DOI: 10.5061/dryad.6wwpzgn72
title: Anatomy of a range contraction: Flow-phenology mismatches threaten salmonid fishes near their trailing edge

description: Climate change is redistributing life on Earth, with profound impacts for
 ecosystems and human well-being. While repeat surveys separated by
 multi-decadal intervals can determine whether observed shifts are in the
 expected direction (e.g., poleward or upslope due to climate change), they
 do not reveal their mechanisms or time scales: whether they were gradual
 responses to environmental trends or punctuated responses to disturbance
 events. Here we document population reductions and temporary range
 contractions at multiple sites resulting from drought for three Pacific
 salmonids at their ranges’ trailing edge. During California’s 2012-2016
 historic multi-year drought, the 2013-14 winter stood apart because
 rainfall was both reduced and delayed. Extremely low river flows
 during the breeding season (‘flow-phenology mismatch’) reduced or
 precluded access to breeding habitat. While Chinook (Oncorhynchus
 tshawytscha) experienced a down-river range shift, entire cohorts failed
 in individual tributaries (steelhead trout, O. mykiss) and in entire
 watersheds (coho salmon, O. kisutch). Salmonids returned to impacted sites
 in subsequent years, rescued by reserves in the ocean, life history
 diversity, and, in one case, a conservation broodstock program. Large
 population losses can, however, leave trailing-edge populations vulnerable
 to extinction due to demographic stochasticity, making permanent range
 contraction more likely. When only a few large storms occur during high
 flow season, the timing of particular storms plays an outsized role in
 determining which migratory fish species are able to access their riverine
 breeding grounds and persist.
description: <strong>Hydrological data</strong>
 Daily flow data were retrieved from USGS for 13 watersheds in
 northern California, including coastal watersheds from Marin County to Del
 Norte County (summarized in Carlson et al., <em>SI
 Appendix</em>, Table S2). The magnitude and timing of flows from the
 2013-14 winter were compared to the long-term record (specifically, the
 most recent 40 complete water years 1983-2022, except in two cases: Walker
 Creek, where gage records commenced after 1983 leading to inclusion of 39
 complete water years, and Austin Creek, where the gage was reactivated in
 2004, leading to inclusion of 18 complete water years). A water year in
 California is defined as October 1 – September 30 (e.g., the 1983 water
 year corresponds to the period October 1, 1982 to September 30, 1983). We
 include gage data from Russian River, Austin Creek, Noyo River, Elder
 Creek, South Fork Eel River, and the Mattole River as representative of
 conditions in systems where we also have biological observations.
 Additionally, we present hydrologic data for 7 additional watersheds that
 spanned a north-south gradient of coastal northern California watersheds,
 providing a broader regional context for the conditions experienced during
 the 2013-14 winter. See <em>SI Appendix</em>, Table S1 for a
 summary of gage data included in our analysis. For each
 of the 13 watersheds, we used the e-flows Functional Flows Calculator to
 identify the onset of winter flow conditions using the
 <em>ffcAPIClient </em>package in R (version 0.9.8.3,
 https://github.com/ceff-tech/ffc_api_client). This tool identifies the
 wet-season start timing as the date that sufficient baseflow has accrued
 based on a magnitude threshold and a rate of change threshold (46). We
 obtained the winter onset timing for each year from 1983-2022. The dates
 were then ranked from smallest to largest using data from the 1983-2022
 water years, and the 2013-14 conditions were identified within these
 ranked conditions. Here, the higher the rank, the later the winter onset
 date. We considered the “typical” adult salmonid
 migration window to extend from 1 November to 31 January, capturing the
