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. 2022 Dec 6;17(12):e0278608. doi: 10.1371/journal.pone.0278608

Native annual forbs decline in California coastal prairies over 15 years despite grazing

Josephine C Lesage 1,2, Grey F Hayes 3, Karen D Holl 1,*
Editor: Mehdi Heydari4
PMCID: PMC9725146  PMID: 36472993

Abstract

Livestock grazing is often used as a land management tool to maximize vegetation diversity in grassland ecosystems worldwide. Prior research has shown that cattle grazing benefits native annual forb species in California’s coastal prairies, but drought and increasing aridity may alter this relationship. In 2016 and 2017, we resurveyed the vegetation structure, native annual forb cover, and native annual forb richness in ten grazed and ungrazed prairies that were originally measured in 2000 and 2001 along a 200-km gradient from Monterey to Sonoma counties in California. We found that grazed prairies continued to have significantly lower vegetation height and thatch depth than ungrazed prairies, and that shrub encroachment over the 15-year period was significantly greater in ungrazed prairies. Furthermore, grazed prairies continued to have greater native annual forb richness (4.9 species per site) than ungrazed sites (3.0 species per site), but native annual forb richness declined by 2.8 species per site in grazed prairies and 0.1 species per site in ungrazed prairies between survey periods. We suggest that severe drought and increasing aridity may be driving declines in native annual forb richness in grazed prairies. The species we recorded only in earlier surveys were disproportionately wetland-associated and had higher average specific leaf area than species that remained through the second survey period. Finally, the cover of native annual species increased regardless of whether prairies were grazed, suggesting that the high precipitation in 2017 may have benefitted the native annual forb species that persisted at sites between surveys. Our study shows that weather conditions affect the outcomes of land management strategies.

Introduction

Most of the Earth’s grassland biomes evolved with large ungulate grazing [1], but humans have substantially altered grazing regimes by introducing domesticated ungulate grazers and managing grazing systems across more than a quarter of global land surface [2]. Inappropriate grazing regimes can result in widespread ecosystem degradation and diversity loss, especially in arid and semi-arid environments [35]. Well-managed livestock grazing, however, can benefit native vegetation diversity and cover in grass-dominated ecosystems [69]. At moderate stocking rates in mesic grasslands, large mammal grazing increases the floral diversity of South American steppe [10], Mediterranean-climate grasslands [9, 11], midwestern United States tallgrass prairies [12], and northern European semi-natural grasslands [13]. Furthermore, livestock grazing often reduces the spread of woody shrubs and trees into grasslands, precluding successional conversion to shrubland or forest in the absence of disturbance [1417], also known as shrub or forest encroachment. However, overgrazing in shrubland ecosystems can facilitate woody encroachment, highlighting the importance of considering the ecosystem type and grazing regime in evaluating the ecological impacts of grazing [2].

In Mediterranean climates, grazing generally benefits short-statured species [1820], though the strength and direction of this effect can vary depending on annual precipitation [2123]. In systems like California coastal prairies, where non-native vegetation grows quickly and can limit native species germination and growth, grazing in grasslands has been promoted as a conservation strategy to enhance the diversity of native species [18, 24, 25], as it serves to reduce shrub encroachment and both cover and litter (thatch) of fast-growing, tall-statured exotic annual grasses.

We focus on California’s coastal prairies, a highly diverse grassland type. These grasslands are present from Santa Barbara county into Oregon, where winter precipitation is relatively high and coastal fog alleviates summer drought [26]. Among North American grassland ecosystems, coastal prairies are exceptional for their high native species richness and they have higher native species cover than most other grassland types in California [27]. Native annual forbs represent between 25–60% of the recorded species in California’s coastal prairies, although they often do not contribute greatly to vegetation cover [18, 2628].

In 2000 and 2001, Hayes and Holl (18) found strong evidence that moderate levels of cattle grazing favored small-statured native annual forbs in California coastal prairies. In 2016 and 2017, we sought to answer whether such grazing continues to benefit native annual forbs in California’s coastal prairies, particularly given the extreme drought and temperature conditions in the years preceding the study. California is already experiencing, 1) progressively more ‘extreme’ precipitation, wherein rainfall events occur less frequently, but in larger magnitudes; 2) increasing ‘whiplash’ weather, when exceptionally dry and wet periods follow one another with minimal change in net precipitation; and 3) rising temperatures [2931]. Over the last few decades, California grasslands have experienced increasing temperatures and aridity [32] and a 1-in-1200-year drought from 2012–2014 [33]. Both these climatic anomalies have impacted the species composition of California grasslands, leading to declines of some drought-sensitive species, particularly native annual forbs [34, 35].

