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Loxodonta Localizer: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA.

Zhao K, Ishida Y, Green CE, Davidson AG, Sitam FAT, Donnelly CL, De Flamingh A, Perrin-Stowe TIN, Bourgeois S, Brandt AL, Mundis SJ, van Aarde RJ, Greenberg JA, Malhi RS, Georgiadis NJ, McEwing R, Roca AL.

J Hered. 2019 Dec 17;110(7):761-768. doi: 10.1093/jhered/esz058.


African elephant genetics: enigmas and anomalies.

Roca AL.

J Genet. 2019 Sep;98. pii: 83.


Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion.

Löber U, Hobbs M, Dayaram A, Tsangaras K, Jones K, Alquezar-Planas DE, Ishida Y, Meers J, Mayer J, Quedenau C, Chen W, Johnson RN, Timms P, Young PR, Roca AL, Greenwood AD.

Proc Natl Acad Sci U S A. 2018 Aug 21;115(34):8609-8614. doi: 10.1073/pnas.1807598115. Epub 2018 Aug 6.


Influence of the geographic distribution of prion protein gene sequence variation on patterns of chronic wasting disease spread in white-tailed deer (Odocoileus virginianus).

Brandt AL, Green ML, Ishida Y, Roca AL, Novakofski J, Mateus-Pinilla NE.

Prion. 2018;12(3-4):204-215. doi: 10.1080/19336896.2018.1474671. Epub 2018 Jul 25.


Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species, the African forest elephant (Loxodonta cyclotis).

Ishida Y, Gugala NA, Georgiadis NJ, Roca AL.

Ecol Evol. 2018 Apr 19;8(10):4919-4931. doi: 10.1002/ece3.4062. eCollection 2018 May.


Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola.

Grigorev K, Kliver S, Dobrynin P, Komissarov A, Wolfsberger W, Krasheninnikova K, Afanador-Hernández YM, Brandt AL, Paulino LA, Carreras R, Rodríguez LE, Núñez A, Brandt JR, Silva F, Hernández-Martich JD, Majeske AJ, Antunes A, Roca AL, O'Brien SJ, Martínez-Cruzado JC, Oleksyk TK.

Gigascience. 2018 Jun 1;7(6). doi: 10.1093/gigascience/giy025.


Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis).

Brandt JR, van Coeverden de Groot PJ, Witt KE, Engelbrektsson PK, Helgen KM, Malhi RS, Ryder OA, Roca AL.

J Hered. 2018 Jun 27;109(5):553-565. doi: 10.1093/jhered/esy019.


A comprehensive genomic history of extinct and living elephants.

Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To TH, Kortschak RD, Raison JM, Qu Z, Chin TJ, Alt KW, Claesson S, Dalén L, MacPhee RDE, Meller H, Roca AL, Ryder OA, Heiman D, Young S, Breen M, Williams C, Aken BL, Ruffier M, Karlsson E, Johnson J, Di Palma F, Alfoldi J, Adelson DL, Mailund T, Munch K, Lindblad-Toh K, Hofreiter M, Poinar H, Reich D.

Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):E2566-E2574. doi: 10.1073/pnas.1720554115. Epub 2018 Feb 26.


Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals.

Springer MS, Murphy WJ, Roca AL.

Mol Phylogenet Evol. 2018 Apr;121:158-165. doi: 10.1016/j.ympev.2018.01.007. Epub 2018 Jan 10.


Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions.

Greenwood AD, Ishida Y, O'Brien SP, Roca AL, Eiden MV.

Microbiol Mol Biol Rev. 2017 Dec 13;82(1). pii: e00044-17. doi: 10.1128/MMBR.00044-17. Print 2018 Mar. Review.


Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution.

Meyer M, Palkopoulou E, Baleka S, Stiller M, Penkman KEH, Alt KW, Ishida Y, Mania D, Mallick S, Meijer T, Meller H, Nagel S, Nickel B, Ostritz S, Rohland N, Schauer K, Schüler T, Roca AL, Reich D, Shapiro B, Hofreiter M.

Elife. 2017 Jun 6;6. pii: e25413. doi: 10.7554/eLife.25413.


Innate immune responses induced by lipopolysaccharide and lipoteichoic acid in primary goat mammary epithelial cells.

