Ecology and Vegetation Dynamics Studies

Maximum entropy modeling of species geographic distributions

Generalized linear mixed models: a practical guide for ecology and evolution

Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation

Accurate modeling of geographic distributions of species is crucial to various applications in ecology and conservation. The best performing techniques often require some parameter tuning, which may be prohibitively time‐consuming to do separately for each species, or unreliable for small or biased datasets. Additionally, even with the abundance of good quality data, users interested in the application of species models need not have the statistical knowledge required for detailed tuning. In such cases, it is desirable to use “default settings”, tuned and validated on diverse datasets. Maxent is a recently introduced modeling technique, achieving high predictive accuracy and enjoying several additional attractive properties. The performance of Maxent is influenced by a moderate number of parameters. The first contribution of this paper is the empirical tuning of these parameters. Since many datasets lack information about species absence, we present a tuning method that uses presence‐only data. We evaluate our method on independently collected high‐quality presence‐absence data. In addition to tuning, we introduce several concepts that improve the predictive accuracy and running time of Maxent. We introduce “hinge features” that model more complex relationships in the training data; we describe a new logistic output format that gives an estimate of probability of presence; finally we explore “background sampling” strategies that cope with sample selection bias and decrease model‐building time. Our evaluation, based on a diverse dataset of 226 species from 6 regions, shows: 1) default settings tuned on presence‐only data achieve performance which is almost as good as if they had been tuned on the evaluation data itself; 2) hinge features substantially improve model performance; 3) logistic output improves model calibration, so that large differences in output values correspond better to large differences in suitability; 4) “target‐group” background sampling can give much better predictive performance than random background sampling; 5) random background sampling results in a dramatic decrease in running time, with no decrease in model performance.

The Population Biology of Invasive Species

▪ Abstract Contributions from the field of population biology hold promise for understanding and managing invasiveness; invasive species also offer excellent opportunities to study basic processes in population biology. Life history studies and demographic models may be valuable for examining the introduction of invasive species and identifying life history stages where management will be most effective. Evolutionary processes may be key features in determining whether invasive species establish and spread. Studies of genetic diversity and evolutionary changes should be useful for understanding the potential for colonization and establishment, geographic patterns of invasion and range expansion, lag times, and the potential for evolutionary responses to novel environments, including management practices. The consequences of biological invasions permit study of basic evolutionary processes, as invaders often evolve rapidly in response to novel abiotic and biotic conditions, and native species evolve in response to the invasion.

Progress in invasion biology: predicting invaders

Niche Conservatism: Integrating Evolution, Ecology, and Conservation Biology

▪ Abstract Niche conservatism is the tendency of species to retain ancestral ecological characteristics. In the recent literature, a debate has emerged as to whether niches are conserved. We suggest that simply testing whether niches are conserved is not by itself particularly helpful or interesting and that a more useful focus is on the patterns that niche conservatism may (or may not) create. We focus specifically on how niche conservatism in climatic tolerances may limit geographic range expansion and how this one type of niche conservatism may be important in (a) allopatric speciation, (b) historical biogeography, (c) patterns of species richness, (d) community structure, (e) the spread of invasive, human-introduced species, (f) responses of species to global climate change, and (g) human history, from 13,000 years ago to the present. We describe how these effects of niche conservatism can be examined with new tools for ecological niche modeling.

The merging of community ecology and phylogenetic biology

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.

A conceptual map of invasion biology: Integrating hypotheses into a consensus network

Abstract Background and aims Since its emergence in the mid‐20th century, invasion biology has matured into a productive research field addressing questions of fundamental and applied importance. Not only has the number of empirical studies increased through time, but also has the number of competing, overlapping and, in some cases, contradictory hypotheses about biological invasions. To make these contradictions and redundancies explicit, and to gain insight into the field’s current theoretical structure, we developed and applied a Delphi approach to create a consensus network of 39 existing invasion hypotheses. Results The resulting network was analysed with a link‐clustering algorithm that revealed five concept clusters (resource availability, biotic interaction, propagule, trait and Darwin’s clusters) representing complementary areas in the theory of invasion biology. The network also displays hypotheses that link two or more clusters, called connecting hypotheses , which are important in determining network structure. The network indicates hypotheses that are logically linked either positively (77 connections of support) or negatively (that is, they contradict each other; 6 connections). Significance The network visually synthesizes how invasion biology’s predominant hypotheses are conceptually related to each other, and thus, reveals an emergent structure – a conceptual map – that can serve as a navigation tool for scholars, practitioners and students, both inside and outside of the field of invasion biology, and guide the development of a more coherent foundation of theory. Additionally, the outlined approach can be more widely applied to create a conceptual map for the larger fields of ecology and biogeography.

