Nunzio Knerr

Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia

Understanding spatial patterns of biodiversity is critical for conservation planning, particularly given rapid habitat loss and human-induced climatic change. Diversity and endemism are typically assessed by comparing species ranges across regions. However, investigation of patterns of species diversity alone misses out on the full richness of patterns that can be inferred using a phylogenetic approach. Here, using Australian Acacia as an example, we show that the application of phylogenetic methods, particularly two new measures, relative phylogenetic diversity and relative phylogenetic endemism, greatly enhances our knowledge of biodiversity across both space and time. We found that areas of high species richness and species endemism are not necessarily areas of high phylogenetic diversity or phylogenetic endemism. We propose a new method called categorical analysis of neo- and paleo-endemism (CANAPE) that allows, for the first time, a clear, quantitative distinction between centres of neo- and paleo-endemism, useful to the conservation decision-making process.

Quantifying Phytogeographical Regions of Australia Using Geospatial Turnover in Species Composition

The largest digitized dataset of land plant distributions in Australia assembled to date (750,741 georeferenced herbarium records; 6,043 species) was used to partition the Australian continent into phytogeographical regions. We used a set of six widely distributed vascular plant groups and three non-vascular plant groups which together occur in a variety of landscapes/habitats across Australia. Phytogeographical regions were identified using quantitative analyses of species turnover, the rate of change in species composition between sites, calculated as Simpsons beta. We propose six major phytogeographical regions for Australia: Northern, Northern Desert, Eremaean, Eastern Queensland, Euronotian and South-Western. Our new phytogeographical regions show a spatial agreement of 65% with respect to previously defined phytogeographical regions of Australia. We also confirm that these new regions are in general agreement with the biomes of Australia and other contemporary biogeographical classifications. To assess the meaningfulness of the proposed phytogeographical regions, we evaluated how they relate to broad scale environmental gradients. Physiographic factors such as geology do not have a strong correspondence with our proposed regions. Instead, we identified climate as the main environmental driver. The use of an unprecedentedly large dataset of multiple plant groups, coupled with an explicit quantitative analysis, makes this study novel and allows an improved historical bioregionalization scheme for Australian plants. Our analyses show that: (1) there is considerable overlap between our results and older biogeographic classifications; (2) phytogeographical regions based on species turnover can be a powerful tool to further partition the landscape into meaningful units; (3) further studies using phylogenetic turnover metrics are needed to test the taxonomic areas.

A comparison of network and clustering methods to detect biogeographical regions

Bioregions are an important concept in biogeography, and are key to our understanding of biodiversity patterns across the world. The use of networks in biogeography to produce bioregions is a relatively novel approach that has been proposed to improve upon current methods. However, it remains unclear if they may be used in place of current methods and/or offer additional biogeographic insights. We compared two network methods to detect bioregions (modularity and map equation) with the conventional distance-based clustering method. We also explored the relationship between network and biodiversity metrics. For the analysis we used two datasets of iconic Australian plant groups at a continental scale, Acacia and eucalypts, as example groups. The modularity method detected fewer large bioregions produced the most succinct bioregionalisation for both plant groups corresponding to Australian biomes, while map equation detected many small bioregions including interzones at a natural scale of one. The clustering method was less sensitive than network methods in detecting bioregions. The network metric called participation coefficient from both network partition methods identified interzones or transition zones between bioregions. Furthermore, another network metric (betweenness) was highly correlated to richness and endemism. We conclude that the application of networks to biogeography offers a number of advantages and provides novel insights. More specifically, our study showed that these network partition methods were more efficient than the clustering method for bioregionalisation of continental-scale data in: 1) the identification of bioregions and 2) the quantification of biogeographic transition zones using the participation coefficient metric. The use of network methods and especially the participation coefficient metric adds to bioregionalisation by identifying transition zones which could be useful for conservation purposes and identifying biodiversity hotspots.

