The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a...
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Taiwan has a long history of fishery operations and contributes significantly to global fishery harvest. The East and South China seas are important fishing grounds with very limited public data. More efforts are needed to digitize and analyze historical catch rate data to illuminate species and community changes in this region. In this study, we digitize historical records of catch and effort from government fishery reports for nine commercial species caught by otter trawl, reported...
Supplemental material for Climate forcing by battered-and-breaded fillets and crab-flavored sticks from Alaska pollockBrandi McKuin, Jordan Watson, Alan Haynie & J. Elliott Campbell
Detailed supplemental datasets: inputs and output information and emission factors for ingredients, non-ingredient materials, and embodied energy of pollock products.
Data from: Avoiding tipping points in fisheries management through Gaussian process dynamic programmingCarl Boettiger, Marc Mangel, Stephan Munch, C. Boettiger & S. Munch
Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some...
Data from: Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and driftAndre E. Moura, John G. Kenny, Roy Chaudhuri, Margaret A. Hughes, Andreanna Welch, Ryan R. Reisinger, P. J. Nico De Bruyn, Marilyn E. Dahlheim, Neil Hall, A. Rus Hoelzel & Andreanna J. Welch
The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species...
The effective population size (Ne) is a fundamental parameter in population genetics that determines the relative strength of selection and random genetic drift, the effect of migration, levels of inbreeding, and linkage disequilibrium. In many cases where it has been estimated in animals, Ne is on the order of 10-20% of the census size. In this study, we use 12 microsatellite markers and 14,888 single nucleotide polymorphisms (SNPs) to empirically estimate Ne in Aedes aegypti,...
We investigated the extent that the 2010 Deepwater Horizon oil spill potentially affected oceanic-stage sea turtles from populations across the Atlantic. Within an ocean-circulation model, particles were backtracked from the Gulf of Mexico spill site to determine the probability of young turtles arriving in this area from major nesting beaches. The abundance of turtles in the vicinity of the oil spill was derived by forward-tracking particles from focal beaches and integrating population size, oceanic-stage duration...
Information on drivers of dispersal is critical for wildlife conservation but is rare for long-lived marine mammal species with large geographic ranges. We fit multi-state mark-recapture models to resighting data of 369 known-aged Steller sea lion (Eumetopias jubatus) females marked as pups on their natal rookeries in southeastern Alaska from 1994-2005 and monitored from 2001-15. We estimated probabilities of females being first observed parous at their natal site (natal philopatry), and of not moving breeding...
Data from: Predator-driven brain size evolution in natural populations of Trinidadian killifish (Rivulus hartii)Matthew R. Walsh, Whitnee Broyles, Shannon M. Beston & Stephan B. Munch
Vertebrates exhibit extensive variation in relative brain size. It has long been assumed that this variation is the product of ecologically driven natural selection. Yet, despite more than 100 years of research, the ecological conditions that select for changes in brain size are unclear. Recent laboratory selection experiments showed that selection for larger brains is associated with increased survival in risky environments. Such results lead to the prediction that increased predation should favour increased brain...
Data from: Migratory culture, population structure and stock identity in North Pacific beluga whales (Delphinapterus leucas)Greg O'Corry-Crowe, Robert Suydam, Lori Quakenbush, Brooke Potgieter, Lois Harwood, Dennis Litovka, Tatiana Ferrer, John Citta, Vladimir Burkanov, Kathy Frost, Barbara Mahoney & Greg O’Corry-Crowe
The annual return of beluga whales, Delphinapterus leucas, to traditional seasonal locations across the Arctic may involve migratory culture, while the convergence of discrete summering aggregations on common wintering grounds may facilitate outbreeding. Natal philopatry and cultural inheritance, however, has been difficult to assess as earlier studies were of too short a duration, while genetic analyses of breeding patterns, especially across the beluga's Pacific range, have been hampered by inadequate sampling and sparse information on...
Data from: Feather corticosterone reveals stress associated with dietary changes in a breeding seabirdAlexis P. Will, Yutaka Watanuki, Dale M. Kikuchi, Nobuhiko Sato, Motohiro Ito, Matt Callahan, Katherine Wynne-Edwards, Scott Hatch, Kyle H. Elliott, Leslie Slater, Akinori Takahashi, Alexander S. Kitaysky, Kyle Elliott, Alexis Will & Alexander Kitaysky
Changes in climate and anthropogenic pressures might affect the composition and abundance of forage fish in the world's oceans. The junk-food hypothesis posits that dietary shifts that affect the quality (e.g., energy content) of food available to marine predators may impact their physiological state and consequently affect their fitness. Previously, we experimentally validated that deposition of the adrenocortical hormone, corticosterone, in feathers is a sensitive measure of nutritional stress in seabirds. Here, we use this...
Data from: Predator-induced phenotypic plasticity within- and across-generations: a challenge for theory?Matthew R. Walsh, Kelsey Biles, Frank Cooley, Stephan B. Munch, S. B. Munch, K. Biles, F. Cooley & M. R. Walsh
Much work has shown that the environment can induce non-genetic changes in phenotype that span multiple generations. Theory predicts that predictable environmental variation selects for both increased within- and across-generation responses. Yet, to the best of our knowledge, there are no empirical tests of this prediction. We explored the relationship between within- versus across-generation plasticity by evaluating the influence of predator cues on the life-history traits of Daphnia ambigua. We measured the duration of predator-induced...
Environmental signals can induce phenotypic changes that span multiple generations. Along with phenotypic responses that occur during development (i.e., ‘within-generation’ plasticity), such ‘transgenerational plasticity’ (TGP) has been documented in a diverse array of taxa spanning many environmental perturbations. New theory predicts that temporal stability is a key driver of the evolution of TGP. We tested this prediction using natural populations of zooplankton from lakes in Connecticut that span a large gradient in the temporal dynamics...
