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Items: 1 to 50 of 81

1.

Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle.

Lambert MR, McKenzie JM, Screen RM, Clause AG, Johnson BB, Mount GG, Shaffer HB, Pauly GB.

PeerJ. 2019 Aug 15;7:e7444. doi: 10.7717/peerj.7444. eCollection 2019.

2.

An empirical pipeline for choosing the optimal clustering threshold in RADseq studies.

McCartney-Melstad E, Gidiş M, Shaffer HB.

Mol Ecol Resour. 2019 Sep;19(5):1195-1204. doi: 10.1111/1755-0998.13029. Epub 2019 Jun 1.

PMID:
31058458
3.

Landscape genomic signatures indicate reduced gene flow and forest-associated adaptive divergence in an endangered neotropical turtle.

Gallego-García N, Forero-Medina G, Vargas-Ramírez M, Caballero S, Shaffer HB.

Mol Ecol. 2019 Jun;28(11):2757-2771. doi: 10.1111/mec.15112. Epub 2019 Jun 26.

PMID:
31013379
4.

Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle.

Wielstra B, McCartney-Melstad E, Arntzen JW, Butlin RK, Shaffer HB.

Mol Phylogenet Evol. 2019 Apr;133:120-127. doi: 10.1016/j.ympev.2018.12.032. Epub 2019 Jan 7.

5.

Follow-up ecological studies for cryptic species discoveries: Decrypting the leopard frogs of the eastern U.S.

Schlesinger MD, Feinberg JA, Nazdrowicz NH, Kleopfer JD, Beane JC, Bunnell JF, Burger J, Corey E, Gipe K, Jaycox JW, Kiviat E, Kubel J, Quinn DP, Raithel C, Scott PA, Wenner SM, White EL, Zarate B, Shaffer HB.

PLoS One. 2018 Nov 9;13(11):e0205805. doi: 10.1371/journal.pone.0205805. eCollection 2018.

6.

Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short-necked turtles (Chelidae: Emydura) of eastern Australia.

Georges A, Gruber B, Pauly GB, White D, Adams M, Young MJ, Kilian A, Zhang X, Shaffer HB, Unmack PJ.

Mol Ecol. 2018 Dec;27(24):5195-5213. doi: 10.1111/mec.14925. Epub 2018 Dec 10.

PMID:
30403418
7.

Genomic data recover previously undetectable fragmentation effects in an endangered amphibian.

McCartney-Melstad E, Vu JK, Shaffer HB.

Mol Ecol. 2018 Nov;27(22):4430-4443. doi: 10.1111/mec.14892. Epub 2018 Oct 30.

PMID:
30307076
8.

Assessing effects of non-native crayfish on mosquito survival.

Bucciarelli GM, Suh D, Lamb AD, Roberts D, Sharpton D, Shaffer HB, Fisher RN, Kats LB.

Conserv Biol. 2019 Feb;33(1):122-131. doi: 10.1111/cobi.13198. Epub 2018 Sep 28.

PMID:
30079610
9.

Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog.

McCartney-Melstad E, Gidiş M, Shaffer HB.

Heredity (Edinb). 2018 Aug;121(2):112-125. doi: 10.1038/s41437-018-0097-7. Epub 2018 Jun 25.

10.

Occurrence of Batrachochytrium dendrobatidis in anurans of the Mediterranean region of Baja California, México.

Peralta-García A, Adams AJ, Briggs CJ, Galina-Tessaro P, Valdez-Villavicencio JH, Hollingsworth BD, Shaffer HB, Fisher RN.

Dis Aquat Organ. 2018 Mar 5;127(3):193-200. doi: 10.3354/dao03202.

11.

Molecular phylogeny and divergence of the map turtles (Emydidae: Graptemys).

Thomson RC, Spinks PQ, Shaffer HB.

Mol Phylogenet Evol. 2018 Apr;121:61-70. doi: 10.1016/j.ympev.2017.11.012. Epub 2017 Dec 11.

PMID:
29242165
12.

An amphibian chemical defense phenotype is inducible across life history stages.

Bucciarelli GM, Shaffer HB, Green DB, Kats LB.

Sci Rep. 2017 Aug 15;7(1):8185. doi: 10.1038/s41598-017-08154-z.

13.

Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).

Shaffer HB, McCartney-Melstad E, Near TJ, Mount GG, Spinks PQ.

Mol Phylogenet Evol. 2017 Oct;115:7-15. doi: 10.1016/j.ympev.2017.07.006. Epub 2017 Jul 12.

PMID:
28711671
14.

Population genetic and field-ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian.

Wang IJ, Shaffer HB.

Evol Appl. 2017 Apr 27;10(6):630-639. doi: 10.1111/eva.12479. eCollection 2017 Jul.

15.

The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander.

Hime PM, Hotaling S, Grewelle RE, O'Neill EM, Voss SR, Shaffer HB, Weisrock DW.

