Trans‐species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): implications for the long‐term maintenance of genetic diversity in trees

For each of three nuclear gene loci, intraspecific‐ as well as trans‐specific shared polymorphisms were detected in DNA among three distantly related species in the genus Picea . Few fixed interspecific polymorphisms were observed. Allele genealogies did not match species phylogenies, and species lineages were not reciprocally monophyletic. Based on molecular clocks and morphological evidence from the fossil record, the divergence time between species was estimated at 13–20 million years (my), and a mutation rate of 2.23 × 10 −10 to 3.42 × 10 −10 per site per year was estimated. Large historical population sizes in excess of 100 000 were inferred, which would have delayed the fixation of polymorphisms. These numbers translated into allele coalescence times in the order of 10 to 18 my, which implies the sharing of polymorphisms since common ancestry. These results suggest that trans‐species shared polymorphisms might be frequent at plant nuclear gene loci, leading to high allelic diversity. Such a trend is more likely in trees and plants characterized by ecological and life‐history determinants favoring large population sizes such as an outcrossing mating system, wind pollination, and a dominant position in ecosystem. These polymorphisms also call for caution in estimating congeneric species phylogenies from nuclear gene sequences in such plant groups.