Lower alpha, higher beta, and similar gamma diversity of saproxylic beetles in unmanaged compared to managed Norway spruce stands.

Strong anthropogenic pressures on global forests necessitate that managed forests be evaluated as habitat for biodiversity. The complex pattern of habitat types created in forestry systems is ideal for analyses through the theoretical framework of alpha (local), gamma (total) and beta (compositional) diversity. Here I use saproxylic beetles, a species-rich threatened group, to compare four Norway spruce-dominated habitats representative of the boreal forest landscape of northern Europe: unmanaged semi-natural stands, nature reserves, unthinned middle-aged production stands and commercially thinned production stands. The beetles (in total 38 085 individuals of 312 species), including red-listed ones and three feeding guilds (wood consumers, fungivores and predators) were studied in 53 stands in central-southern Sweden, in two regions with differing amounts of conservation forest. Alpha diversity of saproxylic, but not red-listed, beetles was higher in the thinned stands than in the semi-natural stands, and did not differ for the other forest types. Beta diversity of saproxylic beetles was higher in unmanaged semi-natural stands than in the other forest types, but species composition did not differ noticeably. Furthermore, red-listed saproxylic beetles had higher gamma diversity in unmanaged semi-natural stands in the region with more conservation forest, but not in the one with less such forest. The local factors dead wood volume and dead wood diversity did not influence alpha diversity of beetles, but increasing canopy openness had a minor negative influence on saproxylic and red-listed beetles. While the local scale (alpha diversity) indicates the potential for managed forests to house many saproxylic beetle species associated with spruce forests in this boreal landscape, the larger scales (beta and gamma diversity) indicate the value of unmanaged forests for the conservation of the entire saproxylic beetle fauna. These results show the importance of analyses at multiple levels of diversity (alpha, beta, gamma) for identifying patterns relevant to conservation.

Introduction

Globally, forest biodiversity faces many anthropogenic pressures, with European forests among the most affected [1]. Conservationists have emphasized the role of modern forestry practices, especially clearcutting, in driving homogenization and extinctions among forest species [2-7]. While more protected forest is needed, there is increasing recognition of the need for conservation measures also within the managed forest matrix [8-11] in order to reach goals of sustainable forest management (e.g. the Convention on Biological Diversity, UN Sustainable Development Goal 15, and the EU Biodiversity Strategy for 2030). It is necessary to identify taxa that are especially sensitive to forestry operations, and other taxa that may be maintained within managed forests. In this study, I compare species diversity and composition of saproxylic (wood-living) beetles between two managed and two unmanaged Norway spruce (Picea abies (L.) H. Karst.) forest types, to clarify how a diverse species group of conservation concern is distributed in and affected by the managed forest matrix in boreal central-southern Sweden.

Saproxylic insects are ecologically important and diverse, and beetles are the most diverse saproxylic insects [12]. In Europe, 18% of assessed saproxylic beetle species are classified as threatened (red-list classes VU, EN, CR), with logging singled out as a primary cause of species declines [13]. In Sweden, 400 out of 1153 (35%) saproxylic beetle species are red-listed (18% classified as threatened, [14]).

The fauna of saproxylic beetles may differ not only between managed and unmanaged forests, but also between management stages [15]. In a previous study we found as many saproxylic beetle species overall, but fewer red-listed species, in pre-commercially thinned young spruce stands compared to unmanaged stands [16]. In many countries, thinning (pre-commercial and commercial) is done on much larger areas each year than final felling—in Sweden nearly three times larger [17] (see [16] for further examples). Young to middle-aged forestry stands are now much more common in Fennoscandian landscapes than before industrialization [18], but are often overlooked in conservation research. At the same time, the long-term effect of thinning on saproxylic beetles is unclear [19,20], and middle-aged stands that have not been recently thinned are also an important part of the forestry landscape.

In the present study I use recently commercially thinned spruce-dominated stands (“thinned stands” below) and spruce-dominated stands without recent forestry intervention (“unthinned stands” below). As a semi-natural reference I use Woodland Key Habitats (“WKHs” below); small, semi-natural forest stands, identified by their biodiversity values and scattered throughout the managed forest landscape in northern Europe [21]. WKHs are important in regional forest conservation [22-25], but to complement them, I use spruce-dominated nature reserves as larger natural forests (“reserves” below). Given the importance of geographic context to biodiversity patterns, and in light of earlier results showing the importance of the amount of WKH in the surrounding landscape to red-listed saproxylic beetles associated with oak [26], I use sites from two large regions that differ in the concentration of WKHs. Contrasting results between these two regions could indicate the importance of the surrounding landscape in determining these patterns.

I use a framework of diversity divided into alpha-, beta- and gamma diversities [27,28], where alpha diversity represents the local diversity of a single stand, beta diversity represents the degree of variation in community composition among stands within a forest type, and gamma diversity represents the total diversity of all stands of one type in the region studied. Many studies of diversity differences between managed and unmanaged forests deal only with the average diversity of individual stands (i.e. alpha diversity). However, species diversity patterns are highly scale dependent [28,29], and patterns at the local scale are often different or reversed at larger scales [30,31]. The framework of alpha, beta, and gamma diversity can give a more complete view, and reveal patterns that would otherwise be missed (e.g. [32-34]). Forestry may increase, decrease or leave unaffected alpha, beta and gamma diversity separately [35], and failing to properly consider the scale of diversity patterns may lead to e.g. poor management recommendations [36]. For example, a higher degree of habitat heterogeneity among unmanaged than managed forests [4,5] could mean that clear differences in species diversity are seen only at the beta or gamma scale.

The amount and diversity of dead wood in a forest seem to be major determinants of saproxylic beetle diversity [37]. Canopy openness is also important, with many species preferring sun-exposed dead wood [38] while others are associated with more shaded wood [39]. These local environmental factors are highly affected by forestry operations. Dead wood recruitment in managed forests follows thinning and felling operations, creating temporary pulses of dead wood [40-42]. On average, dead wood volume and diversity are lower in managed than in unmanaged conifer forests in northern Europe [3,43]. Canopy openness in even-aged forestry is cyclical, with open conditions after clear-cutting and increasingly closed conditions as stands age, counteracted by thinnings. In unmanaged forests, dead wood recruitment and canopy openness is governed by natural succession, disturbances, and ‘gap dynamics’ [2,44]. This study consequently also examines the influence of these local environmental variables on beetle diversity.

Because of the high ecological diversity of saproxylic organisms, it is useful to divide them into functional groups which may respond differently to environmental factors [45,46]. Here I study saproxylic beetles as a whole (“saproxylic beetles” below) and divide them into three feeding guilds (wood consumers, fungivores and predators) and red-listed beetles.

The study aims to test the following specific predictions:

The alpha diversity of saproxylic beetles does not differ between thinned spruce production stands, spruce-dominated Woodland Key Habitats and reserves, as there are many species adapted to each forest type. Unthinned spruce production stands, with less dead wood and canopy openness, have lower alpha diversity of saproxylic beetles than the other forest types.

The alpha diversity of red-listed beetles is higher in unmanaged than in managed stands, owing to a higher concentration of rare and valuable dead wood substrates. Unthinned stands have lower alpha diversity than the other forest types.

Certain species are better adapted to unmanaged stands than managed stands and vice versa, consequently species composition differs between managed and unmanaged forest types.

The alpha diversity of saproxylic and red-listed beetles increases with the amount and diversity of dead wood, and with canopy openness.

The beta diversity of saproxylic beetles is higher in unmanaged than in managed stands due to higher among-habitat heterogeneity of substrates and structures, especially dead wood.

The gamma diversity of saproxylic beetles is higher in unmanaged than in managed stands due to higher habitat heterogeneity. Unthinned stands have lower gamma diversity than the other stand types.

The gamma diversity of red-listed beetles is higher in unmanaged than in managed stands, and the difference is larger in the region with a higher concentration of WKHs. Unthinned stands have lower gamma diversity than the other stand types.

The gamma diversity of fungivores is highest in WKHs and reserves because of higher dead wood and fungal diversity; wood consumers are most diverse in thinned stands because of the pulse of newly dead wood; and predators are most diverse in the WKHs and reserves owing to a higher sensitivity to forestry; alternatively, predators are most diverse in the thinned stands because of high numbers and diversity of wood consumer prey.

