Centre for Australian National Biodiversity Research

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Abstract Aim Interest in species distribution models ( SDM s) and related niche studies has increased dramatically in recent years, with several books and reviews being prepared since 2000. The earliest SDM studies are dealt with only briefly even in the books. Consequently, many researchers are unaware of when the first SDM software package ( bioclim ) was developed and how a broad range of applications using the package was explored within the first 8 years following its release. The purpose of this study is to clarify these early developments and initial applications, as well as to highlight bioclim 's continuing relevance to current studies. Location Mainly Australia and New Zealand, but also some global applications. Methods We outline the development of the bioclim package, early applications (1984–1991) and its current relevance. Results bioclim was the first SDM package to be widely used. Early applications explored many of the possible uses of SDM s in conservation biogeography, such as quantifying the environmental niche of species, identifying areas where a species might be invasive, assisting conservation planning and assessing the likely impacts of climate change on species distributions. Main conclusions Understanding this pioneering work is worthwhile as bioclim was for many years one of the leading SDM packages and remains widely used. Climate interpolation methods developed for bioclim were used to create the WorldClim database, the most common source of climate data for SDM studies, and bioclim variables are used in about 76% of recent published MaxEnt analyses of terrestrial ecosystems. Also, some of the bioclim studies from the late 1980s, such as measuring niche (both realized and fundamental) and assessing possible impacts of climate change, are still highly relevant to key conservation biogeography issues.

Evolution occurs rapidly and is an ongoing process in our environments. Evolutionary principles need to be built into conservation efforts, particularly given the stressful conditions organisms are increasingly likely to experience because of climate change and ongoing habitat fragmentation. The concept of evolutionary resilience is a way of emphasizing evolutionary processes in conservation and landscape planning. From an evolutionary perspective, landscapes need to allow in situ selection and capture high levels of genetic variation essential for responding to the direct and indirect effects of climate change. We summarize ideas that need to be considered in planning for evolutionary resilience and suggest how they might be incorporated into policy and management to ensure that resilience is maintained in the face of environmental degradation.

A working checklist of accepted taxa worldwide is vital in achieving the goal of developing an online flora of all known plants by 2020 as part of the Global Strategy for Plant Conservation. We here present the first-ever worldwide checklist for liverworts (Marchantiophyta) and hornworts (Anthocerotophyta) that includes 7486 species in 398 genera representing 92 families from the two phyla. The checklist has far reaching implications and applications, including providing a valuable tool for taxonomists and systematists, analyzing phytogeographic and diversity patterns, aiding in the assessment of floristic and taxonomic knowledge, and identifying geographical gaps in our understanding of the global liverwort and hornwort flora. The checklist is derived from a working data set centralizing nomenclature, taxonomy and geography on a global scale. Prior to this effort a lack of centralization has been a major impediment for the study and analysis of species richness, conservation and systematic research at both regional and global scales. The success of this checklist, initiated in 2008, has been underpinned by its community approach involving taxonomic specialists working towards a consensus on taxonomy, nomenclature and distribution.

As climates change across already stressed ecosystems, there is no doubt that species will be affected, but to what extent and which will be most vulnerable remain uncertain. The fossil record suggests that most species persisted through past climate change, whereas forecasts of future impacts predict large-scale range reduction and extinction. Many species have altered range limits and phenotypes through 20th-century climate change, but responses are highly variable. The proximate causes of species decline relative to resilience remain largely obscure; however, recent examples of climate-associated species decline can help guide current management in parallel with ongoing research.

Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny. We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected with only 50% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies.

