DOI: 10.5061/dryad.g1jwstqxv
title: Rodent ectoparasite diversity in response to anthropogenic disturbance

description: Rodents are important hosts for ectoparasites such as fleas, ticks, and
 mites, which means they are also important intermediate hosts for many
 zoonotic diseases. As anthropogenic environments bring humans and rodents
 into closer contact, an understanding of host-ectoparasite ecology is
 essential to predict and manage disease spillover risks. We aimed to
 understand how disturbances in vegetation cover affect rodent ectoparasite
 diversity, prevalence, spatial segregation, host (i.e. sex, genus, size,
 habitat domain), and environmental (i.e. vegetation structure, forest
 cover, rainfall) variables in the state of Michoacan, Mexico. We compared
 these variables by trapping rodents in five paired disturbed (reduced
 vegetation cover, regular human presence) and undisturbed (no reduction in
 vegetation cover, no human presence) sites in the summer and autumn of
 2022. From 108 trapped rodents, we collected 123 ectoparasites on 34
 individuals. We found no difference in rodent diversity, ectoparasite
 diversity, or ectoparasite prevalence between disturbed and undisturbed
 sites. However, ground-dwelling and male rodents had a higher probability
 of carrying ectoparasites than arboreal and female rodents. Rodents with
 ectoparasites were not spatially clustered; rather, they were randomly
 distributed across trapping grids. We also identified two rodent genera
 (Rattus and Sigmodon) that carry ectoparasites of medical importance and
 that are in close contact with humans. Our results highlight the necessity
 of constant monitoring of rodents, ectoparasites, and their associated
 transmittable diseases. Assessing these interactions and how they are
 affected by anthropogenic disturbance could better inform management
 decisions and support the need for rodent conservation programs in the
 area.
description: <em>Study sites. </em>Our study sites were in the
 municipalities of Nuevo San Juan, Tancitaro, and Uruapan in the state of
 Michoacan, Mexico, in the Trans-Mexican Volcanic Belt.  Our aim was to
 find the relationship between ectoparasite diversity and anthropogenic
 disturbance. We defined the disturbance status of our sampling sites based
 on their forest structure and cover. Five paired disturbed and undisturbed
 sampling sites were chosen to be, on average, 300 m apart between sites
 within a pair. Undisturbed sites had high forest cover (see results
 below), while disturbed sites had highly disturbed vegetation due to human
 activities. At each site, we measured plant (trees and shrubs) height,
 density, and growth form along three transects. Each transect was 50 m
 long and 2 m wide (Perkins et al., 2019). Each plant was identified at the
 species level with the help of community professionals from the Forestry
 Direction of Nuevo San Juan. To sample rodents, at each
 site, we placed 50 Sherman traps in a 5 × 10 grid arrangement (spaced at
 10 m). We baited the traps with a mixture of peanut butter, vanilla
 essence, and oats, which have given good results in similar environments
 (Vázquez, Medellín, and Cameron, 2000). Paired disturbed and undisturbed
 sites were sampled simultaneously on each event. Sites were sampled for
 two nights in both dry (May 2022) and wet (August 2022) seasons. As
 rodents can be sensitive to light, we avoided sampling on full moon
 nights. Each captured rodent was identified, photographed, and measured
 (total length, tail length, ear length, hind foot length measured in
 millimetres, and weight measured in grams). We inspected the fur of each
 rodent with entomological tweezers systematically on the dorsal area, the
 ears, and limbs, for approximately 2 min. All observed ectoparasites were
 removed. The use of anaesthetics during the inspections was not
 necessarily due to the docile nature of the individuals captured. However,
 signs of distress were assessed prior to inspecting each individual, and
 stressed individuals were immediately released and monitored until
 recovery. Our procedures were approved by the Secretaría de Medio Ambiente
 y Recursos Naturales from Mexico (SEMARNAT), under the permit number
 SGPA/DGVS/02787/22. Collected ectoparasites were preserved in 70% ethanol
 for later identification and counting. In the laboratory, collected mites
 (Mesostigmata) and chiggers (Trombidiformes) were submerged in a chloral
 hydrate solution until translucid, and then individually mounted in
 Hoyer's medium (Moravvej et al., 2016). Fleas were submerged in KOH
 until transparent and mounted in Canada balsam (Wirth and Marston, 1968).
 All ectoparasite species were identified based on taxonomic keys specific
 for each ectoparasite order, family, or genus if necessary (Acosta and
 Morrone, 2003; Hoffmann, 1990; Keirans et al., 1989; Loomis, 1971;
 McDaniel, 1979; Pratt, 1956). <em>Data analyses.