We hypothesized that native annual forb richness and cover had declined in these grasslands since 2001 due to the recent severe drought and overall increasing aridity, but that declines in richness and cover would be less severe in grazed grasslands. To evaluate whether potential declines were related to changes in weather and/or changes in the surrounding vegetation structure, we analyzed climate-relevant traits of the native annual forb species in our sites and changes in vegetation structure over time. We compared the wetland indicator status of species that were recorded in the earlier but not later surveys, which should reflect whether those species were more adapted to mesic environments. We also examined species’ specific leaf area (SLA), which is often associated with drought tolerance [3537]. We hypothesized that the native annual forb species missing in the later survey would largely be adapted to moister conditions.

Materials and methods

Site descriptions

In 2000 and 2001, we surveyed 26 paired grazed and ungrazed coastal prairie sites across 400 km of coastline between San Luis Obispo and Mendocino counties in California, USA [18]. In 2016 and 2017, we resampled sites along 200 km of coastline, in the central area of the prior survey extent (Monterey to Sonoma Counties) where we could obtain permission from landowners for access and grazing patterns had been maintained since 2000–2001 (Fig 1; S1 Table). All analyses presented in this paper include only data from these ten sites, which are a subset of the original 26 sites. For simplicity, we refer to the 2000–2001 sampling period as Time 1 (T1) and the 2016–2017 sampling period at Time 2 (T2). Thus, each sampling period represents two subsequent years of sampling, and all but two sites were sampled four times (S1 Table).

Fig 1. Locations of sites sampled.

Fig 1

For site details see S1 Table. Data for state perimeters are from the US Department of Commerce, Census Bureau.

At all sites paired plots are >2 km apart; are on similar slopes and aspects; and range from 1–20 ha and from 20–350 m in elevation. All sites have 1970–2000 30-year temperature and precipitation means within 1.3°C and 544 mm of one another based on interpolated climate data [S1 Table; 38]. There was no evidence of prior mechanical soil disturbance, and soils were deeper than 40 cm and not ultramafic (serpentine).

We compiled available grazing regime information from landowners and agency reports, but in many cases, specific data on the intensity and timing of grazing for our sites were not available. Cattle were the only domestic grazing animals at our sites. The typical grazing regime in the region is at 1 cow-calf pair per 2–4 ha with grazing occurring year-round at most sites by beef or dairying operations. Based on our conversations with landowners, grazing pressure at the second sampling period (T2) was maintained at or slightly below T1 levels. The only wild ungulate at these sites is the Colombian black tailed mule deer (Odocoileus hemionus columbianus); we did not find evidence of grazing by this species, but access is not restricted at our sites. Deer primarily eat broadleaved plants and cattle primarily graminoids [39]. Moreover, a recent study suggests that wild ungulate grazing in California has minor impacts on plant communities relative to cattle grazing [40].

Climate and weather data

California’s Mediterranean ecosystems have high interannual variability in rainfall quantity and timing, though all precipitation generally falls between October and April and rainfall between May and September is rare. We gathered all precipitation and temperature information available from weather stations in Santa Cruz, Monterey, San Francisco, and Marin counties from NOAA’s Climate Data Online archive (https://www.ncdc.noaa.gov/cdo-web/). Precipitation in the 2000 water year (1 October 1999 to 30 September 2000) was near the 100-year average (449 to 1328 mm) and in 2001 was below average (416 to 912 mm) at our study sites. Precipitation was close to average in the 2016 water year (511 to 1085 mm) and substantially greater than average in 2017 (673 to 1958 mm). Growing season precipitation (November-April) followed similar trends, and temperatures were similar in both sets of sampling years (Fig 2). However, the second set of sampling years occurred immediately after an exceptional 1-in-1200-year drought [33, 41], which was accompanied by above-average temperatures (Fig 2).

Fig 2. Mean annual temperature (points) and precipitation (bars) for meteorological stations in the sampling region (including Monterey, Santa Cruz, San Francisco, and Marin counties).