Abstract Long‐term ecological studies are critical for providing key insights in ecology, environmental change, natural resource management and biodiversity conservation. In this paper, we briefly discuss five key values of such studies. These are: (1) quantifying ecological responses to drivers of ecosystem change; (2) understanding complex ecosystem processes that occur over prolonged periods; (3) providing core ecological data that may be used to develop theoretical ecological models and to parameterize and validate simulation models; (4) acting as platforms for collaborative studies, thus promoting multidisciplinary research; and (5) providing data and understanding at scales relevant to management, and hence critically supporting evidence‐based policy, decision making and the management of ecosystems. We suggest that the ecological research community needs to put higher priority on communicating the benefits of long‐term ecological studies to resource managers, policy makers and the general public. Long‐term research will be especially important for tackling large‐scale emerging problems confronting humanity such as resource management for a rapidly increasing human population, mass species extinction, and climate change detection, mitigation and adaptation. While some ecologically relevant, long‐term data sets are now becoming more generally available, these are exceptions. This deficiency occurs because ecological studies can be difficult to maintain for long periods as they exceed the length of government administrations and funding cycles. We argue that the ecological research community will need to coordinate ongoing efforts in an open and collaborative way, to ensure that discoverable long‐term ecological studies do not become a long‐term deficiency. It is important to maintain publishing outlets for empirical field‐based ecology, while simultaneously developing new systems of recognition that reward ecologists for the use and collaborative sharing of their long‐term data sets. Funding schemes must be re‐crafted to emphasize collaborative partnerships between field‐based ecologists, theoreticians and modellers, and to provide financial support that is committed over commensurate time frames.

Orchids are the most diverse family of angiosperms, with over 25 000 species,more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here,we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. Asupermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras),and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp(-1) My(-1)) is 6.8 times that at the Asparagales crown.

We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation. PE has a number of desirable properties not combined in previous approaches. It assesses endemism consistently, independent of taxonomic status or level, and independent of previously defined political or biological regions. The results can be directly compared between areas because they are based on equivalent spatial units. PE builds on previous phylogenetic analyses of endemism, but provides a more general solution for mapping endemism of lineages. We illustrate the broad applicability of PE using examples of Australian organisms having contrasting life histories: pea-flowered shrubs of the genus Daviesia (Fabaceae) and the Australian species of the Australo-Papuan tree frog radiation within the family Hylidae.

Current approaches to biodiversity conservation are largely based on geographic areas, ecosystems, ecological communities and species, with less attention ongenetic diversity and the evolutionary continuum from populations to species. Conservation management generally rests on discrete categories, such as identified species, and, for threated taxa, intraspecific units. Species, in particular, provide a common measure of biodiversity yet in both theory and nature, speciation is typically a protracted process progressing from connected populations to unambiguous species with variable rates of phenotypic, ecological and genetic divergence. Thus, most recognised species are not genetically uniform and are sometimes highly structured into historically isolated populations worthy of consideration as intraspecific units that represent unique genetic diversity for conservation. Genome screens offer unprecedented resolution of structure across taxonomic boundaries in species complexes, and have the potential to oversplit species if not interpreted conservatively. This highlights the blurred line between populations and species, and can confound simple dichotomies of ‘species’ versus ‘not species’. At the same time, like plants, there is increasing evidence than even distantly related animal species can hybridize and exchange genes. A review of conservation legislation reveals that legal definitions of ‘species’ are quite flexible and can accommodate a range of infra-specific taxa and divergent populations, as well as taxonomically recognised species. For example, the legislative definition of a species around the world can include: species, subspecies, varieties, and geographically and/or genetically distinct populations. In principle, this flexibility allows for protection of genetic diversity and maintenance of evolutionary processes at a broad range of infra-specific levels. However, evolutionary biologists often fail to adequately justify and then translate their evidence for genetically defined units into categories suited to assessment under local legislation. We recommend that (i). genomic data should be interpreted conservatively when formally naming species, (ii). concomitantly, there should be stronger impetus and a more uniform approach to identifying clearly justified intraspecific units, (iii). guidelines be developed for recognising and labelling intraspecific data that align with best scientific practice, and (iv). that the more nuanced view of species and speciation emerging from genomic analyses is communicated more effectively by scientists to decision makers.

