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Items: 32

1.

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.

Andermann T, Torres Jiménez MF, Matos-Maraví P, Batista R, Blanco-Pastor JL, Gustafsson ALS, Kistler L, Liberal IM, Oxelman B, Bacon CD, Antonelli A.

Front Genet. 2020 Feb 21;10:1407. doi: 10.3389/fgene.2019.01407. eCollection 2019. Review.

2.

Drivers of bromeliad leaf and floral bract variation across a latitudinal gradient in the Atlantic Forest.

Neves B, Zanella CM, Kessous IM, Uribbe FP, Salgueiro F, Bered F, Antonelli A, Bacon CD, Costa AF.

J Biogeogr. 2020 Jan;47(1):261-274. doi: 10.1111/jbi.13746. Epub 2019 Nov 24.

3.

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae.

Loiseau O, Olivares I, Paris M, de La Harpe M, Weigand A, Koubínová D, Rolland J, Bacon CD, Balslev H, Borchsenius F, Cano A, Couvreur TLP, Delnatte C, Fardin F, Gayot M, Mejía F, Mota-Machado T, Perret M, Roncal J, Sanin MJ, Stauffer F, Lexer C, Kessler M, Salamin N.

Front Plant Sci. 2019 Jul 12;10:864. doi: 10.3389/fpls.2019.00864. eCollection 2019.

4.

Travel for two.

Bacon CD.

Science. 2019 May 31;364(6443):902. doi: 10.1126/science.364.6443.902. No abstract available.

PMID:
31147522
5.

Ancient Polyploidy and Genome Evolution in Palms.

Barrett CF, McKain MR, Sinn BT, Ge XJ, Zhang Y, Antonelli A, Bacon CD.

Genome Biol Evol. 2019 May 1;11(5):1501-1511. doi: 10.1093/gbe/evz092.

6.

Adjacency and Area Explain Species Bioregional Shifts in Neotropical Palms.

Freitas CG, Bacon CD, Souza-Neto AC, Collevatti RG.

Front Plant Sci. 2019 Feb 5;10:55. doi: 10.3389/fpls.2019.00055. eCollection 2019.

7.

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics.

Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV.

PeerJ. 2019 Feb 14;7:e6399. doi: 10.7717/peerj.6399. eCollection 2019.

8.

Challenging transitions.

Wasalathanthri ND, Zaidi SS, Mahrt E, Srivastava S, Yu KH, Johansson KSL, Li F, Jimenez MFT, Lo C, Allareddy V, Romero-Molina C, Mosegaard S, Heaton SM, Park JJ, Bacon CD, Yu S, Polat EO, Wasalathanthri D, Wang W, Agarwal D.

Science. 2019 Jan 4;363(6422):24-26. doi: 10.1126/science.aaw2641. No abstract available.

PMID:
30606829
9.

Soil fertility and flood regime are correlated with phylogenetic structure of Amazonian palm communities.

Muscarella R, Bacon CD, Faurby S, Antonelli A, Kristiansen SM, Svenning JC, Balslev H.

Ann Bot. 2019 Mar 14;123(4):641-655. doi: 10.1093/aob/mcy196.

10.

Rivers shape population genetic structure in Mauritia flexuosa (Arecaceae).

Sander NL, Pérez-Zavala F, Da Silva CJ, Arruda JC, Pulido MT, Barelli MAA, Rossi AB, Viana AP, Boechat MSB, Bacon CD, Cibrián-Jaramillo A.

Ecol Evol. 2018 Jun 11;8(13):6589-6598. doi: 10.1002/ece3.4142. eCollection 2018 Jul.

11.

phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R.

Bennett DJ, Hettling H, Silvestro D, Zizka A, Bacon CD, Faurby S, Vos RA, Antonelli A.

Life (Basel). 2018 Jun 5;8(2). pii: E20. doi: 10.3390/life8020020.

12.

Amazonia is the primary source of Neotropical biodiversity.

Antonelli A, Zizka A, Carvalho FA, Scharn R, Bacon CD, Silvestro D, Condamine FL.

Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):6034-6039. doi: 10.1073/pnas.1713819115. Epub 2018 May 14.

13.

The road to evolutionary success: insights from the demographic history of an Amazonian palm.

Melo WA, Freitas CG, Bacon CD, Collevatti RG.

Heredity (Edinb). 2018 Aug;121(2):183-195. doi: 10.1038/s41437-018-0074-1. Epub 2018 Mar 28.

14.

Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot.

Bacon CD, Velásquez-Puentes FJ, Hinojosa LF, Schwartz T, Oxelman B, Pfeil B, Arroyo MTK, Wanntorp L, Antonelli A.

PeerJ. 2018 Mar 16;6:e4388. doi: 10.7717/peerj.4388. eCollection 2018.

15.

Comment (1) on "Formation of the Isthmus of Panama" by O'Dea et al.

Jaramillo C, Montes C, Cardona A, Silvestro D, Antonelli A, Bacon CD.

Sci Adv. 2017 Jun 14;3(6):e1602321. doi: 10.1126/sciadv.1602321. eCollection 2017 Jun.

