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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., Bighorn sheep populations impacted by infectious pneumonia may experience long‐term recovery complications due to chronically infected individuals shedding pathogen and suppressing lamb recruitment in years following outbreak events. We investigated genetic associations with the chronic carrier phenotype in bighorn sheep to better understand underlying dynamics influencing pathogen persistence in wild sheep populations.

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., Development of GEOME has been supported by NESCent, the National Evolutionary Synthesis Center (2012 Catalysis Meeting to EDC and CR; 2013‐2014 Working Group to CR, EDC and RJT); the National Science Foundation (OISE‐1243541 to CM, DEB‐0956426 to CM and JD, and DEB‐1457848 to EDC and RJT); the Gordon and Betty Moore Foundation (CM and JD), the Berkeley Natural History Museums, and contracts from the Smithsonian National Museum of Natural History as components of the Global ARMS Programme, Global Genome Initiative and the SI Barcoding Network. The implementation of some metadata fields in GEOME were jointly initiated by the Ira Moana – Genes of the Sea – Project (www.massey.ac.nz/iramoana) and the project ‘Te Tuākiri o te Tāonga: Recognizing Indigenous Interests in Genetic Resources' both supported by Catalyst Seeding funds provided by the New Zealand Ministry of Business, Innovation and Employment and administered by the Royal Society Te Apārangi (17‐MAU‐309‐CSG to LL, CR, EDC, MRG, JD, RJT and seven others; and 19‐UOW‐008‐CSG to Maui Hudson and Jane Anderson, respectively), as well as a Massey University Research Fund to L.L. We thank Dr Karen Chambers and Dr Benjamin Sibbett from Wiley for providing encouragement and suggestions, alongside reviewers including Dr Shawn Narum and Dr Nick Fountain‐Jones. NESCent, we miss you.

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., Diet and foraging behavior are the foundation of an herbivore's life history strategy and it is imperative that we know the species of plants they prefer. We used DNA metabarcoding techniques to noninvasively sample the threatened northern Idaho ground squirrel (Urocitellus brunneus) diet. We used three gene regions and found that diets differed on the genus level between season, availability, and survival was associated with particular plants.

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.

Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.

Evolutionary genetic patterns in shallow coastal fishes are documented with dozens of studies, but corresponding surveys of deepwater fishes (>200m) are scarce. Here we investigate the evolutionary history of deepwater snappers (genus Etelis), comprised of three recognized Indo-Pacific species and one Atlantic congener, by constructing a phylogeny of the genus with two mtDNA loci and two nuclear introns. Further, we apply range-wide Indo-Pacific sampling to test for the presence and distribution of a putative cryptic species pair within E. carbunculus using morphological analyses and mtDNA cytochrome b sequences from 14 locations across the species range (N=1696). These analyses indicate that E. carbunculus is comprised of two distinct, non-interbreeding lineages separated by deep divergence (d=0.081 in cytochrome b). Although these species are morphologically similar, we identified qualitative differences in coloration of the upper-caudal fin tip and the shape of the opercular spine, as well as significant differences in adult body length, body depth, and head length. These two species have overlapping Indo-Pacific distributions, but one species is more widespread across the Indo-Pacific, whereas the other species is documented in the Indian Ocean and Western Central Pacific. The dated Etelis phylogeny places the cryptic species divergence in the Pliocene, indicating that the biogeographic barrier between the Indian and Pacific Oceans played a role in speciation. Based on historic taxonomy and nomenclature, the species more widespread in the Pacific Ocean is E. carbunculus, and the other species is previously undescribed (referred to here as E. sp.). The Atlantic congener E. oculatus has only recently (∼0.5Ma) diverged from E. coruscans in the Indo-Pacific, indicating colonization via southern Africa. The pattern of divergence at the Indo-Pacific barrier, and Pleistocene colonization from the Indian Ocean into the Atlantic, is concordant with patterns observed in shallow coastal fishes, indicating similar drivers of evolutionary processes.

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.

In a recent article, vonHoldt and colleagues ( 1 ) use whole-genome sequence data to address the relationships and evolutionary origins of several North American canid taxa. The authors conclude that two taxa, the red wolf ( Canis rufus ) and the eastern wolf ( Canis lycaon ), are not long-diverged lineages as other researchers have concluded from genetic ( 2 – 7 ) and fossil evidence ( 8 , 9 ) but are, rather, populations resulting from recent admixture between gray wolves ( Canis lupus ) and coyotes ( Canis latrans ). They use this conclusion to argue that endangered species policy should better account for hybridization and admixture. We agree that hybridization and admixture are widespread in the natural world and that the conservation policy needs to be updated to account for this biological reality. However, we strongly disagree with their conclusion that red and eastern wolves are of recent hybrid origin and we conclude that their analysis does not actually test the hypothesis of a recent hybrid origin. Their data are consistent with multiple hypotheses for the origins of red and eastern wolves, including relatively old origins of these taxa. Furthermore, we argue that their data do not support “a lack of unique ancestry in red and eastern wolves” ( 1 ); rather, substantial evidence still supports the conclusion that red and eastern wolves represent genetically distinct taxa among North American canids. Below, we detail this perspective and argue for further analyses that would directly test competing hypotheses for the evolutionary origins of these groups. Analysis of whole-genome sequence data necessarily relies on a relatively small number of individual samples that are taken to be representative of larger populations or taxa. In this case, the choice of representative samples is problematic in several respects. First, of the three individuals chosen as representative nonadmixed coyotes, …

High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.