Pollination biology of the Proteaceae in Australia and southern Africa

Abstract Proteaceae are most diverse in southern Africa and Australia, especially in the south‐western portions of these regions. Most genera have some species in flower at all times of the year, although generally there is a preponderance of species that flower between late winter and early summer. The one genus that is an exception to this generalization is Banksia, which either has approximately the same percentage of species in flower at various times of the year (southwestern Australia) or peaks in autumn (southeastern Australia). Within particular communities, opportunities for hybridization among congeneric species are minimized by staggered flowering times, different pollen vectors and/or various incompatibility mechanisms. Birds, mammals and arthropods have been identified as visitors to the inflorescences of many Proteaceae. The most common avian visitors to the majority of genera in Australia are honeyeaters, although lorikeets, silvereyes and approximately 40 other species sometimes may be important. Sugarbirds and sunbirds are seen most frequently at inflorescences of Protea, Leucospermum and Mimetes in southern Africa, although they rarely visit other genera. In most cases, avian visitors forage in a manner that permits the acquisition and transfer of pollen. Limited evidence supports the hypothesis that birds are selective in their choice of inflorescences, responding to morphological and/or colour changes and usually visiting those inflorescences that offer the greatest nectar rewards. Arthropods may be equally selective, although it is possible that only the larger moths, bees and beetles are important pollinators, even for those plant species that rely entirely on arthropods for pollen transfer. Mammals are pollen vectors for some Proteaceae, especially those that have geoflorous and/or cryptic inflorescences. In Australia, small marsupials may be the most important mammalian pollinators, although rodents fill this niche in at least some southern African habitats. All but two genera of Proteaceae are hermaphroditic and protandrous, the exceptions being the dioecious southern African genera Aulax and Leucadendron. For hermaphroditic species, the timing of visits by animals to inflorescences is such that they not only acquire pollen from freshly opened flowers but also brush against pollen presenters and stigmas of others that have lost self‐pollen and become receptive. Birds and insects (and probably mammals) generally forage in such a way as to facilitate both outcrossing and selfing. Some species are self‐compatible, although many require outcrossing if viable seed is to be formed. Regardless of which animals are the major pollen vectors, fruit set is low relative to the number of flowers available, especially in Australian habitats. Functional andromonoecy of the majority of flowers is advanced as the major cause of poor fruit set. The pollination biology and breeding systems of Australian and southern African Proteaceae resemble one another in many ways, partly because of their common ancestry, but also due to convergence. Divergence is less obvious, apart from the dichotomy between dioecious and hermaphroditic genera, and differences in the levels of seed set for Australian and African species. Future studies should concentrate on identifying the most important pollinators for various Proteaceae, the manner in which their visits are integrated with floral development and factors responsible for limiting fruit set.

Reproductive biology of Australian acacias: important mediator of invasiveness?

Abstract Aim Reproductive traits are important mediators of establishment and spread of introduced species, both directly and through interactions with other life‐history traits and extrinsic factors. We identify features of the reproductive biology of Australian acacias associated with invasiveness. Location Global. Methods We reviewed the pollination biology, seed biology and alternative modes of reproduction of Australian acacias using primary literature, online searches and unpublished data. We used comparative analyses incorporating an Acacia phylogeny to test for associations between invasiveness and eight reproductive traits in a group of introduced and invasive (23) and non‐invasive (129) species. We also explore the distribution of groups of trait ‘syndromes’ between invasive and non‐invasive species. Results Reproductive trait data were only available for 126 of 152 introduced species in our data set, representing 23/23 invasive and 103/129 non‐invasive species. These data suggest that invasives reach reproductive maturity earlier (10/13 within 2 years vs. 7/26 for non‐invasives) and are more commonly able to resprout (11/21 vs. 13/54), although only time to reproductive maturity was significant when phylogenetic relationships were controlled for. Our qualitative survey of the literature suggests that invasive species in general tend to have generalist pollination systems, prolific seed production, efficient seed dispersal and the accumulation of large and persistent seed banks that often have fire‐, heat‐ or disturbance‐triggered germination cues. Conclusions Invasive species respond quicker to disturbance than non‐invasive taxa. Traits found to be significant in our study require more in‐depth analysis involving data for a broader array of species given how little is known of the reproductive biology of so many taxa in this species‐rich genus. Sets of reproductive traits characteristic of invasive species and a general ability to reproduce effectively in new locations are widespread in Australian acacias. Unless there is substantial evidence to the contrary, care should be taken with all introductions.

