Barriers decouple population dynamics of riverine fish, and asynchrony of subpopulations promotes stability within fragments
Data files
Apr 15, 2025 version files 6.70 MB
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all_data_synchrony.csv
5.74 MB
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pop_perf_minnow.csv
9.61 KB
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pop_perf_pike.csv
8.54 KB
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pop_perf_trout.csv
13.54 KB
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rawdf.csv
894.06 KB
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README.md
5.74 KB
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synchrony_final.R
26.52 KB
Apr 15, 2025 version files 6.70 MB
-
all_data_synchrony.csv
5.74 MB
-
pop_perf_minnow.csv
9.61 KB
-
pop_perf_pike.csv
8.54 KB
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pop_perf_trout.csv
13.54 KB
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rawdf.csv
894.06 KB
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README.md
8.49 KB
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synchrony_final.R
26.52 KB
Abstract
The spatial synchrony framework suggests that asynchrony among subpopulations in different branches of a river network should stabilise the metapopulation. However, how barriers affect this framework remains poorly understood. This is a significant knowledge gap given that population synchrony arises from dispersal and environmental similarity, both of which are influenced by barriers. Here, we empirically evaluated how barriers impact fish population synchrony and, subsequently, the associations between synchrony and metapopulation persistence, productivity, stability, and trajectory within fragments. We found that barriers demographically decouple populations by decreasing synchrony in brown trout (Salmo trutta) and Eurasian minnow (Phoxinus phoxinus) but not northern pike (Esox lucius), suggesting species-specific responses to fragmentation. Additionally, asynchrony had a stabilising portfolio effect on metapopulation stability at the fragment level that was statistically significant for S. trutta. Higher fragment synchrony also made S. trutta and P. phoxinus populations less stable. The impact of barriers on riverine fish population synchrony emphasises the need to include barriers in future studies on the causes and consequences of synchrony in rivers. That asynchrony stabilises populations in some riverine fishes suggests that conservation prioritisations should lie in restoring or retaining larger fragment sizes and higher branching complexity with intact connectivity.
https://doi.org/10.5061/dryad.05qfttf9z
Submitted files
1.1 Data files:
all_data_synchrony.csv: This is the full data set for analysing synchrony patterns in rivers (with multimember models) for all three species (S. trutta, P. phoxinus, and E. lucius). Each row is a site-pair with its associated synchrony, between site distance (both euclidean and watercourse), flow-connectedness, etc.
rawdf.csv: This contains the raw time-series abundance data used to calculate the portfolio effect for each fragment for all three species. The code will call this dataset at the appropriate time to calculate the portfolio effect.
pop_perf_trout.csv: This contains the population performance metrics for each fragment for S. trutta. Each row is the mean synchrony and the population metrics for all sites in a fragment.
pop_perf_minnow.csv: This contains the population performance metrics for each fragment for P. phoxinus. Each row is the mean synchrony and the population metrics for all sites in a fragment.
pop_perf_pike.csv: This contains the population performance metrics for each fragment for E. lucius. Each row is the mean synchrony and the population metrics for all sites in a fragment.
1.2 Code files:
synchrony_final.R: This contains the annotated/commented code to reproduce the statistics, data manipulations, and figures in this study. The code will call each data file at the appropriate moment.
Variable descriptions
2.1 For full data (all_data_synchrony.csv):
- variable name: explanation [unit]
- fromid: identifier of from-site
- toid: identifier of to-site
- fromXY: identifier of from-site
- toXY: identifier of to-site
- pythdist: pythagoran/euclidean distance between site-pairs [m]
- rivdist: watercourse distance between site-pairs [m]
- fromXKOORLOK: X coordinate in RT90 of from-site
- fromYKOORLOK: Y coordinate in RT90 of to-site
- toXKOORLOK: X coordinate in RT90 of from-site
- toYKOORLOK: Y coordinate in RT90 of to-site
- n_years: Number of matching sampling years between site-pairs [years]
- over_frag01: Dichotomous variable (1/0) describing whether site-pair were in different (1) or same (0) fragment (i.e., if calculation was OVER FRAGment border)
- flowconn01: Dichotomous variable (1/0) describing whether site-pair were FLOW-CONNected.
- rivdistlg: watercourse distance between site-pairs but log-transformed [log-transformed meters]
- river_id: ID given to river (synonymous with catchment)
- trout_rho: the synchrony in TROUT fluctuations between to-site and from-site [Spearman’s rho]
- trout_n_gt0_two: how many pair-wise observations where both sites have more than 0 density.
- pike_rho: the synchrony in PIKE fluctuations between to-site and from-site [Spearman’s rho]
- pike_n_gt0_two: how many pair-wise observations where both sites have more than 0 density.
- minnow_rho: the synchrony in MINNOW fluctuations between to-site and from-site [Spearman’s rho]
- minnow_n_gt0_two: how many pair-wise observations where both sites have more than 0 density.
