DOI: 10.5061/dryad.8931zcrxq
title: Data associated with: A phylogenetic perspective on ecological specialisation reveals hummingbird and insect pollinators have generalist diets

description: Specialisation in food resource use is a crucial process that fosters
 species coexistence in plant-animal networks, contributing to the
 maintenance of biodiversity, ecological complexity, and community
 stability. Notably, although there is a vast literature on ecological
 specialisation in pollination systems, the evolutionary similarity among
 the plant species visited by particular pollinators has been largely
 ignored. Here, we apply a robust phylogenetic approach to analyse whether
 the evolutionary relatedness of plant species is a significant factor in
 mediating pollinator visits and how it relates to the morphology of
 interacting species. We quantified ecological and clade specialisation of
 hummingbird and insect species in three mutualistic networks from the
 Costa Rican highlands and associated these metrics with species traits. We
 found that hummingbirds were overall ecologically more specialised than
 insects (i.e. visited a less diverse set of plant species). However, when
 evaluating the phylogenetic relatedness among the visited plant species,
 all hummingbird species and most insects had overdispersed diets, which
 indicates they visited phylogenetically distant plant species in the
 community. Moreover, a great proportion of these clade generalists visited
 plant species with a great variation in corolla length, showing a lack of
 preference for this morphological trait. Altogether, our results
 demonstrate that by incorporating plant phylogeny to network analysis,
 pollinator species were generalists and that corolla length weakly
 influences plant-pollinator interactions in the three studied networks. A
 phylogenetic perspective should occupy a central role in the study of
 specialisation since it contributes to understanding the interplay between
 ecological and evolutionary processes in mutualistic networks. Future
 research should focus on evaluating whether the phylogenetic structure of
 animal diets mediates patterns of interactions in different types of
 mutualisms and environmental contexts, linking these patterns to other
 floral traits. This knowledge may be valuable for deepening our
 comprehension of the underlying mechanisms shaping ecological networks.
description: The study was conducted in central–southern Costa Rica on the
 Caribbean and Pacific slopes of the Talamanca mountains, a volcanic
 mountain range that forms the spine of the Central American Isthmus from
 central Costa Rica through western Panama. This area includes the Cerro de
 la Muerte, which has the largest extent of páramo in the country (09°
 60' N, 83° 76' W). The páramo is a neotropical grass- and
 shrub-dominated ecosystem that occupies the cool and wet upper slopes of
 neotropical mountains. Field data collection was conducted at three sites
 of about 12 ha each: Cerro las Vueltas Biological Reserve, Cerro Sákira,
 and Cerro Buena Vista (hereafter Reserve, Sákira, and Buena Vista,
 respectively) at elevations between 3000 and 3400 m a.s.l. We collected
 data on plant-pollinator interactions as well as on abundance and
 morphological traits of interacting species. Because the two types of
 studied organisms (plants and mobile pollinators) differ in space use,
 different approaches for sampling them are required. We used different
 plots distributed across each study site to sample plants and pollinators,
 as in other studies (López-Segoviano et al. 2023). In order to accurately
 record interactions and pollinator species abundance, given the great
 differences in size and behaviour between hummingbirds and insects, we
 used different survey techniques for these groups following similar
 protocols used in previous research (Lehmann et al. 2019). Field data were
 collected during sampling periods ca. every 12 days in every month at each
 study site over an entire year, from January to December 2016.
description: **Data associated with: A phylogenetic perspective on ecological
 specialisation reveals hummingbird and insect pollinators have generalist
 diets** This repository contains three folders, each of them includes *R*
 codes and the respective data files in csv format; some of these data
 files include cells with "NA", which means data not available.
 The folders are named: DSI & phylo signal, Index d' and Models.
