Estimate of within clones and between clone selection suggests a multi-stage selection process in the production of high affinity B cell receptors.

During an immune response, B cells undergo a process of clonal expansion, somatic hypermutation of the immunoglobulin genes and affinity-dependent selection. Over a lifetime, each B cell may participate in multiple rounds of affinity maturation as part of different immune responses. We characterized these two time-scales for selection which are apparent in the structure of B cell lineage trees. The “trunk” of the tree consists of mutations that are shared across all members of a clone, and the branches form a “canopy” consisting of mutations that are shared by a subset of clone members.

We show that the framework regions are subjected to a negative selection at all stages. However, CDR regions are affected to purifying and antigen-driven positive selection on the short term, which leads to a net positive selection in the long term. Overall, we found that long-term selection is strongly dependent on the heavy chain variable gene family.

To the selection in the tree canopy, we propose a novel mixed lineage tree/sequence based method to detect within population selection as defined by the effect of mutations on the average number of offspring. Specifically, we propose to measure the log of the ratio between the number of leaves in lineage trees branches following synonymous and non-synonymous mutations (LONR), and show that selection in CDR region occur at a different stage.