Bulgari O, Dong X, Roca AL, Caroli AM, Loor JJ.

J Anim Sci Biotechnol. 2017 Apr 1;8:29. doi: 10.1186/s40104-017-0162-8. eCollection 2017.


Polymorphisms of the Toll-Like Receptor 2 of Goats (Capra hircus) may be Associated with Somatic Cell Count in Milk.

Ruiz-Rodriguez CT, Brandt JR, Oliverio R, Ishida Y, Guedj N, Garrett EF, Kahila Bar-Gal G, Nikolaidis N, Cardoso FC, Roca AL.

Anim Biotechnol. 2017 Apr 3;28(2):112-119. doi: 10.1080/10495398.2016.1232267. Epub 2016 Oct 28.


Genetic connectivity across marginal habitats: the elephants of the Namib Desert.

Ishida Y, Van Coeverden de Groot PJ, Leggett KE, Putnam AS, Fox VE, Lai J, Boag PT, Georgiadis NJ, Roca AL.

Ecol Evol. 2016 Aug 3;6(17):6189-201. doi: 10.1002/ece3.2352. eCollection 2016 Sep.


Koalas (Phascolarctos cinereus) From Queensland Are Genetically Distinct From 2 Populations in Victoria.

Ruiz-Rodriguez CT, Ishida Y, Murray ND, O'Brien SJ, Graves JA, Greenwood AD, Roca AL.

J Hered. 2016;107(7):573-580. Epub 2016 Aug 11.


Development and characterization of microsatellite markers in the African forest elephant (Loxodonta cyclotis).

Gugala NA, Ishida Y, Georgiadis NJ, Roca AL.

BMC Res Notes. 2016 Jul 26;9:364. doi: 10.1186/s13104-016-2167-3.


Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia).

Alfano N, Michaux J, Morand S, Aplin K, Tsangaras K, Löber U, Fabre PH, Fitriana Y, Semiadi G, Ishida Y, Helgen KM, Roca AL, Eiden MV, Greenwood AD.

J Virol. 2016 Aug 26;90(18):8169-80. doi: 10.1128/JVI.00723-16. Print 2016 Sep 15.


Mitogenomic sequences support a north-south subspecies subdivision within Solenodon paradoxus.

Brandt AL, Grigorev K, Afanador-Hernández YM, Paulino LA, Murphy WJ, Núñez A, Komissarov A, Brandt JR, Dobrynin P, Hernández-Martich JD, María R, O'Brien SJ, Rodríguez LE, Martínez-Cruzado JC, Oleksyk TK, Roca AL.

Mitochondrial DNA A DNA Mapp Seq Anal. 2017 Sep;28(5):662-670. doi: 10.3109/24701394.2016.1167891. Epub 2016 Apr 20.


Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome.

Cui P, Löber U, Alquezar-Planas DE, Ishida Y, Courtiol A, Timms P, Johnson RN, Lenz D, Helgen KM, Roca AL, Hartman S, Greenwood AD.

PeerJ. 2016 Mar 28;4:e1847. doi: 10.7717/peerj.1847. eCollection 2016.


Erratum for Alfano et al., Episodic Diversifying Selection Shaped the Genomes of Gibbon Ape Leukemia Virus and Related Gammaretroviruses.

Alfano N, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD.

J Virol. 2016 Mar 28;90(8):4254. doi: 10.1128/JVI.00210-16. Print 2016 Apr. No abstract available.


Space Maintenance Using Tenting Screws in Atrophic Extraction Sockets.

Reddy TS, Shah NR, Roca AL, Sullivan A, Pascuzzi J, Drew HJ.

J Oral Implantol. 2016 Aug;42(4):353-7. doi: 10.1563/aaid-joi-D-15-00048. Epub 2016 Feb 29. No abstract available.


Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae.

Darfour-Oduro KA, Megens HJ, Roca AL, Groenen MA, Schook LB.

BMC Evol Biol. 2016 Feb 9;16:33. doi: 10.1186/s12862-016-0602-7.


Episodic Diversifying Selection Shaped the Genomes of Gibbon Ape Leukemia Virus and Related Gammaretroviruses.

Alfano N, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD.

