# The return of the Allis shad (Alosa alosa) to the navigable lower reaches of the Seine: what are the migratory routes of future spawners?

Céline Le Pichon, F. Bau, Armand Michelot, Evelyne Tales, Sébastien Grall, Eric Rochard

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Céline Le Pichon, F. Bau, Armand Michelot, Evelyne Tales, Sébastien Grall, et al.. The return of the Allis shad (Alosa alosa) to the navigable lower reaches of the Seine: what are the migratory routes of future spawners?. 2025. hal-05323939

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# The return of the Allis shad (Alosa alosa) to the navigable lower reaches of the Seine: what are the migratory routes of future spawners?

Céline Le Pichon<fnref n="1" />*, Frédérique Bau<fnref n="2" />, Armand Michelot<fnref n="1" />,<fnref n="4" />, Evelyne Tales<fnref n="1" />, Sébastien Grall<fnref n="3" /> and Eric Rochard<fnref n="2" />

## ABSTRACT

Allis shad (Alosa alosa L., 1758) is an anadromous fish globally listed as «critically endangered» (IUCN, 2024). In France, it is estimated that shad has lost 69% (7,000 km) of its historic distribution due to human activities, especially the disruption of connectivity between growth areas at sea and reproduction areas in rivers. After an absence of almost one century, signs of its return in the Seine River have been recorded for the past two decades. Despite scarce data, specimens of both adult and juvenile Allis shad were caught by anglers or recorded at video-counting stations up to 400 km from the sea. To acquire knowledge about the migratory behaviour and routes of these recolonising shads in the navigable lower reaches of the Seine River, an acoustic telemetry study was

<footnote n="1">¹ Université Paris-Saclay, INRAE, HYCAR Hydrosystèmes Continentaux Anthropisés: Ressources, Risques, Restauration, 1 rue Pierre-Gilles de Gennes, CS10030, 92761 Antony cedex, France</footnote>

<footnote n="2">² INRAE, UR EABX, 50 avenue de Verdun, 33612 Cestas cedex, France</footnote>

<footnote n="3">³ Association Seine Normandie Migrateurs</footnote>

<footnote n="4">⁴ current affiliation : INRAE, UR DECOD, L'Institut Agro, IFREMER, INRAE, Rennes, France.</footnote>

<footnote>*Corresponding author</footnote>

<footnote>Correspondence: celine.lepichon@inrae.fr</footnote>

<footnote>ORCID</footnote>

<footnote>Céline Le Pichon : https://orcid.org/0000-0001-8055-7164</footnote>

<footnote>Frederique Bau: https://orcid.org/0000-0002-5983-6430</footnote>

<footnote>Eric Rochard: https://orcid.org/0000-0003-4518-7342</footnote>

<footnote>Evelyne Tales: https://orcid.org/0000-0001-8811-6830</footnote>
conducted. Nineteen shads were captured, tagged and released at the first weir from the sea and tracked over a 188 km channelized reach, fragmented by five navigation weirs and locks, up to Paris. Most individuals quickly resumed their upstream migration, providing an opportunity to analyse their behaviour in the face of cumulative obstacles and multiple crossing routes. Our results highlighted the interest of quantifying, in a complementary way, the overall crossing rate, the time spent below weirs waiting for crossing and the cumulative effects of navigation weirs on migration delays. This is the first time that the presumed low effectiveness of these fishways, assessed using a structural analysis by experts, has been confirmed by the low crossing rate observed (7%). Nevertheless, 16% of shads reached the Oise tributary or Paris by using navigation locks voluntarily, as no fish lockage are operated in the Seine River. While all day long trajectories were direct in open-river reaches with median cruising speeds around 0.8 m.s⁻¹, time delays varied downstream navigation weirs (median time of 27h to 87h) and crossings were observed during daytime. This study revealed that both short- and long-distance repeated retreats and attempts downstream weirs occurred during the upstream migration of shad, probably in an endeavour to locate alternative passage routes. Individual variation in time delay or retreat and attempt movements at navigation weirs affected neither the subsequent upstream migration speed nor the final upstream extent of their migration. The behavioural variation among the recolonising shads, composed of multi-aged and mixed-experience groups, could help to explain their return to the lower reaches of the Seine River.

**Keywords:** anadromous fish, Allis shad, river, spawning migration, behaviour, navigation lock, fishway, telemetry.
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Introduction

Allis shad (Alosa alosa L., 1758) is an anadromous clupeid globally listed as «critically endangered» (IUCN, 2024). Historically present in most North East Atlantic River basins from Morocco to Norway, it was particularly abundant in Douro, Tagus, Mondego, Lima, Minho, Adour, Garonne-Dordogne, Loire, Seine and Rhine basins (Baglinière et al., 2003). Allis shad's distribution range has been progressively constrained by impacts from anthropogenic activities: commercial harvesting, impassable barriers (Lassalle et al., 2009; Merg et al., 2020), hydromorphological modifications and climate change (Lassalle et al., 2009). In France, it is estimated that shad have lost 69% (7,000 km) of their historic potential distribution due to the disruption of connectivity (Merg et al., 2020). In most cases, as for other diadromous fish (Limburg et al., 2009), the disappearance is the result of varying combinations of these pressures (Costa et al., 2001). In addition, restricted migration in basins with high levels of fragmentation generate "forced" shared spawning grounds and hybridization with the wider spread twaite shad (Alosa fallax Lacépède, 1803) (Alexandrino et al., 1996), that could threaten the long-term persistence of these declining species (Taillebois et al., 2020; Rougemont et al., 2022). On the Severn River, fragmented by navigation weirs, the decline of A. alosa has coincided with hybridization with A. fallax on the remaining accessible spawning grounds (current populations show evidence of past introgression) (Antognazza et al., 2022).

In the 2000's, the species was considered extinct in Northern Africa (UICN, 2010) and its' distribution range was restricted to the Atlantic Coast of Portugal and France (Baglinière et al., 2003). The Adour and Loire populations were depleted and the Gironde population collapsed at the beginning of the 2000th without a clear understanding of what happened (Rougier et al., 2012). In the same time, we noticed more frequent observations of shads in rivers of the northern part of the range (Brittany and Normandy). That partly results of strayers from southern populations (Martin et al., 2015; Randon et al., 2017). Actions were initiated (Paumier, 2019; Poulet et al., 2022) and are still in progress to identify the reasons of these ancient or recent declines. A Life Nature project (LIFE06 NAT/D//000005) initiated the reintroduction of the Allis shad in the Rhine basin, with offsprings produced from adults of the Gironde population (LANUV, 2010). Following these stockings, evidence of natural reproduction were observed in the Rhine (Hundt et al., 2015).

The Seine River has a long history of human presence and impacts dating back to the Gallo-Roman era, coinciding with the development of the city of Paris and its activities (Guillerme, 1990). But its diadromous fish community has experienced severe declines and extinctions particularly from the middle of the XIXth century (Belliard et al., 1999; Belliard et al., 2009). Its progressive disappearance resulted from modifications of the river for navigation, i) building of the first weir from the sea (Poses in 1850) and upstream nine "needle" type navigation weirs (Le Pichon et al., 2020), ii) channelization (Lestel et al., 2021) and iii) degradation of the water quality due to domestic and industrial pollutions (Boët et al., 1999). At the end of the 20th century, the Seine was
one of the most impacted French River basins, since all anadromous species have disappeared in 85% of the locations with historical occurrences (mid-18th - 20th century) (Merg et al., 2020). The water quality only started to improve from the 1990s thanks to wastewater treatment following the Water Law (1964) (Romero et al., 2016). Since that period, rebuilding new fishpasses was supported thanks to the implementation of the French Fishing Law in 1984, European regulations and the first management plans for migratory fish.

In the first part of the 19th century, Allis shad was one of the most widely spread diadromous species in the Seine basin; with records of its presence up to 500-600 km from the sea on large tributaries (Belliard et al., 2009). But at the beginning of the 20th century, this species was considered as very rare, and only the twaite shad was present in the lower Seine downstream the first navigation weir (Roule, 1920). After an absence of almost one century, in 2004 and 2007 the first specimens of adult Allis shad were observed again, caught by anglers in the median part of the basin (Belliard et al., 2009). allis shad have been recorded every year at the video counting station, installed in 2008 at the Poses weir. Since that date, some mature and juvenile shads are regularly caught in the Seine, Marne and Oise rivers by anglers (Seinormigr, pers. comm.). Moreover, In a second fish pass, built in 2017 on the other bank of the Seine River at Poses weir, 3000-4000 shads were recorded in 2019-2020, with a seasonal spawning run extending from April to June. For these recolonising shads, this raises questions about their ability to achieve spawning migration and produce viable offspring in the navigated Seine River. As projections of the species distribution range up to 2100 consider the Seine River basin as suitable (Barber-O'Malley et al., 2022; Lassalle et al., 2009), efforts to promote the success of their spawning migration should be continued.

Waterways such as regulated rivers and shipping canals generate threats for fish species (Jeliazkov et al., 2024). In particular, infrastructures such as navigation locks, dams and hydroelectric power plants, as well as regulated water flows, can hamper migratory behaviour of anadromous species. While they can provide energetically favorable migration routes for diadromous fish due to lowered current velocities, they can accentuate fish disorientation and slow down their migratory rhythm due to insufficient unidirectional current. This has been observed for American shad *Alosa sapidissima* (Bailey et al., 2004; Moser et al., 2000), Atlantic salmon (Gerlier et al., 1998; Croze et al., 2008; Ben Jebria et al., 2023), sea and river lamprey *Lampetra fluviatilis* (Pereira et al., 2017; Kerr et al., 2023) and European eel *Anguilla anguilla* (Drouineau et al., 2017; Verhelst et al., 2018). Alosa sp. migrations may occur in regulated rivers when dams and weirs are equipped with fish passage facilities. But unlike few other diadromous species such as eel and salmon, we lack information on the behaviour and ability of allis shad to overcome obstacles, particularly in regulated and navigated rivers.

