Mammal species richness and habitat use in rainforest and abandoned agricultural fields in Chiapas, Mexico

1. We evaluated the potential of small, isolated cornfields embedded in a large forest matrix as an appropriate compromise between conservation and sustainable development.
2. We examined the relationship between habitat structure and diversity with overall mammal species richness and abundance of six common small mammals in four 6-year-old abandoned cornfields (oldfields) and four continuous rainforest sites in the most speciose region in Mexico, the Selva Lacandona, Chiapas.
3. Species richness did not differ between forests and oldfields, indicating that forest-dependent mammals penetrate oldfields of size 0·9–2·9 ha, presumably because forest cover and resources are nearby. Even species which strongly selected forest habitat, such as H. desmarestianus and D. marsupialis , were present in oldfields, and only the latter showed a significant decline in the number of captures as a function of distance from forest edge.
4. The Lacandon Indian use of the land for agriculture in the form of small (> 3 ha) agricultural plots embedded in a large forest matrix increases spatial heterogeneity and promotes mammal diversity.
5. Those small plots (in agricultural production terms) are intermediate in size when the whole continuum of the local natural and anthropogenic disturbance sizes are considered; more common are the extensive clearings for agriculture or cattle ranching, whereas the most common forest disturbance is treefall gaps, at least 20 times smaller than oldfields.
6. This form of land use should be considered as an important, appropriate productive element when decisions are made about managing reserves and pursuing sustainable development.     

Burning and logging differentially affect endemic vs. widely distributed butterfly species in Borneo

We assess the differential impact of logging and ENSO (El Niño Southern Oscillation)-induced disturbance on the relative butterfly abundance and species richness of range-restricted and widespread species within the island of Borneo. Relative abundance and species richness were assessed using rarefaction and species accumulation curves in unburned isolates surrounded by burned forest, the burned forest itself, and continuous forest unaffected by ENSO-induced disturbance in addition to logged and unlogged landscapes in unburned forest. The relative abundance of endemics was significantly higher in unlogged forest than logged forest and significantly higher in unburned forest than burned forest. Rarefied species richness of range categories was similar (Bornean endemics) or higher (other categories) in selectively logged than unlogged forest. In contrast, rarefied species richness of range-restricted species was highest in continuous forest, intermediate in unburned isolates, and lowest in burned forest. Only two individuals of a single Bornean endemic species were found in all the burned forest. Although species richness was higher in all range categories in continuous forest than in unburned isolates and in burned forest, the difference was most pronounced for range-restricted species. Logging and ENSO-induced fires thus have contrasting effects on range-restricted species. While both increase the relative abundance of widely distributed species at the expense of range-restricted species, only ENSO-induced disturbance lowers the rarefied number of restricted range species. Our research highlights the threat that severe ENSO events pose to geographically restricted classes of biodiversity.     

Comparisons of butterfly richness and abundance measures in prairie and barrens

Transect surveys of adult butterflies were conducted along fixed routes at 27 study sites grouped into three subregions of tallgrass prairie and one subregion of pine-oak barrens in the midwestern USA. Within subregion, each site was visited the same number of times over 5–7 years on similar dates with similar weather. For each site, five indices of species richness and/or abundance were calculated both for total butterflies and for specialist species primarily restricted to native herbaceous vegetation. These indices were then analysed as to how much they agreed or conflicted in site ranking and how site rankings based on total butterflies compared to those based on specialists. Variation in site ranking by different indices was relatively low. Mean site rank by specialist indices covaried significantly with mean site rank by indices for total butterflies. Numerous studies have shown that on a regional scale, areas of higher richness for all species in a taxonomic group are different habitat types (based on amount of canopy or degree of degradation) from hotspots for that taxon's subset of species of conservation concern (endemics or specialists). But in this study, within a habitat type, site rankings based on total butterflies significantly tended to agree with site rankings based on specialist butterflies. This suggests that site prioritization and management favouring specialist butterflies would also favour the overall butterfly fauna possible in the same habitat.     

