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.     

Adjusting count period strategies to improve the accuracy of forest bird abundance estimates from point transect distance sampling surveys

Although point transect distance sampling methods have become widely used in surveys of forest birds, there has been no attempt to tailor field methods to maximize the accuracy of abundance estimates by minimizing the effects of violations of the method's critical assumptions, which are: (1) birds at distance 0 m are detected with certainty, (2) birds are detected at their initial location and (3) distances to objects are measured accurately. We investigate the effects on abundance estimates for Philippine forest birds of varying the count period from 2 to 10 min, and of including and excluding a pre‐count settling down period. Encounter rates were highly sensitive to count period length but density estimates from 10‐min count periods were, on average, only 13% higher than those from 2‐min periods, and in several cases were actually lower than those from periods of 6–8 min. This was because birds tended to be recorded at greater distances from the recorder as the count period went on, thus ‘stretching out’ detection functions while having little effect on detection rates close to the recorder. For some bird groups, including canopy frugivores and upperstorey gleaning insectivores, density estimates were more than twice as high without than with a settling down period. We suggest that movement away from the recorder is more common than attraction to the recorder, and that unless pilot studies show otherwise, similar studies should not use a settling down period for surveying many species. Count periods that maximized probability of bird detection close to the central point while minimizing the unwanted effects of bird movement during the count period were: 4 min for omnivores, 6 min for nectarivores and upperstorey gleaning insectivores, 8 min for understorey insectivores and canopy frugivores, and a full 10 min for sallying insectivores, ground‐dwellers, carnivores and coucals/koels. We use the results to suggest ‘group‐specific’ count period regimes that could help maximize the accuracy of density estimates from similar studies of tropical forest birds.     

Caterpillars escape predation in habitat and thermal refuges

1. Climate and, therefore, abiotic conditions, are changing rapidly, and many ecological interactions depend on them. In this study, how abiotic conditions mediate a predator–prey interaction were examined. 2. Caterpillars of Platyprepia virginalis (Boisduval) (Arctiidae) were found previously to be more abundant in wet habitats and thick litter cover compared with drier habitats and little or no litter. We hypothesised that wet litter provided caterpillars with refuges from an important ant predator, Formica lasioides. It was further hypothesised that caterpillars would be able to move at lower temperatures than ants, thus providing them with a thermal refuge. 3. In the lab, caterpillars were more likely to escape ant predation and survive on wet litter and at lower temperatures. At all temperatures, ant recruitment was lower in wet litter than dry litter although ants were more active on litter than bare soil. Thus, wet litter may serve as a habitat refuge for caterpillars from ants. 4. Caterpillars were able to maintain activity at temperatures 8–14 °C lower than F. lasioides. Thus colder temperatures may serve as a thermal refuge for caterpillars from ants. 5. It was hypothesised that caterpillars can escape ant predation when precipitation causes wet litter and at temperatures that they experience commonly in the field. This mismatch between caterpillars and their predators in ability to tolerate wet litter and low temperatures may affect their field distribution and abundance. Expected future warmer and drier conditions may not provide these refuges.     

Using multitemporal digital elevation model data for detecting canopy gaps in tropical forests due to cyclone damage: An initial assessment

Abstract The detection and mapping of canopy disturbance caused by natural events such as cyclones in tropical rainforests is important for monitoring and understanding rainforest dynamics and recovery. In February 1999 tropical cyclone Rona crossed the coastline of Far North Queensland, Australia, causing significant damage to the rainforest canopy in some areas. This paper examines the application of multitemporal canopy digital elevation models (DEMs) generated by a NASA‐operated airborne radar mapping system called TOPSAR in 1996 and 2000, for detection of canopy disturbance caused by cyclone damage. Canopy damage was mapped here by identifying areas with a significant decrease in canopy height estimated from the difference of the 1996 and 2000 TOPSAR DEMs. Conventional aerial photographs, flown shortly after the cyclone (March 1999), were used to validate the resulting map of cyclone damaged rainforest canopy. The results showed that the DEM‐derived canopy damage map performed reasonably well when comparing the spatial distribution and size of damaged areas, while taking into account the time difference between cyclone damage and the second radar acquisition. Some errors were encountered on the steeper slopes which were related to terrain distortions inherent in radar images of steep terrain. The height accuracy of the DEM was close to the depth of some of the gaps being mapped, which also contributed to errors. Even so, the results demonstrate there may be potential for weather‐independent, regional‐scale mapping of forest canopy change from imaging radar that is not always possible from traditional optical means of measuring canopy elevation, for example, airborne laser data and stereo aerial photography. This may be possible in relatively flat areas, provided the second radar acquisition occurs within months of the damaging event. Further algorithm refinement is required to improve its robustness and the range of topographies where this approach can provide reliable estimates of the extent of canopy disturbance.     

A late Quaternary phylogeography for Metrosideros (Myrtaceae) in New Zealand inferred from chloroplast DNA haplotypes

Because of its remoteness and mid-latitude position, New Zealand lacks access to the tropical climates that might have ensured straightforward survival for frost-sensitive species during glacial times. Nevertheless, the New Zealand lowland flora retains a substantial complement of plants sourced in the tropics. While there have been extinction pulses for elements of the frost-sensitive flora under glacial/stadial regimes, the surviving remnants have been able to recolonize large areas of habitat during successive warm climate periods. Refugia for such species in stadial New Zealand are likely to have been localized and ecologically suboptimal. To examine these relationships we have applied chloroplast DNA sequence data to the investigation of phylogeographical pattern for five endemic species of Metrosideros subg. Metrosideros , a wide-ranging group of mostly frost-sensitive woody plants in New Zealand. The results of this research verify the location of two generally mooted stadial refugia for the country and provide support for the existence of a third. A simple pattern of chloroplast haplotype diversity was recorded in extra-refugial areas, compared with a greater complexity in the vicinity of the identified refugia. This pattern was independently repeated in both main islands. The proposed refugia correspond to contemporary localities of high average winter temperatures. The sharing of chloroplast haplotypes between the different species of Metrosideros examined suggests that there has been a history of repeated hybridization and introgression for these plants, possibly initiated by periods of refugial confinement.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 399–412.