scholarly journals Distribution and seasonal differences in Pacific Lamprey andLampetraspp eDNA across 18 Puget Sound watersheds

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4496 ◽  
Author(s):  
Carl O. Ostberg ◽  
Dorothy M. Chase ◽  
Michael C. Hayes ◽  
Jeffrey J. Duda
Keyword(s):  
North America ◽  
Detection Rate ◽  
Puget Sound ◽  
Environmental Dna ◽  
Probe Design ◽  
Significant Finding ◽  
Ecological Communities ◽  
Detection Rates ◽  
Pacific Lamprey ◽  
The Pacific

Lampreys have a worldwide distribution, are functionally important to ecological communities and serve significant roles in many cultures. In Pacific coast drainages of North America, lamprey populations have suffered large declines. However, lamprey population status and trends within many areas of this region are unknown and such information is needed for advancing conservation goals. We developed two quantitative PCR-based, aquatic environmental DNA (eDNA) assays for detection of Pacific Lamprey (Entosphenus tridentatus) andLampetraspp, using locked nucleic acids (LNAs) in the probe design. We used these assays to characterize the spatial distribution of lamprey in 18 watersheds of Puget Sound, Washington, by collecting water samples in spring and fall. Pacific Lamprey andLampetraspp were each detected in 14 watersheds and co-occurred in 10 watersheds. Lamprey eDNA detection rates were much higher in spring compared to fall. Specifically, the Pacific Lamprey eDNA detection rate was 3.5 times higher in spring and theLampetraspp eDNA detection rate was 1.5 times higher in spring even though larval lamprey are present in streams year-round. This significant finding highlights the importance of seasonality on eDNA detection. Higher stream discharge in the fall likely contributed to reduced eDNA detection rates, although seasonal life history events may have also contributed. These eDNA assays differentiate Pacific Lamprey andLampetraspp across much of their range along the west coast of North America. Sequence analysis indicates the Pacific Lamprey assay also targets otherEntosphenusspp and indicates theLampetraspp assay may have limited or no capability of detectingLampetrain some locations south of the Columbia River Basin. Nevertheless, these assays will serve as a valuable tool for resource managers and have direct application to lamprey conservation efforts, such as mapping species distributions, occupancy modeling, and monitoring translocations and reintroductions.

Status, Distribution, and Conservation of Native Freshwater Fishes of Western North America

2007 ◽  
Keyword(s):  
North America ◽  
River Basin ◽  
Ecological Niche ◽  
Snake River ◽  
Pacific Lamprey ◽  
The Pacific ◽  
Coarse Substrate ◽  
The One ◽  
Clearwater River ◽  
Water Depths

ABSTRACT The Pacific lamprey <em>Lampetra tridentata</em> is a native Snake River basin fish species occupying a unique ecological niche. The recent decline in numbers of returning Pacific lamprey adults to the Snake River basin has focused attention on the species. In 2000–2002, we employed electrofishing surveys to determine habitat utilization and distribution of Pacific lamprey ammocoetes in Red River, South Fork Clearwater River drainage, Idaho. Ammocoete average densities were 25.7/100 m<sup>2</sup> in scour pools, 4.4/100 m<sup>2</sup> in riffles, 2.1/100 m<sup>2</sup> in rapids, and 253.3/100 m<sup>2</sup> in the one alcove sampled. Ammocoetes were found in water depths ranging from 1.0 cm to 1.0 m; however, the two greatest densities were observed in habitat units with maximum depths greater than 0.50 m. Pacific lamprey ammocoete density decreased with increased velocity and coarse substrate, and increased with fine and medium substrates and riparian shade.

scholarly journals Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae

2020 ◽  
Author(s):  
Emily Jacobs-Palmer ◽  
Ramón Gallego ◽  
Kelly Cribari ◽  
Abigail Keller ◽  
Ryan P. Kelly
Keyword(s):  
Algal Blooms ◽  
Cold Water ◽  
Global Climate ◽  
Puget Sound ◽  
Environmental Dna ◽  
Harmful Algae ◽  
Social Consequences ◽  
Ecological Communities ◽  
Ecological Context ◽  
Dna Metabarcoding

AbstractHarmful algae can have profound economic, environmental, and social consequences. As the timing, frequency, and severity of harmful algal blooms (HABs) change alongside global climate, efficient tools to monitor and understand the current ecological context of these taxa are increasingly important. Here we employ environmental DNA metabarcoding to identify patterns in a wide variety of harmful algae and associated ecological communities in the Hood Canal of Puget Sound in Washington State, USA. We track trends of presence and abundance in a series of water samples across nearly two years. We find putative harmful algal sequences in a majority of samples, suggesting that these groups are routinely present in local waters. We report patterns in variants of the economically important genus Pseudo-nitzschia (family Bacillariaceae), as well as multiple harmful algal taxa previously unknown or poorly documented in the region, including a cold-water variant from the saxitoxin-producing genus Alexandrium (family Gonyaulacaceae), two variants from the karlotoxin-producing genus Karlodinium (family Kareniaceae), and one variant from the parasitic genus Hematodinium (family Syndiniaceae). We then use data on environmental variables and the biological community surrounding each algal taxon to illustrate the ecological context in which these species are commonly found. Environmental DNA metabarcoding thus simultaneously (1) alerts us to potential new or cryptic occurrences of harmful algae, (2) expands our knowledge of the co-occurring conditions and species associated with the growth of these organisms in changing marine environments, and (3) provides a tool for monitoring and management moving forward.

