Applying time series models with spatial correlation to identify the scale of variation in habitat metrics related to threatened coho salmon (Oncorhynchus kisutch) in the Pacific Northwest

2012 ◽  
Vol 69 (11) ◽  
pp. 1773-1782 ◽  
Author(s):  
Eric J. Ward ◽  
George R. Pess ◽  
Kara Anlauf-Dunn ◽  
Chris E. Jordan
Keyword(s):  
Time Series ◽  
Spatial Correlation ◽  
Pacific Northwest ◽  
Coho Salmon ◽  
Spatial Scales ◽  
Oncorhynchus Kisutch ◽  
Fine Sediment ◽  
Environmental Stochasticity ◽  
Observation Error ◽  
Data Set

Trend analyses are common in the analysis of fisheries data, yet the majority of them ignore either observation error or spatial correlation. In this analysis, we applied a novel hierarchical Bayesian state-space time series model with spatial correlation to a 12-year data set of habitat variables related to coho salmon ( Oncorhynchus kisutch ) in coastal Oregon, USA. This model allowed us to estimate the degree of spatial correlation separately for each habitat variable and the importance of observation error relative to environmental stochasticity. This framework allows us to identify variables that would benefit from additional sampling and variables where sampling could be reduced. Of the eight variables included in our analysis, we found three metrics related to habitat quality correlated at large spatial scales (gradient, fine sediment, shade cover). Variables with higher observation error (pools, active channel width, fine sediment) could be made more precise with more repeat visits. Our spatio-temporal model is flexible and extendable to virtually any spatially explicit monitoring data set, even with large amounts of missing data and no repeated observations. Potential extensions include fisheries catch data, abiotic indicators, invasive species, or species of conservation concern.

Environmental factors influencing freshwater survival and smolt production in Pacific Northwest coho salmon (Oncorhynchus kisutch)

2004 ◽  
Vol 61 (3) ◽  
pp. 360-373 ◽  
Author(s):  
P W Lawson ◽  
E A Logerwell ◽  
N J Mantua ◽  
R C Francis ◽  
V N Agostini
Keyword(s):  
Pacific Northwest ◽  
Air Temperature ◽  
Coho Salmon ◽  
Oncorhynchus Kisutch ◽  
Stream Flows ◽  
Factors Influencing ◽  
Life Phase ◽  
Air Temperatures ◽  
Queets River ◽  
Marine Survival

Climate variability is well known to affect the marine survival of coho salmon (Oncorhynchus kisutch) in Oregon and Washington. Marine factors have been used to explain up to 83% of the variability in Oregon coastal natural coho salmon recruitment, yet about half the variability in coho salmon recruitment comes from the freshwater life phase of the life cycle. This seeming paradox could be resolved if freshwater variability were linked to climate and climate factors influencing marine survival were correlated with those affecting freshwater survival. Effects of climate on broad-scale fluctuations in freshwater survival or production are not well known. We examined the influence of seasonal stream flows and air temperature on freshwater survival and production of two stock units: Oregon coastal natural coho salmon and Queets River coho salmon from the Washington Coast. Annual air temperatures and second winter flows correlated strongly with smolt production from both stock units. Additional correlates for the Oregon Coast stocks were the date of first fall freshets and flow during smolt outmigration. Air temperature is correlated with sea surface temperature and timing of the spring transition so that good freshwater conditions are typically associated with good marine conditions.

Metrics and sampling designs for detecting trends in the distribution of spawning Pacific salmon (Oncorhynchus spp.)

2012 ◽  
Vol 69 (4) ◽  
pp. 681-694 ◽  
Author(s):  
Stephanie J. Peacock ◽  
Carrie A. Holt
Keyword(s):  
Population Dynamics ◽  
Environmental Variability ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Oncorhynchus Kisutch ◽  
Sensitivity Analyses ◽  
Observation Error ◽  
Simulated Population ◽  
Age At Maturity ◽  
Status Assessment

The distribution of individuals among populations and in space may contribute to their resilience under environmental variability. Changes in distribution may indicate the loss of genetically distinct subpopulations, the deterioration of habitat capacity, or both. The distribution of Pacific salmon ( Oncorhynchus  spp.) among spawning locations has recently been recognized as an important component of status assessment by USA and Canadian management agencies, but metrics of spawning distribution have not been rigorously evaluated. We evaluated three metrics of spawning distribution and four sampling designs for their ability to detect simulated contractions in the production of coho salmon ( Oncorhynchus kisutch ). We simulated population dynamics at 100 sites using a spawner–recruit model that incorporated natural variability in recruitment, age-at-maturity, dispersal, and measurement error in observations of abundance. Sensitivity analyses revealed that high observation error and straying of spawners from their natal streams may mask changes in distribution. Furthermore, monitoring only sites with high spawner abundance, as is often practiced, failed to capture the simulated contraction of production, emphasizing the importance of matching monitoring programs with assessment objectives.