Methods

Study regions and stands

The present study combines data from two different sampling years and regions in the hemiboreal zone of southern/central Sweden; Jönköping (roughly corresponding to Jönköping county) in 2017 and Örebro (roughly corresponding to Örebro county) in 2018.

The 2017 Jönköping sample region consists of 10 sites, each with a thinned production stand paired in proximity to a Woodland Key Habitat (WKH) stand. In addition to these 10 pairs, I included three sites with (unpaired) nature reserve stands in the same region. The 2018 Örebro sample region consists of 10 sites, each with one thinned production stand, one unthinned production stand and one WKH in proximity. Consequently, the complete sample from both regions consists of 20 WKH stands, 20 thinned stands, 10 unthinned stands and 3 reserve stands (Fig 1).

Fig 1

Map of study sites.

a) Study sites in the northern region, corresponding roughly to Örebro county. Each red dot represents a study site consisting of one thinned production stand, one unthinned production stand and one Woodland Key Habitat stand. b) Study sites in the southern region, corresponding roughly to Jönköping county. Each red dot represents a study site consisting of one thinned production stand and one Woodland Key Habitat stand. Blue dots represent unpaired nature reserve stands. Green is forested land, teal is wetland, yellow is open (agricultural) land, and grey is urban land. Coordinates are in WGS84, with decimal degrees as units. Background map provided by [47].

Both regions are forested at around 70% of land area [17], and dominated by Norway spruce (~45–50% of tree volume) followed by Scots pine (Pinus sylvestris L., ~35%) and birches (Betula pendula Roth/Betula pubescens Ehrh., ~11%) [48]. Although the two regions have many similarities, including a long history of human forest use [49,50], Örebro county has a markedly higher percentage of forest area that is strictly protected; 4.5% vs 1.8% in Jönköping county [51]. The number and total area of WKHs is also markedly higher in Örebro than in the Jönköping region (defined here by a rectangle encompassing all study sites in each region): ~4.4 WKHs/1000 ha, ~1.4% of total area in Örebro vs ~2.6 WKHs/1000 ha, ~0.5% of total area in Jönköping [52].

Mean yearly temperature in the two regions was 6°C and mean yearly precipitation was between 700–1000 mm during the current standard period of 1991–2020. During the sampling period in 2017 (May-July), the mean temperature in the Jönköping study region was 11–15°C and mean monthly precipitation 20–125 mm. During the sampling period in 2018 (May-July, a hot and dry summer), the mean temperature in the Örebro study region was 14–21°C, and mean monthly precipitation 25–50 mm [53]. Jönköping sites are on average 237, and Örebro sites on average 153 meters above sea level.

All sampled sites except the natures reserves are owned by the state forest company Sveaskog. The thinned stands were recently commercially thinned Norway spruce production stands. The unthinned stands were middle-aged Norway spruce production stands without recent forestry interventions. The WKHs were older Norway spruce-dominated stands. The following criteria were used in selecting sites from the Sveaskog database: forest type (WKH or managed), stand age (over 35 for managed forests), time since intervention (more than 10 years for unthinned stands, 1–5 years for thinned stands), size (above 0.5 ha for WKHs), distance between paired stands (within 2.5 km), tree species (at least 70% Norway spruce). The three reserves in Jönköping were selected as the largest in the region dominated by old Norway spruce forest. All sites were embedded in a forestry mosaic dominated by Norway spruce stands, typical of central-southern Sweden. Stand characteristics per forest type and region are given in Table 1.

Table 1

Stand characteristics.

Descriptive statistics for environmental factors and stand characteristics per forest type and region. The number of stands of each forest type per region is given in parentheses. WKH = Woodland Key Habitat.

Region	Forest type	Dead wood volume (m3/ha)			Dead wood diversity
		min	max	mean (±SD)	min	max	mean (±SD)
Jönköping	WKH (10)	7.3	214.4	72.6 (±50.2)	3	24	12.6 (±4.9)
Jönköping	Thinned (10)	4.7	36.7	15.2 (±8.3)	9	17	12.1 (±2.6)
Jönköping	Reserve (3)	27.5	89.5	57.7 (±26.1)	6	13	9.3 (±2.3)
Örebro	WKH (10)	6.7	267.4	92.2 (±74.2)	6	20	11.6 (±3.8)
Örebro	Thinned (10)	4.5	67.0	17.3 (±15.5)	7	21	12.8 (±3.8)
Örebro	Unthinned (10)	0.7	41.8	13.0 (±11.2)	5	21	10.3 (±4.2)
Region	Forest type	Stand age (years)			Stand size (ha)
		min	max	mean (±SD)	min	max	mean (±SD)
Jönköping	WKH (10)	55	149	111 (±26)	0.9	7.8	3.1 (±2.5)
Jönköping	Thinned (10)	37	51	43 (±5)	0.9	31.7	7.6 (±9.4)
Jönköping	Reserve (3)				70.3	284.5	187.6 (±108.6)
Örebro	WKH (10)	81	161	114 (±28)	0.9	20.7	5.4 (±6.0)
Örebro	Thinned (10)	35	50	41 (±6)	1.1	17.8	6.9 (±6.1)
Örebro	Unthinned (10)	35	68	49 (±11)	1.0	6.8	3.4 (±2.0)
Region	Forest type	Basal area (m 2 /ha)			Average living tree height (m)
		min	max	mean (±SD)	min	max	mean (±SD)
Jönköping	WKH (10)	19.1	137.1	59.8 (±24.1)	8.9	22.5	16.2 (±4.6)
Jönköping	Thinned (10)	19.6	58.2	32.3 (±9.6)	10.8	19.7	14.5 (±2.6)
Jönköping	Reserve (3)	34.9	76.9	54.4 (±16.5)	12.3	23.2	16.9 (±4.5)
Örebro	WKH (10)	17.2	136.4	57.1 (±29.4)	7.9	29.9	17.4 (±6.3)
Örebro	Thinned (10)	13.4	50.5	34.1 (±9.4)	11.4	19.3	15 (±2.3)
Örebro	Unthinned (10)	23.1	70.4	49.7 (±14.0)	8.4	23.4	15.8 (±4.3)
Region	Forest type	Canopy openness (%)			Time since thinning
		min	max	mean (±SD)	min	max	mean (±SD)
Jönköping	WKH (10)	19	41	27 (±6)
Jönköping	Thinned (10)	19	53	34 (±7)	1	5	2.9 (±1.4)
Jönköping	Reserve (3)	24	37	30 (±5)
Örebro	WKH (10)	14	48	24 (±9)
Örebro	Thinned (10)	16	38	24 (±6)	1	5	3.3 (±1.6)
Örebro	Unthinned (10)	17	30	22 (±4)

Measurement of local environmental factors

I sampled beetles in each stand using two insect traps, and recorded environmental variables around traps. In a 5.5 m radius from each trap, I measured living stems 2 m and taller, for each stem recording tree species, height and diameter at breast height (1.3 m). I measured the diameter of multi-stemmed hazel (Corylus avellana L.) at the ground (not individual stems). Fig 2 shows tree composition for each forest type. Norway spruce dominated all sites, followed by birches (Betula pubescens/B. pendula, similar taxa, pooled in this study) and Scots pine. WKHs had the greatest diversity of tree species.

Fig 2

Living tree measurements.

Stems measured within 5.5 m radius around each trap, summed for each forest type. Black circles represent median values. Corylus avellana was measured at base, not breast height. Note the logarithmic scale on the x-axis. A slight jitter has been applied to increase readability of overlapping points. Sample sizes are not equal for the four forest types (reserves: 3, Woodland Key Habitats (WKHs): 20, thinned stands: 20, unthinned stands: 10).

I sampled all dead wood objects over 1 cm in diameter within a 10 m radius around each trap. I recorded tree species, diameter at both ends, height/length, type, and decay stage. In cases of large piles of small objects (diameter 1–3 cm), I measured representative objects and extrapolated to the full count. Dead wood type was classified in 4 categories: logs & branches (lying objects), stumps (height < 1 m), snags (height > 1 m) and dead trees (branches in crown more or less intact). For some snags where the top was too high to reach, diameter at the top was estimated visually. I classified wood decay in 4 stages: 1) newly dead wood (around 1 year or younger), leaves and/or small twigs still attached, bark intact, 2) older than one year but wood still hard, bark still mostly intact but looser, 3) older wood, partly soft, much bark gone, 4) old, heavily decayed and deformed wood.

