Papers by Alex J. Dumbrell
Abstract
We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis—deat... more Abstract
We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis—death adders; Oxyuranus—taipans; Pseudechis—blacksnakes), using parsimony, maximum likelihood, and Bayesian analysis of sequences of the mitochondrial cytochrome b and ND4 genes. In Acanthophis and Pseudechis, we find evidence of multiple trans-Torresian sister-group relationships. Analyses of the timing of cladogenic events suggest crossings of the Torres Strait on several occasions between the late Miocene and the Pleistocene. These results support a hypothesis of repeated land connections between Australia and New Guinea in the late Cenozoic. Additionally, our results reveal undocumented genetic diversity in Acanthophis and Pseudechis, supporting the existence of more species than previously believed, and provide a phylogenetic framework for a reinterpretation of the systematics of these genera. In contrast, our Oxyuranus scutellatus samples from Queensland and two localities in New Guinea share a single haplotype, suggesting very recent (late Pleistocene) genetic exchange between New Guinean and Australian populations.
PloS one, 2015
Termites and ants contribute more to animal biomass in tropical rain forests than any other singl... more Termites and ants contribute more to animal biomass in tropical rain forests than any other single group and perform vital ecosystem functions. Although ants prey on termites, at the community level the linkage between these groups is poorly understood. Thus, assessing the distribution and specificity of ant termitophagy is of considerable interest. We describe an approach for quantifying ant-termite food webs by sequencing termite DNA (cytochrome c oxidase subunit II, COII) from ant guts and apply this to a soil-dwelling ant community from tropical rain forest in Gabon. We extracted DNA from 215 ants from 15 species. Of these, 17.2 % of individuals had termite DNA in their guts, with BLAST analysis confirming the identity of 34.1 % of these termites to family level or better. Although ant species varied in detection of termite DNA, ranging from 63 % (5/7; Camponotus sp. 1) to 0 % (0/7; Ponera sp. 1), there was no evidence (with small sample sizes) for heterogeneity in termite consu...
Commercial selective logging is a major cause of habitat disturbance in Southeast Asian rainfores... more Commercial selective logging is a major cause of habitat disturbance in Southeast Asian rainforests, yet despite much research there is little consensus on impacts of disturbance on biodiversity. There is also little consensus on the most appropriate methods for sampling ...
PLoS ONE, 2014
Arbuscular mycorrhizal (AM) fungi are widely distributed microbes that form obligate symbioses wi... more Arbuscular mycorrhizal (AM) fungi are widely distributed microbes that form obligate symbioses with the majority of terrestrial plants, altering nutrient transfers between soils and plants, thereby profoundly affecting plant growth and ecosystem properties. Molecular methods are commonly used in the study of AM fungal communities. However, the biases associated with PCR amplification of these organisms and their ability to be utilized quantitatively has never been fully tested. We used Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis to characterise artificial community templates containing known quantities of defined AM fungal genotypes. This was compared to a parallel in silico analysis that predicted the results of this experiment in the absence of bias. The data suggest that when used quantitatively the TRFLP protocol tested is a powerful, repeatable method for AM fungal community analysis. However, we suggest some limitations to its use for population-level analyses. We found no evidence of PCR bias, supporting the quantitative use of other PCR-based methods for the study of AM fungi such as next generation amplicon sequencing. This finding greatly improves our confidence in methods that quantitatively examine AM fungal communities, providing a greater understanding of the ecology of these important fungi.
Applied and Environmental Microbiology, 2014
The New phytologist, Jan 5, 2015
Understanding the natural dynamics of arbuscular mycorrhizal (AM) fungi and their response to glo... more Understanding the natural dynamics of arbuscular mycorrhizal (AM) fungi and their response to global environmental change is essential for the prediction of future plant growth and ecosystem functions. We investigated the long-term temporal dynamics and effect of elevated atmospheric carbon dioxide (CO2 ) and ozone (O3 ) concentrations on AM fungal communities. Molecular methods were used to characterize the AM fungal communities of soybean (Glycine max) grown under elevated and ambient atmospheric concentrations of both CO2 and O3 within a free air concentration enrichment experiment in three growing seasons over 5 yr. Elevated CO2 altered the community composition of AM fungi, increasing the ratio of Glomeraceae to Gigasporaceae. By contrast, no effect of elevated O3 on AM fungal communities was detected. However, the greatest compositional differences detected were between years, suggesting that, at least in the short term, large-scale interannual temporal dynamics are stronger m...