scholarly journals The Hamburg Ocean Atmosphere Parameters and Fluxes from Satellite Data – HOAPS-3

2010 ◽  
Vol 2 (2) ◽  
pp. 215-234 ◽  
Author(s):  
A. Andersson ◽  
K. Fennig ◽  
C. Klepp ◽  
S. Bakan ◽  
H. Graßl ◽  
...  
Keyword(s):  
Time Series ◽  
Satellite Data ◽  
Spatial Scales ◽  
Heat Fluxes ◽  
Freshwater Flux ◽  
Climate Modelling ◽  
Turbulent Heat ◽  
Data Sampling ◽  
Data Set ◽  
Ocean Atmosphere

Abstract. The availability of microwave instruments on satellite platforms allows the retrieval of essential water cycle components at high quality for improved understanding and evaluation of water processes in climate modelling. HOAPS-3, the latest version of the satellite climatology "Hamburg Ocean Atmosphere Parameters and Fluxes from Satellite Data" provides fields of turbulent heat fluxes, evaporation, precipitation, freshwater flux and related atmospheric variables over the global ice-free ocean. This paper describes the content, methodology and retrievals of the HOAPS climatology. A sophisticated processing chain, including all available Special Sensor Microwave Imager (SSM/I) instruments aboard the satellites of the Defense Meteorological Satellites Program (DMSP) and careful inter-sensor calibration, ensures a homogeneous time-series with dense data sampling and hence detailed information of the underlying weather situations. The completely reprocessed data set with a continuous time series from 1987 to 2005 contains neural network based algorithms for precipitation and wind speed and Advanced Very High Resolution Radiometer (AVHRR) based SST fields. Additionally, a new 85 GHz synthesis procedure for the defective SSM/I channels on DMSP F08 from 1988 on has been implemented. Freely available monthly and pentad means, twice daily composites and scan-based data make HOAPS-3 a versatile data set for studying ocean-atmosphere interaction on different temporal and spatial scales. HOAPS-3 data products are available via http://www.hoaps.org.

Spatial and temporal factors affecting survival in coho salmon (Oncorhynchus kisutch) in the Pacific Northwest

1998 ◽  
Vol 55 (9) ◽  
pp. 2067-2077 ◽  
Author(s):  
Claribel Coronado ◽  
Ray Hilborn
Keyword(s):  
British Columbia ◽  
Pacific Northwest ◽  
Coho Salmon ◽  
Survival Rates ◽  
Oncorhynchus Kisutch ◽  
Dominant Factor ◽  
Spatial And Temporal Patterns ◽  
Factors Affecting ◽  
The Pacific ◽  
Ocean Conditions

Survival rates for coho salmon (Oncorhynchus kisutch) were estimated for all coded wire tag release groups in the Pacific Northwest between 1971 and 1990. The spatial and temporal patterns show considerable geographic variation, with most regions south of northern British Columbia showing declining survival since 1983, while northern areas have shown increasing survival during that period. The number of years of operation explained very little of the variation in survival, and many hatcheries showed major increases in survival after several years of operation. Survival of marked wild fish generally showed the same trend as hatchery fish. We conclude that the dominant factor affecting coho salmon survival since the 1970s is ocean conditions and that there are major geographic differences in the pattern of ocean conditions. The decline in survival seen in British Columbia and south over the last decade suggests that a major reduction in exploitation rates is necessary to maintain the populations.

Estimating the Population Dynamics of Coho Salmon (Oncorhynchus kisutch) Using Pooled Time-Series and Cross-Sectional Data

1985 ◽  
Vol 42 (3) ◽  
pp. 459-467 ◽  
Author(s):  
James L. Anderson ◽  
James E. Wilen
Keyword(s):  
Time Series ◽  
Population Dynamics ◽  
River Flow ◽  
Coho Salmon ◽  
Oncorhynchus Kisutch ◽  
Cross Sectional ◽  
Factors Affecting ◽  
River Region ◽  
Parent Stock ◽  
Pooled Time Series

The population dynamics of natural and hatchery coho salmon (Oncorhynchus kisutch) were estimated for three regions, (1) Washington coastal, (2) Columbia River region, and (3) Oregon/California coastal, using pooled time-series and cross-sectional data. Two functional forms were compared: the Beverton–Holt and Ricker models. Both models yielded very similar results. In both cases, we found that the natural coho stock recruitment is significantly affected by parent stock level (positive), parent stock density (negative), river flow (positive), and hatchery smolt release (negative). The significant factors affecting hatchery coho salmon were smolt release level (positive), smolt release density (negative), and upwelling (positive).

