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Items: 21

1.

ABLE: blockwise site frequency spectra for inferring complex population histories and recombination.

Beeravolu CR, Hickerson MJ, Frantz LAF, Lohse K.

Genome Biol. 2018 Sep 25;19(1):145. doi: 10.1186/s13059-018-1517-y.

2.

Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research.

Velsko IM, Frantz LAF, Herbig A, Larson G, Warinner C.

mSystems. 2018 Jul 17;3(4). pii: e00080-18. doi: 10.1128/mSystems.00080-18. eCollection 2018 Jul-Aug.

3.

The evolutionary history of dogs in the Americas.

Ní Leathlobhair M, Perri AR, Irving-Pease EK, Witt KE, Linderholm A, Haile J, Lebrasseur O, Ameen C, Blick J, Boyko AR, Brace S, Cortes YN, Crockford SJ, Devault A, Dimopoulos EA, Eldridge M, Enk J, Gopalakrishnan S, Gori K, Grimes V, Guiry E, Hansen AJ, Hulme-Beaman A, Johnson J, Kitchen A, Kasparov AK, Kwon YM, Nikolskiy PA, Lope CP, Manin A, Martin T, Meyer M, Myers KN, Omura M, Rouillard JM, Pavlova EY, Sciulli P, Sinding MS, Strakova A, Ivanova VV, Widga C, Willerslev E, Pitulko VV, Barnes I, Gilbert MTP, Dobney KM, Malhi RS, Murchison EP, Larson G, Frantz LAF.

Science. 2018 Jul 6;361(6397):81-85. doi: 10.1126/science.aao4776.

PMID:
29976825
4.

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events.

Frantz LAF, Rudzinski A, Nugraha AMS, Evin A, Burton J, Hulme-Beaman A, Linderholm A, Barnett R, Vega R, Irving-Pease EK, Haile J, Allen R, Leus K, Shephard J, Hillyer M, Gillemot S, van den Hurk J, Ogle S, Atofanei C, Thomas MG, Johansson F, Mustari AH, Williams J, Mohamad K, Damayanti CS, Wiryadi ID, Obbles D, Mona S, Day H, Yasin M, Meker S, McGuire JA, Evans BJ, von Rintelen T, Ho SYW, Searle JB, Kitchener AC, Macdonald AA, Shaw DJ, Hall R, Galbusera P, Larson G.

Proc Biol Sci. 2018 Apr 11;285(1876). pii: 20172566. doi: 10.1098/rspb.2017.2566.

5.

Rabbits and the Specious Origins of Domestication.

Irving-Pease EK, Frantz LAF, Sykes N, Callou C, Larson G.

Trends Ecol Evol. 2018 Mar;33(3):149-152. doi: 10.1016/j.tree.2017.12.009. Epub 2018 Feb 14.

PMID:
29454669
6.

The dental calculus metabolome in modern and historic samples.

Velsko IM, Overmyer KA, Speller C, Klaus L, Collins MJ, Loe L, Frantz LAF, Sankaranarayanan K, Lewis CM Jr, Martinez JBR, Chaves E, Coon JJ, Larson G, Warinner C.

Metabolomics. 2017;13(11):134. doi: 10.1007/s11306-017-1270-3. Epub 2017 Oct 3.

7.

Genomic and archaeological evidence suggest a dual origin of domestic dogs.

Frantz LA, Mullin VE, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Teasdale MD, Dimopoulos EA, Tresset A, Duffraisse M, McCormick F, Bartosiewicz L, Gál E, Nyerges ÉA, Sablin MV, Bréhard S, Mashkour M, Bălăşescu A, Gillet B, Hughes S, Chassaing O, Hitte C, Vigne JD, Dobney K, Hänni C, Bradley DG, Larson G.

Science. 2016 Jun 3;352(6290):1228-31. doi: 10.1126/science.aaf3161. Epub 2016 Jun 2.

8.

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs.

