using simulation modeling to inform management of invasive species: A case study of eastern brook trout suppression and eradication. Biological Conservation 221: 10-22. https://doi.org/10.1016/j.biocon.2018.01.017
  4. Robinson, Z. L., J. A. Coombs, M. Hudy, K. H. Nislow, B. H. Letcher, A. R. Whiteley (2017) Experimental test of genetic rescue in isolated populations of brook trout. Molecular Ecology 26: 4418-4433. DOI 10.1111/mec.14225.
  5. Rosset, J., A. H. Roy, B. I. Gahagan, J. J. Sheppard, A. R. Whiteley, and A. Jordaan (2017) Temporal patterns of migration and spawning of river herring in coastal Massachusetts. Transactions of the American Fisheries Society. DOI: 10.1080/00028487.2017.1341851
  6. Suni, S. S., Z. Scott, A. Averill, and A. R. Whiteley (2017) Population genetics of wild and managed pollinators: implications for crop pollination and the genetic integrity of wild bees. Conservation Genetics 18: 667-677. DOI 10.1007/s10592-017-0955-5.
  7. Kovach†, R. P. Muhlfeld, C. C., R. Al-Chokhachy, S. J. Amish, J. L. Kershner, R. F. Leary, W. H. Lowe, G. Luikart, P. Matson, D. A. Schmetterling, B. B. Shepard, P. A. H. Westley, D. Whited, A. R. Whiteley, and F. W. Allendorf (2017) No evidence for ecological segregation protecting native trout from invasive hybridization. Global Change Biology. DOI: 10.1111/gcb.13825 [Response to Editor]
  8. Muhlfeld, C. C., R. P. Kovach, R. Al-Chokhachy, S. J. Amish, J. L. Kershner, R. F. Leary, W. H. Lowe, G. Luikart, P. Matson, D. A. Schmetterling, B. B. Shepard, P. A. H. Westley, D. Whited, A. R. Whiteley, and F. W. Allendorf (2017) Legacy introductions and climatic variation explain spatiotemporal patterns of invasive hybridization in a native trout. Global Change Biology 23: 4663-4674. DOI 10.1111/gcb.13681
  9. Whiteley, A. R., J. A. Coombs, M. J. O’Donnell, K. H. Nislow, and B. H. Letcher (2017) Keeping things local: subpopulation Nb and Ne in a stream network with partial barriers to fish migration. Evolutionary Applications 10: 348-365. DOI  10.1111/eva.12454.
  10. Letcher, B. H., D. J. Hocking, K. O’Niel, A. R. Whiteley, K. H. Nislow, and M. J. O’Donnell (2016) A hierarchical model of daily stream temperature using air-water temperature synchronization, autocorrelation, and time lags. PeerJ 4:e1727. DOI 10.7717/peerj.1727.
  11. Wilcox, T. M., K. S. McKelvey, M. K. Young, A. J. Sepulveda, B. B. Shepard, S. F. Jane, A. R. Whiteley, W. H. Lowe, and M. K. Schwartz (2016) Understanding environmental DNA detection probabilities: a case study using a stream-dwelling char Salvelinus fontinalis. Biological Conservation 194:209-216. DOI: 10.1016/j.biocon.2015.12.023.
  12. Suni, S. S., A. R. Whiteley (2015) Genetic structure of a montane perennial plant: the influence of landscape and flowing phenology. Conservation Genetics 16: 1431-1442. DOI: 10.1007/s10592-015-0751-z.
  13. Bassar, R., B. H. Letcher, K. H. Nislow, and A. R. Whiteley (2015) Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout. Global Change Biology 22: 577-593.
  14. Whiteley, A. R., J. A. Coombs, M. Cembrola, M. J. O’Donnell, M. Hudy, K. H. Nislow, and B. H. Letcher (2015) Effective number of breeders provides a link between interannual variation in stream flow and individual reproductive contribution in a stream salmonid. Molecular Ecology 24: 3585-3602.
  15. Uusi-Heikkilä, S., A. R. Whiteley, A. Kuparinen, S. Matsumura, P. A. Venturelli, C. Wolter, J. Slate, C. R. Primmer, T. Meinelt, S. S. Killen, D. Bierbach, G. Polverino, A. Ludwig, and R. Arlinghaus (2015) The evolutionary legacy of size-selective harvest extends from genes to populations. Evolutionary Applications 8: 597-620.
  16. Snook, E.L., B. H. Letcher, T. Dubreuil, J. Zydlewski, A.R. Whiteley, S. Hurley, A.J. Danylchuk (2015). Movement patterns of brook trout in a restored coastal stream system in southern Massachusetts. Ecology of Freshwater Fish. DOI: 10.1111/eff.12216
  17. Whiteley, A. R., W. C. Funk, S. Fitzpatrick, and D. A. Tallmon (2015) Genetic rescue to the rescue. Trends in Ecology and Evolution 30:42-49.