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.

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.

Understanding the factors driving spatial and temporal variation in genetic diversity in cetaceans and primates is crucial in directing conservation and management decisions for these taxa. Spatial variation in genetic diversity can be driven by geographic barriers to dispersal, such as rivers for primates or land masses for cetaceans. Spatial variation in diversity can also be driven by population size differences across habitat patches that vary in resource abundance, with smaller populations typically exhibiting lower genetic diversity than larger populations. However, cetaceans and primates often exhibit complex genetic structure that cannot be explained by simple geographic barriers or variation in habitat abundance. In many cases this complex structure is attributed to behavioral philopatry or social structure. Many cetaceans and primates exhibit philopatry to natal ranges or philopatry to particular habitat types, and many species also exhibit complex social structure features that can influence genetic structure, such as strong group stability and sex-biased dispersal. Finally, genetic diversity can vary temporally; genetic coalescent analyses indicate that diversity has declined in the recent past for several cetacean and primate species, often with evidence for population bottlenecks during times of historical anthropogenic impact, such as habitat fragmentation or whaling. The complexity of factors influencing genetic structure over space and time for cetacean and primate species illustrates that multidisciplinary studies are required to truly understand genetic structure for these species. These studies are becoming increasingly important as cetaceans and primates face severe anthropogenic threats around the world.

Integration of ecological and genetic data to study patterns of biological connectivity can aid in ecosystem-based management. Here we investigated connectivity of the Hawaiian grouperEpinephelus quernus, a species of management concern within the Main Hawaiian Islands (MHI), by comparing genetic analyses with simulated larval dispersal patterns across the species range in the Hawaiian Archipelago and Johnston Atoll. Larval simulations revealed higher dispersal from the MHI to the Northwestern Hawaiian Islands (NWHI) than in the opposite direction and evidence for a dispersal corridor between Johnston and the middle of the Hawaiian Archipelago. Genetic analyses using mitochondrial DNA (mtDNA) control region sequences and microsatellites revealed relatively high connectivity across the Hawaiian Archipelago, with the exception of genetically distinct populations and higher mtDNA diversity in the mid-Archipelago. These analyses support the preservation of the mid-archipelago as a source of genetic diversity and a region of connectivity with locations outside the Hawaiian Archipelago. Additionally, our evidence for directional dispersal away from the MHI lends caution to any management decisions that would rely on the NWHI replenishing depleted MHI stocks.

The population structure of marine species is variable along the Hawaiian Archipelago; thus, it is important to understand dispersal and recruitment patterns for economically and ecologically important taxa to inform Ecosystem-based Management. Connectivity of the coral-eating crown-of-thorns sea star, Acanthaster planci, was examined from Johnston Atoll and 12 locations across the Hawaiian Archipelago. Sequences of mitochondrial DNA from 383 individuals were analyzed to infer patterns of gene flow among the Northwestern Hawaiian Islands (NWHIs), the main Hawaiian Islands, and Johnston Atoll. Population samples were genetically similar across the Hawaiian Archipelago with the exception of the west side of the Big Island of Hawaii, which was significantly differentiated from the majority of Hawaiian samples (pairwise Φ S T = 0 . 0 6 0 7 - 0 . 1 0 6 8 , 𝑃 < . 0 5 ). Although differentiated, Hawai`i West shares haplotypes with every other site across the Hawaiian Archipelago. Johnston Atoll was genetically distinct from every location (pairwise Φ S T = 0 . 0 6 4 - 0 . 1 3 , 𝑃 < . 0 5 ) except French Frigate Shoals ( Φ S T = 0 . 0 3 , 𝑃 = . 1 0 ), supporting connectivity between the central NWHIs and Johnston Atoll. Taken together with the lack of geographic population structure and haplotypes shared among all populations, these results indicate widespread larval dispersal with few restrictions to gene flow along the 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.

Although stochasticity in oceanographic conditions is known to be an important driver of temporal genetic change in many marine species, little is known about whether genetically distinct plankton populations can persist in open ocean habitats. A prior study demonstrated significant population genetic structure among oceanic gyres in the mesopelagic copepod Haloptilus longicornis in both the Atlantic and Pacific Oceans, and we hypothesized that populations within each gyre represent distinct gene pools that persist over time. We tested this expectation through basin-scale sampling across the Atlantic Ocean in 2010 and 2012. Using both mitochondrial (mtCOII) and microsatellite markers (7 loci), we show that the genetic composition of populations was stable across two years in both the northern and southern subtropical gyres. Genetic variation in this species was partitioned among ocean gyres (FCT = 0.285, P < 0.0001 for mtCOII, FCT = 0.013, P < 0.0001 for microsatellites), suggesting strong spatial population structure, but no significant partitioning was found among sampling years. This temporal persistence of population structure across a large geographic scale was coupled with chaotic genetic patchiness at smaller spatial scales, but the magnitude of genetic differentiation was an order of magnitude lower at these smaller scales. Our results demonstrate that genetically distinct plankton populations persist over time in highly-dispersive open ocean habitats, and this is the first study to rigorously test for temporal stability of large scale population structure in the plankton.

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.