Search

Scleractinian corals are the main modern builders of coral reefs, which are major hot spots of marine biodiversity. Southern Atlantic reef corals are understudied compared to their Caribbean and Indo‐Pacific counterparts and many hypotheses about their population dynamics demand further testing. We employed thousands of single nucleotide polymorphisms (SNPs) recovered via ezRAD to characterize genetic population structuring and species boundaries in the amphi‐Atlantic hard coral genus Favia. Coalescent‐based species delimitation (BFD* – Bayes Factor Delimitation) recovered F. fragum and F. gravida as separate species. Although our results agree with depth‐related genetic structuring in F. fragum, they did not support incipient speciation of the 'tall' and 'short' morphotypes. The preferred scenario also revealed a split between two main lineages of F. gravida, one from Ascension Island and the other from Brazil. The Brazilian lineage is further divided into a species that occurs throughout the Northeastern coast and another that ranges from the Abrolhos Archipelago to the state of Espírito Santo. BFD* scenarios were corroborated by analyses of SNP matrices with varying levels of missing data and by a speciation‐based delimitation approach (DELINEATE). Our results challenge current notions about Atlantic reef corals because they uncovered surprising genetic diversity in Favia and rejected the long‐standing hypothesis that Abrolhos Archipelago may have served as a Pleistocenic refuge during the last glaciations. [ABSTRACT FROM AUTHOR]

The diversity and distribution of marine species in eastern Australia is influenced by one of the world's strongest western boundary currents, the East Australia Current, which propels water and propagules poleward, a flow intensifying due to climate change.Population genetic structure of the asterinid sea star Meridiastra calcar was investigated across its range in eastern Australia (12° of latitude, 2,500 km) from northern New South Wales to its poleward‐extending range in Tasmania at the southern edge influence of the East Australia Current.Population structure and connectivity of M. calcar were examined across six bioregions using six microsatellite loci (nuclear DNA) and the control region (mitochondrial DNA). The potential influence of the extent of M. calcar's intertidal rock platform habitat was also assessed.Genetic structure analysis indicated that the Hawkesbury Shelf contained distinct genetic clusters, whereas the two sites in the Batemans Shelf differed from each other, with Jervis Bay Marine Park having just one genetic cluster. The Manning Shelf, Twofold Shelf, and Bruny bioregions all had similar genetic composition.Strong self‐seeding (68–98%) was indicated by microsatellite loci for all bioregions, with lower (0.3–6.5%) migration between bioregions. Poleward (New South Wales to Tasmania) migration was low except from the Manning Shelf (30%).Contemporary population connectivity and genetic structure of M. calcar appear to be influenced by ocean currents, habitat distribution, and its short planktonic larval duration, which was a minimum of 12–14 days, depending on availability of a settlement cue.The dominance of unique genetic groups in the Hawkesbury bioregion shows the importance of this region for M. calcar and possibly a diversity of co‐distributed rock platform species. This highlights how important it is to have a large marine park in the Hawkesbury bioregion, which is presently lacking. [ABSTRACT FROM AUTHOR]

Seagrass habitats are declining worldwide, placing several seagrass‐associated animals at risk of extinction. The Critically Endangered limpet Siphonaria compressa is one of the rarest molluscs in Africa, and has been reported from only two disjunctive lagoons in South Africa. Being a highly specialized grazer that lives exclusively on the narrow blades of Cape eelgrass, Zostera capensis, which is itself listed as Endangered in the South African Red List and has decreased in abundance, conservation initiatives are urgently needed to ensure the long‐term survival of S. compressa.Molecular data (sequence data from the mitochondrial genome and single nucleotide polymorphism data of the nuclear genome) and morphological data were analysed to determine whether the two populations are conspecific, with implications for whether translocation between localities could be a viable management strategy to restore either population in the event of a collapse, or to maintain the genetic diversity of each population.Strong evidence emerged for the distinctness of the two populations, including a lack of shared mtDNA haplotypes that indicate an absence of contemporary gene flow, a divergence time that dates to the late Pleistocene, and a number of morphological characters that distinguish their shells. These findings indicate that the two populations are distinct cryptic subspecies.As the two populations occur in different temperature‐defined marine biogeographical regions, they are probably adapted to different thermal environments. Translocations are not recommended, as this management strategy has considerable potential to result in outbreeding depression and exacerbate the extinction risk. Instead, each population should be managed separately, and several alternative conservation measures are discussed, including the protection and restoration of seagrass beds. [ABSTRACT FROM AUTHOR]

The gap between spawning and settlement location of marine fishes, where the larvae occupy an oceanic phase, is a great mystery in both natural history and conservation. Recent genomic approaches provide some resolution, especially in linking parent to offspring with assays of nucleotide polymorphisms. Here, the authors applied this method to the endemic Hawaiian convict tang (Acanthurus triostegus sandvicensis), a surgeonfish with a long pelagic larval stage of c. 54–77 days. They collected 606 adults and 607 juveniles from 23 locations around the island of Oʻahu, Hawaiʻi. Based on 399 single nucleotide polymorphisms, the authors assigned 68 of these juveniles back to a parent (11.2% assignment rate). Each side of the island showed significant population differentiation, with higher levels in the west and north. The west and north sides of the island also had little evidence of recruitment, which may be due to westerly currents in the region or an artefact of uneven sampling. In contrast, the majority of juveniles (94%) sampled along the eastern shore originated on that side of the island, primarily within semi‐enclosed Kāneʻohe Bay. Nearly half of the juveniles assigned to parents were found in the southern part of Kāneʻohe Bay, with local settlement likely facilitated by extended water residence time. Several instances of self‐recruitment, when juveniles return to their natal location, were observed along the eastern and southern shores. Cumulatively, these findings indicate that most dispersal is between adjacent regions on the eastern and southern shores. Regional management efforts for Acanthurus triostegus and possibly other reef fishes will be effective only with collaboration among adjacent coastal communities, consistent with the traditional moku system of native Hawaiian resource management. [ABSTRACT FROM AUTHOR]

