Theory suggests that pairs of mutualist species will often co-disperse and share the same dispersal patterns, though the extent to which this happens remains unclear. Photosynthetic corals constitute an example of this dynamic, as they rely on algal symbionts to meet their energetic needs, yet many acquire their symbionts environmentally after their larval dispersal phase. Consequently, corals and their symbionts may exhibit similar or contrasting patterns of genetic variation across the seascape, with implications for their evolutionary and ecological processes. Here, we densely sample corals of the key reef-building taxon Acropora cf. tenuis and their algal symbionts across a reefscape in the central Philippines to examine genetic variation across space. Four distinct coral taxa show genetic evidence of long-distance dispersal, including weak or absent isolation by distance signals and parent-offspring pairs at widely spaced sites. These coral taxa all host a single group of algal symbionts from the genus Cladocopium, which shows landscape genetic structure independent from its coral hosts. In fact, Cladocopium genetics vary with both latitude and depth, potentially indicating genome-wide local adaptation at a finer spatial scale than that seen in their hosts. Genetic variation at markedly different spatial scales between host and symbiont may be beneficial for hosts if these differences enable them to acquire symbionts adapted to their settlement environments.

Field sampling was conducted from January to April 2016 across 47 sites in the Visayas region of the central Philippines, including areas surrounding the Camotes Sea and Cebu Strait. Sites were distributed across Cebu Province, including Cebu Island (n = 27 sites) and the Camotes Islands (n = 5), as well as Leyte Province (n = 15). Sites were selected to be approximately 10 km apart to capture ecologically relevant dispersal distances and enable testing for isolation by distance patterns in the study region. At each site, we characterized benthic cover using line point intercept transects. Three 15 m transects were deployed haphazardly parallel to shore, and the bottom type was recorded at 20 cm intervals along each transect. Following benthic surveys, we collected tissue samples from Acropora cf. tenuis colonies at each site. To locate colonies, we conducted a separate belt transect survey at each site by swimming parallel to shore within a 2 m wide belt for approximately one hour or until 20 samples were collected. During these surveys, we measured the maximum length, width, and depth of every A. cf. tenuis colony encountered and recorded the time of collection. We collected small tissue samples (approximately 2 cm × 2 cm) from 20 colonies per site, ensuring that sampled colonies were spaced at least 10 m apart to avoid resampling the same genet. Detailed close-up photographs were taken of each collected specimen.