title: Genomic variation among populations of threatened coral: Acropora cervicornis.
abstract: BACKGROUND
  Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species' ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef Tract (FRT) and in the Dominican Republic.
  
  
  RESULTS
  Genotyping by Sequencing (GBS) identified 4,764 single nucleotide polymorphisms (SNPs). Pairwise nucleotide differences (π) within a population are large (~37 %) and similar to π across all individuals. This high level of genetic diversity along the FRT is similar to the diversity within a small, isolated reef. Much of the genetic diversity (>90 %) exists within a population, yet GBS analysis shows significant variation along the FRT, including 300 SNPs with significant FST values and significant divergence relative to distance. There are also significant differences in SNP allele frequencies over small spatial scales, exemplified by the large FST values among corals collected within Miami-Dade county.
  
  
  CONCLUSIONS
  Large standing diversity was found within each population even after recent declines in abundance, including significant, potentially adaptive divergence over short distances. The data here inform conservation and management actions by uncovering population structure and high levels of diversity maintained within coral collections among sites previously shown to have little genetic divergence. More broadly, this approach demonstrates the power of GBS to resolve differences among individuals and identify subtle genetic structure, informing conservation goals with evolutionary implications.
authors.affiliation: Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
authors.forename: C
authors.initials: C
authors.lastname: Drury
authors.affiliation: Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
authors.forename: K E
authors.initials: KE
authors.lastname: Dale
authors.affiliation: Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
authors.forename: J M
authors.initials: JM
authors.lastname: Panlilio
authors.affiliation: Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
authors.forename: S V
authors.initials: SV
authors.lastname: Miller
authors.affiliation: Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
authors.forename: D
authors.initials: D
authors.lastname: Lirman
authors.affiliation: Nova Southeastern University Oceanographic Center, 8000 N Ocean Drive, Dania Beach, FL, 33004, USA.
authors.forename: E A
authors.initials: EA
authors.lastname: Larson
authors.affiliation: Center for Coral Reef Research, Mote Marine Laboratory, 24244 Overseas Highway, Summerland Key, FL, 33042, USA.
authors.forename: E
authors.initials: E
authors.lastname: Bartels
authors.affiliation: Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
authors.forename: D L
authors.initials: DL
authors.lastname: Crawford
authors.affiliation: Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA. moleksiak@rsmas.miami.edu.
authors.forename: M F
authors.initials: MF
authors.lastname: Oleksiak
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000235:genetics*; D003247:Conservation of Natural Resources; D004293:Dominican Republic; D056727:Endangered Species; D005431:Florida; D014644:Genetic Variation; D005828:Genetics, Population; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: Coral reefs; Florida reef tract; Genotyping by sequencing; Population genomics; Restoration genetics