Abstract The Leguminosae, the third–largest angiosperm family, has a global distribution and high ecological and economic impor tance. We examine how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the ca. 751 genera and ca. 19,500 species of legumes and then translate it into a phylogeny–based classification. We review the current state of knowledge of legume phylogeny and highlight where problems lie, for example in taxon sampling and phylogenetic resolution. We review approaches from bioinformatics and next–generation sequencing, which can facilitate the production of better phylogenetic estimates. Finally, we examine how morphology can be incorporated into legume phylogeny to address issues in comparative biology and classification. Our goal is to stimulate the research needed to improve our knowledge of legume phylogeny and evolution; the approaches that we discuss may also be relevant to other species–rich angiosperm clades.

Natural history museum collections provide unique resources for understanding how species respond to environmental change, including the abrupt, anthropogenic climate change of the past century. Ideally, researchers would conduct genome-scale screening of museum specimens to explore the evolutionary consequences of environmental changes, but to date such analyses have been severely limited by the numerous challenges of working with the highly degraded DNA typical of historic samples. Here, we circumvent these challenges by using custom, multiplexed, exon capture to enrich and sequence ~11,000 exons (~4 Mb) from early 20th-century museum skins. We used this approach to test for changes in genomic diversity accompanying a climate-related range retraction in the alpine chipmunks (Tamias alpinus) in the high Sierra Nevada area of California, USA. We developed robust bioinformatic pipelines that rigorously detect and filter out base misincorporations in DNA derived from skins, most of which likely resulted from postmortem damage. Furthermore, to accommodate genotyping uncertainties associated with low-medium coverage data, we applied a recently developed probabilistic method to call single-nucleotide polymorphisms and estimate allele frequencies and the joint site frequency spectrum. Our results show increased genetic subdivision following range retraction, but no change in overall genetic diversity at either nonsynonymous or synonymous sites. This case study showcases the advantages of integrating emerging genomic and statistical tools in museum collection-based population genomic applications. Such technical advances greatly enhance the value of museum collections, even where a pre-existing reference is lacking and points to a broad range of potential applications in evolutionary and conservation biology.

Trait-based approaches have improved our understanding of plant evolution, community assembly and ecosystem functioning. A major challenge for the upcoming decades is to understand the functions and evolution of early life-history traits, across levels of organization and ecological strategies. Although a variety of seed traits are critical for dispersal, persistence, germination timing and seedling establishment, only seed mass has been considered systematically. Here we suggest broadening the range of morphological, physiological and biochemical seed traits to add new understanding on plant niches, population dynamics and community assembly. The diversity of seed traits and functions provides an important challenge that will require international collaboration in three areas of research. First, we present a conceptual framework for a seed ecological spectrum that builds upon current understanding of plant niches. We then lay the foundation for a seed-trait functional network, the establishment of which will underpin and facilitate trait-based inferences. Finally, we anticipate novel insights and challenges associated with incorporating diverse seed traits into predictive evolutionary ecology, community ecology and applied ecology. If the community invests in standardized seed-trait collection and the implementation of rigorous databases, major strides can be made at this exciting frontier of functional ecology.

Minimizing the impact of invasive alien species (IAS) on islands and elsewhere requires researchers to provide cogent information on the environmental and socioeconomic consequences of IAS to the public and policy makers. Unfortunately, this information has not been readily available owing to a paucity of scientific research and the failure of the scientific community to make their findings readily available to decision makers. This review explores the vulnerability of islands to biological invasion, reports on environmental and socioeconomic impacts of IAS on islands and provides guidance and information on technical resources that can help minimize the effects of IAS in island ecosystems. This assessment is intended to provide a holistic perspective on island-IAS dynamics, enable biologists and social scientists to identify information gaps that warrant further research and serve as a primer for policy makers seeking to minimize the impact of IAS on island systems. Case studies have been selected to reflect the most scientifically-reliable information on the impacts of IAS on islands. Sufficient evidence has emerged to conclude that IAS are the most significant drivers of population declines and species extinctions in island ecosystems worldwide. Clearly, IAS can also have significant socioeconomic impacts directly (for example human health) and indirectly through their effects on ecosystem goods and services. These impacts are manifest at all ecological levels and affect the poorest, as well as richest, island nations. The measures needed to prevent and minimize the impacts of IAS on island ecosystems are generally known. However, many island nations and territories lack the scientific and technical information, infrastructure and human and financial resources necessary to adequately address the problems caused by IAS. Because every nation is an exporter and importer of goods and services, every nation is also a facilitator and victim of the invasion of alien species. Wealthy nations therefore need to help raise the capacity of island nations and territories to minimize the spread and impact of IAS.