I calculated dead wood diversity around each trap as the number of unique combinations of 4 different factors with a varying number of levels, similar to the method used in [54]: tree species (12 species), type (4 types), decay stage (4 stages) and diameter class (3 classes). For diameter class, I used the average of the diameters at the two ends, and used the classes 1–10 cm, 10–30 cm, 30+ cm from [55].

I calculated the volume of each dead wood object using the formula for a conical frustum: V = πh/3 × (R2 + R × r + r2), where h is length, and R and r are the radiuses at each end. For dead trees, I used volume functions intended for the specific tree species [56]. Finally, I pooled the volume of all objects around each trap to obtain m3/ha. Fig 3 shows characteristics for all 2896 recorded dead wood objects, which were dominated by Norway spruce in all forest types, followed by birches.

Fig 3

Dead wood measurements.

Dead wood objects measured in a 10 m radius around each trap. Black circles represent median values. Decay stage 1 is newly dead wood, 2 and 3 are intermediate decay, and 4 is heavily decayed. Diameter is the average of the diameter at the two ends. Note the logarithmic scale on the x-axis. A slight jitter has been applied to increase readability of overlapping points and draw order has been randomized. Sample sizes are not equal for the four forest types (reserves: 3, Woodland Key Habitats (WKHs): 20, thinned stands: 20, unthinned stands: 10).

I estimated canopy openness from photos taken from the ground straight up at both sides of each trap. The images were processed with a high-contrast, greyscale filter, then analyzed for “mean grey value” in ImageJ 1.50b, to estimate percentage canopy openness. Environmental variables per forest type and region are summarized in Table 1.

Sampling of beetles and handling of species data

I sampled beetles using IBL-2 flight interception traps (CHEMIPAN, Warsaw), consisting of 0.3 m2 triangular plastic sheets suspended between a white plastic roof and two gutters, with a collection jar at the bottom. These were hung between two living Norway spruces, at breast height. I used two traps per stand, about 25 m apart. In both years, traps were set up early May, emptied once in mid-June, and once at the end of July. Permission to sample stands outside of protected areas was given by Sveaskog, and no further permits were required under Swedish law. Permission to sample the three nature reserves was given by the county administrative board of Jönköping, permit number 521-2288-17.

All saproxylic beetles were identified to species level based on morphological characters. The families Staphylinidae and Ptilidae were excluded due to difficulty in identification, except for subfamilies Pselaphinae, Scydmaeninae and Scaphidiinae. I classified saproxylic beetles into feeding guilds (wood consumers, fungivores, predators) based on [55,57]. When appropriate, species were classified in more than one feeding guild. I further classified red-listed beetles, based on inclusion in any of the Swedish red-lists since 2000 [14,58-61]. Using older red-lists allowed for a bigger pool of species, as red-listed species are by their very nature often difficult to sample [62]. Previously red-listed species are generally still of conservation interest.

Trap-level data were used for all analyses except for species accumulation curves, where I used stand level data (two traps per stand pooled) to avoid pseudoreplication in that method. The sample consists of 40 traps in WKHs, 40 traps in thinned stands, 20 traps in unthinned stands and 6 traps in reserves.

Statistical analyses

I used generalized linear mixed models (GLMMs) to test the influence of forest type and local environmental factors on the average per-trap number of saproxylic and red-listed species (i.e. alpha diversity). Model 1 used number of saproxylic species per trap as the response variable, and model 2 used the number of red-listed species per trap, with the other factors being the same in both models. Forest type (WKH, reserve, thinned stand, unthinned stand), Region (Jönköping, Örebro) and the three continuous environmental variables (Deadwood volume, Deadwood diversity, Canopy openness) were fixed factors. All continuous variables were standardized before analysis. WKHs and Jönköping were reference levels for the two categorical variables, meaning that effect estimates in the results for the other levels represent deviations from these. I included random intercepts per Site, and Stand nested within Site. I ran the models in R 4.1.0 [63] using the R package glmmTMB [64], with a Poisson distribution and log link function. I inspected residual plots using the DHARMa R package [65], and checked for overdispersion by comparing the sum of squared Pearson residuals to the residual degrees of freedom [66], finding no issues in either case. Statistical significance in the GLMM models was assessed using profile likelihood confidence intervals calculated with glmmTMB, as these are generally more informative and less prone to misinterpretation than p-values [67,68].

I compared gamma diversity of each category (saproxylic beetles, red-listed beetles, the three feeding guilds) among the forest types using species accumulation curves and conservative 95% confidence intervals constructed in EstimateS v.9.1.0 [69]. I extrapolated each sample to twice the sample size using the Chao2 asymptotic estimator [70]. To obtain a measure of evenness for each forest type, I constructed rank-abundance curves per stand type and region.

I tested differences in beta diversity of saproxylic beetles among the four forest types using PERMDISP, with p-values calculated based on 999 permutations using PRIMER v.7.0.13 [71] and the PERMANOVA+ add-on [72]. P-values were used as confidence intervals are not available for this analysis. The choice of dissimilarity measure can have a drastic effect on results [73], so I used both the modified Gower dissimilarity measure with log base 10 [74] which takes into account species abundances, and the Sørensen dissimilarity measure, which does not.

Given a significant result in the PERMDISP analysis, I did not perform a PERMANOVA to test for differences in community composition as it cannot tell apart multivariate dispersion (i.e. beta diversity) and location (i.e. differences in community composition) [75]. Instead, I visualized species assemblages using NMDS, based on the modified Gower dissimilarity measure. In the NMDS, lack of overlap between sample points from different forest types would indicate differences in community composition, and forest types with less clustered points would indicate higher beta diversity. The stress in the two-dimensional NMDS was slightly above the recommended limit of 0.2 (0.24). Analyses of beta diversity and community composition were done only for saproxylic beetles, as red-listed beetles were too few for meaningful analysis. All plots were drawn using the ‘ggplot2′ R package [76].

Results

The total sample consisted of 38 085 saproxylic beetle individuals of 312 species (18 283 individuals, 248 species in Jönköping in 2017; 19 802 individuals, 273 species in Örebro in 2018), representing 45 beetle families. For three of the forest types (commercially thinned stands, unthinned stands and Woodland Key Habitats) the proportion of species associated with Norway spruce was around 50–60% while the proportion associated with broadleaved trees was around 50% (with some species associated with both, and around 10% associated with Scots pine). For the nature reserves, the proportion associated with spruce was higher (around 70%) and the proportion associated with broadleaves lower (around 40%). Summary species data for the four forest types is given in Table 2.

Table 2

Summary species data.

Species (spec.) and individuals (ind.) per species group and forest type. The number of stands per forest type is given in parentheses. WKH = Woodland Key Habitat.

	Thinned (20)		Unthinned (10)		WKH (20)		Reserve (3)		Total (53)
	Spec.	Ind.	Spec.	Ind.	Spec.	Ind.	Spec.	Ind.	Spec.	Ind.
Red-listed species	29	226	22	145	27	228	6	20	37	619
Wood consumers	68	7211	56	4473	64	8342	26	1132	79	21 158
Fungivores	141	4418	115	2347	146	4594	69	502	171	11 861
Predators	54	2082	44	905	52	2014	22	308	63	5309
All saproxylics	260	13 480	215	7699	262	14 944	118	1962	312	38 085

Alpha diversity and environmental factors

The GLMM for saproxylic beetles indicated a higher alpha diversity in thinned stands than in WKHs. Both of the managed stand types had effect estimates higher than the WKH reference level, although only thinned stands had confidence intervals not overlapping 1, indicating statistical significance (an estimated ~12% more species per trap, Table 3). For the reserves, the estimate was lower than the WKHs, although with overlapping confidence intervals. Region, dead wood volume and dead wood diversity had small estimates, all of which with confidence intervals indicating a lack of statistical significance. Canopy openness had a small, statistically significant negative influence on saproxylic beetles (equal to ~1% fewer species per percentage point of canopy openness). The among-site random effect was larger than any of the fixed effect estimates, while the among-stand random effect was smaller than for sites, although still larger than all fixed effects except the estimate for thinned stands (Table 3).

Table 3

Saproxylic alpha diversity and environmental factors.

GLMM results for all saproxylic species. For the categorical predictors “Forest type” and “Region”, Woodland Key Habitat (WKH) and Jönköping are the respective reference levels. The continuous predictors (Dead wood volume, Dead wood diversity, Canopy openness) have been unstandardized and all values have been back-transformed, giving odds ratios for the fixed effect estimates. The random factor “Stand” is nested within “Site”. Confidence intervals (CI) not overlapping 1 (indicating statistical significance) have been marked in bold.