Trade-offs between monitoring objectives and monitoring effort when classifying regional conservation status of Pacific salmon (Oncorhynchus spp.) populations

2011 ◽  
Vol 68 (5) ◽  
pp. 880-897 ◽  
Author(s):  
Kendra R. Holt ◽  
Randall M. Peterman ◽  
Sean P. Cox
Keyword(s):  
Missing Data ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Conservation Status ◽  
Temporal Trends ◽  
Spatial And Temporal Variation ◽  
Spatial And Temporal Variability ◽  
Sampling Effort ◽  
Observation Error ◽  
Data Set

Conservation objectives aimed at maintaining the diversity of Pacific salmon ( Oncorhynchus spp.) are often expressed as a desire to ensure that spawner abundance is spread out over a number of spawning sites. However, sampling is not usually possible at all sites or in all years. For such incomplete data sets, rotating panel sampling designs and hierarchical estimation models have been suggested as ways to improve monitoring performance. To evaluate the potential benefits of using these approaches to assess the conservation status of coho salmon ( O. kisutch ), we developed a simulation procedure that modelled spatial and temporal variation in salmon abundance at multiple sites within a region. Results show that both approaches were largely unsuccessful at reducing classification errors for conservation status. Furthermore, indicators describing distributions of abundance levels and temporal trends in abundance within a region were more sensitive to missing data than to observation error variance on annual abundance estimates. Thus, sampling effort might be better spent reducing the level of missing data within a regional data set, as opposed to obtaining more precise estimates for only a few site–year combinations. Our results also show that the best monitoring plans for regions depend on monitoring objectives as well as the relative magnitudes of spatial and temporal variability.

Family Size and Effective Population Size in a Hatchery Stock of Coho Salmon (Oncorhynchus kisutch)

1986 ◽  
Vol 43 (12) ◽  
pp. 2434-2442 ◽  
Author(s):  
Raymond C. Simon ◽  
John D. McIntyre ◽  
A. R. Hemmingsen
Keyword(s):  
Population Size ◽  
Family Size ◽  
Coho Salmon ◽  
Oncorhynchus Kisutch ◽  
Effective Size ◽  
Effective Population ◽  
Data Set ◽  
Hatchery Stock ◽  
Study Population ◽  
Related Population

Means and variances of family size measured in five year-classes of wire-tagged coho salmon (Oncorhynchus kisutch) were linearly related. Population effective size was calculated by using estimated means and variances of family size in a 25-yr data set. Although numbers of age 3 adults returning to the hatchery appeared to be large enough to avoid inbreeding problems (the 25-yr mean exceeded 4500), the numbers actually contributing to the hatchery production may be too low. Several strategies are proposed to correct the problem perceived. Argument is given to support the contention that the problem of effective size is fairly general and is not confined to the present study population.

scholarly journals An Empirical Assessment of the MODIS Land Cover Dynamics and TIMESAT Land Surface Phenology Algorithms

2019 ◽  
Vol 11 (19) ◽  
pp. 2201 ◽  
Author(s):  
Stanimirova ◽  
Cai ◽  
Melaas ◽  
Gray ◽  
Eklundh ◽  
...  
Keyword(s):  
Time Series ◽  
Land Cover ◽  
Land Surface ◽  
Vegetation Index ◽  
Spatial Scales ◽  
Regional Scale ◽  
Vegetation Indices ◽  
Data Set ◽  
Land Cover Dynamics ◽  
The Impact