J Virol. 2015 Dec 4;90(4):1757-72. doi: 10.1128/JVI.02745-15. Print 2016 Feb 15. Erratum in: J Virol. 2016 Apr;90(8):4254.


Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse.

Hartmann S, Hasenkamp N, Mayer J, Michaux J, Morand S, Mazzoni CJ, Roca AL, Greenwood AD.

BMC Genomics. 2015 Aug 18;16:613. doi: 10.1186/s12864-015-1766-z.


Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes.

Ganu RS, Ishida Y, Koutmos M, Kolokotronis SO, Roca AL, Garrow TA, Schook LB.

PLoS One. 2015 Jul 27;10(7):e0134084. doi: 10.1371/journal.pone.0134084. eCollection 2015.


Evolution: The Island of Misfit Mammoths.

Roca AL.

Curr Biol. 2015 Jun 29;25(13):R549-51. doi: 10.1016/j.cub.2015.05.006.


Variation in koala microbiomes within and between individuals: effect of body region and captivity status.

Alfano N, Courtiol A, Vielgrader H, Timms P, Roca AL, Greenwood AD.

Sci Rep. 2015 May 11;5:10189. doi: 10.1038/srep10189.


Adaptive Evolution of Toll-Like Receptors (TLRs) in the Family Suidae.

Darfour-Oduro KA, Megens HJ, Roca AL, Groenen MA, Schook LB.

PLoS One. 2015 Apr 20;10(4):e0124069. doi: 10.1371/journal.pone.0124069. eCollection 2015.


SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations.

Guiblet WM, Zhao K, O'Brien SJ, Massey SE, Roca AL, Oleksyk TK.

Gigascience. 2015 Jan 14;4:1. doi: 10.1186/2047-217X-4-1. eCollection 2015.


Elephant natural history: a genomic perspective.

Roca AL, Ishida Y, Brandt AL, Benjamin NR, Zhao K, Georgiadis NJ.

Annu Rev Anim Biosci. 2015;3:139-67. doi: 10.1146/annurev-animal-022114-110838. Epub 2014 Dec 8. Review.


Sequence variation of koala retrovirus transmembrane protein p15E among koalas from different geographic regions.

Ishida Y, McCallister C, Nikolaidis N, Tsangaras K, Helgen KM, Greenwood AD, Roca AL.

Virology. 2015 Jan 15;475:28-36. doi: 10.1016/j.virol.2014.10.036. Epub 2014 Nov 22.


Proliferation of endogenous retroviruses in the early stages of a host germ line invasion.

Ishida Y, Zhao K, Greenwood AD, Roca AL.

Mol Biol Evol. 2015 Jan;32(1):109-20. doi: 10.1093/molbev/msu275. Epub 2014 Sep 25.


Hybridization capture reveals evolution and conservation across the entire Koala retrovirus genome.

Tsangaras K, Siracusa MC, Nikolaidis N, Ishida Y, Cui P, Vielgrader H, Helgen KM, Roca AL, Greenwood AD.

PLoS One. 2014 Apr 21;9(4):e95633. doi: 10.1371/journal.pone.0095633. eCollection 2014.


Reconstruction of the narrow ridge using combined ridge split and guided bone regeneration with rhPDGF-BB growth factor-enhanced allograft.

Chiang T, Roca AL, Rostkowski S, Drew HJ, Simon B.

Int J Periodontics Restorative Dent. 2014 Jan-Feb;34(1):123-30. doi: 10.11607/prd.1633.


The elephants of Gash-Barka, Eritrea: nuclear and mitochondrial genetic patterns.

Brandt AL, Hagos Y, Yacob Y, David VA, Georgiadis NJ, Shoshani J, Roca AL.

J Hered. 2014 Jan-Feb;105(1):82-90. doi: 10.1093/jhered/est078. Epub 2013 Nov 27.


Impact of population expansion on genetic diversity and structure of river otters (Lontra canadensis) in Central North America.

Brandt JR, Brandt AL, Ammer FK, Roca AL, Serfass TL.

J Hered. 2014 Jan-Feb;105(1):39-47. doi: 10.1093/jhered/est069. Epub 2013 Oct 23.


Triangulating the provenance of African elephants using mitochondrial DNA.