Finding the entrance of passage is the first difficulty for shads according to the downstream hydraulic conditions, the number of available routes and their locations (Groux et al., 2015). American shad are repelled by turbulent flow, which negatively affects their ability to locate fish
passage (Young *et al.*, 2012). As shads travel in shoals, individuals are reluctant to leave the group to enter narrow passages (Haro *et al.*, 2012). This behaviour dictates that the fish passage must be as wide as possible to avoid the spreading of shoals (Larinier *et al.*, 2002). But migration in shoals has an increasingly recognized advantage: collective navigation, whereby social interactions improve the individuals ability to find their way. Collective navigation enables passages to be found more quickly and crossed in fewer attempts, as has been seen with Chinook salmon *Oncorhynchus tshawytscha* (Okasaki *et al.*, 2020).

Fishways, fish lifts and locks (e.g. Borland-type fish locks designed and built specifically for fish passage) and navigation locks can help migrating individuals (Clay, 2017), although their effectiveness can vary widely (Haro *et al.*, 2012; Larinier *et al.*, 2002; Moser *et al.*, 2000). Unable to leap, adult shad must swim to ascend high-velocity zones or to cross obstacles; they seek out laminar streaming flow and avoid highly turbulent swirling areas and emulsified water (recirculation zones, bends, etc.) (Haro *et al.*, 2001; Larinier *et al.*, 2002). Shad tend to travel in the upper layer of the water column (1.5-4.5 m) and prefer using wide and sufficiently deep (minimum 1.20 m) fish passage facilities; surface passage must therefore be provided in the fishway. As a result, most French fish locks were considered ineffective for allis shad, potentially due to siphon passages (Larinier *et al.*, 2002). The same results was provided at the first dam on the Douro River where shads never enter the Borland-type fish lock despite their presence below the dam (Godinho *et al.*, 2023). Shad orientate visually, crossing obstacles during the day, according to hydrological, turbidity and thermal conditions (Bayse *et al.*, 2019; Belo *et al.*, 2021; Moser *et al.*, 2000). Thus, shads are very sensitive to sudden changes in light, avoiding dark areas (Larinier *et al.*, 2002).

Among various fish passage facilities, navigation locks represent a cost-effective alternative as fishways. American shad, Alabama shad (*Alosa alabamae*), and other diadromous clupeids are known to voluntary use navigation locks when locking operations are proceeded for boats (Young *et al.*, 2012). Passage success may be variable and related to the time spent at the lock entrance, the attraction discharge and current velocity inside the lock, and the daily locking schedule (Moser *et al.*, 2000; Bailey *et al.*, 2004). However, the efficiency of Allis shad passage via navigation locks without specific management measures is largely unknown.

The aim of this work was to study the Allis shad's migration run in the lower Seine River up to Paris, using an approach based on tracking fish with acoustic telemetry. More precisely we aimed at i) characterizing their spatio-temporal migration patterns; ii) quantifying individual variation in the movement behaviour according to different equipments of navigation weirs; iii) determining how several successive weirs can impose cumulative effects on migrants and iv) assessing the impact of environmental conditions and navigation activities on upstream migration.
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### Study area and environmental data

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The Seine River rises in the Langres plateau (480 m elevation) and flows 777 km north-west through Paris before entering the English Channel at Le Havre. Its catchment area drains 76,260 km², 12 % of France's surface, but currently concentrates 25-30 % of the French industrial activity and 23 % of its population (Meybeck et al., 2018). The Seine River is a major axis for French river traffic with 55% of national river freight. Below Paris, it is a great traffic waterway, where commercial boats (from 60 to 135 m long and 8 to 15 m wide) transport bulk goods or containers. The study area is a wide-gauge canal of 188 km long from the first obstacle (Poses weir, 165 km upstream from the sea) to Paris. Modified from the original Seine River and equipped with navigation weirs (Figure 1, Table 1), it is today a succession of deep and low-current velocity forebays.

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<figure><img src="image_2.png" /></figure>

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<caption>**Figure 1** - The Seine River basin and A - the 188 km long study area with tributaries, location of the 6 navigation weirs (W0 to W5) and 39 acoustic receivers. B- Schematic representation of the study site with number of fish tagged (grey), approaching weir (black) and crossing weir (red).</caption>

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The study area encompasses confluences with one major tributary, the River Oise (Strahler order 6), and three minor tributaries (Strahler order 3) in a succession of deep and low-current velocity forebays. Navigation weirs were built in the second half of the 19th century, their renovation in the mid-20th century leads to increasing waterfall height to address navigation needs (Le Pichon
et al., 2020) (Table 1). Today, from the sea to Paris, there are five forebays separated by six navigation weirs, associated locks (short locks: 141-160 mx12 m; long locks: 185-220 m x 17-24 m), new fishways and hydropower plants (Table 1, Figure 1). Fishway types are mainly vertical slot fishways, their functionality are considered low by experts, and the Suresnes weir (W5) is not even equipped with a fishway (Table 1). In that context, navigation weirs may slow down or even prevent the migration of shad. The average boat traffic over April-June 2021 period ranged from 48 boats/day at Chatou (W4) to 18 boats/day at Suresnes (W5) (Table 1). Unlike the Rhône basin (Guillard et al., 2000), there is no manipulation of the locks on the Seine River specifically to improve fish passage. In addition, the flow of the Seine in the study reach is regulated by several storage reservoirs in the upper Seine basin, which buffer floods and maintain minimum low flows to ensure that the water lines and current speeds are compatible with navigation (Boët et al., 1999).

Environmental data were obtained from Environmental Agencies. Daily discharge at gauging station of Vernon (Eure) was downloaded from the hydroportail (SCHAPI - HydroPortail (eaufrance.fr) (Figure 1). The discharge at Vernon is strongly correlated with discharge at Paris and is representative of fluctuations over the study period (Figure 2). The daily median discharge for the 1989-2020 period was calculated using R statistical Software (R version 4.2.1 R Core Team 2022). Water temperature and dissolved oxygen measurements at 15 min resolution are available at Méricourt navigation weir W2 (Figure 1) from the MeSeine observatory of Paris sanitation authority (SIAAP) (Figure 2).

The period of the day (daytime, nighttime) was calculated with the suncalc R package (v0.5.1; Thieurmel 2022). For navigation weirs W1 to W5, data on inland commercial boats traffic were obtained from the regional service of the French navigable waterways organization (VNF-UTI Boucles de la Seine). These data recorded the date and time of passage of commercial or tourist vessels through the various locks and their direction (upstream or downstream). In addition, the regional diadromous fish association (Seinormigr) provided video counts of fish passages at W0 (Figure 2).
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<caption>**Table 1** - Characteristics of navigation weirs built on the Seine River from the sea to Paris. Hydropower plant Ⓔ, derelict lock 🚕 and used lock 🚕, Fish pass 🤝, Functionality: ⊗ bad, ⊙ medium, 😊 good. Average numbers of boats per day are calculated for April-June 2021 period.</caption>

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<table><thead><tr><th>Navigation weir</th><th>Dates<br>(creation—renovation)</th><th>Site structure<br>Right bank-Left bank</th><th>Locks: Tot-used<br>(Boat number/day)</th><th>Waterfall<br>height (m)</th><th>Type of fishway</th><th>Functionality<br>(Cassiopee freeware¹ and experts)</th></tr></thead><tbody><tr><td>Poses<br>(W0)</td><td>1850—1967</td><td>Navigation weir</td><td>3-2<br>(27)</td><td>4.2</td><td>Two vertical slot passes 1991,<br>2014</td><td>Attractivity: ⊗<br>Crossing ⊙<br>Maintenance ⊗</td></tr><tr><td>Port-Mort<br>(W1)</td><td>1847—1962</td><td>Navigation weir</td><td>4-2<br>(36)</td><td>3.8</td><td>Old Vertical slot pass right bank<br>Bypass channel 2010 left bank</td><td>Attractivity: ⊗<br>Crossing ⊗ P>150W.m<sup>-3</sup>,<br>Maintenance ⊗</td></tr><tr><td>Méricourt<br>(W2)</td><td>1886—1965</td><td>Navigation weir</td><td>3-2<br>(35)</td><td>4.8</td><td>Vertical slot pass 1998</td><td>Attractivity: ⊗<br>Crossing ⊗ P>150W.m<sup>-3</sup>,<br>Maintenance ⊙</td></tr><tr><td>Andrésy<br>(W3)</td><td>1846—1953</td><td>Navigation weir</td><td>2-2<br>(46)</td><td>2.7</td><td>Bypass channel 2010</td><td>Attractivity: ⊗<br>Crossing ⊙<br>Maintenance ⊙</td></tr><tr><td>Chatou<br>(W4)</td><td>1880—2014</td><td>Navigation weir</td><td>1-1<br>(48)</td><td>3.2</td><td>Vertical slot pass 2014</td><td>Attractivity: ?<br>Crossing ⊗ P>150W.m<sup>-3</sup>,<br>Maintenance ⊗</td></tr><tr><td>Suresnes<br>(W5)</td><td>1869—1930</td><td>Navigation weir</td><td>3-3<br>(18)</td><td>3.1</td><td>No</td><td></td></tr></tbody></table>
<figure><img src="image_3.png" /><figcaption>**Figure 2** - Temporal dynamic of the upstream migration of shads and environmental conditions between March and July 2021. A- Daily count of shads at the video-counting station of Poses weir (W0) and cumulated count in percentage over the migration period. Vertical arrows indicate tagging periods. B- Daily discharge at the gauging station of Vernon. The dotted line represents the daily median discharge for the period 1989-2020. C- Daily mean water temperature and dissolved oxygen at Méricourt navigation weir (W2). The grey line indicates the period of the upstream migration for tagged fishes.</figcaption></figure>

