Question

Define

Incomplete lineage sorting and using a diagram explain its consequences for phylogenetic reconstruction, label your diagram

Answer 1

"Deep coalescence" or "incomplete lineage sorting" refer to the failure of gene copies to coalesce within the duration of the species - the lineages coalesce in an ancestral species. Where Coalesce means if we choose any two alleles from a current generation and go backward in time, their separate genealogies will eventually coalesce (join) into a single ancestral allele. Whereas coalescence is the process by which, looking back through time, the genealogy of any pair of homologous alleles merges in a common ancestor.  An example of incomplete lineage sorting is sex determination in honeybees because they have haplodiploid sex determination means a species where the females develop from fertilized eggs and are diploid and the males develop from unfertilized eggs and are haploid.

Depends on the population size of the ancestor. Is small, the coalescence would be rapid and would have occurred only a few generations before the population split. If large, coalescence could be much deeper in the past. When representing phylogenetic trees as thick branches with the population genetics processes such as coalescence/lineage sorting occurring inside,  the width represents the population size and the length represents the generation time. If a gene tree is discordant, It means that it does not match the species tree. Incomplete Lineage Sorting or Deep Coalescence cause discordance between the gene tree and the species tree.