REPRODUCTIVE BIOLOGY OF AUSTRALIAN ACACIAS IN THE SOUTH-WESTERN CAPE PROVINCE, SOUTH AFRICA

Several Australian members of the genus Acacia L. have attained weed status in the Cape Province, South Africa. It is shown that in the Cape the plants are pollinated but lack effective seed predators. Mature plants drop seeds numbering usually in the range 1 100 to 7 000 m−2yr−1. They have a seed-bank in the soil about two to five times this magnitude, about 95 per cent of which is dormant. It appears that the decline of viability with age may be relatively very slow. These findings are shown to be critical in planning control-methods. (Miss S. J. Milton and Dr A. V. Hall, Bolus Herbarium, University of Cape Town.)

Beyond the various contrivances by which orchids are pollinated: global patterns in orchid pollination biology

Abstract Orchidaceae show remarkable diversity in pollination strategies, but how these strategies vary globally is not entirely clear. To identify regions and taxa that are data-rich and lend themselves to rigorous analyses or are data-poor and need attention, we introduce a global database of orchid reproductive biology. Our database contains > 2900 species representing all orchid subfamilies and 23 of 24 tribes. We tabulated information on habit, breeding systems, means of pollinator attraction and the identity of pollinators. Patterns of reproductive biology by habit, geography and taxonomy are presented graphically and analysed statistically. On the basis of our database, most orchid species sampled are pollinator dependent (76%) and self-compatible (88%). Pollinator attraction based on rewards occurs in 54% of the species, whereas 46% use some means of deceit. Orchids generally have highly specific pollinator interactions (median number of pollinator species = 1). Nonetheless, on average, specificity is lower for species offering rewards, occurring in multiple continental regions or Northern America (as defined by the Taxonomic Database Working Group Level 1 regions). Although our database reveals impressive knowledge gains, extensive gaps in basic observations of orchid reproductive biology exist, particularly in tropical regions and diverse lineages of fly-pollinated species. The database is expected to facilitate targeted studies, further elucidating the ecological and evolutionary drivers of orchid diversity.

How wide is the “knowing-doing” gap in invasion biology?

An Overview of the Biology of the Desiccation-tolerant Resurrection Plant Myrothamnus flabellifolia

BACKGROUND: Myrothamnus flabellifolia is unique as the only woody resurrection plant. It is an important plant in southern Africa because of its widespread occurrence and usage in African medicine and traditional culture. Many reports have investigated facets of its biology and the mechanisms associated with its desiccation tolerance. SCOPE: The general biology of the woody resurrection plant Myrothamnus flabellifolia is reviewed. The review focuses on the geography and ecology, systematic placement, evolution, morphology and reproductive ecology of M. flabellifolia as well as the wood anatomy and re-filling mechanism. In addition, the desiccation tolerance, ethnobotanical importance and medicinal properties of the plant are reviewed. Also, future research avenues are suggested, in particular the necessity to research the biogeography and systematics of the species and the role of the polyphenols present, as well as the molecular basis of the plant's desiccation tolerance.

Invasion biology and conservation biology: time to join forces to explore the links between species traits and extinction risk and invasiveness

Expansion and decline of species are natural phenomena (Levin, 2000). However, owing to the increasing infl uence of humans worldwide, the processes driving expansion and decline have speeded up dramatically. Hence, we have the current biodiversity crisis. Humanmediated forces are making some species rarer (ie, driving them towards extinction) while at the same time making some species expand their ranges (‘invasive’ sensu Richardson et al., 2000). Undisputedly, the immediate causes for extinction of native species and invasiveness of aliens are extrinsic factors, such as habitat destruction and climate change. However, the ultimate causes have to be ecological and life-history characteristics of species (Kotiaho et al., 2005). Therefore, important research directions in conservation biology and invasion biology are the analyses of species traits associated with rarity (Murray et al., 2002) and invasiveness (Pyšek and Richardson, 2007), respectively. The first are important for prioritizing conservation efforts, and the second are important for prioritizing eradication efforts and the development of screening protocols of potential invasiveness of species considered for introduction to other regions. Unravelling the links between species traits and extrinsic factors is highly complex, particularly because assessment of the causes of rarity and invasiveness relies mainly on retrospective analyses since large-scale controlled experiments are often not feasible (Richardson et al., 2004). However, with the increasing availability of large, widely accessible databases and analytical approaches (eg, Wilson et al., 2007), it is becoming easier to test which traits are associated with rarity and invasiveness, and under which conditions.