Aim Isolation by distance (IBD) analyses are an effective tool for determining genetic connectivity among populations, providing a basis for estimating dispersal and thus contributing to spatial biodiversity planning. Here, we use an IBD approach to determine patterns of connectivity to infer dispersal distances for a phylogenetically diverse range of marine species. Location Two thousand and eight hundred kilometre of South African coastline. Methods mtDNA data sets for 11 rocky shore and reef‐dwelling marine species with diverse life history strategies (broadcast spawning, brooding and live‐bearing) were used to quantify intraspecific genetic connectivity by means of global and pairwise Φst. Mantel tests were used to assess the significance of genetic structure with geographic distance. Significant, positive slopes were used to estimate dispersal distances. For all species, we also plotted genetic diversity along the coast and compared this to patterns of species richness. Results For seven of the 11 species tested, we report positive IBD relationships, with patterns of IBD of similar magnitude in broadcast spawners and live‐bearers. Dispersal estimates were low, with effective distances of < 10 km per generation. We find discordance between pelagic larval development and population structure and that genetic structure and the physio‐geographic features of the coastline considered to be important biogeographic barriers do not overlap. Genetic diversity and species richness show congruent patterns, with both variables lowest on the west coast, and increasing towards the east. Main conclusions Our study highlights the complexity of marine systems and the clear need for regional assessments of connectivity, rather than more general management plans which may not otherwise effectively encompass area‐specific conservation needs. Importantly, we show that the current marine protected area (MPA) network in South Africa is not effective in protecting evolutionary processes and strongly recommend a network of more closely spaced MPAs in the region that reflects the low average connectivity between distant marine populations.

A common way of illustrating phylogeographic results is through the use of haplotype networks. While these networks help to visualize relationships between individuals, populations, and species, evolutionary studies often only quantitatively analyze genetic diversity among haplotypes and ignore other network properties. Here, we present a new metric, haplotype network branch diversity (HBd), as an easy way to quantifiably compare haplotype network complexity. Our metric builds off the logic of combining genetic and topological diversity to estimate complexity previously used by the published metric haplotype network diversity (HNd). However, unlike HNd which uses a combination of network features to produce complexity values that cannot be defined in probabilistic terms, thereby obscuring the values’ implication for a sampled population, HBd uses frequencies of haplotype classes to incorporate topological information of networks, keeping the focus on the population and providing easy-to-interpret probabilistic values for randomly sampled individuals. The goal of this study is to introduce this more intuitive metric and provide an R script that allows researchers to calculate diversity and complexity indices from haplotype networks. A group of datasets, generated manually (model dataset) and based on published data (empirical dataset), were used to illustrate the behavior of HBd and both of its terms, haplotype diversity, and a new index called branch diversity. Results followed a predicted trend in both model and empirical datasets, from low metric values in simple networks to high values in complex networks. In short, the new combined metric joins genetic and topological diversity of haplotype networks, into a single complexity value. Based on our analysis, we recommend the use of HBd, as it makes direct comparisons of network complexity straightforward and provides probabilistic values that can readily discriminate situations that are difficult to resolve with available metrics.

Pricklebacks (Family Stichaeidae) are generally cold-temperate fishes most commonly found in the north Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Monkeyface Prickleback, Cebidichthys violaceus, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on forthcoming population genomic data. The genome of C. violaceus is typical of many marine fishes at less than 1Gb (genome size = 575.6 Mb), and our assembly is near-chromosome level (contig N50 = 1 Mb, scaffold N50 = 16.4 Mb, BUSCO completeness = 93.2%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects, enhancing our knowledge of the population structure of the species and more generally, the efficacy of Marine Protected Areas as a primary conservation tool across California’s marine ecosystems.

Sculpins (Family Cottidae) are generally cold-temperate intertidal reef fishes most commonly found in the North Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Woolly Sculpin, Clinocottus analis, to establish a genomic model for understanding phylogeographic structure of inshore marine taxa along the California coast. These patterns, in turn, should further inform the design of marine protected areas using dispersal models based on genomic data. The small genome of C. analis is typical of marine fishes at less than 1 Gb (genome size = 538 Mb), and our assembly is near-chromosome level (contig N50 = 9.1 Mb, scaffold N50 = 21 Mb, BUSCO completeness = 97.9%). Within the context of the CCGP, the Woolly Sculpin genome will be used as a reference for future whole genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of Marine Protected Areas across the state.