Bosse M, Lopes MS, Madsen O, Megens HJ, Crooijmans RP, Frantz LA, Harlizius B, Bastiaansen JW, Groenen MA.

Proc Biol Sci. 2015 Dec 22;282(1821):20152019. doi: 10.1098/rspb.2015.2019.

9.

Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks.

Bunnefeld L, Frantz LA, Lohse K.

Genetics. 2015 Nov;201(3):1157-69. doi: 10.1534/genetics.115.179861. Epub 2015 Sep 3.

10.

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.

Frantz LA, Schraiber JG, Madsen O, Megens HJ, Cagan A, Bosse M, Paudel Y, Crooijmans RP, Larson G, Groenen MA.

Nat Genet. 2015 Oct;47(10):1141-8. doi: 10.1038/ng.3394. Epub 2015 Aug 31.

PMID:
26323058
11.

Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors.

Paudel Y, Madsen O, Megens HJ, Frantz LA, Bosse M, Crooijmans RP, Groenen MA.

BMC Genomics. 2015 Apr 22;16:330. doi: 10.1186/s12864-015-1449-9.

12.

Evolution of Tibetan wild boars.

Frantz LA, Madsen O, Megens HJ, Schraiber JG, Paudel Y, Bosse M, Crooijmans RP, Larson G, Groenen MA.

Nat Genet. 2015 Mar;47(3):188-9. doi: 10.1038/ng.3197. No abstract available.

13.

Hybrid origin of European commercial pigs examined by an in-depth haplotype analysis on chromosome 1.

Bosse M, Madsen O, Megens HJ, Frantz LA, Paudel Y, Crooijmans RP, Groenen MA.

Front Genet. 2015 Jan 5;5:442. doi: 10.3389/fgene.2014.00442. eCollection 2014.

14.

Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South-East Asian Sus species during the Plio-Pleistocene climatic fluctuations.

Frantz LA, Madsen O, Megens HJ, Groenen MA, Lohse K.

Mol Ecol. 2014 Nov;23(22):5566-74. doi: 10.1111/mec.12958. Epub 2014 Nov 5.

15.

Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression.

Bosse M, Megens HJ, Frantz LA, Madsen O, Larson G, Paudel Y, Duijvesteijn N, Harlizius B, Hagemeijer Y, Crooijmans RP, Groenen MA.

Nat Commun. 2014 Jul 15;5:4392. doi: 10.1038/ncomms5392.

16.

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations.

Bosse M, Megens HJ, Madsen O, Frantz LA, Paudel Y, Crooijmans RP, Groenen MA.

Mol Ecol. 2014 Aug;23(16):4089-102. doi: 10.1111/mec.12807. Epub 2014 Jun 16.

17.

Neandertal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes.

Lohse K, Frantz LA.

Genetics. 2014 Apr;196(4):1241-51. doi: 10.1534/genetics.114.162396. Epub 2014 Feb 13.

18.

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus.

Frantz LA, Schraiber JG, Madsen O, Megens HJ, Bosse M, Paudel Y, Semiadi G, Meijaard E, Li N, Crooijmans RP, Archibald AL, Slatkin M, Schook LB, Larson G, Groenen MA.

Genome Biol. 2013;14(9):R107.

19.

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication.

Paudel Y, Madsen O, Megens HJ, Frantz LA, Bosse M, Bastiaansen JW, Crooijmans RP, Groenen MA.

BMC Genomics. 2013 Jul 5;14:449. doi: 10.1186/1471-2164-14-449.

20.

Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape.

Bosse M, Megens HJ, Madsen O, Paudel Y, Frantz LA, Schook LB, Crooijmans RP, Groenen MA.

PLoS Genet. 2012;8(11):e1003100. doi: 10.1371/journal.pgen.1003100. Epub 2012 Nov 29.

21.

Analyses of pig genomes provide insight into porcine demography and evolution.

Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB.

Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.

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