Giant clams are ecologically important, benefitting species of all trophic levels. But numerous populations have declined drastically in numbers due to past intensive exploitation that led to their listing in both CITES Appendix II and IUCN Red List of Threatened Species. However, giant clams are notoriously difficult to identify, and recent molecular work has revealed that morphological misidentification of giant clams have confounded current population assessments and extinction risk. The most recent study of the status of giant clams in the Samoan Archipelago was published in a journal over 20 years ago, without molecular corroboration of visual identifications. Using morphologic characteristics and ezRAD genetic techniques, we identify the existence of Tridacna noae in the Samoan Archipelago, presenting the first observation and a resulting range expansion. Accurately identifying the extant species in the archipelago is the first step toward a much‐needed population status assessment to effectively manage these long‐lived species. [ABSTRACT FROM AUTHOR]

Fish have one of the highest occurrences of individual specialization in trophic strategies among Eukaryotes. Yet, few studies characterize this variation during trophic niche analysis, limiting our understanding of aquatic food web dynamics. Stable isotope analysis (SIA) with advanced Bayesian statistics is one way to incorporate this individual trophic variation when quantifying niche size. However, studies using SIA to investigate trophodynamics have mostly focused on species‐ or guild‐level (i.e., assumed similar trophic strategy) analyses in settings where source isotopes are well‐resolved. These parameters are uncommon in an ecological context. Here, we use Stable Isotope Bayesian Ellipses in R (SIBER) to investigate cross‐guild trophodynamics of 11 reef fish species within an oceanic atoll. We compared two‐ (δ15N and δ13C) versus three‐dimensional (δ15N, δ13C, and δ34S) reconstructions of isotopic niche space for interpreting guild‐, species‐, and individual‐level trophic strategies. Reef fish isotope compositions varied significantly among, but also within, guilds. Individuals of the same species did not cluster together based on their isotope values, suggesting within‐species specializations. Furthermore, while two‐dimensional isotopic niches helped differentiate reef fish resource use, niche overlap among species was exceptionally high. The addition of δ34S and the generation of three‐dimensional isotopic niches were needed to further characterize their isotopic niches and better evaluate potential trophic strategies. These data suggest that δ34S may reveal fluctuations in resource availability, which are not detectable using only δ15N and δ13C. We recommend that researchers include δ34S in future aquatic food web studies. [ABSTRACT FROM AUTHOR]

Novel methodologies now make it possible to track the complete geographical movements of seafood species from reproduction to human consumption. Doing so will better inform consumers and assist resource managers in matching fisheries and conservation policies with natural borders and pathways, including stock boundaries, networks of marine protected areas, and fisheries management areas. Such mapping necessitates an unprecedented synthesis of natural and social sciences, including knowledge of adult fish population abundance and movements, egg output, larval dispersal, and recruitment to juvenile and adult habitats, as well as fisheries stock assessment, capture, and distribution through human social networks. The challenge is to fully integrate oceanography, population genetics, ecology, and social sciences with fisheries biology to reveal the patterns and mechanisms of "Fish Flow" from spawning to supper. As practitioners representing all five of these disciplines, we believe that Fish Flow analyses will promote sustainable fisheries management and marine conservation efforts, and may foster public knowledge, wise seafood choices, and appreciation of social–ecological interconnections involving fisheries. [ABSTRACT FROM AUTHOR]

Corals obtain nutrition from the photosynthetic products of their algal endosymbionts and the ingestion of organic material and zooplankton from the water column. Here, we use stable carbon (δ13C) and nitrogen (δ15N) isotopes to assess the proportionate contribution of photoautotrophic and heterotrophic sources to seven Hawaiian coral species collected from six locations around the island of O'ahu, Hawaiʻi. We analyzed the δ13C and δ15N of coral tissues and their algal endosymbionts, as well as that of dissolved inorganic matter, particulate organic matter, and zooplankton from each site. Estimates of heterotrophic contribution varied among coral species and sites. Bayesian mixing models revealed that heterotrophic sources (particulate organic material and zooplankton) contributed the most to Pocillopora acuta and Montipora patula coral tissues at 49.3% and 48.0%, respectively, and the least to Porites lobata at 28.7%, on average. Estimates of heterotrophic contribution based on the difference between δ13C of the host and algal endosymbiont (δ13Ch–e) and isotopic niche overlap often differed, while estimates based on δ15Nh–e were slightly more aligned with the estimates produced using Bayesian mixing models. These findings suggest that the utility of each approach may vary with coral health status, regions, and coral species. Overall, we find that the mean heterotrophic contribution to Hawaiian coral tissues ranges from 20% to 50%, suggesting a variety of trophic strategies. However, these findings did not always match past direct measurements of heterotrophic feeding, indicating that heterotrophically acquired nutrition does not necessarily get incorporated into tissues but can be respired or exuded in mucus. [ABSTRACT FROM AUTHOR]

Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA‐based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome‐db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards‐compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology. [ABSTRACT FROM AUTHOR]

The extent to which populations persist under environmental stress depends on the reproductive output of individuals that survive the stress. In coral systems, corals bleach in response to stress from elevated water temperature. However, little is known of the extent to which thermal stress impairs the reproductive capacity of the survivors over the following years, limiting the capacity to predict how populations will persist in the Anthropocene.Using histology to quantify the abundance and size of oocytes and spermaries per polyp, we tested how bleaching impairs the reproductive response of the coral Pocillopora meandrina over two reproductive seasons following the 2015 mass bleaching event in the Hawaiian Islands.We found that smaller colonies not only had a greater probability of bleaching but also suffered greater reproductive impacts over a longer time. In contrast, larger colonies generated comparable reproductive output regardless of bleaching severity, although bleached colonies generated smaller oocytes the year after bleaching.These results show that reproductive impacts of bleaching are more complex and size‐specific than commonly assumed. Therefore, estimates of bleaching mortality may underestimate the true impact of thermal stress on populations, especially as populations lose larger individuals from repeated and co‐occurring stressors. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

Aim: To test hypothesized biogeographic partitions of the tropical Indo‐Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo‐Pacific Ocean. Time period: Pliocene through the Holocene. Major taxa studied: Fifty‐six marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo‐Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise ΦST with a distance‐based redundancy analysis (dbRDA). Results: We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographic or environmental barriers other than distance. Main conclusions: Although there is support for three previously described barriers, phylogeographic discordance in the Indo‐Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo‐Pacific species, even hard vicariance for tens of thousands of years can yield ΦST values that range from 0 to nearly 0.5. [ABSTRACT FROM AUTHOR]

