I am creating a tree for my sequences of an avian reovirus. The data is from 1973-2019. The tree keeps creating a common ancestor in the 1700’s which is beyond my data. I am just making sure my tree is correct. If there is a problem how do I fix it.
Thank you for your help
What makes you think that this tree is wrong? May the common ancestor not be from a few hundred years ago?
It can indeed be that the inferred common ancestor is wrong - but one would need more information. Is there a time tree in the literature for this virus? So you know what you expect?
It could be that you use a hard coded clock rate that is set too low for this virus. What is your augur refine command? In particular, what are the timetree parameters?
Thank you for responding and thanks for the help
There doesn’t seem to be a time tree in the literature. The virus is endemic in poultry. It was discovered in the 1950’s. I expect there to be a common ancestor just not that far back.
My refine command in my snakemake file is the following.
rule refine:
message:
“”"
Refining tree
- estimate timetree
- use {params.coalescent} coalescent timescale
- estimate {params.date_inference} node dates
- filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
“”"
input:
tree = rules.tree.output.tree,
alignment = rules.align.output,
metadata = input_metadata
output:
tree = “results/tree.nwk”,
node_data = “results/branch_lengths.json”
params:
coalescent = “opt”,
date_inference = “marginal”,
clock_filter_iqd = 4
shell:
“”"
augur refine
–tree {input.tree}
–alignment {input.alignment}
–metadata {input.metadata}
–output-tree {output.tree}
–output-node-data {output.node_data}
–timetree
–coalescent {params.coalescent}
–date-confidence
–date-inference {params.date_inference}
–clock-filter-iqd {params.clock_filter_iqd}
“”"
Can’t see any obvious problem in the command.
What does the tree look like in divergence view?
Is there a non-time-tree in the literature?
It could be a tree building mistake but it’s hard to check remotely.
What makes you expect the common ancestor to be recent? Do you have good reasons for that prior?
It could also be that there’s reassortment/recombination happening which would throw off tree building I would imagine.