Mol Ecol. 2016 Dec;25(23):5959-5974. doi: 10.1111/mec.13883. Epub 2016 Nov 12.

PMID:
27748559
16.

Phylogeny and temporal diversification of the New World pond turtles (Emydidae).

Spinks PQ, Thomson RC, McCartney-Melstad E, Shaffer HB.

Mol Phylogenet Evol. 2016 Oct;103:85-97. doi: 10.1016/j.ympev.2016.07.007. Epub 2016 Jul 9.

PMID:
27400630
17.

Exon capture optimization in amphibians with large genomes.

McCartney-Melstad E, Mount GG, Shaffer HB.

Mol Ecol Resour. 2016 Sep;16(5):1084-94. doi: 10.1111/1755-0998.12538. Epub 2016 Jul 12.

PMID:
27223337
18.

Individual fluctuations in toxin levels affect breeding site fidelity in a chemically defended amphibian.

Bucciarelli GM, Green DB, Shaffer HB, Kats LB.

Proc Biol Sci. 2016 May 25;283(1831). pii: 20160468. doi: 10.1098/rspb.2016.0468.

19.

Hybridization and endangered species protection in the molecular era.

Wayne RK, Shaffer HB.

Mol Ecol. 2016 Jun;25(11):2680-9. doi: 10.1111/mec.13642. Epub 2016 May 11.

PMID:
27064931
20.

Ecological equivalency as a tool for endangered species management.

Searcy CA, Rollins HB, Shaffer HB.

Ecol Appl. 2016 Jan;26(1):94-103.

PMID:
27039512
21.

Do Ecological Niche Models Accurately Identify Climatic Determinants of Species Ranges?

Searcy CA, Shaffer HB.

Am Nat. 2016 Apr;187(4):423-35. doi: 10.1086/685387. Epub 2016 Feb 22.

PMID:
27028071
22.

Amphibian molecular ecology and how it has informed conservation.

McCartney-Melstad E, Shaffer HB.

Mol Ecol. 2015 Oct;24(20):5084-109. doi: 10.1111/mec.13391. Epub 2015 Oct 12. Review.

PMID:
26437125
23.

Conservation genetics and genomics of amphibians and reptiles.

Shaffer HB, Gidiş M, McCartney-Melstad E, Neal KM, Oyamaguchi HM, Tellez M, Toffelmier EM.

Annu Rev Anim Biosci. 2015;3:113-38. doi: 10.1146/annurev-animal-022114-110920. Epub 2015 Jan 2. Review.

PMID:
25580719
24.

Cryptic diversity in metropolis: confirmation of a new leopard frog species (Anura: Ranidae) from New York City and surrounding Atlantic coast regions.

Feinberg JA, Newman CE, Watkins-Colwell GJ, Schlesinger MD, Zarate B, Curry BR, Shaffer HB, Burger J.

PLoS One. 2014 Oct 29;9(10):e108213. doi: 10.1371/journal.pone.0108213. eCollection 2014.

25.

The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle.

Spinks PQ, Thomson RC, Shaffer HB.

Mol Ecol. 2014 May;23(9):2228-41. doi: 10.1111/mec.12736. Epub 2014 Apr 18.

PMID:
24673803
26.

Delayed life history effects, multilevel selection, and evolutionary trade-offs in the California tiger salamander.

Searcy CA, Gray LN, Trenham PC, Shaffer HB.

Ecology. 2014 Jan;95(1):68-77.

PMID:
24649647
27.

Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus Pseudemys.

Spinks PQ, Thomson RC, Pauly GB, Newman CE, Mount G, Shaffer HB.

Mol Phylogenet Evol. 2013 Aug;68(2):269-81. doi: 10.1016/j.ympev.2013.03.031. Epub 2013 Apr 12.

PMID:
23583419
28.

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK.

Genome Biol. 2013 Mar 28;14(3):R28. doi: 10.1186/gb-2013-14-3-r28.

29.

Lethal effects of water quality on threatened California salamanders but not on co-occurring hybrid salamanders.

Ryan ME, Johnson JR, Fitzpatrick BM, Lowenstine LJ, Picco AM, Shaffer HB.

Conserv Biol. 2013 Feb;27(1):95-102. doi: 10.1111/j.1523-1739.2012.01955.x. Epub 2012 Nov 9.

PMID:
23140535
30.

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex.

O'Neill EM, Schwartz R, Bullock CT, Williams JS, Shaffer HB, Aguilar-Miguel X, Parra-Olea G, Weisrock DW.

Mol Ecol. 2013 Jan;22(1):111-29. doi: 10.1111/mec.12049. Epub 2012 Oct 12.

PMID:
23062080
31.

Thyroid hormone responsive QTL and the evolution of paedomorphic salamanders.

