DOI: 10.5061/dryad.ghx3ffbxt
title: Hydrochory, a key ecological function of a tropical dry forest river threatened by a dam and open-pit coal mining in Colombia

description: Aims: Freshwater ecosystems have complex spatial and temporal connections
 that support multiple processes essential for life. Since two of the most
 critical impacts on riparian ecosystems is the regulation of river flows
 and water pollution, we aimed to investigate whether a dam and mining
 activities on the Ranchería River affect hydrochory. Location: Tropical
 dry forest of La Guajira, Colombia; a region in need of water. Methods: We
 evaluated hydrochory and compared seed richness, abundance and composition
 with the unaltered Cesar River over two seasons. We sampled both upstream
 and downstream of the dam and the mining site. At these same sites, we
 quantified levels of turbidity and 15 chemical compounds that affect water
 quality. Results: There was significant spatial heterogeneity of the seed
 communities sampled along both rivers, with particularly distinct
 communities collected downstream from the open pit mine. We also found a
 significant effect of the dam on seed composition and abundance in the
 Ranchería River. Seed assemblages, but not seed numbers, differed between
 seasons and rivers. We also found significantly higher levels in chemical
 compounds and turbidity downstream of the mine compared to upstream.
 Conclusions: There is a significant effect of the dam and the open pit
 mine on the Ranchería River in Colombia. The alteration of natural flows,
 environmental conditions and water quality affects hydrochory, a key
 ecological function of the river. Urgent measures are imperative to
 address these challenges effectively and ensure the long-term
 sustainability of the ecosystem.
description: Tropical dry forests are among the most floristically rich
 ecosystems and have high rates of endemism (Gentry 1982); however, they
 are also one of the most threatened in the world (Janzen 1988,
 Portillo-Quintero and Sánchez-Azofeifa 2010, IUCN 2012). It is estimated
 that about 54% of the area covered by this ecosystem is distributed in
 South America (Ceccon 2001, Portillo-Quintero and Sánchez-Azofeifa 2010,
 Blackie et al. 2014). In Colombia, this ecosystem crosses six bioregions
 that vary widely in climate, soils, and anthropogenic pressures; four of
 these regions are in a critical state of fragmentation, with an average
 maximum patch area of only 100 ha (Ariza et al. 2014, Pizano et al. 2017).
 One of these, the La Guajira region, has a long history of anthropogenic
 alteration; since colonial times, the establishment of large and intensive
 crops promoted land use change and the alteration of rivers (Guerra
 Curvelo and Egurrola Hinojosa 2015). The Ranchería River, one of the most
 important in the region, has been one of the most affected since
 colonization and has since undergone repeated modifications (Guerra
 Curvelo and Egurrola Hinojosa 2015). Currently, due to severe anthropic
 changes, the river’s flow has decreased sharply, causing several economic,
 social and environmental problems (Guerra Curvelo and Egurrola Hinojosa
 2015). Coal mining activities began 46 years ago in the
 region, transforming and threatening human and environmental health (Urrea
 and Calvo 2014, Moreno Rodríguez and Montero Torres 2016, Galvis 2018) by
 affecting ecosystem services (Environmental Justice Atlas 2015). One of
 the critical problems associated with open pit coal mining is acid mine
 drainage (AMD). Mineral exploitation generates a high level of dissolved
 solids, such as bicarbonate, chlorides, sodium calcium sulfur, magnesium
 and iron in drainage waters (Akcil and Koldas 2006, Goswami 2015).
 Additionally, there is an excess of nitrates and phosphates, nutrients
 strongly associated with the growth of algae, which generate a strong
 decrease in oxygen in the water (Castro et al. 1998, Talukdar et al.
 2016). These impacts make the water extremely acidic and very high in
 minerals, thus affecting the biodiversity and life cycles of hundreds of
 organisms in wetlands near the mines (Castro et al. 1998, Akcil and Koldas
 2006, Munnik 2010, Goswami 2015, Talukdar et al. 2016, Pat-Espadas et al.
