DOI: 10.5061/dryad.bg79cnph4
title: Maritime international trade and bioinvasions: a three-year long survey of small mammals in Autonomous Port of Cotonou, Benin

description: International trade has been favoring the dissemination of a wide panel of
 invasive alien species. Upstream prevention through the monitoring of
 entry points is identified as an appropriate strategy to achieve control
 of bioinvasions and their consequences. Maritime transports have been
 responsible for the introduction worldwide of exotic rodents that are
 major pests for crops and food stocks as well as reservoirs of many
 zoonotic pathogens. In order to limit further dissemination, the
 International Health Regulation constrains decision makers and
 socio-economic stakeholders to manage ship-mediated import/export of
 rodents within seaports. Unfortunately, eco-evolutionary insights into
 rodent introduction events that could guide preventive actions in seaports
 are very scarce. In order to bridge this gap, we here describe the results
 of a three-year-long survey of small mammals conducted in the Port of
 Cotonou, Benin, that aims at assessing the spatio-temporal distribution,
 diversity and relative abundance of invasive and native rodents. 960 small
 mammal individuals were captured in nine within-seaport sites. We found
 (i) a marked predominance of invasive species (84% of the individuals
 belonging to Mus musculus, Rattus rattus, R. norvegicus), (ii) with native
 species (i.e., Mastomys natalensis and the shrew Crocidura olivieri)
 essentially restricted to peripheral non-industrial areas, as well as
 (iii) a fine-scale spatial segregation stable over time between the
 invasive Norway rats and house mice on the one hand, and the black rats
 and shrews on the other hand. Furthermore, trapping before and after two
 successive rodent anticoagulant-based control campaigns indicates that
 they were poorly efficient and that subsequent rodent recolonization
 occurs 6–12 months following intervention. Synthesis and applications: Our
 results are discussed in terms of ecological processes at play (e.g.,
 interspecific interactions) and operational actions that may be
 implemented to improve rodent control (e.g., assessment of proper
 eradication units, environmental modifications) and to limit
 re-infestation (e.g., rat-proofing of moors and buildings).
description: 1- Sampling
 design,  2- Trapping and identification of small
 mammals,  3- Trapping
 data analysis (Trap-specific and species-specific trapping
 effort, Species-specific
 relative abundance according, Specific diversity, Co-occurrence analyses, Occupancy modelling)
description: # Maritime international trade and bioinvasions: a three-year long survey
 of small mammals in Autonomous Port of Cotonou, Benin
 [https://doi.org/10.5061/dryad.bg79cnph4] In this study of three years of
 monitoring, we assessed the spatio-temporal distribution, diversity and
 relative abundance of invasive and native rodents in a West African
 autonomous port. Data useful for interpreting the results were collected
 during each sampling campaign at each of the surveyed sites. Details for
 each dataset are provided in the README file. Datasets included: 1. Small
 mammal captures by wire and shermans traps. Number of small mammals caught
 per trapping campaign. 2. Sampling design. Description of the
 characteristics of each sampled site. 3. Trapping and identification of
 small mammals Sampling protocol in detail. Morphological identification
 using morphometric measurements (body mass, length of body, tail, hind leg
 and ear). 4. Trapping data analysis Trap-specific and species-specific
 trapping effort under the R software (R Core Team, 2011). Species-specific
 relative abundance according under the R software (R Core Team, 2011).
 Specific diversity using EstimateS v.9.1.0. Co-occurrence analyses using
 the program Pairs v.1.0. Occupancy modelling under R using the unmarked
 v.0.13-2 package. There are not missing values. Supplementaries are
 available in the README file. Supplementary 1 Sampling sites in the port,
 their descriptions and GPS coordinates Supplementary 2 Distribution of the
 number of captures according to sessions, sites and trap type for each
 species Supplementary 3 Proportion of each type of trap (wire and sherman)
 set at the nine sites during sessions Supplementary 4 Comparison of the
 two types of traps in APC3 Supplementary 5 Species-specific success for
 Rattus rattus in APC1 and APC2 Supplementary 6 Species diversity in the
 artisanal (APC1-2) vs the industrial seaport (APC3-9) Supplementary 7
 Detection probabilities as a function of sessions and trap types at sites
 for each species Supplementary 8 Model comparison procedure for all
 species and datasets to detection and occupancy probabilities A) Organized
 by File type DatasetA I- Data/ * Data used for analyses and overall raw
 sampling data I I- Processed/ Data used for analyses. I I 1- Co occurence
 * Excel spreadsheet of the 960 small mammals captured per sampling site
 per session, by species. * Excel spreadsheet of 849 small mammals captured
 per sampling site per session, according to species with numbers greater
 than or equal to 10. * These analyses were performed using Pairs v.1.0
 software with a 95% confidence interval. I I 2- Occupancy modelling *
 Encoded spreadsheets for calculating the probability of detection and
