How can I adjust branches that are outside my phylogeny?
17:31 25 Nov 2025

I am working on phylogenetic tree manipulation in R, and I'm encountering a visualization issue with one of my trees. A few branches are being drawn with lengths that go past the terminal nodes (tips)

#Beast Tree

beast_tree_N <- read.beast("Filogenia/Opuntia_tree_Norte_10_burnin.trees")

#Dataframe

meta_datos <- read.csv("Filogenia/info_especies.csv")

#Tree options

options(ignore.negative.edge = TRUE)

#Add dataframe

beast_p <- ggtree(beast_tree_N, size = 1.3) %<+% meta_datos

#Node number

beast_p + geom_text2(aes(label = node), subset = (isTip = FALSE), hjust = -0.1, size = 2.5, color = "gray25")

enter image description here

I thought the problem was with my code, but I tested it with another tree dated using BEAST, and the issue did not occur, even when using the exact same code

#Beast Tree

beast_tree_SN <- read.beast("Filogenia/Opuntia_tree_sin_norte_10_burnin.trees")

#Tree options

options(ignore.negative.edge = TRUE)

#Add dataframe

beast_p <- ggtree(beast_tree_SN, size = 1.3) %<+% meta_datos

#Node number

beast_p + geom_text2(aes(label = node),subset = (isTip = FALSE), hjust = -0.1, size = 2.5, color = "gray25")

enter image description here

Do you have any recommendations or ideas as to why this is happening? And, how might I fix or solve it?"

Thank you very much

r phylogeny ggtree