Biology subjects

Prada, C.

Publications and source records attributed to Prada, C..

5 recordsLinked to original sources

bioRxiv2026

Genetic connectivity in US Caribbean queen conch (Aliger gigas):Implications for management and forensic assignment

Understanding genetic connectivity among marine populations is central to conservation biology, informing how exploited species are managed, and how marine protected area (MPA) networks are designed. The queen conch (Aliger gigas) is a large, heavily exploited Caribbean gastropod listed under CITES Appendix II and provides an ideal system for examining connectivity in species with high dispersal potential. Its extended pelagic larval phase promotes gene flow across broad spatial scales, limiting detectable population structure. Here we used low-coverage whole-genome sequencing (lcWGS) of queen conch sampled from three regions within United States waters, Florida (FL), Puerto Rico (PR), and the US Virgin Islands (VI), to characterize connectivity and to evaluate the implications for management. Using genotype-likelihood approaches, we inferred patterns across principal component analysis, admixture analysis, pairwise FST, contemporary migration, and historical coalescent-based demographic modeling. Genome-wide analyses revealed little structure with individuals from all three regions intermixed in ordination space and similar ancestry profiles, consistent with high gene flow. In contrast, analyses restricted to the upper tail of the FST distribution recovered geographically concordant structure, resolving FL, PR, and VI as distinguishable groups, with PR individuals showing intermediate, admixed ancestry between FL and VI. Estimates of contemporary migration indicated a partially open system in which 72-98% of each population's ancestry was locally derived, with substantial bidirectional gene flow between PR and VI, moderate immigration from VI into FL and VI to PR, and negligible direct exchange from FL to either PR or VI. Historical demographic analyses suggest long-term genetic effective population sizes (Ne) on the order of 2.2-7.6 x 105; individuals and a hierarchical population divergence during the early Pleistocene (~ 2 Mya) with ongoing symmetric migration among the three populations, with the strongest historical connectivity between PR and VI with 10 diploid migrants per generation (2Nm = 20.0). Together, these results indicate that queen conch populations across US waters are neither fully panmictic nor completely isolated. Instead, they form a connected population system in which substantial gene flow occurs alongside geographically differentiated genomic variation. These findings argue against treating the US range as either a single management unit or as a set of completely independent stocks. They also highlight the potential importance of the US Virgin Islands within the regional connectivity network and suggest that highly differentiated loci could be useful for developing forensic SNP panels to identify the geographic origin of queen conch products and support enforcement against illegal, unreported, and unregulated fishing.

ecology↗

bioRxiv2022

A cnidarian phylogenomic tree fitted with hundreds of 18S leaves

Cnidarians are critical members of aquatic communities and have been an experimental system for a diversity of research areas ranging from development to biomechanics to global change biology. Yet we still lack a well-resolved, taxonomically balanced, cnidarian tree of life to place this research in appropriate phylogenetic context. To move towards this goal, we combined data from 26 new anthozoan transcriptomes with 86 previously published cnidarian and outgroup datasets to generate two 748-locus alignments containing 123,051 (trimmed) and 449,935 (untrimmed) amino acids. We estimated maximum likelihood phylogenies for both matrices under partitioned and unpartitioned site-homogeneous and site-heterogenous models of substitution. We used the resulting topology to constrain a phylogenetic analysis of 1,814 small subunit ribosomal (18S) gene sequences from GenBank. Our results confirm the position of Ceriantharia (tube-dwelling anemones), a historically recalcitrant group, as sister to the rest of Hexacorallia across all phylogenies regardless of data matrix or model choice. We also find unanimous support for the sister relationship of Endocnidozoa and Medusozoa and propose the name Operculozoa for the clade uniting these taxa. Our 18S hybrid phylogeny provides insight into relationships of 15% of extant taxa. Together these data are an invaluable resource for comparative cnidarian research and provide perspective to guide future refinement of cnidarian systematics.

evolutionary biology↗

bioRxiv2021

Linking photoacclimation responses and microbiome shifts between depth-segregated sibling species of reef corals

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea, and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depths, we studied adaptive divergence in the Caribbean corals Orbicella annularis and O. franksi. When transplanted from deep to shallow, O. franksi experienced fast photoacclimation, low mortality, and maintained a consistent bacterial community. In contrast, O. annularis experienced higher mortality, and limited photoacclimation when transplanted from shallow to deep. The photophysiological collapse of O. annularis in the deep environment was associated with an increased microbiome variability and reduction of some bacterial taxa. Differences in the symbiotic algal community were more pronounced between coral species than between depths. Our study suggests that these sibling species are adapted to distinctive light environments partially driven by the algae photoacclimation capacity and the microbiome robustness, highlighting the importance of niche specialization in symbiotic corals for the maintenance of species diversity. Our findings have implications for the management of these threatened Caribbean corals and the effectiveness of coral reef restoration efforts.

microbiology↗

bioRxiv2020

Mesophotic gorgonian corals evolve multiple times and faster than deep and shallow lineages

1.Mesophotic Coral Ecosystems (MCEs) develop on a unique environment, where abrupt environmental changes take place. Using a time-calibrated molecular phylogeny (mtDNA: mtMutS), we examined the lineage membership of mesophotic gorgonian corals (Octocorallia: Cnidaria) in comparison to shallow and deep-sea lineages of the wider Caribbean-Gulf of Mexico and the Tropical Eastern Pacific. Our results show mesophotic gorgonians originating multiple times from old deep-sea octocoral lineages, whereas shallow-water species comprise younger lineages. The mesophotic gorgonian fauna in the studied areas are related to their zooxanthellate shallow-water counterparts in only two clades (Gorgoniidae and Plexauridae), where the shallow-deep gradient could serve as a driver of diversification. Interestingly, mesophotic clades have diversified faster than either shallow or deep clades. One of this groups with fast diversification is the family Ellisellidae, a major component of the mesophotic gorgonian coral assemblage worldwide.

evolutionary biology↗

bioRxiv2017

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the [~]7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 {+/-} 222, with more loci recovered from octocorals (783 {+/-} 138 loci) than hexacorals (475 {+/-}187 loci). Phylogenetically informative sites ranged from 26-49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The percent of variable sites within each of three genera (Acropora, Alcyonium, and Sinularia) for which multiple species were sequenced ranged from 4.7-30%. Maximum likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target-enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Re-designing the baits with improved affinities to capture loci within each sub-class will provide a valuable toolset to address systematic questions and further our understanding of the timing of diversifications in the class Anthozoa.

genomics↗