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USGS2003

Kelp forest ecosystems: Biodiversity, stability, resilience and future

Kelp forests are phyletically diverse, structurally complex and highly productive components of coldwater rocky marine coastlines. This paper reviews the conditions in which kelp forests develop globally and where, why and at what rate they become deforested. The ecology and long archaeological history of kelp forests are examined through case studies from southern California, the Aleutian Islands and the western North Atlantic, well-studied locations that represent the widest possible range in kelp forest biodiversity. Global distribution of kelp forests is physiologically constrained by light at high latitudes and by nutrients, warm temperatures and other macrophytes at low latitudes. Within mid-latitude belts (roughly 40–60° latitude in both hemispheres) well-developed kelp forests are most threatened by herbivory, usually from sea urchins. Overfishing and extirpation of highly valued vertebrate apex predators often triggered herbivore population increases, leading to widespread kelp deforestation. Such deforestations have the most profound and lasting impacts on species-depauperate systems, such as those in Alaska and the western North Atlantic. Globally urchin-induced deforestation has been increasing over the past 2–3 decades. Continued fishing down of coastal food webs has resulted in shifting harvesting targets from apex predators to their invertebrate prey, including kelp-grazing herbivores. The recent global expansion of sea urchin harvesting has led to the widespread extirpation of this herbivore, and kelp forests have returned in some locations but, for the first time, these forests are devoid of vertebrate apex predators. In the western North Atlantic, large predatory crabs have recently filled this void and they have become the new apex predator in this system. Similar shifts from fish- to crab-dominance may have occurred in coastal zones of the United Kingdom and Japan, where large predatory finfish were extirpated long ago. Three North American case studies of kelp forests were examined to determine their long history with humans and project the status of future kelp forests to the year 2025. Fishing impacts on kelp forest systems have been both profound and much longer in duration than previously thought. Archaeological data suggest that coastal peoples exploited kelp forest organisms for thousands of years, occasionally resulting in localized losses of apex predators, outbreaks of sea urchin populations and probably small-scale deforestation. Over the past two centuries, commercial exploitation for export led to the extirpation of sea urchin predators, such as the sea otter in the North Pacific and predatory fishes like the cod in the North Atlantic. The large-scale removal of predators for export markets increased sea urchin abundances and promoted the decline of kelp forests over vast areas. Despite southern California having one of the longest known associations with coastal kelp forests, widespread deforestation is rare. It is possible that functional redundancies among predators and herbivores make this most diverse system most stable. Such biodiverse kelp forests may also resist invasion from non-native species. In the species-depauperate western North Atlantic, introduced algal competitors carpet the benthos and threaten future kelp dominance. There, other non-native herbivores and predators have become established and dominant components of this system. Climate changes have had measurable impacts on kelp forest ecosystems and efforts to control the emission of greenhouse gasses should be a global priority. However, overfishing appears to be the greatest manageable threat to kelp forest ecosystems over the 2025 time horizon. Management should focus on minimizing fishing impacts and restoring populations of functionally important species in these systems.

Environmental Conservation↗
USGS2026

Navigating uncertainty and competing objectives: Spring chinook salmon recovery in the upper Willamette river

Globally, anadromous fish populations are threatened with extinction due to multiple factors, including river impoundments that block migration, widespread alteration of physical habitat, temperature, and flow regimes, commercial and recreational harvest, changes in biological communities, and long-term climate trends. In this synthesis, we describe how physical and biological factors, policy and law, and public resource allocation affect management of spring-run Chinook Salmon ( Oncorhynchus tshawytscha ) in the Upper Willamette River (UWR), Oregon, USA. Efforts to restore salmon populations often involve trade-offs, for example, water management decisions must account for flood control, agricultural and municipal water use, and management of other species. UWR Chinook Salmon recovery efforts are also governed by multiple laws, policies, and action agencies that in some cases have incongruent objectives. Competing and conflicting objectives, combined with uncertainty regarding the outcomes of proposed management actions, create significant challenges for decision makers. Resource limitations, regulatory constraints, and incongruent objectives have created challenges for managers in the UWR, but opportunities exist for improved adaptive management and collaboration, which could build trust and engagement among stakeholders and ultimately support the successful implementation of decision tools. A suite of decision support tools that have been used in the Willamette River basin and elsewhere across the range of Pacific salmon have the potential to enhance decision processes. These tools can be effective when decision makers and stakeholders commit to long-term, collaborative utilization of the tools for decision making, and when available resources and regulatory environments are conducive to implementation and adaptive refinement of both the decision-support tools and management plans. The general biological and institutional principles discussed for UWR Chinook Salmon in this work apply more generally to populations of anadromous fishes across their range, especially to populations in highly regulated river systems.