Fixed effects
Factor		Estimate	CI 2.5%	CI 97.5%
Intercept		55.00	49.26	61.41
Forest type (Reserves)		0.94	0.74	1.18
Forest type (Thinned stands)		1.12	1.01	1.24
Forest type (Unthinned stands)		1.07	0.95	1.21
Region (Örebro)		1.02	0.88	1.18
Dead wood volume (m 3 /ha)		1.00	0.99	1.09
Dead wood diversity		1.00	0.98	1.05
Canopy openness		0.99	0.92	0.99
Random effects
Factor	SD
Stand:Site	1.09
Site	1.13

For red-listed beetles, the effect estimates for all forest types was lower than for WKHs, although all had confidence intervals overlapping 1, indicating a lack of statistical significance (Table 4). The estimate for the Örebro region was considerably higher than for the Jönköping reference level, although with wide confidence intervals overlapping 1. Dead wood volume and dead wood diversity had small estimates, with confidence intervals overlapping 1. Also for red-listed species, canopy openness had a small, statistically significant negative influence (equal to ~2% fewer species per percentage point of canopy openness). The among-site random effect was larger than any of the fixed effects, while the among-stand random effect was very small (Table 4).

Table 4

Red-listed alpha diversity and environmental factors.

GLMM results for red-listed species. For the categorical predictors “Forest type” and “Region”, Woodland Key Habitat (WKH) and Jönköping are the respective reference levels. The continuous predictors (Dead wood volume, Dead wood diversity, Canopy openness) have been unstandardized and all values have been back-transformed, giving odds ratios for the fixed effect estimates. The random factor “Stand” is nested within “Site”. Confidence intervals (CI) not overlapping 1 (indicating statistical significance) have been marked in bold.

Fixed effects
Factor		Estimate	CI 2.5%	CI 97.5%
Intercept		2.74	2.02	3.70
Forest type (Reserves)		0.68	0.31	1.37
Forest type (Thinned stands)		0.99	0.71	1.40
Forest type (Unthinned stands)		0.98	0.67	1.44
Region (Örebro)		1.28	0.88	1.88
Dead wood volume (m 3 /ha)		1.00	0.88	1.19
Dead wood diversity		1.00	0.87	1.12
Canopy openness		0.98	0.73	0.99
Random effects
Factor	SD
Stand:Site	1.00
Site	1.30

None of the rank-abundance curves were noticeably different (Figs 1, 2 and S1), indicating similar evenness in all of the forest types.

In summary, the results indicate that for saproxylic beetles as a whole, commercially thinned spruce production stands have moderately higher local (alpha) diversity than spruce-dominated Woodland Key Habitats, but I found no difference for red-listed species or the other forest types. Furthermore, the results indicate that for both saproxylic beetles as a whole and for red-listed beetles, canopy openness has a small but significant negative effect on alpha diversity.

Beta diversity and community composition

In the PERMDISP analysis of saproxylic beetles based on modified Gower dissimilarity, WKHs had the highest multivariate dispersion (e.g. beta diversity), followed by thinned stands, unthinned stands, then reserves (Table 5). The differences were statistically significant except unthinned stands with thinned stands and reserves (overall results: F(3, 102) = 9.5, p = 0.002; pairwise comparisons in Table 5). The results were not substantially different using the Sørensen dissimilarity measure instead (S1 Table). The NMDS further corroborated this pattern in multivariate dispersion, with WKH points more spread out than those for thinned stands. The plot did not indicate any differences in multivariate location (i.e. community composition) among the forest types, with groups of points largely overlapping (Fig 4). However, the two regions were clearly separated in multivariate location in the NMDS (as indicated by almost all points grouped with points from the same region).

Table 5

Beta diversity.

Multivariate dispersion (mean distances from centroid) for traps of each forest type with associated standard error (SE), from PERMDISP analysis based on modified Gower dissimilarity of saproxylic species abundance data. P-values below 0.05 in bold. WKH = Woodland Key Habitat.

			Pairwise comparisons
	Mean	SE	Reserve	Thinned	Unthinned
WKH	0.67	0.007	t = 4.4; p = 0.001	t = 2.5; p = 0.015	t = 2.8; p = 0.012
Reserve	0.55	0.010		t = 4.6; p = 0.005	t = 2.7; p = 0.095
Thinned	0.64	0.009			t = 1.3; p = 0.319
Unthinned	0.62	0.014

Fig 4

Species assemblages.

NMDS of all traps, based on modified Gower dissimilarity of saproxylic species abundance data. Pairs of traps from the same stand have been connected with a line, and a hull has been drawn around all traps from the same forest type. K = 2, stress = 0.24. WKH = Woodland Key Habitat.

In summary, the results indicate that spruce-dominated Woodland Key Habitats have a higher variation in community composition (beta diversity) than commercially thinned spruce production stands. Between the forest types, there are no clear overall differences in community composition.

Gamma diversity and feeding guilds

For the Jönköping region, most accumulation curves were similar (Fig 5). Regardless of species group, the reserve curves were generally lower than for the other forest types, but with wide and overlapping confidence intervals. For both saproxylic beetles (Fig 5A) and red-listed beetles (Fig 5B), the WKH curve was slightly higher than the thinned stand curve, but confidence intervals were overlapping. For wood consumers (Fig 5C) and fungivores (Fig 5D), the WKH and thinned stand curves were largely identical. For predators, the WKH curve was higher than the curves for thinned stands and reserves, with largely non-overlapping confidence intervals (Fig 5E), indicating higher gamma diversity in the WKHs.

Fig 5

Gamma diversity Jönköping.

a-e) Species accumulation curves with 95% confidence intervals for each forest type and species group from the Jönköping sample. Samples are forest stands (data from two traps per stand pooled), extrapolated to twice the original sample size.

For the Örebro region, accumulation curves were also mostly similar (Fig 6). For saproxylic beetles (Fig 6A) curves were virtually identical between the forest types. However, for red-listed beetles the WKH curve was higher (37.4 ± CI 7.6 species at highest extrapolation) than the unthinned and especially the thinned stand curves, with the confidence interval largely non-overlapping with the thinned stands (27.2 ± CI 6.7 species at highest extrapolation; Fig 6B), indicating higher gamma diversity in the WKHs. The curve for wood consumers was slightly higher for the thinned stands than for the unthinned stands, which in turn was higher than for the WKHs, although the confidence intervals for all three forest types were overlapping (Fig 6C). The curves for fungivores (Fig 6D) and predators (Fig 6E) were largely identical between the forest types.

Fig 6

Gamma diversity Örebro.

a-e) Species accumulation curves with 95% confidence intervals for each forest type and species group from the Örebro sample. Samples are forest stands (data from two traps per stand pooled), extrapolated to twice the original sample size. In b), the inlay shows the curves for the Woodland Key Habitats and the thinned stands, with the unthinned stands removed for clarity.

In summary, the results indicate that for most of the species groups, total (gamma) diversity does not differ between the forest types. An exception is the red-listed species, for which gamma diversity is higher in spruce-dominated Woodland Key Habitats than in commercially thinned spruce production stands in one region (Örebro) but not the other (Jönköping).

Discussion

For saproxylic beetles, I found lower alpha diversity in WKHs than in managed stands, but a higher beta and similar gamma diversity. For red-listed beetles, I found no statistically significant differences in alpha diversity, but gamma diversity was higher in WKHs in one region but not the other, possibly reflecting a biologically richer landscape in the former. These results highlight consequences of the choice of diversity measure and indicate the importance of spatial scale for the diversity of saproxylic beetles, especially red-listed ones.

Alpha diversity and species composition

Prediction 1 predicted no difference in alpha diversity of saproxylic beetles between managed and unmanaged stands. Perhaps surprisingly, alpha diversity was higher in thinned stands than in WKHs. Clear differences in beetle diversity are often lacking between unmanaged forests and production forest stages older than clear-cuts [77-81]. In a related study, we found no difference in alpha diversity between pre-commercially thinned spruce stands and WKHs [16]. These results mirror global trends, where hypothesized reductions in alpha diversity of various species groups as a consequence of anthropogenic influence on habitats are seldom found, or increases are seen instead [82-85].