The ISME Journal, 2010
Most attempts to identify the processes that structure natural communities have focused on conspi... more Most attempts to identify the processes that structure natural communities have focused on conspicuous macroorganisms whereas the processes responsible for structuring microbial communities remain relatively unknown. Two main theories explaining these processes have emerged; niche theory, which highlights the importance of deterministic processes, and neutral theory, which focuses on stochastic processes. We examined whether neutral or niche-based mechanisms best explain the composition and structure of communities of a functionally important soil microbe, the arbuscular mycorrhizal (AM) fungi. Using molecular techniques, we surveyed AM fungi from 425 individual plants of 28 plant species along a soil pH gradient. There was evidence that both niche and neutral processes structured this community. Species abundances fitted the zerosum multinomial distribution and there was evidence of dispersal limitation, both indicators of neutral processes. However, we found stronger support that niche differentiation based on abiotic soil factors, primarily pH, was structuring the AM fungal community. Host plant species affected AM fungal community composition negligibly compared to soil pH. We conclude that although niche partitioning was the primary mechanism regulating the composition and diversity of natural AM fungal communities, these communities are also influenced by stochastic-neutral processes. This study represents one of the most comprehensive investigations of community-level processes acting on soil microbes; revealing a community that although influenced by stochastic processes, still responded in a predictable manner to a major abiotic niche axis, soil pH. The strong response to environmental factors of this community highlights the susceptibility of soil microbes to environmental change.
PLoS ONE, 2014
Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring si... more Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases.
Journal of Ecology, 2010
1. Most studies of species abundance patterns focus on conspicuous macroorganisms while microbial... more 1. Most studies of species abundance patterns focus on conspicuous macroorganisms while microbial communities remain relatively understudied. This bias is a concern given the functional importance and high diversity of microbes. 2. We determine whether a common species abundance distribution (SAD) is observed in communities of a widespread group of soil microbes, the Glomeromycota or arbuscular mycorrhizal (AM) fungi. Using molecular techniques, we intensively sampled the AM fungal community of a woodland-grassland ecotone in Yorkshire, UK. Observed species abundances were compared to theoretical models describing SADs. We also reanalysed 32 previously published data sets in a similar manner.
Journal of Applied Ecology, 2008
Many studies have examined the impacts of tropical habitat disturbance. However, the effects of m... more Many studies have examined the impacts of tropical habitat disturbance. However, the effects of moderate habitat disturbance on species diversity show little consensus, with both increased and decreased diversity following disturbance being reported with approximately equal frequency. Previous work has shown that the spatial scale of sampling affects the reported changes in diversity following habitat disturbance, and here we present new theoretical and empirical data which explain why this is so. 2. We assume that habitat disturbance reduces the slope of the species-area relationship (SAR), and we show theoretically that this reduction in the slope results in a scale-dependent response of diversity to disturbance. Thus, following moderate habitat disturbance, diversity is reported to increase when measured at small spatial scales but declines when measured at large spatial scales. Our findings suggest that even a very small change in the SAR slope following disturbance corresponds with a scale-dependent response of diversity to disturbance. 3. We analyse new empirical data for tropical butterflies at a range of spatial scales ( ≈ 3-80 ha). Our results support our theoretical findings and the notion of scale-dependence in estimates of diversity. We show that this scale-dependence occurs because α and β diversity increase with spatial scale at a significantly faster rate in undisturbed forest compared with disturbed forest. This is due to reduced habitat heterogeneity and reduced spatial autocorrelation of butterfly diversity data following disturbance. 4. Synthesis and applications . There is little consensus in the reported responses of species diversity to moderate tropical habitat disturbance, and the spatial scale at which studies are carried out largely pre-determines the findings. Here we demonstrate, both theoretically and empirically, the mechanisms that produce a scale-dependent response of diversity to habitat disturbance. There is little agreement among researchers about the best methods for sampling tropical species in the field, and our findings highlight the problems of using diversity changes that do not account for the spatial scale of sampling. We conclude that in the future, studies should assess spatial patterns in diversity over a range of spatial scales and should not evaluate changes in diversity at a single spatial scale.
