Alan Thomas Sam, I think concatenation can involve two or more independent data sets regardless of their origins. It means a concatenation could be done between two or more nuclear genes or within two or more chloroplast genes (with similar rates of evolution). I think only goal of concatenation is to increase the number of characters. More characters would yield more reliable phylogenetic relationships. Before concatenation, however, there is an important step of assessing the two data sets for data congruence. In PAUP, it is called partition homogeneity test .

Hope this helps.

Organelle genes (mitochondria and chloroplasts for example) evolve roughly ten-fold faster than genes in the nucleus. Also, the organelles don't have much chance for horizontal gene transfer or recombination. So the organelle genes can help differentiate very closely related groups (such as modern humans from various groups, South African, northern African, Australian, Asian) while the nuclear genes can sometimes give more accurate information about other aspects of deeper relationships such as gorilla/chimpanzee/orangutan date of common ancestor, or introgression of Neanderthal DNA into modern Europeans.

Pr Madhav Nepal ,

what's partition homogeneity test ? and what's the importance of this test, which information can give it?

Thanks

Hello Khammassi Manel , it looks like there has been another post on this test, so please follow the thread at this link: https://www.researchgate.net/post/How_do_I_perform_a_partition_homogeneity_test_in_PAUP

Khammassi Manel , you might find these resources useful. Regarding the software, if you do not use PAUP, I heard other programs such as RAxML and HyPhy can be used for the test.

• https://academic.oup.com/sysbio/article/45/1/92/1631747

• Article Let Them Fall Where They May: Congruence Analysis in Massive...

Pr Madhav Nepal , Thanks for response and advice.