Bird richness and composition along an agricultural gradient in New Guinea: The influence of land use,habitat heterogeneity and proximity to intact forest

Abstract We examined variation in bird species richness, abundance and guild composition along an agricultural gradient in New Guinea, and looked for any additive influence of habitat heterogeneity on these variables. The study was based on a grid of survey plots, six plots wide and 24 plots long with the long axis running from a settlement 2.4 km through active and abandoned agricultural plots towards a large area of forest. Each circular survey plot (25 m radius) was assigned to a broad habitat type, ten habitat measures taken, and birds counted for 1 h in each plot. Principal component analysis (PCA) habitat axis 1 described an axis of decreasing forest alteration (larger trees, greater tree densities, fuller canopy) that was positively correlated with distance from the settlement. Bird richness and abundance were highest at intermediate disturbance levels (plots with mid‐range axis 1 scores). Proportions of insectivores and frugivores increased with decreasing forest alteration, while proportions of nectarivores decreased. We calculated three measures of habitat heterogeneity by comparing each plot's PCA score to those of eight neighbouring plots (50–110 m away). These measures reflected how different the plot was to its neighbours, how variable the habitat was around the plot, and the degree to which the plot bordered less disturbed forest. We related these measures to plot bird variable scores independently, and to residuals following regressions of bird scores against PCA scores. Heterogeneity measures had no significant influence on abundance or richness measures, but there were greater proportions of frugivores in plots showing a given degree of habitat alteration if they bordered more pristine habitat. While we readily identified differences in bird communities along the agricultural gradient, the influences of habitat heterogeneity were not striking for birds at this fine scale.     

Habitat influences on urban avian assemblages

Urbanization is increasing across the globe and there is growing interest in urban ecology and a recognition that developed areas may be important for conservation. We review the factors influencing urban avian assemblages, focusing on habitat type and anthropogenic resource provision, and analyse data from a common bird monitoring scheme to assess some of these issues. The review suggests that (1) local factors are more important than regional ones in determining the species richness of urban avian assemblages, raising the potential for the management of urban sites to deliver conservation; (2) habitat fragmentation frequently influences urban avian assemblages, with the effects of patch size being greater than those of isolation, and (3) urban bird assemblages appear to respond positively to increasing the structural complexity, species richness of woody vegetation and supplementary feeding, and negatively to human disturbance. Data from Britain's Breeding Bird Survey, combined with habitat data obtained from aerial photographs, were used to assess a number of these issues at the resolution of 1‐km squares. Green‐space constituted 45% of these squares, and domestic gardens contributed 50% of this green‐space, though their contribution to large continuous patches of green‐space was negligible. There was no significant positive correlation between the densities of individual species in urban areas and surrounding rural areas. Rural species richness declined with increasing latitude, but urban species richness was not correlated with latitude. This contrast contributes to slightly higher avian species richness in rural squares in Southern England than urban ones. Occupancy and abundance were strongly positively correlated in urban avian assemblages, and some indicator species of conservation concern occurred in few urban areas and at low densities. Such species will require conservation action to be precisely targeted within urban areas. Of the urban indicators of conservation concern, only the House Sparrow Passer domesticus and Common Starling Sturnus vulgaris were more abundant in urban than rural areas. Moreover, the densities of these two species were strongly and positively correlated, indicating that they may be limited by shared resources, such as nest‐sites or supplementary food. There was little evidence that high densities of nest‐predating corvids were associated with reduced densities of their prey species. Species richness and the densities of individual species frequently declined with an increasing number of buildings. Current trends for the densification of many British urban areas are thus likely to be detrimental for many bird species.     

CHARGE CONTRAST IMAGING OF EXCEPTIONALLY-PRESERVED FOSSILS

Abstract:  Charge contrast images are a variant of secondary electron images acquired by operating a variable pressure scanning electron microscope in low vacuum mode; i.e. a gas is present in the specimen chamber. Spatial variation in the amount of charge that accumulates on the surface of the specimen is expressed as differences in greyscale tone; areas that are charging less are darker in tone. The precise mechanisms by which charge contrast images are generated are not known fully. Various different properties of a mineral may create a charge contrast; electrical conductivity is known to be one potentially important variable. As carbon is highly conductive but typical host lithologies (carbonates, silicates) less so or dielectric, the technique is potentially very suitable for imaging organically preserved fossils such as those from the Solite and Jehol biotas. It can also be applied to Burgess Shale fossils: complex films comprising 'aluminosilicates' with or without carbonaceous remains. Charge contrast images reveal anatomical detail not visible using either optical or other scanning electron microscope-based imaging methods.     

