In fungi, stress-related genes tend to undergo many duplications and losses [ 17].
In particular, stress-related genes exhibited many duplications and losses, whereas growth-related genes showed selection against such changes.
In nontranscribed regions the process creates many duplications and expansions with no deletions, causing mitochondria to accumulate large sections of nonfunctional DNA.
As expected, the seven human members of the sirtuin family experienced many duplications and losses over the course of their evolution.
They also have performed many duplications and deletions within the HoxD cluster and shown that these manipulations can lead to heterochronic expression of HoxD genes in the tail bud.
Many of the 22 regions also show nucleotide-level homology to one-another (supplementary fig. S3, Supplementary Material online), with many duplications and inversions, indicating that they were often copied into themselves or similar REs that subsequently were the targets of RIP.
TreeMap [ 37], which seeks to minimize host shifts, inferred a significantly higher number of cospeciation events than expected from a random distribution but required many duplications and extinctions to achieve this (Table 3, upper half) and five distinct smut species were inferred on the ancestral host.
The high degree of sequence similarity shared by these different copies strongly suggests that they belong to a paralogous gene family, originated from an ancestral ceoB-like sequence that underwent many duplication events and existing long before the appearance of the ancestor of Burkholderia.
This is particularly problematic when analyzing genomes of distantly related organisms, because a high degree of divergence over long periods of evolutionary time can obscure many duplications, losses, and transfers, and they will not be reflected in the phyletic profile.
Our analysis show that mitochondrial β-barrel channels from Archaeplastida (plants) and Opisthokonta (animals and fungi) experienced many duplication events that resulted in multiple paralogous isoforms and form well-defined monophyletic clades that match the current model of eukaryotic evolution.