Assessing the geographic structure of populations has relied heavily on Sewell Wright's F‐statistics and their numerous analogues for many decades. However, it is well appreciated that, due to their nonlinear relationship with gene flow, F‐statistics frequently fail to reject the null model of panmixia in species with relatively high levels of gene flow and large population sizes. Coalescent genealogy samplers instead allow a model‐selection approach to the characterization of population structure, thereby providing the opportunity for stronger inference. Here, we validate the use of coalescent samplers in a high gene flow context using simulations of a stepping‐stone model. In an example case study, we then re‐analyze genetic datasets from 41 marine species sampled from throughout the Hawaiian archipelago using coalescent model selection. Due to the archipelago's linear nature, it is expected that most species will conform to some sort of stepping‐stone model (leading to an expected pattern of isolation by distance), but F‐statistics have only supported this inference in ~10% of these datasets. Our simulation analysis shows that a coalescent sampler can make a correct inference of stepping‐stone gene flow in nearly 100% of cases where gene flow is ≤100 migrants per generation (equivalent to FST = 0.002), while F‐statistics had mixed results. Our re‐analysis of empirical datasets found that nearly 70% of datasets with an unambiguous result fit a stepping‐stone model with varying population sizes and rates of gene flow, although 37% of datasets yielded ambiguous results. Together, our results demonstrate that coalescent samplers hold great promise for detecting weak but meaningful population structure, and defining appropriate management units. [ABSTRACT FROM AUTHOR]

Life-history traits, especially the mode and duration of larval development, are expected to strongly influence the population connectivity and phylogeography of marine species. Comparative analysis of sympatric, closely related species with differing life histories provides the opportunity to specifically investigate these mechanisms of evolution but have been equivocal in this regard. Here, we sample two sympatric sea stars across the same geographic range in temperate waters of Australia. Using a combination of mitochondrial DNA sequences, nuclear DNA sequences, and microsatellite genotypes, we show that the benthic-developing sea star, Parvulastra exigua, has lower levels of within- and among-population genetic diversity, more inferred genetic clusters, and higher levels of hierarchical and pairwise population structure than Meridiastra calcar, a species with planktonic development. While both species have populations that have diverged since the middle of the second glacial period of the Pleistocene, most P. exigua populations have origins after the last glacial maxima ( LGM), whereas most M. calcar populations diverged long before the LGM. Our results indicate that phylogenetic patterns of these two species are consistent with predicted dispersal abilities; the benthic-developing P. exigua shows a pattern of extirpation during the LGM with subsequent recolonization, whereas the planktonic-developing M. calcar shows a pattern of persistence and isolation during the LGM with subsequent post-Pleistocene introgression. [ABSTRACT FROM AUTHOR]

Aim To resolve phylogeographical partitions in the pronghorn spiny lobster, Panulirus penicillatus, which has a nine-month pelagic larval phase and the broadest distribution among spiny lobsters. With samples from the Red Sea to the East Pacific, we test genetic partitions across two-thirds of the planet, in a species with one of the longest pelagic phases. Location Red Sea, Indian and Pacific Oceans. Methods A fragment of the mt DNA cytochrome c oxidase subunit I gene ( COI) was resolved in 774 individuals from 28 locations, plus 55 sequences (10 locations) from public databases. Portions of COI, 12S and 16S mt DNA regions were resolved for phylogenetic analyses on a subset of individuals. Phylogenetic and population-level analyses were used to detect evolutionary partitions and dispersal barriers. Results Significant population structuring was detected (overall ΦST = 0.310, P < 0.001). Samples from the Red Sea and East Pacific Provinces (western and eastern range edges) comprise distinct phylogenetic lineages, divergent at d = 1.1% and 1.8%, respectively, from the Indo-Pacific. Coalescent analyses indicate a Pleistocene isolation for the Red Sea (0.71 Ma) and East Pacific (1.52 Ma). Excluding the Red Sea and East Pacific, structure across the rest of the range was comparatively low, but significant (ΦST = 0.018, P < 0.001). Main conclusions The Red Sea and East Pacific populations are phylogenetically distinct from populations elsewhere in the range. The East Pacific population diverged earliest, and may represent a distinct subspecies. Phylogeographical divisions align with the major Indo-Pacific biogeographical barriers, and with subsets of provincial designations from two frameworks: one based on levels of endemism and one on species composition. Tropical and temperate regions in the Pacific are significantly differentiated, potentially indicating an ecological partition. Isolation at eastern and western peripheral provinces may serve as a starting point for evolutionary diversification within this group. [ABSTRACT FROM AUTHOR]

Aim The Red Sea is characterised by a unique fauna and historical periods of desiccation, hypersalinity and intermittent isolation. The origin and contemporary composition of reef-associated taxa in this region can illuminate biogeographical principles about vicariance and the establishment (or local extirpation) of existing species. Here we aim to: (1) outline the distribution of shallow water fauna between the Red Sea and adjacent regions, (2) explore mechanisms for maintaining these distributions and (3) propose hypotheses to test these mechanisms. Location Red Sea, Gulf of Aden, Arabian Sea, Arabian Gulf and Indian Ocean. Methods Updated checklists for scleractinian corals, fishes and non-coral invertebrates were used to determine species richness in the Red Sea and the rest of the Arabian Peninsula and assess levels of endemism. Fine-scale diversity and abundance of reef fishes within the Red Sea were explored using ecological survey data. Results Within the Red Sea, we recorded 346 zooxanthellate and azooxanthellate scleractinian coral species of which 19 are endemic (5.5%). Currently 635 species of polychaetes, 211 echinoderms and 79 ascidians have been documented, with endemism rates of 12.6%, 8.1% and 16.5% respectively. A preliminary compilation of 231 species of crustaceans and 137 species of molluscs include 10.0% and 6.6% endemism respectively. We documented 1071 shallow fish species, with 12.9% endemic in the entire Red Sea and 14.1% endemic in the Red Sea and Gulf of Aden. Based on ecological survey data of endemic fishes, there were no major changes in species richness or abundance across 1100 km of Saudi Arabian coastline. Main conclusions The Red Sea biota appears resilient to major environmental fluctuations and is characterized by high rates of endemism with variable degrees of incursion into the Gulf of Aden. The nearby Omani and Arabian Gulfs also have variable environments and high levels of endemism, but these are not consistently distinct across taxa. The presence of physical barriers does not appear to explain species distributions, which are more likely determined by ecological plasticity and genetic diversity. [ABSTRACT FROM AUTHOR]