- sqrt_rivdist: watercourse distance between site-pairs but square root-transformed [square root-transformed meters]
- sqrt_pythdist: pythagoran/euclidean distance between site-pairs but squareroot-transformed [square root-transformed meters]
- random_site3: Random effect site identifier for LmerMultiMember to function
- unique_frag: Unique identifier for all fragments
- dedw: euclidean distance (ed) divided by watercourse distance (dw) [unitless]
- median_ed: catchment specific median for ed [unitless]
- median_dedw: catchment specific median for ed/dw [unitless]
- cat: The synchrogram category (see Larsen et al., 2021) describing what type of distance that separates the site-pairs
2.2 For raw density data (rawdf.csv)
- variable name: explanation [unit]
- XKOORLOK: X coordinate in RT90 of site
- YKOORLOK: Y coordinate in RT90 of site
- unique_frag: Unique identifier for all fragments
- riverID: ID given to river (synonymous with catchment)
- year: sampled year [year]
- ÖringTOT_mean: mean density of brown trout [individuals per 100m²]
- Elrit_mean: mean density of Eurasian minnow [individuals per 100m²]
- Gädda_mean: mean density of northern pike [individuals per 100m²]
2.3 For fragment data (pop_perf_trout.csv, pop_perf_minnow.csv, pop_perf_pike.csv):
(Replace “SPECIES” with either “trout”, “minnow”, or “pike” in the variable names below depending on the species dataset.)
- variable name: explanation [unit]
- unique_fragment: Unique identifier for all fragments
- river_id: ID given to river [synonymous with catchment)
- arith_rho: arithmetic mean synchrony of fragment [mean rho]
- SPECIES_occ: mean occurrence of SPECIES within fragment [mean occurrence rate]
- SPECIES_mean: mean log(density +1) of SPECIES within fragment [log-transformed individuals per 100m^2]
- SPECIES_sd: standard deviation in log-density of SPECIES within fragment [log-transformed individuals per 100m^2]
- SPECIES_rsd: residual standard deviation of SPECIES within fragment [log-transformed individuals per 100m^2]
- SPECIES_slope: population trajectory (mean slope) of SPECIES within fragment [log-transformed individuals per 100m^2]
- n_occasions: number of unique fishing occasions within fragment [years]
- n_sites: number of sites within fragment [sampling sites]
3.0 R and R package versions
> sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=Swedish_Sweden.utf8 LC_CTYPE=Swedish_Sweden.utf8
[3] LC_MONETARY=Swedish_Sweden.utf8 LC_NUMERIC=C
[5] LC_TIME=Swedish_Sweden.utf8
time zone: Europe/Stockholm
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.5.1 gridExtra_2.3 flextable_0.9.7
[4] broom.mixed_0.2.9.6 lme4_1.1-36 Matrix_1.7-1
[7] stringr_1.5.1 dplyr_1.1.4 pacman_0.5.1
[10] lmerMultiMember_0.11.8
loaded via a namespace (and not attached):
[1] gtable_0.3.6 xfun_0.50 insight_1.0.1
[4] lattice_0.22-6 vctrs_0.6.5 sjstats_0.19.0
[7] tools_4.4.2 Rdpack_2.6.4 generics_0.1.3
[10] datawizard_1.0.0 parallel_4.4.2 tibble_3.2.1
[13] pkgconfig_2.0.3 data.table_1.16.4 ggeffects_2.1.0
[16] uuid_1.2-1 lifecycle_1.0.4 compiler_4.4.2
[19] textshaping_1.0.0 sjmisc_2.8.10 munsell_0.5.1
[22] codetools_0.2-20 fontLiberation_0.1.0 fontquiver_0.2.1
[25] htmltools_0.5.8.1 pillar_1.10.1 furrr_0.3.1
[28] nloptr_2.1.1 tidyr_1.3.1 MASS_7.3-61
[31] openssl_2.3.1 reformulas_0.4.0 boot_1.3-31
[34] nlme_3.1-166 parallelly_1.42.0 fontBitstreamVera_0.1.1
[37] zip_2.3.2 tidyselect_1.2.1 sjlabelled_1.2.0
[40] digest_0.6.37 performance_0.13.0 stringi_1.8.4
[43] future_1.34.0 purrr_1.0.2 listenv_0.9.1
[46] forcats_1.0.0 splines_4.4.2 fastmap_1.2.0
[49] grid_4.4.2 colorspace_2.1-1 cli_3.6.3
[52] magrittr_2.0.3 broom_1.0.7 withr_3.0.2
[55] gdtools_0.4.1 scales_1.3.0 backports_1.5.0
[58] rmarkdown_2.29 officer_0.6.7 globals_0.16.3
[61] ragg_1.3.3 askpass_1.2.1 sjPlot_2.8.17
[64] evaluate_1.0.3 knitr_1.49 rbibutils_2.3
[67] rlang_1.1.5 Rcpp_1.0.14 glue_1.8.0
[70] xml2_1.3.6 rstudioapi_0.17.1 minqa_1.2.8
[73] R6_2.5.1 systemfonts_1.2.1
- D1: Populations with small and similar dE and dW values are likely on the same network branch, displaying high synchrony. They are close both in terms of physical distance and water flow, suggesting a strong potential for interaction and shared dynamics.
- D2: Populations with large and equal dE and dW values are likely located on the same branch but are more distant. They are still expected to show intermediate synchrony, influenced by a combination of dispersal and a Moran effect.
- D3: Populations with small dE but much larger dW values are likely situated in separate but nearby branches. They should display intermediate synchrony, primarily driven by a Moran effect. This suggests that even though they may not be directly connected by water flow, there might still be shared environmental influences.
- D4: Populations with large dE and much larger dW values are positioned on distant and separate branches. They are expected to show the lowest degree of synchrony due to their significant spatial and hydrological separation.