Ishida Y, Georgiadis NJ, Hondo T, Roca AL.

Evol Appl. 2013 Feb;6(2):253-65. doi: 10.1111/j.1752-4571.2012.00286.x. Epub 2012 Aug 1.


Evidence for selection at HIV host susceptibility genes in a West Central African human population.

Zhao K, Ishida Y, Oleksyk TK, Winkler CA, Roca AL.

BMC Evol Biol. 2012 Dec 6;12:237. doi: 10.1186/1471-2148-12-237.


Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus).

Tsangaras K, Ávila-Arcos MC, Ishida Y, Helgen KM, Roca AL, Greenwood AD.

BMC Genet. 2012 Oct 24;13:92. doi: 10.1186/1471-2156-13-92.


One hundred twenty years of koala retrovirus evolution determined from museum skins.

Ávila-Arcos MC, Ho SY, Ishida Y, Nikolaidis N, Tsangaras K, Hönig K, Medina R, Rasmussen M, Fordyce SL, Calvignac-Spencer S, Willerslev E, Gilbert MT, Helgen KM, Roca AL, Greenwood AD.

Mol Biol Evol. 2013 Feb;30(2):299-304. doi: 10.1093/molbev/mss223. Epub 2012 Sep 14. Erratum in: Mol Biol Evol. 2013 May;30(5):1237.


Forest elephant mitochondrial genomes reveal that elephantid diversification in Africa tracked climate transitions.

Brandt AL, Ishida Y, Georgiadis NJ, Roca AL.

Mol Ecol. 2012 Mar;21(5):1175-89. doi: 10.1111/j.1365-294X.2012.05461.x. Epub 2012 Jan 19.


Successful genotyping of microsatellites in the woolly mammoth.

Ishida Y, Roca AL, Fratpietro S, Greenwood AD.

J Hered. 2012 May-Jun;103(3):459-64. doi: 10.1093/jhered/esr139. Epub 2012 Jan 10.


Distinguishing forest and savanna African elephants using short nuclear DNA sequences.

Ishida Y, Demeke Y, van Coeverden de Groot PJ, Georgiadis NJ, Leggett KE, Fox VE, Roca AL.

J Hered. 2011 Sep-Oct;102(5):610-6. doi: 10.1093/jhered/esr073. Epub 2011 Jul 20.


10th International Feline Retrovirus Research Symposium 2010. Preface.

Roca AL.

Vet Immunol Immunopathol. 2011 Oct 15;143(3-4):177-8. doi: 10.1016/j.vetimm.2011.06.001. Epub 2011 Jun 12. No abstract available.


Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants.

Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, Stephens RM, Kolokotronis SO, Roca AL.

PLoS One. 2011;6(6):e20642. doi: 10.1371/journal.pone.0020642. Epub 2011 Jun 8.


Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants.

Rohland N, Reich D, Mallick S, Meyer M, Green RE, Georgiadis NJ, Roca AL, Hofreiter M.

PLoS Biol. 2010 Dec 21;8(12):e1000564. doi: 10.1371/journal.pbio.1000564.


Evolutionary dynamics of endogenous feline leukemia virus proliferation among species of the domestic cat lineage.

Polani S, Roca AL, Rosensteel BB, Kolokotronis SO, Bar-Gal GK.

Virology. 2010 Sep 30;405(2):397-407. doi: 10.1016/j.virol.2010.06.010. Epub 2010 Jul 7.


Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

Roca AL, Ishida Y, Nikolaidis N, Kolokotronis SO, Fratpietro S, Stewardson K, Hensley S, Tisdale M, Boeskorov G, Greenwood AD.

BMC Evol Biol. 2009 Sep 11;9:232. doi: 10.1186/1471-2148-9-232.


Pathological manifestations of feline immunodeficiency virus (FIV) infection in wild African lions.

Roelke ME, Brown MA, Troyer JL, Winterbach H, Winterbach C, Hemson G, Smith D, Johnson RC, Pecon-Slattery J, Roca AL, Alexander KA, Klein L, Martelli P, Krishnasamy K, O'Brien SJ.

Virology. 2009 Jul 20;390(1):1-12. doi: 10.1016/j.virol.2009.04.011. Epub 2009 May 22.

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