## Capture, tagging and tracking shad

To sample shad throughout the migration period, captures were made during three tagging sessions (26-30 April; 3-4 May; 17-21 May) in 2021 (Figure 2A). Shad were captured in the fishway at Poses (W0) using a net cage installed at the outlet basin upstream of the video-counting station. Due to the sensitive nature of the species, little or no stabling of shad was undertaken. Individuals were carefully handled and tagged without any selection on a just-in-time basis as they were caught. Light anaesthesia by immersion in a bath (2 to 3 mL of a 10% solution of eugenol in 20L of water) and tagging were carried out in the same supple stretcher to limit handling of individuals. The stretcher was closed to limit stress, during anaesthesia induction. Once the shad was fully sedated, a 69 kHz, V9-2L acoustic transmitter (9 mm x 29 mm; 2.7 g in water; 146dB, www.innovasea.com) was inserted into the stomach cavity via the natural route. The risk of
transmitter regurgitation is all the more limited as the tag weight is extremely low (well below 0.5% of fish weight) and this species stops feeding on arrival in freshwaters (the retracted stomach allows the mark to be maintained). This intragastric tagging is a proven standard method (e.g. Acolas et al. 2004) that is minimally traumatic, rapid, does not require long-term recovery and does not affect swimming performance and buoyancy (Mellas & Haynes 1985, Bridger & Booth 2003). After tagging, 4 to 5 scales were sampled for ageing fish and characterise their genetic proximity with other french populations. The entire procedure lasted 3 to 5 minutes and was carried out entirely underwater. Before release, The tagged shad was kept under observation in a 1.5 m diameter circular floating cage set in the Seine until it had fully recovered and resumed swimming. All the individuals were then released 50 m upstream of the Poses weir, near receiver 3 (Figure1). The entire tagging procedure was designed to respect animal welfare, following ethical review and according to an authorization from the French Ministry for Higher Education and Research project.

Individual shads were tracked using a monitoring array of 39 acoustic receivers (VR2-W 69 kHz, www.innovasea.com), operated in continuous receiving mode. They were deployed in the first forebay, upstream and downstream of each navigation weir and at the lower part of main tributaries (Figure 1). An additional one was attached to the floating cage during tagging periods to provide information of individual leaving the release area. Receivers were mainly arranged in pairs, located on each bank of the navigation channel. In upstream part of each weir, receivers were located to provide a differential detection of fish moving from the fish pass or the locks. The overlap in the detection range for pairs of receivers and their ability to identify the route upstream of each weir was tested using a tag hauled by a kayak (Michelot et al., 2023). Distances for the core area of detections ranged from 300 to 600 m according to the channel sinuosity. This design prevents fish from crossing undetected, especially when commercial vessels are navigating. Each receiver was suspended in the water column just below a buoy, which was anchored with a 50 kg ballast.

## Data analysis

Fish presence detections were downloaded from receivers every 2 weeks from June 1st to September 9th via a Bluetooth connection using VUE software (Innovasea v 2.6, 2019) and visualized in a VUE database. At the end of the experiment, all data were stored in a FiloScience database (Fish LOgger for Science, (Quinton, 2021)), a web-based open-source software designed to store and visualize fish tracking operations. To avoid multiple simultaneous detections of the same fish by overlapping receivers, detections were smoothed using a period of 20 min (time to cross the core area of detection by a pair of receivers (Michelot et al., 2023) and weighted locations were obtained as described in (Le Pichon et al., 2015).
## Trajectory analysis

Fish trajectories were characterized using weighted locations with Adehabitat R package v1.8.17 (Calenge, 2015). Each trajectory is composed of several elementary segments, characterized by their start and end times and locations. The start and end locations of each segment were overlaid on a cost surface raster. Each cell of this raster gives the value of the least-cost distance from Poses Weir (W0), with a 1 m resolution (ArcGIS 10.6.1, Spatial Analyst extension). The difference in least-cost values between the end and start locations determines the instream length of the segments and also their orientation (positive difference: upstream movement, negative difference: downstream movement). As least-cost distance of each weir from W0 is known, segments corresponding to crossing events were detected. According to their start and end times, each segment was assigned a period of the day, discharge, dissolved oxygen and water temperature values. These environmental parameters were averaged over the time period of each segment. Segments that straddled two periods of the day were referred “multiple time”. To characterize fish trajectory, four categories of movement were assigned to each segment: upstream movement (in open-river reaches), waiting below weir (continuous detection by the receivers pair and interruptions duration below 3 hours), retreat/attempt (exploratory downstream or upstream movements after waiting below weirs: interruption duration greater than 3 hours) or crossing weir.

To test whether the navigation weirs reduced shad movement, their groundspeeds were calculated immediately after release and for each open-river reach and weir. The groundspeed after release was estimated using the delay between the last detection after release and the first detection 5 km upstream (receiver n°8). In open-river reaches, groundspeed is the ratio of the distance between two weirs to the time taken for the first detection upstream of one weir to the first detection downstream of the next weir. The groundspeed to cross each weir was based on the crossing time because of the varying distance between the locations of the receiver pair below and upstream of each navigation weir (660-2300 m) and the lack of detection within the close neighbourhood of the entrance and exit of potential routes. The crossing time is the difference between the last detection on the receiver pair downstream of the weir and the first detection on the receiver pair upstream. This crossing time included the approach to the structure (fish pass or lock), the passage through the structure and the exit. Distributions of groundspeeds after release, to cross weirs and open-river reaches were compared with the Wilcoxon Rank-Sum (Mann-Whitney) test using a pairwise procedure with corrections for multiple tests using the adjustment methods of Benjamini and Yekutieli, based on the false discovery rate. The null hypothesis that the two distributions were the same was rejected at p-value < 0.05.

The cumulative effect of navigation weirs on upstream migration was assessed using three metrics: (i) the average time to cross navigation weirs (16 shads considered) (Kaplan-Meier curve,
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(Kaplan et al., 1958)), (ii) the cumulative crossing rate for individuals that used only the Seine River to Paris (13 shads considered); and (iii) the individual cumulated time lost for the individuals that reached W5 (4 shads considered). This time lost was calculated as difference between the time observed to reach W5 and the time it would have taken to reach W5, swimming at the median groundspeed observed in open-river reaches calculated in our study.

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## Influence of environmental variables and boats traffic

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The effect of environmental variables (temperature, oxygen saturation and discharge) on the probability of being in a particular movement category during active upstream migration (upstream movement, waiting below the weir, retreating/attempting to cross the weir, or crossing the weir) was tested. A multinomial logistic regression was used (that need a reference category), that generalizes logistic regression to multiclass response variable (Venables et al., 2002). The function multinom from the package 'nnet' (v. 7.3-17, Ripley and Venables, 2022) was used in R 4.2.3 (R Core Team 2023). Waiting below weir was chosen as the reference category, as we want to identify the variables that induce active movement. The three other categories of movement were compared to this reference using the Odds ratio. The analysis is restricted to trajectories from release to the last upstream movement.

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To study specifically weirs crossing delays and the effects of biological and environmental factors on crossing time, we used Cox regression, a type of time-to-event analysis, also known as survival analysis (Castro-Santos et al., 2003). Its relevance has been demonstrated to solve the problems of individuals that fail to pass barriers and to potentially consider time-varying covariates during delay (Goerig et al., 2017; Alcott et al., 2021). To fit mixed effects Cox proportional hazards models, we used the package 'coxme' in R (V2.2-18.1, Terry and Therneau, 2022), including fixed effects and random effects for individual and weir. Fixed covariates were fish total length (TL), weight (W) and Fulton condition factor (K) to test the effect of fish characteristics on crossing capacities. In a second analysis, time-varying covariates were included: the number of boat passages (traffic), the number of lock operations and the number of lockage without boats upstream or downstream (total, short lock, long lock) within a time window of 1/5 of day (2 for night and 3 for day).

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# Results

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## General results

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Among the 19 shads tagged, 74% were caught during the first session (26-30 April), when half of the cumulative annual shad numbers had already been video-counted (Figure 2). During the first two days, individuals entered the cage in three groups (shoals in Table 2), while on subsequent days individuals were captured as singles. Individuals were in good condition and relatively homogeneous in size: median total length (TL): 592 mm (505-710mm), median weight (W): 2 kg (1.0-2.5 kg) and median condition (K) 1.0 (0.61-1.35) (Table 2). The individuals ranged in age from

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4 to 6 years and 75% were 5 years old. Spawning marks were observed on the scales of one-third of the individuals (Table 2).

