Biology subjects

Santos, M. E. A.

Publications and source records attributed to Santos, M. E. A..

3 recordsLinked to original sources

bioRxiv2026

Atlantic and Indo-Pacific separation in Palythoa sibling species: phylogenomic analyses using ultraconserved elements

The delineation of closely related species remains a persistent challenge in Zoantharia, where morphological plasticity and limited genetic differentiation complicate taxonomy. In this study, we investigated the phylogenetic relationship between the widely distributed sibling taxa Palythoa tuberculosa (Indo-Pacific) and Palythoa caribaeorum (Atlantic) using ultraconserved elements (UCEs) recovered from genome skimming. A dataset comprising 116 loci (35,699 bp) across 37 specimens from Brazil, the Red Sea, Okinawa, and New Caledonia was analysed using both concatenated maximum-likelihood and coalescent-based approaches. Phylogenetic reconstructions did not recover monophyletic relationships corresponding to either species or geographic origin, instead revealing intermixed lineages across the Indo-Pacific and Atlantic regions. Concordance factor analyses indicated low gene concordance and moderate site concordance, suggesting pervasive gene tree discordance rather than a lack of phylogenetic signal. These patterns are consistent with previous studies based on mitochondrial, nuclear, and reduced-representation datasets, indicating that increased marker resolution does not resolve species boundaries within this complex. The observed lack of differentiation may reflect ongoing or recent connectivity among populations, potentially facilitated by long-distance dispersal promoted by anthropogenic rafting or historical range expansion, biological invasion, or biological processes such as incomplete lineage sorting. The results support the hypothesis that P. tuberculosa and P. caribaeorum represent a species complex or a case of incipient speciation rather than fully distinct evolutionary lineages. These findings indicate that genome-scale data alone may be insufficient to resolve very recent divergences, supporting the need for integrative approaches to resolve complicated species boundaries in zoantharians.

evolutionary biology↗

bioRxiv2026

Comparing Symbiodiniaceae diversity across unicellular hosts, multicellular hosts, and environmental reservoirs

Symbiodiniaceae dinoflagellates are the primary photosymbionts in reef ecosystems, crucial for reef productivity. Although they are widely recognized as symbionts of animals such as corals and clams, they can occupy a broad range of reef niches, including water, sediment, and macroalgae. Understanding their ecology is typically hampered by their horizontal acquisition. Combining evidence from multiple sample types collected at the same location has the potential to address this issue, but such analyses are surprisingly rare. Here, we analysed Symbiodiniaceae communities across 74 environmental and host samples in one reef flat in Okinawa, Japan. We detected ten Symbiodiniaceae genera or genus-level clades using the ITS2 marker metabarcoding, including Clade J, previously known only from Okinotori Island, Japan. Cladocopium, Symbiodinium, and Durusdinium dominated multicellular hosts (hexacorals and Tridacna). In contrast, foraminiferal hosts were dominated by Cladocopium or genus-specific Freudenthalidium, Fugacium, and Miliolidium. Symbiont communities were mostly specific to the host genera. Water samples, with higher proportions of Durusdinium and free-living Symbiodinium, were distinct from macroalgae and sediment samples. The latter did not differ significantly from each other and contained Freudenthalidium, Fugacium, Miliolidium, Clade I, and Clade J. Only three ITS2 variants were shared across all sample categories, but many variants were unique to hosts or habitats. We highlight that both unicellular and multicellular hosts harbor specific endosymbiont types, with lower diversity than in the surrounding environment. Our results imply that host diversity, availability, and environmental context jointly structure photosymbiont communities at fine spatial scales within coral reef ecosystems.

microbiology↗

bioRxiv2024

Coral microbiomes from the Atlantic and Indo-Pacific oceans have the same alpha diversity but different composition

Corals are early-branching animals highly reliant on diverse symbionts for growth and reproduction. Most coral groups, including stony corals and hydrocorals, exhibit deep genetic divergence between the Atlantic (ATO) and Indo-Pacific (IPO) oceans, hampering their direct comparison. Although sibling zoanthid species (Hexacorallia: Zoantharia) deviate from this pattern, their symbioses have so far only been studied on local scales. Here, we examined the microbiomes of Palythoa caribaeorum from the ATO and P. tuberculosa from the IPO. Our extensive geographical sampling and metabarcoding revealed that Palythoa microbiomes have similar alpha diversity in both oceans. The primary exceptions are the symbiodiniacean Cladocopium and Chlamydiae bacteria, which mirror the global diversity patterns of corals. Despite distinct overall microbial compositions between oceans, some regions shared remarkably similar communities, hinting at the importance of both symbiont phylogeny and function. Finally, we explore the shift from commensal/mutualistic microbes to opportunistic pathogens, crucial amid the ongoing environmental changes.

microbiology↗