Is there any cut off point of genetic distance in phylogenetic tree to determine which category my study isolates are to be counted?
Getting highly confused with different authors giving own views on minimal distances. Some characterizing their isolates with minimal distance as a new variant, while others even though there is a large gap, they are considering it usual. :/
Should not there be a cut off, you think?
There's a good reason for the lack of consensus - to base this on genetic distances is completely arbitrary, and that's not just because mutation rates can vary considerably for a given marker. In addition to reciprocal monophyly of a particular group (based on a large sample size), it makes sense to bring in independent information, including: do different variants look different, are they adapted to different habitats, and, most convincing, do they interbreed?
It is dependent upon what organism, what gene, and other issues. The rules for bacteria are not the same as for viruses or eukaryotes. And even within any one group of organisms there can be differences of opinion, as you already note, as to what the rules should be.
There's a good reason for the lack of consensus - to base this on genetic distances is completely arbitrary, and that's not just because mutation rates can vary considerably for a given marker. In addition to reciprocal monophyly of a particular group (based on a large sample size), it makes sense to bring in independent information, including: do different variants look different, are they adapted to different habitats, and, most convincing, do they interbreed?
Another complicating factor is that different regions of a genome can yield very different phylogenetic trees. A tree for one gene may place a given taxon very near its fellows and another gene may be quite heavily derived. This is also the case for mitochondrial genomes - Meyer et al. recently found that ancient humans from Sima de los Huesos in Spain have nuclear DNA that is very like Neanderthals, but mitochondrial genomes that are very unlike Neanderthals.
http://www.ncbi.nlm.nih.gov/pubmed/26976447
Nature. 2016 Mar 14. doi: 10.1038/nature17405. [Epub ahead of print]
Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins.
Meyer M, Arsuaga JL, de Filippo C, Nagel S, Aximu-Petri A, Nickel B, Martínez I, Gracia A, de Castro JM, Carbonell E, Viola B, Kelso J, Prüfer K, Pääbo S.
Abstract
A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.
PMID: 26976447
It depends on the gene and organism that you working. You should also consider the statistical analysis you used while comparing with the other publications.
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