Abstract Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods 1,2 . A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome 3,4 . Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins 5–7 . However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes 8 . This 15-fold increase in genus-level sampling relative to comparable nuclear studies 9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis. To address the question of whether rapid genomic changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using both methylation-sensitive and methylation-insensitive enzymes, the extent of fragment additivity in newly combined genomes was ascertained for a total of approximately 22,000 genomic loci. Fragment additivity was observed in nearly all cases, with the few exceptions most likely reflecting parental heterozygosity or experimental error. In addition, genomic Southern analysis on six sets of synthetic allopolyploids probed with five retrotransposons also revealed complete additivity. Because no alterations were observed using methylation-sensitive isoschizomers, epigenetic changes following polyploid synthesis were also minimal. These indications of genomic additivity and epigenetic stasis during allopolyploid formation provide a contrast to recent evidence from several model plant allopolyploids, most notably wheat and Brassica, where rapid and unexplained genomic changes have been reported. In addition, the data contrast with evidence from repetitive DNAs in Gossypium, some of which are subject to non-Mendelian molecular evolutionary phenomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa.

Varietal data from 27 crop species from five continents were drawn together to determine overall trends in crop varietal diversity on farm. Measurements of richness, evenness, and divergence showed that considerable crop genetic diversity continues to be maintained on farm, in the form of traditional crop varieties. Major staples had higher richness and evenness than nonstaples. Variety richness for clonal species was much higher than that of other breeding systems. A close linear relationship between traditional variety richness and evenness (both transformed), empirically derived from data spanning a wide range of crops and countries, was found both at household and community levels. Fitting a neutral "function" to traditional variety diversity relationships, comparable to a species abundance distribution of "neutral ecology," provided a benchmark to assess the standing diversity on farm. In some cases, high dominance occurred, with much of the variety richness held at low frequencies. This suggested that diversity may be maintained as an insurance to meet future environmental changes or social and economic needs. In other cases, a more even frequency distribution of varieties was found, possibly implying that farmers are selecting varieties to service a diversity of current needs and purposes. Divergence estimates, measured as the proportion of community evenness displayed among farmers, underscore the importance of a large number of small farms adopting distinctly diverse varietal strategies as a major force that maintains crop genetic diversity on farm.

Abstract Comparative studies investigating relationships between plant traits and species rarity and commonness were surveyed to establish whether global patterns have emerged that would be of practical use in management strategies aimed at the long‐term conservation of species. Across 54 studies, 94 traits have been examined in relation to abundance, distribution and threatened status at local, regional and geographical spatial scales. Most traits (63) have yet to be the focus of more than one study. Half of the studies involved less than 10 species, and one‐quarter did not replicate rare–common contrasts. Although these features of the literature make it difficult to demonstrate robust generalizations regarding trait relationships with species rarity, some important findings surfaced in relation to traits that have been examined in two or more studies. Species with narrow geographical distributions were found to produce significantly fewer seeds (per unit measurement) than common species (in four of six studies), but did not differ with respect to breeding system (five of five studies). The majority of traits (including seed size, competitive ability, growth form and dispersal mode) were related to rarity in different ways from one study to the next. The highly context‐dependent nature of most trait relationships with rarity implies that application of knowledge concerning rare–common differences and similarities to management plans will vary substantially for different vegetation types and on different continents. A comparative analysis of distribution patterns in relation to several life‐history and ecological traits among 700 Australian eucalypt species was then performed. A significantly dispro­portionate number of tall species and species with long flowering durations had wide geographical ranges. Trait relationships with distribution were explored further through the development of a methodology incorporating multiple spatial scales. Eight theoretical categories were described illustrating variation in distribution patterns (and hence rarity and commonness) across small, intermediate and large spatial scales, based on the spatial structure of species occurrence across the Australian landscape. Each eucalypt species was placed into a category, and trait variation was explored across all species in relation to distribution patterns across multiple spatial scales. This approach yielded important information about trait relationships with distribution among the eucalypts, linking the spatial structure of points‐of‐occurrence with patterns of rarity and commonness. With the pressing need to protect increasing numbers of threatened species and slow rates of extinction, the development and refinement of a broadly usable methodology for rarity studies that encompasses multiple spatial scales, which can be used for any geographical location, will be useful in both conservation and management.