Species richness and endemism of Australian bryophytes

Abstract Although understanding the patterns of diversity is essential for conservation and environmental studies, an understanding of bryophyte distributions in Australia has been limited by the absence of continental-scale maps for patterns of bryophyte diversity. The aim of this study was to identify the patterns of species richness and endemism of hornworts, liverworts, and mosses in Australia. A database of 85 383 geo-referenced herbarium records was assembled and aggregated at a grid cell resolution of 0·5°. A one-cell radius neighbourhood analysis was applied to identify the spatial patterns of species richness and endemism. Primary centres of species richness were located on the east of the continent, with the highest number of species occurring in Queensland’s Wet Tropics, the Border Ranges near the Queensland–New South Wales border, the central coast of New South Wales, southern Victoria, and Tasmania. Endemism scores were high in the Wet Tropics, but highly endemic regions were scattered across the continent but not found in arid regions. The spatial patterns of diversity differed among hornworts, liverworts, and mosses, and areas of endemism and species richness did not always overlap. Comparisons with other taxa additionally indicated that areas of bryophyte diversity do not correspond with groups that are currently used as proxies in conservation.

Non-geographic collecting biases in herbarium specimens of Australian daisies (Asteraceae)

Biological collections are increasingly becoming databased and available for novel types of study. A possible limitation of these data, which has the potential to confound analyses based on them, is their biased composition due to non-random and opportunistic collecting efforts. While geographic biases are comparatively well studied and understood, very little attention has been directed at other potential biases. We used Asteraceae specimen data from Australia’s Virtual Herbarium to test for over- and under-representation of plants with specific morphology, phenology and status by comparing observed numbers of specimens against a null distribution of simulated collections. Strong collecting biases could be demonstrated against introduced plants, plants with green or brown inflorescences, and very small plants. Specimens belonging to species with very restricted areas of distribution were also found to be strongly underrepresented. A moderate bias was observed against plants flowering in summer. While spiny plants have been collected only about half as often as should be expected, much of this bias was due to nearly all of them also being introduced (thistles). When introduced species were analyzed alone, a negative effect of spines remained but was much more moderate. The effect of woody or herbaceous habit, other inflorescence colours, tall growth and size of the capitula was comparatively negligible. Our results indicate that care should be taken when relying on specimen databases or the herbaria themselves for studies examining phenology, resource availability for pollinators, or the distribution and abundance of exotic species, and that researchers should be aware of collecting biases against small and unattractively coloured plants.

Continental scale patterns and predictors of fern richness and phylogenetic diversity

Because ferns have a wide range of habitat preferences and are widely distributed, they are an ideal group for understanding how diversity is distributed. Here we examine fern diversity on a broad-scale using standard and corrected richness measures as well as phylogenetic indices; in addition we determine the environmental predictors of each diversity metric. Using the combined records of Australian herbaria, a dataset of over 60,000 records was obtained for 89 genera to infer richness. A molecular phylogeny of all the genera was constructed and combined with the herbarium records to obtain phylogenetic diversity patterns. A hotspot of both taxic and phylogenetic diversity occurs in the Wet Tropics of northeastern Australia. Although considerable diversity is distributed along the eastern coast, some important regions of diversity are identified only after sample-standardization of richness and through the phylogenetic metric. Of all of the metrics, annual precipitation was identified as the most explanatory variable, in part, in agreement with global and regional fern studies. However, precipitation was combined with a different variable for each different metric. For corrected richness, precipitation was combined with temperature seasonality, while correlation of phylogenetic diversity to precipitation plus radiation indicated support for the species-energy hypothesis. Significantly high and significantly low phylogenetic diversity were found in geographically separate areas. These separate areas correlated with different climatic conditions such as seasonality in precipitation. The phylogenetic metrics identified additional areas of significant diversity, some of which have not been revealed using traditional taxonomic analyses, suggesting that different ecological and evolutionary processes have operated over the continent. Our study demonstrates that it is possible and vital to incorporate evolutionary metrics when inferring biodiversity hotspots from large compilations of data.

Range‐weighted metrics of species and phylogenetic turnover can better resolve biogeographic transition zones

Understanding changes of biodiversity across the landscape underlies biogeography and ecology and is important in land management and conservation. Measures of species and phylogenetic turnover used to estimate the rate of change of assemblages between sets of locations are more often influenced by wide-ranging taxa. Transition zones between regions that are associated with range-restricted taxa can be obscured by wide-ranging taxa that span them. We present a set of new range-weighted metrics of taxon and phylogenetic turnover, as modifications of conventional metrics, where the range-restricted components of the assemblages are assigned greater weight in the calculations. We show how these metrics are derived from weighted endemism and phylogenetic endemism and demonstrate their properties using a continent-wide data set of Australian Acacia. The range-weighted metrics result in better delineated transition zones between regions, in that the rate of turnover is steeper than with conventional turnover measures. These metrics provide important complementary information for the interpretation of spatial turnover patterns derived from conventional turnover metrics. Additionally, the phylogenetic variant incorporates information about phylogenetic relatedness while also not saturating at high values of turnover, thus remaining useful for comparisons over greater distances than conventional turnover metrics.

Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups

Abstract Identifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple taxonomic groups can be used jointly to map diversity and endemism. Here, we demonstrate how to apply different phylogenetic approaches to assess biodiversity across multiple taxonomic groups. We map spatial patterns of phylogenetic diversity/endemism to identify concordant areas with the greatest representation of biodiversity across multiple taxa and demonstrate the approach by applying it to the Murray–Darling basin region of southeastern Australia. The areas with significant centers of phylogenetic diversity and endemism were distributed differently for the five taxonomic groups studied (plant genera, fish, tree frogs, acacias, and eucalypts); no strong shared patterns across all five groups emerged. However, congruence was apparent between some groups in some parts of the basin. The northern region of the basin emerges from the analysis as a priority area for future conservation initiatives focused on eucalypts and tree frogs. The southern region is particularly important for conservation of the evolutionary heritage of plants and fishes.

Do soil and climate properties drive biogeography of the Australian proteaceae

AimsThe Proteaceae are a diverse family of approximately 80 genera and 1700 species with a mostly southern-hemisphere distribution. While distributional patterns of various subsets of the Proteaceae have been studied, no quantitative continental-scale study of species-level spatial biodiversity patterns of the Australian Proteaceae has been conducted. The aim of this study is to identify and examine patterns of distribution, diversity and endemism for the Proteaceae (at family, genera and species levels) of continental Australia and to investigate the environmental drivers for the observed patterns.MethodsUsing 151,899 herbarium records for 1179 Australian Proteaceae species, we investigate taxon richness, endemism, and compositional turnover along with climatic and soil correlates.ResultsSpecies richness and endemism was highest in the Southwest phytogeographical region, as well as the Atherton and Southeastern subregions. Genus richness was highest in the Northeastern and Atherton subregions. Highest species turnover occured in the Southwestern region and the Southeastern subregion while lowest species turnover occured in the Northern, Northern Desert and Eremaean regions. Over the entire continent, soil geochemistry and climate explain 37% of the variation in species turnover; however, in areas of high species richness, they account for >75% of the variation in species turnover.ConclusionsThese results suggest that the biogeographic patterns of the Proteaceae are impacted by climate and soils, where Proteaceae specialization has filled novel environmental niches associated with low nutrient and low water availability soils, particularly in southwestern Australia.

Why non-native grasses pose a critical emerging threat to biodiversity conservation, habitat connectivity and agricultural production in multifunctional rural landscapes

ContextLandscape-scale conservation planning is key to the protection of biodiversity globally. Central to this approach is the development of multifunctional rural landscapes (MRLs) that maintain the viability of natural ecosystems and promote animal and plant dispersal alongside agricultural land uses.ObjectivesWe investigate evidence that non-native grasses (NNGs) in rangelands and other low-intensity agricultural systems pose a critical threat to landscape conservation initiatives in MRLs both in Australia and globally.MethodsWe first establish a simple socio-ecological model that classifies different rural landscape elements within typical MRLs based on their joint conservation and agro-economic value. We then quantify the impacts of eight Australian NNGs (Andropogon gayanus, Cenchrus ciliaris, Eragrostis curvula, Hyparrhenia hirta, Nassella neesiana, Nassella trichotoma, Phalaris aquatica and Urochloa mutica) on different landscape elements and then classify and describe the socio-ecological transformations that result at the MRL scale.ResultsOur data indicate that two broad classes of NNGs exist. The first reduces both conservation and agro-economic value (‘co-degrading’ species) of invaded landscapes, while the second improves agro-economic value at the expense of conservation value (‘trade-off’ species). Crucially, however, both classes cause hardening of the landscape matrix, agricultural intensification, reduced habitat connectivity, and the loss of multi-value land use types that are vital for landscape conservation.ConclusionsNNGs drive socio-ecological transformations that pose a growing threat to landscape-scale connectivity and conservation initiatives in Australia and globally. There is an urgent need for further research into the impacts of NNGs on habitat connectivity and biodiversity within multifunctional landscapes, and the socio-ecological goals that can be achieved when landscape transformation and degradation by these species is unavoidable.