Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida Keys Reef Tract

Abstract

Broadcast-spawning coral species have wide geographical ranges spanning strong environmental gradients, but it is unclear how much spatially varying selection these gradients actually impose. Strong divergent selection might present a considerable barrier for demographic exchange between disparate reef habitats. We investigated whether the cross-shelf gradient is associated with spatially varying selection in two common coral species, Montastraea cavernosa and Siderastrea siderea, in the Florida Keys. To this end, we generated a de novo genome assembly for M. cavernosa and used 2bRAD to genotype 20 juveniles and 20 adults of both species from each of the three reef zones to identify signatures of selection occurring within a single generation.Unexpectedly, each species was found to be composed of four genetically distinct lineages, with gene flow between them still ongoing but highly reduced in 13.0%-54.7% of the genome. Each species includes two sympatric lineages that are only found in the deep (20 m) habitat, while the other lineages are found almost exclusively on the shallower reefs (3-10 m). The two "shallow" lineages of M. cavernosa are also specialized for either nearshore or offshore: comparison between adult and juvenile cohorts indicates that cross-shelf migrants are more than twice as likely to die before reaching adulthood than local recruits. S. siderea and M. cavernosa are among the most ecologically successful species on the Florida Keys Reef Tract, and this work offers important insight into the genomic background of divergent selection and environmental specialization that may in part explain their resilience and broad environmental range.

Phylogeography and Taxonomic Revision of the Pen Shell Atrina pectinata Species Complex in the South China Sea

“…This divergence rate is just a rough approximation, causing our estimates of absolute time and population size values to be unreliable. However, the fold-change in Ne and the relative placement of expansions and declines along the temporal axis do not depend on these assumptions and can therefore be evaluated more reliably (Rippe et al, 2021). In our previous study (Xue et al, 2014), the population demographic expansion of A. japonica started approximately 160,000 years ago assuming an mtCOI divergence rate of 2.4%/Myr, which was earlier than those of A. lischkeana (90,000 years ago), Atrina sp.…”

“…Two scenarios may potentially account for this distribution pattern: (1) sympatric speciation, in which the speciation process was unrelated to geographic isolation, or (2) pen shells may have originated in tropical regions and expanded their ranges from southern to northern regions after glaciation, giving rise to new lineages/species (Kim et al, 2017). Recently, sympatric speciation has come to be understood as a major generator of marine biodiversity, but it remains among the most controversial evolutionary processes (Quesada et al, 2007;Bowen et al, 2013;Richards et al, 2019). Nearly all existing case studies of sympatric speciation involve some form of automatic magic traits, such as assortative mating by habitat, along a depth gradient, or environment-induced phenology shifts (Richards et al, 2019).…”

“…Recently, sympatric speciation has come to be understood as a major generator of marine biodiversity, but it remains among the most controversial evolutionary processes (Quesada et al, 2007;Bowen et al, 2013;Richards et al, 2019). Nearly all existing case studies of sympatric speciation involve some form of automatic magic traits, such as assortative mating by habitat, along a depth gradient, or environment-induced phenology shifts (Richards et al, 2019). However, there is little information on any magic traits associated with the three sympatric pen shell species considered herein, and genomic, physiological, environmental, morphological and reproductive datasets must be combined to reveal speciation mechanisms.…”

Alphaflexivirus Genomes in Stony Coral Tissue Loss Disease-Affected, Disease-Exposed, and Disease-Unexposed Coral Colonies in the U.S. Virgin Islands

“… b Reads not mapping to coral or Symbiodiniaceae transcriptomes and retained for further analysis using BBSplit (within BBMap v38.90) ( 9 ). A genome-guided M. cavernosa transcriptome was generated using the draft genome from reference 10 , and de novo Porites astreoides and Pseudodiploria strigosa transcriptomes were assembled using Trinity v2.11.0 ( 11 ). These reference transcriptomes were generated by the Mydlarz lab (University of Texas at Arlington, Arlington, TX, USA) for internal use but will be made available upon request.…”

Adaptive variation in homologue number within transcript families promotes expression divergence in reef‐building coral

“…Genome-derived predicted gene models were obtained from the O. faveolata assembly on NCBI (assembly ofav_dov_v1) (Prada et al, 2016), while for M. cavernosa a draft genome assembly is available (Rippe et al, 2021), and we chose to use this genome assembly to generate a genome-guided transcriptome assembly for M. cavernosa. Reads from our five M. cavernosa colonies were mapped to the draft genome with the read mapping program tophat2 (Kim et al, 2013) using default parameters.…”