Oregon↗
USGS2020

Using advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon

Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus ) are a large-bodied anadromous fish that historically supported important fisheries along the east coast of the United States. Following years of overharvest and habitat degradation, populations experienced severe declines. In 2012, the National Marine Fisheries Service listed Atlantic Sturgeon under the Endangered Species Act (ESA; 61 FR 4722). Their listing named five Distinct Population Segments (DPSs), predicated on genetic groups composed of geographically proximate populations. Federal management of Atlantic Sturgeon presents challenges, as sturgeon from each of the five DPSs mix extensively in coastal and marine habitats yet take and recovery progress must be evaluated separately for each unit. Genetic assignment testing based on mitochondrial and microsatellite markers allows individuals to be assigned back to their natal river and DPS. However, this approach is not perfect and some individuals may be incorrectly assigned. Recent advances in genomics offer the potential of a higher resolution approach to genetic assignment testing, and thus may reduce uncertainty associated with assignment testing. In addition, genomics allows a greater number of markers to be examined from across a broader portion of the sturgeon genome, thus may provide an enhanced perspective of population structure for the species, and potentially allow other previously intractable questions to be addressed (Bernatchez et al. 2017, Supple and Shapiro 2018). We used next-generation sequencing to develop a draft genome for Atlantic Sturgeon and identify single nucleotide polymorphisms (SNPs) that could be used to resolve the natal river and DPS of individual Atlantic Sturgeon. We identified 1,210 candidate SNPs within the nuclear genome as well as 49 SNPs within the mitochondrial genome. After filtering and review, we selected 161 nuclear SNPs and 39 mitochondrial SNPs for further testing and evaluation. We used genotyping-in-thousands by sequencing (GT-seq) to simultaneously sequence nuclear SNP loci, mitochondrial SNP loci, and the existing panel of twelve microsatellite loci. This effort required a pilot sequencing run on a single sturgeon sample to test marker amplification and refine primer strengths, followed by a series of sequencing runs to generate baseline data for 288 individuals representing nine populations of Atlantic Sturgeon in four DPSs. Using baseline data from the nine populations, we ran a series of genomic analyses to characterize diversity within and among populations, providing a benchmark for this species using the new SNP markers. Allelic richness was similar for all populations, although there was a general trend of more northern population containing greater levels of allelic richness. Interestingly, we observed linkage disequilibrium among many pairs of loci within many populations. This might be the result of physical linkage but could also suggest these populations are recovering from genetic bottlenecks and/or are effectively small, leading to specific haplotypes to be favored by chance. Pairwise differentiation among populations varied among the populations ( F ST range: 0.010-0.098) and was significantly correlated ( r = 0.771; P < 0.001) to pairwise F ST observed using microsatellite markers). Population clustering and ordination techniques using the new genomic data both support an overall population structure that is similar to the current DPS management units (which were developed primarily based on microsatellite genetic data). Overall, this suggests that existing microsatellite markers and the panel of SNP markers developed in this study provide similar information about the populations structure and ecology of Atlantic Sturgeon. Given the observed differences in allele frequencies among populations, our genomic baseline supports previous assertations that Atlantic Sturgeon show natal homing, despite mixing extensively in marine waters during non-breeding periods. Lower levels of differentiation between populations in the South Atlantic DPS suggest that populations in this region may have greater levels of gene flow relative to their more northerly conspecifics, which has also previously been suggested based on microsatellite data. The observed differentiation among populations provides the necessary foundation for determining the natal river and DPS of Atlantic Sturgeon using assignment testing. We tested the utility of our new genomic baseline for resolving the population and DPS of Atlantic Sturgeon. Our nuclear SNP markers showed utility for identifying the origin of unknown Atlantic Sturgeon samples, as 86.5% were assigned to the correct DPS and 66.3% were assigned to the correct natal river. However, since this study was funded the Conservation Genetics and Genomics Laboratory at Leetown Science Center has made significant improvements to their microsatellite genetic baseline, which now performs more effectively than our new genomic approach (the genetic baseline includes 12 populations and 5 DPSs, and correctly assigns 95.8% of individuals to DPS and 84.9% of individuals to their natal population using 12 microsatellite loci). We conducted an ad hoc exploration of how additional microsatellite or nuclear SNP loci may further improve the accuracy of assignment testing. We found that additional microsatellite markers are likely to result in greater improvements in assignment efficiency than additional nuclear SNPs. However, a much larger number of SNP loci (which if identified could be sequenced using other methods that are now available; e.g., the RAD-capture approach published by Ali et al. 2016) could produce assignment efficiencies that are greater than what is currently feasible using microsatellites. In the absence of further research and development of additional SNP markers for Atlantic Sturgeon (possibly using an approach other than GT-seq), the existing microsatellite loci are the most effective means available to determine the natal river and DPS of Atlantic Sturgeon encountered in offshore waters. Because our new genomic markers were less effective than the existing panel of 12 microsatellite markers, we chose to use the existing microsatellite markers to assign Atlantic Sturgeon captured in another BOEM-funded study (cooperative agreement M16AC00003; Monitoring endangered Atlantic Sturgeon and commercial finfish habitat use offshore New York) following consultation with our project officer. Using this approach, we genotyped and assigned 186 Atlantic Sturgeon captured in coastal waters off the Rockaway Peninsula, New York. The vast majority of these sturgeon were assigned to the New York Bight DPS (94.62%), and most appear to belong to the Hudson River population (87.10%) with smaller contributions from the Delaware River population (7.53%). Smaller contributions (2.15%) were observed from six other populations, including those from the James, York, Kennebec, Ogeechee, and Edisto rivers. Although most of the fish we assigned were assigned to the nearest spawning rivers (Hudson and Delaware), the contributions from distant rivers is consistent with the propensity of this species to move long distances and form mixed stock aggregations along the continental shelf. This finding indicates that spawning populations (and their corresponding DPS) from distant locations may potentially be impacted by offshore activities. In fact, activities in this region of the New York Bight could negatively impact Atlantic Sturgeon population from at least four different DPSs. Genetic or genomic assignment testing remains an essential tool to characterize potential impacts to Atlantic Sturgeon populations and should be applied more broadly to better characterize potential impacts of activities in other locations.