 onset of migrations for the three salmonids (Chinook, coho, and steelhead
 trout) in the study region.  We computed the mean flow for this window for
 each winter across the 1983-2022 water years, in each watershed, and then
 rank-ordered the observations, again identifying the 2014-14 conditions
 within the ranked conditions. Here, the lower the rank, the more unusually
 low the flow conditions were. <strong>Biological
 data</strong> We then combined observations from
 multiple monitoring efforts to illustrate the consequences of extremely
 delayed rains for three species of salmon and trout near their trailing
 range edge. While sampling designs differed among the monitoring efforts
 (<em>SI Appendix</em>), they fell into two general categories:
 monitoring of adults on the breeding grounds and/or monitoring of newly
 hatched juvenile fish (<em>SI Appendix</em>, Table
 S1).<strong> </strong>Newly hatched salmonids typically have
 restricted movement for the first months of their lives (26), so their
 abundance can indicate the success of adult breeding. The adult monitoring
 data allowed us to explore the timing and location of breeding, while
 juvenile monitoring data revealed patterns of juvenile production and
 cohort strength. We used a bootstrapped
 Kolmogorov-Smirnov test to determine if adult arrival timing in 2013-14
 was delayed relative to the other years of study (where the cumulative
 distribution for “all other years” was calculated from the pooled data set
 across years). We used ks.boot() function in the R package “Matching” with
 1000 bootstraps. The test returns the Kolmogorov D (“distance”) statistic
 and associated p-value (in our case, for a one-tailed test). We present
 the D statistics in Figure 2, which represents the degree of difference
 measured as the maximum vertical distance between the reference
 distribution (“all other years”) and the 2013-14 distribution.
 To determine whether the juvenile or adult abundance was
 significantly reduced in 2013-14 relative to other years of study, we
 asked whether the abundance estimate fell outside the 95% CI of estimates
 based on “all other years” of data. The 95% CI was estimated by the mean ±
 standard error (SE). SE was calculated as the standard deviation divided
 by square root of the sample size. 
description: # Anatomy of a range contraction: Flow-phenology mismatches threaten
 salmonid fishes near their trailing edge
 [https://doi.org/10.5061/dryad.6wwpzgn72](https://doi.org/10.5061/dryad.6wwpzgn72) ## **Description of the data and file structure** Data are structured by figure. We include 6 zipped data files. Several datasets used in analyses are incompatible with the CC0 license waiver required by Dryad. Consequently, users should contact [smcarlson@berkeley.edu](mailto:smcarlson@berkeley.edu) for access to the data.  **1.“Fig1-Hydro.zip”.** Three  files are supplied at DRYAD: three Matlab m-files (code that can be executed within Matlab).  As a note about the data files, several of the files draw on data archived by the USGS.  The relevant gage names and numbers are listed within the “Flow_means.m” file.  Because these files are large and publicly archived, we have not stored those data files here. We also refer to data obtained by passing these flow data through the e-flows Functional Flows Calculator to identify the onset of winter flow conditions within a given water year using the *ffcAPIClient *package in R (version 0.9.8.3, [https://github.com/ceff-tech/ffc_api_client](https://github.com/ceff-tech/ffc_api_client)), which is an open-access tool for estimating seasonal flow from USGS datasets. Data files: E-flow-metrics.xlsx (available from [smcarlson@berkeley.edu](mailto:smcarlson@berkeley.edu)) BreedingSeasonFlows.xlsx (available from [smcarlson@berkeley.edu](mailto:smcarlson@berkeley.edu)) E-flow-metrics.xlsx is an excel file containing the timing of the wet season onset for each study and reference watershed from 1983-2022 obtained from the e-flows calculator tool. BreedingSeasonFlows.xlsx is an excel file summarizing cumulative flow during the breeding season for each watershed from 1983 – 2022, obtained from the USGS flow data Code files Flow_means.m EFlowsPlot.m Plot20132014Flows.m Flow_means.m computes the mean flow during the breeding window for the study and north coast reference watersheds from the USGS gage data. EFlowsPlot.m sorts the timing of the season onset obtained from the eflows calculator for all years in the dataset and  identifies the relative ranking of the 2013-2013 onset. Plot20132014Flows.m plots hydrographs of the flow in the study basins for the 2013-2014 winter.