Fig 2

The red dotted line shows the average temperature for the region over this period and the blue dashed line shows mean annual precipitation. Error bars indicate ±1 SE. The sampling years are shaded.

Vegetation structure and native annual forbs

Data collection replicated methods used by Hayes and Holl (2003). We sampled from April through May, traveling from southern sites to northern sites to follow the peak flowering phenology of most species. At each site, we relocated 50-m line transects from the first (T1) sampling period using a Garmin eTrex 20 GPS. There were five transects each in the grazed and ungrazed portions at each site. Transects within sites were separated by 15 m to 1 km and placed at least 5 m from fence lines to avoid edge effects.

We quantified community composition by recording the identity of each species that intersected a 1.8-mm-diameter pin at 1-m intervals. We recorded each species that intercepted the pin once. Our nomenclature and species origin information follow the Jepson Manual and online Jepson eFlora database [42]. We measured vegetation height at 5-m intervals using a piece of paper dropped onto foliage and recording the lowest point. We quantified thatch depth (i.e., build-up of dead plant biomass) by pushing a 1.8-mm pin to the soil surface and measuring the tallest standing dead biomass. We calculated shrub cover as the number of woody shrub pin intercepts as a percent of the 50 intercepts total along the transect. Finally, we carefully searched for and measured the aerial cover (to the nearest cm2) of all native annual forbs present within a 1-m belt transect centered over the 50-m transect.

We compiled specific leaf area (SLA, leaf area/leaf dry mass) for 43 of the 56 native annual forbs species from the TRY Plant Trait Database and data collected by others [35, 43, 44]. We also collected data from species present in and near our sites during spring and summer 2018. Most of these data came from grazed plots, since this is where the species were more prevalent, though we selected individuals that showed no evidence of recent grazing. When data for a single species were available from multiple sources, we averaged the values. High SLA is associated with drought-intolerance and low water use efficiency [45, 46]. We used the United States Army Corps of Engineers National Wetland Plant List to determine the wetland indicator status of all native annual forbs found in our sites [47].

Data analysis

We conducted all data analyses in R version 4.1.2 [48]. To model the effects of time and grazing treatment on vegetation structure (i.e., vegetation height, thatch depth, and shrub cover) and native annual forbs (i.e., richness and cover), we used generalized linear mixed models in the glmmTMB package [49]. We treated sampling period and grazing treatment (both categorical with two levels) as fixed effects and treated year and transect as nested within-site random factors. We fit vegetation and thatch height with normal distributions, shrub cover using a beta distribution, and native richness using a Poisson distribution. Cover data were fit using a Tweedie distribution [50] because our data were overdispersed and zero-inflated. Model fit was checked using the DHARMa package to plot residuals against fitted values [51]. We summarized the SLA of native annual forb species for the sampling period when they were found (i.e.: lost, observed in only T1; still present, observed in both T1 and T2; and new, observed in only T2) and compared the values using one-way ANOVA.

Results

Vegetation height was greater in both ungrazed and grazed prairies in the second sampling period than in the first, and, as expected, vegetation was consistently shorter in grazed than ungrazed prairies across both periods (Fig 3A; Table 1). Grazed prairies had lower thatch depth than ungrazed prairies across all sampling years, and thatch depth did not change significantly over time (Fig 3B; Table 1). Shrub cover increased significantly more in ungrazed prairies than in grazed prairies between the two sampling periods (Fig 3C; Table 1). More than 95% of total shrub cover was comprised of three native species Baccharis pilularis (66.4%), Rubus ursinus (26.5%), and Toxicodendron diversilobum (2.8%).

Fig 3. Vegetation height, thatch depth, and shrub cover over time in grazed and ungrazed prairies.

Fig 3

Values represent means for n = 10 sites and error bar indicate 1 SE.

Table 1. Generalized linear model results for changes in vegetation factors across treatments and over time.