Observations of vegetation phenology at regional-to-global scales provide important information regarding seasonal variation in the fluxes of energy, carbon, and water between the biosphere and the atmosphere. Numerous algorithms have been developed to estimate phenological transition dates using time series of remotely sensed spectral vegetation indices. A key challenge, however, is that different algorithms provide inconsistent results. This study provides a comprehensive comparison of start of season (SOS) and end of season (EOS) phenological transition dates estimated from 500 m MODIS data based on two widely used sources of such data: the TIMESAT program and the MODIS Global Land Cover Dynamics (MLCD) product. Specifically, we evaluate the impact of land cover class, criteria used to identify SOS and EOS, and fitting algorithm (local versus global) on the transition dates estimated from time series of MODIS enhanced vegetation index (EVI). Satellite-derived transition dates from each source are compared against each other and against SOS and EOS dates estimated from PhenoCams distributed across the Northeastern United States and Canada. Our results show that TIMESAT and MLCD SOS transition dates are generally highly correlated (r = 0.51-0.97), except in Central Canada where correlation coefficients are as low as 0.25. Relative to SOS, EOS comparison shows lower agreement and higher magnitude of deviations. SOS and EOS dates are impacted by noise arising from snow and cloud contamination, and there is low agreement among results from TIMESAT, the MLCD product, and PhenoCams in vegetation types with low seasonal EVI amplitude or with irregular EVI time series. In deciduous forests, SOS dates from the MLCD product and TIMESAT agree closely with SOS dates from PhenoCams, with correlations as high as 0.76. Overall, our results suggest that TIMESAT is well-suited for local-to-regional scale studies because of its ability to tune algorithm parameters, which makes it more flexible than the MLCD product. At large spatial scales, where local tuning is not feasible, the MLCD product provides a readily available data set based on a globally consistent approach that provides SOS and EOS dates that are comparable to results from TIMESAT.

Landscape characteristics and coho salmon (Oncorhynchus kisutch) distributions: explaining abundance versus occupancy

2012 ◽  
Vol 69 (3) ◽  
pp. 457-468 ◽  
Author(s):  
E.A. Steel ◽  
D.W. Jensen ◽  
K.M. Burnett ◽  
K. Christiansen ◽  
J.C. Firman ◽  
...  
Keyword(s):  
Coho Salmon ◽  
Full Range ◽  
Model Performance ◽  
Oncorhynchus Kisutch ◽  
Monitoring Data ◽  
Published Data ◽  
Data Sets ◽  
Data Set ◽  
Landscape Characteristics ◽  
Oregon Plan

Distribution of fishes, both occupancy and abundance, is often correlated with landscape-scale characteristics (e.g., geology, climate, and human disturbance). Understanding these relationships is essential for effective conservation of depressed populations. We used landscape characteristics to explain the distribution of coho salmon ( Oncorhynchus kisutch ) in the Oregon Plan data set, one of the first long-term, probabilistic salmon monitoring data sets covering the full range of potential habitats. First we compared data structure and model performance between the Oregon Plan data set and two published data sets on coho salmon distribution. Most of the variation in spawner abundance occurred between reaches but much also occurred between years, limiting potential model performance. Similar suites of landscape predictors are correlated with coho salmon distribution across regions and data sets. We then modeled coho salmon spawner distribution using the Oregon Plan data set and determined that landscape characteristics could not explain presence vs. absence of spawners but that the percentage of agriculture, winter temperature range, and the intrinsic potential of the stream could explain some variation in abundance (weighted average R2 = 0.30) where spawners were present. We conclude that the previous use of nonrandom monitoring data sets may have obscured understanding of species distribution, and we suggest minor modifications to large-scale monitoring programs.

scholarly journals Current landscapes and legacies of land-use past: understanding the distribution of juvenile coho salmon (Oncorhynchus kisutch) and their habitats along the Oregon Coast, USA

2017 ◽  
Vol 74 (4) ◽  
pp. 546-561 ◽  
Author(s):  
E. Ashley Steel ◽  
Ariel Muldoon ◽  
Rebecca L. Flitcroft ◽  
Julie C. Firman ◽  
Kara J. Anlauf-Dunn ◽  
...  
Keyword(s):  
Land Use ◽  
Surface Area ◽  
Coho Salmon ◽  
Spatial Scales ◽  
Oncorhynchus Kisutch ◽  
River Management ◽  
Land Ownership ◽  
Weak Rock ◽  
Oregon Coast ◽  
Pool Surface

The Oregon Coast landscape displays strong spatial patterns in air temperature, precipitation, and geology, which can confound our ability to detect relationships among land management, instream conditions, and fish at broad spatial scales. Despite this structure, we found that a suite of immutable or intrinsic attributes (e.g., reach gradient, drainage area, elevation, and percent weak rock geology of the catchments draining to each of our 423 study reaches) could explain much of the variation in pool surface area across the landscape and could contribute to an estimate of how many juvenile coho salmon (Oncorhynchus kisutch) one might expect to find in those pools. Further, we found evidence of differences in pool surface area across land ownership categories that reflect differing management histories. Our results also suggest that historical land and river management activities, in particular splash dams that occurred at least 50 years ago, continue to influence the distribution of juvenile coho salmon and their habitats today.

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