Publications
(In Press).
Comparing and Integrating Fish Surveys in the San Francisco Estuary: Why Diverse Long-Term Monitoring Programs are Important.
San Francisco Estuary and Watershed Science. 18(2),
(2020). Detrital food web contributes to aquatic ecosystem productivity and rapid salmon growth in a managed floodplain.
PLoS. 15(9),
Jeffres et al. 2020.pdf (2.26 MB)
(2020). 
Drought and the Sacramento-San Joaquin Delta, 2012–2016: Environmental Review and Lessons.
San Francisco Estuary and Watershed Science.
(2020). Dynamic river processes drive variability in particulate organic matter over fine spatiotemporal scales.
Freshwater Biology. 65(9), 1569-1584.
fwb.13522.pdf (1.3 MB)
(2020). 
Estuarine-terrestrial habitat gradients enhance nursery function for resident and transient fishes in the San Francisco Estuary.
Marine Ecology Progress Series. 637,
(2020). Food Web Fuel Differs Across Habitats and Seasons of a Tidal Freshwater Estuary.
Estuaries and Coasts. 188,
(2020). A functional flows approach to selecting ecologically relevant flow metrics for environmental flow applications.
River Research and Applications. 36(2), 318–324.
Yarnell et al. 2020 RRA (759.84 KB)
(2020).
(2020). 
Improving Infrastructure for Wildlife.
Natural Resources & Environment. 34, 38–42.
(2020). North Delta Arc Study 2019 annual report: Cache and Lindsey Slough water quality, productivity, and fisheries.
2019 North Delta Arc Annual Report Final.pdf (5.72 MB)
(2020). 
Sacramento River Predator Diet Analysis: A Comparative Study.
San Francisco Estuary and Watershed Science. 18(1),
(2020). Small Populations in Jeopardy: A Delta Smelt Case Study.
Envtl. L. Rep.. 10714.
(2020). Source Water Apportionment of a River Network: Comparing Field Isotopes to Hydrodynamically Modeled Tracers.
Water. 12(4), 1128.
water-12-01128.pdf (4.43 MB)
(2020). 
Suisun Marsh Fish Study: trends in fish and invertebrate populations of Suisun Marsh January 2018 - December 2018.
Suisun Marsh Fish Report 2018 Final.pdf (3.16 MB)
(2020). 
Tidal effects on marsh habitat use by three fishes in the San Francisco Estuary.
Environmental Biology of Fishes.
(2020). Eye in the Sky: Using UAV Imagery of Seasonal Riverine Canopy Growth to Model Water Temperature.
Hydrology. 6(1),
(2019). Hybridization between two parapatric ranid frog species in the northern Sierra Nevada, California, USA.
Molecular ecology. 28, 4636–4647.
(2019).
(2019). Little Shasta River 2017-2019: Pre-Project Assessment of the Proposition 1 Ecosystem Restoration Grant Activities.
LS_Pre-ProjectReport2019.pdf (3.97 MB)
(2019). 
Noteworthy collections, California (Alternanthera philoxeroides).
Madrono. 66(1),
(2019). Novel life history tactic observed in fall-run Chinook Salmon.
Ecology. 100(10),
(2019). River research and applications across borders.
River Research and Applications. early view online,
(2019). Strontium isotopes reveal ephemeral streams used for spawning and rearing by an imperilled potamodromous cyprinid Clear Lake hitch Lavinia exilicauda chi.
Marine and Freshwater Research. https://doi.org/10.1071/MF18264,
(2019). Suisun Marsh Fish Study: trends in fish and invertebrate populations of Suisun Marsh January 2017 - December 2017.
Suisun Marsh Fish Report 2017 Final - No Appendix (low res).pdf (2 MB)
Suisun Marsh Fish Report 2017 Final - Appendix (low res).pdf (398.3 KB)
(2019). 

Warm, dry winters truncate timing and size distribution of seaward‐migrating salmon across a large, regulated watershed.