We quantified benthic community structure on shallow (10 m isobath) reefs separated by 3-130 km on four islands in the south Pacific, and evaluated the roles of disturbances vs. coral recruitment as causes of spatial heterogeneity. Reefs were surveyed in 2013 on Moorea, Tahiti, Tetiaroa, and Maiao, with community structure sampled at two sites on each island using photoquadrats. The effects of coral recruitment on population structure were evaluated through genetic analyses of Pocillopora on three of the islands. Benthic community structure with functional group resolution differed among islands and generally among sites, but coral community structure (generic resolution) differed among islands, but generally not among sites. Genetic analyses of Pocillopora using the open reading frame of host mtDNA revealed varying relative abundances of Pocillopora meandrina/Pocillopora eydouxi, Pocillopora verrucosa, Pocillopora effuses, and two unnamed haplotypes on each island. These results suggest that corals on each island represent unique samplings of genetically discrete larval assemblages rather than random samplings of a single larval assemblage. Together, our findings emphasize the extent to which coral community structure varies over a scale of <200 km, and suggests that recruitment from spatially discrete pools of coral larvae plays an important role in creating spatial variation in community structure, even where reefs are connected by prevailing currents. [ABSTRACT FROM AUTHOR]

Aim The geological and palaeo-climatic forces that produced the unique biodiversity in the Red Sea are a subject of vigorous debate. Here, we review evidence for and against the hypotheses that: (1) Red Sea fauna was extirpated during glacial cycles of the Pleistocene and (2) coral reef fauna found refuge within or just outside the Red Sea during low sea level stands when conditions were inhospitable. Location Red Sea and Western Indian Ocean. Methods We review the literature on palaeontological, geological, biological and genetic evidence that allow us to explore competing hypotheses on the origins and maintenance of shallow-water reef fauna in the Red Sea. Results Palaeontological (microfossil) evidence indicates that some areas of the central Red Sea were devoid of most plankton during low sea level stands due to hypersaline conditions caused by almost complete isolation from the Indian Ocean. However, two areas may have retained conditions adequate for survival: the Gulf of Aqaba and the southern Red Sea. In addition to isolation within the Red Sea, which separated the northern and southern faunas, a strong barrier may also operate in the region: the cold, nutrient-rich water upwelling at the boundary of the Gulf of Aden and the Arabian Sea. Biological data are either inconclusive or support these putative barriers and refugia, but no data set, that we know of rejects them. Genetic evidence suggests that many endemic lineages diverged from their Indian Ocean counterparts long before the most recent glaciations and/or are restricted to narrow areas, especially in the northern Red Sea. Main conclusions High endemism observed in the Red Sea and Gulf of Aden appears to have multiple origins. A cold, nutrient-rich water barrier separates the Gulf of Aden from the rest of the Arabian Sea, whereas a narrow strait separates the Red Sea from the Gulf of Aden, each providing potential isolating barriers. Additional barriers may arise from environmental gradients, circulation patterns and the constriction at the mouth of the Gulf of Aqaba. Endemics that evolved within the Red Sea basin had to survive glacial cycles in relatively low salinity refugia. It therefore appears that the unique conditions in the Red Sea, in addition to those characteristics of the Arabian Peninsula region as a whole, drive the divergence of populations via a combination of isolation and selection. [ABSTRACT FROM AUTHOR]

In this age of data-driven science and high-throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long-standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373-389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context-specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade-offs that are not obvious to the uninitiated. [ABSTRACT FROM AUTHOR]

We are writing in response to the population and phylogenomics meeting review by Andrews & Luikart () entitled 'Recent novel approaches for population genomics data analysis'. Restriction-site-associated DNA ( RAD) sequencing has become a powerful and useful approach in molecular ecology, with several different published methods now available to molecular ecologists, none of which can be considered the best option in all situations. A& L report that the original RAD protocol of Miller et al. () and Baird et al. () is superior to all other RAD variants because putative PCR duplicates can be identified (see Baxter et al. ), thereby reducing the impact of PCR artefacts on allele frequency estimates (Andrews & Luikart ). In response, we (i) challenge the assertion that the original RAD protocol minimizes the impact of PCR artefacts relative to that of other RAD protocols, (ii) present additional biases in RADseq that are at least as important as PCR artefacts in selecting a RAD protocol and (iii) highlight the strengths and weaknesses of four different approaches to RADseq which are a representative sample of all RAD variants: the original RAD protocol (mb RAD, Miller et al. ; Baird et al. ), double digest RAD (dd RAD, Peterson et al. ), ez RAD (Toonen et al. ) and 2b RAD (Wang et al. ). With an understanding of the strengths and weaknesses of different RAD protocols, researchers can make a more informed decision when selecting a RAD protocol. [ABSTRACT FROM AUTHOR]

Hybridization in the ocean was once considered rare, a process prohibited by the rapid evolution of intrinsic reproductive barriers in a high-dispersal medium. However, recent genetic surveys have prompted a reappraisal of marine hybridization as an important demographic and evolutionary process. The Hawaiian Archipelago offers an unusual case history in this arena, due to the recent arrival of the widely distributed Indo-Pacific sergeant ( Abudefduf vaigiensis), which is hybridizing with the endemic congener, A. abdominalis. Surveys of mt DNA and three nuclear loci across Hawai'i ( N = 396, Abudefduf abdominalis and N = 314, A. vaigiensis) reveal that hybridization is significantly higher in the human-perturbed southeast archipelago (19.8%), tapering off to 5.9% in the pristine northwest archipelago. While densities of the two species varied throughout Hawai'i, hybridization was highest in regions with similar species densities, contradicting the generalization that the rarity of one species promotes interspecific mating. Our finding of later generation hybrids throughout the archipelago invokes the possibility of genetic swamping of the endemic species. Exaptation, an adaptation with unintended consequences, may explain these findings: the endemic species has transient yellow coloration during reproduction, whereas the introduced species has yellow coloration continuously as adults, in effect a permanent signal of reproductive receptivity. Haplotype diversity is higher in Hawaiian A. vaigiensis than in our samples from the native range, indicating large-scale colonization almost certainly facilitated by the historically recent surge of marine debris. In this chain of events, marine debris promotes colonization, exaptation promotes hybridization, and introgression invokes the possible collapse of an endemic species. [ABSTRACT FROM AUTHOR]