Misprescription and misuse of one‐tailed tests

One‐tailed statistical tests are often used in ecology, animal behaviour and in most other fields in the biological and social sciences. Here we review the frequency of their use in the 1989 and 2005 volumes of two journals (Animal Behaviour and Oecologia), their advantages and disadvantages, the extensive erroneous advice on them in both older and modern statistics texts and their utility in certain narrow areas of applied research. Of those articles with data sets susceptible to one‐tailed tests, at least 24% in Animal Behaviour and at least 13% in Oecologia used one‐tailed tests at least once. They were used 35% more frequently with nonparametric methods than with parametric ones and about twice as often in 1989 as in 2005. Debate in the psychological literature of the 1950s established the logical criterion that one‐tailed tests should be restricted to situations where there is interest only in results in one direction. ‘Interest’ should be defined; however, in terms of collective or societal interest and not by the individual investigator. By this ‘collective interest’ criterion, all uses of one‐tailed tests in the journals surveyed seem invalid. In his book Nonparametric Statistics, S. Siegel unrelentingly suggested the use of one‐tailed tests whenever the investigator predicts the direction of a result. That work has been a major proximate source of confusion on this issue, but so are most recent statistics textbooks. The utility of one‐tailed tests in research aimed at obtaining regulatory approval of new drugs and new pesticides is briefly described, to exemplify the narrow range of research situations where such tests can be appropriate. These situations are characterized by null hypotheses stating that the difference or effect size does not exceed, or is at least as great as, some ‘amount of practical interest’. One‐tailed tests rarely should be used for basic or applied research in ecology, animal behaviour or any other science.     

Systematics of a widespread Southeast Asian frog,Rana chalconota (Amphibia: Anura: Ranidae)

The abundant Sundaland forest frog, Rana chalconota, has long been considered a single widespread species, although some authors have recommended its division into regional subspecies. The discovery of co‐occurring pairs of morphologically distinct populations in three widely separated parts of the range led to a morphological and molecular analysis of populations from all parts of the known range. The results suggest that R. chalconota consists of at least seven species from Thailand through Borneo and Java. Existing names are applied to three of these species, R. chalconota (Schlegel), R. raniceps (Peters) and R. labialis Boulenger. We describe four others as new species and suggest the existence of one or two additional, unnamed species. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 123–147.     

Genetic divergence and echolocation call frequency in cryptic species of Hipposideros larvatus s.l. (Chiroptera: Hipposideridae) from the Indo-Malayan region

The intermediate leaf-nosed bat ( Hipposideros larvatus ) is a medium-sized bat distributed throughout the Indo-Malay region. In north-east India, bats identified as H. larvatus captured at a single cave emitted echolocation calls with a bimodal distribution of peak frequencies, around either 85 kHz or 98 kHz. Individuals echolocating at 85 kHz had larger ears and longer forearms than those echolocating at 98 kHz, although no differences were detected in either wing morphology or diet, suggesting limited resource partitioning. A comparison of mitochondrial control region haplotypes of the two phonic types with individuals sampled from across the Indo-Malay range supports the hypothesis that, in India, two cryptic species are present. The Indian 98-kHz phonic bats formed a monophyletic clade with bats from all other regional populations sampled, to the exclusion of the Indian 85-kHz bats. In India, the two forms showed 12–13% sequence divergence and we propose that the name Hipposideros khasiana for bats of the 85-kHz phonic type. Bats of the 98-kHz phonic type formed a monophyletic group with bats from Myanmar, and corresponded to Hipposideros grandis , which is suggested to be a species distinct from Hipposideros larvatus . Differences in echolocation call frequency among populations did not reflect phylogenetic relationships, indicating that call frequency is a poor indicator of evolutionary history. Instead, divergence in call frequency probably occurs in allopatry, possibly augmented by character displacement on secondary contact to facilitate intraspecific communication.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 119–130.     