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<caption>**Table 2** - Characteristics of tagged shads sorted by date of capture. The furthest upstream location is indicated: below or upstream weirs, in open reach or at release site. ALA for *Alosa alosa*.</caption>

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<table><thead><tr><th>ID fish<br>Shoal ID</th><th>Release<br>date</th><th>Days of<br>detection</th><th>Age-age at<br>spawning</th><th>TL<br>(mm)</th><th>W<br>(kg)</th><th>K</th><th colspan="5">Crossing site (yes/no) and migration<br>route if yes (except W4)</th><th>Most upstream<br>location</th></tr><tr><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th>W1</th><th>W2</th><th>W3</th><th>W4</th><th>W5</th><th></th></tr></thead><tbody><tr><td>ALA0<sup>a</sup></td><td>04-28</td><td>49</td><td>5</td><td>610</td><td>1.9</td><td>0.84</td><td>Yes,<br>lock</td><td>No</td><td></td><td></td><td></td><td>Below W2</td></tr><tr><td>ALA1<sup>a</sup></td><td>04-28</td><td>15</td><td>5</td><td>615</td><td>2.3</td><td>0.99</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes</td><td>Yes,<br>lock</td><td>Upstream Paris</td></tr><tr><td>ALA2<sup>a</sup></td><td>04-28</td><td>22</td><td>6</td><td>710</td><td>2.2</td><td>0.61</td><td>Yes,<br>lock</td><td>No</td><td></td><td></td><td></td><td>Below W2</td></tr><tr><td>ALA3<sup>b</sup></td><td>04-28</td><td>1</td><td>5-4</td><td>565</td><td>2</td><td>1.11</td><td></td><td></td><td></td><td></td><td></td><td>Release site</td></tr><tr><td>ALA4<sup>b</sup></td><td>04-28</td><td>23</td><td>5</td><td>555</td><td>2.3</td><td>1.35</td><td>No</td><td></td><td></td><td></td><td></td><td>Below W1</td></tr><tr><td>ALA5<sup>b</sup></td><td>04-28</td><td>111</td><td>4</td><td>527</td><td>1.6</td><td>1.09</td><td>No</td><td></td><td></td><td></td><td></td><td>Below W1</td></tr><tr><td>ALA6<sup>b</sup></td><td>04-28</td><td>15</td><td>4</td><td>505</td><td>1</td><td>0.78</td><td>Yes,<br>lock</td><td>No</td><td></td><td></td><td></td><td>Below W2</td></tr><tr><td>ALA7<sup>b</sup></td><td>04-28</td><td>1</td><td>6</td><td>612</td><td>2.5</td><td>1.09</td><td></td><td></td><td></td><td></td><td></td><td>Release site</td></tr><tr><td>ALA8<sup>b</sup></td><td>04-28</td><td>27</td><td>5-4</td><td>575</td><td>2</td><td>1.05</td><td>No</td><td></td><td></td><td></td><td></td><td>Below W1</td></tr><tr><td>ALA9<sup>c</sup></td><td>04-29</td><td>33</td><td>5-4</td><td>610</td><td>2</td><td>0.88</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>no</td><td></td><td></td><td>Below W3</td></tr><tr><td>ALA10<sup>c</sup></td><td>04-29</td><td>33</td><td>5</td><td>543</td><td>1.6</td><td>1</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Oise</td><td></td><td>Upstream Oise</td></tr><tr><td>ALA11<sup>c</sup></td><td>04-29</td><td>7</td><td>5</td><td>615</td><td>2.2</td><td>0.95</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Oise</td><td></td><td>Upstream Oise</td></tr><tr><td>ALA12</td><td>04-30</td><td>2</td><td>5-4</td><td>626</td><td>1.7</td><td>0.69</td><td></td><td></td><td></td><td></td><td></td><td>Forebay W0-W1</td></tr><tr><td>ALA13</td><td>04-30</td><td>29</td><td>5</td><td>584</td><td>1.9</td><td>0.95</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes,<br>fish<br>pass</td><td>Yes</td><td>No</td><td>Below W5</td></tr><tr><td>ALA14</td><td>05-04</td><td>10</td><td>5</td><td>595</td><td>2.2</td><td>1.04</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes</td><td>Yes,<br>lock</td><td>Upstream Paris</td></tr><tr><td>ALA15</td><td>05-18</td><td>22</td><td>5-4</td><td>585</td><td>1.9</td><td>0.95</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Oise</td><td></td><td>Upstream Oise</td></tr><tr><td>ALA16</td><td>05-18</td><td>6</td><td>4-3</td><td>592</td><td>1.8</td><td>0.87</td><td>no</td><td></td><td></td><td></td><td></td><td>Below W1</td></tr><tr><td>ALA17</td><td>05-19</td><td>15</td><td>5</td><td>615</td><td>2</td><td>0.86</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes,<br>lock</td><td>Yes</td><td>Yes,<br>lock</td><td>Upstream Paris</td></tr><tr><td>ALA18</td><td>05-19</td><td>5</td><td>5</td><td>542</td><td></td><td></td><td>Yes,<br>lock</td><td>No</td><td></td><td></td><td></td><td>Below W2</td></tr></tbody></table>
Two individuals (ALA3 and ALA7) were removed for further analysis as they were detected for only one day near the release site. No downstream migration was detected after release and 17 individuals quickly resumed their upstream migration with almost no delay (mean time between the release site and the first pair of receivers 500 m upstream: 87 min). These 17 shads were detected between 2 and 111 days (median 22 days) with an upstream migration range of 27.0 km to 187.5 km at least, according to the number of weir crossed. A few days after tagging, ALA12 (K=0.69) definitely stopped migrating 27 km upstream from the release site, and was not considered for trajectory analysis. Sixteen shads reached W1, twelve shads crossed it and all reached W2; among them, eight individuals crossed W2 and all reached W3 (Figure 1B). Seven shads crossed W3, three towards the Oise and four towards the upper Seine. The four shads heading towards the upper Seine reached and crossed W4, reached W5, where three of them managed to cross towards Paris (Figure 1B, Table 2). The upstream migration of tagged shads lasted 44 days after release. The last weir crossing event occurred on 10 June (W3, ALA15) and coincided with the water temperature reaching 21°C. None of them entered any of the three minor tributaries during the study period.

## Trajectory analysis of upstream migrants

All trajectories started with upstream straight movements after release in the first open-river reach (W0-W1: forebay F1) (Figure 3). The monitoring array enabled the detection of approaches up to 700 m downstream of W1, as well as short or long distance retreats and attempts. There was inter-individual variability in retreat movements, which represented on average 53% of the total time spent in F1. Nine individuals (among the sixteen reaching W1) made long-distance retreats and were detected by the receivers 5.3 km downstream, or as far downstream as 12 km in the case of the longest retreats, before returning to W1 (Figure 3, ex ALA2, ALA8, ALA15 and ALA17). Four shads reached W1 and stayed in F1 over the study period (6-111 days), two of them below W1 (Figure 3, line A); four shads reached W2, then either stayed below it or returned upstream of W1 (Figure 3, line B); one shad reached and stayed below W3 and three migrated to the Oise River, crossing W3 (Figure 3, line C) and four shads reached Paris or stayed below W5 (Figure 3, line D). When the last crossing event occured, data from the video-counting station at W0, indicated that the annual cumulated shad count reached 95% of the run (Figure 2). For shads crossing W1, the global number of weir crossed was linearly correlated with the condition factor ($R^2=0.62$). Ten individuals (53%) achieved a maximum upstream extent that was immediately downstream of a navigation weir, while the remaining stayed in F1 or went upstream of the monitoring array (Oise or Paris forebay) (Table 2). Four trajectories ended with a waiting period (from 14 to 25 days) just downstream of a weir, before the end of the detections (ALA2, ALA4, ALA13 and ALA18). Other trajectories terminated by downstream movements to the previous weir (ALA0, ALA1, ALA10, ALA6) or to the release site for two shads with spawning marks on their scales (ALA8 and ALA9).
<figure><img src="image_4.png" /><figcaption>Figure 3 - Trajectories of 16 individuals reaching only W1 (line A), reaching only W2 (line B), reaching W3 and three migrating to Oise River (line C), reaching W4 and W5 with 3 migrating to Paris (line D).</figcaption></figure>

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Groundspeeds after release were in the same range (N=17, 0.28-1.11 m.s⁻¹) as the groundspeeds observed in F1 (0.1-1.09 m.s⁻¹; median 0.65 m.s⁻¹) and non-significantly different from the median groundspeeds calculated for all open-river reaches (0.8 m.s⁻¹, Figure 4). In the first open-reach F1, upstream migration took place both at night and during the day at similar speeds and 16 of the 17 shads reached the pair of receivers downstream of W1 (in 11 hours to 4 days), half of them in less than 24 hours. In the two open-river reaches (F2 and F3), no individual stopped and their median swimming groundspeed was 0.9 m.s⁻¹, slightly higher than in F1 (Figure 4). No relationships were observed between TL, W, K and mean groundspeeds and between individual groundspeeds in the different forebays.
<figure><img src="image_5.png" /><figcaption>**Figure 4** - Individual and global swimming groundspeeds in open-river reaches (Forebays F1 to F5) and during weir crossing (W1 to W5). Red boxes indicate crossing by the locks and the two orange dots by the fish pass (W3). Modalities sharing at least one common superscript are not significantly different at p < 0.05 (Wilcoxon rank sum test).</figcaption></figure>

The results from the multinomial model suggested that increasing value in river discharge, oxygen saturation and water temperature were significantly associated with greater or lower chance of being in some categories of movement relative to the reference category "wait below weir" (Supp.Mat. Figure 1). Greater chances for upstream migration were significant with increasing oxygen saturation, water temperature and discharge, but odds ratios were small for the last two compared to those for oxygen saturation. Increasing oxygen saturation and water temperature were significant variables for lower chance of being in retreat/attempt than being waiting below weirs. Only increasing oxygen saturation was significant for greater chance of crossing weirs than being waiting below weirs.