 2018). It has been reported that water acidification generates
 modifications in seed morphology by damaging specialized structures for
 buoyancy and viability, which also affects seed germination and
 establishment (Fulbright 1988, Fargašová 1994). Additionally, the
 decomposition of nutrients, microorganisms and mycorrhizae generates
 strong transformations in the ecological conditions of soils and water
 (Fulbright 1988, Fargašová 1994, Clark 1997). It has been reported that
 the accumulation of salts or heavy metals together with water
 acidification completely inhibit the seed germination process (Fulbright
 1988, Fargašová 1994, Clark 1997, Pérez-Fernández et al. 2006, Reichman et
 al. 2006, Donggan et al. 2011, Pat-Espadas et al. 2018). Coal mining also
 has major physical (mechanical) effects, including altering and diversion
 of water courses and banks and the disconnection between surface and
 groundwater flows (Seybold et al. 2004, Anawar 2013). These can completely
 change water and soil conditions and the composition of seed species
 transported by the river (Ghose 2004, Pandey et al. 2014). This, in turn,
 affects seed establishment sites and leaves soils poorly drained, eroded
 and poor in organic matter (Ghose 2004, Seybold et al. 2004, Donggan et
 al. 2011, Anawar 2013, Pandey et al. 2014). Sixteen
 years have passed since the diversion of the Rancheria River for the
 construction of the El Cercado dam, causing several environmental impacts
 including the fragmentation of the river network and the alteration of the
 flow regime, the generation of a new ecosystem (reservoir), and impeding
 the downstream movement of aquatic organisms, sediments and nutrients
 (Contraloría General de la República 2010, Corpoguajira 2020). Various
 studies report reduction in hydrochory and decreased floristic diversity
 downstream of dams (Nilsson et al. 1989, Nilsson and Jansson 1995, Jansson
 et al. 2000, Andersson and Nilsson 2002). For example, Brown and Chenoweth
 (2008) found a 90% reduction in abundance and an 84% reduction in seed
 species richness in sampling downstream of a dam; they also report that
 the germination of seeds collected downstream of the dam was very low.
 Likewise, the decomposition of biomass accumulated in dams can generate
 water toxicity and eutrophication of the ecosystem, affecting the
 germination of seeds downstream of the dam (Merritt and Wohl 2006).
 Therefore, based on the above, we hypothesized that damming and mining of
 the Ranchería River will affect the seed community composition flowing
 with the river; for example, a marked decrease in richness and abundance
 of seeds transported downstream of the dam and the mining area.
 In order to test the effects of the anthropogenic alterations of
 the Ranchería River on hydrochory, 1. we assessed the composition,
 richness, and abundance of the seed community transported by the
 Ranchería, both upstream and downstream of a dam and of the coal mine;  2.
 we then compared these parameters to zones with similar physiographic
 features in the nearby Cesar River, which has undergone much less intense
 modification. We conducted these survey activities during both the dry and
 rainy season, which are highly contrasting in this tropical dry forest
 ecosystem. We expected distinct composition and higher richness and
 abundance of seeds in the Cesar than in the Ranchería River, with
 particularly marked differences at sites downstream of the dam and mine.
 Furthermore, 3. to complement ecological results and to investigate the
 effects of the coal mine on the physical and chemical characteristics of
 the Ranchería River water, we analyzed physical-chemical water parameters
 in this River. Understanding the role of rivers and mechanisms that
 determine the geographic range of seed dispersal is of vital importance to
 determine the intensity of human impacts on wetland transformation, and
 may point to ways to successfully restore biodiversity and their lost
 ecosystem services (Richter and Stromberg 2005). There
 was significant spatial heterogeneity of the seed communities sampled
 along both rivers, with especially strong separation of the community
 collected downstream from the open pit mine. We also found a significant
 effect of the dam on seed composition and abundance in the Ranchería
 River. Seed community assemblages, but not seed numbers, were
 significantly different between seasons and rivers. We also found
 significantly higher turbidity, chloride, carbonate, iron, nitrate and
 sulfate levels downstream of the mine compared to upstream samples. There
 is a clear effect of the dam and the open pit* *mine on the Ranchería
 River in Colombia. The alteration of natural flows, environmental
 conditions and water quality triggers a radical change in the composition,
 abundance and structure of the riparian plant communities and affect key
 ecological functions of the river. Urgent measures are imperative to
 address these challenges effectively and ensure the long-term
 sustainability of the ecosystem. <em>2.2.1. The
 flow pattern of the Ranchería River</em> In order
 to characterize the flow pattern of the Rancheria River, we calculated
 mean monthly flows and total mean flows
 (m<sup>3</sup>s<sup>-1</sup>) for each of four
 hydrological stations located along the Ranchería river for a period of 13
 to 15 years (dataset: IDEAM 2023) according to data availability (see Fig.
