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Global invasion history of the agricultural pest butterfly Pieris rapae revealed with genomics and citizen science.

Ryan SF, Lombaert E, Espeset A, Vila R, Talavera G, Dincă V, Doellman MM, Renshaw MA, Eng MW, Hornett EA, Li Y, Pfrender ME, Shoemaker D.

Proc Natl Acad Sci U S A. 2019 Sep 10. pii: 201907492. doi: 10.1073/pnas.1907492116. [Epub ahead of print]


Pattern of DNA Methylation in Daphnia: Evolutionary Perspective.

Kvist J, Gonçalves Athanàsio C, Shams Solari O, Brown JB, Colbourne JK, Pfrender ME, Mirbahai L.

Genome Biol Evol. 2018 Aug 1;10(8):1988-2007. doi: 10.1093/gbe/evy155.


Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome.

Perry BW, Card DC, McGlothlin JW, Pasquesi GIM, Adams RH, Schield DR, Hales NR, Corbin AB, Demuth JP, Hoffmann FG, Vandewege MW, Schott RK, Bhattacharyya N, Chang BSW, Casewell NR, Whiteley G, Reyes-Velasco J, Mackessy SP, Gamble T, Storey KB, Biggar KK, Passow CN, Kuo CH, McGaugh SE, Bronikowski AM, de Koning APJ, Edwards SV, Pfrender ME, Minx P, Brodie ED 3rd, Brodie ED Jr, Warren WC, Castoe TA.

Genome Biol Evol. 2018 Aug 1;10(8):2110-2129. doi: 10.1093/gbe/evy157.


Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys.

Grey EK, Bernatchez L, Cassey P, Deiner K, Deveney M, Howland KL, Lacoursière-Roussel A, Leong SCY, Li Y, Olds B, Pfrender ME, Prowse TAA, Renshaw MA, Lodge DM.

Sci Rep. 2018 Jun 11;8(1):8843. doi: 10.1038/s41598-018-27048-2.


Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling.

Ryan SF, Deines JM, Scriber JM, Pfrender ME, Jones SE, Emrich SJ, Hellmann JJ.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2284-E2291. doi: 10.1073/pnas.1714950115. Epub 2018 Feb 20.


The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera.

Li Y, Zhang R, Liu S, Donath A, Peters RS, Ware J, Misof B, Niehuis O, Pfrender ME, Zhou X.

BMC Evol Biol. 2017 Dec 28;17(1):269. doi: 10.1186/s12862-017-1111-z.


Evolutionary transition from blood feeding to obligate nonbiting in a mosquito.

Bradshaw WE, Burkhart J, Colbourne JK, Borowczak R, Lopez J, Denlinger DL, Reynolds JA, Pfrender ME, Holzapfel CM.

Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):1009-1014. doi: 10.1073/pnas.1717502115. Epub 2017 Dec 18.


Gene Coexpression Networks Drive and Predict Reproductive Effects in Daphnia in Response to Environmental Disturbances.

Asselman J, Pfrender ME, Lopez JA, Shaw JR, De Schamphelaere KAC.

Environ Sci Technol. 2018 Jan 2;52(1):317-326. doi: 10.1021/acs.est.7b05256. Epub 2017 Dec 15.


Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae).

Dowle EJ, Bracewell RR, Pfrender ME, Mock KE, Bentz BJ, Ragland GJ.

Mol Ecol. 2017 Nov;26(21):6071-6084. doi: 10.1111/mec.14342. Epub 2017 Nov 8.


Environmental DNA metabarcoding: Transforming how we survey animal and plant communities.

Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L.

Mol Ecol. 2017 Nov;26(21):5872-5895. doi: 10.1111/mec.14350. Epub 2017 Oct 26. Review.


Is there more than one way to skin a newt? Convergent toxin resistance in snakes is not due to a common genetic mechanism.

Feldman CR, Durso AM, Hanifin CT, Pfrender ME, Ducey PK, Stokes AN, Barnett KE, Brodie ED 3rd, Brodie ED Jr.

Heredity (Edinb). 2017 Dec;119(6):468. doi: 10.1038/hdy.2017.39. Epub 2017 Aug 9.


Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes.

Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, Stoiber MH, Spanier KI, Gilbert D, Jansen M, Rusch DB, Pfrender ME, Colbourne JK, Frilander MJ, Kvist J, Decaestecker E, De Schamphelaere KAC, De Meester L.

