evolutionary trees of sepecies

Question

[zhu]

I try to construct phylogenetic trees for multiple species. So I use orthofinders to run so that to find Single_Copy_Orthologue_Sequences. But their no Single_Copy_Orthologue_Sequences. So I want to know wether or not ia can use the species_tree about the orthofinder's run. Or their have an any other way to construct phylogenetic trees for multiple species.

[dthorbur]

What kind of organisms are you trying to infer a species tree for? It would sound alarm bells about data quality if no single copy orthologs were found in any of the organisms. Can you check how many copies you have of BUSCO genes?

[zhu]

I'm trying to inferring the evolutionary tree of the genus Solanum. I've added two species about Cooperation-88 and qingshu9 that they're all tetraploids but other species are diploid. If i don't add these two species when using orthofinder, there will have single_copy_orthologus_sequences. Otherwise there would be no single_copy_orthologus_sequences. These species are are hybrids. There have a lot of duplicate genes. So how is it better to deal with both species?

[dthorbur]

There are tools for whole genome phylogenies, though it's been a while since I've used one. Another option would be mtDNA. There was also an interesting tool I saw recently that used raw reads. Paper here. Otherwise, I'm used to working on vertebrates where single copy orthologs are usually easier to find. So Dave's recommendation is likely more appropriate than mine.

Answer 1

[Dave Carlson]

In my experience, it's pretty common to have relatively few single-copy orthologs (sometimes zero) if you run orthofinder on a fairly large or diverse group of plant species. Presumably this is due to the relatively high rate of polyploidy in plants.

The good news is that there are now methods available that can do species tree inference in the presence of paralogs/gene families. For example, Astral-Pro2.