Molecular Phylogenetics and Evolution, 2005
We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis—death adders;... more We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis—death adders; Oxyuranus—taipans; Pseudechis—blacksnakes), using parsimony, maximum likelihood, and Bayesian analysis of sequences of the mitochondrial cytochrome b and ND4 genes. In Acanthophis and Pseudechis, we find evidence of multiple trans-Torresian sister-group relationships. Analyses of the timing of cladogenic events suggest crossings of the Torres Strait on several occasions
FEMS Microbiology Ecology, 2013
Within intertidal sediments, much of the dissolved organic carbon (DOC) consists of carbohydrate-... more Within intertidal sediments, much of the dissolved organic carbon (DOC) consists of carbohydrate-rich extracellular polymeric substances (EPS) produced by microphytobenthic biofilms. EPS are an important source of carbon and energy for aerobic and anaerobic microorganisms owing to burial of microphytobenthos and downward transport of their exudates. We established slurries of estuarine biofilms to determine the fate of organic carbon and EPS fractions, differing in size and complexity, under oxic and anoxic conditions. DOC and hot-water-extracted organic matter (predominately diatom chrysolaminarin) were utilised rapidly at similar rates in both conditions. Concentrations of insoluble, high-molecular-weight EPS were unchanged in oxic microcosms, but were significantly degraded under anoxic conditions (39% degradation by day 25). Methanogenesis and sulphate reduction were major anaerobic processes in the anoxic slurries, and 16S rRNA gene pyrosequencing revealed that Desulfobacteraceae (relative sequence abundance increased from 1.9% to 12.2%) and Desulfobulbaceae (increased from 1.5% to 4.3%) were the main sulphate reducers, whilst Clostridia and Bacteroidetes were likely responsible for anaerobic hydrolysis and fermentation of EPS. We conclude that a diverse consortium of anaerobic microorganisms (including coexisting sulphate reducers and methanogens) degrade both labile and refractory microphytobenthic-derived carbon and that anaerobic degradation may be the primary fate of more structurally complex components of microphytobenthic EPS.
Biotropica, 2009
Epiphytic plants are a dominant component of the rain forest canopy biota. They represent a signi... more Epiphytic plants are a dominant component of the rain forest canopy biota. They represent a significant proportion of canopy plant biomass and diversity, play a key role in nutrient cycling, and support highly abundant and diverse animal communities. Understanding the factors affecting their distribution in this three-dimensional habitat is consequently of great importance, not least because they may be particularly vulnerable to climate change and habitat conversion. Here we investigate how canopy architecture affects the distribution of two species of bird's nest fern (Asplenium spp.) in pristine rain forest. Both species were found at high abundances (Asplenium phyllitidis: 136/ha, SE AE 31.6, Asplenium nidus: 44/ha, SE AE 9.2) and their distributions were differentially affected by canopy architecture. Asplenium phyllitidis was found only at heights o 30 m in areas with a thicker lower canopy layer. Asplenium nidus was found at all heights in the canopy and was associated with emergent trees and areas with an open understory. Larger A. phyllitidis were found higher in the canopy while larger A. nidus were found on trunks and branches with a wider diameter. Asplenium nidus seems adapted to withstand the hot dry conditions in the upper canopy and in gaps, and its size is consequently limited only by the size of its support. Asplenium phyllitidis is dominant in areas that are cooler and damper, and so the growth rate of individuals may be limited by light levels. We discuss possible implications of this partitioning for epiphyte communities in the face of climate change and habitat conversion.
Biological Conservation, 2005
Commercial selective logging is a major cause of habitat disturbance in Southeast Asian rainfores... more Commercial selective logging is a major cause of habitat disturbance in Southeast Asian rainforests, yet despite much research there is little consensus on impacts of disturbance on biodiversity. There is also little consensus on the most appropriate methods for sampling ...