## Behaviour at navigation weirs and cumulated impacts

The time spent below weirs, including detections in close neighbourhood and retreats/attempt, was highlighted with the Kaplan-meier curves, calculating the time to fail crossing the weir for each weir or for all weirs (Figure 5). On each curve, the shads crossing the weir are added successively and the proportions that have never crossed are indicated by the final horizontal line. Overall, half the individuals spend 66 h to cross the weirs, but there were differences between the five weirs. The longest duration, with 87 h for half the individuals to cross corresponds to W2; for the three upstream weirs, median time was 46 h (W3), 58 h (W4) and 27 h (W5). For W4, all shads crossed in a maximal time of 157 h. On the global curve, the ratio between all approaching events and
crossing (the end of the line) reached 78% for a maximal time spent of 240 h. No fixed covariates related to fish were significant to explain the time to fail for shads attempting to cross.

From W1 to W5, 34 crossings events were recorded for 12 shads, with 28 over 30 crossing routes assigned to a lock (Table 2); the two remaining passages were observed at W3 where the fishpass is a bypass channel. The crossing routes at W4, lock or fishway, could not be distinguished by the receiver array.

<figure><img src="image_6.png" /><figcaption>**Figure 5** -Time to fail for shads attempting to cross navigation weirs (All fish). Kaplan-Meier curves (KM) for failure at each navigation weir and for all weirs (Each curve describes the expected cumulative failure probability, based on all the fish remaining in the system until a crossing event time). In brackets, the value indicated the number of shads attempting to cross (Figure 1B).</figcaption></figure>

The crossing of the bypass channel at W3 took place at 14:00 and 19:00, consistent with the range of crossing times (7:00 - 19:00) recorded at W0. For crossings attributed to passage through locks, they mainly occurred between 5:00 and 18:00 and relatively more frequently between 14:00 and 17:00 (Supp.Mat. Figure 2). During the Allis shad spawning run (28 April to 10 June 2021), boat passage times were mainly between 5:00 and 19:00, although some night-time boat traffic was also recorded. The number of boats using the navigation locks in the April-June 2021 period ranged from 18/day (W5) to 48/day (W4) (Table 2), with an average of 30% of empty lock operations recorded at W1 (VNF, pers. comm., 2021).

Among the single parameter Cox models with an AIC value lower than the value of the null model, those that consider empty lockage upstream (total or short lock) were significant at P-value < 0.005 while traffic (total and long lock) and lock operations (long lock) were slightly
significant *P*-value < 0.10 (Table 3). For each variable included in the models, the proportional hazards assumption was confirmed. The best multiple model included empty lockage upstream (short lock) associated with traffic (long lock), both had a positive effect on crossing rate (Hazard ratio >0 and *P*-value= 0.009 and 0.035). An increase of one empty lockage more than doubles the hazard of crossing (HR=2.36, Table 3) while an increase of one boat (long lock) led to an 13% increase in the hazard of crossing (HR=1.13, Table 3). Regarding random effects, we found that the weir had a greater impact than the fish, around fifteen times greater.

<table><caption>**Table 3** - Cox models of the effect of boat traffic, lock operation or empty lockage on the crossing rate at W1, W2, W3 and W5.</caption><thead><tr><th>Parameter in model</th><th>Hazard Ratio</th><th>P-value</th><th>AIC</th></tr></thead><tbody><tr><td rowspan="2">Empty lockage upstream (short lock)+Traffic (long lock)</td><td>2.36</td><td>0.009</td><td rowspan="2">126.25</td></tr><tr><td>1.13</td><td>0.035</td></tr><tr><td>Empty lockage upstream (total)</td><td>1.82</td><td>0.002</td><td>128.26</td></tr><tr><td>Empty lockage upstream (short lock)</td><td>2.15</td><td>0.001</td><td>128.59</td></tr><tr><td>Traffic (long lock)</td><td>1.1</td><td>0.071</td><td>132.3</td></tr><tr><td>Traffic (total)</td><td>1.07</td><td>0.096</td><td>132.31</td></tr><tr><td>Lock operations (long lock)</td><td>1.15</td><td>0.089</td><td>132.75</td></tr><tr><td>Lock operations (total)</td><td>1.01</td><td>0.104</td><td>133.42</td></tr><tr><td>null model</td><td></td><td></td><td>133.76</td></tr><tr><td>Empty lockage downstream (short lock)</td><td>0.6</td><td>0.286</td><td>133.87</td></tr><tr><td>Empty lockage upstream (long lock)</td><td>1.54</td><td>0.177</td><td>134.12</td></tr><tr><td>Lock operations (short lock)</td><td>1.1</td><td>0.211</td><td>134.55</td></tr><tr><td>Traffic (short lock)</td><td>1.09</td><td>0.274</td><td>134.85</td></tr><tr><td>Empty lockage downstream (long lock)</td><td>1.16</td><td>0.589</td><td>135.44</td></tr><tr><td>Empty lockage downstream (total)</td><td>0.93</td><td>0.733</td><td>135.58</td></tr></tbody></table>

The cumulated impact of navigation weirs on the number of shads migrating upstream to Paris was assessed using the cumulated crossing rate (Figure 6A). The cumulated crossing rate dropped by 30% at the first two weirs (W1, W2), then less drastically (8-9%) for the next three (W3-W5), reaching 23% upstream W5. For the three shads crossing W5, the cumulated individual time lost, relative to the theoretical time needed to cover the whole distance for shads swimming at a median swimming speed of 0.8 m.s⁻¹, ranged from 6 to 12 days (Figure 6B). Globaly, mean time lost ranged from 0.77 to 1.53 hours/km. Using these values and also mean groundspeed, we estimated a total of 12-20 days (free travel time 5d + 7-15d time lost) to reach the non-navigated upper Oise River. The time losses were mainly observed at the weirs; in the open-river reaches, the horizontal curves indicate that the swimming speeds of the shads were almost 0.8 m.s⁻¹, while decreasing curves indicate shads swimming at higher speeds. There was an individual variability of time lost at each weir, with no real tendency; for example ALA17 lost nearly 7 days at W1 then only 6 on the next four weirs, while ALA1 lost 1 day at W1, 4 days at W2 and 2 days on the last three weirs.
<figure><img src="image_7.png" /><figcaption>**Figure 6** - A) Cumulative crossing rate for individuals that used only the Seine River to Paris. B) Cumulated time lost for the four individuals that reached W5, relative to the time needed to cover the same hydrographic distance with a median swimming speed of 0.8 m.s⁻¹. Note: in open reaches where individuals navigated at higher speed than 0.8 m.s⁻¹, cumulated time lost decreases.</figcaption></figure>

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We have shown for the first time that recolonising adult Allis shad have managed to pass the six navigation weirs on the lower Seine. Although the present tracking study involved a small sample of nineteen fish, it provides the opportunity to analyze behaviours in the face of cumulative obstacles with multiple crossing routes. Our results highlighted the interest of quantifying, in a complementary way, the overall crossing rate, the time spent below weirs waiting for crossing and the cumulative effects of navigation weirs on migration delay. Considering migration as a time-limited process may contribute to a better understanding of the effects of migration distance and delays at weirs on spawning success and survival (Castro-Santos et al., 2010).

Widely used in the marine environment, acoustic telemetry is becoming increasingly popular in Europe's freshwater ecosystems to study spawning runs, downstream migration or crossing routes at weirs and dams, but mainly for the conservation of salmonids and eels (Matley et al., 2022). This study shows how acoustic telemetry can enhance our understanding of shad return conditions in a river that has been deserted by this species for a century, and the management implications. The deployment of a receivers' network over a large area (188 km), including a succession of six navigation weirs, has enabled the assessment of the continuity for fish of the Seine River and the cumulative impact of the navigation infrastructures. The number of receiver pairs in the first forebay provided trajectory resolution fine enough to detect diel movements and long-distance retreats and attempts. For subsequent navigation weirs, the use of downstream and upstream receivers provided sufficient resolution to distinguish crossing routes. Nevertheless, adding receivers downstream of each crossing routes would have allowed for a more detailed study of the behaviour involved in approaching and searching for a crossing routes.

## Tagging effects

Shad and other clupeids are fragile species (Hendricks, 2003) sensitive to capture, handling and tagging method (Bolland et al., 2019; Eakin, 2017; Larinier et al., 2000; Bunch et al., 2023) particularly at emersion (Grote et al., 2014; Smith et al., 2009). Considering this vulnerability, we optimized these three steps and observed negligible post-tagging effects on motivation to migrate. The capture with a mobile net-cage, localized at the exit of the video-counting basin, was optimized to maximize catchability while limiting physical trauma and behavioural bias. The video-counting station displayed shad crossing in nearly real time to adjust the frequency of trap lifting, in order to limit waiting times and the density of fish in the trap. Shad capture at the exit of the fishway guarantees that they were actively moving upstream. In addition, the gastric tagging procedure used in our study, carried out rapidly underwater and under light sedation, does not have significantly affected the migratory behaviour of individuals. However, two shad did not resume their progression (Table 2) and it is difficult to conclude what happened to them since their signal disappeared after being detected for varying duration (58-585 min) 500 m upstream of the
navigation weir W0. We cannot rule out the possibility of regurgitation or post-marking mortality
due to stomach rupture (Nielsen, 1992; Winter, 1996) despite the precautions taken and the low
weight of the transmitter (Jepsen et al., 2005; Bunch et al., 2023). However, the rate of post-tagging
losses remains lower than those found in other monitoring studies of anadromous shad spp.
(Moser et al., 2000; Travade, 2002; Grote et al., 2014; McCartin et al., 2019; Tétard et al., 2016).

