是否可以通过将分类群绑定到姐妹分类群而不是节点来将分类群添加到系统发育中? [英] Is it possible to add taxa to a phylogeny by binding them to sister taxa, rather than nodes?

问题描述

我正在尝试创建一棵树来计算系统发育信号并进行系统发育广义最小二乘分析.然而，我用于此分析的文献树中缺少我的一些分类群，主要是因为这些分类群在父研究时被认为是包含的分类群的亚种，后来被提升到物种等级.因此，我确切地知道这些分类群需要去哪里(它们以前包含的分类群的姐妹)，但我无法将它们添加到树中.

I am trying to create a tree to calculate phylogenetic signal and conduct a phylogenetic generalized least squares analysis. However, some of my taxa are missing from the literature tree I am using for this analysis, mostly because these were taxa at the time of the parent study that were considered subspecies of included taxa have since been raised to species rank. As a result, I know exactly where these taxa need to go (sister to the taxon they were formerly included in), but I am having trouble adding them to the tree.

我一直在使用以下代码将分类群添加到我的树中.

I have been adding taxa to my tree using the following code.

library(ape)
library(phytools)
orig_tree<-rtree(n=20)
tip<-list(edge=matrix(c(2,1),1,2),
          tip.label="t6a",
          edge.length=1.0,
          Nnode=1)
class(tip)<-"phylo"
btree<-bind.tree(orig_tree,tip,where=22)
plotTree(btree)

然而，这有几个问题.一方面，这通过创建一个多分体来添加新的分类群，然后我必须使用像 bifurcatr 这样的包来随机解析.然而，这对于已知的系统发育来说是不准确的.这不是真正的多分法，这种情况下的拓扑结构是已知的:t6a 和 t6 是姐妹分类群.如果我尝试将任何化石分类群添加到数据中，这也是一个问题，因为如果化石靠近两个主要进化枝的基部，则随机解析多聚体可能会将其作为错误进化枝的基本成员.

However, there are several problems with this. On the one hand this adds new taxa by creating a polytomy that I then have to randomly resolve using a package like bifurcatr. However, this is inaccurate to the known phylogeny. This is not a true polytomy, the topology in this case is known: t6a and t6 are sister taxa. This is also a problem if I try to add any fossil taxa into the data, because if the fossil is near the base of two major clades randomly resolving the polytomy could place it as a basal member of the wrong clade.

另外，我使用节点数可变的树，因为在某些情况下，某些分类群的数据丢失，我必须运行数据的子集，而忽略分类群.因此，树之间的 then 节点的数量并不总是相同的.所以我想找出一种方法来添加分类群，并且不依赖于特定树中特定节点的数量.

Additionally I am using trees with variable numbers of nodes, because in some cases data is missing for certain taxa and I have to run subsets of the data with taxa omitted. Therefore, the numbers of then nodes are not always the same between trees. So I would like to figure out a way to add taxa that and is not dependent on the number of a specific node in a specific tree.

我想知道是否有任何方法可以通过将它们作为姐妹分类群绑定到已知尖端而不是在内部节点创建多分体来将分类群添加到树中?这将允许我更容易将分类群绑定到树上，因为有一个一致的点，无论树的长度如何(作为任何尖端的姐妹都有特定标签).

I was wondering if there was any way to add taxa to a tree by binding them as a sister taxa to a known tip, rather than creating a polytomy at an internal node? This would allow me to more easily bind taxa to the tree because there is a consistent point at which they can be bound regardless of the tree length (as the sister to whatever tip has a certain label).

推荐答案

使用TreeTools"功能很容易实现AddTip().

This is simple to achieve using the 'TreeTools' function AddTip().

orig_tree <- ape::rtree(n = 20)
leaf_labelled_6 <- which(orig_tree$tip.label == 't6')
new_tree <- TreeTools::AddTip(orig_tree, leaf_labelled_6,  't6a')

我对bind.tree()的体验是，它有时会使树的内部节点编号混乱，导致某些下游功能出现问题.

My experience of bind.tree() is that it can sometimes make a mess of the internal node numbering of trees, causing problems with certain downstream functions.

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