Studies in several organisms have shown that eukaryotic centromere regions contain proteins involved in chromosome inheritance functions such as centromere structure, heterochromatin assembly and sister chromatid cohesion.
So far we have argued the large role vertical inheritance of function has played in evolution is larger than the network of genomes implies.
Monism is not a necessary concomitant of the standard ontology, but we think that it fits easily with the linear focus on vertical inheritance: the function of an entity is its role in driving the evolving lineage along its branch of the tree.
Natural selection, like most complex scientific theories, runs counter to common experience and therefore competes usually unsuccessfully with intuitive ideas about inheritance, variation, function, intentionality, and probability.
These are also homologous with the bones of human arms, dog legs, and whale flippers because homology is defined on the basis of shared inheritance, not function (Wagner 2007).
Large-scale genomic analysis are fraught with uncertainties related to the inheritance of function among remotely homologous proteins.
Not all genes contribute equally to the cell, and we will demonstrate that vertical inheritance of function has a more pronounced signal than vertical inheritance of genetic material.
Alternatively, LUCA's genome dynamics may have simply been a by-product of early genome evolution in which inheritance and function were not fully separated or coordinated; such a system might even have emerged during (or soon following) a transition from RNA to DNA-based genomes.
To derive the transition probabilities between any types of relationships, we introduce the inheritance-generating function, which can conveniently aggregate all possible inheritance patterns between their common ancestors and this pair of individuals.
Actually, our definition of the inheritance-generating function can explicitly list the number of all possible inheritance paths and their lengths between a pair of alleles.
