Publications

Publications

Kaganer, Alyssa W., G.S. Stapleton, E.M. Bunting and M.P. Hare. 2022. Aquatic eDNA can advance monitoring of a small-bodied terrestrial salamander and amphibian pathogen. Environmental DNA 00, 1– 12. https://doi.org/10.1002/edn3.316

Kaganer, Alyssa W., L.D. Nagel, T.E. Youker‐Smith, E.M. Bunting, and M.P. Hare. 2021. Environmental DNA‐derived pathogen gene sequences can expand surveillance when pathogen titers are decoupled in eDNA and hosts. Environmental DNA 3, 6:1192-1207.

Albecker M.A., L.G.E. Wilkins, S.A. Krueger-Hadfield, S.M. Bashevkin, M.W. Hahn, M.P. Hare, H.K. Kindsvater, M.A. Sewall, K.E. Lotterhos and A.M. Reitzel. 2021. Does a complex life cycle affect adaptation to environmental change? Genome-informed insights for characterizing selection across complex life cycle. Proc. R. Soc. B 288: 20212122. https://doi.org/10.1098/rspb.2021.2122

Mao, X., S. Augyte, M. Huang, M.P. Hare, D. Bailey, S. Umanzor, M. Marty-Rivera, K.R. Robbins, C. Yarish, S. Lindell and J.L. Jannink. 2020. Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers. Frontiers in Marine Science, 7:694. DOI:10.3389/fmars.2020.00694

Bruce, S.A., Y. Kutsumi, C. Van Maaren, M.P. Hare. 2020. Habitat effects on stocking-induced changes in wild brook trout (Salvelinus fontinalis) genetic structure. Transactions of the American Fisheries Society online early, https://doi.org/10.1002/tafs.10239

McFarland, K and M.P. Hare. 2018. Restoring oysters to urban estuaries: Redefining habitat quality for eastern oyster performance near New York City. PLoS ONE 13(11): e0207368.

Holley, J., K. McComas and M.P. Hare. 2018. Troubled Waters: Risk Perception and the Case of Oyster Restoration in the Hudson-Raritan Estuary. Marine Policy 91:104-112, doi.org/10.1016/j.marpol.2018.01.024

Bruce, S.A., M.P. Hare, M.W. Mitchell, & J.J. Wright. 2018. Identification of a unique and genetically diverse strain of brook trout (Salvelinus fontinalis) in a remote Adirondack watershed. Conservation Genetics DOI: 10.1007/s10592-017-1019-6

Sutherland, C., Fuller, A.K., Royle, J.A., Hare, M.P. and Madden, S., 2018. Large-scale variation in density of an aquatic ecosystem indicator species. Scientific Reports 8, 8958 (2018) doi:10.1038/s41598-018-26847-x

George, E., M.P. Hare, D. Crabtree, B. Lantry and L. Rudstam. 2017. Comparison of genetic and visual identification of cisco and lake whitefish larvae from Chaumont Bay, Lake Ontario. Canadian Journal of Fisheries and Aquatic Sciences DOI: 10.1139/cjfas-2017-0186

Linden, D.W., A.K. Fuller, J.A. Royle and M.P. Hare. 2017. Examining the occupancy-density relationship for a low-density carnivore. J. Animal Ecology 54:2043-2052, DOI: 10.1111/1365-2664.12883

Sun, C.C., A.K. Fuller, M.P. Hare and J.E. Hurst. 2017. Evaluating population expansion of black bears using noninvasive, genetic spatial capture-recapture. J. Wildlife Management 81: 814–823, DOI:10.1002/jwmg.21248

Sethi, S.A., D. Linden, J. Wenburg, C. Lewis, P. Lemons, A. Fuller and M.P. Hare. 2016. Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering. Royal Society Open Science, 3(12), p.160457, DOI: 10.1098/rsos.160457

Fuller, A.K., C. Sutherland, J.A. Royle and M.P. Hare. 2016. Estimating population density and space usage of American mink using spatial capture-recapture. Ecological Applications 26:1125-1135

Eierman, L.E. and M.P. Hare. 2015. Reef specific patterns of gene expression plasticity in eastern oysters (Crassostrea virginica). Journal of Heredity, special issue on phenotypic plasticity and evolution 107(1):90-100.

Sutherland, J., F. Acker, J. Bloomfield, C. Boylen, D. Charles, R. Daniels, L. Eichler, J. Farrell, R. Feranec, M.P. Hare, S. Kanfoush, R. Preall, S. Quinn, H. Rowell, W. Schoch, W. Shaw, C. Siegfried, T. Sullivan, D. Winkler and S. Nierzwicki-Bauer. 2015. Brooktrout Lake Case Study – Biotic Recovery from Acid Deposition 20 Years after the 1990 Clean Air Act Amendments. Environmental Science and Technology 49(5): 2665–2674.