While downstream movements may be part of the normal alosine migratory behaviour (Frank et al., 2009), post-tagging downstream movements are often attributed to the effects of adverse handling. Such movements appear in variable proportions depending on the tagging methodology and the environmental conditions of the migration (Barry et al., 1986; Acolas et al., 2004; Moser et al., 2000; Bailey et al., 2004; Gahagan et al., 2020; Sprankle, 2005; Hightower et al., 2003). As no downstream movement was observed immediately after release, this reinforces the conclusion that tagging had little effect on our individuals. Furthermore, the observed rate of repeat spawners, although the species is usually considered semelparous, could potentially pose a survival problem for intragastrally tagged individuals returning to the sea.

Shads characteristics

Among the shad caught at W0, multi-aged shoals with or without spawning marks on their
scales were observed (ALA3-ALA8 for example, Table2). Individuals were between 4 and 6 years
old and 75% of them were 5 years old. It coincided with the fish body size estimated by analysing
video-counting data at Poses in April-May between 2008 and 2022 (quantile 25-50% : 475-580
mm). This age range is consistent with the analysis from Lassalle et al. (2008) on allis shad
populations along the eastern Atlantic coast; by Lambert et al. (2001) in the Gironde basin and by
Boisneau et al. (2011) in the Loire River. The maximum number of spawners goes back to the age
of 5 years, but males tend to migrate younger than females. Also, males tend to migrate
seasonnally earlier. In our study, we did not identify sex of individuals but as they were caught in
the second half of the 2021 spawning run, we could hypothesize that there may be more females
in our samples. The age range observed at Poses corresponds to cohorts born in 2015-2017. As
juveniles were regularly observed, especially in 2017 and 2021, some of the spawners migrating
could have their natal origin in the Seine basin. However, around 2015-2017, high numbers of
spawners were recorded in the Vire River, a neighbouring river of the Seine River in the English
Channel (data provided by Seinormigr https://www.seinormigr.fr/). Therefore, the recolonising
shad from our study could have their origins in breeding populations from Normandy coastal rivers,
as confirmed by genetic similarity between individuals from the Seine River and from the Vire River
(Launay et al., 2024, pers. Com). They would represent a proportion of strayers from neighbouring
rivers, which was found to be 10-23% in a study of 15 rivers on the French Atlantic coast (Martin
et al., 2015). The arrival of strayers in the Seine River basin since 2000 could be hypothesized to
several factors: (i) a regional regain of allis shad in northwestern France, especially in some coastal
streams in Brittany and Normandy, (ii) a more attractive basin with an improved water quality,
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without hypoxic events since 2007 (Romero *et al.*, 2016) and (iii) a shift in the starting point of migration associated with more favorable marine wintering habitats in the British channel (Elliott *et al.*, 2023).

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Among the individuals captured at Poses, 31% had already spawned in the previous year or at least had migrated in freshwater. Considering the usually semelparous reproductive strategy of allis shad (implying high energy expenditure but higher fecundity), this is relatively high. The maximum recorded rate of individuals reproducing more than once is around 15% in the Gironde estuary (Taverny, 1991), 1.3% in the Loire River and 6% in the Mondego River (Baglinière *et al.*, 2000). In *A. sapidissima*, variation in iteroparity rates is controlled by the interannual stability of spawning conditions: semelparity is favoured in the core of the distribution range, where conditions are stable and predictable (Glebe & Leggett, 1981; Castro-Santos & Letcher, 2010), whereas iteroparity rates increased in the northern range of the species. In addition, the more energy shad expend during migration, the less likely they are to return to the sea and resume a spawning migration the following year, increasing the rate of semelparity in these populations (Binder *et al.*, 2011). Post-spawning conditions would also be of prime importance, with the decrease of shad iteroparity rate in the Connecticut River potentially linked to a restoration of upstream continuity but a difficult downstream migration (Zydlewski *et al.*, 2021). At the fish population level, changes in size, age structure and iteroparity rates may be a demographic trend triggered by presence of barriers (Zydlewski *et al.*, 2023).

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The latitude of the study area lies to the north of the distribution range, suggesting a potential tendency towards increasing rates of iteroparity. In addition, despite the restoration of continuity through fishways, the conditions of upstream migration remain costly with cumulated time lost to reach Paris between 6 to 14 days. A high proportion of individuals stopped their migration after crossing only a few navigation weirs; for them energy stores may be sufficient to allow a return to the coastal environment of the Seine basin where they will feed and grow again. In particular because the downstream migration on the Seine is favored by the hydraulic conditions of the waterway. Similarly, in a small population blocked downstream of the first barrier in the Penobscot river, 75-95% of repeat spawners are observed, indicating low upstream connectivity (Grote *et al.*, 2014). However, the small number of individuals considered in our study suggests that we should remain cautious about this rate of repeat spawners. In addition, the mortality rate at sea between two years of spawning migrations should be taken into account.

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Multi-aged shoals (see Table 2), made up of first-time and repeat spawners, could constitute mixed-experience groups. These tagged shads were captured in the last pool of a large vertical slot fishway and thus experienced the crossing of this fish pass with success. Our tagged shads are a selection of individuals with good swimming capacities, which have found the fish pass entrance of their first barrier encountered from the sea. We noticed that individuals released at 1-hour intervals were also detected at this interval by successive receiver pairs up to W1. It is generally accepted that tagging and successive weirs break up shoals and in Katz (1986), the

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acoustically tagged shad swam upstream individually. Multi-age groups can regroup at each weir and collectively search for an opportunity to cross. For example, we observed two individuals from different shoals (ALA11 and ALA6; 4 and 5 years old) arriving at W1 with a difference of 12 hours and crossing W1 using the same boat lockage. It is recognised that collective behaviour enhances individual-level orientation capacity and increase the ability of individuals in groups to migrate to natal sites (Couzin, 2009). For migrating fish, collective navigation may play an important role in guiding individuals back to their natal river, as has been observed in salmonids (Berdahl et al., 2016; Okasaki et al., 2020). In addition, social learning through observational or collective interactions with a few well-informed individuals could help others to find crossing routes (Aikens et al., 2022). It as been observed for few well-informed older birds, which reduced migration route deviation for the group (Mueller et al., 2013). Fish can learn routes by using landmarks or spatially "informed" conspecifics (Odling-Smee et al., 2003). For example, naïve, first-time winterers of Atlantic herring (*Clupea harengus*) learn about favorable wintering areas by schooling with older, experienced winterers (Macdonald et al., 2018). In our study, even if the release time delay of around one hour between individuals at W0 has disrupted the cohesion of shoals, these "solitary" shads could rely on indirect signals and long-distance communication with conspecifics (Aikens et al., 2022).

## Behaviour in the regulated and fragmented Seine River

### Swimming in open-river reaches

After release, most of the tagged shads resumed their upstream migration within a few hours and adopted an average groundspeed of 0.56 m.s⁻¹ in the first forebay F1. This is slightly lower, but not significantly different, from the average groundspeed recorded in all open-river reaches: 0.8 m.s⁻¹. These speeds were comparable to the mean 0.6 m.s⁻¹ (0.24-1.06 m.s⁻¹) observed for tagged Allis shads crossing the Loire estuary (Tétard et al., 2016) and higher than those estimated in the Gironde estuary : 0.19-0.27 m.s⁻¹ (Rochard, 2001) and in the Loire River : 0.24 m.s⁻¹ (Steinbach et al., 1986). As allis shad shows similar swimming behaviour and biological characteristics as American shad (Castro-Santos et al., 2010; Larinier et al., 2002), these values are also consistent with the optimal cruising speeds calculated (0.35-0.83 m.s⁻¹) for 500-700mm long shads using the 0.7-1.7 body lengths (BL)·s⁻¹ rule for open-reach by Castro-Santos et al. (2010) and Stich et al. (2019). Katz (1986) points out that the groundspeed remains stable if the current speed remains below 0.6 m.s⁻¹, whereas speeds above 0.6 m.s⁻¹ lead to a significant increase in the ground speed. In the context of the navigated Seine, transformed into a succession of still waters reaches generally with a current velocity of less than 0.5 m.s⁻¹, migration should be less costly than through river reaches with turbulent flows (Hinch et al., 1998). This meant that the shad would only need to swim at intermediate speeds, involving only the red muscles for locomotion and limiting exhaustion (Binder et al., 2011).
During the 2021 spawning run, the relatively stable temperature of 18-20°C may have been a contributing factor to the optimal and relatively uniform cruising speeds observed in the open-river reaches. Indeed, cruising swimming capacity increases with temperature to an optimum level (20°C observed for American shad, see Katz (1986)), beyond which temperature negatively affects swimming performance. Furthermore, no relationship was observed between shads characteristics and mean cruising speed; and individual speeds were not consistent among forebays. Tétard *et al.* (2016) also observed this absence of length effect on shad swimming speed in the Loire estuary, that could be attributed to differences in performance between the sexes as previously discussed by Castro-Santos (2002). But variation in cruising speed may be associated with other physical and physiological differences among fish (Katz, 1986). The lipid content and fork length of shad females and males differ and can influence their endurance, which can also change during migration (Bayse *et al.*, 2019). Likewise, even though females are larger than males, much of their mass is devoted to eggs rather than muscle for swimming (Haro *et al.*, 2004). Furthermore, in the case of shad using locks, the regulated lentic areas for boat traffic located just upstream of the locks may also cause disorientation due to insufficient unidirectional current. This may result in a minor delay, thereby reducing the calculated global swimming speed for the open-reaches.

