The application of genetics to marine management and conservation: examples from the Indo-Pacific

Molecular tools and analyses have played pivotal roles in uncovering the processes and patterns of biodiversity in the Indian and Pacific oceans. However, integrating genetic results into management and conservation objectives has been challenging, with few examples that show practical applicability. This review aims to address some of the perceived barriers to an enhanced approach that integrates molecular data into management and conservation goals, by reviewing papers relevant to both conservation and fisheries management in the Indo-Pacific region, particularly with respect to phylogeography, connectivity, and species identification, as well as stock delineation, restoration of depleted wild stocks, mislabeled marine resources and "molecular forensics." We also highlight case studies from each of these areas that illustrate how molecular analyses are relevant to conservation and management in the Indo- Pacific, spanning a variety of vertebrate and invertebrate species. We discuss the application of genetic data to the design and evaluation of the effectiveness of marine protected area networks, stock delineation, and restoration and the usage of exclusion tests and parentage analyses for fisheries management. We conclude that there is a distinct need for increasing public awareness and ownership of genetically unique lineages and, ultimately, the increased inclusion of genetic research into management policy and conservation. Finally, we make a case for the importance of clear and effective communication for promoting public awareness, public ownership, and for achieving conservation goals within the region

Siganus fuscescens_Microsat_Genotypes_RRGotanco et al 2017

Microsatellite genotype data in csv format. Data collected from 12 microsatellite loci for 343 individuals. File description in the first row. Locus names are in the second row. Individual names are in the first column, followed by alleles.Alleles are coded as fragment sizes, in separate columns. Missing data are indicated by ‘?.

Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabra

The genotype data used for the assignment analyses provided as a GenePop file (.gen

Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea

Abstract Connectivity of marine populations is shaped by complex interactions between biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications for the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (FST = 0.0057, p < .001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p < .001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating significant contribution of asymmetric ocean currents to neutral genetic variation (Radj2 = 0.133, p = .035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (Ne < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p < .001), significantly correlated with sea surface temperature variabilities during peak spawning months for S. olivacea (Radj2 = 0.692–0.763; p < .050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of S. olivacea across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly dispersive marine species, and provides information useful for spatial management of the fishery resource

Genetic diversity and stock delineation of Philippine populations of the orange mud crab, Scylla olivacea

Abstract only.The orange mud crab, Scylla olivacea, is regarded as an important fishery resource due to high demand and high market value. However, mud crab populations are threatened by over exploitation and habitat degradation, and would benefit from resource management interventions. The study examined patterns of genetic diversity and connectivity of orange mud crab populations across the Philippines, with the aim of identifying putative management units. A total of 387 Scylla olivacea were collected from ten localities across the Philippine archipelago. Phylogenetic analysis of mitochondrial control region (mtDNA-CR) DNA sequences revealed cryptic diversity among Scylla olivacea specimens with four mitochondrial lineages recovered. Analysis of molecular variance revealed that Philippine populations do not constitute a single genetic stock (0ST=0.00262; P=0.00015). Thirteen microsatellite loci were also utilized as additional markers to infer population structure and estimate genetic variation. Overall, S. olivacea populations exhibit high haplotype diversity (mean h=0.9803) and nucleotide diversity (mean ~p3.46%), which may be indicative of a large, stable population within Philippine archipelagic waters. This study provides information on genetic diversity and population structure of S. olivacea, which will be useful towards developing management and conservation strategies for sustainable development of natural S. olivacea populations in the Philippines

Data from: Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region

Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markers

Abstract Morphologically cryptic and pseudo-cryptic species pose a challenge to taxonomic identification and assessments of species diversity and distributions. Such is the case for the sea cucumber Stichopus horrens, commonly confused with Stichopus monotuberculatus. Here, we used mitochondrial cytochrome oxidase subunit I (COI) and microsatellite markers to examine genetic diversity in Stichopus cf. horrens throughout the Philippine archipelago, to aid species identification and clarify species boundaries. Phylogenetic analysis reveals two recently diverged COI lineages (Clade A and Clade B; c. 1.35–2.54 Mya) corresponding to sequence records for specimens identified as S. monotuberculatus and S. horrens, respectively. Microsatellite markers reveal two significantly differentiated genotype clusters broadly concordant with COI lineages (Cluster 1, Cluster 2). A small proportion of individuals were identified as later-generation hybrids indicating limited contemporary gene flow between genotype clusters, thus confirming species boundaries. Morphological differences in papillae distribution and form are observed for the two species, however tack-like spicules from the dorsal papillae are not a reliable diagnostic character. An additional putative cryptic species was detected within Clade B-Cluster 2 specimens warranting further examination. We propose that these lineages revealed by COI and genotype data be referred to as Stichopus cf. horrens species complex

Comparison of genotype cluster assignment and mtDNA lineage membership for <i>Siganus fuscescens</i> individuals.

<p>Each individual is represented by a vertical bar where the apportion of ancestry is represented by segments of different colors corresponding to different mitochondrial lineages and nuclear genotype clusters. Individuals with mixed ancestry are indicated by different colors corresponding to the inferred proportion of ancestry in a particular group. (a) MtDNA lineage membership; (b) Assignment to nuclear genotype cluster based on correspondence analysis; (c) Individual ancestry coefficient (<i>q</i>) inferred from STRUCTURE analysis when <i>K</i> = 2; (d) Individual ancestry coefficient (<i>q</i>) inferred from STRUCTURE analysis when <i>K</i> = 3. Putative hybrids are marked (‘h’).</p

Seawater carbonate chemistry and survival, growth rate, zooxanthellae density, maximum photosynthetic efficiency of Favites colemani

Tropical coral reefs are threatened by local-scale stressors that are exacerbated by global ocean warming and acidification from the post-industrial increase of atmospheric CO2 levels. Despite their observed decline in the past four decades, little is known on how Philippine coral reefs will respond to ocean warming and acidification. This study explored individual and synergistic effects of present-day (pH 8.0, 28°C) and near-future (pH 7.7, 32°C) scenarios of ocean temperature and pH on the adult Favites colemani, a common massive reef-building coral in Bolinao-Anda, Philippines. Changes in seawater temperature drive the physiological responses of F. colemani, whereas changes in pH create an additive effect on survival, growth, and photosynthetic efficiency. Under near-future scenarios, F. colemani showed sustained photosynthetic competency despite the decline in growth rate and zooxanthellae density. F. colemani exhibited specificity with the Cladocopium clade C3u. This coral experienced lower growth rates but survived projected near-future ocean warming and acidification scenarios. Its pH-thermal stress threshold is possibly a consequence of acclimation and adaptation to local environmental conditions and past bleaching events. This research highlights the importance of examining the susceptibility and resilience of Philippine corals to climate-driven stressors for future conservation and restoration efforts in the changing ocean

Isolation-with-migration analysis of mtDNA control region sequences for three pairwise comparisons of nuclear genotype clusters (Cluster 1, Cluster 2A, Cluster 2B) in <i>Siganus fuscescens</i> from the northern Philippines and Hong Kong.

<p>Isolation-with-migration analysis of mtDNA control region sequences for three pairwise comparisons of nuclear genotype clusters (Cluster 1, Cluster 2A, Cluster 2B) in <i>Siganus fuscescens</i> from the northern Philippines and Hong Kong.</p