16.

Endemic palm species shed light on habitat shifts and the assembly of the Cerrado and Restinga floras.

Bacon CD, Moraes R M, Jaramillo C, Antonelli A.

Mol Phylogenet Evol. 2017 May;110:127-133. doi: 10.1016/j.ympev.2017.03.013. Epub 2017 Mar 10.

PMID:
28288942
17.

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.

Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA.

Syst Biol. 2017 Mar 1;66(2):152-166. doi: 10.1093/sysbio/syw066.

18.

Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data.

Silvestro D, Zizka A, Bacon CD, Cascales-Miñana B, Salamin N, Antonelli A.

Philos Trans R Soc Lond B Biol Sci. 2016 Apr 5;371(1691):20150225. doi: 10.1098/rstb.2015.0225.

19.

Reply to Lessios and Marko et al.: Early and progressive migration across the Isthmus of Panama is robust to missing data and biases.

Bacon CD, Silvestro D, Jaramillo C, Smith BT, Chakrabarty P, Antonelli A.

Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):E5767-8. doi: 10.1073/pnas.1515451112. Epub 2015 Oct 21. No abstract available.

20.

Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar.

Bacon CD, Simmons MP, Archer RH, Zhao LC, Andriantiana J.

Mol Phylogenet Evol. 2016 Jan;94(Pt A):365-82. doi: 10.1016/j.ympev.2015.09.013. Epub 2015 Sep 30.

PMID:
26432393
21.

Biological evidence supports an early and complex emergence of the Isthmus of Panama.

Bacon CD, Silvestro D, Jaramillo C, Smith BT, Chakrabarty P, Antonelli A.

Proc Natl Acad Sci U S A. 2015 May 12;112(19):6110-5. doi: 10.1073/pnas.1423853112. Epub 2015 Apr 27. Erratum in: Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):E3153. Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3631.

22.

An engine for global plant diversity: highest evolutionary turnover and emigration in the American tropics.

Antonelli A, Zizka A, Silvestro D, Scharn R, Cascales-Miñana B, Bacon CD.

Front Genet. 2015 Apr 8;6:130. doi: 10.3389/fgene.2015.00130. eCollection 2015.

23.

Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record.

Silvestro D, Cascales-Miñana B, Bacon CD, Antonelli A.

New Phytol. 2015 Jul;207(2):425-436. doi: 10.1111/nph.13247. Epub 2015 Jan 26.

24.

Geographic and taxonomic disparities in species diversity: dispersal and diversification rates across Wallace's line.

Bacon CD, Michonneau F, Henderson AJ, McKenna MJ, Milroy AM, Simmons MP.

Evolution. 2013 Jul;67(7):2058-71. doi: 10.1111/evo.12084. Epub 2013 Mar 15.

PMID:
23815659
25.

Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia).

Bacon CD, McKenna MJ, Simmons MP, Wagner WL.

BMC Evol Biol. 2012 Feb 22;12:23. doi: 10.1186/1471-2148-12-23.

26.

Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae).

Bacon CD, Baker WJ, Simmons MP.

Syst Biol. 2012 May;61(3):426-42. doi: 10.1093/sysbio/syr123. Epub 2012 Jan 5.

PMID:
22223444
27.

Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes.

Simmons MP, McKenna MJ, Bacon CD, Yakobson K, Cappa JJ, Archer RH, Ford AJ.

Mol Phylogenet Evol. 2012 Jan;62(1):9-20. doi: 10.1016/j.ympev.2011.08.022. Epub 2011 Aug 30.

PMID:
22001302
28.

Development of microsatellites in the Hawaiian endemic palm Pritchardia martii (Arecaceae) and their utility in congeners.

Bacon CD, Johnson GP, Meimberg H, Puppo P, Simmons MP, Wagner WL.

Am J Bot. 2011 Jun;98(6):e139-40. doi: 10.3732/ajb.1100073. Epub 2011 May 27.

29.

Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation.

Cibrián-Jaramillo A, Bacon CD, Garwood NC, Bateman RM, Thomas MM, Russell S, Bailey CD, Hahn WJ, Bridgewater SG, DeSalle R.

BMC Genet. 2009 Oct 9;10:65. doi: 10.1186/1471-2156-10-65.

30.

Novel nuclear intron-spanning primers for Arecaceae evolutionary biology.

Bacon CD, Feltus FA, Paterson AH, Bailey CD.

Mol Ecol Resour. 2008 Jan;8(1):211-4. doi: 10.1111/j.1471-8286.2007.01928.x.

PMID:
21585759
31.

Leveraging the rice genome sequence for monocot comparative and translational genomics.

Lohithaswa HC, Feltus FA, Singh HP, Bacon CD, Bailey CD, Paterson AH.

Theor Appl Genet. 2007 Jul;115(2):237-43. Epub 2007 May 24.

PMID:
17522835
32.

Taxonomy and conservation: A case study from Chamaedorea alternans.

Bacon CD, Bailey CD.

Ann Bot. 2006 Oct;98(4):755-63. Epub 2006 Jul 24.

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