Coral reef ecosystems are under threat from the frequent and severe impacts of anthropogenic climate change, particularly rising sea surface temperatures. The effects of thermal stress may be ameliorated by adaptation and/or acclimation of the host, symbiont, or holobiont (host + symbiont) to increased temperatures. We examined the role of the symbiont in promoting thermal tolerance of the holobiont, using Antillogorgia bipinnata (octocoral host) and Breviolum antillogorgium (symbiont) as a model system. We identified five distinct genotypes of B. antillogorgium from symbiont populations isolated from Antillogorgia colonies in the Florida Keys. Three symbiont genotypes were cultured and maintained at 26 °C (ambient historical temperature), and two were cultured and maintained at 30 °C (elevated historical temperature) for 2 yrs. We analyzed the growth rate and carrying capacity of each symbiont genotype at both ambient and elevated temperatures in culture (in vitro). All genotypes grew well at both temperatures, indicating that thermal tolerance exists among these B. antillogorgium cultures. However, a history of long-term growth at 30 °C did not yield better performance for B. antillogorgium at 30 °C (as compared to 26 °C), suggesting that prior culturing at the elevated temperature did not result in increased thermal tolerance. We then inoculated juvenile A. bipinnata polyps with each of the five symbiont genotypes and reared these polyps at both ambient and elevated temperatures (in hospite experiment). All genotypes established symbioses with polyps in both temperature treatments. Survivorship of polyps at 30 °C was significantly lower than survivorship at 26 °C, but all treatments had surviving polyps at 56 d post-infection. Our results suggest broad thermal tolerance in B. antillogorgium, which may play a part in the increased resilience of Caribbean octocorals during heat stress events.

Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree–species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.

Coral reef ecosystems are under threat from the frequent and severe impacts of anthropogenic climate change, particularly rising sea surface temperatures. The effects of thermal stress may be ameliorated by adaptation and/or acclimation of the host, symbiont, or holobiont (host + symbiont) to increased temperatures. We examined the role of the symbiont in promoting thermal tolerance of the holobiont, using Antillogorgia bipinnata (octocoral host) and Breviolum antillogorgium (symbiont) as a model system. We identified five distinct genotypes of B. antillogorgium from symbiont populations isolated from A. bipinnata colonies. Three symbiont genotypes were maintained at 26°C (ambient historical temperature) and two were maintained at 30°C (elevated historical temperature) for two years. We analyzed the in vitro growth rate and carrying capacity of each genotype at both ambient and elevated temperatures. All genotypes grew well at both temperature treatments, indicating thermal tolerance among these B. antillogorgium genotypes. We also inoculated juvenile A. bipinnata polyps with each of the five symbiont genotypes, and reared these polyps at both ambient and elevated temperatures. All genotypes were able to infect polyps at both temperature treatments. Survivorship of polyps at 30°C was significantly lower than survivorship at 26°C, but all treatments had surviving polyps at 56 days post-infection, suggestive of broad-scale thermal tolerance in this system. The widespread thermal tolerance observed in B. antillogorgium may play a part in the increased resilience of Caribbean octocorals during heat stress events.

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Fishes of the family Catostomidae (“suckers”; Teleostei: Cypriniformes) are hypothesized to have undergone an allopolyploidy event approximately 60 million years ago. However, genomic evidence has previously been unavailable to assess this hypothesis. We sequenced and assembled the first chromosome-level catostomid genome, Chinese sucker (Myxocyprinus asiaticus), and present clear evidence of a catostomid-specific whole genome duplication (WGD) event (“Cat-4R”). Our results reveal remarkably-strong, conserved synteny since this duplication event, as well as between Myxocyprinus and an unduplicated outgroup, zebrafish (Danio rerio). Gene content and repetitive elements are also approximately evenly distributed across homeologous chromosomes, suggesting that both sub-genomes retain some function, with no obvious bias in gene fractionation or sub-genome dominance. The Cat-4R duplication provides another independent example of genome evolution following WGD in animals, in this case at the extreme end of conserved genome architecture over at least 25.2 million years since the duplication. The Myxocyprinus asiaticus genome is a useful resource for researchers interested in understanding genome evolution following WGD in animals.

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Octocorals are conspicuous members of coral reefs and deep-sea ecosystems. Yet, species boundaries and taxonomic relationships within this group remain poorly understood, hindering our understanding of this essential component of the marine fauna. We used a multifaceted approach to revisit the systematics of the Caribbean octocorals Plexaura homomalla and Plexaura kükenthali, two taxa that have a long history of taxonomic revisions. We integrated morphological and reproductive analyses with high-throughput sequencing technology to clarify the relationship between these common gorgonians. Although size and shape of the sclerites are significantly different, there is overlap in the distributions making identification based on sclerites alone difficult. Differences in reproductive timing and mode of larval development were detected, suggesting possible mechanisms of pre-zygotic isolation. Furthermore, there are substantial genetic differences and clear separation of the two species in nuclear introns and single-nucleotide polymorphisms obtained from de novo assembled transcriptomes. Despite these differences, analyses with SNPs suggest that hybridization is still possible between the two groups. The two nascent species also differed in their symbiont communities (genus Breviolum) across multiple sampling sites in the Caribbean. Despite a complicated history of taxonomic revisions, our results support the differentiation of P. homomalla and P. kükenthali, emphasizing that integrative approaches are essential for Anthozoan systematics.