DOI: 10.5061/dryad.nvx0k6f0t
title: Resource availability alters breeding strategies in a small mammal community

description: Following a resource pulse, animals may finance reproduction by consuming
 concurrently available resources (income breeding) or by storing resources
 for future reproduction (capital breeding). Understanding how these
 reproductive strategies are used is important for determining the
 ecological mechanisms that structure the timing of reproduction and that
 drive interannual population fluctuations in animals. We gathered a
 reproductive dataset for five small mammal species over a 12-year period
 in Northeastern USA during which six masting events of American beech
 (Fagus grandifolia) and eastern hemlock (Tsuga canadensis) occurred.
 Masting created alternate years where seeds were either available late
 (masting year) or early (cached from the previous year) in the breeding
 season. The small mammal species differed in reliance on seeds and
 overwintering strategies. We quantified the diet using stable isotopes and
 recorded reproduction timing, proportion breeding, and litter size in
 females and testes size in males. Timing of seed availability minimally
 affected litter size but strongly affected proportion breeding and timing
 of reproduction. During masting years (late seed availability), a higher
 proportion of females reproduced, with breeding taking place later in the
 season (lactation timed with peak seed availability), although the delay
 was restricted in Napaeozapus insignis, an obligate hibernator.
 After a fall mast, cached seeds were used as capital in the following
 spring (early seed availability) to support a litter that, depending on
 the species, occurred 24 to 79 days sooner than a mast year. No
 late-season reproduction occurred in years with early seed availability
 except for Myodes gapperi which produced a second litter, likely financed
 by fungal consumption. Males also showed strong responses to seed
 availability, mirroring female reproduction with testes size staying
 constant in years with late seed availability and sharply decreasing over
 the breeding season in years with early seed availability. Our results
 highlight that although photoperiod and temperature broadly set the bounds
 of the breeding season in temperate environments, resource availability
 influences the reproductive strategies that species use, which in turn
 alters reproductive timing and can drive large inter-annual population
 fluctuations. Differences in overwintering strategies and diet may further
 modulate reproductive timing and output relative to resource pulses.
description: # Resource availability alters breeding strategies in a small mammal
 community
 [https://doi.org/10.5061/dryad.nvx0k6f0t](https://doi.org/10.5061/dryad.nvx0k6f0t) ## **List of Data Files** Beech_Hemlock_Bartlett_m2.csv Food_All.csv Isotope_2013_2015.csv Isotope_2014_2015.csv Mixing_model_output.csv Small_mammal_data_Final.csv ## **List of R Scripts** Figure_1_Seed_fall.R Mixing_Model_Scripts.R Figure_2_niche_diet_season.R Figure_3_EMB_Pscars.R Figure_4_Probability_reproduction.R Figure_5_Proportion_breeding.R Figure_6_lact_Timing.R ## **Descriptions of Data Files and R Code** ##### **Beech\_Hemlock\_Bartlett\_m2.csv** American beech and eastern hemlock seedfall was measured from seed baskets at Bartlett Experimental Forest. Column headers are as follows. * **Grid:** Sampling grid that seeds were collected on (1 - 12). * **Station:** Station that seeds were collected on (ranges between 1 – 64). * **Month:** Month that seeds were collected. * **Day:** Day that seeds were collected. * **Year:** Year that seeds were collected. * **Season:** The season that seeds were collected (Spring, Summer, Fall). * **Tree_Species:** The tree species that seeds came from (American beech, Eastern hemlock). Only viable beech seeds (Beech_V) were included. * **Seeds_m2:** Seeds per square meter. This was calculated from seeds collected from a 0.24 m^2 area. ##### **Food\_All.csv** Potential food items available to small mammals at Bartlett Experimental Forest. Column headers are as follows. * **Type:** Food source name (AM fungi, Arthropods, Beech, Berries, EM fungi, Hemlock, Red maple). * **d13C:** The δ13C value of the sample. * **d15N:** The δ15N value of the sample. * **Concd15N:** Proportion of the sample composed of nitrogen. * **Concd13C:** Proportion of the sample composed of carbon. * **Forest_Type:** Forest type of the grid (hardwood, mixed, softwood). ##### **Isotope\_2013\_2015.csv** Isotopic values from small mammal hair samples collected from Bartlett Experimental Forest. This is a larger data set collected from 2013 – 2014, of which isotopic values were drawn to create ‘Isotope_2014_2015.csv’ to assess niches and diets. Blank rows are filled with NA. Column headers are as follows. * **ID:** Unique ID for each hair sample. * **Weight:** Mass of the hair sample in mg. * **X15N:** The δ15N value of the sample. * **X13C:** The δ13C value of the sample. * **C.:** Proportion of the sample composed of carbon.  * **N.:** Proportion of the sample composed of nitrogen. * **C.N:** The C:N ratio of the sample. * **Grid:** Sampling grid that the animal was captured on (1 – 12; additionally, a few samples of *Blarina brevicauda* were included from USFS sites 41, 42, 45). * **Forest_Type:** Forest type of the grid (Hardwood, Mixed, Softwood). * **Year:** Year animal was captured. * **Month:** Month animal was captured. * **Day:** Day animal was captured. * **Station:** Station that animal was captured on (1 – 64). * **Species:** Species abbreviation codes that include the first two letters of the genus and species (BLBR = *Blarina brevicauda*; GLVO = *Glaucomys volans*; MYGA = *Myodes gapperi*; NAIN = *Napaeozapus insignis*; PELE = *Peromyscus leucopus*; PEMA = *Peromyscus maniculatus*, SOCI = *Sorex cinereus*; SOFU = *Sorex fumeus*; TAST = *Tamias striatus*). * **Tag:** Unique tag number for the animal. * **W:** Mass of the animal in grams. * **Sex:** Sex of the animal (F = female, M = male). * **Age:** Age of the animal (A = adult, SA = sub-adult, J = juvenile). ##### **Isotope\_2014\_2015.csv** Isotopic values from small mammal hair samples collected from Bartlett Experimental Forest used to assess niches and diets. Blank rows are filled with NA. Column headers are as follows. * **ID:** Unique ID for each hair sample. * **Weight:** Mass of the hair sample in mg. * **X15N:** The δ15N value of the sample. * **X13C:** The δ13C value of the sample. * **C.:** Proportion of the sample composed of carbon. * **N.:** Proportion of the sample composed of nitrogen. * **C.N:** The C:N ratio of the sample.  * **Grid:** Sampling grid that the animal was captured on (1 – 12; Additionally, a few samples of *Blarina brevicauda* were included from USFS sites 41, 42, 45). * **Forest_Type:** Forest type of the grid (Hardwood, Mixed, Softwood). * **Year:** Year animal was captured. * **Month:** Month animal was captured. * **Day:** Day animal was captured. * **Station:** Station that animal was captured on (1 – 64). * **Species:** Species abbreviation codes that include the first two letters of the genus and species (BLBR = *Blarina brevicauda*; MYGA = *Myodes gapperi*; NAIN = *Napaeozapus insignis*; PELE = *Peromyscus leucopus*; PEMA = *Peromyscus maniculatus*). * **Tag:** Unique tag number for the animal. * **W:** Mass of the animal in grams. * **Sex:** Sex of the animal (F = female, M = male). * **Age:** Age of the animal (A = adult, SA = sub-adult, J = juvenile). * **Date:** Date that the hair sample was collected.    * **DOY:** Day of the year that the hair sample was collected.  * **CommonDate:** Standardized date used for graphing (i.e., year is stripped off). * **Season:** Season that the hair was grown (note that this may differ from the time that it was collected).     * **Year_molt:** Year that the hair was grown (note that this may differ from the time that it was collected). * **Seed_Avail:** Timing of seed availability within a year relative to reproduction. ##### **Mixing\_model\_output.csv** Mixing model output for diet contribution of food sources for each small mammal species for the summer and fall of 2014 and 2015. Column headers are as follows. * **Number:** Model iteration number. * **Source:** Food source including AM_fungi = arbuscular mycorrhizal fungi (*Glomus* spp.); Arthropods = beetles (Coleoptera), grasshoppers (Orthoptera), and spiders (Araneae); Beech = American beech seeds (*Fagus grandifolia*); Beech_hemlock = combined posterior of beech and hemlock; Berries (hobblebush [*Viburnum lantanoides*] and partridge berries [*Mitchella repens*]); ECM_fungi = ectomycorrhizal (EM) fungal sporocarps (*Elaphomyces *and *Hydnotrya* spp.); Fungi = total fungal contribution that combines posterior of AM and ECM fungi; Hemlock = eastern hemlock seeds (*Tsuga canadensis*); Red_Maple = red maple seeds (*Acer rubrum*). * **Value:** Posterior value of food source contribution. * **Season:** Season of the diet (Summer or fall) * **Year:** Year of the diet. * **Seed_avail:** Timing of seed availability within a year relative to reproduction. * **Species:** Species abbreviation codes that include the first two letters of the genus and species (BLBR = *Blarina brevicauda*; MYGA = *Myodes gapperi*; NAIN = *Napaeozapus insignis*; PELE = *Peromyscus leucopus*; PEMA = *Peromyscus maniculatus*). ##### **Small\_mammal\_data\_Final.csv** Small mammals collected from Bartlett Experimental Forest and prepared as museum specimens. Blank rows are filled with NA. Column headers are as follows. * **Code:** Sampling location where the specimen was collected.     * **Preparator:** Name of the person who measured and prepared the specimen.          * **Initials:** Initials of the person who measured and prepared the specimen.    * **Field_num:** The field number of the person who measured and prepared the specimen.           * **Month_prep:** Month the specimen was prepared.    * **Day_prep:** Day the specimen was prepared. * **Year_prep:** Year the specimen was prepared.          * **Month_coll:** Month the specimen was collected.    * **Day_coll:** Day the specimen was collected.  * **Year_coll:** Year the specimen was collected.            * **Skin:** ‘x’ if the specimen was prepared as a skin.      * **Skeleton:** ‘x’ if the specimen was prepared as a skeleton.    * **Skull:** ‘x’ if the specimen was prepared as a skull.   * **Tissues:** ‘x’ if the specimen has a tissue sample.        * **Hair:** ‘x’ if the specimen had a hair sample taken (these were retained at UNH).   * **Fluid:** ‘x’ if the specimen was preserved in 70% ethanol. * **Species:** Species of the specimen.      * **Sex:** Sex of the specimen (m = male, f = female).     * **Testes_mm:** testes length in mm.      * **No_embryo:** ‘x’ if the specimen was a female and had no embryos. * **Lactating:** ‘x’ if the specimen was lactating. * **EMB_R:** Number of embryos on the right uterine horn.       * **EMB_L:** Number of embryos on the left uterine horn.          * **CR_mm:** Crown to rump length in mm of the embryos.       * **P_Scar_R:** Number of placental scars on the right uterine horn.      * **P_Scar_L:** Number of placental scars on the left uterine horn.         * **TL:** Total length of the specimen in mm.      * **T:** Tail length of the specimen in mm.           * **HF:** Hind food length of the specimen in mm.          * **E:** Ear length of the specimen in mm.            * **W:** Body mass of the specimen in grams.      * **Museum:** Museum that the specimen was deposited in. Note that at the time of submission, not all the specimens had been sent to a museum. Additionally, specimens prepared as skull preps were retained at UNH.            * **Catalog_num:** Museum catalog number. * **Latitude:** Latitude of the location where the specimen was collected.         * **Longitude:** Longitude of the location where the specimen was collected. * **Trap:** Trap type used to collect the specimen.           * **Collector:** Collector of the specimen.            * **Notes:** Notes related to the specimen.            * **Accession:** Museum accession number if available.  * **NK.Number:** Pre-catalog number used by the Museum of Southwestern Biology. * **Seed_avail:** Timing of seed availability within a year relative to reproduction. * **EMB:** Total number of embryos that a specimen had.          * **Pscars:** The total number of placental scars that a specimen had. * **Date:** Date that a specimen was collected.    * **DOY:** Day of the year that a specimen was collected.          * **CommonDate:** Standardized date used for graphing (i.e., year is stripped off). ##### **Figure\_1\_Seed\_fall.R** Code to produce Figure 1 which uses seed fall data from Bartlett Experimental Forest (Beech_Hemlock_Bartlett_m2.csv) and Hubbard Brook Experimental Forest (data available from authors of Cleavitt and Fahey 2017, Canadian Journal of Forest Research upon request). ##### **Mixing\_Model\_Scripts.R** Code to run Bayesian mixing models for five small mammal species at Bartlett Experimental Forest. This script uses isotopic values from potential food items (Food_All.csv) and hair from live-trapped small mammals at Bartlett Experimental Forest (Isotope_2014_2015.csv) to determine the proportions of food items in the diet of small mammals depending on seed availability. ##### **Figure\_2\_niche\_diet\_season.R** Code to produce Figure 2 which visually shows isotopic niches of small mammals in the summer and fall of 2014 and 2015. The script uses isotopic data from hair samples (Isotope_2014_2015.csv) to show bivariate plots representing niches and mixing model output (Mixing_model_output.csv) to visually show the predicted contributions of different food sources. ##### **Figure\_3\_EMB\_Pscars.R** Code to produce Figure 3 which uses embryo and placental scar counts from small mammals collected at Bartlett Experimental Forest (Small_mammal_data_Final.csv) to assess how seed availability influences litter size. #####  **Figure\_4\_Probability\_reproduction.R** Code to produce Figure 4 which uses generalized linear mixed effects models to assess the probability of reproduction of females and linear mixed effects models to assess testes size in males relative to early and late seed availability. Data come from ‘Small_mammal_data_Final.csv’. ##### **Figure\_5\_Proportion\_breeding.R** Code that uses reproductive data from female small mammals collected at Bartlett Experimental Forest (Small_mammal_data_Final.csv) to assess how seed availability influences the proportion of individuals breeding in the population in years with early and late seed availability. ##### **Figure\_6\_lact\_Timing.R** Code to produce Figure 6 which uses female small mammals collected at Bartlett Experimental Forest (Small_mammal_data_Final.csv) to assess how seed availability influences the timing of reproduction.