DOI: 10.5061/dryad.j0zpc86k7
title: Data from: Non-native mammals are weak candidates to substitute ecological function of native avian seed-dispersers in an island ecosystem

description: Although prominent examples exist of non-native species causing
 substantial ecological harm, many have neutral or positive effects,
 including filling surrogate roles once performed by extinct native
 organisms. We tested the ecological roles of two non-native mammals as
 seed dispersers or seed predators in Guåhan, which, due to invasive brown
 treesnakes (Boiga irregularis), is devoid of native seed dispersers –
 birds and bats. We conducted feeding trials with captive rats (Rattus
 spp.), which are present but uncommon due to predation by snakes, and pigs
 (Sus scrofa), which are abundant. We examined if and how they interacted
 with common forest fruits. We then compared how any gut-passed or handled
 seeds germinated compared to seeds left in whole fruit or depulped seeds.
 Rats and pigs interacted with most of the fruits and seeds (&gt;80%)
 that they were fed. Of those, most seeds were destroyed – 78% for rats and
 90% for pigs, across both native and non-native plant species. Compared to
 seeds germinating within whole fruits, rats improved germination of the
 seeds that they handled without ingesting, while pigs diminished the
 germination of seeds that they handled. The small percentage of seeds
 (approximately 1.5% for rats and 5% for pigs) that survived gut passage
 germinated in higher proportions than those in whole fruits. Percentages
 of seed survival to germination are lower than those found in similar
 studies with native avian frugivores. Our results indicate that pigs and
 rats have mixed effects on seeds, but are not suitable surrogates for
 native seed dispersers.
description: Fruit
 collection We collected common fruit
 species present in Guåhan’s limestone forests to use in feeding and
 germination trials. This included both native and non-native
 fleshy-fruited plant species varying in fruit and seed size and in growth
 form (trees, shrubs, and vines) (Table 1). Most species were collected on
 the day of the feeding trials. In cases when these fruits were not ripe at
 the time of picking, <em>Morinda citrifolia</em> (ladda) and
 <em>Premna serratifolia</em> (åhgao) were held for up to four
 days to allow for ripening before feeding. Fruits of a single species were
 picked from different sites and at least three different individual trees
 per site to account for individual effects. Fruits were mixed and divided
 into four groups: 1) a depulped treatment (to approximate flesh-removal
 without digestion) where we extracted seeds from the fruit by hand, 2) a
 whole-fruit treatment (representing fruits falling to the ground in the
 wild), where fruits were left intact, and two treatments, 3) seeds that
 had passed through the gut or 4) had been spat out by rats or pigs, that
 were determined after being fed to animals. Fruits were fed to captive
 animals within a mix of multiple species collected that day, or less
 commonly, as a single species. Rat feeding trials – immediate
 seed fate Rat feeding trials occurred
 from July 2017 until February 2018. Rats were captured from the wild in
 Guåhan and kept in a captive outdoor facility. After collecting fruits, we
 reserved some for whole fruit and depulped treatments, while the rest of
 the fruits were fed to rats. We fed rats in the late afternoon or
 evening.  As rats normally did not begin feeding immediately, fruits were
 left overnight. Based on preliminary trials, any ingested seeds were
 passed within 12 hours. All remaining fruits and seeds, and all scats were
 collected the following morning and again later in the day to allow enough
 time for gut passage. Seeds that had flesh removed, which we considered
 “rat-handled,” were set aside to be planted as one of our germination
 treatments. Scats were picked apart under a dissecting scope to locate all
 gut-passed seeds, and, if they appeared mostly intact, these were also set
 aside to be planted as our gut-passed germination treatment.