Voss SR, Kump DK, Walker JA, Shaffer HB, Voss GJ.

Heredity (Edinb). 2012 Nov;109(5):293-8. doi: 10.1038/hdy.2012.41. Epub 2012 Aug 1.

32.

Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora.

Spinks PQ, Thomson RC, Zhang Y, Che J, Wu Y, Shaffer HB.

Mol Phylogenet Evol. 2012 Jun;63(3):656-67.

PMID:
22649793
33.

A new species of leopard frog (Anura: Ranidae) from the urban northeastern US.

Newman CE, Feinberg JA, Rissler LJ, Burger J, Shaffer HB.

Mol Phylogenet Evol. 2012 May;63(2):445-55. doi: 10.1016/j.ympev.2012.01.021. Epub 2012 Feb 2.

34.

Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time.

Savage WK, Fremier AK, Shaffer HB.

Mol Ecol. 2010 Aug;19(16):3301-14. doi: 10.1111/j.1365-294X.2010.04718.x.

PMID:
20701683
35.

Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles.

Thomson RC, Shaffer HB.

Syst Biol. 2010 Jan;59(1):42-58. doi: 10.1093/sysbio/syp075. Epub 2009 Nov 11.

PMID:
20525619
36.

Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders.

Johnson JR, Fitzpatrick BM, Shaffer HB.

BMC Evol Biol. 2010 May 18;10:147. doi: 10.1186/1471-2148-10-147.

37.

Rapid progress on the vertebrate tree of life.

Thomson RC, Shaffer HB.

BMC Biol. 2010 Mar 8;8:19. doi: 10.1186/1741-7007-8-19.

38.

Rapid spread of invasive genes into a threatened native species.

Fitzpatrick BM, Johnson JR, Kump DK, Smith JJ, Voss SR, Shaffer HB.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3606-10. doi: 10.1073/pnas.0911802107. Epub 2010 Feb 2.

39.

Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle, Emys marmorata in California.

Spinks PQ, Thomson RC, Shaffer HB.

Mol Ecol. 2010 Feb;19(3):542-56. doi: 10.1111/j.1365-294X.2009.04451.x. Epub 2009 Dec 30.

PMID:
20051011
40.

Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life.

Barley AJ, Spinks PQ, Thomson RC, Shaffer HB.

Mol Phylogenet Evol. 2010 Jun;55(3):1189-94. doi: 10.1016/j.ympev.2009.11.005. Epub 2009 Nov 12.

PMID:
19913628
41.

Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders.

Fitzpatrick BM, Johnson JR, Kump DK, Shaffer HB, Smith JJ, Voss SR.

BMC Evol Biol. 2009 Jul 24;9:176. doi: 10.1186/1471-2148-9-176.

42.

Landscape genetics and least-cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense).

Wang IJ, Savage WK, Shaffer HB.

Mol Ecol. 2009 Apr;18(7):1365-74. doi: 10.1111/j.1365-294X.2009.04122.x.

PMID:
19368644
43.

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles.

Spinks PQ, Thomson RC, Lovely GA, Shaffer HB.

BMC Evol Biol. 2009 Mar 12;9:56. doi: 10.1186/1471-2148-9-56.

44.
45.

Rapid color evolution in an aposematic species: a phylogenetic analysis of color variation in the strikingly polymorphic strawberry poison-dart frog.

Wang IJ, Shaffer HB.

Evolution. 2008 Nov;62(11):2742-59. doi: 10.1111/j.1558-5646.2008.00507.x. Epub 2008 Sep 1.

PMID:
18764916
46.

Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles.

Thomson RC, Shedlock AM, Edwards SV, Shaffer HB.

Mol Phylogenet Evol. 2008 Nov;49(2):514-25. doi: 10.1016/j.ympev.2008.08.006. Epub 2008 Aug 12.

PMID:
18761096
47.

Calculating biologically accurate mitigation credits: insights from the California tiger salamander.

Searcy CA, Shaffer HB.

Conserv Biol. 2008 Aug;22(4):997-1005. doi: 10.1111/j.1523-1739.2008.00971.x. Epub 2008 Jul 10.

PMID:
18616742
48.

Species limits and phylogeography of North American cricket frogs (Acris: Hylidae).

Gamble T, Berendzen PB, Shaffer HB, Starkey DE, Simons AM.

Mol Phylogenet Evol. 2008 Jul;48(1):112-25. doi: 10.1016/j.ympev.2008.03.015. Epub 2008 Mar 16.

PMID:
18462953
49.

Delimiting species in recent radiations.

Shaffer HB, Thomson RC.

Syst Biol. 2007 Dec;56(6):896-906.

PMID:
18066926
50.

Hybrid vigor between native and introduced salamanders raises new challenges for conservation.

Fitzpatrick BM, Shaffer HB.

Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15793-8. Epub 2007 Sep 20.

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