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Jean J. de Klerk1 & Nico L. Avenant1,2

1Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa

2*Department of Mammalogy, National Museum, Bloemfontein, South Africa

*Corresponding Author:


Small mammal communities are potential indicators of habitat integrity in southern African grassland ecosystems. As such, the assessment of small mammal diversity and community structure in rehabilitated areas could allow judgments to be made regarding the success of implemented eradication programs. In this study evidence in support of their status as ecological indicators is presented by investigating small mammals in an area cleared of alien vegetation in the Albany Thicket Biome of the Eastern Cape, South Africa. Small mammal community variables were studied in a degraded area infested with alien black wattle Acacia mearnsii, an area cleared of black wattle, and a control area with no records of alien vegetation. During 5400 trap nights 690 individuals were caught, with an overall trap success of 12.8%. Significant differences were found between degraded, rehabilitated and control plots. Small mammal total abundance, individual species’ abundance, relative abundance, species richness, and diversity were highest in the control plot and lowest in the infested plot. Intermediate values were obtained in the rehabilitated plot; most of these were significantly higher than in the infested area. One year after rehabilitation the rehabilitated plot shared a Bray-Curtis similarity value of 0.93 with the control plot, markedly lower (0.67) than the infested plot. This case study is applicable to rehabilitation, habitat integrity and environmental management.

Key words: community structure, ecological integrity, indicators, small mammals, succession.


Alien invasive plant species pose a major threat to biodiversity worldwide. In South Africa over 200 introduced plant species have been classified as invasive (Poona 2001; Chamier et al. 2012) and are considered to be the most significant threat to biodiversity after direct habitat destruction (Holmes et al. 2000). Alien invasives are associated with various negative impacts, both direct (e.g. native species loss and increased fire intensity) and indirect (e.g. decreased soil absorption and river flow) (Chamier et al. 2012).

Alien invasive plant species eradication programs have been ongoing across many areas of South Africa for a long time, and their schemes have been classified as some of the most ambitious in the world (Rouget et al. 2004; Galatowitsch & Richardson 2005). These eradicated areas reportedly recover to a natural ecological state and therefore improve the biodiversity and ecosystem functioning of the area. Apart from vegetation itself, a number of other indicators of recovery, such as insects (Pearson 1992) and reptiles (Letnic et al. 2004), have been considered, but these are relatively cumbersome, require long periods of time, are season-dependent, specialists must be involved, and interpretation of results is not always clear.

A limited number of studies have identified small mammal communities (including mouse, shrew and sengi) as indicators of ecological integrity and have suggested that this group is useful for sustainable habitat management (see Carey & Johnson 1995; Ferreira & Van Aarde 1997; Avenant 2000, 2003, 2011; Kaminski et al. 2004; Avenant & Cavallini 2007; Avenant, Watson & Schulze 2008). This group responds relatively quickly to changing environmental conditions, is adapted to microhabitats (and is therefore affected by small-scale changes), and can be utilised as an inexpensive, relatively quick, estimate of habitat health and improvement (Avenant & Cavallini 2007; Avenant et al. 2008; Avenant 2011). Small mammals have not, however, been used as indicators in studies relating to alien vegetation eradication programs.

In areas with invasive plants in southern Africa, small mammal species richness and diversity have been found to be lower in areas with Lantana sp. than in less disturbed areas (Avenant & Kuyler 2002), and the community structure changes with vegetation succession and ecological integrity (Fox 1982, 1990; Foster & Gaines 1991; Avenant 2000; Schweiger et al. 2000; Avenant & Cavallini 2007; Avenant et al. 2008; Avenant 2011). By assessing the small mammal diversity and community structure in rehabilitated areas, judgments can therefore be made about the recovery of ecosystems post-eradication. Avenant (2005, 2011) suggested a hypothesis where small mammal species richness and diversity increase with succession of an area, as more specialist species enter the habitat and the relative contribution of generalist species decreases in the pre-climax phase; in the post-climax phase the process is reversed.

Using a standard capture-mark-release-recapture technique, our study explored the extent to which small mammal community variables indicate improved integrity in southern Africa’s Albany Thicket Biome about one year after alien invasive black wattle Acacia mearnsii (De Wildeman 1925) was eradicated.


The study was conducted at Kariega Game Reserve (lat -33.58°, lon 26.61°), located in the Albany Thicket Biome, approximately 45 km south of Grahamstown, Eastern Cape Province, South Africa. Mean temperatures range from 9°C in June and July (mid-winter) to 26°C in January and February (mid- to late-summer) (Weather Bureau 1986). Three homogenous plots were selected in the dominant vegetation type, Kowie Thicket (Parker 2004; Hoare et al. 2006): (i) an area heavily infested with black wattle, (ii) an area cleared of black wattle 12 months prior to the study, and (iii) a control area with no black wattle. These plots were between 3 km and 8 km apart, on similar substrate (sandy soil with some lithosols), aspect and elevation (570 m a.s.l.).