scholarly journals Seasonal monitoring of Hida salamander Hynobius kimurae using environmental DNA with a genus-specific primer set

2020 ◽  
Vol 43 ◽  
pp. 341-352
Author(s):  
T Jo ◽  
S Tomita ◽  
Y Kohmatsu ◽  
M Osathanunkul ◽  
A Ushimaru ◽  
...  
Keyword(s):  
Detection Rate ◽  
Habitat Restoration ◽  
Site Occupancy ◽  
Environmental Dna ◽  
Taqman Probe ◽  
Morphological Identification ◽  
Target Species ◽  
Amphibian Species ◽  
Detection Rates ◽  
Occupancy Probability

The diversity and the abundance of amphibians have dramatically declined globally over the past 30 years, and the monitoring and conservation of their habitats is essential. However, traditional methods such as bait trapping and mark-recapture are costly, and morphological identification usually requires a high level of taxonomic expertise. Here, seasonal surveillances of Hida salamander Hynobius kimurae were performed by means of environmental DNA (eDNA) analysis with Hynobius-specific primers and a species-specific TaqMan probe. Water sampling and visual surveys were conducted seasonally in a stream in Kyoto Prefecture, Japan. Detection rates of eDNA were then calculated by real-time PCR, and eDNA site occupancy probability was estimated by multi-scale occupancy modeling. The eDNA-based detection rate of Hida salamander was 76.7%, whereas the visual survey-based detection rate was 23.3%, and target eDNA was detected at almost all sites where the presence of target species was visually confirmed. Moreover, factors relating to the site- and sample-level occurrence probabilities of the target eDNA differed depending on the developmental stage of the target species. Our findings support previous studies showing that eDNA analysis enables an effective assessment of amphibian distributions without damaging the organisms or their habitat, and we compare for the first time the site occupancy probability of amphibian eDNA throughout the life cycle of an amphibian species. The present study contributes to the development of eDNA analysis as a tool for understanding the distribution and seasonal activity of amphibian species and will thus aid in the planning of conservation measures and habitat restoration for these species.

Coexistence of three specialist predators of the hemlock woolly adelgid in the Pacific Northwest USA

2019 ◽  
Vol 110 (3) ◽  
pp. 303-308 ◽  
Author(s):  
Alexander Rose ◽  
Darrell W. Ross ◽  
Nathan P. Havill ◽  
Kyle Motley ◽  
Kimberly F. Wallin
Keyword(s):  
Biological Control ◽  
North America ◽  
Pacific Northwest ◽  
Puget Sound ◽  
Hemlock Woolly Adelgid ◽  
Adelges Tsugae ◽  
Laricobius Nigrinus ◽  
The Pacific ◽  
Eastern Usa ◽  
Specialist Predators

AbstractThe hemlock woolly adelgid (Hemiptera: Adelgidae: Adelges tsugae Annand) is an invasive insect, introduced from Japan to eastern North America, where it causes decline and death of hemlock trees. There is a closely related lineage of A. tsugae native to western North America. To inform classical biological control of A. tsugae in the eastern USA, the density and phenology of three native western adelgid specialist predators, Leucopis argenticollis (Zetterstedt), Le. piniperda (Malloch) (Diptera: Chamaemyiidae), and Laricobius nigrinus Fender (Coleoptera: Derodontidae), were quantified in the Pacific Northwest. Infested branches were collected from western hemlock (Pinaceae: Tsuga heterophylla (Raf.) Sarg.) at four sites around the Puget Sound, Washington and three sites in Oregon. Immature Leucopis were identified to species using DNA barcodes. Leucopis argenticollis was roughly twice as abundant as Le. piniperda. Laricobius nigrinus larvae were more abundant than the two species of Leucopis during the egg stage of the first adelgid generation, but Leucopis were present as feeding larvae during the second adelgid generation when La. nigrinus was aestivating in the soil, resulting in Leucopis being more abundant than La. nigrinus across the entire sampling period. Adelges tsugae and La. nigrinus densities were not correlated, while A. tsugae and Leucopis spp. densities were positively correlated. Leucopis spp. and La. nigrinus densities were negatively correlated. These results support the complementary use of La. nigrinus and the two Leucopis species for biological control of A. tsugae in the eastern USA, and point to the need for further investigation of spatial and temporal niche partitioning among the three predator species.