**\ 2. “Fig2-Phenology.zip”** One file is supplied at DRYAD: one R Markdown file (.RMD)  Three data files are available from [smcarlson@berkeley.edu](mailto:smcarlson@berkeley.edu): Mattole_timing_data_2025-02-16.csv RR_timing_data_2025-02-16.csv SouthForkEel_timing_data_2025-02-16.csv Mattole_timing_data_2025-02-16.csv is an excel file containing the adult return timing information for Chinook salmon monitoring in the Mattole River for the 2010-11 to 2022-23 winters. This file contains three columns: “ObsDate1” (date of observation), “Year” (year of observation), and “CommonName” (common name of the species observed). RR_timing_data_2025-02-16.csv is an excel file containing the adult return timing information for coho salmon monitoring in the Russian River for the 2010-11 to 2021-22 winters. This file contains three columns: “Winter” (winter of antenna detection), “Date” (date of antenna detection), and “antenna” (category denoting whether a detection was on the mainstem or a tributary antenna). SouthForkEel_timing_data_2025-02-16.csv is an excel file containing the adult return timing information for Chinook salmon, coho salmon, and steelhead trout monitoring in the South Fork Eel River for the years of 2010-11 to 2017-18 and 2020-21 to 2021-22 winters. This file contains three columns: “ObsDate1” (date of observation), “Year” (year of observation), and “CommonName” (common name of the species observed). Code files Carlson_etal_PNAS_Fig2_2025-02-14.RMD  Carlson_etal_PNAS_Fig2_2025-02-14.RMD creates the Figure 2 plot of adult return timing comparing the 2013-2014 to all other available years for each system (South Fork Eel River, Mattole River, Russian River). **3.“Fig3-Distribution.zip”** One file is supplied at DRYAD: One R Markdown file (.RMD)  Twenty-seven data files are available from [smcarlson@berkeley.edu](mailto:smcarlson@berkeley.edu) *GIS files:* Mattole_tribs1.shp (and associated files with .cpg, .dbf, .prj, .sbn, .shx extensions needed to view .shp shapefile) Mattole_tribs2.shp (and associated files with .cpg, .dbf, .prj, .sbn, .shx extensions needed to view .shp shapefile) RR_tribs1.shp (and associated files with .cpg, .dbf, .prj, .sbn, .shx extensions needed to view .shp shapefile) RR_tribs2.shp (and associated files with .cpg, .dbf, .prj, .sbn, .shx extensions needed to view .shp shapefile) Mattole_tribs1.shp and Mattole_tribs2.shp are two shapefiles that contain all of the tributary geometry for our map of the Mattole River. RR_tribs1.shp and RR_tribs2.shp are two shapefiles that contain all of the tributary geometry for our map of the Mattole River. *Excel files (available from [smcarlson@berkeley.edu](mailto:smcarlson@berkeley.edu)):* Mattole_Chinook_map_data_2025-02-16.csv RR_coho_map_data_2025-02-16.csv Mattole_Chinook_map_data_2025-02-16.csv contains the adult Chinook salmon count observations by reach in the Mattole River. We can match this information to our tributary names in the GIS shapefiles (using RMD file described below) to visualize the distribution of adult counts in the Mattole River. This file has 14 columns: “Reach_ID” (the ID number for each reach sampled), columns 2-14 beginning with “SY” denote the sample year and values the number of adults observed, and “avg” denotes the average across all years except for the 2013-2014 winter. Sample years with missing data (i.e., empty excel cell) means no survey was performed, these empty cells will display as “NA” when loaded into