Plots were sampled by using 77 x 65 x 290 mm PVC live traps. Traps were placed on three parallel transects within each plot, and left open for four consecutive days and nights during each of three survey periods. These survey periods were once monthly, from October till December 2013, and excluded the three days prior and post full moon when many nocturnal species are less active (Price et al. 2013; Upham & Hafner 2013; N.L. Avenant pers. obs.).

Each transect had 50 traps, spaced 5 m apart (Tew & Todd 1994; Ferreira & Avenant 2003). Considering a 10 m attraction zone, the total area covered by each transect was at least 5 300 m2, and the total area covered in each plot at least 15 900 m2. All transects were more than 200 m apart, and more than 100 m from the edge of any homogenous area. A total of 150 traps in each plot, and therefore a total of 450 traps on the three plots, were placed simultaneously per survey period. Standardised bait consisted of a mixture of peanut butter, rolled oats, sunflower oil and marmite, to attract as wide a variety of small mammal species as possible (see Avenant 2011; Kok, Parker & Barker 2013). All individuals caught were hair-clipped on the left buttock (first survey period), right buttock (second survey period) and left buttock again (third survey period) to enable recording of recaptures. Trapped animals were all released at capture sites.

A trap night was defined as one trap set for a 24 h period (Rowe-Rowe & Lowry 1982; Avenant 2011). Each plot therefore had a total of 600 trap nights per survey period (150 traps per area for four days) and a total of 1800 trap nights at completion of the study. Traps were checked twice a day, at 06H00–08H00 and 18H00–19H00 , to ensure consistency, prevent mortalities , and rebait traps if needed.

The measures of abundance used were trap success, species richness and species diversity. Trap success (an indication of density) was determined on each plot as the number of small mammals captured per 100 trap nights (Avenant 2011). Species richness is the number of species collected, and diversity is expressed using both the Shannon and Simpson indices (Magurran 2004). Species evenness was calculated using Smith and Wilson’s Evar formula (Smith & Wilson 1996; Tuomisto 2012). The Bray-Curtis similarity index was used to test similarity between the three areas (Magurran 2004).

Data were tested for normality using a Shapiro-Wilks’ W test. To investigate any differences in the number of species and number of individuals trapped between plots, Friedman Anovas were used. Wilcoxon matched pairs tests then indicated between which groups the differences lay. For a comparison of diversity and evenness scores per trap session, t-tests for dependent samples were used, and Spearman rank order was used for correlations. Statistical analyses were done with Statistica for Windows (Statsoft Inc., Tulsa, OK) and the 95% level (p<0.05) was regarded as statistically significant for all tests.


A total of 690 individuals were caught during the 5400 trap nights of the study, giving an overall trap success of 12.78% (Table 1). In total five small mammal species were caught: one musk shrew (Crocidura flavescens Geoffroy, 1827) and four rodents. In all three areas Rhabdomys pumilio (Sparrmann, 1784) was the most abundant, followed by Otomys irroratus (Brants, 1827) and Micaelamys namaquensis (A. Smith, 1834).

All five species were collected in the control plot (Table 1). This plot also had the highest trap success (16.55 ± 4.71), total abundance (N = 298 individuals; 43.19% of the total number of individuals trapped), species richness (4.33 ± 0.58), and both Shannon H (0.732 ± 0.048) and Simpson’s D (1.654 ± 0.039) diversities. The Evar evenness value at the control plot was low (0.300 ± 0.034).

In comparison, only three species were recorded from the black wattle infested plot. This plot also had the lowest trap success (7.277 ± 2.343), total abundance (N = 131; 18.99% of the total number of individuals trapped), species richness (2.67 ± 0.58), and Shannon H’ (0.530 ± 0.026) and Simpson’s D (1.440 ± 0.046) diversities (Table 1). This plot’s evenness value (0.494 ± 0.196) was the highest of the three (Table 1).

In the cleared plot all five species were caught, with most community variables (trap success, total abundance, species richness, diversity, evenness) intermediate (Table 1; Figs 1–3). The total of 261 individuals caught contributed 37.83% to the total number of individuals for all areas.

