1 Introduction

Considering the spatial patterns and scales of dispersal, population connectivity has key implications for management and conservation (Moritz, 1994, Palumbi, 2003). For marine organisms, connectivity is primarily driven by complex interactions between life history characteristics and environmental conditions which influence the dynamics and persistence of populations (Cowen and Sponaugle, 2009). The absence of apparent physical barriers in the ocean combined with high dispersal potentials characteristic of most marine organisms shaped the paradigm of genetic homogeneity in the marine environment (Hauser and Carvalho, 2008). Advances in DNA sequencing technologies now provide the ability to interrogate genetic variation genome-wide, providing adequate resolution to study population genetic processes (Davey et al., 2011, Andrews et al., 2016). High-throughput genotyping of single nucleotide polymorphisms (SNPs) employing restriction-site associated DNA sequencing approaches (RAD-sequencing; Baird et al., 2008) is a widely-used approach having several variants, e.g ddRAD (Peterson et al., 2012), 2b-RAD (Wang et al., 2012), and ezRAD (Toonen et al., 2013). Genetic approaches, coupled with increased capabilities in numerical modeling to simulate and track larval dispersal in the marine environment (reviewed in Swearer et al., 2019), have resulted in considerable interest and wide use of seascape genomics approaches to examine the processes that shape genetic variation in the marine environment (Riginos and Liggins, 2013, Selkoe et al., 2016).
Seascape genomics studies have improved our understanding of the environmental conditions influencing population connectivity and the spatial distribution of genetic variation in the ocean. The ability to interrogate population diversity using thousands of SNPs, and to identify loci which may be under the influence of selection versus neutral loci (Davey et al., 2011, Gagnaire et al., 2015) allows the examination of environmental factors and their influence on genetic structure. There is a growing body of literature documenting genetic structure either due to neutral variation or adaptive polymorphisms, at finer spatial scales than expected from species dispersal potentials. Recent studies have reported environmental factors influencing neutral and adaptive genetic variation, among them: ocean currents (Benestan et al., 2016, Gilg and Hilbish, 2003, Lal et al., 2017, Paterno et al., 2017, Riginos et al., 2019, Schunter et al., 2011, Teske et al., 2016, Truelove et al., 2017, Van Wyngaarden et al., 2018, Xuereb et al., 2018), temperature  (Wang et al. 2013; Chu et al. 2014, Sandoval-Castillo et al. 2018, Hoey and Pinsky 2018), and salinity (Sjöqvist et al., 2015).
Mud crabs (genus: Scylla de Haan, 1833) are commercially important species with a wide distribution in mangrove areas throughout the Indo-West Pacific and other tropical and subtropical regions (Alberts-Hubatsch et al., 2015). Three mud crab species occur in the Philippines (S. olivacea, S. tranquebarica, and S. serrata), with S. olivacea (Herbst, 1796) being the most abundant (Lebata et al., 2007). While adult mud crabs exhibit limited movement (Hyland et al., 1984), larvae are thought to be highly dispersive due to their long pelagic larval duration (PLD) of 20 to 30 days (Jantrarotai et al., 2002, Motoh et al., 1977, Thirunavukkarasu et al., 2014), which can extend up to 75 days depending on environmental conditions (Baylon, 2010). Although ocean currents may play a huge role in larval dispersal and settlement success (Cowen and Sponaugle, 2009), survival and development of mud crab larvae strongly depends on water temperature and salinity (Baylon, 2011, Hamasaki, 2003, Hill, 1974, Nurdiani and Zeng, 2007). In the Sulu Sea basin, S. olivacea populations are distributed along regions influenced by temporally-varying environmental gradients (Oppo et al., 2003) and complex sea surface circulation such as the southward-flowing Sulu Sea throughflow from the South China Sea, the westward-flowing Bohol Sea current exiting via the Dipolog strait, and the southern Sulu Sea gyre (Han et al., 2009, Hurlburt et al., 2011). Oceanographic features in the Sulu Sea have been suggested to act as barriers to gene flow among populations for other taxa with relatively lower dispersal potentials than S. olivacea such as the seahorse Hippocampus spinosissimus (Lourie et al., 2005), damselfish Dascyllus aruanus (Raynal et al., 2014) and sea cucumber Holuthuria scabra (Ravago-Gotanco and Kim, 2019). There is limited information however, on the genetic structure of Philippine populations of S. olivacea, with one study reporting weak but significant genetic differentiation of Philippine populations based on microsatellite loci (Paran and Ravago-Gotanco, 2017). Moreover, there are no studies to date that explicitly examined the influence of asymmetric ocean currents and environmental heterogeneity on population connectivity and genetic structure of a highly dispersive species in the Sulu Sea.
This study examined patterns of connectivity among populations of the orange mud crab (S. olivacea) in the Sulu Sea basin. Using a seascape genomics approach, we aimed to (1) characterize genetic structure of S. olivacea across the Sulu Sea and examine spatial patterns of genetic connectivity using SNP markers generated by RADseq; (2) examine the influence of oceanographic circulation on genetic structure and connectivity of S. olivacea populations in the Sulu Sea; and (3) examine the SNP dataset for signatures of local adaptation which may be correlated with other environmental factors. First we developed a biophysical model of larval dispersal parameterized using the life-history characteristics of S. olivacea, to generate realistic predictions of larval dispersal and connectivity in the Sulu Sea. We combined larval dispersal estimates with empirical genetic observations at neutral loci to determine the influence of asymmetric ocean currents on spatial patterns of connectivity. Second, we performed analyses to recover loci putatively under selection to examine signatures of local adaptation. We assessed the potential impact of environmental factors, specifically sea surface temperature and rainfall (as a proxy for salinity) on adaptive divergence of S. olivacea. This study provides valuable insights into the spatial scales of dispersal, patterns of genetic structure, and the influence of environmental and evolutionary processes on population connectivity of S. olivacea in the Sulu Sea basin. The results provide information useful to support the development of management and conservation strategies for the fishery resource.