Background:

In western Mexico, the Magnolia pacifica complex includes three morphologically defined, endemic, and endangered species, distributed along a 215 km continentality and moisture gradient: Magnolia pugana, M. pacifica s.s., and M. vallartensis.

Hypothesis:

Genetic evidence supports the taxonomical classification of the M. pacifica complex.

Study site and dates:

Western Mexico, samples were collected in 2012-2015.

Methods:

Six Inter-Simple Sequence Repeats (ISSR) primers amplified 76 clear and reproducible fragments in 278 individuals from 10 representative localities of the M. pacifica complex. ISSR dataset was analyzed using STRUCTURE 2.3.4, UPGMA clustering, Barrier 2.2, and AMOVA. Genetic diversity parameters were also estimated.

Results:

Genetic analyses revealed two main groups: M. pugana and M. pacifica s.s.-M. vallartensis. Two subpopulations within each group were evidenced, particularly M. pacifica s.s. was separated from M. vallartensis. Geographical barriers to gene flow were identified. AMOVA revealed a similar and significant proportion of variation between and within groups. M. pugana has lower genetic diversity and higher differentiation than the M. pacifica s.s-M. vallartensis group.

Conclusions:

Our results support the recognition of M. pugana as a genetically distinct lineage from M. pacifica s.s and M. vallartensis, but did not reveal a clear species boundary between the last two taxa. Geographical barriers and distance isolation might explain the genetic structure and differentiation pattern within the M. pacifica s.s. species complex. All main groups and subgroups defined in this study should be considered as separate conservation units, and concerted efforts are needed to protect them.