In addition, we observed a fairly similar swimming speed in the first forebay all day long. This has also been noticed in a forebay of the Connecticut River for American shads (Katz, 1986). It suggested that they use their positive rheotactic behaviour all day long in the turbid Seine River. This behaviour has been demonstrated to enable shads to navigate fluvial habitats, as outlined by Dodson *et al.* (1974) with anosmic and blind American shads.

*Migratory delays at navigation weirs*

The migration duration depends on the swimming speed in the open-river reaches, but the main factor relies on the migratory delays at navigation weirs. It was observed for upstream migration of sea lamprey, for which the overall delay at the dams was considerable (median delay = 13.6-14.6 days) (Castro-Santos *et al.*, 2017) or for downstream migration of European eels, for which important delays at shipping locks were recorded (Verhelst *et al.*, 2018). In our case, while the groundspeed in open reaches was relatively homogeneous and quick (0.8 m.s⁻¹), the groundspeed to cross weirs -mainly by the locks- was reduced by half. This groundspeed observed to cross weir may be that observed in a natural reach with difficult passages, such as in the Loire, or with strong currents, such as in the Gironde estuary.

Delays for those individuals that ultimately crossed the weirs included the time spent below the weirs and the time spent retreating/attempting; which for example accounted for half of the time from release to crossing W1. In average, half of the individuals crossed the weirs in less than 3 days and the delays at the entry of the bypass channel at W3 were not lower (48-108h) than those observed for locks.
Whether exploratory downstream retreats and upstream attempts are successful or not, the energetic costs incurred may be additional impacts on their migration. Migration delays due to barriers, prolonged waiting and searching for crossing routes are known to deplete energy reserves for salmonids (Hinch et al., 1998). If upstream and downstream movements are taken into account (Frank et al., 2009), a single obstacle can cause a cumulative delay that drains energy and reduces success for shad (Castro-Santos et al., 2010).

Navigation weirs induced migration delay that increases the duration and distance of the migration when multiple retreats/attempts are made by shad before crossing the multiple navigation weirs on their way to spawning habitats, located far upstream. This has also been observed for downstream- migrating wild- caught and hatchery- released Atlantic salmon smolts (Nyqvist et al., 2017). The consequence of increased migration duration and distance travelled is greater energy expenditure that cannot be mitigated by food consumption. This could reduce the amount of energy available for gamete production or development (Minke-Martin et al., 2018).

## Retreats and attempts during upstream migration: locate alternative passage routes

In addition to temporal delays experienced by shads at navigation weirs, this study highlighted that short and long-distance downstream retreats and upstream attempts occurred during their upstream migration. As highlighted in Frank et al. (2009), diverse and complex post-tagging downstream movements in Alosine species could be recorded, that need to be carefully interpreted using metrics such as direction of initial movement, sequence, timing and spatial extent of movements. Downstream movements in the Seine River were observed after a more or less long period of time spent downstream a weir, then for a part associated with upstream movements and the crossing of the weir. These downstream movements might represent a behavioural mechanism to find alternative passage ways when upstream access is impeded (Davies, 2022). This hypothesis is supported by observations of three individuals who made no retreat/attempt and for which delay before crossing was short (4-7-17 hours). Below weirs, individuals of *Alosa agone* search for a passage at the limit of turbulent waters (Abdallah, 2024 pers.com.) and Katz (1986) observed groups of up to 75 American shad that shoaled and swam in large circles, moving neither up- nor downstream. This milling behaviour or fallback activity has also been observed in fishway pools, suggesting poor passage efficiency (Larinier et al., 2002; Haro et al., 2012). We hypothesized that this behaviour was also at work for *Alosa alosa* in the Seine River as several spatio-temporal small-scale retreats and attempts were observed.

In addition, as observed for American shad, after an attempt below the weir, individuals may prefer more downstream areas of non-turbulent flow to rest (Barry et al., 1986). At the weir of Saint-Laurent-des-Eaux in the Loire River, Allis shad made on average two attempts and stayed for an average of 22 hours within the 500 m downstream of the weir (Steinbach et al., 1986). Considerable exploratory behaviour downstream of an impassable weir was also observed in the small Aulne River (Brittany) and 1.5 km downstream of the spawning site (Acolas et al., 2004).
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This site could also be used as a resting area by actively migrating individuals at the time of their
exploration of the dam before trying to cross it. The search for an alternative passage way can
also involve long-distance downstream movements: up to 2.5 km downstream of W5, up to 12 km
downstream W1 before returning to the weir. These long-distance retreats have not been
documented previously to our knowledge, but could be related to the search for an alternative
passage in a secondary channel or a tributary. In the literature on salmonids, these downstream
movements or 'failbacks' are considered as intentional behaviour in search for natal site, when fish
miss natal confluences (Keefer et al., 2006). In all cases, they increased the distances covered
and could reduced spawning success. This behaviour in shads can increase the chances of finding
another more favorable migration route with spawning sites, being in the right place at the right
time: actively searching for a "transient window of connectivity" (Zeigler et al., 2014).

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Cumulated impacts of navigation weirs

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Acoustic telemetry provided strong evidence that navigation weirs consistently hindered the upstream migration of adult allis shad. These impacts were both spatial: inhibiting access to potential natural spawning areas in upstream reaches (Oise, Aisle, Marne, Seine), and temporal: increasing cumulated time lost along the trajectories. Whilst no weir was considered to be a complete barrier to upstream migration of shad, the majority of navigation structures hindered some of the upstream migrating cohort to the extent that only 16% of tagged individuals migrated to the furthest upstream weir on the Seine or Oise equipped with receivers. Despite this low percentage, we observed that the upstream extent of shads spawning run reached at least Paris (354 km from the sea) which is consistent with the observation of individuals in the alluvial floodplain of the Seine upstream Paris (Belliard et al., 2009; Lamarche, 2013). These individuals reaching Paris were 5 years old, had high condition factors K and no spawning marks, indicating shads with high energy reserves and certainly high motivation to spawn.

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In addition, we highlighted that tagged shads did not enter medium tributaries along their migration route, but a significant proportion enter the large Oise tributary and confirm the historical use of this river known through 1850's shad distribution (Belliard et al., 2019; Le Pichon et al., 2020). The use of this tributary has been recently confirmed by the video-counting data at the station of Pontoise, installed in 2023 in the fish pass of the lowest navigation weir on the Oise River. Furthermore, the emphasis placed on navigation has significantly impacted the diversity of fish habitats, especially with a loss of habitats with high current velocities. As shad have only recently recolonised the Seine basin, it is not certain that they will find a suitable spawning habitat in navigable areas, which could lead them to migrate far upstream towards their historic tributaries, but they will then have to pass dozens of weirs in their allocated migration time. This was observed for the sea lamprey in the highly impounded River Ulla (Spain), where individuals would need a cumulated time of 5 months to pass the 23 barriers present before reaching the first spawning areas (Silva et al., 2019). In this case, it is likely that the energy expenditure will reduce their
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chance to spawn in good conditions and survive this ordeal (Castro-Santos *et al.*, 2010). However, among our tagged individuals, six were repeat spawners, meaning that they had completed a previous spawning run with sufficient reserves to return to the marine environment to start feeding and growing again. This could be consistent with our observation of half of the tagged shads stopping their trajectory and staying long time downstream weirs, potentially spawning in "forced" sub-optimal habitats after crossing a limited number of weirs.

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The cumulative crossing rate at navigation weirs for shads reaching Paris did not demonstrate a linear trend, and individual cumulative time lost along the Seine River exhibited variability. The cumulative crossing rate drops by 30% at the first two weirs then less drastically (0-9%) at the next three weirs, possibly indicating that these individuals, captured in a fishway at Poses are predisposed to find a passage way or that they learned how to find it. For example, individuals of American shad that had been caught in a lock were more likely to pass through it (Moser *et al.*, 2000). Higher passage rates were observed during successive spawning migrations of iteroparous twaite shad for individuals that had been successful the year before (Davies *et al.*, 2023). This study suggests that the motivation to cross barriers is maintained and/or that there is an inherent ability to do so. In our study, an individual variability in cumulative time lost at each weir was emphasized. While 4 days was necessary for ALA1 to cross W2 and 6 days for ALA17 to cross W1, the next three/four navigation weirs were crossed with reduced delays, suggesting potential learning of crossing locks. This kind of individuals could represent leaders for small groups of shads searching for a route below obstacles. For example, ALA1 was detected downstream of W2 with ALA0,6,9,10 searching for a route the 1st of May and with ALA10,11 at W3 the 5th of May. Leadership by a small number of individuals may be a key mechanism in finding and using a crossing route, because populations typically consist of a large proportion of individuals that use a socially facilitated movement behaviour (Guttal *et al.*, 2010).

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As highlighted by Davies *et al.* (2022) for sea lamprey, we found that individual variation in time lost or retreat and attempts movements at navigation weirs influenced neither the subsequent upstream migration speed nor the final upstream extent of tagged shads. This behavioural variation both within individuals over time and across individuals is recognized in behavioural ecology (Shaw, 2020). The idea put forward by Dingemanse *et al.* (2010) is that individuals vary in terms of their average behaviour across a range of contexts (i.e. their 'animal personality') along with their responsiveness to environmental variation (i.e. their 'plasticity').