 Pig feeding trials – immediate
 seed fate Pig feeding trials occurred
 between July 2018 and May 2019. Again, a portion of fruits and seeds were
 set aside for whole fruit and depulped germination treatments. The
 remaining fruits were placed in pens in feeding bowls or in spots where
 each pig’s food was normally placed. Because feeding trials were
 coordinated with private landowners, timing of feeding depended on when we
 had permission to access their pigs. However, all feeding trials were done
 in the afternoon or early evening. We left fruits with pigs for
 approximately one hour while we remained out of sight before collecting
 any remnant fruits. Seeds that were spat out and partially-eaten fruits
 were set aside for our “pig-handled” treatment. We collected scat once
 daily until seeds of those species ceased to appear in scats, usually four
 to five days, which was consistent with gut passage time in other studies
 (Elston, et al., 2005; Schmidt, et al., 2004). Scats were processed by
 spraying water through size-appropriate mesh sieves. Any intact or mostly
 intact seeds caught in the mesh were identified, counted, and then planted
 in the nursery within one day as our gut-passed treatment. Scats collected
 in the days after feeding the very small-seeded species of <em>Ficus
 prolixa</em> and <em>Pipturus argenteus</em> were placed
 intact in soil mix and germination trays, and the entire scat was watered
 and monitored for germination. 
 We fed 14 species of fruits to both rats
 and pigs. An additional four species were fed only to rats, and four
 species only to pigs due to differences in fruit availability during the
 respective feeding trials (Table 1). Germination
 Trials We planted seeds as one of four
 treatments, as mentioned above and repeated here: 1) a depulped treatment
 (to approximate flesh-removal without digestion) where we extracted seeds
 from the fruit by hand, 2) a whole-fruit treatment (representing fruits
 falling to the ground in the wild), where fruits were left intact, and two
 treatments, 3) seeds that had passed through the gut or 4) had been spat
 out by rats or pigs, that were determined after being fed to animals.
 While preparing seeds for our depulped treatment, we also selected several
 fruits from which to tally seed counts – this allowed us to estimate
 average seed counts for whole fruits with multiple seeds. If whole fruit
 treatments did not fit in seedling trays, as in the case of larger fruits
 with many seeds (<em>Carica papaya</em>, <em>Morinda
 citrifolia</em>) which normally break when they fall to the ground
 in the wild, we divided the fruit into chunks and planted each chunk
 separately.  We conducted germination trials
 in an open-air shadehouse covered by 70 percent shadecloth. We sowed seeds
 from all treatments in a 1:1 mix of peat moss and perlite and watered them
 daily, and recorded germination three times a week. When a seedling
 sprouted in a cell, we took one of two courses of action: 1) if only one
 seedling was expected to grow from the cell, then the seedling and all
 contents of that cell were discarded or 2) if the cell contained
 additional seeds that could germinate, the seedling was clipped and other
 contents left undisturbed. Germination was monitored from July 2017 until
 June 2018 for treatments planted with rat feeding trials, and from July
 2018 until November 2019 for treatments planted with pig feeding trials.
 Based on knowledge from previous germination studies (Fricke et al.,
 2018), we did not expect most species to be viable after six months, and
 therefore, discontinued our monitoring of these species if they had not
 germinated within seven months. One species, <em>Elaeocarpus joga
 </em>(yoga), can germinate after more than a year, so we monitored
 this species for 14 months after planting. Analyses
 Overview We ran separate parallel
 analyses for pig trials and for rat trials. All analyses were run in R (R
 Core Team 2020) using the <em>lme4</em> (Bates et al. 2015)
 and <em>emmeans</em> (Lenth, et al., 2020) packages. Each
 analysis consisted of three separate steps (Figure 1). First, we analyzed
 whether an animal interacted with a fruit. Second, for the fruits with
 which animals interacted, we analyzed whether seeds were handled (cleaned
 of flesh), ingested and passed, or destroyed. Finally, we analyzed
 germination, comparing germination success between separate animal
 treatments (gut passed by an animal or handled by an animal), with seeds
 that were depulped by us, and those planted in whole fruit. In addition,
 we estimated the overall cumulative effect of each animal species on each
 plant species by multiplying the probability of a seed reaching each
 subsequent step in the feeding to germination
 process. Immediate seed fate
 analysis We used a generalized linear
 mixed-effects model (GLMM) with a binomial error distribution to determine
 if animals ignored or interacted with fruit. The response variable