scholarly journals Fault locking, block rotation and crustal deformation in the Pacific Northwest

2007 ◽  
Vol 169 (3) ◽  
pp. 1315-1340 ◽  
Author(s):  
Robert McCaffrey ◽  
Anthony I. Qamar ◽  
Robert W. King ◽  
Ray Wells ◽  
Giorgi Khazaradze ◽  
...  
Keyword(s):  
North America ◽  
Shear Deformation ◽  
Pacific Northwest ◽  
Puget Sound ◽  
Vancouver Island ◽  
Block Rotation ◽  
The Pacific ◽  
Juan De Fuca ◽  
Gps Velocities ◽  
Relative Motions

Summary We interpret Global Positioning System (GPS) measurements in the northwestern United States and adjacent parts of western Canada to describe relative motions of crustal blocks, locking on faults and permanent deformation associated with convergence between the Juan de Fuca and North American plates. To estimate angular velocities of the oceanic Juan de Fuca and Explorer plates and several continental crustal blocks, we invert the GPS velocities together with seafloor spreading rates, earthquake slip vector azimuths and fault slip azimuths and rates. We also determine the degree to which faults are either creeping aseismically or, alternatively, locked on the block-bounding faults. The Cascadia subduction thrust is locked mainly offshore, except in central Oregon, where locking extends inland. Most of Oregon and southwest Washington rotate clockwise relative to North America at rates of 0.4–1.0 ° Myr−1. No shear or extension along the Cascades volcanic arc has occurred at the mm/yr level during the past decade, suggesting that the shear deformation extending northward from the Walker Lane and eastern California shear zone south of Oregon is largely accommodated by block rotation in Oregon. The general agreement of vertical axis rotation rates derived from GPS velocities with those estimated from palaeomagnetic declination anomalies suggests that the rotations have been relatively steady for 10–15 Ma. Additional permanent dextral shear is indicated within the Oregon Coast Range near the coast. Block rotations in the Pacific Northwest do not result in net westward flux of crustal material—the crust is simply spinning and not escaping. On Vancouver Island, where the convergence obliquity is less than in Oregon and Washington, the contractional strain at the coast is more aligned with Juan de Fuca—North America motion. GPS velocities are fit significantly better when Vancouver Island and the southern Coast Mountains move relative to North America in a block-like fashion. The relative motions of the Oregon, western Washington and Vancouver Island crustal blocks indicate that the rate of permanent shortening, the type that causes upper plate earthquakes, across the Puget Sound region is 4.4 ± 0.3 mm yr−1. This shortening is likely distributed over several faults but GPS data alone cannot determine the partitioning of slip on them. The transition from predominantly shear deformation within the continent south of the Mendocino Triple Junction to predominantly block rotations north of it is similar to changes in tectonic style at other transitions from shear to subduction. This similarity suggests that crustal block rotations are enhanced in the vicinity of subduction zones possibly due to lower resisting stress.

scholarly journals Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae

2021 ◽  
Vol 9 ◽  
Author(s):  
Emily Jacobs-Palmer ◽  
Ramón Gallego ◽  
Kelly Cribari ◽  
Abigail G. Keller ◽  
Ryan P. Kelly
Keyword(s):  
Algal Blooms ◽  
Cold Water ◽  
Global Climate ◽  
Puget Sound ◽  
Environmental Dna ◽  
Harmful Algae ◽  
Social Consequences ◽  
Ecological Communities ◽  
Ecological Context ◽  
Dna Metabarcoding

Harmful algae can have profound economic, environmental, and social consequences. As the timing, frequency, and severity of harmful algal blooms (HABs) change alongside global climate, efficient tools to monitor and understand the current ecological context of these taxa are increasingly important. Here we employ environmental DNA metabarcoding to identify patterns in a wide variety of potentially harmful algae and associated ecological communities in the Hood Canal of Puget Sound in Washington State, USA. Tracking trends of occurrence in a series of water samples over a period of 19 months, we find algal sequences from genera with harmful members in a majority of samples, suggesting that these groups are routinely present in local waters. We report patterns in variants of the economically important genus Pseudo-nitzschia (of which some members produce domoic acid; family Bacillariaceae), as well as multiple potentially harmful algal taxa previously unknown or poorly documented in the region, including a cold-water variant from the genus Alexandrium (of which some members produce saxitoxin; family Gonyaulacaceae), two variants from the genus Karlodinium (of which some members produce karlotoxins; family Kareniaceae), and one variant from the parasitic genus Hematodinium (family Syndiniaceae). We then use data on environmental variables and the biological community surrounding each algal taxon to illustrate the ecological context in which they are commonly found. Environmental DNA metabarcoding thus simultaneously (1) alerts us to potential new or cryptic occurrences of algae from harmful genera, (2) expands our knowledge of the co-occurring conditions and species associated with the growth of these organisms in changing marine environments, and (3) suggests a pathway for multispecies monitoring and management moving forward.

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