Genomic features of subspecies defined by phenotypic criteria：Analyses
of the mangrove species complex, Avicennia marina
The designation of subspecies has often been uncertain in systematics.
In addition to phenotypic divergence, designation of subspecies may need
to be supplemented by population genetic analyses. In this study, we
perform such a survey of the mangrove tree Avicennia marina on Indo-West
Pacific coasts. This species harbors three morphological groups. We
collected samples from 16 populations (577 individuals) and sequenced 94
nuclear genes. Three genetic features support the subspecies designation
for the three morphological subgroups. First, the observed genetic
divergence is concordant with the morphological differences, with
discordance found in zones of coexistence. Second, the three groups
differ in the level of genetic diversity as well as in the demographic
history, suggesting a degree of ecological differentiation. Third, and
most important, the divergence level varies from locus to locus across
the genome. A small portion of the genome is most informative about
subspecies delineation, thus hinting the uneven exchange of genes. Such
locus-dependent gene flow is expected for incompletely isolated groups.
This last point suggests that the reduction in gene flow can be observed
at some loci, thus hinting incipient reproductive isolation. In short,
the three groups of A. marina appear to have evolved far beyond the
stage of structured populations, but not to the point of full species.
Hence, the subspecies designation is warranted. We believe these
considerations can be generalized to other taxa.