Abstract Aim Australian acacias (1012 recognized species native to Australia, which were previously grouped in Acacia subgenus Phyllodineae ) have been moved extensively around the world by humans over the past 250 years. This has created the opportunity to explore how evolutionary, ecological, historical and sociological factors interact to affect the distribution, usage, invasiveness and perceptions of a globally important group of plants. This editorial provides the background for the 20 papers in this special issue of Diversity and Distributions that focusses on the global cross‐disciplinary experiment of introduced Australian acacias. Location Australia and global. Methods The papers of the special issue are discussed in the context of a unified framework for biological invasions. Distributions of species were mapped across Australia, their representation in bioclimatic zones examined and the potential global distribution of the group modelled. By collating a variety of different lists, we determined which Australian acacias have reached different stages in the introduction‐naturalization‐invasion continuum in different parts of the world. Paradigms and key research questions relating to barriers to invasion, stages of invasion and management perceptions are sketched. Results According to our global database of Australian acacia records, 386 species have been moved outside Australia by human agency, 71 species are naturalized or weedy, and 23 are unequivocally invasive. Climatic models suggest that about a third of the world’s land surface is climatically suitable for Australian acacias. Many species are commercially important crops or are useful for other purposes and have been extensively planted, and many different human perceptions of Australian acacias exist in different parts of the world. The papers in the special issue cover all the barriers, stages and processes that define biological invasions and touch on many aspects: history and the human dimension; aspects of the species pool; species traits; biotic interactions; climate and niche; and management. Main conclusions Australian acacias are an excellent model group for examining interactions between evolutionary, ecological and socio‐economic drivers of species introductions. New insights have emerged on the biological, ecological and evolutionary correlates of naturalization and invasion, but human usage factors permeate all explanatory models. Understanding and managing introduced Australian acacias requires a fundamental and integrative appreciation of both intrinsic (e.g. species traits) and extrinsic (e.g. human usage and perceptions) aspects.

When negotiating a narrow gap, honeybees tend to fly through the middle of the gap, balancing the distances to the boundary on either side. To investigate the basis of this "centering response," bees were trained to fly through a tunnel on their way to a feeding site and back, while their flight trajectories were filmed from above. The wall on either side carried a visual pattern. When the patterns were stationary vertical gratings, bees tended to fly through the middle of the tunnel, i.e. along its longitudinal axis. However, when one of the gratings was in motion, bees flying in the same direction as the moving grating tended to fly closer to it, while bees flying in the opposite direction tended to fly closer to the stationary grating. This demonstrates, directly and unequivocally, that flying bees estimate the distances of surfaces in terms of the apparent motion of their images. A series of further experiments revealed that the distance to the gratings is gauged in terms of their apparent angular speeds, and that the visual system of the bee is capable of measuring angular speed largely independently of the spatial period, intensity profile, or contrast of the grating. Thus, the motion-sensitive mechanisms mediating range perception appear to be qualitatively different from those that mediate the well-known optomotor response in insects, or those involved in motion detection and ocular tracking in man.