 </em>The diversity of rodent and ectoparasite communities was
 compared between disturbed and undisturbed sites using a Hutcheson t-test
 o compare the Shannon Diversity Index performed in the <em>ecolTest
 </em>R package (R Core Team, 2022; Salinas and Ramirez-Delgado,
 2021). We compared ectoparasite species richness among site types using
 species accumulation curves inferred using the <em>iNEXT</em>
 package from R (Hsieh, Ma, and Chao, 2016; R Core Team, 2022). We also
 calculated the sample coverage, defined as a measure of sample
 completeness, giving the proportion of the total number of individuals in
 a community that belong to the species represented in the sample (Chao and
 Jost, 2012). We compared the relative abundance of ectoparasite orders
 between site types (i.e., Siphonaptera, Ixodida, Mesostigmata, and
 Trombidiformes) using a Mann-Whitney test in the R base package (R Core
 Team, 2022). Pielou’s evenness index was used to compare ectoparasite
 communities between site types using a Mann-Whitney test (see F2 in
 Supplementary material S2) implanted in the R <em>base</em>
 package (R Core Team, 2022). We calculated the prevalence of taxonomic
 orders of ectoparasites on rodents per sampling event and compared them
 among disturbed and undisturbed sites using a Mann-Whitney test. To
 compare beta diversity of ectoparasite communities, we applied a
 non-metric multidimensional scaling (NMDS) using the ‘metaMDS’ function in
 <em>vegan</em> (Oksanen et al., 2022; R Core Team, 2022). We
 used the Bray-Curtis distance, and the treatment factor using 1,000
 permutations. We then performed an analysis of similarity (ANOSIM) using
 the ‘anosim’ function from <em>vegan </em>under the same
 parameters. We developed binomial generalised linear
 models to predict the presence of ectoparasites in rodents. We generated a
 global model in the <em>MuMIn</em> R package (Barton, 2018) to
 assess the influence of rodent life-history traits, rodent genus, rodent
 relative abundance, and habitat condition on the presence/absence of
 ectoparasites on rodents. Rodent host variables included activity patterns
 (nocturnal/crepuscular), habitat domain (arboreal/ground-dwelling), sex,
 body mass index, host genus, and rodent relative abundance per season for
 each site. The environmental variables included in the global model were
 season (wet/dry), shrub density, tree density, and site type
 (disturbed/undisturbed). As more than one model met the ΔAICc &lt; 2
 criterion, we applied a model full averaging to produce an average of the
 estimates with these models (Burnham and Anderson, 2002).
 We calculated the spatial patterns of ectoparasite presence on
 rodent hosts through the segregation index (<em>S</em>) using
 the <em>dixon2002</em> function from the
 <em>ecespa</em> R package (de la Cruz, Dixon, and
 Blanco-Moreno, 2023; R Core Team, 2022). This index describes the tendency
 of one species to be associated with itself or with other species (Dixon,
 2002). <em>S</em> &gt; 0 indicates that rodents hosting
 ectoparasites are segregated, whereas <em>S</em> &lt; 0
 indicates that rodents with ectoparasites are clustered and found near one
 another. <em>S</em> close to 0 suggests a random distribution
 of rodents with ectoparasites (de la Cruz et al., 2023).
description: # Rodent ectoparasite diversity in response to anthropogenic disturbance
 [https://doi.org/10.5061/dryad.g1jwstqxv](https://doi.org/10.5061/dryad.g1jwstqxv) The data sets contain information on the rodents and associated ectoparasites in response to anthropogenic disturbance in five pairs of disturbed and undisturbed sites in Nuevo San Juan, Michoacan, Mexico. ## Description of the data and file structure We imported .csv files into RStudio to do the analyses. The databases used were: * **20240123_plant_transects_V2.csv** - Contains information on vegetation communities and structure collected in disturbed and undisturbed sites of Nuevo San Juan, Michoacan, Mexico. The variables in this database are: * ID: Consecutive number of the individual plant measured. * site: It refers to the site where the data were collected. It is composed of the identifier of the treatment (D=Disturbed, and C=Undisturbed), and the pair number (1 to 5). * sampling_line: identifier of the sampling line. We carried out three sampling lines per site. However, there were highly homogeneous sites where the number of lines was less. * height: height in meters of the plant measured. * habit: plants were classified into trees or shrubs depending on height and life history. * morpho_id: Identification of the plant per species, genus or morpho species. * code_sp: A letter assigned to each different taxonomic group of plants. It is based on the morpho_id column. * **20240124_mice-ectoparasites_MX.csv** - Contains information of the captured rodents in Nuevo San Juan, Michoacan, Mexico. The variables in this database are: * site: identifier of the site where the rodent was captured. * pair: sites were sampled simultaneously in pairs of disturbed and undisturbed sites. Thus, P1 contains both undisturbed site 1 and disturbed site 1. * treatment: disturbed or undisturbed sites. * date: day of the rodent capture. * event: sampling event of the capture. * season: we sampled in two seasons, dry (May 2022) and rainy (August 2022). * latitude: decimal degrees latitude of the site. * longitude: decimal degrees longitude of the site. * dshrub: average shrub density in the site calculated by line transects. * dtree: average tree density in the site calculated by line transects. * pcover: percentage of forest cover of the site calculated by satellite images. * id_individual: identifier per captured individual rodent. * x: spatial identifier of the trap within the grid where the rodent was caught. Empty cells represent missing values where we failed to record the trap