Model Parameter Estimate Std. Error z-value p-value
Vegetation height Intercept 25.87 2.44 10.60 <0.001
Sampling Period 10.43 1.93 5.42 <0.001
Treatment -11.24 1.56 -7.21 <0.001
Sampling Period × Treatment -3.47 1.96 -1.77 0.077
Thatch depth Intercept 4.84 0.72 6.76 <0.001
Sampling Period 0.49 0.34 1.44 0.151
Treatment -3.31 0.46 -7.24 <0.001
Sampling Period × Treatment -0.17 0.44 -0.38 0.707
Shrub cover Intercept -3.03 0.45 -6.79 <0.001
Sampling Period 1.24 0.22 5.52 <0.001
Treatment -1.14 0.27 -4.18 <0.001
Sampling Period × Treatment -0.85 0.34 -2.47 0.014

We recorded a total of 56 annual forb species in grazed and ungrazed prairies during the four survey years (S2 Table). The mean richness of native annual forbs declined between T1 and T2 by 2.8 species in grazed prairies and 0.1 species in ungrazed prairies, resulting in a significant interactive effect of time and grazing treatment on the richness of native annual forbs (Fig 4A; Table 2). Native annual forb richness remained higher in grazed than ungrazed sites in T2, but the difference was much smaller than in T1. Native annual forb cover was greater in grazed than in ungrazed prairies during T1 (Fig 4B; Table 2). During T2, mean native annual forb cover in grazed sites was more than twice as high in 2017 as compared to 2016, but was similar in both years in ungrazed sites.

Fig 4. Richness and cover of native annual forbs in grazed and ungrazed prairies in four survey years (n = 9 in 2000, 2016, n = 10 in 2001, 2017).

Fig 4

Error bars indicate 1 SE.

Table 2. Fitted models for the effects of grazing and year on native annual forb richness and cover.

Model Parameter Estimate Std. Error z-value p-value
Native annual forb richness Intercept -1.10 0.37 -3.01 0.003
Sampling Period -0.02 0.14 -0.14 0.892
Treatment 1.09 0.16 7.01 <0.001
Sampling Period × Treatment -0.39 0.16 -2.40 0.017
Native annual forb cover Intercept -0.41 0.50 -0.82 0.411
Sampling Period 1.16 0.41 2.83 0.005
Treatment 1.60 0.45 3.57 <0.001
Sampling Period × Treatment -0.73 0.48 -1.51 0.132

The average SLA of species observed only in T1 (342.7 ± 43.0 mm2 g-1) was greater than those found in both (227.3 ± 18.0 mm2 g-1) periods or only in T2 (168.9 ± 17.0 mm2 g-1; n = 43 species, F = 3.3, p = 0.020). Most species observed in both sampling periods are classified as upland or facultative upland species (Fig 5). The proportion of species classified as ‘obligate wetland’, ‘facultative wetland’, or ‘facultative’ by the US Army Corps of Engineers declined from T1 (30%) to T2 (23%) and the proportion of facultative upland and upland species increased (Fig 5).

Fig 5. Wetland indicator status of native annual forbs observed in T1 (2000–2001) and in T2 (2016–2017).

Fig 5

Discussion

Grassland structure

The effects of grazing on vegetation structure (i.e., height, cover) were similar over time. In both sampling periods, grazed prairies had shorter standing living canopies and reduced thatch, as expected. The vegetation was significantly taller in both grazed and ungrazed plots in the second than in the first sampling period (T1:19.5 cm; T2: 29.0 cm, Table 1), though the net difference in vegetation height between grazed and ungrazed plots was consistent over time (T1: Δ11.2 cm; T2: Δ14.6). Mean vegetation height in grazed prairies during the second sampling period approached but did not quite reach the T1 height of ungrazed prairies (Fig 3). The greater vegetation height in T2 could be attributed either to more precipitation in T2 than T1 (Fig 2) or lower grazing pressure. Although we cannot conclusively distinguish between these two hypotheses, the fact that vegetation height was similar in both years of each sampling period, despite interannual differences in precipitation, suggests that grazing pressure was lower during T2. This trend towards reduced grazing intensity concurred with anecdotal information from landowners.

Our resurvey supports the use of cattle grazing to reduce the rate of shrub encroachment into California coastal prairies. Many native coastal prairie species are adapted to disturbance regimes that prevent shrub encroachment, having evolved under grazing by Pleistocene megafauna [52] and later, frequent burning by Native peoples [53]. Shrub cover increased substantially more in ungrazed than grazed prairies over a 15-year period. The most common shrub species are mostly native, and their rate of spread is similar to those described from other coastal California sites [25, 54].