program R. RR_coho_map_data_2025-02-16.csv contains the juvenile coho salmon count observations by reach in the Russian River. We can match this information to our tributary names in the GIS shapefiles (using RMD file described below) to visualize the distribution of adult counts in the Russian River. This file has three columns “year” (year of survey), “reach” (reach ID), and “coho_yoy_count” (number of juveniles observed). Code files Carlson_etal_PNAS_Fig3_2025-02-14.RMD  Carlson_etal_PNAS_Fig3_2025-02-14.RMD creates the Figure 3 map plot showing the distribution of breeding adults in the Mattole River and juveniles in the Russian River. **4.“Fig4_FigS2_SigS3-Boxplot.zip”** One file is supplied at DRYAD: one R Markdown file (.RMD)  Three data files are available from [smcarlson@berkeley.edu](mailto:smcarlson@berkeley.edu): Fay_Fox_Tannery_boxplot_data_2025-02-16.csv Mendocino_boxplot_data_2025-02-16.csv Russian_River_boxplot_data_2025-02-16.csv Fay_Fox_Tannery_boxplot_data_2025-02-16.csv is an excel file containing the juvenile count information for coho salmon and steelhead trout monitoring in Fay Creek (tributary of the Salmon River, 2012-2016 summers), Fox Creek (tributary of the South Fork Eel River, 2014-2016 summers), and Tannery Creek (tributary of the Salmon River, 2012-2016 summers). This file contains five columns: “stream” (stream name), “year” (year of sample), “date” (date of sample), “species” (name of species observed), and “num_YOY” (the number of juveniles observed).  Mendocino_boxplot_data_2025-02-16.csv is an excel file containing the adult count information for coho salmon monitoring for each of the Mendocino coastal streams (Big River, Caspar Creek, Garcia River, Navarro River, Noyo River, Pudding Creek, South Fork Albion River, Ten Mile River) ranging from 2008-09 to 2022-23 winters. This file has nine columns: “year” (winter sampled), and columns two through nine correspond to each Mendocino coastal stream and the values are the number of adults observed. “NA” means no survey was performed for that year/stream. Russian_River_boxplot_data_2025-02-16.csv is an excel file containing juvenile count data for coho salmon monitoring in the Russian River for the 2014-2022 summers. This file has three columns: “year” (year of sample), “subwatershed” (which of the four subwatersheds where surveys occurred), and “coho_yoy_count” (the number of juveniles observed).  Code files Carlson_etal_PNAS_Fig4_FigS2_FigS3_2025-02-04.RMD  Carlson_etal_PNAS_Fig4_FigS2_FigS3_2025-02-04.RMD creates the boxplots for Figure 4, and supplemental Figure S2 and Figure S3 comparing the 2013-2014 drought year to all other years available. **5.“FigS5_FigS6-AnnualAdultAbundance.zip”** One file is supplied at DRYAD: one R Markdown file (.RMD)  Four data files are available from [smcarlson@berkeley.edu](mailto:smcarlson@berkeley.edu): Mattole_timing_data_2025-02-16.csv Mendocino_boxplot_data_2025-02-16.csv RR_timing_data_2025-02-16.csv SouthForkEel_timing_data_2025-02-16.csv Mattole_timing_data_2025-02-16.csv is an excel file containing the adult return timing information for Chinook salmon monitoring in the Mattole River for the 2010-11 to 2022-23 winters. This file contains three columns: “ObsDate1” (date of observation), “Year” (year of observation), and “CommonName” (common name of the species observed). Mendocino_boxplot_data_2025-02-16.csv is an excel file containing the adult count information for coho salmon monitoring for each of the Mendocino coastal streams (Big River, Caspar Creek, Garcia River, Navarro River, Noyo River, Pudding Creek, South Fork Albion River, Ten Mile River) ranging from 2008-09 to 2022-23 winters. This file has nine columns: “year” (winter sampled), and columns two through nine correspond to each Mendocino coastal stream and the values are the number of adults observed. “NA” means no survey was performed for that year/stream. RR_timing_data_2025-02-16.csv is an excel file containing the adult return timing information for coho salmon monitoring in the Russian River for