Effects of selective logging on the arboreal ants of a Bornean rainforest

We examined the effect of selective logging and corresponding forest canopy loss on arboreal ant diversity in a tropical rainforest. Arboreal ants were collected from an unlogged forest plot and from forest plots selectively logged 14 years and 24 years earlier in Danum Valley, Sabah, Malaysia, using a canopy fogging method. Selective logging was associated with a significant decrease in canopy cover and an increase in understory vegetation density relative to unlogged forest. Our study showed that selective logging in primary forest might not dramatically decrease total species number and overall abundance of arboreal ants; however, it may influence the species composition and dominance structure of the ant community, accompanied by an increase in abundance of shrub‐layer species and trophobiotic species. In view of the results of this study, management techniques that minimize logging impact on understory vegetation structure are likely to help maintain the conservation value of logged forests for arboreal ants. Our results also suggest that accurate assessment of the impacts on biodiversity should not be based only on measurement of species number and overall abundance, but also on analysis of species composition and community structure.     

An elevational shift in butterfly species richness and composition accompanying recent climate change

The geographic ranges of many species have shifted polewards and uphill in elevation associated with climate warming, leading to increases in species richness at high latitudes and elevations. However, few studies have addressed community‐level responses to climate change across the entire elevational gradients of mountain ranges, or at warm lower latitudes where ecological diversity is expected to decline. Here, we show uphill shifts in butterfly species richness and composition in the Sierra de Guadarrama (central Spain) between 1967–1973 and 2004–2005. Butterfly communities with comparable species compositions shifted uphill by 293 m (± SE 26), consistent with an upward shift of approximately 225 m in mean annual isotherms. Species richness had a humped relationship with elevation, but declined between surveys, particularly at low elevations. Changes to species richness and composition primarily reflect the loss from lower elevations of species whose regional distributions are restricted to the mountains. The few colonizations by specialist low‐elevation species failed to compensate for the loss of high‐elevation species, because there are few low‐elevation species in the region and the habitat requirements of some of these prevent them from colonizing the mountain range. As a result, we estimated a net decline in species richness in approximately 90% of the region, and increasing community domination by widespread species. The results suggest that climate warming, combined with habitat loss and other drivers of biological change, could lead to significant losses in ecological diversity in mountains and other regions where species encounter their lower latitudinal‐range margins.     

Mixed effects of habitat fragmentation on species richness and community structure in a microarthropod microecosystem

Abstract.  1. Theory is unclear about the optimal degree of isolation of habitat fragments where the aim is to maximise species richness. In a field-based microecosystem of Collembola and predatory and non-predatory mites, moss patches of the same total area were fragmented to varying degrees. The habitat was left for several months to allow the communities to approach a new state of equilibrium.
2. The species richness (in particular of predatory mites) of a given area of habitat was greater when it was part of a large mainland area than part of an island, in agreement with theory.
3. Conversely, species richness and abundance were largely unaffected by fragmentation of a fixed area of island habitat. In this case, it is suggested here that the advantages of several small patches (e.g. reduced impact of environmental stochasticity, wider range of habitats overall) were equally balanced by the advantages of a single large patch (e.g. reduced effect of demographic stochasticity, wider range of habitats within a single patch, reduced edge effect), or that both effects were small.
4. The shapes of rank–abundance curves were similar among the levels of fragmentation of a fixed area of island habitat, implying that fragmentation had little impact on community structure. Conversely, the species composition of non-predatory mites varied weakly, but significantly, by fragmentation.     

Land-use,environment, and their impact on butterfly populations in a mountainous pastoral landscape: species richness and family-level abundance