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The cumulative impact of navigation weirs may also be considered in terms of downstream passage issues. If navigation weirs allow shad to cross upstream but do not ensure the survival of their offspring to the sea and potential returning adults, upstream fish passage may be considered as an ecological trap (Ohms *et al.*, 2022). This is particularly the case when habitats upstream of dams are unfavourable for fish recruitment due to the absence of spawning grounds and nurseries (Pelicice *et al.*, 2008). Using a stochastic life-history based simulation model for American shad

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Stich *et al.* (2019) observed that increased downstream passage was required to maintain or
increase population abundance in conjunction with increased upstream passage.

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Crossing way and boat traffic

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We clearly observed that the existing fishways were not effective for the passage of shad
upstream of the navigation weirs. These low crossing rates confirmed the expert's evaluation of
fishways on the lower Seine River, which pointed out their low downstream attractiveness and the
too high maximum volumetric power dissipation factor in their pools (Table 1). A similar situation
was observed in the Cape Fear River, where only 8% of American shad used the fishway, due to
design deficiencies and the lack of attraction flow at the fishway entrance, and most individuals
used the locks instead (Moser *et al.*, 2000). Only the W3 bypass channel, considered effective by
experts, was used by two shads. Large fishways with lower slopes and fewer eddies are thought
to be more effective for crossing American shad (Larinier *et al.*, 2002). Alewife (*Alosa
pseudoharengus*) passage rates were related to fishway type, design and functionality, with
greater passage for the Denils than the pool-and-weir fishway (Nau *et al.*, 2017). In this study, an
increase in passage rate for alewife was observed when the dysfunctional pool-and-weir fishway
was repaired and then replaced, highlighting the importance of regular structural maintenance.

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As there are no fish lockages on the Seine, we observed a high rate of allis shad passage
through the voluntary use of navigation locks (93%) without specific maneuvers and attraction.
Although accidental, this deliberate use of navigation locks during boat lockage operations has
been observed for other clupeids (Young *et al.*, 2012) and lamprey (Silva *et al.*, 2017). Fish
passage coincided with specific sequence of boats lockage and boat traffic, as observed for other
species in the navigated upper Mississippi River (Fritts *et al.*, 2021). We found that the choice of
this passage way was significantly related to the occurrence of a particular sequence of two
successive downstream boats lockages, leading to one lock operation without boats. This
sequence is similar to fish lockages proposed for Rhone shads *Alosa agone* on the navigated
Rhone River (Guillard *et al.*, 2000). In addition, higher crossing rates were observed with increasing
boat traffic in the long lock. The use of this long lock is indicative of larger boats using it, which
would generate a higher attraction flow volume of water. This enhances the attractiveness of the
channel downstream of locks. When large boats leave the long lock downstream, they generate
reverse currents that could help shad enter the short lock, provided that the downstream gate is
open. However, entering the lock does not mean crossing the structure. Without attractive currents
when the upstream gates open, shad may become disorientated and trapped in the lock when the
gates close, and then return downstream. This was observed for tagged allis shad in a recent
experiment on the Oise River, where only half of the individuals entering a lock crossed it
(Cherbero, M. pers. comm., 2025). This impediment to crossing has been observed during
upstream migration of American shad and is associated with its positive rheotactic behaviour (Katz,
1986). Moser *et al.* (2000) also observed that shad did not accumulate in the lock for more than

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two hours, and concluded that the best crossing rates were observed when as many lockages as possible occured in a day. We noticed that this crossing route was used despite the fact that all tagged individuals have been caught in the first fishway from the sea at W0 and for individuals also using the bypass channel. This undoubtedly indicates an opportunistic behaviour, with shad actively seeking favorable hydraulics conditions and then finding alternative passages, such as two successive downstream boat passages in the short lock when a high traffic occurred in the long lock. The favorable sequence of two successive downstream boats lockages occurred in average 22% of total downstream boats passages, representing 1 to 3 favorable lockages per day (range 13-25% considering each lock at the different weirs). Two lockages per day were efficient at a lock in the Apalachicola River (Florida) for an annual passage success ranging from 33% to 45% for Alabama shad (Young *et al.*, 2012). Furthermore, three fish lockages per day were proposed for crossing American shad at three low-head lock-and-dam structures on the Cape Fear River, resulting in high passage rates (64-85%) (Smith *et al.*, 2012).

Whatever the crossing route, shads from our study were mainly observed crossing weirs during daytime, whereas fish passes and locks could be used all the day round. Unlike swimming in open water, crossing weirs through fishways, with their turbulent currents, or through locks, with no currents, may require vision. Observation from (Keefer *et al.*, 2013) suggest that diel activity patterns vary with the degree of effort required for migration. The movement of salmonids and American shad, which are active all day in river habitats and reservoirs with low hydraulic complexity, shifted to mainly diurnal activity in fishways where hydraulic complexity was high. Crossings through locks were mostly recorded early in the morning and in the afternoon in the Seine River; although the locks are open all day, the busiest times are between 4:00 and 18:00. Most Alabama shad entered and crossed lock during the afternoon locking cycle (lock operates between 08:00-16:00) (Young *et al.*, 2012). Similar studies on American shad illustrate that the diel timing of fish lockage is critical for passage success, and that the highest passage was observed during the day (Moser *et al.*, 2000; Bailey *et al.*, 2004).

## Conclusion

Using a large monitoring array of receivers, this study highlights how acoustic telemetry can refine our understanding of the spatial and temporal patterns of spawning migrations in the context of the recolonisation of Allis shad in the Seine. It is the first time, since their construction, that crossing efficiency of fishways equipping navigation weirs in the lower Seine River was evaluated. The low utilisation rate of fishways confirmed the experts' structural assessment that they were not only inappropriate for shad, but also for other migratory species (unpublished data). By using navigation locks voluntarily, some Allis shads have nevertheless reached Paris. Evidence was given that specific fish lockages could improve the crossing rate of all the navigation weirs on the Seine. Using locks to overcome weirs is not necessarily easy, because individuals need to find the
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entrance and the exit, but it may require probably less energy to cross (no current velocities during
the lockage) than using vertical slot fishways. On one hand, It is crucial for these population
dynamics to improve the attractiveness of fishways, their hydraulics with an adequate
management of the upstream waterline, as well as their long-term maintenance; and to replace
old poorly designed fishways by more efficient ones. But also to take greater advantage of this
species' voluntary use of locks, fish lockages should be implemented as frequently as possible, in
line with commercial navigation.

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However, one might wonder the benefit of a prolonged upstream migration to reach natural
spawning habitats in historic tributaries located nearly 400-500 km from the sea, but with
cumulative time lost at each navigation weir and a fragmented route for juveniles to travel back to
the sea. Another observation that can be drawn from our findings is that a significant proportion of
individuals cross few navigation weirs. This may limit energy expenditure and could explain
iteroparity rates, but exposes them to suboptimal spawning and nursery habitats in navigable
areas. Furthermore, there have been few observations of juvenile shad in the Seine, highlighting
the urgent need to locate and assess the suitability of potential spawning habitats in both the main
channel and tributaries.

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The diversity of characteristics among the mixed-experience groups of shad, as well as their
migration routes and behaviour when recolonising the lower Seine, could help to explain their
return. Populations with diverse life histories and behaviours are hypothesized to be more robust
in the face of environmental change, a phenomenon known as the portfolio effect, observed for
salmonids (Schindler et al., 2010). For shads their capacity for expansion and re-colonization is
related to differences in life history such as iteroparity versus semelparity and the extent of natal
homing (Pess et al., 2014).

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Discharge

<figure><img src="image_8.png" /></figure>

Oxygen saturation

<figure><img src="image_9.png" /></figure>

Temperature

<figure><img src="image_10.png" /></figure>

Odds Ratio

Supp.Mat. Figure 1 – Forest plot of odds ratio based on multinomial logistic regression model
explaining the type of movement. Horizontal bars represented 95% Confidence interval.
<figure><img src="image_11.png" /><figcaption>**Supp.Mat. Figure 2** - Hours of shads crossing the vertical slot fishway at W0 (2008-2015 period) and crossing weirs during the present telemetry study. Hours of boat traffic at the same period for the studied weirs.</figcaption></figure>

## Acknowledgements

This study was carried out as part of the CONSACRE project, managed by the GIP Seine-Aval and INRAE-HYCAR. We thank Nicolas Bacq (GIP Seine-Aval) for all support, ideas and helfull management of the project. We thank all people from INRAE and Seinormigr that help during capture and tagging sessions. We thank Vincent Morel from VNF navigation service for providing data on boat traffic. We thank Aaron Bluche (INRAE) for his help in writing and running R scripts. This work was carried out with the support (equipment and personnel) provided by the XPO scientific infrastructure (LIFE research infrastructure - Living in Freshwater and Estuaries, INRAE), of EABX research unit, and we would like to thank Guillaume Lefebvre in particular for his contribution.
Funding

The state-interregional planning contract "Vallée de la Seine" (2015–2020) and the ZA Seine (LTSER, Long-Term Ecosystem Research in Europe) provided financial support, especially the Normandy and Ile-de-France regions and the Water Agency Seine-Normandy.

Conflict of interest disclosure

The authors declare that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.

Data, scripts, code, and supplementary information availability

Ethical authorization obtained from the French Ministry for Higher Education and Research project licence APAFIS#23377-2021011509593471 v1.

Data are available online: https://filo.eabx.inrae.fr/ with password request.

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