Halophila johnsonii phylogenetic analysis alignments

Halophila johnsonii is an endangered seagrass species that is restricted
to the Florida Bay region of Florida, USA. Its taxonomic status has been
called into question, in particular, given the close morphological and
genetic similarity of H. johnsonii and the widely distributed and
morphologically variable H. ovalis, which is largely restricted to the
Indo-Pacific region. While a close relationship to H. ovalis is
uncontroversial, it remains uncertain whether H. johnsonii represents a
distinct lineage or is a recent introduction to the Florida region. Given
the conservation status of H. johnsonii, distinguishing these alternatives
has important implications for the management of the species and its
habitat. Here, we develop molecular data sets for samples of H. johnsonii
and H. ovalis including DNA sequences, genome-wide SNPs and
microsatellites with the view to resolving the affinities of H. johnsonii
with respect to the wider H. ovalis complex. Phylogenetic hypotheses based
upon plastid (~18000 bp) and low copy nuclear DNA (~6500 bp) sequences
derived from hybrid capture, along with 990 genome-wide ddRAD SNPs
consistently resolved H. johnsonii within H. ovalis. Specifically, we
found a close affinity between H. johnsonii and H. ovalis sampled from the
east coast of Africa. In addition, Halophila specimens collected in
Antigua, which are within the range of morphological variation typical for
H. ovalis, are virtually identical to H. johnsonii and the East African H.
ovalis samples based upon DNA sequence analyses and these group together
using Bayesian clustering analyses of microsatellites and ddRAD SNPs. We
conducted population genetic analyses using large number of H. johnsonii
samples collected over a 17-year period. Genotypic data generated through
microsatellites and ddRAD SNPs revealed genetic uniformity for all 132 H.
johnsonii samples across the Indian River Lagoon, Florida, while samples
of H. ovalis from Antigua shared the same genotype as H. johnsonii. We
conclude that the lack of genetic diversity and the absence of sexual
reproduction strongly indicates that the total range of H. johnsonii is
actually one clone that is closely related to populations in Africa and
Antigua and may be derived from a recent introduction from one of those
regions.