Extensive grasslands are considered to be of high biodiversity value, but are under threat from intensification and abandonment. We studied butterfly species richness and abundance in 47 hay and grazing meadows in the Picos de Europa, northern Spain in 2004. Nine transects were walked around the perimeter of the meadows from the 1 June to 28 July with butterflies recorded to species or species-group. Land-use, abiotic, and sward variables were also recorded. Change in meadow extent was estimated by comparing a digital map of open meadows with a cadastral map with 1950s provenance. We found: A decrease in open area, mostly attributable to reduction in grazing meadows. 75 or more butterfly species with species richness principally, and positively, influenced by altitude and presence of scrub in the body of the meadow. Hay meadow management was a positive influence on richness of satyrids. When all butterflies were considered together, the only significant factor influencing abundance was Plantago lanceolata (−ve). For sub-groups of the butterfly community there was no consistent pattern, although P. lanceolata was identified as a (−ve) factor in relation to hesperiid, nymphalid, satyrid, and Viola-feeding fritillary groups. Several regression models included components that could be linked to abiotic influences (water, aspect, altitude) but many were indicative of abandonment or relaxation of management intensity (scrub, Pteridium aquilinum, Asphodelus albus), sward components, fragmentation (distance to nearest meadow, number of meadows within 100 m), and land use (hay management, summer grazing). The results are discussed in relation to changing socio-economics, including the potential impact of tourism, and the need for financial instruments to support extensive farming.     

Functional diversity (FD), species richness and community composition

Functional diversity is an important component of biodiversity, yet in comparison to taxonomic diversity, methods of quantifying functional diversity are less well developed. Here, we propose a means for quantifying functional diversity that may be particularly useful for determining how functional diversity is related to ecosystem functioning. This measure of functional diversity “FD” is defined as the total branch length of a functional dendrogram. Various characteristics of FD make it preferable to other measures of functional diversity, such as the number of functional groups in a community. Simulating species' trait values illustrates how the relative importance of richness and composition for FD depends on the effective dimensionality of the trait space in which species separate. Fewer dimensions increase the importance of community composition and functional redundancy. More dimensions increase the importance of species richness and decreases functional redundancy. Clumping of species in trait space increases the relative importance of community composition. Five natural communities show remarkably similar relationships between FD and species richness.     

Elevational species richness patterns for vascular plants on Mount Kinabalu, Borneo

Aim  We quantify the elevational patterns of species richness for all vascular plants and some functional and taxonomic groups on a regional scale on a tropical mountain and discuss some possible causes for the observed patterns.
Location  Mount Kinabalu, Sabah, Borneo.
Methods  A data base containing elevational information on more than 28,000 specimens was analysed for vascular plant distribution, taking into account sampling effort. The total species richness pattern was estimated per 300-m elevational interval by rarefaction analyses. The same methods were also applied to quantify species richness patterns of trees, epiphytes, and ferns.
Results  Total species richness has a humped relationship with elevation, and a maximum species richness in the interval between 900 and 1200 m. For ferns and epiphytes the maximum species richness is found at slightly higher elevations, whereas tree species did not have a statistically significant peak in richness above the lowest interval analysed.
Main conclusions  For the first time a rigorous estimate of an elevational pattern in species richness of the whole vascular plant flora of a tropical mountain has been quantified. The pattern observed depends on the group studied. We discuss the differences between the groups and compare the results with previous studies of elevational patterns of species richness from other tropical areas. We also discuss the methods used to quantify the richness pattern and conclude that rarefaction gives an appropriate estimate of the species richness pattern.     

Fine‐scale determinants of butterfly species richness and composition in a mountain region

Aim Global patterns of species richness are often considered to depend primarily on climate. We aimed to determine how topography and land cover affect species richness and composition at finer scales. Location Sierra de Guadarrama (central Iberian Peninsula). Methods We sampled the butterfly fauna of 180 locations (89 in 2004, 91 in 2005) at 600–2300 m elevation in a region of 10800 km². We recorded environmental variables at 100‐m resolution using GIS, and derived generalized linear models for species density (number of species per unit area) and expected richness (number of species standardized to number of individuals) based on variables of topoclimate (elevation and insolation) or land cover (vegetation type, geology and hydrology), or both (combined). We evaluated the models against independent data from the alternative study year. We also tested for differences in species composition among sites and years using constrained ordination (canonical correspondence analysis), and used variation partitioning analyses to quantify the independent and combined roles of topoclimate and land cover. Results Topoclimatic, land cover and combined models were significantly related to observed species density and expected richness. Topoclimatic and combined models outperformed models based on land cover variables, showing a humped elevational diversity gradient. Both topoclimate and land cover made significant contributions to models of species composition. Main conclusions Topoclimatic factors may dominate species richness patterns in regions with pronounced elevational gradients, as long as large areas of natural habitat remain. In contrast, both topoclimate and land cover may have important effects on species composition. Biodiversity conservation in mountainous regions therefore requires protection and management of natural habitats over a wide range of topoclimatic conditions, which may assist in facilitating range shifts and alleviating declines in species richness related to climate change.     