Hare, M.P. and H. Borchardt-Wier. 2014. Microsatellite primers designed from pyrosequences to compare two subspecies of surf clam, Spisula solidissima. Conservation Genetics Resources, 6(4):1039-1041.

Ilut, D.C., M.L. Nydam and M.P. Hare. 2014. Defining loci in restriction-based reduced representation genomic data from nonmodel species: Sources of bias and diagnostics for optimal clustering. BioMed Research International vol. 2014, Article ID 675158, 9 pages. doi:10.1155/2014/675158

Eierman, L.E. and M.P. Hare. 2014. Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica. BMC Genomics 15:503 doi:10.1186/1471-2164-15-503.

Burford M.O., J. Scarpa, B.J. Cook, M.P. Hare. 2014. Local adaptation of a marine invertebrate with high dispersal potential: evidence from a reciprocal transplant experiment of the eastern oyster (Crassostrea virginica). Marine Ecology Progress Series 505:161-175,. DOI: 10.3354/meps10796

Thompson, P., B. Rosenthal, and M.P. Hare. 2014b. Hybridization between previously isolated ancestors may explain the persistence of exactly two ancient lineages in the genome of the oyster parasite Perkinsus marinus. Infection, Genetics and Evolution 24C(2014)167-176. DOI: 10.1016/j.meegid.2014.03.003.

Thompson, P., B. Rosenthal, and M.P. Hare. 2014a. Microsatellite genotypes reveal some long distance gene flow in Perkinsus marinus, a major pathogen of eastern oysters. Journal of Shellfish Research. 33(1):195-206.

Anderson, J.D., W.J. Karel1, C.E. Mace, B.L. Bartram and M.P. Hare. 2014. Spatial genetic features of eastern oysters (Crassostrea virginica Gmelin) in the Gulf of Mexico: northward movement of a secondary contact zone. Ecology and Evolution, DOI: 10.1002/ece3.1064.

Eierman, L.E. and M.P. Hare. 2013. Survival of oyster larvae in different salinities depends on source population within an estuary. Journal of Experimental Marine Biology and Ecology449:61-68, Early Online: http://dx.doi.org/10.1016/j.jembe.2013.08.015

Thompson, C.M., M.P. Hare, and S.M. Gallager. 2012. Semi-automated image-analysis for the identification of bivalve larvae from a Cape Cod estuary. Limnology & Oceanography Methods 10:538-554 (2012).

Zhang, H. and M.P. Hare. 2012. Identifying and reducing AFLP genotyping error: An example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters. Heredity DOI: 10.1038/hdy.2011.132.

Kruse, I., M.P. Hare & A.H. Hines. 2011. Genetic relationships of the marine invasive crab parasite Loxothylacus panopaei: an analysis of DNA sequence variation, host specificity, and distributional range. Biological Invasions DOI: 10.1007/s10530-011-0111-y.

Chen, G. and M.P. Hare. 2011. Cryptic diversity and comparative phylogeography of the estuarine copepod Acartia tonsa on the US Atlantic coast. Molecular Ecology20(11): 2425-2441.

Hare, M., L. Nunney, M. Schwartz, D. Ruzzante, M. Burford, R. Waples, K. Ruegg, and F. Palstra. 2011. Understanding and estimating effective population size for practical applications in marine species management. Conservation Biology 25(3): 438-449.

Thompson, P., B. Rosenthal, and M.P. Hare. 2011. An evolutionary legacy of sex and clonal reproduction in the protistan oyster parasite Perkinsus marinus. Infection, Genetics and Evolution 11(3): 598-609.

Hare, M.P., J. Weinberg, O. Peterfalvy and M. Davidson.2010. The “southern” surfclam (Spisula solidissima) found north of its reported range: A commercially harvested population in Long Island Sound, New York. Journal of Shellfish Research. 29(4):799-807.

Zhang, H., J. Scarpa, and M.P. Hare. 2010. Differential fertilization success between two populations of eastern oyster, Crassostrea virginica. Biological Bulletin 219:142-150.

Carlsson, J., R.B. Carnegie, J.F. Cordes, M.P. Hare, T. Leggett, K.S. Reece. 2008. Evaluating recruitment contribution of a selectively bred aquaculture line of the oyster, Crassostrea virginica used in restoration efforts. Journal of Shellfish Research 27(5):1117-1124.

Chen, G. and M.P. Hare. 2008. Cryptic ecological diversification of a planktonic estuarine copepod, Acartia tonsa. Molecular Ecology 17:1451-1468.

Wangchuk, T.,  D.W. Inouye, and M.P. Hare. 2008. The emergence of an endangered species: Evolution and phylogeny of the Trachypithecus geei of Bhutan.International Journal of Primatology 29(3):565-582.

