Daniel F. R. Cleary, Timothy J. B. Boyle, Titiek Setyawati, Celina D. Anggraeni, E. Emiel Van Loon, and Steph B. J. Menken. 2007. Bird species and traits associated with logged and unlogged forest in Borneo. Ecological Applications 17:1184–1197.

Appendix E. Estimates of bird species richness per area (P, L89, L93) using sample based rarefaction, and species richness estimators (the incidence-based coverage estimator [ICE] and the Chao2 estimator) in addition to the number of uniques (species only sampled in a single sample site) and duplicates (species sampled in exactly two sample sites).

For each forest type/landscape species richness was estimated using sample based rarefaction, and species richness estimators (the incidence-based coverage estimator [ICE] and the Chao2 estimator) within the programme Estimates! (Colwell 2000) using 1000 randomisations for each landscape. Rarefied species richness is the expected number of species for a given number of randomly sampled individuals (McCabe and Gotelli 2000) and facilitates comparison of areas in which densities may differ. Disturbance, for example, is known to have a strong effect on abundance so it is important to disentangle the effects of disturbance on species richness by rarefying (McCabe and Gotelli 2000). In the results, sample-based rarefaction curves are plotted using the accumulated number of individuals, and not the accumulated number of samples, as suggested by Gotelli and Colwell (2001). ICE and Chao2 are nonparametric richness estimators that have been evaluated for a number of biological data sets (Longino et al. 2002). Both have shown promise as estimators of true species richness and have been shown to give reliable estimates from relatively small sample sizes (Colwell and Coddington 1994). The numbers of uniques (species present in a single sample) and duplicates (species present in exactly two samples) were examined as indicators of inventory completeness ( Longino et al. 2002).

A total of 177 ( n = 9747) bird species were recorded in the study area including 54 globally threatened bird species (Collar et al. 2001). These species belonged to 30 families and 103 genera. The most speciose families were the Timaliidae (23 species), Pycnonotidae (17 species), Muscicapidae (14 species), Nectariniidae (13 species), Picidae (13 species) and Cuculidae (13 species). The most speciose genera were Pycnonotus (10 species), Stachyris (6 species), Pitta (5 species) and Malacopteron (5 species). Total observed species richness was highest in L89 followed by P and L93 but the species accumulation curves from each landscape were well within the 95% confidence intervals of curves from other landscapes thereby indicating similar levels of species richness in all three areas. Although the sample-based rarefaction curves of observed species richness were still increasing, the two non-parametric estimators had clearly stabilized and reached an asymptote (Fig. E1). The final species richness estimates varied from 154 species (ICE and Chao2) in P to 157 (Chao2) – 158 (ICE) species in L89 and 156 (ICE) – 157 species (Chao2) in L93. Total species richness across the whole study area was estimated at 184 species (ICE and Chao2). Overall bird density (± 95% CI) was higher in P (284 ± 39) than in L89 (260 ± 46) and L93 (244 ± 41) but there was no significant difference among landscapes (F_2,34 = 1.052, P = 0.361). Importantly, virtually the same number of species have been observed in Gunung Palung National Park (178), the only remaining large intact area of true lowland forest in Kalimantan (Curran et al. 2004).

FIG. E1. Species accumulation curves for (a) unlogged forest P, (b) older logged forest L89 and (c) recently logged forest L93 . In each landscape two nonparametric richness estimators, ICE and Chao2, sample based rarefaction, uniques and duplicates are shown as a function of the number of individuals observed. (d) Sample based rarefaction curves for P, L89 and L93. Solid lines represent mean estimated species richness and dashed lines represent 95% confidence intervals. Ch2: Chao2 richness estimator, ICE: Incidence-based coverage estimator, Obs: observed species richness; Uni: number of uniques (present in a single sample site), Dup: number of duplicates: present in two sample sites.

LITERATURE CITED

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Colwell R. K. 2000. EstimateS version 6.0b1: Statistical estimation of species richness and shared species from samples. Freeware published at http://viceroy.eeb.uconn.edu/EstimateS.

Colwell, R. K., and J. A. Coddington. 1994. Estimating terrestrial biodiversity through extraolation. Philosophical Transactions of the Royal Society London B 345:101–118.

Curran, L. M., S. N. Trigg, A. K. McDonald, D. Astiani, Y. M. Hardiono, P. Siregar, I. Caniago, and E. Kasischeke. 2004. Lowland forest loss in protected areas of Indonesian Borneo. Science 303:1000–1003.

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Longino , J. T., J. Coddington, and R. K. Colwell. 2002. The ant fauna of a tropical rain forest: estimating species richness three different ways. Ecology 83:689–702.

McCabe D. J., and N. J. Gotelli. 2000. Effects of disturbance frequency, intensity, and area on assemblages of stream macroinvertebrates. Oecologia 124:270–279.