Copyright of Conservation Biology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global FST. Pelagic larval duration ( PLD) was not a strong predictor of variation in population structure ( R2 = 0.22), but accounting for higher FST values of chaotic and invertebrate species, compared to regionally structured and fish species, doubled the power of PLD to explain variation in global FST (adjusted R2 = 0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e. fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawaìi marine species may be generated by demographic variability due to species-specific abundance and migration patterns and/or seascape and historical factors. [ABSTRACT FROM AUTHOR]

Aim To explore the spatial and temporal genetic structure of four tropical hermit crabs in the genus Calcinus with varying habitat use in order to test for impacts of sea-level change and demography in shaping contemporary population structure and to understand how this structure relates to the process of speciation in the genus. Location Central Pacific. Methods We sequenced 586 bp of the cytochrome c oxidase subunit I gene ( COI) ( n = 702) and analysed the data for population differentiation and demographic changes. We complemented the sequences with abundance surveys of targeted species and modelled potential habitat availability in response to sea-level change. Results Sequence data revealed high haplotype diversity ( h = 0.685-0.983) and low nucleotide diversity (π = 0.002-0.018) for all species. There was little population differentiation and extensive geographical haplotype sharing within all species, despite dramatic shifts in the abundance of species among locations, which appear to result from ecological interactions rather than limits to contemporary larval dispersal. Population expansion occurred most recently in the subtidal species Calcinus haigae (30-70 ka), whereas the intertidal species showed earlier expansions: Calcinus seurati: 110-140 ka, and Calcinus laevimanus: 220-250 ka. Differences in timing can be linked to the prediction that subtidal habitat area is strongly affected by changing sea level, while intertidal habitat area is affected less strongly. Interestingly, unlike the West Pacific, habitat in the Central Pacific remains relatively equidistant. Main conclusions Habitat availability during sea-level fluctuations, rather than dispersal limitation per se, appears to be a potential force shaping the population genetic patterns of subtidal species, and perhaps speciation of tropical Calcinus hermit crabs. Insofar as this represents a general pattern, historical sea-level change may play a role in structuring Central Pacific reef species through alteration of habitat availability rather than isolation and vicariance. [ABSTRACT FROM AUTHOR]

We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster ( Panulirus interruptus) and find slight, but significant global population differentiation in mt DNA (ΦST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites ( FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo- F16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance ( P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites ( Dest_Chao, R2 = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity ( R2 = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low FST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal. [ABSTRACT FROM AUTHOR]

The susceptibility of the Y chromosome to sexual selection may make this chromosome an important player in the formation of reproductive isolating barriers, and ultimately speciation. Here, we investigate the role of the Y chromosome in phenotypic divergence and reproductive isolation of spinner dolphin ( Stenella longirostris) ecotypes. This species contains six known ecotypes (grouped into four subspecies) that exhibit striking differences in morphology, habitat and mating system, despite having adjacent or overlapping ranges and little genetic divergence at previously studied mt DNA and autosomal markers. We examined the phylogeographic structure for all six ecotypes across the species range ( n = 261, 17 geographic locations) using DNA sequences from three Y chromosome markers, two maternally inherited mitochondrial (mt DNA) markers, and a biparentally inherited autosomal intron. mt DNA and autosomal analyses revealed low divergence (most ΦST values <0.1) between ecotypes and geographic regions, concordant with previous studies. In contrast, Y intron analyses revealed fixed differences amongst the three most phenotypically divergent groups: S. l. longirostris vs. S. l. roseiventris vs. combined S. l. orientalis/ S. l. centroamericana/Tres Marias ecotypes). Another ecotype (whitebelly), previously postulated to be a hybrid between the two phenotypically most divergent ecotypes, had Y haplotypes from both putative parent ecotypes, supporting a hybrid designation. Reduced introgression of the Y chromosome has previously been observed in other organisms ranging from insects to terrestrial mammals, and here we demonstrate this phenomenon in a marine mammal with high dispersal capabilities. These results indicate that reduced introgression of the Y chromosome occurs in a wide taxonomic range of organisms and support the growing body of evidence that rapid evolution of the Y chromosome is important in evolutionary diversification. [ABSTRACT FROM AUTHOR]

Aim Phylogeographic analyses have confirmed high dispersal in many marine taxa but have also revealed many cryptic lineages and species, raising the question of how population and regional genetic diversity arise and persist in dynamic oceanographic settings. Here we explore the geographic evolution of Emerita analoga, an inter-tidal sandy beach crab with an exceptionally long pelagic larval phase and wide latitudinal, amphitropical, distribution. We test the hypothesis that eastern Pacific E. analoga constitute a single panmictic population and examine the location(s), timing and cause(s) of phylogeographic differentiation. Location Principally the eastern Pacific Ocean. Methods Wesequenced cytochrome c oxidase subunit I (COI) from 742 E. analoga specimens collected between 1997 and 2000 and downloaded homologoussequences of congeners from GenBank. We reconstructed a phylogeny for Emerita species using maximum likelihood and Bayesian methods and estimated times to most recent common ancestors (TMRCAs), using a COI divergence rate of 1% Myr)1 and timing of closure of the Central American Seaway. We constructed the COI haplotype network of E. analoga using statistical parsimony, calculated population genetic and spatial structure statistics in Arlequin, and estimated the demographic history of E. analoga using Bayesian skyline analysis. Results Population subdivision and allele frequency differences were insignificant among north-eastern Pacific locations over 2000 km apart (FST = 0.00, P = 0.70), yet two distinct phylogroups were recovered from the north-eastern and southeastern Pacific (FCT = 0.87, P < 0.001). Amphitropical differentiation of these temperate clades occurred after TMRCA1.9 ± 0.02 (mean ±± SE)Maand E. analoga has expanded into its present-day north-eastern Pacific range since c. 250 ka. Main conclusions Emerita analoga is not panmictic but is very widely dispersed and approaching genetic homogeneity, i.e. 'eurymixis', in the north-eastern Pacific. North-eastern and south-eastern Pacific populations of E. analoga probably became isolated c. 1.5 Ma as the tropical eastern Pacific Ocean warmed and expanded, intensifying barriers to gene flow. The fragmentation of a widespread ancestral species previously connected by long-distance gene flow ('soft vicariance') coincident with changing oceanographic conditions may be a common theme in the evolution of Emerita species and in other highly dispersive taxa. Highly dispersive species may differentiate because of, not despite, the dynamic oceanographic setting. [ABSTRACT FROM AUTHOR]

