Phylogenomics reveals coincident divergence between giant host sea anemones and the clownfish adaptive radiation
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (Arcadia Science)
Abstract
The mutualism between clownfishes (or anemonefishes) and their giant host sea anemones are among the most immediately recognizable animal interactions on the planet and have attracted a great deal of popular and scientific attention [1-5]. However, our evolutionary understanding of this iconic symbiosis comes almost entirely from studies on clownfishes— a charismatic group of 28 described species in the genus Amphiprion [2]. Adaptation to venomous sea anemones (Anthozoa: Actiniaria) provided clownfishes with novel habitat space, ultimately triggering the adaptive radiation of the group [2]. Clownfishes diverged from their free-living ancestors 25-30 MYA with their adaptive radiation to sea anemones dating to 13.2 MYA [2, 3]. Far from being mere habitat space, the host sea anemones also receive substantial benefits from hosting clownfishes, making the mutualistic and co-dependent nature of the symbiosis well established [4, 5]. Yet the evolutionary consequences of mutualism with clownfishes have remained a mystery from the host perspective. Here we use bait-capture sequencing to fully resolve the evolutionary relationships among the 10 nominal species of clownfish-hosting sea anemones for the first time (Figure 1). Using time-calibrated divergence dating analyses we calculate divergence times of less than 25 MYA for each host species, with 9 of 10 host species having divergence times within the last 13 MYA (Figure 1). The clownfish-hosting sea anemones thus diversified coincidently with clownfishes, potentially facilitating the clownfish adaptive radiation, and providing the first strong evidence for co-evolutionary patterns in this iconic partnership.
Article activity feed
-
We employed multiple divergence dating analyses
Given that the dates inferred from your time calibration are of such critical importance to the conclusions made herein, I might strongly suggest using more robust methods that can take advantage of your fantastic UCE dataset. In particular, I would recommend looking into either using BEAST or MCMCTree.
-
24.9 MYA (95% CI = 21-45.5 MYA; Figure 1, S2).
Which dates are you reporting here and throughout? Presumably these are dates from only one of the two methods (Chronos and LSD2).
-
Divergence times for all host anemone species were calculated at less than 25 MYA, with 9 of 10 host species having divergence times between 6.9-11.6 MYA
What were the times inferred from each method respectively?
-
We employed multiple divergence dating analyses to convert phylogenetic trees into ultrametric chronograms and estimate divergence times for the clownfish-hosting sea anemones for the first time [8] (see Supplemental Methods).
I understand that the detailed methods are in the supplement, but you really should at least state which methods you are using, otherwise this statement is not particularly informative.
One thing I did notice when reading the supplement - it doesn't really make sense to use the IQ-TREE implementation of LSD2 here if the only constraints you have are for the root age. This method is primarily intended for use in phylodynamic contexts wherein you have tip-dates for most or all of your rapidly evolving pathogen samples. At its core, the method dates the tree by regressing the tip-to-root distance against sampling …
We employed multiple divergence dating analyses to convert phylogenetic trees into ultrametric chronograms and estimate divergence times for the clownfish-hosting sea anemones for the first time [8] (see Supplemental Methods).
I understand that the detailed methods are in the supplement, but you really should at least state which methods you are using, otherwise this statement is not particularly informative.
One thing I did notice when reading the supplement - it doesn't really make sense to use the IQ-TREE implementation of LSD2 here if the only constraints you have are for the root age. This method is primarily intended for use in phylodynamic contexts wherein you have tip-dates for most or all of your rapidly evolving pathogen samples. At its core, the method dates the tree by regressing the tip-to-root distance against sampling date - if you only have a date for the root, the method is unlikely to be accurate.
From the LSD2 github page (https://github.com/tothuhien/lsd2): "The input date file should contain the date of most of the tips and possiblly some internal nodes if known."
-
Diversification of the clownfish-hosting sea anemones was coincident with the clownfish adaptive radiation.
This plot is a bit misleading, as diversification events plotted here include both geographic subdivision within species (e.g. Entacmaea) as well as diversification among species. Furthermore, without seeing the clownfish phylogeny, it's quite difficult to correspond the tempo of their diversification to the tempo of diversification in anenomes as seen here.
-
Figure 1.
I would strongly suggest plotting the clownfish phylogeny alongside this one as "co-phylogenies", such as implemented within phytools: http://blog.phytools.org/2016/08/empirical-co-phylogenetic-cophylo.html
If you have information about which specific host species each clownfish is paired with, this would be a useful way of more intuitively visualizing whether the diversification of mutualistic species pairs truly is coincident.
-
The clownfish-hosting sea anemones thus diversified coincidently with clownfishes, potentially facilitating the clownfish adaptive radiation, and providing the first strong evidence for co-evolutionary patterns in this iconic partnership.
This statement really is quite strong, however I'm not convinced that it's warranted simply given a coincident interval in which extant species of both groups diversified.
For instance, given the close ecological interactions among the anemones and clownfishes, they certainly share many ecological conditions. From this, it seems clear that although one hypothesis to explain the pattern of co-diversification is that of coevolution, an alternative hypothesis is that each diversification in each group was driven by some shared feature of their life history, independent of the interactions between …
The clownfish-hosting sea anemones thus diversified coincidently with clownfishes, potentially facilitating the clownfish adaptive radiation, and providing the first strong evidence for co-evolutionary patterns in this iconic partnership.
This statement really is quite strong, however I'm not convinced that it's warranted simply given a coincident interval in which extant species of both groups diversified.
For instance, given the close ecological interactions among the anemones and clownfishes, they certainly share many ecological conditions. From this, it seems clear that although one hypothesis to explain the pattern of co-diversification is that of coevolution, an alternative hypothesis is that each diversification in each group was driven by some shared feature of their life history, independent of the interactions between anemones and clownfishes.
I might suggest including a description of alternative hypotheses, and the extent to which your data and analyses support/refute them.
-