  18. Letcher, B. H., P. Schueller, R. Bassar, K. H. Nislow, J. A. Coombs, K. Sakrejda, M. Morrissey, D. Sigourney, A. R. Whiteley, M. O’Donnell, and T. Dubreuil (2014) Robust estimates of seasonal environmental effects on population vital rates: an integrated capture-recapture model of brook trout growth, survival and movement in a stream network. Journal of Animal Ecology 84: 337-352.
  19. Whiteley, A. R., J. A. Coombs, B. H. Letcher, and K. H. Nislow (2014) Simulation and empirical analysis of novel sibship-based genetic determination of fish passage. Canadian Journal of Fisheries and Aquatic Sciences 71: 1667-1679. DOI: 10.1139/cjfas-2014-0137.
  20. Jane, S. P., T. M. Wilcox, K. S. McKelvey, M. K. Young, M. K. Schwartz, W. H. Lowe, B. H. Letcher, and A. R. Whiteley (2014) Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams. Molecular Ecology Resources 15: 216-227. DOI: 10.1111/1755-0998.12285.
  21. Whiteley, A. R., M. Schwartz and K. McGarigal (2014) Pronounced differences in genetic structure despite overall ecological similarity for two Ambystoma salamanders in the same landscape. Conservation Genetics 15:573-591.
  22. Kanno, Y., B. H. Letcher, J. A. Coombs, K. H. Nislow, and A. R. Whiteley (2014) Linking movement and reproductive history of brook trout to assess habitat connectivity in a heterogeneous stream network. Freshwater Biology 59:142-154.
  23. Jane, S. F., K. H. Nislow, and A. R. Whiteley (2014) The use (and misuse) of archaeological salmon data to infer historical abundance in North America with a focus on New England. Reviews in Fish Biology and Fisheries 24, 943-954. DOI 10.1007/s11160-013-9337-3.
  24. Shimomura, K., V. Kumar, N. Koike, T.- K. Kim, J. Chong, E. D. Buhr, A. R. Whiteley, S. S. Low, C. Omura, D. Fenner, J. R. Owens, M. Richards, S.- H. Yoo, H.- K. Hong, M. H. Vitaterna, J. Bass, M. T. Pletcher, T. Wiltshire, J. B. Hogenesch, H. Kadotani, A. Hida, K. Mishima, P. L. Lowrey, and J. S. Takahashi (2013) Usf1, a suppressor of the circadian clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex. eLife 2013:2:e00426.
  25. Whiteley A. R., J. A. Coombs, M. Hudy, Z. Robinson, A. R. Colton, K. H. Nislow, and B. H. Letcher (2013) Fragmentation and patch size shape genetic structure of brook trout populations. Canadian Journal of Fisheries and Aquatic Sciences 70:678-688. DOI: 10.1139/cjfas-2012-0493.
  26. Wilcox, T. M., K. S. McKelvey, M. K. Young, S. F. Jane, W. H. Lowe, A. R. Whiteley, and M. K. Schwartz (2013) Robust detection of rare species using environmental DNA. PLoS ONE 8:e59520. DOI: 10.1371/journal.pone.0059520.
  27. Bergstrom, C. A., A. R. Whiteley, and D. A. Tallmon (2012) The heritable basis and cost of color plasticity in coastrange sculpins. Journal of Evolutionary Biology 25:2526-2536.
  28. Annett, B., G. Gerlach, T. L. King, and A. R. Whiteley (2012) Conservation genetics of remnant coastal brook trout populations at the southern limit of their distribution: population structure and effects of stocking. Transactions of the American Fisheries Society 141:1399-1410. DOI: 10.1080/00028487.2012.694831.
  29. Zeller, K. A., K. McGarigal, and A. R. Whiteley (2012) Estimating landscape resistance to movement: a review. Landscape Ecology 27:777-797. DOI: 10.1007/s10980-012-9737-0.
  30. Whiteley A. R., J. A. Coombs, M. Hudy, Z. Robinson*, K. H. Nislow, and B. H. Letcher (2012) Sampling strategies for estimating brook trout effective population size. Conservation Genetics 13:625-637. DOI: 10.1007/s10592-011-0313-y.
  31. Whiteley A. R., A. Bhat, E. P. Martins, R. Mayden, M. Arunachalam, S. Uusi-Heikkila, and L. Bernatchez (2011) Population genomics of wild and laboratory zebrafish (Danio rerio). Molecular Ecology 20:4259-4276. DOI: 10.1111/j.1365-294X.2011.05272.x.
  32. Whiteley A. R., C. A. Bergstrom, T. Linderoth*, and D. A. Tallmon (2011) The specter of past spectral conditions: color plasticity, crypsis, and predation risk in newly deglaciated streams. Ecology of Freshwater Fish 20:80-91. DOI: 10.1111/j.1600-0633.2010.00461.x.