Mol Ecol. 2018 Feb;27(4):886-897. doi: 10.1111/mec.14261. Epub 2017 Aug 19.


Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient.

Ryan SF, Fontaine MC, Scriber JM, Pfrender ME, O'Neil ST, Hellmann JJ.

Mol Ecol. 2017 Sep;26(18):4725-4742. doi: 10.1111/mec.14236. Epub 2017 Aug 21.


A New Reference Genome Assembly for the Microcrustacean Daphnia pulex.

Ye Z, Xu S, Spitze K, Asselman J, Jiang X, Ackerman MS, Lopez J, Harker B, Raborn RT, Thomas WK, Ramsdell J, Pfrender ME, Lynch M.

G3 (Bethesda). 2017 May 5;7(5):1405-1416. doi: 10.1534/g3.116.038638.


Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

Orsini L, Gilbert D, Podicheti R, Jansen M, Brown JB, Solari OS, Spanier KI, Colbourne JK, Rusch DB, Decaestecker E, Asselman J, De Schamphelaere KA, Ebert D, Haag CR, Kvist J, Laforsch C, Petrusek A, Beckerman AP, Little TJ, Chaturvedi A, Pfrender ME, De Meester L, Frilander MJ.

Sci Data. 2017 Jan 31;4:170006. doi: 10.1038/sdata.2017.6. No abstract available.


Bisulfite Sequencing with Daphnia Highlights a Role for Epigenetics in Regulating Stress Response to Microcystis through Preferential Differential Methylation of Serine and Threonine Amino Acids.

Asselman J, De Coninck DI, Beert E, Janssen CR, Orsini L, Pfrender ME, Decaestecker E, De Schamphelaere KA.

Environ Sci Technol. 2017 Jan 17;51(2):924-931. doi: 10.1021/acs.est.6b03870. Epub 2016 Dec 28.


Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure.

Orsini L, Marshall H, Cuenca Cambronero M, Chaturvedi A, Thomas KW, Pfrender ME, Spanier KI, De Meester L.

Mol Ecol. 2016 Dec;25(24):6024-6038. doi: 10.1111/mec.13907. Epub 2016 Nov 25.


Genome-wide profiling of 24 hr diel rhythmicity in the water flea, Daphnia pulex: network analysis reveals rhythmic gene expression and enhances functional gene annotation.

Rund SS, Yoo B, Alam C, Green T, Stephens MT, Zeng E, George GF, Sheppard AD, Duffield GE, Milenković T, Pfrender ME.

BMC Genomics. 2016 Aug 18;17:653. doi: 10.1186/s12864-016-2998-2.


Estimating species richness using environmental DNA.

Olds BP, Jerde CL, Renshaw MA, Li Y, Evans NT, Turner CR, Deiner K, Mahon AR, Brueseke MA, Shirey PD, Pfrender ME, Lodge DM, Lamberti GA.

Ecol Evol. 2016 May 30;6(12):4214-26. doi: 10.1002/ece3.2186. eCollection 2016 Jun.


Historical Contingency in a Multigene Family Facilitates Adaptive Evolution of Toxin Resistance.

McGlothlin JW, Kobiela ME, Feldman CR, Castoe TA, Geffeney SL, Hanifin CT, Toledo G, Vonk FJ, Richardson MK, Brodie ED Jr, Pfrender ME, Brodie ED 3rd.

Curr Biol. 2016 Jun 20;26(12):1616-1621. doi: 10.1016/j.cub.2016.04.056. Epub 2016 Jun 9.


Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

Orsini L, Gilbert D, Podicheti R, Jansen M, Brown JB, Solari OS, Spanier KI, Colbourne JK, Rusch DB, Decaestecker E, Asselman J, De Schamphelaere KA, Ebert D, Haag CR, Kvist J, Laforsch C, Petrusek A, Beckerman AP, Little TJ, Chaturvedi A, Pfrender ME, De Meester L, Frilander MJ.

Sci Data. 2016 May 10;3:160030. doi: 10.1038/sdata.2016.30. Erratum in: Sci Data. 2017 Jan 31;4:170006. Rush, Douglas [corrected to Rusch, Douglas B].


Genomic Appraisal of the Multifactorial Basis for In Vitro Acquisition of Miltefosine Resistance in Leishmania donovani.

Vacchina P, Norris-Mullins B, Abengózar MA, Viamontes CG, Sarro J, Stephens MT, Pfrender ME, Rivas L, Morales MA.