Atlantic Coast↗
USGS1957

Geology of possible petroleum provinces in Alaska

The history of petroleum exploration in Alaska and the geology of possible petroleum provinces in Alaska are reviewed. Maps showing Alaska's major Mesozoic and Tertiary tectonic elements, possible petroleum provinces, and indications of petrol, are included in this report. Annotated references in Geological Survey publications relating to petroleum and oil shale in Alaska are given at the end of the report. For the purpose of appraising its petroleum possibilities, Alaska is divided into the southern, central, and northern major geologic-physiographic regions. Southern Alaska includes the arcuate mountain chain formed by the Alaska and Aleutian Ranges and the Mentasta- Nutzotin Mountains, the coastal range and valley area to the south, and the southeastern Alaska "panhandle" -- an area of 185,000 square miles. Oil seeps on the west shore of Cook Inlet in southern Alaska were known as early as 1853, and claims were staked in this region in 1882. Drilling began near the oil seeps in the Katalla district about 1901, and this started Alaska's first period of oil activity. From 1902 to 1933 the Katalla field produced 154,000 barrels of oil from fractured shale and sandstone of Tertiary age the- first and only commercial production in Alaska. On the basis of geology, surficial indications of petroleum, and test wells drilled, six possible petroleum provinces are indicated in southern Alaska. They are Heceta Island area, Keku Islands area, Cook Inlet Mesozoic province, Gulf of Alaska Tertiary province, Cook Inlet Tertiary province, and Copper River basin. The exposed rocks in the Heceta Island area include lower Paleozoic graywacke-type sandstone, sandstone, conglomerate, and massive limestones with reeflike structures; igneous rocks are rare or lacking in much of the area. The Kosciusko-Tuxekan-Heceta synclinorium, the main structural feature, is modified by minor folds and faults. Some of the minor folds are reported to be broad and open, with flanks dipping 20°-145°. As far as known, the Heceta Island area has not heretofore been seriously considered as a possible petroleum province. Rocks of Silurian to Cretaceous age are exposed in the Keku Island area and include moderately folded and relatively unaltered limestone and other marine sedimentary rocks. The Cook Inlet Mesozoic province, a land area of approximately 18,500 square miles, includes a great thickness of unmetamorphosed marine sedimentary rocks of Jurassic and Cretaceous age. At least 23 test wells were drilled or started in this province by the end of 1955. Shows of oil and gas were encountered in many of these wells. During 1955 at least ten oil companies were active in this area and by the end of 1955 about 1 1/2 million acres were included in oil and gas leases applied for or granted. The Gulf of Alaska Tertiary province includes about 5,200 square miles in which rocks of Tertiary age are exposed or are believed to underlie Quaternary deposits. Between 1901 and the end of 1955 about 47 wells were drilled or started in this province. The Cook Inlet Tertiary province embraces an area of about 9,500 square miles, of which about 4,100 is covered by the shallow waters of Cook Inlet. Petroleum exploration has been in that part of the area which overlaps the Cook Inlet Mesozoic province. Eocene or younger Tertiary nonmarine sedimentary rocks are believed to underlie much of the province, and marine rocks of Tertiary age may also be present. The Copper River basin is a topographic basin underlain by unconsolidated deposits of Quaternary age. Tertiary rocks favorable for the accumulation of petroleum may underlie part of the basin but this is not believed likely. Except for some leasing activity no petroleum exploration has been recorded in the Copper River Basin to the end of 1955. Central Alaska is a region of about 275,000 square miles and consists of an irregular assemblage of intricately dissected uplands and alluvium-floored lowland basins. Scattered peaks of resistant intrusive igneous rocks surmount most of the upland areas. In the vast region of central Alaska only six test wells are known to have been drilled for the purpose of finding oil and gas. The maximum depth reached was 350 feet and the holes were mostly or entirely in Quaternary deposits. In recent years several oil companies have investigated some parts of the region and large areas in the Yukon-Koyukuk province are now under lease. Oil seeps, gas seeps, and other indications of petroleum have been reported from many localities; samples from two localities have been analyzed and reported to be petroleum. The geology of central Alaska is similar in a general way to that of the