. Black corals (Cnidaria: Antipatharia) are ecologically important members of the sessile invertebrate fauna, but due to their typical deep-water environments (>50 m), very little is known about their basic biology, including reproduction. We used histological techniques to examine the sexual reproduction of members of eight species of antipatharians collected from the Hawaiian Islands over a wide depth range (10-1327 m). Gametes of all species examined were found in association with the primary transverse mesenteries, which in some cases reached into the cavity of lateral tentacles. Specimens contained either spermatocysts or oocytes, but never both within the same individual, suggesting either a gonochoric or a sequentially hermaphroditic mode of reproduction. No developing embryos or larvae were observed in any of the samples, indicating that fertilization and larval development likely occur externally in the water column and not internally within polyps. We compared our results with previously published information on the sexual reproduction of antipatharians. Our review suggests that in antipatharians, more generally, (1) entire colonies are either female or male (although sequential hermaphroditism cannot be ruled out in most cases and has been reported previously for one species), (2) gametes are confined to the primary transverse mesenteries in most species, and (3) there is no evidence of internal fertilization. Further studies are needed to determine whether gonochorism or sequential hermaphroditism is more prevalent within the Antipatharia, whether dimorphic polyps occur within this taxonomic order, and to examine the reproductive seasonality and larval behavior of individual species. [ABSTRACT FROM AUTHOR]

Speciation remains a central enigma in biology, and nowhere is this more apparent than in shallow tropical seas where biodiversity rivals that of tropical rainforests. Obvious barriers to gene flow are few and most marine species have a highly dispersive larval stage, which should greatly decrease opportunities for speciation via geographic isolation. The disparity in the level of geographic isolation for terrestrial and marine species is exemplified in Hawai'i where opportunities for allopatric speciation abound in the terrestrial realm. In contrast, marine colonizers of Hawai'i are believed to produce only a single endemic species or population, due to the lack of isolating barriers. To test the assertion that marine species do not diversify within Hawai'i, we examine the evolutionary origin of three endemic limpets ( Cellana exarata, C. sandwicensis and C. talcosa) that are vertically segregated across a steep ecocline on rocky shores. Analyses of three mtDNA loci (12S, 16S, COI; 1565 bp) and two nDNA loci (ATPSβ, H3; 709 bp) in 26 Indo-Pacific Cellana species ( N = 414) indicates that Hawai'i was colonized once ∼3.4-7.2 Ma from the vicinity of Japan. Trait mapping demonstrates that high-shore residence is the ancestral character state, such that mid- and low-shore species are the product of subsequent diversification. The Hawaiian Cellana are the first broadcast-spawners demonstrated to have speciated within any archipelago. The habitat stratification, extensive sympatry, and evolutionary history of these limpets collectively indicate a strong ecological component to speciation and support the growing body of evidence for non-allopatric speciation in the ocean. [ABSTRACT FROM AUTHOR]

Copyright of Conservation Biology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

There is an ongoing debate on the scale of pelagic larval dispersal in promoting connectivity among populations of shallow, benthic marine organisms. The linearly arranged Hawaiian Islands are uniquely suited to study scales of population connectivity and have been used extensively as a natural laboratory in terrestrial systems. Here, we focus on Hawaiian populations of the lobe coral Porites lobata, an ecosystem engineer of shallow reefs throughout the Pacific. Patterns of recent gene flow and population structure in P. lobata samples ( n = 318) from two regions, the Hawaiian Islands ( n = 10 sites) and from their nearest neighbour Johnston Atoll, were analysed with nine microsatellite loci. Despite its massive growth form, ∼6% of the samples from both regions were the product of asexual reproduction via fragmentation. Cluster analysis and measures of genetic differentiation indicated that P. lobata from the Hawaiian Islands are strongly isolated from those on Johnston Atoll ( F = 0.311; P < 0.001), with the descendants of recent migrants ( n = 6) being clearly identifiable. Within the Hawaiian Islands, P. lobata conforms to a pattern of isolation by distance. Here, over 37% ( P = 0.001) of the variation in genetic distance was explained by geographical distance. This pattern indicates that while the majority of ongoing gene flow in Hawaiian P. lobata occurs among geographically proximate reefs, inter-island distances are insufficient to generate strong population structure across the archipelago. [ABSTRACT FROM AUTHOR]

Marine species frequently show weak and/or complex genetic structuring that is commonly dismissed as ‘chaotic’ genetic patchiness and ecologically uninformative. Here, using three datasets that individually feature weak chaotic patchiness, we demonstrate that combining inferences across species and incorporating environmental data can greatly improve the predictive value of marine population genetics studies on small spatial scales. Significant correlations in genetic patterns of microsatellite markers among three species, kelp bass Paralabrax clathratus, Kellet’s whelk Kelletia kelletii and California spiny lobster Panulirus interruptus, in the Southern California Bight suggest that slight differences in diversity and pairwise differentiation across sampling sites are not simply noise or chaotic patchiness, but are ecologically meaningful. To test whether interspecies correlations potentially result from shared environmental drivers of genetic patterns, we assembled data on kelp bed size, sea surface temperature and estimates of site-to-site migration probability derived from a high resolution multi-year ocean circulation model. These data served as predictor variables in linear models of genetic diversity and linear mixed models of genetic differentiation that were assessed with information–theoretic model selection. Kelp was the most informative predictor of genetics for all three species, but ocean circulation also played a minor role for kelp bass. The shared patterns suggest a single spatial marine management strategy may effectively protect genetic diversity of multiple species. This study demonstrates the power of environmental and ecological data to shed light on weak genetic patterns and highlights the need for future focus on a mechanistic understanding of the links between oceanography, ecology and genetic structure. [ABSTRACT FROM AUTHOR]