Abundance of small mammals differed between the three plots (F2,12 = 19.5; p<0.0001), with the number of individuals caught differing significantly between all plots (Fig. 1). Similar patterns were observed for the three most abundant species Rhabdomys pumilio (F2,12 = 18.178; p<0.001), Micaelamys namaquensis (F2,12 = 7.590; p<0.024) and Otomys irroratus (F2,12 = 9.50; p<0.009), with significantly fewer individuals caught in the infested plot than in the control or rehabilitated plots (Wilcoxon matched pairs tests; p<0.03); for all three species more individuals were trapped in the control plot compared to the rehabilitated plot, but none of the comparisons were significant (p>0.05). Saccostomus campestris (Peters, 1846) and Crocidura flavescens were found in both the control and rehabilitated plots, but not in the infested plot.

Species richness per plot differed in a similar way between plots (F2,12 = 11.029; p<0.004), with more species caught in the control and rehabilitated plots than in the infested plot (Z = 2.521 and Z=2.395, respectively; p<0.02) (Fig. 2). No significant difference could be found between the rehabilitated and control plots.

Both the Shannon and Simpson’s diversities were highest in the control plot (H’ = 0.731 ± 0.048; D = 1.654 ± 0.039), intermediate in the rehabilitated plot (H’ = 0.641 ± 0.107; D = 1.490 ± 0.106) and lowest in the infested plot (H’ = 0.530 ± 0.026; D = 1.440 ± 0.046) (Fig. 3). The differences were significant between the control and infested plots only. Species evenness scores were highest in the infested plot, intermediate in the rehabilitated plot, and lowest in the control plot. These differences were, however, not significant (t-tests for dependent samples; p>0.2). Evar correlated significantly with Shannon H’ (R = -0.7; p< 0.04), but not with Simpson’s D (R = -0.57; p> 0.1).

The Bray-Curtis index (Fig. 4) indicates that the small mammal community in the rehabilitated area, cleared of alien black wattle, was markedly more similar to that in the control area (0.93) compared to that in the black wattle infested area (0.67).


Small mammal communities have been investigated as bioindicators in many different environmental contexts (Fox & Fox 1984; Kirkland 1990; Ferreira & Van Aarde 2000; Carey & Wilson 2001; Klenner & Sullivan 2003; Pearce & Venier 2005; Hoffmann & Zeller 2005; Klinger 2006; Glennon & Porter 2007; Hauptfleisch & Avenant 2015). The variable most often referred to in such studies is species richness. According to Tilman’s hump-shaped curve model (Tilman 1982), species richness increases with advancing successional stage up to the point of ecological climax, followed by a post-climax decline. Studies that have demonstrated correlations between species richness and declines in ecosystem function, resilience and resistance support this model (e.g. Wootton 1998; Cardinale, Nelson & Palmer 2000; Johnson 2000; McCann 2000; Petchey 2000; Fonseca & Ganade 2001). The model has also been supported by several studies conducted on rodents in southern African (Joubert & Ryan 1999; Rowe-Rowe 1995; Rowe-Rowe & Lowry 1982; Monadjem & Perrin 2003; Avenant & Cavallini 2007; Avenant et al. 2008; Avenant 2011) and Chinese grasslands (Wang et al. 1999), and in other biomes in Africa (e.g. Joubert & Ryan 1999; Eccard, Walther & Milton 2000; Avenant & Kuyler 2002) and North America (e.g. Abramsky & Rosenzweig 1984).

Other small mammal variables referred to in Avenant’s (2011) hypothesis—that reflect the integrity of the environment—are species diversity (which often correlates positively with species richness), presence or absence of generalist species (their domination of small mammal communities is often associated with lower ecological integrity/higher disturbance), presence or absence of specialist species (occur more frequently in areas with higher ecological values), and presence or absence of specific indicator species known to enter or leave the system at certain successional stages (Avenant 2011). These variables are correlated and together they indicate the successional position on the hump-shaped integrity curve. This acquiescence of variables is most useful, especially as the number of small mammal species trapped, as well as trap success (e.g. ranging between 0% and 23.20% in South Africa’s Grassland Biome, with a seasonal mean of 1.91 ± 1.29 for specific transects), can be very low in some systems; the sole use of species richness and diversity scores is, therefore, not sufficient (Avenant 2011). The initial use of evenness values (Avenant 2005) has also been considered, but was dropped from the hypothesis as no consequent trend could be found (Avenant 2011). Trap success and density estimates are also of no use in this hypothesis, but are an indication of primary productivity/grazing capacity (Van Horne 1983; Joubert & Ryan 1999; Avenant 2003, 2011).

The current alien eradication study supports Avenant’s (2011) hypothesis. Higher species richness and diversities were found in the more pristine control plot compared to the black wattle infested plot. Although habitat specific to some extent, all species found in the infested plot (O. irroratus, R. pumilio, M. namaquensis) can be regarded as generalist species in the study area (see Avenant 2011). On the other hand the control plot also had a specialist species (C. flavescens; insectivores are considered good indicators of increased habitat health; Avenant 2011, Pocock & Jennings 2008) plus another species, S. campestris, which is not associated with disturbed areas. One year after eradication of black wattle, the rehabilitated area already had scores for all of these variables falling in between the scores for disturbed and more pristine sites, and already showed markedly closer similarity to the more pristine control site (Bray-Curtis value of 0.93). Taking all information into account, the rehabilitated area can therefore be assumed to lie in a succession position between the disturbed infested area and the more pristine control area.