area between the Rocky Mountains and Sierra-Cascade belts of the United States. Sedimentary rocks, probably equivalent to the Precambrian Belt series, and rocks of the Cambrian and all younger geologic systems have been recognized in central Alaska. The structure of the region is known to be complex, but except in local mineral districts, it has not been mapped in detail. Based on the limited amount of available information, the region cannot be regarded as distinctly favorable for significant accumulations of petroleum. However, three pre-Cenozoic provinces, the Yukon-Koyukuk, the Kobuk, and the Kandik, and several large Cenozoic basin provinces may be worthy of further investigation. Northern Alaska includes the Brooks Range and all the treeless tundra north to the Arctic Coast, an area of about 125,000 square miles. The presence of oil seeps along the Arctic Coast has been known at least since 1900 and a description of the Cape Simpson oil seeps vas published in 1909. Since then oil and gas seeps have been described from nine localities, and oil shales and oil-bearing sandstones are known from many localities in the Arctic Foothills province. Oil and gas deposits have been discovered and geologic conditions are favorable for oil and gas accumulations in approximately half of the region. In 1923 approximately 37,000 square miles in northern Alaska was reserved by Executive order as Naval Petroleum Reserve No. 4. In 1944 the U. S. Navy began a vast petroleum exploration program which was suspended in 1953. In the years 1945 through 1955, 37 test wells and 45 core tests were drilled on 18 structures. Three oil fields, Umiat, Simpson, and Fish Creek, and two gas fields, South Barrow and Gubik, were discovered. Total reserve estimates for all discoveries of oil to 1955 range from 30 to 100 million barrels, and for gas, from 370 billion to 900 billion cubic feet. All northern Alaska, with the exception of the Brooks Range, can be considered a possible petroleum province, but the region can be subdivided into provinces of somewhat different potentialities. These subdivisions roughly correspond with the geomorphic provinces and sections, which in turn reflect differences in geology. The known oil-bearing beds are of Mesozoic age, primarily Cretaceous, and thus the possible petroleum provinces could be designated as Mesozoic. However, Paleozoic and Cenozoic rocks with favorable reservoir characteristics are exposed in the region and possibly underlie, in favorable structural situations, some of the areas as yet not tested. The Arctic Coastal Plain province includes gently folded and flat-lying Mesozoic beds that overlie a basement complex of Paleozoic and early Mesozoic age. Near the southern edge of this province the basement rocks are at depths of at least 20,000 feet, and to the north these rocks rise to within 2,500 feet of the surface. The Teshukpuk Lake section of the Arctic Coastal plain includes many of the known oil seeps; it is the most accessible to sea transportation, and lies almost completely within NPR 4. Thirteen test wells and 35 core tests have been drilled here; one gas field and two (at present, noncommercial) oil fields have been discovered. The possibility of further discoveries may depend largely on locating porous sandstones in stratigraphic rather than anticlinal traps. The White Hills section is distinguished topographically from the Teshukpruk section by its white-gravel-covered hills and fever lakes, and geologically by the presence of Tertiary rocks, including 2,000 feet of nonmarine beds in the west and at least 7,000 feet of marine beds to the east, in the vicinity of Carter Creek. This section appears to be more complex structurally. No test wells have been drilled in the White Hills section. The Northern Foothills section includes many closed anticlines. Twenty-four test wells and ten core tests have been drilled on 11 structures and two discoveries have been made -the Umiat oil field and the Gubik gas field. All these tests have been drilled in Cretaceous rocks. The Southern Foothills section is structurally similar to the Alberta Foothills and to the northern part of the Brooks Range. Great thicknesses of marine shale of Lover Cretaceous, Jurassic, and Triassic age are exposed. The outcropping Mesozoic sandstones are generally poorly sorted, nonporous, and impermeable. To the south the section is bordered by mountainous exposures of Mississippian limestone, which probably underlie at least part of this section. The rocks that underlie the deeply eroded complex structures of the Brooks Range include schist, slate, argillite, and limestone. Some exposed limestones have a strong petroleum-like odor and contain traces of petroleum residues.

Alaska↗