Biology subjects

Vermeij, M. J.

Publications and source records attributed to Vermeij, M. J..

4 recordsLinked to original sources

bioRxiv2022

Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths

Mesophotic coral communities are increasingly gaining attention for the unique biological species they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies rarely include mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Here, we used reduced-representation genome sequencing to provide a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed substantial undescribed diversity (at least 24 molecular clades across the 8 species), including deep divergences within genera and current taxonomic species. Five of the eight focal species consisted of at least two sympatrically-occurring, genetically distinct clades, which were consistently detected across different methods. The repeated observation of genetically divergent clades associated with mesophotic depths highlights that there are many more mesophotic-specialist coral species than currently acknowledged, and that an urgent assessment of this largely unstudied biological diversity is warranted.

evolutionary biology↗

bioRxiv2020

Taxonomy of the apicomplexan symbionts of coral, including Corallicolida ord. nov., reassignment of the genus Gemmocystis, and description of new species Corallicola aquarius gen. nov. sp. nov. and Anthozoaphila gnarlus gen. nov. sp. nov.

Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called corallicolids, are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, Gemmocystis cylindrus (described from the coral Dendrogyra cylindrus), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, Corallicola aquarius gen. nov. sp. nov. from its Rhodactis sp. host, and also describe a second species, Anthozoaphila gnarlus gen. nov. sp. nov., from the coral host Madracis mirabilis. Finally, we propose reassigning the incertae sedis taxon G. cylindrus from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.

microbiology↗

bioRxiv2020

Juvenile corals inherit mutations acquired during the parents lifespan

128 years ago, August Weismann proposed that the only source of inherited genetic variation in animals is the germline1. Julian Huxley reasoned that if this were true, it would falsify Jean-Baptiste Lamarcks theory that acquired characteristics are heritable2. Since then, scientists have discovered that not all animals segregate germline cells from somatic cells permanently and early in development3. In fact, throughout their lives, Cnidaria4-6 and Porifera7 maintain primordial stem cells that continuously give rise to both germline and somatic cells. The fate of mutations generated in this primordial stem cell line during adulthood remains an open question. It was unknown whether post-embryonic mutations could be heritable in animals8-10--until now. Here we use two independent genetic marker analyses to show that post-embryonic mutations are inherited in the coral Acropora palmata (Cnidaria, Anthozoa). This discovery upends the long-held supposition that post-embryonic genetic mutations acquired over an animals lifetime in non-germline tissues are not heritable2. Over the centuries-long lifespan of a coral, the inheritance of post-embryonic mutations may not only change allele frequencies in the local larval pool but may also spread novel alleles across great distances via larval dispersal. Thus, corals may have the potential to adapt to changing environments via heritable somatic mutations10. This mechanism challenges our understanding of animal adaptation and prompts a deeper examination of both the process of germline determination in Cnidaria and the role of post-embryonic genetic mutations in adaptation and epigenetics of modular animals. Understanding the role of post-embryonic mutations in animal adaptation will be crucial as ecological change accelerates in the Anthropocene.

evolutionary biology↗

bioRxiv2018

A universal set of primers to study animal associated microeukaryotic communities

BackgroundUnlike the study of bacterial microbiomes, the study of the microeukaryotes associated with animals has largely been restricted to visual identification or molecular targeting of particular groups. The application of high-throughput sequencing (HTS) approaches, such as those used to look at bacteria, has been restricted because the barcoding gene traditionally used to study microeukaryotic ecology and distribution in the environment, the Small Subunit of the Ribosomal RNA gene (18S rRNA), is also present in the animal host. As a result, when host-associated microbial eukaryotes are analyzed by HTS, the obtained reads tend to be dominated by host sequences.\n\nResultsWe have done an in-silico validation against the SILVA 18S rRNA reference database of contrametazoan primers that cover the V4 region of the 18S rRNA, and compared these with universal V4 18S rRNA primers that are widely used by the microbial ecology community. We observe that the contrametazoan primers recover only 2.6% of all the metazoan sequences present in SILVA, while the universal primers recover up to 20%. Among metazoans, the contrametazoan primers are predicted to amplify 74% of Porifera sequences and 4% and 15% of ctenophore and Cnidaria, respectively, while amplifying almost no sequences within Bilateria.\n\nWe tested these predictions in-vivo, and observed that contrametazoan primers amplify the 18SrRNA from two ctenophore species, but reduce significantly the metazoan signal from material derived from coral and from human samples. When compared in-vivo against universal primers, contrametazoan primers worked in 8 out of 9 samples, providing at worst a 2-fold decrease in the number of metazoan reads, and at best a 2800-fold decrease.\n\nConclusionsWe have validated an easy, inexpensive, and near-universal method for the study of microeukaryotes associated with animal hosts using 18S rRNA Illumina metabarcoding. This method will contribute to a better understanding of microbial communities, as they related to the wellbeing of animals and humans.

microbiology↗