Effects of catchment perturbations by logging and wildfires on zooplankton species richness and composition in Boreal Shield lakes

SUMMARY 1. Forest logging and wildfires are important perturbations of the boreal forest, but their effects on lake biota remain largely unknown. Here, we test whether zooplankton species richness and species assemblages differed among three groups of lakes in Eastern Canada characterised by different catchment conditions: logged in 1995 ( n =9); burnt in 1995 ( n =9); unperturbed ( n =20). Lakes were sampled in June, July and September 1 year after catchment perturbations.
2. Cumulative species richness in reference lakes averaged 46 (33–60) of which 63% were rotifers. Mean cumulative species richness and mean diversity in logged and burnt lakes did not differ from those in reference lakes.
3. Lake species assemblages were described by the density of 62 species (41 rotifers and 21 crustaceans). Among-group differences in species assemblages were not significant. Eighteen per cent of the total variability in species assemblages could be explained by 13 environmental factors, among which dissolved oxygen concentration and cyanobacteria biovolume were the most important. About 5% of species assemblage variability was attributed to covariation between environmental factors and time of sampling, while 4.1% was attributed to temporal variation.
4. Variations in zooplankton species richness and assemblages in Boreal Shield lakes are important, both among lakes and among sampling dates. They seem to depend on environmental factors unrelated to catchment-based perturbations, at least on the short-term of 1 year.     

The impact of tropical forest logging and oil palm agriculture on the soil microbiome

Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land‐use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once‐logged and twice‐logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell–cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land‐use changes on the interaction of soil microbes.     

Contribution of tree species to the biodiversity of a 1ha Old World rainforest in Brunei, Borneo

Tree biodiversity data is presented for a 1-ha permanent study plot on a low slope position of the Kuala Belalong valley in Temburong District, Brunei, Borneo. This is the first study in the region to document the tree flora of a low slope. All trees 5cm at 1.3m were mapped, measurements of dbh and height taken, and identified to species and morpho-species level. The total and relative values of each family for density, diversity, dominance and Importance Value Indices were calculated. A total of 1062 stems were recorded on the plot (1019 live, 43 dead) with a total of 278 species representing 110 genera in 49 families. The most ecologically significant family as determined by the Family Importance Value (FIV) was Euphorbiaceae with a value of 40 and'the'most significant species, using the Importance Value (IV), was morpho-speciesFordia splendissima with an IV of 29. The total basal area of all living trees was 31.43m². Forest structure was marked by a few tall (>45m) emergents, for example,Koompassia excelsa, Crypteronia griffithii and two species of the Dipterocarpaceae family, however, lower understorey and sub-canopy species dominated the plot with the average height of all individuals over the hectare being 11m.     

海南岛尖峰岭山地雨林的群落结构、物种多样性以及在世界雨林中的地位

位于海南岛西南部的尖峰岭是目前我国为数不多、保存得较为完好的具有热带雨林性质的森林类型。在较典型的山地雨林中,设置1hm^2的固定样地,记录到DBH≥5．0cm的乔木171种,隶属于52科93属,总株数1099株,其中乔木种株数为1024。样地的Shannon—Wiener指数(H')、均匀度指数(E)和Simpson指数(D)分别为4．11、0．80和0．97,但取样面积和测定个体的起始大小等取样技术对物种多样性指数有显著的影响。随着取样面积的增加,H’值逐渐增加;但超过了4000m^2以后,增加不明显。E和D值在取样面积达到2000m^2后,基本保持不变：随着测定个体起始直径的增加,物种数、科数、H'和D都呈现出明显的减少趋势,而E值增加。径级频度分布的分析表明,该山地雨林的垂直结构可以划分成4个层次,每个层次的个体大小在空间上呈均匀或随机分布。从气候学、科属组成以及与世界热带雨林物种多样性的比较等方面,讨论了尖峰岭山地雨林在世界雨林中的地位。气候学分析表明,尖峰岭山地雨林在温度带上属于亚热带／暖温带范围,但由于其丰沛的降水量,使物种多样性较为丰富,具备了雨林的特点。对科属组成的分析表明,亚热带／暖温带科属占优势,其中典型的亚热带／暖温带科——壳斗科和樟科占总重要值的34％以上,而热带科属成份较少。与世界其他地区的典型热带林相比较,尖峰岭山地雨林的物种丰富度显著偏低,但高于某些降水量少的地区的热带林。因此,我们认为尖峰岭山地雨林与典型热带雨林有较大差别,具有由热带雨林向亚热带／暖温带雨林过渡的性质。此外,文本提出了平均种群密度(MPD)和种数一个体数关系这两种反映物种多样性测度的指标和表达式,并利用样地资料进行了分析。     