 combined the number of “successes” (fruits interacted with) and the number
 of failures (fruits ignored), using the <em>cbind</em>
 function in R. The fixed effect was the fruit species, and the random
 effect was the individual identity of the pig or rat to account for
 individual variation between animals, and the date of feeding trial, to
 account for the variation in viability of fruits between collection
 bouts.  We ran further analyses using
 the subset of species with which pigs or rats interacted to determine what
 type of interaction an animal had with a seed. For species that were gut
 passed (which tended to be smaller-seeded), we used GLMMs with binomial
 error distributions to determine if seeds were gut passed or destroyed by
 rats and pigs. For species that were handled (which tended to be
 larger-seeded), we again used GLMMs with binomial error distributions to
 determine if seeds were handled or destroyed by rats or pigs. For each
 GLMM, the response variable was the number of seeds gut passed or the
 number of seeds spat out combined with the number of seeds destroyed,
 again using the <em>cbind</em> function; the fixed effect was
 fruit species, and the random effect was individual pig or rat. There was
 almost no overlap between gut-passed and handled seeds for either pigs or
 rats. Only one species, <em>Carica papaya</em>, had seeds that
 were both gut-passed and handled by rats, so we used a GLMM to determine
 how many seeds were either gut-passed or handled and used these respective
 numbers in the models above. We did not conduct post-hoc tests, as we were
 not interested in the differences between species, but instead report the
 predicted proportion of seeds that were gut passed or handled relative to
 the proportion destroyed for each species. Germination
 analysis  We used separate generalized
 linear models (GLMs) to compare germination proportions between
 animal-treated seeds (gut-passed or handled) and control seeds (planted in
 whole fruit or depulped). Similar to the immediate seed fate analysis,
 this analysis was split into plant species where seeds passed through the
 gut intact or species where seeds were handled and not passed. We used the
 <em>emmeans</em> package (Lenth et al., 2020) to determine if
 treatment (animal handled or gut-passed) significantly improved
 germination over the other two treatments (whole fruit or depulped).
 Overall
 effects We estimated overall frugivore
 effects on seeds by sequentially combining our model-predicted proportions
 for fruit fate, immediate seed fate, and germination. To do this, we
 multiplied predicted proportions, from GLMMs described above, across each
 step for each plant species to get a cumulative proportion of seeds that
 germinated out of total seeds fed to each animal.
description: The datasheets contain data from feeding trials of captive rats and pigs,
 the fruits that they were fed, and the fate of the seeds that they
 interacted with.   A germination trial was also conducted to compare the
 seeds that they interacted with and seeds that they did not interact with.
   Five datasheet files are to be uploaded to run the .rmd and .r files in
 R or Rstudio:   1\. "rats\_fate\.csv" is run with the \.Rmd file
 "ratseedanalysis\_share\.Rmd\." These are data from rat feeding
 trials and the associated .rmd file runs models to determine which fruits
 rats interacted with and which seeds (of the fruits that they interacted
 with) they gut passed, handled (spat out), or destroyed. Generalized
 linear mixed models (GLMM's)are used in the code to determine this
 and create ggplots of these results. Column headings are as follows for
 "rats\_fate.csv": * datefed: the date the feedings on this line
 occurred * site: forest site from which fruit were collected *
 datefruitcollected: date that fruit were collected * ratID: individual
 name of the captive rat fed on this line * numberadded: number of fruits
 of that species fed to rat * timeadd: time that fruits were placed in the
 rat's cage * datechecked: date after datefed on which the rat's
 cage was checked for remnant fruit parts, seeds, or scat * timechecked:
 time on datechecked at which the rat's cage was checked for remnant
 fruit parts, seeds, or scat * remain: the number of fruits remaining
 uneaten in a rat's cage (this could be a partial number to represent
 part of a fruit remaining, ie. 0.25) * notes.scat: any notes taken *
 handle: number of seeds handled and spat out by a rat * species: species
 of fruit fed to rat * seedsperfruit: number of seeds expected in the fruit
 added during the given feeding * seedsadded: number of seeds in fruit of
 that species during this feeding (a multiple of numberadded and the
 seedsperfruit) * seedsleft: number of seeds left uneaten (should be equal
 to the seedsadded minus remain\*seedsperfruit) * numseedsscat: number of
 seeds found in scat * seedsdestroyed: number of seeds destroyed - not
 found remaining in cage, not handled, and not found in scat 2\.
