Seascape genomics reveals fine‐scale patterns of dispersal for a reef fish along the ecologically divergent coast of Northwestern Australia

Abstract

Understanding the drivers of dispersal among populations is a central topic in marine ecology and fundamental for spatially explicit management of marine resources. The extensive coast of Northwestern Australia provides an emerging frontier for implementing new genomic tools to comparatively identify patterns of dispersal across diverse and extreme environmental conditions. Here, we focused on the stripey snapper (Lutjanus carponotatus), which is important to recreational, charter-based and customary fishers throughout the Indo-West Pacific. We collected 1,016 L. carponotatus samples at 51 locations in the coastal waters of Northwestern Australia ranging from the Northern Territory to Shark Bay and adopted a genotype-by-sequencing approach to test whether realized connectivity (via larval dispersal) was related to extreme gradients in coastal hydrodynamics. Hydrodynamic simulations using CONNIE and a more detailed treatment in the Kimberley Bioregion provided null models for comparison. Based on 4,402 polymorphic single nucleotide polymorphism loci shared across all individuals, we demonstrated significant genetic subdivision between the Shark Bay Bioregion in the south and all locations within the remaining, more northern bioregions. More importantly, we identified a zone of admixture spanning a distance of 180 km at the border of the Kimberley and Canning bioregions, including the Buccaneer Archipelago and adjacent waters, which collectively experiences the largest tropical tidal range and some of the fastest tidal currents in the world. Further testing of the generality of this admixture zone in other shallow water species across broader geographic ranges will be critical for our understanding of the population dynamics and genetic structure of marine taxa in our tropical oceans.

Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula

“…Genome‐wide single nucleotide polymorphisms (SNPs), generated by restriction site‐associated DNA sequencing (RAD‐seq), have proven valuable for studying divergence driven by natural selection in model fishes adapted to freshwater (cichlids, Wagner et al, 2013) and euryhaline environments (threespine stickleback, Hohenlohe et al, 2010), and a number of nonmodel reef fishes (Beltrán, Schizas, Appeldoorn, & Prada, 2017; Bernal, Gaither, Simison, & Rocha, 2017; DiBattista, Travers, et al, 2017; Gould & Dunlap, 2017; Harrison et al, 2017; Picq, McMillan, & Puebla, 2016; Puebla, Bermingham, & McMillan, 2014; Stockwell et al, 2016). Using RAD‐seq technology, Gaither et al (2015) demonstrated that the strongest signals of selection in a widespread surgeonfish ( Acanthurus olivaceus ) were associated with divergent environmental conditions in a peripheral population.…”

Random PCR‐based genotyping by sequencing technology GRAS‐Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes

“…The number of SNPs is an important factor for genetic analysis because analyses with a large number of SNPs often increase the power to detect population structure, which cannot be unveiled with a limited number of molecular markers (Attard et al, 2018;Weiss, Weigand, Weigand, & Leese, 2018). This is typically the case for marine organisms, where geographically distant populations are often connected via passive larval dispersal, making it difficult to detect genetic differentiation with few SNPs (Carreras et al, 2017;DiBattista et al, 2017;Vendrami et al, 2017). Moreover, this method is expected to be tolerant to degraded DNA samples as it utilizes short amplicons.…”

Genetic population structure of the convict surgeonfish Acanthurus triostegus: a phylogeographic reassessment across its range

“…However, the relationship between PLD and genetic population structure is not straightforward (Selkoe et al ., ), as a positive correlation between the two is reported in some studies (Gaither et al ., , ), but not in others (Barber et al ., ; Weersing & Toonen, ). This ambiguity suggests that larval dispersal in marine species is not only influenced by PLD but also local oceanographic current conditions (DiBattista et al ., ; Otwoma & Kochzius, ), larval behaviour (Fisher et al ., ) and historical processes (Otwoma & Kochzius, ).…”