Roger Cousens - Academia.edu (original) (raw)

Papers by Roger Cousens

There is debate amongst ecologists concerning the validity of particular experimental designs for... more There is debate amongst ecologists concerning the validity of particular experimental designs for the study of interference (competition) and the quest for a "best" design. The debate has become increasingly dogmatic and confusing to outsiders. Most of the criticisms relate not to the validity of the designs themselves, as is usually claimed, but to the interpretability of indices calculated from them. It is argued that it is illogical to condemn a group of experimental treatments for all purposes simply because of the ways in which some researchers choose to interpret the results. Assertions that one particular design, the Replacement Series, is totally unusable are argued to be unwarranted and driven by an assumption that every researcher has the same objective. Each experimental design has both its merits and its restrictions; it is unreasonable to expect that any design will be universally applicable. A researcher must match the aim of the experiment with an appropriat...

Biological Invasions, 2017

Management of an invasive plant species can be viewed as two separate and successive processes. T... more Management of an invasive plant species can be viewed as two separate and successive processes. The first, survey, aims to find infested areas and remove individuals. The second, monitoring, consists of repeated visits to these areas in order to prevent possible re-emergence. As detection probability may vary over time, the timing and number of monitoring visits can dramatically impact monitoring efficacy. We explore the optimal timing and number of monitoring visits, by focusing on one infested site. Our decision-analysis framework defines an optimal monitoring schedule which accounts for a time-dependent probability of detection, based on the presence/absence of a flower. We use this framework to investigate the optimal monitoring schedule for Hieracium aurantiacum, an invasive species in the Australian Alps and many other countries. We also perform a sensitivity analysis to draw more general conclusions. For Hieracium aurantiacum eight monitoring visits (compared to 12 visits in the current program) are sufficient to obtain a 99% monitoring efficacy. When four or fewer visits to a site are allowed, it is optimal to visit during the high season, when the weed is likely to initiate flowering. Any extra visits should be scheduled in the early season, before the plants flower. The sensitivity analysis shows that increasing the detection probability early in the season has a greater impact than increasing it late in the season. An effective treatment method increases the value of site visits late in the season, when the detection probability is higher. Our decision-analysis framework can assist invasive species managers to reduce or reallocate management resources by determining the minimum number of monitoring visits required to satisfy an acceptable risk of re-emergence.

Biological Invasions, 2015

Current methods for using herbarium data as time series, for example to estimate the length of th... more Current methods for using herbarium data as time series, for example to estimate the length of the invasion lag phase, often make assumptions that are both statistically and logically inappropriate. We present an alternative statistical approach, estimating the lag phase based on annual rather than cumulative data, a generalized linear model incorporating a log link for overall collection effort, and piecewise linear splines. We demonstrate the method on two species representing good and poor data quality, then apply it to two data sets comprising 448 species/region combinations. Significant lags were detected in only 28% and 40% of time series, a much lower level than the 95% and 77% found in previous analyses of the same data. In a case with high quality data, a lag was concluded even though during the "lag" the locations of herbarium collections indicated that it was spreading rapidly at a continental scale. In species with few records, results were sensitive to the way in which zeroes were included. Overall, our method gives very good fit to the data, avoids unrealistic assumptions of other methods and gives more reliable estimates of confidence. However, given the poor representation of herbarium samples in the early stages of invasions and the fact that they do not constitute a structured survey of abundance, we warn against overreliance on statistical analysis of such data to reach conclusions about the dynamics of invasions. Keywords Lag phase  invasion  herbarium  statistical analysis

Seedling densities were recorded in large numbers of small quadrats (225,000 in 1998) every two y... more Seedling densities were recorded in large numbers of small quadrats (225,000 in 1998) every two years at a single site in Victoria. Soil analyses were made in a single year. An 'adaptive analysis' approach was used to investigate the processes that generate spatial pattern. The four most abundant species exhibited very different patterns resulting from different processes. One was widespread but its pattern varied considerably from year to year, another appeared to be patterned by competition from the first, a third occupied dense patches that were highly consistent between years, while a fourth occurred sporadically in patches of low density.