Species dispersal has a positive (or unimodal) relationship to alpha diversity [31,86], and species associated with managed habitats should have little difficulty dispersing between patches in managed forest landscapes. Dispersal is likely more difficult for species associated with unmanaged forests, which are few, small and fragmented. Dispersal-limitation among species associated with unmanaged forests could mean that managed forests are more “fully-stocked” than unmanaged forests. If the regions used in this study consisted of mostly unmanaged forest, another pattern might be seen.

Contrary to prediction 2, I found no statistically significant differences in alpha diversity of red-listed beetles between the forest types, although the estimate for WKHs was higher than for the other types. This may be due to sampling: red-listed beetles are often rare, requiring very large samples to be properly assessed [62]. Furthermore, the diversity of red-listed saproxylic beetles may also need to be analyzed at larger scales than the local.

In contrast to the prediction of prediction 3, I found no clear differences in species composition among the forest types. It seems plausible that many species move freely between the forest types and do not view one or the other type as an impassable matrix [8], at least not in forests past the clear-cut stage [87]. Furthermore, nearby forest stands may not be the most appropriate scale to evaluate compositional differences, instead manifesting between e.g. regions with differing amounts of the forest types. If the amount of unmanaged, semi-natural forest (such as WKH) is much lower than that of managed forests, it is also possible that a potentially distinct fauna associated with unmanaged forests is strongly diluted by common immigrant species from surrounding managed stands [88,89]. In addition, associations of individual species to the different forest types may be obscured by a general community composition measure, and could be interesting to explore in more detail.

Environmental factors

In contrast to prediction 4, I found no positive association of the environmental factors dead wood volume and dead wood diversity with saproxylic beetles, or red-listed beetles. Saproxylic beetle species are generally thought to follow the species-area relationship, with dead wood volume instead of area [90,91]. Thresholds of increasing saproxylic diversity at around 20 m3/ha of dead wood in boreal forests have been proposed [92]. Given that this is well below what I found in the unmanaged stands (~82 m3/ha on average in WKHs) and above what I found in the managed stands (~16 m3/ha on average in thinned stands) it is perhaps surprising that I found no positive association with dead wood volume, and no difference in alpha diversity among the forest types. However, it should be noted that several of the WKH sites may have had inflated dead wood volume due to recent bark beetle attacks (pers. obs).

More important than dead wood volume per se may be dead wood diversity [37,93-95]. The span of dead wood diversity was quite limited in the current study, which may explain the absence of an association with saproxylic diversity. In a previous study, higher gamma diversity of certain saproxylic beetle groups in WKHs than in pre-commercially thinned spruce stands may have been partly explained by higher tree species diversity in the WKHs [16]. In this study, the WKHs were spruce-dominated, with quite similar dead wood diversity between managed and unmanaged stands. Roughly 60% of WKHs in southern and mid-Sweden are coniferous forests [96], dominated by Norway spruce or Scots pine. This spruce dominance in Fennoscandian forests, managed and unmanaged, is largely a product of historical forest management [97].

Canopy openness had a slight negative influence on both saproxylic and red-listed beetles. This is contrary not just to prediction 4 but seems to contradict previous literature concluding that more saproxylic beetles prefer sun-exposed dead wood than shaded [38,98]. However, Norway spruce is late-successional, adapted to closed-canopy, small-scale gap-dynamics and old-growth stands that characterized much of pre-industrial Fennoscandia [99], and spruce-associated species likely have similar preferences.

Beta and gamma diversity of saproxylic beetles

Consistent with prediction 5, I found higher beta diversity of saproxylic beetles in the WKHs than in the thinned stands. This suggests that largely the same “managed stand fauna” reoccurs, whilst the unmanaged stands are more heterogeneous. Beta diversity is negatively associated with dispersal, as it lets the same set of species populate many sites [31,86]. If, as reasoned above, the managed stand fauna exhibits higher dispersal, this could explain the lower beta diversity. Alternatively, the lower beta diversity in the managed stands could be due to lower among-stand diversity of forest structure and substrates (e.g. dead wood, see Fig 2).

In contrast to prediction 6, I did not find significantly higher gamma diversity of saproxylic beetles in the WKHs than in the other types. The definition of gamma or “regional” diversity is dependent on the scope of the study [31], and it is tightly linked to alpha and beta diversity [100]. In the scope of the present study, the higher alpha diversity in the thinned stands than in the WKHs may have compensated for the lower beta diversity. Given the difference in beta diversity between the forest types, a difference in gamma diversity would be expected if the scope of the study increased.

Gamma diversity of red-listed beetles and feeding guilds

Consistent with prediction 7, there was a clear difference in the gamma diversity of red-listed beetles between managed and unmanaged stands in the region with a higher concentration of WKHs, but not in the region with lower concentration. This is in line with previous studies indicating the importance of the surrounding landscape for saproxylic beetle diversity, especially of red-listed beetles [26,101-103]. Given the paucity of semi-natural and unmanaged spruce forests in the Jönköping region, it is likely that many species dependent on these forest types are locally extinct. Although the Örebro region has a relatively higher concentration of WKHs than the Jönköping region, it still has a long history of anthropogenic influence [49]. Repeated in a more pristine region, it is possible the difference between the forest types would be even larger.

A hint at the increased importance of the larger spatial context for red-listed as compared to saproxylic beetles is also given by the random effect estimates in the GLMMs. While saproxylic beetles had variance associated with both sites and stands, red-listed beetles had considerable variance associated with sites, but virtually none with stands. This indicates that although the number of saproxylic beetles varied to some extent both among sites and between stands within sites, the red-listed beetles varied primarily at the larger, among-site scale.

As catches often vary between sampling years [104,105], and year is confounded with region in the present study, an alternate explanation of the contrast between regions/years is that WKHs functioned as better refuges for red-listed beetles during the hot and dry 2018 summer. Given climate change, this has potentially important implications for the coming value of unmanaged stands.

There were mixed results for the three feeding guilds, although largely not consistent with prediction 8. For the fungivores, which did not differ between the forest types, the prediction presumed a substantially higher dead wood diversity and associated fungal diversity [106] in the WKHs, which seems not to have been the case. It is possible that the fine woody debris commonly left after thinning supports a relatively diverse and overlooked fungal diversity [107]. Wood consumers did indeed show higher gamma diversity in the thinned stands in the Örebro sample in accordance with the prediction, although the confidence intervals were partly overlapping. The pattern for predators was the reverse of the pattern for red-listed beetles, with higher gamma diversity in the WKHs in Jönköping but not in Örebro. Previous studies would suggest that predators should follow a similar pattern to red-listed beetles, being sensitive to forestry [108-110]. The pattern could either be caused by Jönköping WKHs being enriched in terms of predators, or thinned stands being impoverished. If the latter scenario is the case, a possible explanation could be that managed stands require nearby unmanaged stands in order to maintain a diverse fauna of predatory beetles. This might then be the case in Örebro, with a higher density of WKHs in the surrounding landscape, but not in Jönköping.

Unthinned stands and reserves

Contrary to hypotheses 1, 2, 6 and 7, I did not find consistently lower alpha, beta or gamma diversity of saproxylic or red-listed beetles in the unthinned stands than in the other forest types. While thinning can clearly have a beneficial influence on saproxylic beetles living on tree species associated with more open conditions, such as oak [111,112], many species associated with spruce may instead prefer relatively shaded and undisturbed conditions, and self-thinning dead wood dynamics. This is congruent with results from northern Sweden, where [79] found similar alpha diversity of saproxylic beetles and red-listed saproxylic beetles in unthinned, commercially thinned and “unprotected mature” stands.

However, [79] found higher alpha diversity, and [90] both higher alpha and gamma diversity, in old-growth coniferous forests than in mature managed stands, contrasting with the results of the present study. Given the low sample size of reserves included in this study, no clear conclusion should be drawn. Furthermore, the differing results could once again be due to differing regional contexts of forest continuity or quality.

Conclusions

This study helps clarify the importance of small, semi-natural unmanaged spruce stands for the conservation of forest biota, through a higher beta diversity of saproxylic beetles. Although managed stands seem to harbor many species, relative to other habitats, at the local scale, unmanaged stands are needed to counteract biotic homogenization.

