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Phylogenetics

Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

Blischak PD, Latvis M, Morales-Briones DF, Johnson JC, Di Stilio VS, Wolfe AD, Tank DC.  2018.  Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons. Applications in Plant Sciences. 6(6)

Scent matters: differential contribution of scent to insect response in flowers with insect vs. wind pollination traits

Wang TN, Clifford MR, Martínez-Gómez J, Johnson JC, Riffell JA, Di Stilio VS.  2018.  Scent matters: differential contribution of scent to insect response in flowers with insect vs. wind pollination traits. Annals of Botany.

Phylogenomic Analysis of the Ranunculales resolves branching events across the order

Lane AK, Augustin MM, Ayyampalayam S, Plant A, Gleissberg S, Di Stilio VS, dePamphillis CW, Wong GK-S, Kutchan TM, Leebens-Mack JH.  2018.  Phylogenomic Analysis of the Ranunculales resolves branching events across the order. Botanical Journal of the Linnean Society. 187(2)

Molecular evolution of Drosophila Cdc6, an essential DNA replication-licensing gene, suggests an adaptive choice of replication origins

Wiggins BL, Malik HS.  2007.  Molecular evolution of Drosophila Cdc6, an essential DNA replication-licensing gene, suggests an adaptive choice of replication origins. Fly. 1(3):-163.

Darwin’s Phylogenetic Reasoning

Darwin claimed that similarity is evidence for common ancestry, and that adaptive similarities provide weaker evidence than neutral or deleterious similarities.  He also used phylogenetic trees to reason critically about adaptive hypotheses.  In this talk I'll analyze his bits of reasoning and describe frameworks for evaluating their correctness.

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