DOI: 10.5061/dryad.6t1g1jx29
title: Data for: Effects of habitat management on rodent diversity, abundance, and virus infection dynamics

description: As anthropogenic factors continue to degrade natural areas, habitat
 management is needed to restore and maintain biodiversity. However, the
 impacts of different habitat management regimes on ecosystems have largely
 focused on vegetation analyses, with limited evaluation of downstream
 effects on wildlife. We compared the effects of grassland management
 regimes (prescribed burning, cutting/haying, or no active management) on
 rodent communities and the viruses they hosted. Rodents were trapped in 13
 existing grassland sites in Northwest Arkansas, USA during 2020 and 2021.
 Rodent blood samples were screened for antibodies against three common
 rodent-borne virus groups: orthohantaviruses, arenaviruses, and
 orthopoxviruses. We captured 616 rodents across 5953 trap nights. Burned
 and unmanaged sites had similarly high abundance and diversity, but burned
 sites had a higher proportion of grassland species than unmanaged sites;
 cut sites had the highest proportion of grassland species but the lowest
 rodent abundance and diversity. A total of 38 rodents were seropositive
 for one of the three virus groups (34 orthohantavirus, three arenavirus,
 and one orthopoxvirus). Thirty-six seropositive individuals were found in
 burned sites, and two orthohantavirus-seropositive individuals were found
 in cut sites. Cotton rats and prairie voles, two grassland species,
 accounted for 97% of the rodents seropositive for orthohantavirus. Our
 study indicates that prescribed burns lead to a diverse and abundant
 community of grassland rodent species when compared to other management
 regimes; as keystone taxa, these results also have important implications
 for many other species in food webs. Higher prevalence of antibodies
 against rodent-borne viruses in burned prairies shows an unexpected
 consequence likely resulting from robust host population densities
 supported by the increased habitat quality of these sites. Ultimately,
 these results provide empirical evidence that can inform grassland
 restoration and ongoing management strategies.
description: <em>Study
 sites</em> Rodents were captured
 in grasslands throughout Benton and Washington Counties, Arkansas, USA.
 This area lies near the edge of the historical tallgrass prairie
 ecoregion, and like other tallgrass prairie ecosystems, most of the
 landscape has been altered by humans, with few remnant prairies remaining.
 Instead, many of the modern grasslands in this region are restored
 prairies or non-prairie grasslands. Trapping was conducted at 13 sites
 within six distinct grasslands (Figure 1). Neighboring sites within the
 same grassland were considered separate areas as they are distinctly
 managed and separated by physical barriers (i.e., roadway, riparian
 habitat, and/or firebreak). Although these barriers do not act as complete
 physical barriers, they limit rodent movement among sites and distinguish
 separately-managed parcels. Grasslands ranged in size from 6.7–32.6 ha,
 and distinct management sites within each grassland ranged in size from
 1.5–23.6 ha. Site management was classified as one of three regimes:
 prescribed burning, reminiscent of natural ecosystem functioning
 (designated burn; five sites); haying, mowing, or other means of
 mechanical cutting, which result in managed yet artificial landscapes
 (designated cut; six sites); or no active management of vegetation,
 leading to heavy woody encroachment (designated unmanaged; 2 sites; Figure
 1). Management regimes at the study sites have been continuous for several
 decades, and our results thus represent long-term effects of management
 regimes. <em>Rodent
 trapping and sampling</em> Rodent trapping was
 conducted once every two months at each site from June-November 2020 and
 April-July 2021. Because of the number of sites and distances between
 grasslands, sites were trapped in several groups over the course of the
 trapping month. To maintain consistency of time between trapping at each
 site, site groups were trapped in the same order each trapping month. For
 each trapping occasion, approximately 50 Sherman live traps (H. B. Sherman
 Traps, Inc.) were set for two consecutive nights approximately 10m apart
 in a series of transect lines (see Table 1 for deviations of trap
 numbers). Traps were baited with a mixture of millet and black oil
 sunflower seeds and set at dusk. Traps were checked and captured rodents
 were processed the following morning. Initially, all rodents were
 euthanized for tissue collection except for species classified as species
 of conservation need by Arkansas Game and Fish Commission
 (<em>Reithrodontomys humulis</em>,<em>
 megalotis</em>, and <em>montanus</em>). Due to permit
 limitations, we were unable to euthanize all individuals of abundant
 species (<em>Reithrodontomoys fulvescens</em> and
 <em>Sigmodon hispidus</em>) in fall
 2020. Captured rodents were
 identified to species level based on morphology (pelage and lengths of
 ear, tail, head/body, and hind foot; Sealander & Heidt, 1990; Reid
 2006). Visual inspection was used to determine sex and reproductive
 condition; males were considered to be reproductive if their testes were
 descended into the scrotum, and females were considered to be reproductive
 if their nipples were enlarged or lactating or if their vagina was
 perforate or plugged. Rodent blood samples were collected via either the
 submandibular vein directly into a microcentrifuge tube during processing
 and immediately placed on ice or a heart sample that was placed into
 phosphate-buffered saline (PBS) during dissection (see below; Forbes et
 al., 2014). To promote efficiency and minimize handling time and
 associated distress to wild rodents, most rodent species were quickly
 euthanized via cervical dislocation without anesthetic; cotton rats were
 the exception due to their larger size and were anesthetized with
 inhalation isoflurane prior to cervical dislocation. Euthanized rodents
 were placed in individual labeled grip-lock bags and stored in a cooler
 with ice while in the field. Rodents that were not euthanized were
 ear-tagged and released at their point of capture following sample and
 data collection. Euthanized rodents
 were stored in a -20°C freezer and later dissected under a biosafety hood.
