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Given that the compared genes come from closely related organisms, such that in many cases the number of substitutions is small, one might expect a significant contribution from sampling error.
While the two samples come from closely related organisms, we also used tblastx to compare at the predicted amino acid level in case divergence at the nucleotide level was too high.
2. If they come from closely related genomes (e.g., genomes from two strains of the same species), the similarity is high (usually greater than 90% identity), and the context on the chromosome (i.e., the adjacent genes) can easily be seen to correspond, then they can be placed in the same family (even if the function they implement is yet to be determined).
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Furthermore, genome-based methods do not allow for genomic-scale grouping of sequences with certain characteristics most likely coming from closely related individuals, which can be used for reconstruction of species genomes.
Alternatively, a number of studies have focused on measuring causal signatures based on very specific upstream perturbations, either performed directly in the system of interest [ 9] or coming from closely-related published data [ 10].
The lab family also has a real family's "intense personal relationships" that in this case "come from working closely with other people with different backgrounds, from different countries, from different cultures, and different ages.
This individuality in diversity is presumably also the fundamental basis of the high discriminatory potential of the human palette to distinguish rice varieties after cooking, even when the grains come from genetically closely related varieties ([Calingacion et al. 2011];[Champagne et al. 2010]).
Down-regulation of secondary metabolite production in a heterologous host by ammonia [6], [23] might be expected in cases where the genes for the heterologous pathway come from a closely related organism using similar regulatory networks sensitive to ammonia.
Additional support for this hypothesis may come from the closely related, North American C. clupeaformis-complex.
Taxonomically speaking, all these 346 accessions come from two closely related subspecies: M. truncatula ssp longeaculata and M. truncatula ssp truncatula.
The 40 Acorus genes used here come from two closely related species – A. calamus (14 genes) and A. gramineus (26 genes) – and correspond to 65.6% (40/61) of the genes and 71.4% (32,072/44,937) of the nucleotide characters analyzed by Goremykin et al. [ 19].
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