 2a, b). Hydrological stations were located close to our sampling zones
 (Appendix S1a, b). The location of the stations from upstream to
 downstream of the river were: Caracolí (located before the dam), El
 Silencio (located after the dam), Pte. Guajiro (located before the mining
 area), and Cuestecitas (located immediately after the mining area)
 (Appendix S1a, b). <em>2.3 Selection of sampling
 zones and sites </em> To evaluate the effect of
 the dam on seed dispersal in the Ranchería River, we collected seeds
 transported along the Cesar River, as well as from upstream and downstream
 sections of both the dam and mining zones of the Ranchería River. The
 Cesar River, unaffected by major anthropogenic modifications, was used as
 a control. Two sampling zones in the Cesar River were selected based on
 their similar physiographic traits -such as altitude, geographic and
 environmental characteristics, and orientation- to the upper and middle
 zones of the Ranchería River. In total, we designated five sampling zones:
 the Ranchería upper zone (UR), located upstream of the dam; the Ranchería
 middle zone (MR), located downstream from the dam: the Ranchería lower
 zone (LR), located downstream of the mine area; and two zones in the Cesar
 River, the Cesar upper zone (UC) and the Cesar middle zone (MC) (Fig. 1a;
 Appendix S1a). Within each zone, we chose three sampling sites (Fig. 1a,
 Appendix S1a), separated from each other by at least 200 m. We placed
 three seed traps at each site (i.e., nine traps per zone).
 <em>2.4 Seed sampling</em> Our
 seed traps were made following the model proposed by Vogt et al. (2004)
 and used in Esper-Reyes et al. (2018) from PVC pipe with a cloth funnel
 and cap. The cloth forming the funnel and the outer part of the cap
 consisted of synthetic fiber gauze with a mesh size of 0.5 mm, and the
 inner part consisted of gauze with a mesh size of 0.1 mm. Thirty traps
 were constructed as follows: each trap consisted of a section of PVC pipe
 measuring 15.24 cm in diameter × 30 cm long and a 7.62 cm PVC pipe
 coupling was fitted with caps at the end of each trap (Fig. 1b).
 Two field trips were conducted to the study areas, one in July
 and the other in December 2019. The trips were planned based on logistical
 considerations to ensure the feasibility of carrying out sampling in the
 field. According to the climate regime, July is the driest month of the
 shorter dry season, and December is a transitional month between the end
 of the rainy season and the beginning of the longer dry season (Arregocés
 et al. 2024). Thus, in the subsequent analyses we used
 'transitional' season for December and 'dry' season
 for July. The mean monthly flows obtained in hydrographs show a contrast
 between the two dates, with December having a higher river flow because of
 the end of the more extended rainy period of the year. At each sampling
 site the traps were placed hanging from rocks and surrounding vegetation,
 to remain hidden to prevent removal by local people. Traps were suspended
 so that half of the mouth of the trap was submerged in the river (Fig.
 1b). These remained suspended in the river for 48 hours, after which the
 material collected was placed in resealable plastic bags. Likewise, we
 sampled the flowers/fruits of herbs, shrubs and trees that were within 50
 m of the riverbank for approximately 100–200 meters. This material was
 pressed and stored for later identification, in order to be used as
 support for the identification of the seed species found in the traps. The
 material that was collected by the traps was placed in drying trays and
 kept in the sun for fourth days. After this time, rocks, leaves and large
 dry branches were discarded, and the seeds were separated by using a
 Hubbard #548 six-screen sieve. In some cases, such as
 <em>Ficus</em> spp., fruits were considered the dispersal unit
 rather than individual seeds. Finally, the selected material was placed in
 labeled paper bags for later identification at the Colombian National
 Herbarium, at the National University of Colombia, in Bogotá, Colombia.
