There is a genus I focused, whose phylogenetic histories were obvious different based on chloroplast and nuclear loci. Both topologies were well support. In this case, maybe commonly, how to classify such taxa? Which one evidence should be used? Why? Any advice or references are good, thanks everyone.
additionally: In fact, i focus on how to treat the different genealogies based on nuclear and organelle data, rather than methodological, whatever they are based on gene trees, genomics trees or species trees. In a word, hypothesis there are two different genealogies based on nuclear and organelle data (not uncommon, given maternal inheritance), how I treat reasonably two history?
Hello
From what I understand, you have two genealogies based on two distinct genes, so you do not have a phylogeny, but rather two genes tree. To infer evolutionary relationships, you need the species tree.
read this: https://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/46.3.523
As mentioned by MS. Saravia if what you are trying to unveil is the taxonomic rank of an organism, you need the species tree. It is no uncommon that by using different genes the topology of the resulting trees might differ, specially when comparing organelle genes (from mitochondria or chloroplast, as in your case) and from the nucleus.
Generally speaking, the 16S (archea/bacteria) or 18S (eukaryotes) ribosomal genes are used for defining the taxonomy of an organism. A part from being one of the most studied regions (lots of data to compare with), they also tend to have constant evolutionary rates, as well as not usually being involved in horizontal gene transfer events. If you can, try to use it as *base line* or species tree for your comparisons.
Then you will see which of the other trees diverges from 18S tree, and try to know why (gene introgression by breeding, horizontal gene transfer, rapid evolving genes, etc).
Cheers
JMC
Saraiva and Martí-Carreras,
Thank your replies. Maybe I haven`t explained clearly my thought. I don`t focus on methodology but how to address two different genealogies. Considering difference of inheritance pattern, it is frequent that genealogies are different based on nuclear and organelle sequences, how and why should I handle such case?
Hello Zhen Zhang , it is not uncommon that a nuclear gene tree is different from the organellar tree. It is very common in the plant genus with often hybridizing species. While I was working on the phylogeny of the genus Morus (Moraceae), I had similar situations as you described. I had to use multiple regions of both nuclear and Chloroplast DNA. If the genealogies (as you described) have fewer discrepancies in topologies, you could run a Partition Homogeneity Test and see if the incongruence is significant. Then you could conduct a maximum parsimony analysis based on the concatenated data set. In your situation, I would use two or more non-coding sequences (i.e. internal transcribed spacer of the nuclear DNA or Intergenic sequences of the organellar DNA).
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