Although no alien vegetation has been recorded in the control area (Kariega Reserve Alien Removal Plan, unpublished), there are a number of indications that this area is not in a pristine condition: 1. Shannon diversities of less than 0.8 are considered low (Avenant & Cavallini 2007; Avenant et al. 2008; Whittington-Jones, Bernard & Parker 2008); 2. species richness was lower than expected, with at least two more small mammal species (i.e. Dendromus melanotis A. Smith, 1834 and/or Dendromus mesomelas Brants, 1827, and Mus minutoides Smith, 1834) expected to also be present in similar, pristine habitat in the study area (following Els & Kerley 1996; Skinner & Chimimba 2005; Krystufek et al. 2007; Whittington-Jones et al. 2008); 3. these “missing” species can all be considered specialist species (Avenant 2011); and 4. the dominance by one diurnal (R. pumilio), one crepuscular (O. irroratus) and one nocturnal (M. namaquensis) species (Avenant 2011). It will therefore be interesting to see how the small mammal variables keep changing on the rehabilitated plot if progressive succession is allowed to occur uninterrupted. Depending on whether the same expected disturbance that influences current community structure on the control plot is allowed to play a role on the rehabilitated plot, integrity in the recovering area may even exceed that of the control area (O’Farrell et al. 2008; Avenant 2011).

In conclusion, where the small mammal variables indentified above indicated the success of the black wattle eradication program in improving the ecological integrity of the rehabilitated area, the higher trap success in the more pristine control and cleared plots also agreed with other rehabilitation studies which indicated that black wattle eradication leads to increased primary productivity and grazing potential in such areas (Dye & Jarmain 2004; Yapi 2013). The inclusion of small mammal community variables as indicators of successful management during alien eradication programs is, therefore, supported.


Stenden South Africa are acknowledged for financial assistance. The owners, management and staff at Kariega Game Reserve are thanked for allowing this work on their premises. Frances van Pletzen provided assistance and co-ordinated this work with the Kariega Game Reserve conservation program. Gerhard van der Westhuizen, Jason Friend and Brendon Jennings assisted with data collection and accommodation during the study period. This paper is also based on research supported in part by the National Research Foundation of South Africa (Grant specific unique reference number UID 86321). 


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Figure legends

Figure 1. Mean, standard error and standard deviation of the number of small mammal individuals trapped per day in the three study plots. Letters in superscript refer to homologous groupings derived from Wilcoxon matched pairs tests.

Figure 2. Mean, standard error and standard deviation of the number of species trapped per day in the three sampling plots. Letters in superscript refer to homologous groupings derived from Wilcoxon matched pairs tests.

Figure 3. A comparison of (a) Shannon and (b) Simpson’s small mammal diversities on the three sampling plots. Vertical bars denote 95% confidence intervals. Letters in superscript refer to homologous groupings derived from t-tests for dependent samples.

Figure 4. Bray-Curtis values indicating small mammal community similarity between three sampling plots at Kariega Nature Reserve, South Africa.

Table 1. Summary of small mammals trapped at three plots and during three months at the Kariega Game Reserve, South Africa. Infested, plot in area infested with alien black wattle Acacia mearnsii;  Cleared, plot in area cleared of black wattle; Control, plot in area with no records of alien vegetation.

Species October 2013 November 2013 December 2013
  Infested Cleared Control Infested Cleared Control Infested Cleared Control
Otomys irroratus 5 11 18 4 10 16 9 9 10
Rhabdomys pumilio 48 90 96 24 65 78 36 58 54
Micaelamys namaquensis 4 5 9 1 6 8 0 4 4
Saccostomus campestris 0 0 2 0 1 2 0 1 1
Crocidura flavescens 0 0 0 0 0 0 0 1 1
Number of individuals 57 106 125 29 82 104 45 73 69
Trap success 9.50 17.67 20.83 4.83 13.67 17.33 7.50 12.17 11.50
Species richness 3 3 4 3 4 4 2 5 5
Shannon Diversity, H’ 0.545 0.518 0.736 0.546 0.686 0.777 0.500 0.718 0.682
Simpsons Diversity, D 1.395 1.367 1.632 1.440 1.552 1.699 1.486 1.550 1.630
Evenness, Evar 0.427 0.377 0.304 0.340 0.270 0.332 0.715 0.260 0.264


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