PoolParty2: An integrated pipeline for analysing pooled or indexed low-coverage whole-genome sequencing data to discover the genetic basis of diversity

Whole-genome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome sub-sampling with estimating recombination rates and linkage between sampled markers and target loci. As sequencing costs decrease, low-coverage whole-genome sequencing of pooled or indexed-individual samples is commonly utilized to identify loci associated with phenotypes or environmental axes in non-model organisms. There are, however, relatively few publicly available bioinformatic pipelines designed explicitly to analyse these types of data, and fewer still that process the raw sequencing data, provide useful metrics of quality control and then execute analyses. Here, we present an updated version of a bioinformatics pipeline called PoolParty2 that can effectively handle either pooled or indexed DNA samples and includes new features to improve computational efficiency. Using simulated data, we demonstrate the ability of our pipeline to recover segregating variants, estimate their allele frequencies accurately, and identify genomic regions harbouring loci under selection. Based on the simulated data set, we benchmark the efficacy of our pipeline with another bioinformatic suite, angsd, and illustrate the compatibility and complementarity of these suites using angsd to generate genotype likelihoods as input for identifying linkage outlier regions using alignment files and variants provided by PoolParty2. Finally, we apply our updated pipeline to an empirical dataset of low-coverage whole genomic data from population samples of Columbia River steelhead trout (Oncorhynchus mykiss), results from which demonstrate the genomic impacts of decades of artificial selection in a prominent hatchery stock. Thus, we not only demonstrate the utility of PoolParty2 for genomic studies that combine sequencing data from multiple individuals, but also illustrate how it compliments other bioinformatics resources such as angsd.

Genomic surveillance identifies potential risk factors for SARS-CoV-2 transmission at a mid-sized university in a small rural town

Understanding transmission dynamics of SARS-CoV-2 in institutions of higher education (IHEs) is important because these settings have potential for rapid viral spread. Here, we used genomic surveillance to retrospectively investigate transmission dynamics throughout the 2020-2021 academic year for the University of Idaho ("University"), a mid-sized IHE in a small rural town. We generated genome assemblies for 1168 SARS-CoV-2 samples collected during the academic year, representing 46.8% of positive samples collected from the University population and 49.8% of positive samples collected from the surrounding community ("Community") at the local hospital during this time. Transmission dynamics differed for the University when compared to the Community, with more infection waves that lasted shorter lengths of time, potentially resulting from high-transmission congregate settings along with mitigation efforts implemented by the University to combat outbreaks. We found evidence for low transmission rates between the University and Community, with approximately 8% of transmissions into the Community originating from the University, and approximately 6% of transmissions into the University originating from the Community. Potential transmission risk factors identified for the University included congregate settings such as sorority and fraternity events and residences, holiday travel, and high caseloads in the surrounding community. Knowledge of these risk factors can help the University and other IHEs develop effective mitigation measures for SARS-CoV-2 and similar pathogens.

High-Resolution Taxonomic Characterization Reveals Novel Human Microbial Strains with Potential as Risk Factors and Probiotics for Prediabetes and Type 2 Diabetes

Alterations in the composition of the gut microbiota is thought to play a key role in causing type 2 diabetes, yet is not fully understood, especially at the strain level. Here, we used long-read DNA sequencing technology of 16S-ITS-23S rRNA genes for high-resolution characterization of gut microbiota in the development of type 2 diabetes. Gut microbiota composition was characterized from fecal DNA from 47 participants divided into 4 cohorts based on glycemic control: normal glycemic control (healthy; n = 21), reversed prediabetes (prediabetes/healthy; n = 8), prediabetes (n = 8), or type 2 diabetes (n = 10). A total of 46 taxa were found to be possibly related to progression from healthy state to type 2 diabetes. Bacteroides coprophilus DSM 18228, Bifidobacterium pseudocatenulatum DSM 20438, and Bifidobacterium adolescentis ATCC 15703 could confer resistance to glucose intolerance. On the other hand, Odoribacter laneus YIT 12061 may be pathogenic as it was found to be more abundant in type 2 diabetes participants than other cohorts. This research increases our understanding of the structural modulation of gut microbiota in the pathogenesis of type 2 diabetes and highlights gut microbiota strains, with the potential for targeted opportunistic pathogen control or consideration for probiotic prophylaxis and treatment.

Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout

Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.