Data from: Does mating behaviour affect connectivity in marine fishes? Comparative population genetics of two protogynous groupers (Family Serranidae)David S. Portnoy, Christopher M. Hollenbeck, Mark A. Renshaw, Nancie J. Cummings, John R. Gold, D. S. Portnoy, C. M. Hollenbeck, M. A. Renshaw, J. R. Gold & N. J. Cummings
Pelagic larval duration (PLD) has been hypothesized to be the primary predictor of connectivity in marine fishes; however, few studies have examined the effects that adult reproductive behaviour may have on realized dispersal. We assessed gene flow (connectivity) by documenting variation in microsatellites and mitochondrial DNA sequences in two protogynous species of groupers, the aggregate spawning red hind, Epinephelus guttatus, and the single-male, harem-spawning coney, Cephalopholis fulva, to ask if reproductive strategy affects connectivity. Samples...
Data from: Discovery and characterization of single nucleotide polymorphisms in coho salmon, Oncorhynchus kisutchHilary A. Starks, Anthony J. Clemento & John Carlos Garza
Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is...
Data from: Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current SystemTyler M. Jackson, G. Curtis Roegner & Kathleen G. O'Malley
Using a combination of population- and individual-based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic structure, and then assessed inter-annual variability in our estimates by sampling again in 2014. Genetic diversity showed little variation among sites or across years. In...
Data from: Spatial distribution, movements, and geographic range of Steller sea lions (Eumetopias jubatus) in AlaskaLauri A. Jemison, Grey W. Pendleton, Kelly K. Hastings, John M. Maniscalco & Lowell W. Fritz
The two stocks of Steller sea lions (Eumetopias jubatus) in Alaska include an endangered western stock, recently recovering in parts of its range following decades of decline, and an eastern stock which was removed from the U.S. Endangered Species List in 2013 following increasing numbers since the 1970s. Information on overlapping distributions of eastern and western sea lions is needed for management considerations. We analyzed >30,000 sightings collected from 2000-2014 of 2,385 sea lions that...
Data from: Long-term population size of the North Atlantic humpback whale within the context of worldwide population structureKristen Ruegg, Howard C. Rosenbaum, Eric C. Anderson, Marcia Engel, Anna Rothschild, C. Scott Baker & Stephen R. Palumbi
Once hunted to the brink of extinction, humpback whales (Megaptera novaeangliae) in the North Atlantic have recently been increasing in numbers. However, uncertain information on past abundance makes it difficult to assess the extent of the recovery in this species. While estimates of pre-exploitation abundance based upon catch data suggest the population might be approaching pre-whaling numbers, estimates based on mtDNA genetic diversity suggest they are still only a fraction of their past abundance levels....
Data from: The importance of standardization for biodiversity comparisons: a case study using Autonomous Reef Monitoring Structures (ARMS) and metabarcoding to measure cryptic diversity on Mo'orea coral reefs, French PolynesiaEmma Ransome, Jonathan B. Geller, Molly Timmers, Matthieu Leray, Angka Mahardini, Andrianus Sembiring, Allen G. Collins & Christopher P. Meyer
The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four...
Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion for City of Ketchikan Removal of Berth II Rock Pinnacle ProjectUnited States. National Marine Fisheries Service
ESA Section 7 Consultation ; AKRO-2019-00553
Revisions to the Incidental Take Statement and Essential Fish Habitat Conservation Recommendations of the Endangered Species Act Section 7 Formal Consultation and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Consultation for the Lolo Insect and Disease Project, Lolo Creek, HUC 17060306, Idaho County, Idaho (One Project)United States. National Marine Fisheries Service
ESA Section 7 Consultation ; WCRO-2019-00351
Endangered Species Act Section 7 Biological Opinion, Concurrence Letter, and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response for Livestock Grazing on the Upper Hayden Cattle and Horse Grazing Allotment, Upper Hayden Creek 5th field Hydrologic Unit Code 1706020406, Lemhi County, Idaho, (One Project)United States. National Marine Fisheries Service
ESA Section 7 Consultation ; WCRO-2019-00305
Endangered Species Act Section 7 Formal Consultation and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Consultation for the Clear Creek Integrated Restoration, Clear Creek, HU Cs 170603040 l O l, 170603040 l 02, l 70603040103, Idaho County, Idaho (One Project)United States. National Marine Fisheries Service
ESA Section 7 Consultation ; WCRO-2019-00545
Endangered Species Act Section 7(a)(2) Biological Opinion, Concurrence Letter, and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response for the Aerial Application of Fire Retardant on National Forest System Land within the jurisdiction of the National Marine Fisheries Service West Coast Region; California, Oregon, Washington, and IdahoUnited States. National Marine Fisheries Service
ESA Section 7 Consultation ; WCRO-2018-00288
Endangered Species Act Section 7(a)(2) Concurrence Letter and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response for the BLM Salmon Field Office Hawley Creek and Leadville Allotments; 1706020402 - Eighteenmile Creek; 1706020403 - Hawley Creek; 1706020404; Lemhi County, IdahoUnited States. National Marine Fisheries Service
ESA Section 7 Consultation ; WCRO-2018-00243
National Marine Fisheries Service142
Pacific Islands Fisheries Science Center8
South Atlantic Fishery Management Council7
Gulf of Mexico Fishery Management Council5
Northeast Fisheries Science Center4
Alaska Department of Fish and Game4
Integrated Statistics (United States)3
The University of Texas at Arlington3
Alaska Fisheries Science Center3
Southwest Fisheries Science Center3
Northwest Fisheries Science Center3
Oregon State University2
University of California, Berkeley2
University of Hawaii at Manoa2
University of Miami2