A half century ago the State of Hawaii began a remarkable, if unintentional, experiment on the population genetics of introduced species, by releasing 2431 Bluestriped Snappers ( Lutjanus kasmira) from the Marquesas Islands in 1958 and 728 conspecifics from the Society Islands in 1961. By 1992 L. kasmira had spread across the entire archipelago, including locations 2000 km from the release site. Genetic surveys of the source populations reveal diagnostic differences in the mtDNA control region ( d = 3.8%; φST = 0.734, P < 0.001) and significant allele frequency differences at nuclear DNA loci ( FST = 0.49; P < 0.001). These findings, which indicate that source populations have been isolated for approximately half a million years, set the stage for a survey of the Hawaiian Archipelago ( N = 385) to determine the success of these introductions in terms of genetic diversity and breeding behaviour. Both Marquesas and Society mtDNA lineages were detected at each survey site across the Hawaiian Archipelago, at about the same proportion or slightly less than the original 3.4:1 introduction ratio. Nuclear allele frequencies and parentage tests demonstrate that the two source populations are freely interbreeding. The introduction of 2431 Marquesan founders produced only a slight reduction in mtDNA diversity (17%), while the 728 Society founders produced a greater reduction in haplotype diversity (41%). We find no evidence of genetic bottlenecks between islands of the Hawaiian Archipelago, as expected under a stepping-stone model of colonization, from the initial introduction site. This species rapidly colonized across 2000 km without loss of genetic diversity, illustrating the consequences of introducing highly dispersive marine species. [ABSTRACT FROM AUTHOR]

Spinner dolphins ( Stenella longirostris) exhibit different social behaviours at two regions in the Hawaiian Archipelago: off the high volcanic islands in the SE archipelago they form dynamic groups with ever-changing membership, but in the low carbonate atolls in the NW archipelago they form long-term stable groups. To determine whether these environmental and social differences influence population genetic structure, we surveyed spinner dolphins throughout the Hawaiian Archipelago with mtDNA control region sequences and 10 microsatellite loci ( n = 505). F-statistics, Bayesian cluster analyses, and assignment tests revealed population genetic separations between most islands, with less genetic structuring among the NW atolls than among the SE high islands. The populations with the most stable social structure (Midway and Kure Atolls) have the highest gene flow between populations (mtDNA ΦST < 0.001, P = 0.357; microsatellite FST = −0.001; P = 0.597), and a population with dynamic groups and fluid social structure (the Kona Coast of the island of Hawai’i) has the lowest gene flow (mtDNA 0.042 < ΦST < 0.236, P < 0.05; microsatellite 0.016 < FST < 0.040, P < 0.001). We suggest that gene flow, dispersal, and social structure are influenced by the availability of habitat and resources at each island. Genetic comparisons to a South Pacific location ( n = 16) indicate that Hawaiian populations are genetically depauperate and isolated from other Pacific locations (mtDNA 0.216 < FST < 0.643, P < 0.001; microsatellite 0.058 < FST < 0.090, P < 0.001); this isolation may also influence social and genetic structure within Hawai’i. Our results illustrate that genetic and social structure are flexible traits that can vary between even closely-related populations. [ABSTRACT FROM AUTHOR]

Aim In the Indo-Pacific, the mass of islands of the Indonesian archipelago constitute a major biogeographical barrier (the Indo-Pacific Barrier, IPB) separating the Pacific and Indian oceans. Evidence for other, more localized barriers include high rates of endemism at the Marquesas and other isolated peripheral islands in the Pacific. Here we use mitochondrial-sequence comparisons to evaluate the efficacy of biogeographical barriers on populations of the snappers Lutjanus kasmira and Lutjanus fulvus across their natural ranges. Location Pacific and Indian oceans. Methods Mitochondrial cytochrome b sequence data were obtained from 370 individuals of L. kasmira and 203 individuals of L. fulvus collected from across each species’ range. Allele frequency data for two nuclear introns were collected from L. kasmira. Phylogenetic and population-level analyses were used to determine patterns of population structure in these species and to identify barriers to dispersal. Results Lutjanus kasmira lacks genetic structure across the IPB and throughout 12,000 km of its central Indo-Pacific range. In contrast, L. fulvus demonstrates high levels of population structure at all geographical scales. In both species, highly significant population structure results primarily from the phylogenetic distinctiveness of their Marquesas Islands populations ( L. kasmira, d = 0.50–0.53%; L. fulvus, d = 0.87–1.50%). Coalescence analyses of the L. kasmira data indicate that populations at opposite ends of its range (western Indian Ocean and the Marquesas) are the oldest. Coalescence analyses for L. fulvus are less robust but also indicate colonization from the Indian to the Pacific Ocean. Main conclusions The IPB does not act as a biogeographical barrier to L. kasmira, and, in L. fulvus, its effects are no stronger than isolating mechanisms elsewhere. Both species demonstrate a strong genetic break at the Marquesas. Population divergence and high endemism in that archipelago may be a product of geographical isolation enhanced by oceanographic currents that limit gene flow to and from those islands, and adaptation to unusual ecological conditions. Lutjanus kasmira shows evidence of Pleistocene population expansion throughout the Indo-central Pacific that originated in the western Indian Ocean rather than the Marquesas, further demonstrating a strong barrier at the latter location. [ABSTRACT FROM AUTHOR]

The article presents a study on the evaluation of anthropogenic threats to the Northwestern Hawaiian Islands (NWHI) in Hawaii. It states that NWHI make up one of the most isolated and remote ecosystems in the world, and is subjected to many anthropogenic threats. The study employed a standardized and systematic method in collecting and quantitatively synthesizing expert opinion on the ecological effects anthropological threats to the Papahānaumokuākea Marine National Monument in NWHI. It provides details on the reasons behind the particular ranking of threats, and why the ranking may vary across ecological landscapes. An overview of the methodology and the survey statistics is also offered.

