DOI: 10.5061/dryad.j0zpc86nj
title: Data from: Seasonal host community dynamics constrain the risk of parasite transmission between migrant and resident species

description: Seasonal migration shapes the community dynamics that influence pathogen
 transmission between migrants and resident species. While theoretical and
 empirical evidence has accumulated, whether migration
 increases or decreases the risk of cross-species infection
 remains inconclusive. We studied how the seasonal arrival
 and departure of a single avian migrant species change the
 composition of local communities in breeding areas affecting the
 haemosporidian infection dynamics. The seasonal reordering of resident
 species abundances induced by migrants, minimizes the
 opportunities for contact between highly infected hosts and
 susceptible species, either migrants or residents, thereby
 limiting the transmission of parasites to occasional
 spillover events. The occurrence of spillover dynamics during the
 seasonal sympatry between migrants and residents provides a
 plausible explanation that reconciles empirical inconsistencies in the
 intersection of animal migration and infection risk at the host
 community level. Our findings underscore the critical role played
 by seasonality in shaping infection dynamics in migratory
 systems.
description: Between October 2015 and September 2019, we studied local
 communities of closely related bird species (Order: Passeriformes) and
 their haemosporidian parasites at five study sites in Southern Chile (Fig.
 1A). Each of these sites represents different habitat types, where the
 long-distance migrant <em>Elaenia albiceps</em> occurs in
 sympatry with local resident species during the austral spring and summer,
 between October and March (hereafter, breeding season). The local absence
 of <em>E. albiceps</em> occurs during the austral fall and
 winter, between April and September (hereafter, non-breeding season).
 Llancahue (39°84’ S; 73°14’ W) is an evergreen forest, supporting remnants
 of old-growth temperate rainforest and secondary forests (Biscarra et al.
 2021). Quempillén (41°87’ S; 73°77’ W) is a secondary forest with dense
 understory vegetation covered by a mixture of native berry trees, native
 bamboo, fern species, and exotic shrublands (Díaz & Armesto 2007).
 San José (39°55’ S; 72°98’ W) is an anthropogenic habitat in which native
 temperate rainforests have been largely replaced by agricultural lands and
 exotic tree plantations, followed by recent natural regeneration
 (Zamorano-Elgueta et al. 2015). Santa María (39°68’ S; 73°19’ W) and Teja
 Norte (39°79’ S; 73°26’ W) are riparian habitats within the Río Cruces
 wetland. While Santa María is located on the border of a temperate forest
 patch and presents mainly low marsh vegetation maintained by cattle
 grazing, Teja Norte has a dense reedbed surrounded by scrubs. For
 logistical reasons, Llancahue was subsampled during winter and San José
 was sampled for only one year (Table S1; Fig. S1).
 Individual birds were systematically trapped once per month with
 mist nets operating for 5 h each, beginning at sunrise. Individuals were
 identified at the species level and marked with numbered aluminum leg
 rings to record individual-based abundance. Blood samples were obtained
 from a random subset of the trapped bird species by puncturing the
 brachial vein and were deposited in a 2 ml tube with 96% ethanol for
 further molecular analyses. Additionally, a drop of each blood sample was
 used for parasite quantification in the blood smear, fixed with 100%
 methanol, and stained with a three-step quick stain (Differential Quik
 Stain Kit; Polysciences, Warrington, PA, USA). In infected individuals,
 the intensity of infection was quantified using optical microscopy with
 1000X amplification and was reported as the number of haemosporidian
 gametocytes in 10,000 erythrocytes. DNA was extracted from blood samples
 using an E.Z.N.A. Blood DNA Kit (Omega Bio-tek, Norcross, GA, USA)
 according to the manufacturer’s protocol. We screened all DNA samples for
 infection with either of the haemosporidian genera
 <em>Plasmodium</em>, <em>Haemoproteus</em>, and
 <em>Leucocytozoon</em> using nested PCR that targets a ~1,068
 bp fragment of the cytochrome b gene (cyt <em>b</em>) of the
 parasite mitochondrial DNA, using the primers DW2 and DW4, followed by DW1
 and DW6 (Bensch et al. 2009; Perkins & Schall 2002). All PCR runs
 were performed using positive and negative controls. PCR products were
 purified (E.Z.N.A. Cycle Pure Kit, Omega Bio-tek) and then sequenced in
 both directions with an ABI3100 Genetic Analyzer (AustralOmics, Valdivia,
 Chile). All haemosporidian sequences obtained were submitted to GenBank
 (accession numbers are pending upon publication). Individual sequences
 were compared with the BLAST database and grouped by haemosporidian genus.