The results also highlight the importance of considering scale, both for management and scientific studies of biodiversity. Gamma diversity of red-listed saproxylic beetles in WKHs was higher only in the region with a higher concentration of WKH stands. Without considering this regional context, a potentially important pattern would have been missed. The results indicate that for red-listed saproxylic beetles, the species most in need of conservation action, management should not ignore larger scales. Furthermore, as the contrasting results of alpha and beta diversity of saproxylic beetles in this study indicate, measuring only alpha diversity is insufficient. Studies comparing the diversity of managed and unmanaged forests only at the stand scale are likely to miss important context, resulting in simplified conclusions regarding the relative conservation value of forest types.

Rank abundance curves.

(PDF)

Click here for additional data file.

PERMDISP based on Sørensen dissimilarity.

(PDF)

Click here for additional data file.

19 May 2022

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Reviewer #1: Review of:

Lower alpha, higher beta, and similar gamma diversity of saproxylic beetles in unmanaged compared to managed Norway spruce stands

(PONE-D-22-04886)

General comment:

This is an important contribution dealing with forestry systems and the evaluation of biodiversity therein. Its value lies mainly in assessing a range of habitats produced by a boreal clear-cutting system, including young plantations (first study in project), thinning, harvesting stages, and set-asides for biodiversity (here, saproxylic beetles). The study is unusual and valuable in its approach, and in addition the use of classical diversity concepts in the analysis is well motivated.

The manuscript is well-written and the statistical analysis, as far as I can judge, is competent. See below for how the manuscript can, potentially, become even a bit better.

Minor comments:

Abstract: a good summary, but if possible add number of species and number of individuals (e.g. in parenthesis somewhere)

Row numbers:

48, maybe replace “important” with “species-rich and partly threatened”

60, change “decisions” to “recommendations”?

66, “…threatened with extinction”. Maybe omit ”with extinction”, and instead give the red-list categories used, in parenthesis (CR, EN, …).

76, “…but are often overlooked”. Better, perhaps: “… but are often overlooked in conservation research.”

101, change “looks at” to “examines”

109-110, “Unthinned stands, with less dead wood and canopy openness…” comes sudden and unexpected in wording, you may qualify with a parenthesis “(recall that “unthinned” refers to production stands)”, thus helping the reader

171-172, bedrock sentence may be deleted as long as you don’t present for each region separately (but of little importance anyway, drop?)

315, add “(Table 3)” at end of sentence to help readers.

329-330, add at sentence start (row 329), “Also for this group, canopy openness had a ….”

332, add Table 4, as for 315 (see above)

345, why is Gamma diversity presented second in Results, and not last? (now Beta diversity is last) Compare sequence of listing of hypotheses (Gamma last). And since Gamma diversity represents the largest spatial level, should it not be presented last in Results? Moreover, in title of manuscript the sequence is Alfa-Beta-Gamma.

376, should not “Community composition” have a separate sub-heading? NMDS and Fig 6 seem as related to Gamma as to Beta, since the it shows the whole communities (separated into two regions). For this, and comment 345, you may explain sequency / community composition in Materials and methods (e.g. last there, before Results).

376, as regards PERMDISP and Table 5, the results are clear, and pairwise testing has bearing on Beta diversity. You say in the Intro, “beta diversity represents the difference in species community among stands within a forest type”. Maybe it should be “between stands”, as “among stands” approaches Gamma diversity?

There might be other, complementary ways of illustrating Beta diversity. Could differences in species numbers, and/or differences in species abundances, be analysed by WKH nearest neighbor-distances (WKH site vs WKH site); thinned nearest neighbor-distance (thinned site vs thinned site), unthinned nearest neighbor-distance (unthinned site vs unthinned site)? Could such “between site” paired analysis be of value? (thus, comparing same stand type between sites). Model estimates (Table 5) are valuable, but do not illustrate absolute species/abundance Beta diversity patterns for the reader. This means excluding the real biological units (species, individuals) and showing more abstract statistical measures. (But Figs 2-5 are very good in showing “biology”.)

Discussion

409, change “there were” to “we found”

406-420, very good and interesting

423, change “could possibly” to “may well”

424-425, I suggest change “Furthermore, the main determinants of diversity of red-listed saproxylic beetles may manifest at larger scales than the local.” to “Furthermore, the diversity of red-listed saproxylic beetles must also be analyzed at larger scales than the local.

434, possibly add, “In addition, community composition is not the only test of hypothesis 3; individual species would be interesting to explore in more detail”

459, “…Norway spruce is late-successional, adapted to closed-canopy, small-scale gap-dynamics…”. But so is e.g. beech, with even stronger tolerance to closed canopies than Norway spruce. The contradiction of hypothesis 4 is interesting. What proportion of your species were “spruce species”? Please add, if possible.

469-470, You write “Alternatively, the lower beta diversity in the managed stands could be due to lower among-stand diversity of forest structure and substrates”. I assume this can be tested quantitatively with your data (WKH vs managed), though may be the subject of a different paper.

511-513, a bit hard to follow / understand. Also, were there more bark beetles in Jönköping, attracting predators?

519-520, “…many species associated with spruce…”. Again, what proportion of your species are spruce-connected?

527, drop “from this”

533, ”…seem to harbor many species at the local scale”,

change to “…seem to harbor many species, relative to other habitats, at the local scale”

533-534, consider omitting this part of sentence; “…encouraging for the potential of conservation-oriented management actions within these forests…”. Not necessary, and not clear.

541, consider changing “management might do best focusing on scales larger than the local”

to: “management should focus on both local and larger scales”

Reviewer #2: The artilcle written in thesis formate. Tiltle, abstract, introduction, results, discussion not according to Scinetific manners, it should be revised and resubmit again.

Introduction of subject experiment not well explained. Author should explain briefly why this study required to conduct? What are the study gaps you address? Results presentations not in scientific terms, it should need to revise profoundly. Future directions are also not presented well overloaded text should need to removed.

Reviewer #3: Review for PONE-D-22-04886

Overall, it is a worthwhile piece of work. It presents an important contribution to the scientific community concerning the saproxylic beetles’ diversity across forest types and spatial scales i.e. alpha, beta, and gamma diversity. The paper has no shortcomings, the study appears to be scientifically sound, the language clear, making it easy to follow.

My specific minor comments are outlined:

Lines 91-94: Amount of dead wood, diversity and canopy openness seem to be three different factors affecting saproxylic beetles’ diversity. Please revise “seems to be a major determinant” and “Both of these”.

Line 93: The authors maybe could provide a reference for species preferring shaded wood, too (e.g. Müller et al. 2015 - doi: 10.1111/1365-2664.12421 or other).

Line 154: The authors may specify for clarity that coordinates are in WGS84 coordinate reference system, using Decimal Degrees (DD) as its units. Also, the data source of background map could be added.

Line 156: Instead of “(Nilsson et al., 2019)” the authors could write “[27]”.

Table 1: For consistency, next to Canopy openness the authors should write “(%)” and remove the units from the numbers. Also, in Stand age units must be added i.e. years in order the table to stand on is own without reading the paper.

Line 197: Please also write the scientific name for Scots pine (Pinus sylvestris L.).

In Figures write the full terms, for example of WKH and in Tables explain all abbreviations eg.in Line 322 after “Confidence intervals” you can add CI in parentheses.

Reviewer #4: In this manuscript, the author compares alpha, beta, and gamma diversity of saproxylic beetles in managed versus unmanaged Norway spruce stands in central-southern Sweden. Author used field collected samples across two years from two different sampling region and found that alpha and beta diversity were higher for saproxylic beetles except for red-listed ones in thin stands and semi-natural thinned stands respectively whereas gamma diversity was higher for red-listed beetles in semi-natural thinned stands. The author further argues that all three (alpha, beta, and gamma) diversity measures need to be taken into consideration while carrying out conservation efforts. I really appreciate the amount of work the author has put into measuring plant diameters, and in collection and identification of thousands of beetles. Even though I like the manuscript, I have some suggestions which I feel will make the manuscript better:

My biggest reservation about this manuscript is the introduction section. I am still not convinced if all the hypothesis that the author lists are actual hypothesis as some of these feel like predictions to me. I wonder if it would be possible to narrow them down and a lot of the predictions can be brought into discussion sections when the author is discussing the findings. I also feel the introduction section can be more coherent. I appreciate the fact that the author has tried to put as much information as possible, however the information can be arranged properly such that it will be easier for the reader. For example, author introduces the study system in the first paragraph and do not come back to it until third paragraph and again till fifth or sixth paragraph.

Figure 2 and 3: I think these figures could be supplemental figures as they are not part of the result section of the manuscript.