Native forb richness and cover

Native annual forb species richness and cover continued to be greater in grazed than ungrazed prairies in the second sampling period, although the richness of grazed prairies had declined substantially over time. Our results are consistent with past research showing that shorter vegetation and higher levels of light at the soil surface increase native annual forb germination and growth when competition with exotic annual grasses is high [55, 56]. Reducing the canopy height and dominance of exotic annual grasses through grazing is a common grassland management technique, as exotic species often have faster growth rates and are competitively dominant to many native species in their early stages, reducing native species establishment [5760]. Furthermore, the reduction of thatch by grazing can substantially enhance recruitment of native grassland species [61, 62].

The significant decline in the richness of native annual species we measured in grazed prairies complicates the interpretation of prior work showing a beneficial effect of grazing on native annual forbs in California [18, 19] and other Mediterranean grasslands [6365]. Native annual forb species richness declined significantly more in grazed than ungrazed prairies. This is likely because ungrazed prairies had much lower richness at the first sampling period, comprised of those species best able to compete with tall-statured exotic grasses; consequently, there were fewer species that could disappear during the 15 years between sampling periods. We cannot directly attribute the decline in native annual forb richness to changes in grazing regime or climate, but we use circumstantial evidence to explore the relative importance of these factors.

The significantly taller vegetation height in the second sampling period may explain part of the decline in native annual forb richness, given that many of the native annual forbs in California are low-stature species that benefit from greater light availability afforded by a shorter canopy [18, 19, 60]. However, vegetation height increased in both grazed and ungrazed plots, whereas native annual forb richness only declined in grazed sites. Thatch depth did not differ in grazed plots between the sampling periods and therefore likely did not cause the declines. There was significant treatment × sampling period interaction, as shrub cover increased substantially between sampling periods in ungrazed plots (~7 to 29%), but not in grazed plots (from ~1 to 4%). Thus, it seems unlikely that the primary cause for decline in native annual forb richness in grazed plots was local changes in vegetation structure.

Multiple lines of evidence support the hypothesis that climate and weather factors prior to the second survey led to the decline in native annual forb richness, though we note that we did not conduct manipulative experiments to directly link specific climate variables and species composition. California experienced a severe, 1-in-1200 year drought [33] between our sampling periods and the years immediately preceding our second sampling period were both exceptionally dry and warm (Fig 2). Evidence from wetland indicator status and SLA, both of which are tied to plant water stress tolerance, suggest that increasing aridity, and therefore less plant-available water, may be an important contributor in the richness declines we measured. The native annual forb species absent in the second sampling period were disproportionately adapted to mesic environments according to their wetland indicator status (Fig 5). Moreover, the average SLA of plant species found only in T1 was significantly greater than for those found in T2 or both sampling periods, suggesting that the species that persisted are better adapted to drought. Likewise, other long-term grassland data in California [66] and experimental work by LaForgia and colleagues [67] show that native annual grassland forbs with traits associated with higher moisture conditions are more negatively affected by drought.

Importantly, grazing and precipitation often have interactive effects on native species richness and cover [40, 62, 68, 69]. Species richness generally increases under grazing in mesic and highly productive environments, but richness often declines under grazing in arid environments [10, 19, 70, 71] [but see 40]. Grazing during the extreme drought of 2012–2014 may have directly reduced native annual forb species richness, consistent with prior studies showing that grazing can reduce biodiversity during drought conditions [68, 69].

Overall native annual forb cover was greater in T2 than T1, and native annual forb cover was greater in grazed prairies than ungrazed prairies in three of four survey years (Fig 4). The greater native annual forb cover in ungrazed prairies in T2 as compared to T1 may be attributable to lagged drought-induced declines in exotic annual grasses [46, 72], reducing competitive pressure and allowing some species of native forbs to increase significantly in cover. Furthermore, the large spike in native annual forb cover in some grazed sites in 2017 as compared to 2016, suggests that the higher than typical precipitation in 2017 benefitted the native annual species that persisted through the drought but did little to restore native species richness, reinforcing findings from other sites that ‘drought plus deluge do not equal normal’ [35].

Our results show a pattern of declining native annual forb richness, but we are unable to determine whether the declines we observed are a short-term response to the 2012–2014 drought, changes in grazing, or a sign of longer-term trends. Heavy winter rainfall in 2017 did not result in increased site-level native annual forb species richness, which would be expected if high precipitation stimulated the persistent seedbanks typical of many species in this group, though a single high precipitation year may not be enough for all species to recover following severe drought. Prior work on the dynamics of annual forbs and annual grasses suggests that annual forbs persist alongside exotic annual grasses in part due to precipitation variability and drought [73, 74]. Additional data are necessary to determine whether the declines in richness we observed were due to local extinction or were only temporary responses to drought.