 Sequences were aligned using MAFFT v7 and evaluated in a median-joining
 haplotype network to distinguish any host or seasonal distribution using
 Network 5.0.1.0 (Fluxus Technology Ltd., Suffolk, England) and Network
 Publisher v.2.1.2.3 (Fluxus Technology Ltd.). Seasonal
 host community dynamics The dynamics of host
 communities were analyzed by considering the accumulated abundance of each
 species in a local community over a three-month capture period. Breeding
 communities were formed by individuals captured between October and
 December and between January and March, while non-breeding communities
 were formed by individuals captured between April and June and between
 July and September. To avoid pseudoreplication in community estimates,
 individuals recaptured within the same three-month period in an annual
 cycle were excluded from the analyses (Hurlbert 1984; Schwarz 2002). To
 visualize the two-dimensional distribution of pairwise Bray-Curtis
 dissimilarities between samples, nonmetric multidimensional scaling (NMDS)
 with relative abundance transformation was performed. Permutational
 multivariate analysis of variance (PERMANOVA) was used to test for
 differences in community composition using the “vegan” R package (Oksanen
 et al. 2022). To gain a deeper understanding of the processes underlying
 changes in community composition across seasons in the presence of
 <em>E. albiceps</em>, we calculated two community-change
 metrics based on rank abundance curves (RACs) that incorporate both
 species identities and abundances (Avolio et al. 2015, 2019). We used
 E<sub>var</sub> as a measure of variance in the relative
 abundance of species in a community (Smith & Wilson 1996) and
 calculated the change in E<sub>var</sub> between seasons
 (<em>ΔE</em>) as the difference in evenness between
 the breeding and non-breeding seasons. Additionally, we calculated the
 average change in the rank of each species in the community
 (<em>ΔR</em>), which considered the gains and losses of
 species in each evaluated season, incorporating species turnover. All
 calculations of changes in RAC-based measures between seasons
 were conducted using the “codyn” R package (Avolio et al. 2019; Hallett et
 al. 2016). We tested for statistically significant differences in the
 drivers of seasonal community changes among communities using Welch’s two
 sample t-tests. Host contribution to parasite
 transmission To determine the potential reservoirs of
 infection for each lineage of haemosporidian circulating within the
 communities, we estimated the relative contribution of each host species
 to the overall infectious pool (<em>π</em>) following
 Streicker et al. (2013). Host species were categorized as key hosts,
 indicating their role as infection reservoirs if <em>π</em> ≥
 0.5. Conversely, values of <em>π</em> &lt; 0.5 suggested
 that these host species were only occasionally infected through spillover
 dynamics. To understand how host species contribute to
 parasite transmission and persistence, we explored three asymmetries that
 underlie host heterogeneity: the degree of asymmetry in host abundance
 (<em>θA</em>) which serves as a proxy for encounter
 opportunities between host species, the degree of asymmetry in the
 prevalence of infection (<em>θI</em>) which represent the
 exposure of host species to infected vectors, and the degree of asymmetry
 in infection intensity (<em>θS</em>), which act as a proxy for
 the susceptibility to infection and the capacity to shed parasites
 (Streicker et al. 2013). In order for a host species to be classified as a
 key host, at least one of these asymmetries must be significantly greater
 than 1.
description: # Data from: Seasonal host community dynamics constrain the risk of
 parasite transmission between migrant and resident species
 [https://doi.org/10.5061/dryad.j0zpc86nj](https://doi.org/10.5061/dryad.j0zpc86nj) R script and data used to estimate seasonal host community dynamics and the contribution of each host to the transmission of haemosporidian parasites in resident bird communities seasonally visited by a migrant species within the Neotropical austral bird migration system. ## **File list (files found within Navarrete\_et\_al\_data.zip)** Navarrete_et_al_analyzes.R Navarrete_et_al_relative_abundance_change.csv Navarrete_et_al_NMDS.csv Navarrete_et_al_NMDS_points.csv Navarrete_et_al_community_dynamics.csv Navarrete_et_al_RAC_change.csv ## **File descriptions** **Note:** .csv files are semi-colon delimited. Navarrete_et_al_analyzes.R – The only file that you need to open. Has the code to make the figures of the paper and perform the statistical analyzes related to the seasonal host community dynamics and the contribution of hosts to parasite transmission. Navarrete_et_al_relative_abundance.csv – The relative abundance of each host species (six-letter code, where the first three letters correspond to the genus and the next three letters to the species) at each study site and season. For each species, its seasonal movement behavior is specified. NA indicates that the species was not found in a given study site and season. Navarrete_et_al_NMDS.csv – Species abundance matrix at each study site, sampling year and season. Navarrete_et_al_NMDS_points.csv – Results of the ordination of communities in a two-dimensional space. These points are used for graphing. Navarrete_et_al_community_dynamics.csv – Relative abundance of species at each study site, sampling year and season. It is used to quantify seasonal change in community metrics.  Navarrete_et_al_RAC_change.csv – Seasonal change in the community evenness and reordering of host species at each study site and sampling year. Each community is classified as "forest-type community" or "wetland-type community" according to the NMDS result. Navarrete_et_al_host_contribution.csv – Contribution of each host species to the transmission of haemosporidian parasites in our natural disease system. Each host species is positioned as a vector according to the result of the NMDS. Their relative abundance determines the size of the circle. **Note:** All of the files in “Navarrete_et_al_data.zip” must be within your working directory for the analysis to work.