I also think the background grid and color is making it difficult to read the figure. So, adding “theme_bw()” at the end of the ggplot2 code that the author already has can help give a clean background making it easier to comprehend the figure.

It would also be helpful to label the x-axis as “log (Diameter at breast height)” rather than mentioning it in the figure legend.

Result: All the result section is explained only in statistical terms. On its current form, the manuscript is inaccessible to a person who is not familiar with linear mixed models. So, it would be helpful to provide biological explanations on what those results mean in at least one or two simple sentences such that the manuscript would be accessible to a broader audience.

Line 30 : The sentence starting in “These results..” would make a better final sentence to the abstract.

Line 141, 144, and 145: Replace “sample” with “sampling area or sampling region”

Line 193: Add “,” after trap

Line 210: Please replace “;” with “,” and add “add” before dead trees

Line 211: Is it a common practice to estimate visually?

Line 237&238: Please rewrite the sentence as “environmental variables per forest type and region are summarized in Table 1”

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21 Jun 2022

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Reviewer #4: 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: Review of:

Lower alpha, higher beta, and similar gamma diversity of saproxylic beetles in unmanaged compared to managed Norway spruce stands

(PONE-D-22-04886)

General comment:

This is an important contribution dealing with forestry systems and the evaluation of biodiversity therein. Its value lies mainly in assessing a range of habitats produced by a boreal clear-cutting system, including young plantations (first study in project), thinning, harvesting stages, and set-asides for biodiversity (here, saproxylic beetles). The study is unusual and valuable in its approach, and in addition the use of classical diversity concepts in the analysis is well motivated.

The manuscript is well-written and the statistical analysis, as far as I can judge, is competent. See below for how the manuscript can, potentially, become even a bit better.

Response: I thank reviewer #1 for helpful and insightful comments on the manuscript.

Minor comments:

Abstract: a good summary, but if possible add number of species and number of individuals (e.g. in parenthesis somewhere)

Response: this has been added to lines 20-21.

Row numbers:

48, maybe replace “important” with “species-rich and partly threatened”

Response: the line has been changed to “a diverse species group of conservation concern”, as I believe this fits better in the sentence while still being in line with what reviewer #1 suggests.

60, change “decisions” to “recommendations”?

Response: line changed accordingly, and for same line, “incorrect” changed to “poor” as there is no such thing as the “correct” management.

66, “…threatened with extinction”. Maybe omit ”with extinction”, and instead give the red-list categories used, in parenthesis (CR, EN, …).

Response: line changed accordingly.

76, “…but are often overlooked”. Better, perhaps: “… but are often overlooked in conservation research.”

Response: line changed accordingly.

101, change “looks at” to “examines”

Response: line changed accordingly.

109-110, “Unthinned stands, with less dead wood and canopy openness…” comes sudden and unexpected in wording, you may qualify with a parenthesis “(recall that “unthinned” refers to production stands)”, thus helping the reader

Response: The lines have been changed, clarifying that both thinned stands and unthinned stands are production stands, which hopefully makes the wording less abrupt and easier for the reader to follow.

171-172, bedrock sentence may be deleted as long as you don’t present for each region separately (but of little importance anyway, drop?)

Response: the sentence has been omitted.

315, add “(Table 3)” at end of sentence to help readers.

Response: line changed accordingly.

329-330, add at sentence start (row 329), “Also for this group, canopy openness had a ….”

Response: line changed to “Also for red-listed species…” for clarity.

332, add Table 4, as for 315 (see above)

Response: line changed accordingly.

345, why is Gamma diversity presented second in Results, and not last? (now Beta diversity is last) Compare sequence of listing of hypotheses (Gamma last). And since Gamma diversity represents the largest spatial level, should it not be presented last in Results? Moreover, in title of manuscript the sequence is Alfa-Beta-Gamma.

Response: I have switched the order of the two sections. This also meant that the numbering for figures 4-6 changed, and the text has been updated to for this.

376, should not “Community composition” have a separate sub-heading? NMDS and Fig 6 seem as related to Gamma as to Beta, since the it shows the whole communities (separated into two regions). For this, and comment 345, you may explain sequency / community composition in Materials and methods (e.g. last there, before Results).

Response: The analyses of community composition and beta diversity are very closely related and complement each other, and both differences in location (i.e. composition) and dispersion (i.e. beta diversity) are visualized by the NMDS, so to me it makes much more sense to group these together. I have added some further explanation of the PERMDISP and NMDS in the methods section (lines 297, 299-301).

376, as regards PERMDISP and Table 5, the results are clear, and pairwise testing has bearing on Beta diversity. You say in the Intro, “beta diversity represents the difference in species community among stands within a forest type”. Maybe it should be “between stands”, as “among stands” approaches Gamma diversity?

Response: Beta diversity here is a measure of variation in community composition among multiple stands (in the NMDS, the average distance of a stand from the centroid of all points of the same forest type), so I think among is more fitting than between. But I have rephrased the definition in lines 79-80 to make it more straightforward.

There might be other, complementary ways of illustrating Beta diversity. Could differences in species numbers, and/or differences in species abundances, be analysed by WKH nearest neighbor-distances (WKH site vs WKH site); thinned nearest neighbor-distance (thinned site vs thinned site), unthinned nearest neighbor-distance (unthinned site vs unthinned site)? Could such “between site” paired analysis be of value? (thus, comparing same stand type between sites). Model estimates (Table 5) are valuable, but do not illustrate absolute species/abundance Beta diversity patterns for the reader. This means excluding the real biological units (species, individuals) and showing more abstract statistical measures. (But Figs 2-5 are very good in showing “biology”.)

Response: See Anderson et al. 2006 [75] for problems associated both with using dissimilarities between pairs of sampling units (p. 684 “A test for…”), and using raw abundances, i.e. “real biological units” (p. 685 “Potential pitfalls…”) when testing differences in beta diversity between groups of sampling units (e.g. stands of different forest types). I follow the recommendations from Anderson et al. 2011 [74] on the appropriate way to test differences in multivariate variation (in this case beta diversity) between levels of a categorical factor (in this case forest type).

Discussion

409, change “there were” to “we found”

Response: text changed accordingly

423, change “could possibly” to “may well”

Response: I changed “could possibly” to “may”

424-425, I suggest change “Furthermore, the main determinants of diversity of red-listed saproxylic beetles may manifest at larger scales than the local.” to “Furthermore, the diversity of red-listed saproxylic beetles must also be analyzed at larger scales than the local.

Response: line changed to “Furthermore, the diversity of red-listed saproxylic beetles may also need to be analyzed at larger scales than the local.”

434, possibly add, “In addition, community composition is not the only test of hypothesis 3; individual species would be interesting to explore in more detail”

Response: added “In addition, associations of individual species to the different forest types may be obscured by a general community composition measure, and could be interesting to explore in more detail.”

459, “…Norway spruce is late-successional, adapted to closed-canopy, small-scale gap-dynamics…”. But so is e.g. beech, with even stronger tolerance to closed canopies than Norway spruce. The contradiction of hypothesis 4 is interesting. What proportion of your species were “spruce species”? Please add, if possible.

Response: I have added a section on host tree associations at the start of the results section, lines 309-314.

469-470, You write “Alternatively, the lower beta diversity in the managed stands could be due to lower among-stand diversity of forest structure and substrates”. I assume this can be tested quantitatively with your data (WKH vs managed), though may be the subject of a different paper.

Response: In theory this could be tested, but I believe this to be outside the scope of the present paper, and would perhaps require additional measurements of stand characteristics.

511-513, a bit hard to follow / understand. Also, were there more bark beetles in Jönköping, attracting predators?

Response: I have rephrased the section to make it easier to follow. There were indeed slightly more wood consumers in the Jönköping sample, although this general pattern would not explain the difference between the forest types.

519-520, “…many species associated with spruce…”. Again, what proportion of your species are spruce-connected?

Response: See above.

527, drop “from this”

Response: text change accordingly

533, ”…seem to harbor many species at the local scale”,

change to “…seem to harbor many species, relative to other habitats, at the local scale”

Response: text change accordingly

533-534, consider omitting this part of sentence; “…encouraging for the potential of conservation-oriented management actions within these forests…”. Not necessary, and not clear.