the 2010-11 to 2021-22 winters. This file contains three columns: “Winter” (winter of antenna detection), “Date” (date of antenna detection), and “antenna” (category denoting whether a detection was on the mainstem or a tributary antenna). SouthForkEel_timing_data_2025-02-16.csv is an excel file containing the adult return timing information for Chinook salmon, coho salmon, and steelhead trout monitoring in the South Fork Eel River for the years of 2010-11 to 2017-18 and 2020-21 to 2021-22 winters. This file contains three columns: “ObsDate1” (date of observation), “Year” (year of observation), and “CommonName” (common name of the species observed). Code files Carlson_etal_PNAS_FigS5_FigS6_2025-02-01.RMD  Carlson_etal_PNAS_FigS5_FigS6_2025-02-01.RMD creates the barplots to summarize adult return counts by year for supplemental Figure S5 and Figure S6. **6.“FigS7-AnnualAdultPhenology.zip”** One file is supplied at DRYAD: one R Markdown file (.RMD)  Three data files are available at [smcarlson@berkeley.edu](mailto:smcarlson@berkeley.edu): Mattole_timing_data_2025-02-16.csv RR_timing_data_2025-02-16.csv SouthForkEel_timing_data_2025-02-16.csv Mattole_timing_data_2025-02-16.csv is an excel file containing the adult return timing information for Chinook salmon monitoring in the Mattole River for the 2010-11 to 2022-23 winters. This file contains three columns: “ObsDate1” (date of observation), “Year” (year of observation), and “CommonName” (common name of the species observed). RR_timing_data_2025-02-16.csv is an excel file containing the adult return timing information for coho salmon monitoring in the Russian River for the 2010-11 to 2021-22 winters. This file contains three columns: “Winter” (winter of antenna detection), “Date” (date of antenna detection), and “antenna” (category denoting whether a detection was on the mainstem or a tributary antenna). SouthForkEel_timing_data_2025-02-16.csv is an excel file containing the adult return timing information for Chinook salmon, coho salmon, and steelhead trout monitoring in the South Fork Eel River for the years of 2010-11 to 2017-18 and 2020-21 to 2021-22 winters. This file contains three columns: “ObsDate1” (date of observation), “Year” (year of observation), and “CommonName” (common name of the species observed).\ Code files: Carlson_etal_PNAS_FigS7_2025-02-04.RMD  Carlson_etal_PNAS_FigS7_2025-02-04.RMD creates the density plots for adult return timing by year for the South Fork Eel River, Mattole River, and Russian River for supplemental Figure S7. ## Sharing/Access information With the exception of USGS flow data, which is publicly archived, all data included in this manuscript are uploaded here. The flow data is available from USGS at [https://waterdata.usgs.gov/nwis/rt](http://...) Additionally, some of the biological data analyses are available from publicly accessible locations. In particular, biological observations collected by the California Department of Fish and Wildlife (CDFW) and/or by groups using the same protocol (e.g., California Sea Grant and partners in the Russian River, Mattole Salmon Group) are inputted annually to the California Monitoring Plan for Salmon and Steelhead excel sheet, which is available at[ https://wildlife.ca.gov/Conservation/Fishes/Salmonid-Monitoring/CMP](https://wildlife.ca.gov/Conservation/Fishes/Salmonid-Monitoring/CMP) ## Code/Software Describe any scripts, code, or notebooks (e.g., R, Python, Mathematica, MatLab) as well as the software versions (including loaded packages) that you used to run those files. If your repository contains more than one file whose relationship to other scripts is not obvious, provide information about the workflow that you used to run those scripts and notebooks. For “Fig1-HydroData.zip”, we include three Matlab m-files (code that can be executed within Matlab), which we ran using Matlab R2022a, main release, no additional packages needed. For Figures 2-4, S2-S3, S5-S7, we include 5 RMD files (code that can be executed within R), which we ran using R version 4.4.2.