What is gene tree and species tree? if I am using rbcL, matK and ITS (as eg.) to resolve the phylogeny in a species complex, in that case what is gene tree and what would be the species tree? If I want to do phylogeography, what software do I need to learn?
Hi there, trees inferred using any gene or introns like loci that you were referring are called gene trees. Species tree is the ideal tree that no one knows (this tree is known if you are doing simulation studies with modelling, otherwise tree is not known). So all we can do is to guess species tree from a gene tree, or an array of gene trees. Oftentimes gene tree and species tree are same, but incongruence may also be present. This incongruence (differences) is known as "lineage sorting". for step-by-step protocol to infer phylogeny from a set of sequences, please see my latest paper in "Nature Protocol". If you still have doubt please feel free to ask me. Cheers!
Article Sequence Similarity Search, Multiple Sequence Alignment, Mod...
Hi there, trees inferred using any gene or introns like loci that you were referring are called gene trees. Species tree is the ideal tree that no one knows (this tree is known if you are doing simulation studies with modelling, otherwise tree is not known). So all we can do is to guess species tree from a gene tree, or an array of gene trees. Oftentimes gene tree and species tree are same, but incongruence may also be present. This incongruence (differences) is known as "lineage sorting". for step-by-step protocol to infer phylogeny from a set of sequences, please see my latest paper in "Nature Protocol". If you still have doubt please feel free to ask me. Cheers!
Article Sequence Similarity Search, Multiple Sequence Alignment, Mod...
As Felix says, there really is no way to actually compute an organism species tree, since every phylogenetic tree is derived from some data (genetic, biochemical, morphological, etc) that may or may not represent the evolution of the underlying species form which the data was derived.
That is why the process of making trees to study the evolution of species is referred to as phylogenetic inference - we collect data, say gene sequences, and use that to infer a phylogeny of the species. But there literally is no way to actually know with certainty the evolutionary history of any given species or organism lineage.
People will refer to a "gene" tree in the context of discussing the apparent evolutionary pattern amongst a set of homologous gene sequences (usually where homology itself is merely inferred based on the degree of sequence similarity). They may switch to referring to a "species" tree when the are explicitly discussing the interpretation of a particular phylogenetic tree in terms of the inferred evolutionary history of the species represented in the genetic data set.
So those two terms really indicate the intention or focus of the presenter - are they discussing the actually inferred evolution of the genes themselves, or are they using them to infer something broader about the evolution of the organisms from which the sequence was obtained.
As far as useful software, the free PHYLIP suite of programs is still widely used and has been for decades now. The PHYLIP home page also contains links to a host of alternative programs and tools - take a look there (for links, click on the "Phylogeny programs available elsewhere"): http://evolution.genetics.washington.edu/phylip.html
The Tree Of Life web site also has lists of useful resources:
http://tolweb.org/tree/
I'll just add that since you are using chloroplast loci (matK & rbcL) and a nuclear locus (ITS) you can construct a separate tree for each locus and test for incongruence. If your chloroplast tree and nuclear tree are significantly incongruent with each other, you know that one or both of them must be incongruent with the species tree as well and you can investigate why. You might check out the following review paper about the many possible sources of gene tree/species tree incongruence.
Wendel, J. F. and J. J. Doyle (1998). Phylogenetic incongruence: window into genome history and molecular evolution. Molecular systematics of plants II: DNA sequencing. D. E. Soltis, P. S. Soltis and J. J. Doyle. Norwell, MA, Kluwer Academic Publishers: 265-296.
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