Germination of common heliotrope is principally limited by temperature and water availability, re... more Germination of common heliotrope is principally limited by temperature and water availability, requirements for which are relatively high and cycle seasonally. This provides a mechanism for the species to detect its temporal niche and to germinate only after sufficient rainfall to allow reproduction.

In many weeds, plant architecture will influence dispersal immediately around the parent plant, a... more In many weeds, plant architecture will influence dispersal immediately around the parent plant, as well as determining the proportion of seeds that will be dispersed by harvesting equipment over much greater distances. Since resource availability affects growth, competition with a crop can logically be expected to affect dispersal. This experiment was designed to assess the influence of competition on the final architecture, spatial pattern of pods and pattern of pod dispersal in wild radish (Raphanus raphanistrum L.). The results of this experiment showed that at high crop density, wild radish plants were smaller and produce shorter branches and fewer pods at greater heights. In contrast, plants produced longer branches and more pods were released at greater distances from the base of plant when plants were grown at zero or low crop density. This resulted in greater mean dispersal distance when the weed was grown in zero or low-density wheat than at high density. The scale of the relative frequency distributions of distances were affected by density.

Weed Research, 2010

The correct design of experimental studies, the selection of the appropriate statistical analysis... more The correct design of experimental studies, the selection of the appropriate statistical analysis of data and the efficient presentation of results are key to the good conduct and communication of science. The last Guidance for the use and presentation of statistics in Weed Research was published in 1988. Since then, there have been developments in both the scope of research covered by the journal and in the statistical techniques available. This paper addresses the changes in statistics and provides a reference work that will aid researchers in the design and analysis of their work. It will also provide guidance for editors and reviewers. The paper is organised into sections, which will aid the selection of relevant paragraphs, as we recognise that particular approaches require particular statistical analysis. It also uses examples, questions and checklists, so that non-specialists can work towards the correct approach. Statistics can be complex, so knowing when to seek specialist advice is important. The structure and layout of this contribution should help weed scientists, but it cannot provide a comprehensive guide to every technique. Therefore, we provide references to further reading. We would like to reinforce the idea that statistical methods are not a set of recipes whose mindless application is required by convention; each experiment or study may involve subtleties that these guidelines cannot cover. Nevertheless, we anticipate that this paper will help weed scientists in their initial designs for research, in the analysis of data and in the presentation of results for publication.

Plant Ecology, 2012

Changes to the timing of peak river flows caused by flow regulation affect riparian vegetation co... more Changes to the timing of peak river flows caused by flow regulation affect riparian vegetation composition, but the mechanisms driving such vegetation changes are not well understood. We investigated experimentally the effects of timing of inundation on riparian plant growth and flowering. We collected 168 sods from 14 sites across five lowland rivers in southeastern Australia. Plant cover and flowering within the sods was surveyed each season for a year. During this period, sods were inundated for six weeks in either early spring or in summer. Terrestrial plant taxa (which included most exotic species) senesced in response to inundation, regardless of its timing. In contrast, native amphibious species (particularly amphibious forbs) responded favourably to inundation in spring, but were unaffected by inundation in summer. Native and exotic emergent macrophytes responded favourably to inundation regardless of timing, and flowered frequently in both the spring-and summer-inundation treatments. In contrast, many native annuals flowered only in the spring-inundation treatment, while more exotic grasses flowered in the summerinundation treatment. In temperate climates, inundation in early spring followed by non-flooded conditions is likely to be important for promoting the growth of amphibious forbs and the recruitment and flowering of riparian annuals. Without inundation in spring, many terrestrial exotic weeds may flourish and set seed prior to any subsequent inundation (e.g. in summer). We contend that natural seasonal timing (i.e. winter-early spring) of flow peaks is important for the maintenance of native riverbank vegetation and reducing the extent of terrestrial exotic species within the riparian zone.