The marine environment offers few obvious barriers to dispersal for broadcast-spawning species, yet population genetic structure can occur on a scale much smaller than the theoretical limits of larval dispersal. Comparative phylogeographical studies of sympatric sister species can illuminate how differences in life history, behaviour, and habitat affinity influence population partitioning. Here we use a mitochondrial DNA marker (612 bp of cytochrome c oxidase subunit I) to investigate population structure of three endemic Hawaiian broadcast-spawning limpets ( Cellana spp.) with planktonic larvae that are competent to settle within 4 days. All three species exhibit significant population structure and isolation by distance, but the spatial scales of partitioning differ among the species. Cellana talcosa ( n = 105) exhibits strong population structure between Kauai and the other main Hawaiian Islands (MHI) where the maximum channel width is 117 km, and no shared haplotypes were observed (ΦCT = 0.30, P<0.001). In contrast, populations of Cellana exarata ( n = 149) and Cellana sandwicensis ( n = 109) exhibit weaker population structure within the MHI (ΦST = 0.03–0.04, P<0.05), and between the MHI and the Northwestern Hawaiian Islands (ΦST = 0.03–0.09, P<0.01), where the maximum channel width is 260 km. Biogeographical range and microhabitat use were correlated with estimates of dispersal, while phylogenetic affiliation and minimum pelagic larval duration were poor predictors of population partitioning. Despite similar life histories, these closely related limpets have contrasting patterns of population structure, illustrating the danger of relying on model species in management initiatives to predict population structure and dispersal in the context of marine protected area delineation. [ABSTRACT FROM AUTHOR]

We developed five degenerate primer pairs for the amplification and sequencing of two noncoding regions found in the mitochondrial genome of corals. These primers amplify products ranging from 380 to 950 bp, and work in a wide variety of scleractinian taxa from both the Pacific and Caribbean. Based on our initial analysis of ∼300 sequences from 13 scleractinian taxa, both these noncoding regions appear to have equivalent levels of variability to the most variable of previously published coral mitochondrial loci, but work in a wider variety of taxa. We believe these primers will be of use to coral biologists studying questions above the level of species; as with other mithochondrial DNA markers in corals, these loci will likely provide little resolution for within-species studies. [ABSTRACT FROM AUTHOR]

Recent improvements in genetic analysis and genotyping methods have resulted in a rapid expansion of the power of molecular markers to address ecological questions. Microsatellites have emerged as the most popular and versatile marker type for ecological applications. The rise of commercial services that can isolate microsatellites for new study species and genotype samples at reasonable prices presents ecologists with the unprecedented ability to employ genetic approaches without heavy investment in specialized equipment. Nevertheless, the lack of accessible, synthesized information on the practicalities and pitfalls of using genetic tools impedes ecologists’ ability to make informed decisions on using molecular approaches and creates the risk that some will use microsatellites without understanding the steps needed to evaluate the quality of a genetic data set. The first goal of this synthesis is to provide an overview of the strengths and limitations of microsatellite markers and the risks, cost and time requirements of isolating and using microsatellites with the aid of commercial services. The second goal is to encourage the use and consistent reporting of thorough marker screening to ensure high quality data. To that end, we present a multistep screening process to evaluate candidate loci for inclusion in a genetic study that is broadly targeted to both novice and experienced geneticists alike. [ABSTRACT FROM AUTHOR]

There is considerable interest in the genetic structure of Kelletia kelletii because of its economic, ecological and scientific importance. To that end, we developed species-specific primers which amplify mitochondrial cytochrome c oxidase subunit I as well as 13 hypervariable nuclear microsatellite loci. Using dye-labelled primers, the microsatellite loci can be co-amplified in two multiplex polymerase chain reactions and scored simultaneously on an automated sequencer. [ABSTRACT FROM AUTHOR]

The Dungeness crab, Cancer magister, is the focus of one of the most intensely harvested fisheries in North America. Given its economic importance, there is considerable interest in assessing the degree and spatial pattern of genetic structure in C. magister. To that end, we developed a series of 17 hypervariable microsatellite loci. Six of these 17 loci could be amplified in a single multiplex PCR reaction. Using dye-labelled primers all six loci can be coamplified and scored simultaneously on an automated sequencer. The ability to multiplex multiple loci greatly increases the ease and speed of genotyping for this species. [ABSTRACT FROM AUTHOR]

Signals of natural selection can be quickly eroded in high gene flow systems, curtailing efforts to understand how and when genetic adaptation occurs in the ocean. This long‐standing, unresolved topic in ecology and evolution has renewed importance because changing environmental conditions are driving range expansions that may necessitate rapid evolutionary responses. One example occurs in Kellet's whelk (Kelletia kelletii), a common subtidal gastropod with an ~40‐ to 60‐day pelagic larval duration that expanded their biogeographic range northwards in the 1970s by over 300 km. To test for genetic adaptation, we performed a series of experimental crosses with Kellet's whelk adults collected from their historical (HxH) and recently expanded range (ExE), and conducted RNA‐Seq on offspring that we reared in a common garden environment. We identified 2770 differentially expressed genes (DEGs) between 54 offspring samples with either only historical range (HxH offspring) or expanded range (ExE offspring) ancestry. Using SNPs called directly from the DEGs, we assigned samples of known origin back to their range of origin with unprecedented accuracy for a marine species (92.6% and 94.5% for HxH and ExE offspring, respectively). The SNP with the highest predictive importance occurred on triosephosphate isomerase (TPI), an essential metabolic enzyme involved in cold stress response. TPI was significantly upregulated and contained a non‐synonymous mutation in the expanded range. Our findings pave the way for accurately identifying patterns of dispersal, gene flow and population connectivity in the ocean by demonstrating that experimental transcriptomics can reveal mechanisms for how marine organisms respond to changing environmental conditions. [ABSTRACT FROM AUTHOR]

A correction to an article on pairwise F-statistics for spinner dolphins between locations in the Hawaiian Archipelago and American Sãmoa that was published in a previous issue is presented.