In conclusion, we find that grazed grasslands continue to have a greater richness of native annual forbs than ungrazed grasslands, but that the gap between grazed and ungrazed prairie diversity declined. Our study provides additional evidence that drought and rising temperatures affect community composition in managed grasslands globally [75, 76]. Finally, our study raises the question of whether species adapted to mesic conditions need alternative conservation strategies beyond in situ grazing in areas where aridity is increasing, such as assisted migration to climate refugia or ex situ collections.

Supporting information

S1 Table. Sites visited by sampling year, ordered from North to South.

Elevation extracted from the USGS National Map Elevation Point Query Service. Thirty-year mean temperatures and precipitation values extracted from the WorldClim version 2.1 climate model (Fick & Hijmans 2017).

(PDF)

S2 Table. Native annual forb species observed in sampling periods 1 and 2.

Nomenclature follows Jepson Flora Project (2020).

(PDF)

Acknowledgments

We thank the UC Santa Cruz Reserve System, California State Parks, National Parks Service, Monterey Peninsula Regional Parks District, and private landowners for allowing us to access their land. We thank S. Glascock and M. Voce for their help in the field. We appreciate helpful feedback from A. Huertas-Herrera, M. Loik, and S. Harrison on drafts of this paper.

Data Availability

The data are available at https://datadryad.org/stash/dataset/doi:10.7291/D10X19

Funding Statement

The original survey was funded by a grant (#99-35101-8234) of the U.S. Department of Agriculture (https://nifa.usda.gov/grants) to K.D.H. The resurvey was funded by a small grant from the Santa Clara Valley Chapter of the California Native Plant Society (https://www.cnps-scv.org/education/scholarships/32-scholarships/256-student-research-scholarships) to JCL; funding from the Jean Langenheim graduate fellowship at the University of California, Santa Cruz to JCL; and by the Griswold Endowed Chair funds at UC Santa Cruz to KDH. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Decision Letter 0

Fei Xu

21 Apr 2022

PONE-D-22-07590Native annual forbs decline in California coastal prairies over 15 years despite grazingPLOS ONE

Dear Dr. Holl,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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Reviewer #1: Partly

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

**********

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Reviewer #1: Yes

Reviewer #2: Yes

**********

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Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Authors examined the effects of livestock grazing by cattle on grassland diversity and cover in California. This is a timely topic and adapting grazing management to account for changing climate will be critical for conserving rangelands worldwide. The authors are lacking key pieces of information in the methods section, and the discussion section must draw conclusions more tightly linked to actual findings, and contextualize findings in the context of current literature.

Introduction

Page 3, Line 25: I’m not familiar with the term semi-natural plant community, define?

Page 3, Line 38: Is grazing only beneficial in highly invaded grasslands?

Materials and methods

Page 5: no need to include ‘the two of us’

Page 5: Please provide more information about the grazed and ungrazed plots. At what intensity (AUM) were the plots grazed? What size are the plots? When surveying the vegetation did you avoid the fenceline / edge effects? At what frequency were the plots grazed? How close were the paired sites (are they bisected fields?)? Please discuss herbivory within both grazed and ungrazed plots by wild ungulates.

Page 5: Site descriptions. No need to talk about survey permission, just describe the sites that you actually included in the study. Could you include a map of these study areas and/or a description of the range of conditions across which these plots occur (distance apart, elevational range, etc.). In other words, tailor site description to the actual study sites.

I see here that it was hard to establish a complete grazing history, but could you provide a ball park estimate of grazing intensity in order to contextualize that patterns that you observe with other studies?

Line 99: It is going to be hard to attribute differences in response to grazing to climate (especially with incomplete grazing history), with only two time points (though I agree it is likely). We two sample points, however, many other factors could have changed – for instance, land use in the surrounding habitat matrix, nitrogen deposition, pressure from undomesticated livestock. In other words, attributing differences to drought specifically is challenging, and should be discussed in the discussion.

Line 106: Does this sampling regime recapitulate the original veg sampling?

Line 125: Just the version of R is fine – though I do like ‘Bird Hippie’.

Line 128: How is year different from time period – somehow I didn’t understand that you had multiple years of data within each time period – could you make this more clear?

