Poly-A primed mRNA derived intron loss. (a) Reverse transcriptase mediated intron loss. Step 1: a gene is transcribed by RNA polymerase (RNAP) and the transcript contains both exons (black boxes) and introns (lines between boxes). The transcript is processed to mature mRNA by splicing out introns and adding a poly-A tail to the 3' end. Step 2: reverse transcriptase (RT) primes off of the poly-A tail to create a cDNA (blue boxes), but falls off in a length-dependent fashion. Step 3: the partial cDNA then recombines with the gene. Step 4: the resulting gene has lost any introns that span the recombination junction. (b) Meiotic recombination can create internal intron losses. An individual from a population of Cryptococcus starts with a four-intron wild-type allele (step 1; exons are colored boxes). A subsequent poly-A primed mRNA-mediated mutation of said allele generates a 3' loss allele in this individual (as indicated by asterisks, introns 2, 3, and 4 are lost). This individual mates with another individual in the population that carries the wild-type allele (step 2). During meiosis, the alleles may pair and recombine, as in step 3. Depending upon the location of the recombination event (crossing lines in step 3), various recombinant progeny alleles will be generated (step 4). The final product is a 3' loss allele (missing introns 3 and 4) and an internal intron loss allele (missing only intron 2). Assuming neutrality, both recombinant alleles have an equal probability of eventually being fixed in the population.