Antimicrob Agents Chemother. 2016 Jun 20;60(7):4089-100. doi: 10.1128/AAC.00478-16. Print 2016 Jul.


Gene Body Methylation Patterns in Daphnia Are Associated with Gene Family Size.

Asselman J, De Coninck DI, Pfrender ME, De Schamphelaere KA.

Genome Biol Evol. 2016 Apr 25;8(4):1185-96. doi: 10.1093/gbe/evw069.


Is there more than one way to skin a newt? Convergent toxin resistance in snakes is not due to a common genetic mechanism.

Feldman CR, Durso AM, Hanifin CT, Pfrender ME, Ducey PK, Stokes AN, Barnett KE, Brodie ED 3rd, Brodie ED Jr.

Heredity (Edinb). 2016 Jan;116(1):84-91. doi: 10.1038/hdy.2015.73. Epub 2015 Sep 16. Erratum in: Heredity (Edinb). 2017 Aug 09;:.


Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding.

Evans NT, Olds BP, Renshaw MA, Turner CR, Li Y, Jerde CL, Mahon AR, Pfrender ME, Lamberti GA, Lodge DM.

Mol Ecol Resour. 2016 Jan;16(1):29-41. doi: 10.1111/1755-0998.12433. Epub 2015 Jun 18.


Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia.

Asselman J, Pfrender ME, Lopez JA, De Coninck DI, Janssen CR, Shaw JR, De Schamphelaere KA.

Mol Ecol. 2015 Apr;24(8):1844-55. doi: 10.1111/mec.13148. Epub 2015 Apr 2.


An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits.

Routtu J, Hall MD, Albere B, Beisel C, Bergeron RD, Chaturvedi A, Choi JH, Colbourne J, De Meester L, Stephens MT, Stelzer CP, Solorzano E, Thomas WK, Pfrender ME, Ebert D.

BMC Genomics. 2014 Nov 27;15:1033. doi: 10.1186/1471-2164-15-1033.


Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia.

Yampolsky LY, Zeng E, Lopez J, Williams PJ, Dick KB, Colbourne JK, Pfrender ME.

BMC Genomics. 2014 Oct 4;15:859. doi: 10.1186/1471-2164-15-859.


Parallel evolution of tetrodotoxin resistance in three voltage-gated sodium channel genes in the garter snake Thamnophis sirtalis.

McGlothlin JW, Chuckalovcak JP, Janes DE, Edwards SV, Feldman CR, Brodie ED Jr, Pfrender ME, Brodie ED 3rd.

Mol Biol Evol. 2014 Nov;31(11):2836-46. doi: 10.1093/molbev/msu237. Epub 2014 Aug 18.


Confirmation and distribution of tetrodotoxin for the first time in terrestrial invertebrates: two terrestrial flatworm species (Bipalium adventitium and Bipalium kewense).

Stokes AN, Ducey PK, Neuman-Lee L, Hanifin CT, French SS, Pfrender ME, Brodie ED 3rd, Brodie ED Jr.

PLoS One. 2014 Jun 25;9(6):e100718. doi: 10.1371/journal.pone.0100718. eCollection 2014.


The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments.

Orsini L, Schwenk K, De Meester L, Colbourne JK, Pfrender ME, Weider LJ.

Trends Ecol Evol. 2013 May;28(5):274-82. doi: 10.1016/j.tree.2013.01.009. Epub 2013 Feb 8.


Cast adrift on an island: introduced populations experience an altered balance between selection and drift.

O'Neill EM, Beard KH, Pfrender ME.

Biol Lett. 2012 Oct 23;8(5):890-3. doi: 10.1098/rsbl.2012.0312. Epub 2012 Jun 20.


Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA.

Lodge DM, Turner CR, Jerde CL, Barnes MA, Chadderton L, Egan SP, Feder JL, Mahon AR, Pfrender ME.

Mol Ecol. 2012 Jun;21(11):2555-8. doi: 10.1111/j.1365-294X.2012.05600.x.


The evolution of salinity tolerance in Daphnia: a functional genomics approach.

Latta LC, Weider LJ, Colbourne JK, Pfrender ME.

Ecol Lett. 2012 Aug;15(8):794-802. doi: 10.1111/j.1461-0248.2012.01799.x. Epub 2012 May 15.


Triangulating the genetic basis of adaptation to multifarious selection.

Pfrender ME.

Mol Ecol. 2012 May;21(9):2051-3. doi: 10.1111/j.1365-294X.2012.05494.x.


Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes.

Feldman CR, Brodie ED Jr, Brodie ED 3rd, Pfrender ME.

Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4556-61. doi: 10.1073/pnas.1113468109. Epub 2012 Mar 5.


Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock.

Parnell JJ, Callister SJ, Rompato G, Nicora CD, Paša-Tolić L, Williamson A, Pfrender ME.

Sci Rep. 2011;1:25. doi: 10.1038/srep00025. Epub 2011 Jun 29.


Linking genes to communities and ecosystems: Daphnia as an ecogenomic model.

Miner BE, De Meester L, Pfrender ME, Lampert W, Hairston NG Jr.

Proc Biol Sci. 2012 May 22;279(1735):1873-82. doi: 10.1098/rspb.2011.2404. Epub 2012 Feb 1.


Future human intervention in ecosystems and the critical role for evolutionary biology.

Hellmann JJ, Pfrender ME.

Conserv Biol. 2011 Dec;25(6):1143-7. doi: 10.1111/j.1523-1739.2011.01786.x. No abstract available.


Diet restriction and life history trade-offs in short- and long-lived species of Daphnia.

Latta LC 4th, Frederick S, Pfrender ME.

J Exp Zool A Ecol Genet Physiol. 2011 Dec 1;315(10):610-7. doi: 10.1002/jez.710. Epub 2011 Sep 26.


A proposal to sequence the genome of a garter snake (Thamnophis sirtalis).

Castoe TA, Bronikowski AM, Brodie ED 3rd, Edwards SV, Pfrender ME, Shapiro MD, Pollock DD, Warren WC.

Stand Genomic Sci. 2011 Apr 29;4(2):257-70. doi: 10.4056/sigs.1664145.


Genomics of environmentally induced phenotypes in 2 extremely plastic arthropods.

Simon JC, Pfrender ME, Tollrian R, Tagu D, Colbourne JK.

J Hered. 2011 Sep-Oct;102(5):512-25. doi: 10.1093/jhered/esr020. Epub 2011 Apr 27. Review.


The ecoresponsive genome of Daphnia pulex.

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL.

Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.


Cryptic postzygotic isolation in an eruptive species of bark beetle (Dendroctonus ponderosae).

Bracewell RR, Pfrender ME, Mock KE, Bentz BJ.

Evolution. 2011 Apr;65(4):961-75. doi: 10.1111/j.1558-5646.2010.01201.x. Epub 2010 Dec 22.


Functional biogeography as evidence of gene transfer in hypersaline microbial communities.

Parnell JJ, Rompato G, Latta LC 4th, Pfrender ME, Van Nostrand JD, He Z, Zhou J, Andersen G, Champine P, Ganesan B, Weimer BC.

PLoS One. 2010 Sep 23;5(9):e12919. doi: 10.1371/journal.pone.0012919.


Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches.

Pfrender ME, Hawkins CP, Bagley M, Courtney GW, Creutzburg BR, Epler JH, Fend S, Schindel D, Ferrington LC Jr, Hartzell PL, Jackson S, Larsen DP, Lévesque A, Morse JC, Petersen MJ, Ruiter D, Whiting M.

Q Rev Biol. 2010 Sep;85(3):319-40. Review.


Genomics in the ecological arena.

Orsini L, Decaestecker E, De Meester L, Pfrender ME, Colbourne JK.

Biol Lett. 2011 Feb 23;7(1):2-3. doi: 10.1098/rsbl.2010.0629. Epub 2010 Aug 11.


Predator-induced defences in Daphnia pulex: selection and evaluation of internal reference genes for gene expression studies with real-time PCR.

Spanier KI, Leese F, Mayer C, Colbourne JK, Gilbert D, Pfrender ME, Tollrian R.

BMC Mol Biol. 2010 Jun 29;11:50. doi: 10.1186/1471-2199-11-50.


Genetic architecture of a feeding adaptation: garter snake (Thamnophis) resistance to tetrodotoxin bearing prey.

Feldman CR, Brodie ED Jr, Brodie ED 3rd, Pfrender ME.

Proc Biol Sci. 2010 Nov 7;277(1698):3317-25. doi: 10.1098/rspb.2010.0748. Epub 2010 Jun 3.


Phenotypic plasticity facilitates recurrent rapid adaptation to introduced predators.

Scoville AG, Pfrender ME.

Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4260-3. doi: 10.1073/pnas.0912748107. Epub 2010 Feb 16.

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