 The material was dried in an oven until all the moisture was removed, on
 average for two days. Once dry, the seeds of each of the samples were
 separated using a stereomicroscope. Subsequently, these were grouped into
 similar morphospecies and identified to the finest possible taxonomic
 level, with the help of taxonomists and the support of specimens from the
 fruit and seed collection of the Colombian National Herbarium
 (COL). <em>2.5 Water
 sampling</em> On November 24, 2020, we collected
 water samples from the Ranchería River at two sampling points within each
 of the three zones (UR, MR and LR), with the sampling points spaced more
 than 200 m apart. Additionally, a fourth zone upstream of the mine
 (U-mine) was included to allow for a more thorough evaluation of the
 mine´s impact. All samples were kept cold and taken to the laboratory and
 analyzed the day after collection. A total of fifteen chemical parameters
 of the water were analyzed in the laboratory following the regulations of
 the Institute of Hydrology, Meteorology and Environmental Studies of
 Colombia, IDEAM (Nancy Flórez Garcia S.A.S. Laboratories; IDEAM Accredited
 Laboratory; Appendix S2). To measure water turbidity—an indicator of how
 much light is absorbed by suspended particles or particulate
 contaminants—we used a highly accurate portable HI 98703 Hanna Instruments
 Turbidimeter, which meets or exceeds EPA standards (USEPA Method 180.1 for
 wastewater and Standard Method 2130 B for drinking water). The instrument
 measures the turbidity of a sample in the range of 0.00 to 1000
 nephelometric turbidity units (NTU), with NTU indicating the number of
 particles per unit volume, or a specific light scattering
 coefficient. <em>2.6 Statistical
 analysis</em> <em>2.6.1. The seed community
 transported by the rivers</em> We determined the
 composition, richness and abundance of the seeds dispersed by the
 Ranchería and Cesar Rivers in the sampling zones detailed above. Species
 rank-abundance curves were generated to observe the relationships between
 richness, relative abundance and evenness of the collected seed species.
 Rank-abundance curves can be fitted to various types of models (Wilson
 1991). This analysis is useful not only because they help reveal
 similarities and/or distinctions of seed communities between sampling
 sites and climatic seasons, but also dominance, and this is likely to have
 different effects on the dynamics of riparian ecosystems. To evaluate the
 fit of the different curve models, we used the “radfit” function of the
 “vegan” package in the R statistical program (Oksanen et al.
 2022). To assess the relationships between seed
 community composition, zone, season and river, we performed non-metric
 multidimensional scaling (NMDS) ordinations on Bray-Curtis
 dissimilarities, permuted analysis of variance (PERMANOVA) and permuted
 multivariate analysis using the functions metaMDS, adonis2 and betadisper,
 respectively from the vegan package in R (Oksanen et al., 2022; R
 Development Core Team, 2023). The square root-transformed abundance data
 was used as the input matrix. Plant species with &lt; 3 seeds were not
 included in the analysis. Bray-Curtis dissimilarity matrices were
 visualized using non-metric multidimensional scaling (NMDS) plots. For
 PERMANOVA analyses, the occurrence of 0 seeds for some sites precludes a
 hierarchy analysis using constraining permutations with the adonis2
 procedure. To overcome this limitation, we incorporated into the data
 matrix a “dummy species” (i.e., to set a minimum abundance of one for all
 sites), as recommended by Clarke et al. (2006).