 Tissue samples were collected aseptically using clean forceps and scissors
 and placed in sterilized microcentrifuge tubes. Hearts were placed in PBS
 solution to permit serology assays. All samples and specimens were stored
 at -20°C. All animal handling
 and sampling procedures were approved by the University of Arkansas
 Institutional Animal Care and Use Committee (IACUC) protocol number 20028
 and Arkansas Game and Fish Commission permit numbers 102820194 and
 030820211. Additionally, sampling at Chesney Prairie Natural Area was also
 approved by Arkansas Natural Heritage Commission permit numbers
 S-NHCC-19-025 and S-NHCC-21-007. <em>Assays to
 detect antibodies against rodent viruses</em>
 Blood samples
 were tested for antibodies reactive to orthohantaviruses, arenaviruses,
 and orthopoxviruses using immunofluorescence assays (IFAs), as previously
 described (Kallio-Kokko et al., 2006; Kinnunen et al., 2011; Forbes et
 al., 2014). Briefly, samples were diluted in PBS and then incubated on
 slides with viral antigens followed by several wash cycles to remove
 unbound antibodies. Fluorescent polyclonal rabbit anti-mouse FITC
 conjugate was then added to the slides, which were again incubated and
 washed. Slides were examined under a fluorescence microscope for reactive
 antibodies. These serology assays are cross-reactive within broad virus
 groups and therefore are effective and efficient approaches for
 non-specific screening (e.g., Ogola et al., 2021). 
 <em>Data
 analyses</em> All analyses were
 conducted in R 4.1.0 (R Core Team 2021). We used a chi-square test of
 independence to compare trapping success among management types. Renyi
 diversity profiles were used to compare several indices of rodent
 diversity among management regimes (Tóthmérész 1995; Kindt 2020).
 Additionally, an analysis of similarity (ANOSIM) test was used to
 determine if rodent community composition varied among management regimes
 using the Bray-Curtis dissimilarity index (Herlemann et al., 2016; Zorz
 2019). Because rodents with
 antibodies against the focus virus groups were only detected in sites that
 were burned or cut, a chi-square test of independence was used to test for
 differences in total seroprevalence of all three viruses among habitat
 management regimes. Binomial generalized linear mixed models (GLMMs) with
 seropositivity as the response variable were then used to compare
 seroprevalence between burned and cut sites, with grassland and site
 identity as a nested random effect. Demographic data, including sex,
 reproductive status, abundance index (capture success), and their
 interactions were set as explanatory variables in the GLMMs. Because most
 seropositive cases were from rodents with antibodies against
 orthohantaviruses, we also used GLMMs to compare orthohantavirus
 seroprevalence alone among burned and cut sites. Two separate binomial
 GLMMs were used to analyze orthohantavirus seroprevalence from all sites
 within cotton rats and prairie voles (<em>M.
 ochrogaster</em>), as these two species accounted for the majority
 of seropositive rodents but have different life histories, including
 seasonal dynamics and mass (Brady and Slade, 2001). Large, reproductive
 male rodents are often disproportionately seropositive for
 orthohantaviruses (Douglass, 2007; Polop et al., 2010), so explanatory
 variables for species-level GLMMs included mass, sex, reproductive status,
 abundance index, and their interactions. Finally, a Poisson GLMM, again
 using seropositivity as the response variable, was used to compare
 seroprevalence by trap success at each site and trapping occasion, with
 trapping occasion as a random effect and grassland and site identity as a
 nested random effect. GLMMs were conducted using the
 <em>lme4</em> package (Bates et al., 2022); all other
 statistical analyses were conducted using base R (R Core Team,
 2021). It is worth noting
 that although sites were grouped according to management regime, some
 differences in management schedules, site history, and biogeochemical
 factors were unavoidable and created heterogeneity within group
 categories. In particular, three of the five burned sites were burned
 every three years and the other two were burned annually. These
 differences were unavoidable due to the study design, akin to a natural
 experiment. However, potential differences due to site heterogeneity
 within management categories were assessed to validate groupings; no
 differences in rodent abundance, rodent diversity, or seroprevalence were
 detected between burn frequencies (Appendix 1). Despite several replicates
 of burned and cut sites, only two unmanaged sites were available in this
 study, as these habitats change drastically with the onset of management
 and are prone to ecological succession in the prolonged absence of
 management.