 occupancy of captures from 3 nights of trapping for each locality, by
 session and by trap type for Crocidura olivieri, R. rattus, R. norvegicus
 and Mus musculus. (N1, N2 et N3 : 1=capture, 0=no capture, Blank cell=no
 trap set at this location ; loc : 1=APC1, 2=APC2, 3=APC3, 4=APC4, 5=APC5,
 6=APC6, 7=APC7, 8=APC8 ; Trap: 1=sherman, 0=Wire ; n1=night1, 2=night2 and
 3=night3). * The analysis was performed under R using the unmarked
 v.0.13-2 package. I I 3- Specific diversity * Excel spreadsheet for
 estimating the specific diversity of the number of captures of Rattus
 rattus, Rattus norvegicus, Mus musuclus, Mastomys natalensis and Crocidura
 sp per session in APC1-2 : artisanal seaport versus AP3-9 : industrial
 seaport * The analysis was performed on EstimateS v.9.1.0 I I 4-
 Statistical data * APC-Traps (data original) : Encoded spreadsheet of the
 3 nights' trapping catches for each locality, by session and by trap
 type. * APC1-Traps to APC 9-Traps : Encoded spreadsheet of catches for the
 3 nights of trapping by session and by trap type for APC1 to APC9 *
 tAPC1-species to tAPC9-species : Excel spreadsheet to calculate the
 relative abundance of each site according to species caught, session and
 trap type for APC1 to APC9 for the most abundant species. * tAPC8-Rn-Mus :
 Excel spreadsheet to calculate the relative abundance in APC8 between
 Rattus norvegicus and Mus musculus per session and trap type. *
 tAPC8-Rn-Rr : Excel spreadsheet to calculate the relative abundance in
 APC8 between Rattus norvegicus and Rattus rattus per session and trap
 type. * tAPC8-Rr-Mus : Excel spreadsheet to calculate the relative
 abundance in APC8 between Rattus rattus and Mus musculus per session and
 trap type. * APC3-Proportion of traps per sessions : APC 3 Only site with
 a significant difference between the numbers of each type of trap set per
 session * Database : Database of small mammals captured by collection
 number, species, session, trap type, locality and sites. * Script-SB :
 Script for comparison of trapping yields between species, comparison of
 relative abundance between species and comparison of trapping effort
 between sessions * Traps by sessions : Encoded excel spreadsheet of the
 number of traps set during the 3 nights of trapping for each location and
 session * All analyses were performed under the R software (R Core Team,
 2011) and p-values&lt;0.05 were considered significant. I I- Raw
 Overall raw sampling data. I I 1- APC trapping report * Raw data : Excel
 spreadsheet organizing the raw data from the 6 sampling sessions for each
 site, according to the number of each type of trap set, the total number
 of mammals captured according to each trap type, the number of individuals
 captured per species according to trap type. * APC1-9 : Excel spreadsheet
 organizing sampling data from nine sites (APC1-9) according to species
 captured per session and trap type. * R norvegicus : Excel spreadsheet
 summarizing captures of R norvegicus at each site according to the number
 of traps set and the number of captures according to trap type. * R rattus
 : Excel spreadsheet summarizing captures of R rattus at each site
 according to the number of traps set and the number of captures according
 to trap type. * M musculus: Excel spreadsheet summarizing captures of Mus
 musculus at each site according to the number of traps set and the number
 of captures according to trap type. * Crocidura sp : Excel spreadsheet
 summarizing captures of Crocidura at each site according to the number of
 traps set and the number of captures according to trap type. * Mastomys
 natalensis : Excel spreadsheet summarizing captures of Mastomys natalensis
 at each site according to the number of traps set and the number of
 captures according to trap type. * All species depending on sites : Excel
 spreadsheet summarizing all species captured by site and trap type. * All
 species function atime : Excel spreadsheet summarizing all species
 captured by session. I I 2- Small mammal abundance in APC * Excel
 spreadsheet classifying each species according to its status (invasive or
 native) based on sites, geographical coordinates, number of traps set and
 capture rates for each species. I I 3- Trapping sites Figure : A)
 Assemblage of traditional stores (APC1), B) fresh fish market (APC2), c)
 restaurants and outdoor canteens (APC3), D) four large non-joined
 industrial storehouses (APC4-7), E) garage and mechanical equipment
 storage rooms (APC8) and F) storage area for large equipment (APC9). I I
 4- Trapping yields * Excel spreadsheet of capture yields for different
 species at each site, by session and by trap type. A) Organized by
 Analysis DatasetB I- Results I 1- Statistical analyses * Comparisons of
 wire vs sherman trapping yields ("Chi-squared") for all sessions
 and all sites by species. * Comparisons of wire vs sherman trapping yields
 ("Chi-squared") all sessions per site. * Calculate of the
 relative abundance probability between species at each sampling site. I 2-
 Wilcoxon analyses * Pairwise comparisons using Wilcoxon rank sum test for
 each species I 3- Yields R norvegicus - R rattus - Mus musculus * Yields
 for R norvegicus in APC4-8 captured by the wire, Mus musculus in APC4-8
 captured by the shermans and R rattus captured by the wire and shermans in
 APC1, 2 and 8.