 <em>2.6.2. Spatial variation of seed transport in relation
 to sampling zones </em> PERMANOVA was used to
 test for significant differences in seed communities collected from the
 rivers across five sampling zones, with permutations constrained by
 season. <em>2.6.3. Effects of the dam on seed
 communities transported by the river</em> To
 evaluate the impact of the dam on the seed community of the Ranchería
 River, we used a PERMANOVA nested design considering four sampling zones
 (the upper and middle zones of the Cesar and Rancheria rivers). We
 assessed the effect of river (Cesar, Ranchería), season (dry,
 transitional), zone (upstream and midstream, with the latter representing
 downstream of the dam for Rancheria River), and the two-factor
 interactions: season×river; season×zone, and river×zone. We assumed that a
 significant river×zone effect would indicate an effect of the dam on
 hydrochory. The permutation was constrained with the strata option in
 adonis2 procedure by a “plot” factor with four levels resulting from the
 river/zone combination (i.e., Cesar-upper, Cesar-middle, Ranchería-upper,
 Ranchería-middle). The test was performed with 9999
 permutations. <em>2.6.4.</em>
 <em>Effects of the dam on seed abundances transported by the
 rivers</em> We constructed a mixed nested model
 to evaluate the impact of river (main effect) and zone (subplot effect) on
 the total abundance of seeds, representing the cumulative sum across all
 species. The model incorporated a 'plot' factor as a random
 effect, comprising four consecutive levels (1 to 4), each corresponding to
 unique combinations of season and river (transitional-Cesar,
 transitional-Ranchería, dry-Cesar, dry-Ranchería). Additionally, season
 was included as a blocking factor in the model. This approach allowed for
 a comprehensive examination of the effects of river, zone, and their
 interactions while controlling for seasonal variations. As indicated in
 the multivariate analysis, it was hypothesized that if the dam influenced
 seed transport, a statistically significant river×zone interaction would
 be anticipated. To find the best (simplest) model we used backwards
 stepwise selection, starting with the most complex model (including all
 terms and the specified interaction) and dropping each term sequentially,
 retaining only terms whose removal significantly worsened the model fit (p
 &lt; 0.05). The total number of seeds (the response variable) was
 first transformed to square root of y plus 0.5 to meet the assumptions of
 normality and homogeneity of variance of the model residuals. To perform
 the mixed model, we used the nlme library of R including the varPower
 option to model the variance (Pinheiro and Bates 2023). In all cases, we
 report mean and standard error values for untransformed data.
 <em>2.6.5. Effects of the mine on seed communities
 transported by the river</em> In order to
 evaluate the potential effect of the mine on the seed community
 composition we performed pairwise comparisons (PERMANOVA) of the sampling
 zone downstream of the mine on the Ranchería River to the upstream and
 midstream sampling zones on both rivers. To control family-wise error rate
 following multiple comparisons, P-values were adjusted using the
 Benjamini-Hochberg procedure (Benjamini and Hochberg 1995). All
 permutation tests were carried out with 999 permutations.
 <em>2.6.6. Effects of the mine on seed abundances
 transported by the Rancheria River</em> We then
 assessed whether there was a difference in the total number of seeds
 transported by the Rancheria River between the two seasons upstream versus
 downstream of the mine in the Ranchería River, using an ANOVA (Type III
 sum of squares) for the two main factors and their interaction. Prior to
 analysis, we transformed the response variable by square root + 0.5 to
 achieve normality and homogeneity of variances. To fit the statistical
 model, we used ‘car’ package in R statistical software (Fox and Weisberg
 2019). <em>2.6.7. Effect of the mine and the dam
 on water quality</em> To test whether there were
 effects of the mine and the dam on water quality, we used a PERMANOVA
 analysis with a planned orthogonal comparison model, applying the reverse
 Helmert coding (i.e., comparing each level with the mean of the previous
 levels: downstream of the mine (LR) vs mean of the three upstream sampling
 zones (UR, MR, U-mine); upstream of the mine (U-mine) vs mean of upstream
 and downstream of the dam (UR, MR), and downstream (MR) vs upstream of the
 dam (UR). To perform the analysis, we calculated a Euclidean distance
 matrix on the data transformed by log(x+1). The PERMANOVA was performed
 with 9999 permutations. To visualize the arrangement of chemical water
 compounds, Principal Component Analysis (PCA) was employed. Before PCA,
 sample adequacy was confirmed through the Kaiser-Meyer-Olkin (KMO) Test
 for Sampling Adequacy. For PCA analysis we used prcomp function in the
 “stat” package and biplot from the “vegan” package in the R statistical
 program.
description: # Hydrochory, a key ecological function of a tropical dry forest river
 threatened by a dam and open-pit coal mining in Colombia Dataset DOI:
 [10.5061/dryad.ghx3ffbxt](10.5061/dryad.ghx3ffbxt) ## Description of the
 data and file structure Hydrochory is a key ecological function of a
 tropical dry forest river threatened by a dam and open-pit coal mining in
 Colombia.