  33. Kelly, B. P., A. R. Whiteley, and D. A. Tallmon (2010) The Arctic melting pot. Nature 468:891.
  34. Whiteley A. R., K. Hastings, J. K. Wenburg, C. A. Frissell, J. C. Martin, and F. W. Allendorf (2010) Genetic variation and effective population size in isolated populations of coastal cutthroat trout. Conservation Genetics 11:1929-1943.
  35. Fuller, T.K., S. M. Matthews, S. S. Stevens, N. D. Rayl, C. J. Zieminski, A. R. Whiteley, P. R. Sievert, J. F. Organ, and M. W. Gabriel (2010) Noninvasive survey methods for carnivores. Journal of Wildlife Diseases 46:1055-1058.
  36. Bernatchez L., S. Renaut, A. R. Whiteley, D. Campbell, N. Derôme, J. Jeukens, L. Landry, G. Lu, A. W. Nolte, K. Østbye, S. M. Rogers, J. St-Cyr (2010) On the origin of species: insights from the ecological genomics of whitefish. Philosophical Transactions of the Royal Society of London 365:1783-1800.
  37. Whiteley, A. R., S. M. Gende, A. J. Gharrett, and D. A. Tallmon (2009) Background matching and color change plasticity in colonizing freshwater sculpin populations following rapid deglaciation. Evolution 63:1519-1529.
  38. Whiteley, A. R., K. N. Persaud, N. Derome, R. Montgomerie, and L. Bernatchez (2009) Reduced sperm performance in backcross hybrids between species-pairs of whitefish (Coregonus clupeaformis). Canadian Journal of Zoology 87: 566-572.
  39. Whiteley, A. R., N. Derome, S. M. Rogers, J. St-Cyr, J. Laroche, A. Labbe, A. Nolte, S. Renaut, J. Jeukens and L. Bernatchez (2008) The phenomics and expression quantitative trait locus mapping of brain transcriptomes regulating adaptive divergence in lake whitefish species pairs (Coregonus sp.). Genetics 180: 147-164.
  40. Schlei, O. L., A. Crête-Lafrenière, A. R. Whiteley, R. J. Brown, J. B. Olsen, L. Bernatchez, J. K. Wenburg (2008) DNA barcoding of eight North American coregonine species. Molecular Ecology Resources 8: 1212-1218.
  41. Derome, N., B. Bougas, S. M. Rogers, A. R. Whiteley, A. Labbe, J. Laroche, and L. Bernatchez (2008) Pervasive sex-linked effects on transcription regulation as revealed by expression quantitative trait loci mapping in lake whitefish species pairs (Coregonus sp., Salmonidae). Genetics 179: 1903-191.
  42. Whiteley, A. R. (2007) Morphological, dietary, and genetic analysis of a potential trophic polymorphism in a riverine fish species. Biological Journal of the Linnean Society 92: 253-267.
  43. Whiteley, A. R., P. Spruell, and F. W. Allendorf (2006) Can common species provide valuable information for conservation? Molecular Ecology 15: 2767-2786.
  44. Whiteley, A. R., P. Spruell, B. E. Rieman, and F. W. Allendorf (2006) Fine-scale genetic structure of bull trout at the southern limit of their distribution. Transactions of the American Fisheries Society 135: 1238-1253.
  45. Whiteley, A. R., P. Spruell, and F. W. Allendorf (2004) Ecology and life history characteristics predict the population genetic divergence of two salmonids in the same landscape. Molecular Ecology 13: 3675-3688.
  46. Shimomura, K., S. S. Low-Zeddies, D. P. King, T. D. Steeves, A. R. Whiteley, Kushla, P. D. Zemenides, A. Lin, M. H. Vitaterna, G. A. Churchill, and J. S. Takahashi (2001) Genome-wide epistatic interaction analysis reveals complex genetic determinants of circadian behavior in mice. Genome Research 11: 959-980.
  47. Zhu, H., S. LaRue, A. R. Whiteley, T. D. Steeves, J. S. Takahashi, and C. B. Green (2000) The Xenopus clock gene is constitutively expressed in retinal photoreceptors. Molecular Brain Research 75: 303-308.
  48. Sangoram, A. M., L. Saez, M. P. Antoch, N. Gekakis, D. Staknis, A. R. Whiteley, E. M. Fruechte, M. H. Vitaterna, K. Shimomura, D. P. King, M. W. Young, C. J. Weitz, and J. S. Takahashi (1998) Mammalian circadian autoregulatory loop: a timeless ortholog and mper1 interact and negatively regulate clock-bmal1-induced transcription. Neuron 21: 1101-1113.
  49. Valentinuzzi, V. S., D. E. Kolker, M. H. Vitaterna, K. Shimomura, A. R. Whiteley, S. Low-Zeddies, F. W. Turek, E. A. M. Ferrari, R. Paylor, and J. S. Takahashi (1998) Automated measurement of mouse freezing behavior and its use for quantitative trait locus analysis of contextual fear conditioning of (BALB/cJ x C57BL/6J)F2 mice. Learning & Memory 5: 391-403.