Evaluating the population‐level impact of an invasive species,Ring‐necked Parakeet Psittacula krameri,on native avifauna

The introduction of exotic species to ecosystems can have severe consequences for populations of native organisms, but logistical limitations and shortage of historical data often hinder attempts to quantify the ecological implications of such relationships. The establishment and rapid expansion of Ring‐necked Parakeets Psittacula krameri in England therefore presents a rare opportunity to apply novel analytical methods to existing extensive national bird monitoring data from the UK Breeding Bird Survey for an invasive species. A previous study from Belgium suggests that Ring‐necked Parakeets have the potential to reduce the abundance of Eurasian Nuthatch Sitta europaea through competition for nesting cavities. Our analysis provides no evidence for a significant impact through competition on Nuthatch populations or those of any other cavity‐nesting species within the Parakeet’s current range in the UK. However, we cannot exclude the possibility that competitive exclusion could be occurring at a minority of sites at which availability of nest cavities is limiting. This may yet have significant implications for future conflict if Parakeets continue to increase in numbers and range.     

A comparison of spatially explicit landscape representation methods and their relationship to stream condition

1. Biodiversity, water quality and ecosystem processes in streams are known to be influenced by the terrestrial landscape over a range of spatial and temporal scales. Lumped attributes (i.e. per cent land use) are often used to characterise the condition of the catchment; however, they are not spatially explicit and do not account for the disproportionate influence of land located near the stream or connected by overland flow. 2. We compared seven landscape representation metrics to determine whether accounting for the spatial proximity and hydrological effects of land use can be used to account for additional variability in indicators of stream ecosystem health. The landscape metrics included the following: a lumped metric, four inverse‐distance‐weighted (IDW) metrics based on distance to the stream or survey site and two modified IDW metrics that also accounted for the level of hydrologic activity (HA‐IDW). Ecosystem health data were obtained from the Ecological Health Monitoring Programme in Southeast Queensland, Australia and included measures of fish, invertebrates, physicochemistry and nutrients collected during two seasons over 4 years. Linear models were fitted to the stream indicators and landscape metrics, by season, and compared using an information‐theoretic approach. 3. Although no single metric was most suitable for modelling all stream indicators, lumped metrics rarely performed as well as other metric types. Metrics based on proximity to the stream (IDW and HA‐IDW) were more suitable for modelling fish indicators, while the HA‐IDW metric based on proximity to the survey site generally outperformed others for invertebrates, irrespective of season. There was consistent support for metrics based on proximity to the survey site (IDW or HA‐IDW) for all physicochemical indicators during the dry season, while a HA‐IDW metric based on proximity to the stream was suitable for five of the six physicochemical indicators in the post‐wet season. Only one nutrient indicator was tested and results showed that catchment area had a significant effect on the relationship between land use metrics and algal stable isotope ratios in both seasons. 4. Spatially explicit methods of landscape representation can clearly improve the predictive ability of many empirical models currently used to study the relationship between landscape, habitat and stream condition. A comparison of different metrics may provide clues about causal pathways and mechanistic processes behind correlative relationships and could be used to target restoration efforts strategically.     

Tobraviruses—plant pathogens and tools for biotechnology

The tobraviruses, Tobacco rattle virus (TRV), Pea early‐browning virus (PEBV) and Pepper ringspot virus (PepRSV), are positive‐strand RNA viruses with rod‐shaped virus particles that are transmitted between plants by trichodorid nematodes. As a group, these viruses infect many plant species, with TRV having the widest host range. Recent studies have begun to dissect the interaction of TRV with potato, currently the most commercially important crop disease caused by any of the tobraviruses. As well as being successful plant pathogens, these viruses have become widely used as vectors for expression in plants of nonviral proteins or, more frequently, as initiators of virus‐induced gene silencing (VIGS). Precisely why tobraviruses should be so effective as VIGS vectors is not known; however, molecular studies of the mode of action of the tobravirus silencing suppressor protein are shedding some light on this process.