Ecological Application. https://esajournals.onlinelibrary.wiley.com/doi/epdf/10.1002/eap.1880,
(2019). Associating metrics of hydrologic variability with benthic macroinvertebrate communities in regulated and unregulated snowmelt-dominated rivers.
Freshwater Biology. 63(8), 844-858.
(2018). Delta Smelt and Salmon Habitats Beyond the Estuary.
(Moyle, P. B., & Durand J. R., Ed.).
Delta Smelt Salmon Beyond Estuary (BDSC) - 1 of 2.pdf (1.68 MB)
Delta Smelt Salmon Beyond Estuary (BDSC) - 2 of 2.pdf (1.6 MB)
Delta Smelt and Salmon Beyond the Estuary - Abstract.pdf (95.01 KB)
(2018). 


Delta Smelt and the Politics of Water in California.
Fisheries. 43,
(2018). Ecocorrelates of pelage coloration in pigs and peccaries.
Journal of Mammalogy. 99(5),
(2018). The ecological importance of unregulated tributaries to macroinvertebrate diversity and community composition in a regulated river.
Hydrobiologia. 829, 291-305.
(2018). Endangered winter-run Chinook salmon rely on diverse rearing habitats in a highly altered landscape..
Biological Conservation. 217,
Phillis_et_al_2017_Biological_Conservation.pdf (907.84 KB)
(2018). 
Factors affecting distribution and abundance of jellyfish medusae in a temperate estuary: a multi-decadal study.
Biological Invasions.
(2018). Fishery collapse, recovery, and the cryptic decline of wild salmon on a major California River.
Canadian Journal of Fisheries and Aquatic Sciences.
cjfas-2017-0273.pdf (7.7 MB)
(2018). 
A Freshwater Conservation Blueprint for California: Prioritizing Watersheds for Freshwater Biodiversity.
Freshwater Science. 37(2),
(2018). How Scientists Reveal The Secret Migrations of Fish.
Frontiers for Young Minds. 6(67),
Morais et al 2018 secret migrations of fish frym-06-00067_small.pdf (536.93 KB)
(2018). 
Managing flow regimes and landscapes together: Hydrospatial analysis for evaluating spatiotemporal floodplain inundation patterns with restoration and climate change implications.
Hydrologic Sciences. Doctor of Philosophy, 255.
Whipple_Dissertation_2018.pdf (10.15 MB)
(2018). 
Managing for salmon resilience in California’s variable and changing climate.
(Carlson, SM., Henery R., Johnson RC., Mantua N., Moyle P. B., & Sommer T., Ed.).San Francisco Estuary and Watershed Sciences. 16(2),
SFEWS_Herbold_0818_final.pdf (6.85 MB)
(2018). 
South Fork Scott River: Preliminary Assessment of Bouvier Ranch for Coho Recovery.
Preliminary Assessment of Bouvier Ranch for Coho Recovery_FINAL_8-1-2018.pdf (1.43 MB)
(2018). 
Stream macrophytes increase invertebrate production and fish habitat utilization in a California stream.
River Research and Applications.
Lusardietal2018.pdf (548.37 KB)
(2018).
(2018). 
Assessing Extinction.
Bioscience. 67,
(2017). Confronting the risks of large-scale invasive species control.
Nature Ecology & Evolution. 1,
(2017). Environmental hedging: Theory and method for reconciling reservoir operations for downstream ecology and water supply.
Water Resources Research.
(2017). Is extinction inevitable for Delta Smelt and Longfin Smelt? An opinion and recommendations for recovery..
San Francisco Estuary and Watershed Science . 15(2),
(2017). Flood regime typology for floodplain ecosystem management as applied to the unregulated Cosumnes River of California, United States.
Ecohydrology. 10(e1817),
(2017). Floodplain farm fields provide novel rearing habitat for Chinook salmon.
PLoS ONE. 12(6),
(2017).
(2017). Genomics Clarifies Taxonomic Boundaries in a Difficult Species Complex..
PLoS ONE. 12(12),
(2017).
(2017).