Results

In terms of vegetation height, did you derive this via the trait database or did you collect measurements in the field, and if the latter, were measurements collected after the fields had been grazed? Sorry, that is more of a methods question!

Could you provide more information about the overall community composition – in particular, I’m curious about invasive species cover, perennial grass cover, etc.

Discussion

Line 185: As mentioned, I need a little more information before I can contextualize this height difference.

Line 214: Can you connect your findings here with other studies of grazing in similar habitats?

Line 227: Since your statistical tests indicate no differences, do not discuss as if there are treatment effects.

Line 222: Did changes occur due to composition change or due to increased biomass?

Line 245: This is good – could mention other forms of change in the region that could explain differences, but supporting your finding with the mesic index etc is good.

Line 252: Be clear here about what grazing effects (positive effects on diversity?). Several studies have shown that negative grazing impacts on diversity and native cover are exacerbated during drought years.

Live 253: This transition to annual dominated states has been observed in other studies – maybe cite a few?

Live 276: I don’t feel like you’ve set us up to make conclusions about microhabitat (did you do any spatial studies?) or to mention assisted migration. In order to mention these things, please explain how your findings support this suggestion.

Reviewer #2: Review of PLOS

This is an excellent paper that resamples a coastal prairies to explore how a regional drought influenced species richness. The sampling approach was straightforward, as was the data analysis. The results were unambiguous and certainly worthy of publication. The writing was clear and concise and addressed the key limitations and strengths of the analysis. Overall, a very clean manuscript.

There are a few areas where I believe there are opportunities for improvement or increased impact for this publication. Here are my suggestions:

1. Given the broad regional sampling that was conducted, there may be opportunities to get a more nuanced view of the impact of climate change/drought. It is highly unlikely that the extent of the drought (deviation from mean conditions) or the 2017 pulse in increased precipitation was equal across the entire gradient. I would appreciate seeing the nuance of species loss or increase in vegetation height relative to the extent of drought/2017 pulse across the gradient rather than a single, aggregated measure.

2. Somewhere either in the supplementary materials or in a table in the paper there should be a list of species, their abundance, and an identification of which species were lost. This would be a valuable resource.

A few other minor edits.

Line 40: Provide spatial description for readers not familiar with California geography; consider including biophysical data that capture the environmental gradient.

Line 53: Global patterns don’t help in interpreting these data; need to include weather trends and key disruptive weather events that are useful in understanding the changes observed.

Line 98: More precision here. Much of the explanation hangs on a single source describing an “exceptional drought”. I want to see the actual deviation, including the temporal extent of dry periods, the relative change in water year, increases in mean temperature, etc. for the sampled region.

Line 195: Shrub encroachment as a topic comes out of nowhere. It hasn’t been established as a key metric nor are data presented. I’d drop this argument or add the woody plant data.

Line 221: The most parsimonious explanation is that a higher-than-average water year produced greater plant biomass in this water-limited ecosystem.

Line 237: Unclear what “Climatic Water Deficit” is as a proper noun. First time it is introduced and it isn’t well explained.

Overall, I believe this paper to be valuable to understanding the factorial influence of grazing and weather on forb species richness in a biodiverse ecosystem.

**********

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Reviewer #1: No

Reviewer #2: No

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Attachment

Submitted filename: Review.docx

Decision Letter 1

Mehdi Heydari

13 Sep 2022

PONE-D-22-07590R1Native annual forbs decline in California coastal prairies over 15 years despite grazingPLOS ONE

Dear Dr. Holl,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Oct 28 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Mehdi Heydari

Academic Editor

PLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

Dear Dr. Karen D. Holl

Based on the reviewers comments and my additional control, I am pleased to inform that your manuscript PONE-D-22-07590R1" Native annual forbs decline in California coastal prairies over 15 years despite grazing" can be accepted for publication in PLOS ONE.after minor revision

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #3: All comments have been addressed

Reviewer #4: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #3: Partly

Reviewer #4: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: Yes

Reviewer #4: Yes

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #3: Yes

Reviewer #4: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #3: Yes

Reviewer #4: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: Dear Authors,

Overall the manuscript is a very nice attempt to explore the response of coastal prairies to changes in grazing management (grazed and ungrazed) in California. The paper is well written, and I think it is pleasant to read. However, some details can be improved, e.g., some unsupported sentences could be deleted, several concepts must be standardized, and minor changes in some figures should be made. Note that I do not find the "wetland indicator status" analyses helpful. But, it is up to you keeping or remove it. Beside this, I believe both supplementary figures should be in the manuscript's main text and not as an annexe. In the S1 Figure, please remove the words Longitude and Latitude; they are unnecessary.

