AUTHOR=Waycott Michelle , van Dijk Kor-jent , Calladine Ainsley , Bricker Eric , Biffin Ed 

TITLE=Genomics-Based Phylogenetic and Population Genetic Analysis of Global Samples Confirms Halophila johnsonii Eiseman as Halophila ovalis (R.Br.) Hook.f.

JOURNAL=Frontiers in Marine Science

VOLUME=8

YEAR=2021

URL=https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2021.740958

DOI=10.3389/fmars.2021.740958

ISSN=2296-7745

ABSTRACT=<p><italic>Halophila johnsonii</italic> is an endangered seagrass species that is restricted to the southeast coast of Florida, United States. Its taxonomic status has been called into question, in particular, given the close morphological and genetic similarity of <italic>H. johnsonii</italic> and the widely distributed and morphologically variable <italic>Halophila ovalis</italic>, which is largely restricted to the Indo-Pacific region. While a close relationship to <italic>H. ovalis</italic> is uncontroversial, it remains uncertain whether <italic>H. johnsonii</italic> represents a distinct lineage or is a recent introduction to the Florida region. Given the conservation status of <italic>H. johnsonii</italic>, distinguishing these alternatives has important implications for the management of the species and its habitat. Here, we develop molecular data sets for samples of <italic>H. johnsonii</italic> and <italic>H. ovalis</italic> including DNA sequences, genome-wide SNPs and microsatellites with the view to resolving the affinities of <italic>H. johnsonii</italic> with respect to the wider <italic>H. ovalis</italic> 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 <italic>H. johnsonii</italic> within <italic>H. ovalis.</italic> Specifically, we found a close affinity between <italic>H. johnsonii</italic> and <italic>H. ovalis</italic> sampled from the east coast of Africa. In addition, <italic>Halophila</italic> specimens collected in Antigua, which are within the range of morphological variation typical for <italic>H. ovalis</italic>, are virtually identical to <italic>H. johnsonii</italic> and the East African <italic>H. ovalis</italic> 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 <italic>H. johnsonii</italic> samples collected over a 17-year period. Genotypic data generated through microsatellites and ddRAD SNPs revealed genetic uniformity for all 132 <italic>H. johnsonii</italic> samples across the Indian River Lagoon, Florida, while samples of <italic>H. ovalis</italic> from Antigua shared the same genotype as <italic>H. johnsonii</italic>. We conclude that the lack of genetic diversity and the absence of sexual reproduction strongly indicates that the total range of <italic>H. johnsonii</italic> 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.</p>