Effect of species richness and relative abundance on the shape of the species accumulation curve

Abstract We explain how species accumulation curves are influenced by species richness (total number of species), relative abundance and diversity using computer‐generated simulations. Species richness defines the boundary of the horizontal asymptote value for a species accumulation curve, and the shape of the curve is influenced by both relative abundance and diversity. Simulations with a high proportion of rare species and a few abundant species have a species accumulation curve with a low ‘shoulder’ (inflection point on the ordinate axis) and a long upward slope to the asymptote. Simulations with a high proportion of relatively abundant species have a steeply rising initial slope to the species accumulation curve and plateau early. Diversity (as measured by Simpson's and Shannon–Weaver indices) for simulations is positively correlated with the initial slope of the species accumulation curve. Species accumulation curves cross when one simulation has a high proportion of both rare and abundant species compared with another that has a more even distribution of abundance among species.     

Using soundscape recordings to estimate bird species abundance, richness, and composition

ABSTRACT Point counts are the most frequently used technique for sampling bird populations and communities, but have well‐known limitations such as inter‐ and intraobserver errors and limited availability of expert field observers. The use of acoustic recordings to survey birds offers solutions to these limitations. We designed a Soundscape Recording System (SRS) that combines a four‐channel, discrete microphone system with a quadraphonic playback system for surveying bird communities. We compared the effectiveness of SRS and point counts for estimating species abundance, richness, and composition of riparian breeding birds in California by comparing data collected simultaneously using both methods. We used the temporal‐removal method to estimate individual bird detection probabilities and species abundances using the program MARK. Akaike's Information Criterion provided strong evidence that detection probabilities differed between the two survey methods and among the 10 most common species. The probability of detecting birds was higher when listening to SRS recordings in the laboratory than during the field survey. Additionally, SRS data demonstrated a better fit to the temporal‐removal model assumptions and yielded more reliable estimates of detection probability and abundance than point‐count data. Our results demonstrate how the perceptual constraints of observers can affect temporal detection patterns during point counts and thus influence abundance estimates derived from time‐of‐detection approaches. We used a closed‐population capture–recapture approach to calculate jackknife estimates of species richness and average species detection probabilities for SRS and point counts using the program CAPTURE. SRS and point counts had similar species richness and detection probabilities. However, the methods differed in the composition of species detected based on Jaccard's similarity index. Most individuals (83%) detected during point counts vocalized at least once during the survey period and were available for detection using a purely acoustic technique, such as SRS. SRS provides an effective method for surveying bird communities, particularly when most species are detected by sound. SRS can eliminate or minimize observer biases, produce permanent records of surveys, and resolve problems associated with the limited availability of expert field observers.     