Academic Emergency Medicine, 2003
Research in patients with life-threatening illness such as cardiac arrest is challenging since th... more Research in patients with life-threatening illness such as cardiac arrest is challenging since they can not consent. The Food and Drug Administration addressed research under emergency conditions by publishing new criteria for exception from informed consent in 1996. We systematically reviewed randomized trials over a 10-year period to assess the impact of these regulations. Case-control study of published trials for cardiac arrest (cases) and atrial fibrillation (controls.) Studies were identified by using structured searches of MEDLINE and EMBASE from 1992 to 2002. Included were studies using random allocation in humans with cardiac arrest or atrial fibrillation prior to enrollment. Excluded were duplicate publications. Number of American trials, foreign trials and proportion of trials of American origin were compared by using regression analysis. Changes in cardiac arrest versus atrial fibrillation trials were calculated as risk differences. Of 4982 identified cardiac arrest studies, 57 (1.1%) were randomized trials. The number of American cardiac arrest trials decreased by 15% (95% CI: 8, 22%) annually (P = 0.05). The proportion of cardiac arrest trials of American origin decreased by 16% (95% CI: 10, 22%) annually (P = 0.006). Of 5596 identified atrial fibrillation studies, 197 trials (3.5%) were randomized trials. The risk difference between cardiac arrest versus atrial fibrillation trials being of American origin decreased significantly (annual difference -5.8% (95% CI: -10, -0.1%), P = 0.03). Fewer American cardiac arrest trials were published during the last decade, when federal consent requirements changed. Regulatory requirements for clinical trials may inhibit improvements in care and threaten public health.
Limnology and Oceanography, 2013
ABSTRACT To investigate photoacclimation of phytoplankton adapted to different aquatic light regi... more ABSTRACT To investigate photoacclimation of phytoplankton adapted to different aquatic light regimes, a physiologically explicit phytoplankton optimality model was applied in two contrasting environments: constant irradiance vs. dynamic irradiance associated with oceanic mixed layers. Nitrogen was assumed to be partitioned between cellular components associated with light harvesting, carbon fixation, biosynthesis, and photoprotection. The model was used to predict how resources are (re)distributed to optimize growth in the different environments. Optimal intracellular nitrogen allocation in dynamic environments was associated with constitutive investment in Calvin cycle enzymes; in contrast, in the static environment Calvin cycle allocation was reduced at low light. Furthermore, reduced allocation to components associated with photoprotection in static environments led to heavily inhibited photosynthesis-irradiance response consistent with that of Prochlorococcus adapted to relatively stable oligotrophic gyres. In contrast, photosynthetic response in the diatom Skeletonema costatum was better explained by maintenance of photoprotection components across a range of integrated light doses. Limited range of chlorophyll : C in Thalassiosira pseudonana was consistent with optimization of resource allocation to light-harvesting components in dynamic environments, in contrast to the relatively wide range in allocation to light harvesting predicted by the model in static environments and chlorophyll cell−1 observed in high-light-adapted Prochlorococcus. The model was used to explain variability of the photosynthesis-irradiance response of samples from the Celtic and Irish Seas. Photoacclimation state is a consequence of optimization of resource allocation to the set of environmental parameters (e.g., surface irradiance, depth of mixing, and light attenuation) that influence light variability.
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Papers by Alex J. Dumbrell
We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis—death adders; Oxyuranus—taipans; Pseudechis—blacksnakes), using parsimony, maximum likelihood, and Bayesian analysis of sequences of the mitochondrial cytochrome b and ND4 genes. In Acanthophis and Pseudechis, we find evidence of multiple trans-Torresian sister-group relationships. Analyses of the timing of cladogenic events suggest crossings of the Torres Strait on several occasions between the late Miocene and the Pleistocene. These results support a hypothesis of repeated land connections between Australia and New Guinea in the late Cenozoic. Additionally, our results reveal undocumented genetic diversity in Acanthophis and Pseudechis, supporting the existence of more species than previously believed, and provide a phylogenetic framework for a reinterpretation of the systematics of these genera. In contrast, our Oxyuranus scutellatus samples from Queensland and two localities in New Guinea share a single haplotype, suggesting very recent (late Pleistocene) genetic exchange between New Guinean and Australian populations.
We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis—death adders; Oxyuranus—taipans; Pseudechis—blacksnakes), using parsimony, maximum likelihood, and Bayesian analysis of sequences of the mitochondrial cytochrome b and ND4 genes. In Acanthophis and Pseudechis, we find evidence of multiple trans-Torresian sister-group relationships. Analyses of the timing of cladogenic events suggest crossings of the Torres Strait on several occasions between the late Miocene and the Pleistocene. These results support a hypothesis of repeated land connections between Australia and New Guinea in the late Cenozoic. Additionally, our results reveal undocumented genetic diversity in Acanthophis and Pseudechis, supporting the existence of more species than previously believed, and provide a phylogenetic framework for a reinterpretation of the systematics of these genera. In contrast, our Oxyuranus scutellatus samples from Queensland and two localities in New Guinea share a single haplotype, suggesting very recent (late Pleistocene) genetic exchange between New Guinean and Australian populations.