Oikos, 2004

In previous empirical and modelling studies of rare species and weeds, evidence of fractal behavi... more In previous empirical and modelling studies of rare species and weeds, evidence of fractal behaviour has been found. We propose that weeds in modern agricultural systems may be managed close to critical population dynamic thresholds, below which their rates of increase will be negative and where scale-invariance may be expected as a consequence. We collected detailed spatial data on five contrasting species over a period of three years in a primarily arable field. Counts in 20)/20 cm contiguous quadrats, 225,000 in 1998 and 84,375 thereafter, could be restructured into a wide range of larger quadrat sizes. These were analysed using three methods based on correlation sum, incidence and conditional incidence. We found non-trivial scale invariance for species occurring at low mean densities and where they were strongly aggregated. The fact that the scale-invariance was not found for widespread species occurring at higher densities suggests that the scaling in agricultural weed populations may, indeed, be related to critical phenomena.

Oecologia, 2000

A comparative ecological study of closely related invasive and non-invasive species, Senecio mada... more A comparative ecological study of closely related invasive and non-invasive species, Senecio madagascariensis and S. lautus (Asteraceae), investigated what traits might confer invasive ability in very similar species. Life-history attributes of the weed S. madagascariensis were compared to five habitat-specific subspecies of S. lautus: S. l. alpinus, S. l. dissectifolius, S. l. lanceolatus and two forms of S. l. maritimus. Field populations of each taxon were monitored to compare their population ecology. Relative rates of phenological development were compared at a single location. Seed germination was studied in a laboratory experiment. Transplant experiments were conducted in a range of S. madagascariensis and S. lautus habitats to compare performance in different environments. In monitored field populations S. madagascariensis produced seedlings and reproductive cohorts more frequently, flowered for longer periods, produced more seeds and had fewer germinable achenes in the soil compared to S. lautus taxa. S. madagascariensis achenes had higher rates of germination than S. lautus in both light and dark conditions. S. madagascariensis was found to have higher rates of survival than S. lautus taxa in a range of habitats and to be faster to flower in both transplant and standard glasshouse environments. Overall S. madagascariensis performed better than S. lautus ecotypes in terms of seedling, growth and fecundity measurements and second best for achenes. Despite relatively good performance in terms of life-history traits there is no evidence that S. madagascariensis is invading S. lautus habitats. We speculate that physiological and morphological adaptations to specialised environments are a better explanation for success of Senecio taxa/ecotypes than generalised life-history trait performance. We suggest that invasiveness is essentially unpredictable, due to habitat/plant specific interactions between invader and area of introduction. In the absence of predictive theory, quarantine authorities should use a combination of methods to assess invasive potential including a database of known weeds, performance comparisons between congeneric natives and exotics in a range of habitats at proposed point of introduction and monitoring of introduced species to determine if they spread.

Australian Systematic Botany, 2004

The current taxonomy of the Senecio pinnatifolius complex (formerly Australian S. lautus) is inad... more The current taxonomy of the Senecio pinnatifolius complex (formerly Australian S. lautus) is inadequate in describing intra-specific variation. We present several putative taxa as alternatives to current subspecies, based on variants observed during both herbarium surveys and field studies. We sought to establish whether these taxa were objectively justified in terms of morphology and genetic relationships. This was done in three ways. First, a morphometric study of plants grown under standard conditions was undertaken. Second, isozymes were analysed to establish genetic relationships within the complex. Third, achene morphology was examined by scanning electron microscopy. Variants from central Queensland (BRIGALOW V.) and the deserts of central and Western Australia (DESERT V.) were clearly separated from all other variants based on the number of involucral bracts. This differentiation into two major groups may warrant subspecific recognition. Although variation within each of the...