 [https://doi.org/10.5061/dryad.ghx3ffbxt](https://doi.org/10.5061/dryad.ghx3ffbxt) Tropical dry forests are among the most floristically rich ecosystems and have high rates of endemism (Gentry 1982); however, they are also one of the most threatened in the world (Janzen 1988, Portillo-Quintero and Sánchez-Azofeifa 2010, IUCN 2012). It is estimated that about 54% of the area covered by this ecosystem is distributed in South America (Ceccon 2001, Portillo-Quintero and Sánchez-Azofeifa 2010, Blackie et al. 2014). In Colombia, this ecosystem crosses six bioregions that vary widely in climate, soils, and anthropogenic pressures; four of these regions are in a critical state of fragmentation, with an average maximum patch area of only 100 ha (Ariza et al. 2014, Pizano et al. 2017). One of these, the La Guajira region, has a long history of anthropogenic alteration; since colonial times, the establishment of large and intensive crops promoted land use change and the alteration of rivers (Guerra Curvelo and Egurrola Hinojosa 2015). The Ranchería River, one of the most important in the region, has been one of the most affected since colonization and has since undergone repeated modifications (Guerra Curvelo and Egurrola Hinojosa 2015). Currently, due to severe anthropic changes, the river’s flow has decreased sharply, causing several economic, social and environmental problems (Guerra Curvelo and Egurrola Hinojosa 2015). Coal mining activities began 46 years ago in the region, transforming and threatening human and environmental health (Urrea and Calvo 2014, Moreno Rodríguez and Montero Torres 2016, Galvis 2018) by affecting ecosystem services (Environmental Justice Atlas 2015). One of the critical problems associated with open pit coal mining is acid mine drainage (AMD). Mineral exploitation generates a high level of dissolved solids, such as bicarbonate, chlorides, sodium calcium sulfur, magnesium and iron in drainage waters (Akcil and Koldas 2006, Goswami 2015). Additionally, there is an excess of nitrates and phosphates, nutrients strongly associated with the growth of algae, which generate a strong decrease in oxygen in the water (Castro et al. 1998, Talukdar et al. 2016). These impacts make the water extremely acidic and very high in minerals, thus affecting the biodiversity and life cycles of hundreds of organisms in wetlands near the mines (Castro et al. 1998, Akcil and Koldas 2006, Munnik 2010, Goswami 2015, Talukdar et al. 2016, Pat-Espadas et al. 2018). It has been reported that water acidification generates modifications in seed morphology by damaging specialized structures for buoyancy and viability, which also affects seed germination and establishment (Fulbright 1988, Fargašová 1994). Additionally, the decomposition of nutrients, microorganisms and mycorrhizae generates strong transformations in the ecological conditions of soils and water (Fulbright 1988, Fargašová 1994, Clark 1997). It has been reported that the accumulation of salts or heavy metals together with water acidification completely inhibit the seed germination process (Fulbright 1988, Fargašová 1994, Clark 1997, Pérez-Fernández et al. 2006, Reichman et al. 2006, Donggan et al. 2011, Pat-Espadas et al. 2018). Coal mining also has major physical (mechanical) effects, including altering and diversion of water courses and banks and the disconnection between surface and groundwater flows (Seybold et al. 2004, Anawar 2013). These can completely change water and soil conditions and the composition of seed species transported by the river (Ghose 2004, Pandey et al. 2014). This, in turn, affects seed establishment sites and leaves soils poorly drained, eroded and poor in organic matter (Ghose 2004, Seybold et al. 2004, Donggan et al. 2011, Anawar 2013, Pandey et al. 2014). Sixteen years have passed since the diversion of the Rancheria River for the construction of the El Cercado dam, causing several environmental impacts including the fragmentation of the river network and the alteration of the flow regime, the generation of a new ecosystem (reservoir), and impeding the downstream movement of aquatic organisms, sediments and nutrients (Contraloría General de la República 2010, Corpoguajira 2020). Various studies report reduction in hydrochory and decreased floristic diversity downstream of dams (Nilsson et al. 1989, Nilsson and Jansson 1995, Jansson et al. 2000, Andersson and Nilsson 2002). For example, Brown and Chenoweth (2008) found a 90% reduction in abundance and an 84% reduction in seed species richness in sampling downstream of a dam; they also report that the germination of seeds collected downstream of the dam was very low. Likewise, the decomposition of biomass accumulated in dams can generate water toxicity and eutrophication of the ecosystem, affecting the germination of seeds downstream of the dam (Merritt and Wohl 2006). Therefore, based on the above, we hypothesized that damming and mining of the Ranchería River will affect the seed community composition flowing with the river; for example, a marked decrease in richness and abundance of seeds transported downstream of the dam and the mining area. In order to test the effects of the anthropogenic alterations of the Ranchería River on hydrochory, 1. we assessed the composition, richness, and abundance of the seed community transported by the Ranchería, both upstream and downstream of a dam and of the coal mine;  2. we then compared these parameters to zones with similar physiographic features in the nearby Cesar River, which has undergone much less intense modification. We conducted these survey activities during both the dry and rainy season, which are highly contrasting in this tropical dry forest ecosystem. We expected distinct composition and higher richness and abundance of seeds in the Cesar than in the Ranchería River, with particularly marked differences at sites downstream of the dam and mine. Furthermore, 3. to complement ecological results and to investigate the effects of the coal mine on the physical and chemical characteristics of the Ranchería River water, we analyzed physical-chemical water parameters in this River. Understanding the role of rivers and mechanisms that determine the geographic range of seed dispersal is of vital importance to determine the intensity of human impacts on wetland transformation, and may point to ways to successfully restore biodiversity and their lost ecosystem services (Richter and Stromberg 2005). There was significant spatial heterogeneity of the seed communities sampled along both rivers, with especially strong separation of the community collected downstream from the open pit mine. We also found a significant effect of the dam on seed composition and abundance in the Ranchería River. Seed community assemblages, but not seed numbers, were significantly different between seasons and rivers. We also found significantly higher turbidity, chloride, carbonate, iron, nitrate and sulfate levels downstream of the mine compared to upstream samples. There is a clear effect of the dam and the open pit* *mine on the Ranchería River in Colombia. The alteration of natural flows, environmental conditions and water quality triggers a radical change in the composition, abundance and structure of the riparian plant communities and affect key ecological functions of the river. Urgent measures are imperative to address these challenges effectively and ensure the long-term sustainability of the ecosystem. ## Description of the data and file structure ### seed-matrix.csv Description: The "**seed-matrix.csv**" data file contains abundance data for seed species captured in the study rivers in Colombia, corresponding to 79 plant species and one pseudospecies (used to balance the sampling design). The columns include the acronym for each species. Sampling was conducted in two rivers: Cesar River and Ranchería River. The Cesar River had two collection zones, while the Ranchería River had three collection zones. Each zone contained three sampling sites, and sampling was repeated across two seasons. Variables: * season: seasons of the year with precipitation (rainy) or without precipitation (dry) * river: river identity: Cesar and Rancheria River * zone: studies zones:  Upper (upstream), Middle (downstream of the dam for Rancheria River;  middle-stream for Cesar River), LR (downstream of the mine for Rancheria River) * Species, see table below for abbreviation definitions | Column name | Species | | :---------- | :------------------------------ | | Anacexce | Anacardium excelsum | | Chussp. | Chusquea sp. | | Combfrut | Combretum fruticosum | | Faba2 | Fabaceae sp.2 | | Faba3 | Fabaceae sp. 3 | | Fabo1 | Faboideae sp. 1 | | Ficu1 | Ficus sp. 1 | | Ficuinsi | Ficus insipida | | Ficupequ | Ficus sp. 2 | | Guazulmi | Guazuma ulmifolia | | Hirasp. | Hiraea sp. | | Morph1 | Morphospecies1 | | Morph2 | Morphospecies2 | | Morph3 | Morphospecies3 | | Morph4 | Morphospecies4 | | Morph5 | Morphospecies5 | | Morph6 | Morphospecies6 | | Morph7 | Morphospecies7 | | Morph8 | Morphospecies8 | | Morph9 | Morphospecies9 | | Morph10 | Morphospecies10 | | Morph11 | Morphospecies11 | | Morph12 | Morphospecies12 | | Morph13 | Morphospecies13 | | Morph14 | Morphospecies14 | | Morph15 | Morphospecies15 | | Morph16 | Morphospecies16 | | Morph17 | Morphospecies17 | | Morph18 | Morphospecies18 | | Morph19 | Morphospecies19 | | Morph20 | Morphospecies20 | | Morph21 | Morphospecies21 | | Morph22 | Morphospecies22 | | Morph23 | Morphospecies23 | | Morph24 | Morphospecies24 | | Morph25 | Morphospecies25 | | Morph26 | Morphospecies26 | | Morph27 | Morphospecies27 | | Morph28 | Morphospecies28 | | Morph29 | Morphospecies29 | | Morph30 | Morphospecies30 | | Morph31 | Morphospecies31 | | Morph32 | Morphospecies32 | | Morph33 | Morphospecies33 | | Morph34 | Morphospecies34 | | Morph35 | Morphospecies35 | | Morph36 | Morphospecies36 | | Morph37 | Morphospecies37 | | Morph38 | Morphospecies38 | | Morph39 | Morphospecies39 | | Morph40 | Morphospecies40 | | Morph41 | Morphospecies41 | | Morph42 | Morphospecies42 | | Morph43 | Morphospecies43 | | Morph44 | Morphospecies44 | | Morph45 | Morphospecies45 | | Morph46 | Morphospecies46 | | Morph47 | Morphospecies47 | | Morph48 | Morphospecies48 | | Morph49 | Morphospecies49 | | Morph50 | Morphospecies50 | | Morph51 | Morphospecies51 | | Indisp | Indigofera sp | | Inga1 | Inga sp. 1 | | Inga2 | Inga sp. 2 | | Inga4 | Inga sp. 3 | | Ingavera | Inga vera | | Iseiluxu | Iseia luxurians | | Loncpunc | Lonchocarpus aff. punctatus | | Macharbo | Machaerium arboreum | | Machcapo | Machaerium capote | | Mimopigr | Mimosa pigra | | Paspsp. | Paspalum sp. | | Phytamer | Phytolacca americana | | Piptflav | Piptadenia flava | | Pithungu | Pithecellobium aff. unguis-cati | | Prisverr | Pristimera verrucosa | | Serjsp. | Serjania sp. | | Sponmomb | Spondias mombin | ### seed\_abundance.csv Description: The file ‘**seed_abundance.csv**’ contains data on the total abundance of seeds collected from multiple sampling zones along the Cesar and Rancheria rivers during two distinct seasons: rainy and dry. Variables: | season | seasons of the year with precipitation (rainy) or without precipitation (dry) | | :----- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | river | river identity: Cesar and Rancheria River | | zone | studies zones:  Upper (upstream), Middle (downstream of the dam for Rancheria River;  middle-stream for Cesar River), LR (downstream of the mine for Rancheria River) | | seed | total seed abundance | ### chemical-turbidity.csv Description: The file ‘**chemical-turbidity.csv**’ contains data on concentrations of chemical compounds (mg/L) and turbidity (NTU: nephelometric turbidity units) measured in each of the sampling zones along the Ranchería River. Data were used to test the effect of the mine and the dam on water quality Variables: | Zone: UR | upstream of the dam | | :----------- | :--------------------- | | Zone: MR | downstream of the dam | | Zone: U-mine | upstream of the mine | | Zone: LR | downstream of the mine | | Cl | Chlorides | | CaCO3 | Carbonates | | Fe | Iron | | NO3 | Nitrates | | SO4 | Sulfates | | Turb. | Turbidity | ## Code/Software n/a