Kruse, I. and M.P. Hare. 2007. Genetic diversity and expanding non-indigenous range of the rhizocephalan Loxothylacus panopaei parasitizing mud crabs in the western North Atlantic. J. Parasitology 93(3):575-582.

Murray, M. and M.P. Hare. 2006. A genomic stan for divergent selection in a secondary contact zone between Atlantic and Gulf of Mexico oysters, Crassostrea virginica. Molecular Ecology 15: 4229-4242.

Hare, M. P., S. K. Allen Jr., P. Bloomer, M. D. Camara, M. D. Carnegie, J. Murfree, M. W. Luckenbach, D. Merritt, C. Morrison, K. T. Paynter, K. S. Reece, and C. G. Rose. 2006. A genetic test for recruitment enhancement in Chesapeake Bayoysters, Crassostrea virginica, after population supplementation with a disease tolerant strain. Conservation Genetics 7: 717-734.

Rose, C. G., K. T. Paynter, and M. Hare. 2006. Isolation by distance in the eastern oyster, Crassostrea virginica, in Chesapeake Bay. J. Heredity 97(2): 158-170.

Hare, M.P., C. Guenther and W.F. Fagan. 2005. Nonrandom larval dispersal can steepen marine clines. Evolution59:2509-2517.

Gaines, C.A., M.P. Hare, S.E. Beck and H.C. Rosenbaum.2005. Nuclear markers confirm taxonomic status and relationships among highly endangered and closely related right whale species. Proceedings of the Royal Society B272:533-542.

Hare, M.P. and J. Weinberg. 2005. Phylogeography of surf clams, Spisula solidissima, in the western North Atlanticbased on mitochondrial and nuclear DNA sequences. Marine Biology 146:707-716.

Robinson T.B., C.L. Griffiths, A. Tonin, P. Bloomer & M.P. Hare. 2005. Naturalized populations of Crassostrea gigasalong the South African coast: distribution, abundance and population structure. Journal of Shellfish Research24(2):443-450.

Hare, M.P. and S.R. Palumbi. 2003. High intron sequence conservation across three mammalian orders suggests functional constraints. Molecular Biology and Evolution20(6):969-978.

Wangchuk, T., D.W. Inouye and M.P. Hare. 2003. A new subspecies of golden langur (Trachypithecus geei) from Bhutan. Folia Primatol 74:104-108.

Hare, M.P., F. Cipriano and S.R. Palumbi. 2002. Genetic evidence on the demography of speciation in allopatric dolphin species. Evolution 56:804-816.

Hare, M.P. 2001. Prospects for nuclear gene phylogeography. Trends in Ecology and Evolution 16(12):700-706.

Palumbi, S. R., F. Cipriano and M. P. Hare. 2001. Predicting nuclear gene coalescence from mitochondrial data: The three-times rule. Evolution 55:859-868.

Hare, M.P., S.R. Palumbi and C.A. Butman. 2000. Single-step species identification of bivalve larvae using multiplex polymerase chain reaction. Marine Biology 137:953-961.

Hare, M.P. and S. R. Palumbi. 1999. The accuracy of heterozygous base calling from diploid sequence and resolution of haplotypes using allele-specific sequencing.Molecular Ecology 8:1750-1752.

Hare, M.P. 1998. Using mitochondrial DNA gene trees and nuclear RFLPs to predict genealogical patterns at nuclear loci: examples from the American oyster. Proceedings of the trinational workshop on molecular evolution, M. Uyenoyama and A. von Haeseler, eds. Duke Publications Group, Duke University, Durham, NC.

Hare, M.P. and J.C. Avise. 1998. Population structure in the American oyster as inferred by nuclear gene genealogies. Molecular Biology and Evolution 15:119-128.

Orti, G., M.P. Hare, and J.C. Avise. 1997. Detection and isolation of nuclear haplotypes by PCR-SSCP. Molecular Ecology 6:575-580.

Hare, M.P. and J.C. Avise. 1996. Molecular genetic analysis of a stepped multilocus cline in the American oyster (Crassostrea virginica). Evolution 50:2305-2315.

Hare, M.P., S.A. Karl, and J.C. Avise. 1996. Anonymous nuclear DNA markers in the American oyster and their implications for the heterozygote deficiency phenomenon in marine bivalves. Molecular Biology and Evolution 13:334-345.

Hare, M.P, and G.F. Shields. 1992. Mitochondrial-DNA variation in the polytypic Alaskan Song Sparrow. Auk109(1):126-132.

Foster, N.R. and M.P. Hare. 1990. Cephalopod remains from a Cuvier’s beaked whale (Ziphius cavirostris) stranded in Kodiak, Alaska. Northwestern Naturalist 71:49-51.