The impact of local surface changes in Borneo on atmospheric composition at wider spatial scales: coastal processes, land-use change and air quality

We present results from the OP3 campaign in Sabah during 2008 that allow us to study the impact of local emission changes over Borneo on atmospheric composition at the regional and wider scale. OP3 constituent data provide an important constraint on model performance. Treatment of boundary layer processes is highlighted as an important area of model uncertainty. Model studies of land-use change confirm earlier work, indicating that further changes to intensive oil palm agriculture in South East Asia, and the tropics in general, could have important impacts on air quality, with the biggest factor being the concomitant changes in NO(x) emissions. With the model scenarios used here, local increases in ozone of around 50 per cent could occur. We also report measurements of short-lived brominated compounds around Sabah suggesting that oceanic (and, especially, coastal) emission sources dominate locally. The concentration of bromine in short-lived halocarbons measured at the surface during OP3 amounted to about 7 ppt, setting an upper limit on the amount of these species that can reach the lower stratosphere.     

Landscape composition and habitat area affects butterfly species richness in semi-natural grasslands

During the last 50 years, the distribution and abundance of many European butterfly species associated with semi-natural grasslands have declined. This may be the result of deteriorating habitat quality, but habitat loss, resulting in decreasing area and increasing isolation of remaining habitat, is also predicted to result in reduced species richness. To investigate the effects of habitat loss on species richness, we surveyed butterflies in semi-natural grasslands of similar quality and structure, but situated in landscapes of different habitat composition. Using spatially explicit habitat data, we selected one large (6–10 ha) and one small (0.5–2 ha) grassland site (pasture) in each of 24 non-overlapping 28.2 km² landscapes belonging to three categories differing in the proportion of the area that consisted of semi-natural grasslands. After controlling for local habitat quality, species richness was higher in grassland sites situated in landscapes consisting of a high proportion of grasslands. Species richness was also higher in larger grassland sites, and this effect was more pronounced for sedentary than for mobile species. However, the number of species for a given area did not differ between large and small grasslands. There was also a significant relationship between butterfly species richness and habitat quality in the form of vegetation height and abundance of flowers. In contrast, butterfly density was not related to landscape composition or grassland size. When species respond differently to habitat area or landscape composition this leads to effects on community structure, and nestedness analysis showed that depauperate communities were subsets of richer ones. Both grassland area and landscape composition may have contributed to this pattern, implying that small habitat fragments and landscapes with low proportions of habitat are both likely to mainly contain common generalist species. Based on these results, conservation efforts should aim at preserving landscapes with high proportions of the focal habitat.     

The effects of host-plant distribution and local abundance on the species richness of agromyzid flies attacking British umbellifers

Abstract. 1. The number of agromyzid species (Diptera: Agromyzidae) attacking British Umbelliferae generally increases with the size of the geographic range of the host, measured as occupied 10 km squares in the Atlas of the British Flora (Lawton & Price, 1979). 2. In the present study we tried to explain the large, residual variation in this species—area relationship using two new variables, namely the local abundance of the host plant, and the number of habitats within which it grows. 3. Local abundance was estimated from eight floras that map plant distributions within English countries by tetrads (2 times 2 km squares). Local abundance was defined as: Total number of occupied tetrads Total number of available tetrads within occupied 10 km squares 4. The number of habitats occupied by each host plant was taken from the only county flora to record plant habitats objectively, that for Warwickshire. 5. We expected to find a correlation between local abundance and the residuals from the national species—area relationship, with locally scarce plants having fewer agromyzids than expected from the sizes of their national ranges, and vice versa. 6. What we found was that size of geographic range and local abundance were highly correlated; hence their relative contributions to agromyzid species richness were difficult to disentangle. Residuals from the national species—area relationship were positively correlated with local abundance, but the relationship marginally failed to achieve statistical significance (P= 0.06). 7. In contrast, the number of habitats occupied by each species of umbellifer in Warwickshire had a marked effect upon agrornyzid species richness, with plants that grow in more habitats supporting more species of insects. Not surprisingly, local abundance and number of habitats occupied were highly correlated. 8. Lawton & Price's observation that aquatic umbellifers are faunally impoverished now emerges as part of the general effect of number of habitats occupied by the host plants on agromyzid species richness. 9. Once the number of habitats occupied by each host plant in Warwickshire was entered into a multiple regression, the effect of size of host geographic range on agromyzid species richness was no longer statistically significant. 10. A combination of the number of habitats occupied, and leaf-form of the host (the latter taken from Lawton & Price, 1979), explains 61% of the variation in agromyzid species richness on British Umbelliferae.