Etelis boweni sp. nov., a new cryptic deepwater eteline snapper from the Indo-Pacific (Perciformes: Lutjanidae)

A new species of Etelis is described based on 16 specimens collected from the Red Sea and Western Australia, with confirmed genetic records throughout the Indo-West Pacific. It is similar to and was often misidentified as Etelis carbunculus Cuvier, with both species sharing the diagnostic character of low number of developed gill rakers. Nonetheless, the two species are genetically divergent and differ morphologically in adult body length; proportions of eye, snout, cheek and caudal fin; shape of head, opercular spine and sagittal otolith; and coloration of the tip of the upper caudal fin. Etelis boweni has a wide Indo-west Pacific distribution that largely overlaps with E. carbunculus, and the two species are often caught on the same fishing line.

The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern

Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus - NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both theinter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype-environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographic barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.

Genomic signatures of divergent selection are associated with social behaviour for spinner dolphin ecotypes

Understanding the genomic basis of adaptation is critical for understanding evolutionary processes and predicting how species will respond to environmental change. Spinner dolphins in the eastern tropical Pacific (ETP) present a unique system for studying adaptation. Within this large geographical region are four spinner dolphin ecotypes with weak neutral genetic divergence and no obvious barriers to gene flow, but strong spatial variation in morphology, behaviour and habitat. These ecotypes have large population sizes, which could reduce the effects of drift and facilitate selection. To identify genomic regions putatively under divergent selective pressures between ecotypes, we used genome scans with 8994 RADseq single nucleotide polymorphisms (SNPs) to identify population differentiation outliers and genotype-environment association outliers. Gene ontology enrichment analyses indicated that outlier SNPs from both types of analyses were associated with multiple genes involved in social behaviour and hippocampus development, including 15 genes associated with the human social disorder autism. Evidence for divergent selection on social behaviour is supported by previous evidence that these spinner dolphin ecotypes differ in mating systems and associated social behaviours. In particular, three of the ETP ecotypes probably have a polygynous mating system characterized by strong premating competition among males, whereas the fourth ecotype probably has a polygynandrous mating system characterized by strong postmating competition such as sperm competition. Our results provide evidence that selection for social behaviour may be an evolutionary force driving diversification of spinner dolphins in the ETP, potentially as a result of divergent sexual selection associated with different mating systems. Future studies should further investigate the potential adaptive role of the candidate genes identified here, and could probably find further signatures of selection using whole genome sequence data.

Genomic association with pathogen carriage in bighorn sheep (Ovis canadensis)

Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population-level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well-studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family-based genome-wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome-wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP-based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.

Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research

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.

Range-Wide Population Structure of 3 Deepwater Eteline Snappers Across the Indo-Pacific Basin

Deep-sea habitats may drive unique dispersal and demographic patterns for fishes, but population genetic analyses to address these questions have rarely been conducted for fishes in these environments. This study investigates the population structure of 3 tropical deepwater snappers of the genus Etelis that reside at 100-400 m depth, with broad and overlapping distributions in the Indo-Pacific. Previous studies showed little population structure within the Hawaiian Archipelago for 2 of these species: Etelis coruscans and E. carbunculus. Here we extend sampling to the entire geographic range of each species to resolve the population genetic architecture for these 2 species, as well as a recently exposed cryptic species (Etelis sp.). One goal was to determine whether deepwater snappers are more dispersive than shallow-water fishes. A second goal was to determine whether submesophotic fishes have older, more stable populations than shallow reef denizens that are subject to glacial sea-level fluctuations. Both goals are pertinent to the management of these valuable food fishes. A total of 1153 specimens of E. coruscans from 15 geographic regions were analyzed, along with 1064 specimens of E. carbunculus from 11 regions, and 590 specimens of E. sp. from 16 regions. The first 2 species were analyzed with mtDNA and 9-11 microsatellite loci, while E. sp. was analyzed with mtDNA only. Etelis coruscans had a non-significant microsatellite global FST, but significant global mtDNA Ф ST = 0.010 (P = 0.0007), with the isolation of Seychelles in the western Indian Ocean, and intermittent signals of isolation for the Hawaiian Archipelago. Etelis carbunculus had a non-significant microsatellite global FST, and significant global mtDNA Ф ST = 0.021 (P = 0.0001), with low but significant levels of isolation for Hawai'i, and divergence between Tonga and Fiji. Etelis sp. had mtDNA Ф ST = 0.018 (P = 0.0005), with a strong pattern of isolation for both Seychelles and Tonga. Overall, we observed low population structure, shallow mtDNA coalescence (similar to near-shore species), and isolation at the fringes of the Indo-Pacific basin in Hawai'i and the western Indian Ocean. While most shallow-water species have population structure on the scale of biogeographic provinces, deepwater snapper populations are structured on the wider scale of ocean basins, more similar to pelagic fishes than to shallow-water species. This population structure indicates the capacity for widespread dispersal throughout the Indo-Pacific region.

Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control

The larvae of click beetles (Coleoptera: Elateridae), known as "wireworms," are agricultural pests that pose a substantial economic threat worldwide. We produced one of the first wireworm genome assemblies (Limonius californicus), and investigated population structure and phylogenetic relationships of three species (L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada using genome-wide markers (RADseq) and genome skimming. We found two species (L. californicus and L. infuscatus) are comprised of multiple genetically distinct groups that diverged in the Pleistocene but have no known distinguishing morphological characters, and therefore could be considered cryptic species complexes. We also found within-species population structure across relatively short geographic distances. Genome scans for selection provided preliminary evidence for signatures of adaptation associated with different pesticide treatments in an agricultural field trial for L. canus. We demonstrate that genomic tools can be a strong asset in developing effective wireworm control strategies.

Long-lived marine species may be resilient to environmental variability through a temporal portfolio effect

Maintenance of genetic variation may provide resilience of populations to natural environmental variability. We used Pacific ocean perch (POP; Sebastes alutus) to test for the maintenance of adaptive variation across overlapping generations. POP are a long-lived species characterized by widespread larval dispersal in their first year and a longevity of over 100 years. In order to understand how early marine dispersal affects POP survival and population structure, we used restriction site-associated DNA sequencing (RADseq) to obtain 11,146 single-nucleotide polymorphisms (SNPs) from 401 young-of-the-year (YOY) POP collected during surveys conducted in 2014 (19 stations) and 2015 (4 stations) in the eastern Gulf of Alaska. Population clustering analysis showed that the POP samples represented four distinct ancestral populations mixed throughout the sampling area. Based on prior work on larval dispersal of POP, these larvae are most likely from distinct parturition locations that are mixing during their pelagic dispersal life stage. Latent factor mixed models revealed that POP larvae face significant selection during their first year at sea, which is specific to the year of their birth. Thus each adult cohort's genetic composition is heavily influenced by the environmental conditions experienced during their first year at sea. Long-lived species relying on broadcast spawning strategies may therefore be uniquely resilient to environmental variability by maintaining a portfolio of cohort-specific adaptive genotypes, and age truncation due to overfishing of older cohorts may have detrimental effect on the population viability.

Diet of a rare herbivore based on DNA metabarcoding of feces: Selection, seasonality, and survival

In herbivores, survival and reproduction are influenced by quality and quantity of forage, and hence, diet and foraging behavior are the foundation of an herbivore's life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: (a) They are difficult to observe, (b) collecting stomach contents requires sacrificing animals, and (c) microhistology requires accurately identifying taxa from partially digested plant fragments and likely overemphasizes less-digestible taxa. The northern Idaho ground squirrel (Urocitellus brunneus) is federally threatened in the United States under the Endangered Species Act. We used DNA metabarcoding techniques to identify the diet of 188 squirrels at 11 study sites from fecal samples. We identified 42 families, 126 genera, and 120 species of plants in the squirrel's diet. Our use of three gene regions was beneficial because reliance on only one gene region (e.g., only trnL) would have caused us to miss >30% of the taxa in their diet. Northern Idaho ground squirrel diet differed between spring and summer, frequency of many plants in the diet differed from their frequency within their foraging areas (evidence of selective foraging), and several plant genera in their diet were associated with survival. Our results suggest that while these squirrels are generalists (they consume a wide variety of plant species), they are also selective and do not eat plants relative to availability. Consumption of particular genera such as Perideridia may be associated with higher overwinter survival.

A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data

The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis across SNP panels generated with or without the use of a reference genome, and between SNPs and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome produced SNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across all SNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284 SNPs for Mexican gray wolf and 142 SNPs for bighorn sheep, indicating our pipeline can be used to develop SNP genotyping assays for parentage analysis with relatively small numbers of loci.

Age-specific infectious period shapes dynamics of pneumonia in bighorn sheep

Superspreading, the phenomenon where a small proportion of individuals contribute disproportionately to new infections, has profound effects on disease dynamics. Superspreading can arise through variation in contacts, infectiousness or infectious periods. The latter has received little attention, yet it drives the dynamics of many diseases of critical public health, livestock health and conservation concern. Here, we present rare evidence of variation in infectious periods underlying a superspreading phenomenon in a free-ranging wildlife system. We detected persistent infections of Mycoplasma ovipneumoniae, the primary causative agent of pneumonia in bighorn sheep (Ovis canadensis), in a small number of older individuals that were homozygous at an immunologically relevant genetic locus. Interactions among age-structure, genetic composition and infectious periods may drive feedbacks in disease dynamics that determine the magnitude of population response to infection. Accordingly, variation in initial conditions may explain divergent population responses to infection that range from recovery to catastrophic decline and extirpation.