Annals of Applied Biology, 1993

An eco-physiological simulation model of the growth and development of Avena fatua was parameteri... more An eco-physiological simulation model of the growth and development of Avena fatua was parameterised and tested. The model simulates growth of A. fatua, in kg dry matter ha-1 day-1 , from sowing to maturity as a function of irradiance, temperature and various species characteristics. Parameter values were derived from the literature and from field experiments, including both autumn and spring sowings of A. fatua over three years at two sites in southern England. With two exceptions, a single set of parameter values was sufficient to accurately simulate the emergence, growth and development of both autumn and spring cohorts over all years and sites. The two exceptions were the result of differences between autumn and spring cohorts of A. fatua in the rate of early leaf area growth and in the relationship between specific leaf area and developmental stage.

Annals of Applied Biology, 1994

An eco-physiological simulation model of competition between Avena fatua and winter wheat (Tritic... more An eco-physiological simulation model of competition between Avena fatua and winter wheat (Triticum aestivum cv. Avalon) for light was parameterised and tested. The model simulates growth of each species, in kg dry matter ha-1 day-1 , from sowing to maturity as a function of irradiance, temperature and various species characteristics. Parameter values were derived from the literature and from field experiments with each species grown in monoculture. Model performance was tested against 50:50 mixtures of the two species grown at two sites in southern England. Sensitivity analyses were performed in which the canopy height of each species and the density and time of emergence of A. fatua were systematically varied while all other parameters were left unchanged. Accurate simulations of growth in mixtures depended upon an accurate description of the canopy height of each species throughout the growing season. Model predictions of winter wheat yield losses in relation to A. fatua density and time of emergence showed good agreement with previously published data.

Agronomy Journal, 2003

geous at different times. The competing species may also have very different phenologies, which a... more geous at different times. The competing species may also have very different phenologies, which are likely Previous studies in the United Kingdom (UK) and Australia have to have significant influences over the competitive hierled to the hypotheses that reversals in competitive hierarchy between wheat (Triticum aestivum L.) and oat (Avena spp.) could occur only archies as they develop. Thus, the identification of comin situations in which (i) there is a reversal in the relative heights of petitive traits may not be straightforward. One example the competitors during the year and (ii) there is strong competition of such complex dynamics comes from research on wild for light. Reversals in competitive hierarchy should not, therefore, oat (Avena fatua L.) in competition with wheat and occur where the wheat is either taller or shorter than oat throughout barley (Hordeum vulgare L.) in the UK, in which growth. We grew near-isogenic lines of wheat for height in monocul-Cousens et al. (1991) reported a late reversal of competiture and in replacement mixtures with oat (A. sativa L. and A. strigosa tive hierarchy between wild oat and both crops. On an Schreb.) in 2 yr. In the drier year and with a late-maturing oat cultivar, individual plant basis, the cereals were initially more height of wheat had no influence over its competitive superiority, competitive, but after crop anthesis, the wild oat became which was maintained throughout the season. In a somewhat wetter equal to or more competitive than the crops. One explayear and with an earlier-maturing oat cultivar, the shortest wheat lines were less competitive than corresponding taller near-isolines. nation was that this might be caused by the relative Results were consistent for near-isogenic lines in three contrasting patterns of resource allocation by the species. It was genetic backgrounds. Partial reversals in competitive hierarchy were suggested that if this was the case, by experimentally seen in a late sowing, but these did not correspond with patterns in moving the timing of key developmental stages, the the relative height growth of the species.