I enclose my specific comments in the Word file.

Bests

Reviewer #4: I have reviewed article 7590R1. I was not a reviewer of the original submission and consequently cannot comment on changes that were made to the previous version. Following my read of this version I have no serious concerns about the science contained in this work nor its interpretation. Some minor issues or suggestion for clarification include:

Line 24 – Specify ‘Livestock grazing’ grazing by native animals is typical of all grasslands etc.

Line 32-34 – There are just as many examples of livestock grazing encouraging woody plant encroachment as there are of it discouraging it. I would temper this statement and include the counterpoint that livestock can encourage encroachment.

Line 79 – Emphasize that these 10 sites are a subset of the original 26

Line 84 – how many transects? I believe this question is answered later, but transect spacing is covered here. Perhaps a minor re-organization would put this connected material together in a single paragraph.

Line 92 – Please clarify the stocking. The ‘1 cow per 2-4 ha’ corresponds to 1 cow-calf pair, or a single animal (i.e., does a cow-calf pair = 2 cows in this situation)?

Line 116 – Not necessary to say ‘ are described below’.

Line 118 – Please define ‘T1’

Line 125-128 – Sentence describes two methods. Make separate sentences.

Line 128-130 – Please elaborate on the method for quantifying cover. What technique was used?

Line 135-136 = ‘When data … were available’

Line 141 – This is a really nice, super clear data analysis section!

Line 149 – Not familiar with the Tweedie – maybe provide a reference for this approach to your zero-inflated data.

Line 267-237 – I’m not understanding this argument that declines in native richness are greater in the ungrazed because they had low richness to begin with. Maybe expand on this thinking.

Line 254 – You should do this again – its only gotten worse in CA since 2017…

Line 275 – better word choice for ‘slackening’?

Line 298 – The thing I think this paper is missing – but not something you would address at this stage – is a community analysis because you have clearly observed a community shift toward more drought-tolerant species. Perhaps for the paper with 3 sampling periods in a few years!

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Reviewer #3: Yes: Alejandro Huertas-Herrera

Reviewer #4: No

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Attachment

Submitted filename: GrazingResurveyManuscript_PLOS One_revised-resubmission.docx

Decision Letter 2

Mehdi Heydari

21 Nov 2022

Native annual forbs decline in California coastal prairies over 15 years despite grazing

PONE-D-22-07590R2

Dear Dr. Holl,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Mehdi Heydari

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #3: All comments have been addressed

Reviewer #4: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #3: Yes

Reviewer #4: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: Yes

Reviewer #4: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #3: Yes

Reviewer #4: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #3: Yes

Reviewer #4: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: Dear authors. It is a pleasure to read your manuscript. Thank you for considering my suggestions. Congratulations for your manuscript! Best.

Reviewer #4: This manuscript has been reviewed the authors notified of the manuscript being acceptable. Therefore I have no additional comments.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #3: Yes: Alejandro Huertas Herrera

Reviewer #4: No

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Acceptance letter

Mehdi Heydari

23 Nov 2022

PONE-D-22-07590R2

Native annual forbs decline in California coastal prairies over 15 years despite grazing

Dear Dr. Holl:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Mehdi Heydari

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Table. Sites visited by sampling year, ordered from North to South.

    Elevation extracted from the USGS National Map Elevation Point Query Service. Thirty-year mean temperatures and precipitation values extracted from the WorldClim version 2.1 climate model (Fick & Hijmans 2017).

    (PDF)

    S2 Table. Native annual forb species observed in sampling periods 1 and 2.

    Nomenclature follows Jepson Flora Project (2020).

    (PDF)

    Attachment

    Submitted filename: Review.docx

    Attachment

    Submitted filename: Responses to Reviewers.docx

    Attachment

    Submitted filename: GrazingResurveyManuscript_PLOS One_revised-resubmission.docx

    Attachment

    Submitted filename: Response to reviewers 2.docx

    Data Availability Statement

    The data are available at https://datadryad.org/stash/dataset/doi:10.7291/D10X19


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