Comment on "Whole-genome sequence analysis shows two endemic species of North American wolf are admixtures of the coyote and gray wolf"

Whole-genome data do not support a recent hybrid origin for red and eastern wolves.

Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals

The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.

Measurements of Elliptic and Triangular Flow in High-Multiplicity 3He+Au Collisions at √(s(NN))=200 GeV

We present the first measurement of elliptic (v(2)) and triangular (v(3)) flow in high-multiplicity (3)He+Au collisions at √(s(NN))=200  GeV. Two-particle correlations, where the particles have a large separation in pseudorapidity, are compared in (3)He+Au and in p+p collisions and indicate that collective effects dominate the second and third Fourier components for the correlations observed in the (3)He+Au system. The collective behavior is quantified in terms of elliptic v(2) and triangular v(3) anisotropy coefficients measured with respect to their corresponding event planes. The v(2) values are comparable to those previously measured in d+Au collisions at the same nucleon-nucleon center-of-mass energy. Comparisons with various theoretical predictions are made, including to models where the hot spots created by the impact of the three (3)He nucleons on the Au nucleus expand hydrodynamically to generate the triangular flow. The agreement of these models with data may indicate the formation of low-viscosity quark-gluon plasma even in these small collision systems.

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod

Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open-ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.

Measurement of Long-Range Angular Correlation and Quadrupole Anisotropy of Pions and (Anti)Protons in Central d+Au Collisions at sqrt[s_{NN}]=200 GeV

We present azimuthal angular correlations between charged hadrons and energy deposited in calorimeter towers in central d+Au and minimum bias p+p collisions at sqrt[s_{NN}]=200 GeV. The charged hadron is measured at midrapidity |η|<0.35, and the energy is measured at large rapidity (-3.7<η<-3.1, Au-going direction). An enhanced near-side angular correlation across |Δη|>2.75 is observed in d+Au collisions. Using the event plane method applied to the Au-going energy distribution, we extract the anisotropy strength v_{2} for inclusive charged hadrons at midrapidity up to p_{T}=4.5 GeV/c. We also present the measurement of v_{2} for identified π^{±} and (anti)protons in central d+Au collisions, and observe a mass-ordering pattern similar to that seen in heavy-ion collisions. These results are compared with viscous hydrodynamic calculations and measurements from p+Pb at sqrt[s_{NN}]=5.02 TeV. The magnitude of the mass ordering in d+Au is found to be smaller than that in p+Pb collisions, which may indicate smaller radial flow in lower energy d+Au collisions.

Cold-nuclear-matter effects on heavy-quark production at forward and backward rapidity in d + Au collisions at √sNN = 200 GeV

The PHENIX experiment has measured open heavy-flavor production via semileptonic decay over the transverse momentum range 1 < p(T) < 6  GeV/c at forward and backward rapidity (1.4 < |y| < 2.0) in d+Au and p + p collisions at √sNN = 200  GeV. In central d+Au collisions, relative to the yield in p + p collisions scaled by the number of binary nucleon-nucleon collisions, a suppression is observed at forward rapidity (in the d-going direction) and an enhancement at backward rapidity (in the Au-going direction). Predictions using nuclear-modified-parton-distribution functions, even with additional nuclear-p(T) broadening, cannot simultaneously reproduce the data at both rapidity ranges, which implies that these models are incomplete and suggests the possible importance of final-state interactions in the asymmetric d + Au collision system. These results can be used to probe cold-nuclear-matter effects, which may significantly affect heavy-quark production, in addition to helping constrain the magnitude of charmonia-breakup effects in nuclear matter.

Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (family Lutjanidae) reveal concordant genetic structure across the Hawaiian Archipelago