where the rodent was captured. * y: second spatial identifier of the trap within the grid where the rodent was caught. Empty cells represent missing values where we failed to record the trap where the rodent was captured. * weight: weight of the captured rodent in grams. Empty cells represent missing values where either rodents were recaptured (therefore we did not weight them again) or the rodents escaped before being weighted. * body_length: lenght in milimeters of the body of the captured rodent, from the base of the tail to the tip of the muzzle. Empty cells represent missing values where either rodents were recaptured (therefore we did not measure them again) or the rodents escaped before being measured. * sex: sex of the captured rodent. Empty cells represent missing values where rodents escaped before their sex was determined. * host_genus: genus of the captured rodent. * species: species of the captured rodent. Empty cells represent missing values where the species of rodent could not be determined. * code_sp: code assign to the species based on the species column. Empty cells represent missing values where the species of rodent could not be determined. * habitat_domain: wether the captured rodent is ground-dwelling or arboreal. * activity: wether the captured rodent is nocturnal or crepuscular. * recapture: wether the captured rodent has been captured previously (i.e., if yes, it is a recapture) * n_ectoparasites: number of ectoparasites collected from the captured rodent. Empty cells represent missing values where the number of ectoparasites could not be determined accurately. * ectop_pa: presence or absence of ectoparasites in the captured rodent. * rai_rodents: relative abundance index of the site where the rodent was captured. It was calculated based on the number of captures per site divided by the sampling effort. * **20240124_ectoparasites_V2.csv** - Database focused on the species or taxonomic groups of ectoparasites on captured rodents. A rodent ID can be repetead based on the number of species it was a host for. The variables in this database are: * ID: identifier per captured rodent individual. * date: day of the rodent capture. * event: sampling event of the capture. * site: identifier of the site where the rodent was captured. * latitude: decimal degrees latitude of the site. * longitude: decimal degrees longitude of the site. * dshrub: average shrub density in the site calculated by line transects. * dtree: average tree density in the site calculated by line transects. * pair: sites were sampled simultaneously in pairs of disturbed and undisturbed sites. Thus, P1 contains both undisturbed site 1 and disturbed site 1. * treatment: disturbed or undisturbed sites. * season: we sampled in two seasons, dry (May 2022) and rainy (August 2022). * host_genus: genus of the captured rodent. * species: species of the captured rodent. Empty cells represent missing values where the species of rodent could not be determined. * code_sp: code assign to the species based on the species column. Empty cells represent missing values where the species of rodent could not be determined. * habitat_domain: wether the captured rodent is ground-dwelling or arboreal. * activity: wether the captured rodent is nocturnal or crepuscular. * weight: weight of the captured rodent in grams. Empty cells represent missing values where either rodents were recaptured (therefore we did not weight them again) or the rodents escaped before being weighted. * body_length: lenght in milimeters of the body of the captured rodent, from the base of the tail to the tip of the muzzle. Empty cells represent missing values where either rodents were recaptured (therefore we did not measure them again) or the rodents escaped before being measured. * sex: sex of the captured rodent. Empty cells represent missing values where rodents escaped before their sex was determined. * recapture: wether the captured rodent has been captured previously (i.e., if yes, it is a recapture). * ectop_pa: presence or absence of ectoparasites in the captured rodent. * ect_class: class of the ectoparasite collected from the captured rodent. * ect_order: order of the ectoparasite collected from the captured rodent. * ect_family: family of the ectoparasite collected from the captured rodent. * sp_ect: species of the ectoparasite collected from the captured rodent. Empty cells represent NA, where there were no ectoparasites to determined. * code_ect: code for based on the sp_ect column for species of the ectoparasite collected from the captured rodent. Empty cells correspond to individuals without ectoparasites to be identified. * n_ectoparasites: number of ectoparasites collected from the captured rodent. Empty cells represent missing values where the number of ectoparasites could not be determined accurately. * **20240124_ectoparasites_disturbed_inext.csv** - Database to create species accumulation curves on iNext. It is based on the presence/absense per ectoparasite species (rows) captured on individual hosts (columns) on disturbed sites. * **20240124_ectoparasites_undisturbed_inext.csv** - Database to create species accumulation curves on iNext. It is based on the presence/absense per ectoparasite species (rows) captured on individual hosts (columns) on undisturbed sites. * **20240124_rai_ect_order.csv** - Manually modified database for the relative abundance index based on the number of ectoparasites (nect) of each ectoparasite order per treatment and site. ## Code/Software We created our code on R (version 4.3.2), using RStudio (2023.12.0+369 "Ocean Storm" Release (33206f75bd14d07d84753f965eaa24756eda97b7, 2023-12-17) for Windows. Our RScript contains all the information of the installed packages and the detailed step to obtained the results publised in the manuscript JEN-2023-0288 under review on the Journal of Applied Entomology.