Journal of Vegetation Science, 2006

Questions: To what extent can spatial structure and its causes be determined in a highly disturbe... more Questions: To what extent can spatial structure and its causes be determined in a highly disturbed environment? What are the main determinants of pattern and are these species-specific? How much do spatial patterns change over generations? Location: Wimmera region of southern Australia. Methods: Broad-leaved weeds were counted in 225 000 contiguous 20-cm square quadrats. A substantial number of these quadrats were recorded again after two and four years. An hierarchical 'adaptive analysis' approach was used to select spatial analytical methods to examine specific aspects of pattern and variation in pattern from year to year. Results: Patterns varied among species and included both dense and sparse patches surrounded by areas of zero density, diffuse gradations of density and clear anisotropy. Patterns in Erodium botrys and Oxalis pes-caprae persisted over years, whereas patterns in Arctotheca calendula were less pronounced and varied over time. Edaphic factors appeared to have only a minor influence over the spatial distribution of the weed community as a whole. In Oxalis pes-caprae, whose patches were hypothesized to have been shaped by cultivation, there was no spread in four years, despite further tillage. Outlying plants of O. pes-caprae failed to establish new patches, even in the year of greatest population increase. Little evidence of localised recruitment events was found. Conclusions: Despite repeated annual disturbances by natural and anthropogenic mechanisms, clear and interpretable spatial structure develops in annual weeds over a range of spatial resolutions. Adaptive analysis is a useful approach to the characterization of such patterns.

Journal of Biogeography

Aim: If we are able to determine the geographic origin of an invasion, as well as its known area ... more Aim: If we are able to determine the geographic origin of an invasion, as well as its known area of introduction, we can better appreciate the innate environmental tolerance of a species and the strength of selection for adaptation that colonizing populations have undergone. It also enables us to maximize the success of searches for effective biological control agents. We determined the number of successful colonization events that have occurred throughout the world for two Cakile species and compared the climates from which they originated, in which they established and then spread. Location: Worldwide. Taxon: Sea-Rockets (Cakile spp.), Brassicaceae. Methods: We used a high-throughput sequencing and a genome skimming approach combined with Bayesian Inference phylogenetics to examine variation in entire chloroplast genomes and regions of nuclear ribosomal DNA within native and introduced areas. Databases were used to compare climates between native ranges and introduced regions for multiple clades within each species. Results: At least seven clades have invaded different regions of the world. In most cases we were able to identify their source regions and climates. The environmental bottlenecks differed in intensity: while some clades colonized into climates that were similar to climates in their native range, other clades had a very broad innate environmental tolerance such that new invasions succeeded beyond the climate range of native populations. We found clear evidence of hybridization-specifically, chloroplast capture-between two species in Australia. Conclusions: Results here show that these species are sometimes capable of colonizing in climates that are beyond the climate range of native populations. Whether successful colonization beyond native climate niches requires de novo adaptation, or whether it represents an innate broad fundamental niche requires further investigation. Cakile species provide an excellent opportunity to study replicated climate adaptation trajectories.

Annals of Botany, 2019

Background and AimsHybridization is commonly assumed to aid invasions through adaptive introgress... more Background and AimsHybridization is commonly assumed to aid invasions through adaptive introgression. In contrast, a recent theoretical model predicted that there can be non-adaptive demographic advantages from hybridization and that the population consequences will depend on the breeding systems of the species and the extent to which subsequent generations are able to interbreed and reproduce. We examined cross-fertilization success and inheritance of breeding systems of two species in order to better assess the plausibility of the theoretical predictions.MethodsReciprocal artificial crosses were made to produce F1, F2 and backcrosses between Cakile maritima (self-incompatible, SI) and Cakile edentula (self-compatible, SC) (Brassicaceae). Flowers were emasculated prior to anther dehiscence and pollen was introduced from donor plants to the recipient’s stigma. Breeding system, pollen viability, pollen germination, pollen tube growth and reproductive output were then determined. The ...

Weed Research, 2019

This is the author manuscript accepted for publication and has undergone full peer review but has... more This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record.

Weed Research, 2018

Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequen... more Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequently to human health and wellbeing. However, many currently used weed management approaches are increasingly unsustainable. To address this knowledge and practice gap, in June 2014, 35 weed and invasion ecologists, weed scientists, evolutionary biologists and social scientists convened a workshop to explore current and future perspectives and approaches in weed ecology and management. A horizon scanning exercise ranked a list of 124 pre-submitted questions to identify a priority list of 30 questions. These questions are discussed under seven themed headings that represent areas for renewed and emerging focus for the disciplines of weed research and practice. The themed areas considered the need for transdisciplinarity, increased adoption of