The Hawaiian Archipelago has become a natural laboratory for understanding genetic connectivity in marine organisms as a result of the large number of population genetics studies that have been conducted across this island chain for a wide taxonomic range of organisms. However, population genetic studies have been conducted for only two species occurring in the mesophotic or submesophotic zones (30+m) in this archipelago. To gain a greater understanding of genetic connectivity in these deepwater habitats, we investigated the genetic structure of two submesophotic fish species (occurring ∼200-360 m) in this archipelago. We surveyed 16 locations across the archipelago for submesophotic snappers Etelis coruscans (N = 787) and E. "marshi" (formerly E. carbunculus; N = 770) with 436-490 bp of mtDNA cytochrome b and 10-11 microsatellite loci. Phylogeographic analyses reveal no geographic structuring of mtDNA lineages and recent coalescence times that are typical of shallow reef fauna. Population genetic analyses reveal no overall structure across most of the archipelago, a pattern also typical of dispersive shallow fishes. However some sites in the mid-archipelago (Raita Bank to French Frigate Shoals) had significant population differentiation. This pattern of no structure between ends of the Hawaiian range, and significant structure in the middle, was previously observed in a submesophotic snapper (Pristipomoides filamentosus) and a submesophotic grouper (Hyporthodus quernus). Three of these four species also have elevated genetic diversity in the mid-archipelago. Biophysical larval dispersal models from previous studies indicate that this elevated diversity may result from larval supplement from Johnston Atoll, ∼800 km southwest of Hawaii. In this case the boundaries of stocks for fishery management cannot be defined simply in terms of geography, and fishery management in Hawaii may need to incorporate external larval supply into management plans.

ezRAD: a simplified method for genomic genotyping in non-model organisms

Here, we introduce ezRAD, a novel strategy for restriction site–associated DNA (RAD) that requires little technical expertise or investment in laboratory equipment, and demonstrate its utility for ten non-model organisms across a wide taxonomic range. ezRAD differs from other RAD methods primarily through its use of standard Illumina TruSeq library preparation kits, which makes it possible for any laboratory to send out to a commercial genomic core facility for library preparation and next-generation sequencing with virtually no additional investment beyond the cost of the service itself. This simplification opens RADseq to any lab with the ability to extract DNA and perform a restriction digest. ezRAD also differs from others in its flexibility to use any restriction enzyme (or combination of enzymes) that cuts frequently enough to generate fragments of the desired size range, without requiring the purchase of separate adapters for each enzyme or a sonication step, which can further decrease the cost involved in choosing optimal enzymes for particular species and research questions. We apply this method across a wide taxonomic diversity of non-model organisms to demonstrate the utility and flexibility of our approach. The simplicity of ezRAD makes it particularly useful for the discovery of single nucleotide polymorphisms and targeted amplicon sequencing in natural populations of non-model organisms that have been historically understudied because of lack of genomic information.

Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline

Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.

Cross section and parity-violating spin asymmetries of W± boson production in polarized p + p collisions at sqrt[s] = 500 GeV

Large parity-violating longitudinal single-spin asymmetries A(L)(e+) = -0.86(-0.14) (+0.30) and A(L)(e-) = 0.88(-0.71) (+0.12) are observed for inclusive high transverse momentum electrons and positrons in polarized p+p collisions at a center-of-mass energy of sqrt[s] = 500 GeV with the PHENIX detector at RHIC. These e± come mainly from the decay of W± and Z0 bosons, and their asymmetries directly demonstrate parity violation in the couplings of the W± to the light quarks. The observed electron and positron yields were used to estimate W± boson production cross sections for the e± channels of σ(pp → W+ X) × BR(W+ → e+ ν(e)) = 144.1 ± 21.2(stat)(-10.3) (+3.4) (syst) ± 21.6(norm)  pb, and σ(pp → W- X) × BR(W- → e- ν[over ¯](e)) = 31.7 ± 12.1(stat)(-8.2) (+10.1) (syst) ± 4.8(norm)  pb.

Defining Boundaries for Ecosystem-Based Management: A Multispecies Case Study of Marine Connectivity across the Hawaiian Archipelago

Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to be an obstacle for many marine conservation programs. Generalizations based on geographic proximity, taxonomy, or life history characteristics provide little predictive power in determining overall patterns of connectivity, and therefore offer little in terms of delineating boundaries for marine spatial management areas. Here, we provide a case study of 27 taxonomically and ecologically diverse species (including reef fishes, marine mammals, gastropods, echinoderms, cnidarians, crustaceans, and an elasmobranch) that reveal four concordant barriers to dispersal within the Hawaiian Archipelago which are not detected in single-species exemplar studies. We contend that this multispecies approach to determine concordant patterns of connectivity is an objective and logical way in which to define the minimum number of management units and that EBM in the Hawaiian Archipelago requires at least five spatially managed regions.

Rolling stones and stable homes: social structure, habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris)

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 Phi(ST) < 0.001, P = 0.357; microsatellite F(ST) = -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 < Phi(ST) < 0.236, P < 0.05; microsatellite 0.016 < F(ST) < 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 < F(ST) < 0.643, P < 0.001; microsatellite 0.058 < F(ST) < 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.