 "pigs\_fate\.xlsx" is run with the \.Rmd file
 "pigseedanalysis\_share\.Rmd\." These are data from pig feeding
 trials and the associated .rmd file runs models to determine which fruits
 pigs interacted with and which seeds (of the fruits that they interacted
 with) they gut passed, handled (spat out), or destroyed. GLMM's are
 used in the code to determine this and create ggplots of these results.
 Column headings are as follows for "pigs\_fate.xlsx": * species:
 species of fruit fed to pig * pig: name of individual pig fed on this line
 * datefruitcollected: date that fruit were collected * datefed: the date
 the feedings on this line occurred * datechecked: date after datefed on
 which the pig's pen was checked for remnant fruit parts, seeds, or
 scat * numadded: number of fruits of that species fed to pig * remain: the
 number of fruits remaining uneaten in a pig's pen (this could be a
 partial number to represent part of a fruit remaining, ie. 0.25) *
 truehandled: number of seeds handled and spat out by a pig * seedsadded:
 number of seeds in fruit of that species during this feeding *
 seedsdestroyed: number of seeds destroyed - not found remaining in pen,
 not handled, and not found in scat * gptot: total number of seeds
 gut-passed by pig, total number of seeds found in scats from that species
 in that feeding * notes: notes from feeding trials * notes.y: notes from
 scat collection (they were separate paper datasheets, so combined here)
 3\. "rats\_germcombo\.csv" is run with the \.Rmd file
 "ratgermanalysis\_share\.Rmd" These are data from germination
 trials of the seeds described in the datasets above that were handled or
 gut passed by rats, and then compared to seeds that were planted in these
 germination trials that were left in whole fruits or depulped by hand.
 Generalized mixed models (GLM's)are used to determined proportions
 then used in figures, created using ggplot. Column headings are as follows
 for "rats\_germcombo.csv": * species: species of the seeds/fruit
 * datefrcoll: date that the fruit was collected from the wild * ratID:
 individual rat that either handled or passed the seeds in this seedling
 cell; if this was a comparative seed planted within its flesh or depulped
 by the researchers, sometimes, the ratID is "na" since no rat
 interacted with these seeds * treatment: can be either "mh"-
 seed mechanically handled by the researcher, "wf" - whole fruit,
 seed left in flesh, "rh" - seed handled and spat out by a rat;
 "gp" - seed passed by a rat and found in the scat * round: round
 of scat collection, sometimes, scats were collected again later in the day
 to assure we collected any possible gut-passed seeds * unique: unique
 identifier of a germination tray cell, for example 10-10-b would be tray
 #10, row #10, cell b of that row * datescatcoll: date scat was collected
 from a rat's cage. if this was a comparative seed planted within its
 flesh or depulped by the researchers, sometimes, this value is
 "na" since these seeds did not come from a scat collection *
 date.checked: date that a germination cell was checked to see if any seeds
 germinated * treatment.y: dummy column from merging datasets, real value
 is in column labeled "treatment" * germinants: number of
 seedlings sprouted in that cell at time of checking * native:
 characteristic of the seeds, where they from a native or non-native
 species of fruit? * seedsper: number of seeds that could be found in an
 individual fruit/diaspore of this species * seedsize: a categorical value
 for seeds, could be tiny/small/med/large * fleshiness: a categorical value
 for fruits, could be juicy/not * seedsperdiaspore: number used to
 calculate actual # of seeds per cell * planted: # seeds actually planted
 in that cell * prop: proportion germinated, should be equal to
 germinants/planted   4\. "pigs\_germcombo\.csv" is run with the
 \.Rmd file "piggermanalysis\_share\.Rmd" These are data from
 germination trials of the seeds described in the datasets above that were
 handled or gut passed by pigs, and then compared to seeds that were
 planted in these germination trials that were left in whole fruits or
 depulped by hand. Generalized mixed models (GLM's)are used to