Response: text change accordingly

541, consider changing “management might do best focusing on scales larger than the local”

to: “management should focus on both local and larger scales”

Response: text changed to “management should not ignore larger scales”

Reviewer #2:

Response: I thank reviewer #2 for comments on the manuscript. However, I find some of the comments difficult to follow as they do not refer to specifics, and at times refer to sections that are not present in the manuscript (e.g. no experiment was carried out; the article does not contain a section on future directions).

The artilcle written in thesis formate. Tiltle, abstract, introduction, results, discussion not according to Scinetific manners, it should be revised and resubmit again.

Response: I believe the manuscript follows the structure set out in the PLoS ONE submission guidelines.

Introduction of subject experiment not well explained.

Response: I am unclear as to what reviewer #2 is referring to here. There was no experiment carried out in this study.

Author should explain briefly why this study required to conduct? What are the study gaps you address?

Response: This is addressed several times in the introduction, e.g. lines 45-47, 61-65, 81-83.

Results presentations not in scientific terms, it should need to revise profoundly.

Response: It is hard to address this point without specific examples. I believe the results section uses scientific terminology throughout. The comment also contrasts with comments from reviewer #4 indicating the opposite, i.e. that the results section should use less technical language.

Future directions are also not presented well overloaded text should need to removed.

Response: I am unsure as to what part of the text this comment is concerning, as the manuscript does not contain a "Future directions" section.

Reviewer #3: Review for PONE-D-22-04886

Overall, it is a worthwhile piece of work. It presents an important contribution to the scientific community concerning the saproxylic beetles’ diversity across forest types and spatial scales i.e. alpha, beta, and gamma diversity. The paper has no shortcomings, the study appears to be scientifically sound, the language clear, making it easy to follow.

Response: I thank reviewer #3 for helpful and insightful comments on the manuscript.

My specific minor comments are outlined:

Lines 91-94: Amount of dead wood, diversity and canopy openness seem to be three different factors affecting saproxylic beetles’ diversity. Please revise “seems to be a major determinant” and “Both of these”.

Response: the lines have been changed accordingly.

Line 93: The authors maybe could provide a reference for species preferring shaded wood, too (e.g. Müller et al. 2015 - doi: 10.1111/1365-2664.12421 or other).

Response: the reference has been added.

Line 154: The authors may specify for clarity that coordinates are in WGS84 coordinate reference system, using Decimal Degrees (DD) as its units. Also, the data source of background map could be added.

Response: the figure caption has been changed accordingly, and the source of the background map added.

Line 156: Instead of “(Nilsson et al., 2019)” the authors could write “[27]”.

Response: the reference has been corrected accordingly

Table 1: For consistency, next to Canopy openness the authors should write “(%)” and remove the units from the numbers. Also, in Stand age units must be added i.e. years in order the table to stand on is own without reading the paper.

Response: the table has been changed accordingly

Line 197: Please also write the scientific name for Scots pine (Pinus sylvestris L.).

Response: I have tried to be consistent regarding scientific names, and as Scots pine is mentioned earlier with scientific name in line 161, I have not provided the scientific name here.

In Figures write the full terms, for example of WKH and in Tables explain all abbreviations eg.in Line 322 after “Confidence intervals” you can add CI in parentheses.

Response: I have added explanations for all abbreviations in the table and figure legends, although I have retained the abbreviation WKH in most of the figures as Woodland Key Habitats is too long to fit and would require reducing the text size.

Reviewer #4: In this manuscript, the author compares alpha, beta, and gamma diversity of saproxylic beetles in managed versus unmanaged Norway spruce stands in central-southern Sweden. Author used field collected samples across two years from two different sampling region and found that alpha and beta diversity were higher for saproxylic beetles except for red-listed ones in thin stands and semi-natural thinned stands respectively whereas gamma diversity was higher for red-listed beetles in semi-natural thinned stands. The author further argues that all three (alpha, beta, and gamma) diversity measures need to be taken into consideration while carrying out conservation efforts. I really appreciate the amount of work the author has put into measuring plant diameters, and in collection and identification of thousands of beetles. Even though I like the manuscript, I have some suggestions which I feel will make the manuscript better:

Response: I thank reviewer #4 for helpful and insightful comments on the manuscript.

My biggest reservation about this manuscript is the introduction section. I am still not convinced if all the hypothesis that the author lists are actual hypothesis as some of these feel like predictions to me. I wonder if it would be possible to narrow them down and a lot of the predictions can be brought into discussion sections when the author is discussing the findings.

Response: I accept reviewer #4’s point that they are perhaps more appropriately described as predictions than hypotheses, and have modified the text accordingly. I nevertheless believe they are supported by the preceding introduction, and I think they provide a useful structure to the paper. Having them present from the start should make it easier for the reader to follow the different lines of inquiry present in the paper, and provides a clear connection between the introduction and discussion sections. This being said, if the editor still believes that some of these should be combined, simplified or removed from the introduction, I will not object.

I also feel the introduction section can be more coherent. I appreciate the fact that the author has tried to put as much information as possible, however the information can be arranged properly such that it will be easier for the reader. For example, author introduces the study system in the first paragraph and do not come back to it until third paragraph and again till fifth or sixth paragraph.

Response: The section explaining the theoretical framework of alpha-beta-gamma diversity may be somewhat incongruous with the rest of the introduction, although it is important establishing knowledge. I have moved the paragraph to a later part of the introduction (lines 78-91), in order to hopefully facilitate better flow and coherency.

Figure 2 and 3: I think these figures could be supplemental figures as they are not part of the result section of the manuscript.

Response: While they are not part of the results section, I believe they nonetheless are valuable in characterizing the stands, and have direct bearing on the interpretation of the results. Reviewer #1 also highlights these as good, in showing concrete “biology”. Consequently, I have left them in the main text, but ultimately I leave it up to the discretion of the editor whether they should be moved to the supplementary material.

I also think the background grid and color is making it difficult to read the figure. So, adding “theme_bw()” at the end of the ggplot2 code that the author already has can help give a clean background making it easier to comprehend the figure.

Response: While removing the background will possibly give a cleaner look, it will make it more difficult to identify which series of points are associated with which tree species, especially should the paper be viewed in black and white (e.g. printed). Additionally, for figure 3, leaving out the background will make it harder to identify the discrete facets (i.e. dead wood type x forest type combination). As such, I have chosen to retain the background.

It would also be helpful to label the x-axis as “log (Diameter at breast height)” rather than mentioning it in the figure legend.

Response: Renaming the x-axis as log(Diameter…) would not be correct, as this would indicate that the values have been log transformed. Instead, the raw values have been plotted on a logarithmic scale.

Result: All the result section is explained only in statistical terms. On its current form, the manuscript is inaccessible to a person who is not familiar with linear mixed models. So, it would be helpful to provide biological explanations on what those results mean in at least one or two simple sentences such that the manuscript would be accessible to a broader audience.

Response: To facilitate understanding, I have added a short summary of the main results to the end of each results section: lines 362-366, 391-394, 427-431.

Line 30 : The sentence starting in “These results..” would make a better final sentence to the abstract.

Response: abstract changed accordingly

Line 141, 144, and 145: Replace “sample” with “sampling area or sampling region”

Response: text changed accordingly

Line 193: Add “,” after trap

Response: text changed accordingly

Line 210: Please replace “;” with “,” and add “add” before dead trees

Response: text changed accordingly

Line 211: Is it a common practice to estimate visually?

Response: Ocular estimation is used in forestry, e.g. for standing deadwood in The Swedish National Forest Inventory (see p. 217 of handbook [in Swedish] https://www.slu.se/globalassets/ew/org/centrb/rt/dokument/faltinst/ris_faltinstruktion_2011_hela.pdf). Although physically measuring the top diameter would obviously have been preferable, this was not practically possible in this case. The method is unlikely to have had much influence on the end result, as the difference in diameter between the bottom and tops of snags was usually minor, and the number of snags where this method was employed was small.

Line 237&238: Please rewrite the sentence as “environmental variables per forest type and region are summarized in Table 1”

Response: Response: text changed accordingly

Submitted filename: Response to Reviewers.docx

Click here for additional data file.

24 Jun 2022

Lower alpha, higher beta, and similar gamma diversity of saproxylic beetles in unmanaged compared to managed Norway spruce stands

PONE-D-22-04886R1

Dear Dr. Gran,

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Reviewers' comments:

30 Jun 2022

PONE-D-22-04886R1

Lower alpha, higher beta, and similar gamma diversity of saproxylic beetles in unmanaged compared to managed Norway spruce stands

Dear Dr. Gran:

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