 **DSI & phylo signal**. It includes the *R* scripts “1_DSI
 pollination.R” where the DSI* index is calculated for each pollinator
 species at each of the three study sites and “2_Phylo Signal.R” where the
 phylogenetic signal of pollinator richness is calculated for the three
 studied communities. \- The source files used in “1_DSI pollination.R”
 are: (a) inter.matrix.reserva.2016.csv, inter.matrix.sakira.2016.csv, and
 interact.matrix.all.BuenaVista.csv: quantitative bipartite matrices for
 each of the three study sites, with rows corresponding to plant species
 and columns to pollinator species, where cell entries are integers
 representing the observed frequency of pairwise interactions. (b)
 Abund_flowers.csv is a data frame with the following variables: Year: year
 of the data collection Perio: 15-days periods Date: date of sampling Site:
 sampling site (Reserva, Sakira or BuenaVista) Trans: transect (plot) for
 flower counts PlCode: number assigned at each plant species PlOrder:
 taxonomic order of the plant species PlFamily: taxonomic family of the
 plant species PlantSp: scientific name of the plant species Abund_1:
 number of open flowers counted in the transects where in some plant
 species (for example from the family Asteraceae) inflorescences were
 considered as unit count Unit_Abund: whether the unit count was an
 individual flower or an inflorescence Abund_2: Abund_1 is multiplied by
 the mean number of flowers in a set of inflorescences previously sampled,
 so the unit count in this case is always the individual flower \- The
 source files used in “2_Phylo Signal.R” are: (a) NBV.nex, Nreserva.nex and
 Nsakira.nex: plant phylogenies for each community, obtained using the
 phylocom software based on the species list of each site. (b)
 Plant_traits.csv including the variables PlantSp: scientific name of the
 plant species Type: whether the flower corolla is open or tubular
 corola_length: corolla length in mm curvature: corolla curvature in
 degrees (calculated from trigonometry) diameter: diameter of the corolla
 opening in mm. (c) inter.matrix.bv.csv, inter.matrix.res.csv,
 inter.matrix.sk.csv: the three quantitative bipartite matrices outlined
 before with a slight modification in their format to be used in
 phylogenetic analysis.   **Index d'**. It includes the *R* script
 named “1_Ecol specializ index d.R” where the specialization index d'
 of pollinator species in the three communities is calculated accounting
 for the flower abundance of interacting plant species. The source files
 used in this code are: (a) Abund_flowers_site is a data frame with the
 following variables: Site: study site PlantSp: scientific name of the
 plant species OverallNumFl: total number of flowers counted across
 transects (b) d_pollinators: an output from the *R* code including the
 variables: d: specialization index d’ PollinatorSp: scientific name of the
 pollinator species Site: study site marg.total: total number of
 interactions between a given pollinator species and all the plant species
 it visited. (c) inter.matrix.buenavista.2016.csv,
 inter.matrix.reserva.2016.csv, and inter.matrix.sakira.2016.csv: the
 quantitative bipartite matrices for each of the three study sites outlined
 before, with rows corresponding to plant species and columns to pollinator
 species, where cell entries are integers representing the observed
 frequency of pairwise interactions.   **Models.** It includes three *R*
 codes: “1_Models d-DSI” that contains comparison of specialization indices
 (index d' and DSI*) between birds and insects, and across pollinator
 orders; “2_Ecol Specializ-originality” where the relationship between
 index d' and morphological originality is analysed; and “3_Flower
 morphology” where the plant phylogeny is built. \- The source file used in
 “1_Models d-DSI” is: d_DSI with the following variables: Site: sampling
 site (Reserva, Sakira, BuenaVista) Group: whether the pollinator species
 belong to bird or insect group Order: taxonomic order of the pollinator
 species PollinatorSp: scientific name of the pollinator species
 CorollaType: whether the pollinator visited plant species with flower
 corolla open, tubular or both CorollaShape: whether the pollinator visited
 plant species with flower shape straight, curved or both Family: taxonomic
 family of the pollinator species d: specialization index d’ marg.total:
 total number of interactions between a given pollinator species and all
 the plant species it visited DSI.st: distance-based specialisation index
 Index: a variable used to aggregate the data in the R code \- The source
 file used in “2_Ecol Specializ-originality” is d_DSI_originality including
 the following variables: Site, Group, Order, Family, PollinatorSp, d,
 marg.total and DSI.st as outlined before st.originality: standardized
 originality (distance of a species to the community-weighted mean centroid
 normalised to zero mean and unit variance) log.st.originality:
 log-transformed standardized originality \- The source files used in
 “3_Flower morphology” are: (a) Plant_all_visited_2016: including the
 variables as outlined before for the csv Abund_flowers in the DSI &
 phylo signal: Year, Date, Site, PlOrder, PlFamily, PlantSp. Additionally,
 in this csv file are included the following variables: PoOrder, PoFamily,
 PollinatorSp: taxonomic order, family and scientific name of the
 pollinator species, respectively NFlVisit: number of flowers visited by
 each pollinator Index: a variable used to aggregate the data in the *R*
 code (b) Plant_traits: including the three variables PlantSp (plant
 species), Type (whether the flower corolla is open or tubular) and
 corola_length (corolla length in mm) (c) d_DSI: including the variables
 Site: study site Group: whether the pollinator belongs to bird or insect
 group Order: taxonomic order of the pollinator PollinatorSp: scientific
 name of the pollinator species CorollaType: whether the pollinator visited
 plant species with flower corolla open, tubular or both) CorollaShape:
 whether the pollinator visited plant species with flower shape straight,
 curved or both Family: taxonomic family of the pollinator species d:
 specialization index d´ marg.total: total number of interactions between a
 given pollinator species and all the plant species that it visited DSI.st:
 distance-based specialisation index Index: a variable used to aggregate
 the data in the R code.