 determined proportions then used in figures, created using ggplot. Column
 headings are as follows for "pigs\_germcombo.csv": * species:
 species of fruit/seed planted in this cell * datefruitcoll:date that fruit
 was collected from the wild * site: site that fruit was collected from the
 wild * treatment: can be either "mh"- seed mechanically handled
 by the researcher, "wf" - whole fruit, seed left in flesh,
 "ph" - seed handled and spat out by a pig,"gp" - seed
 passed by a pig and found in the scat * pigname: name of pig that handled
 or passed this seed; could be "na" if treatment was
 "wf" or "mh" * uniqueID: cell in a tray, combination
 of the next headings: trayID, rowID, cellID * round: round of scat
 collection after feeding * datescatcoll:date scat was collected from a
 pig's pen. if this was a comparative seed planted within its flesh or
 depulped by the researchers, could be "na" * dateplanted: date
 seed was planted * notes: notes * entered by/date entered/proofed by/date
 proofed:initials of researchers or assistants who entered/proofed data and
 what date that occurred * native: characteristic of the seeds, where they
 from a native or non-native species of fruit? * seedsper: number of seeds
 that could be found in an individual fruit/diaspore of this species *
 seedsize: a categorical value for seeds, could be tiny/small/med/large *
 fleshiness: a categorical value for fruits, could be juicy/not *
 seedsperdiaspore: number used to calculate actual # of seeds per cell *
 seedsplanted: # seeds actually planted in that cell * numgerm: # of
 seedlings that germinated   notgerm: # of seeds in that cell that did not
 germinate   An additional two information datasets are combined to give #
 of seeds and native/non-native status when running the four .Rmd files
 above: 1\. "spp\_info\_formerging\_rats\.csv" is called in
 "ratseedanalysis\_share\.Rmd" and
 "ratgermanalysis\_share\.Rmd" 2\.
 "spp\_info\_formergin\_pigs\.csv" is called in
 "pigseedanalysis\_share\.Rmd" and
 "piggermanalysis\_share\.Rmd" Both of these files have
 fruit/seed characteristics for each species - native or non-native?,
 seedsper - seedsper fruit, seedsize - tiny/small/medium/large, fleshiness
 - juicy/not, seedsperdiaspore - actual seeds per diaspore (ie. how many
 seedlings we could expect out of a "seed")   A separate dataset
 was used to create a final figure for this study, combining all steps
 above (feeding, germination trials) for pigs and rats:   1\.
 "combined\_props\.csv" is called in
 "combofigure\_share\.Rmd" to create a plot in
 ggplot\,summarizing the feeding\, seed fate\, and germination results laid
 out in the four analysis files \(\.Rmd\) above\. The column headings in
 "combined\_props.csv" are: Pig or rat - whether a pig or rat was
 involved in the interaction Species - species of fruit/seed Interacted -
 proportion of seeds of that species that either rats or pigs interacted
 with Ignored - proportion of seeds ignored Type - the type of interaction
 (handled/gut-passed/both or if they were all destroyed/all ignored) Imm
 seedfate - the proportion of seeds of that species that were fed to rats
 or pigs that fit into that category or "type" Destroyed - the
 proportion of seeds of that species that were destroyed by rats or pigs
 Fruit and seed - Interacted \* Imm seedfate Germ fail - proportion of
 seeds that were already either handled or passed that failed to germinate
 Germinated - proportion of seeds that were already either handled or
 passed that germinated Cumulative - Germinated \* Fruit and seed Native -
 was this species native or non-native? check - a check to see that
 proportions added up to 1 n - number of seeds tested   Sharing/Access
 information   All data is included here. Questions can be directed to
 anngawel@gmail.com.   \*   Data was derived from the following sources:  
 Data is original and collected by the authors of this study (corresponding
 author Ann Marie Gawel) from 2017-2019.   Code/Software   As described
 above, .Rmd files used with the corresponding datasets described above can
 be used to run all of our analyses for this study, and to create four
 figures (figures 2-5) found in this publication.