Biodiversity and evolutionary history: useful extensions of the PD phylogenetic diversity assessment framework

Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage

Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce "EvoHeritage", a generalization of PD that is founded on the joint processes of accumulation and attrition of features. We argue that while PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one-dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.

Biodiversity patterns diverge along geographic temperature gradients

Models applying space-for-time substitution, including those projecting ecological responses to climate change, generally assume an elevational and latitudinal equivalence that is rarely tested. However, a mismatch may lead to different capacities for providing climatic refuge to dispersing species. We compiled community data on zooplankton, ectothermic animals that form the consumer basis of most aquatic food webs, from over 1200 mountain lakes and ponds across western North America to assess biodiversity along geographic temperature gradients spanning nearly 3750 m elevation and 30° latitude. Species richness, phylogenetic relationships, and functional diversity all showed contrasting responses across gradients, with richness metrics plateauing at low elevations but exhibiting intermediate latitudinal maxima. The nonmonotonic/hump-shaped diversity trends with latitude emerged from geographic interactions, including weaker latitudinal relationships at higher elevations (i.e. in alpine lakes) linked to different underlying drivers. Here, divergent patterns of phylogenetic and functional trait dispersion indicate shifting roles of environmental filters and limiting similarity in the assembly of communities with increasing elevation and latitude. We further tested whether gradients showed common responses to warmer temperatures and found that mean annual (but not seasonal) temperatures predicted elevational richness patterns but failed to capture consistent trends with latitude, meaning that predictions of how climate change will influence diversity also differ between gradients. Contrasting responses to elevation- and latitude-driven warming suggest different limits on climatic refugia and likely greater barriers to northward range expansion.

Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.

Cftr deletion in mouse epithelial and immune cells differentially influence the intestinal microbiota

Cystic fibrosis (CF) is a life-threatening genetic disorder, caused by mutations in the CF transmembrane-conductance regulator gene (cftr) that encodes CFTR, a cAMP-activated chloride and bicarbonate channel. Clinically, CF lung disease dominates the adult patient population. However, its gastrointestinal illness claims the early morbidity and mortality, manifesting as intestinal dysbiosis, inflammation and obstruction. As CF is widely accepted as a disease of epithelial dysfunction, it is unknown whether CFTR loss-of-function in immune cells contributes to these clinical outcomes. Using cftr genetic knockout and bone marrow transplantation mouse models, we performed 16S rRNA gene sequencing of the intestinal microbes. Here we show that cftr deletion in both epithelial and immune cells collectively influence the intestinal microbiota. However, the immune defect is a major factor determining the dysbiosis in the small intestine, while the epithelial defect largely influences that in the large intestine. This finding revises the current concept by suggesting that CF epithelial defect and immune defect play differential roles in CF intestinal disease.

Biodiversity priority areas and conservation strategies for seed plants in China

China is known for its abundant plant resources, but biodiversity conservation faces unprecedented challenges. To provide feasible suggestions for sustainable conservation, we used the species richness algorithm and complementary algorithm to study distribution patterns of 34,082 seed plants based on 1,007,196 county-level distribution records. We reconstructed a phylogenetic tree for 95.35% of species and estimated the spatial phylogenetics, followed by correlation analyses between different distribution patterns. We identified 264 counties concentrated in southern and south-western mountainous areas as hotspots which covered 10% of the land area of China and harbored 85.22% of the Chinese seed plant species. The biodiversity conservation priorities we identified were highly representative as we have considered multiple conservation indicators. We evaluated the conservation effectiveness and gaps in the network of nature reserves and identified 31.44, 32.95, and 9.47%, respectively, of the hotspot counties as gaps in the national nature reserves, provincial nature reserves and both together, with respectively 55.77, 61.53, and 28.94% of the species. Analysis of the species composition showed there were a large number of threatened and endemic species occurring in the nature reserves' gaps. The conservation gaps need to be filled by establishing new nature reserves or national parks, especially in south-western China, and more attentions should be paid to strengthen the conservation of specific plant taxa due to the apparent mismatches between different distribution patterns.

Phylogenetic diversity and conservation of crop wild relatives in Colombia

Crop wild relatives (CWR) are an important agricultural resource as they contain genetic traits not found in cultivated species due to localized adaptation to unique environmental and climatic conditions. Phylogenetic diversity (PD) measures the evolutionary relationship of species using the tree of life. Our knowledge of CWR PD in neotropical regions is in its infancy. We analysed the distribution of CWR PD across Colombia and assessed its conservation status. The areas with the largest concentration of PD were identified as being in the northern part of the central and western Andean mountain ranges and the Pacific region. These centres of high PD were comprised of predominantly short and closely related branches, mostly of species of wild tomatoes and black peppers. In contrast, the CWR PD in the lowland ecosystems of the Amazon and Orinoquia regions had deeply diverging clades predominantly represented by long and distantly related branches (i.e. tuberous roots, grains and cacao). We categorized 50 (52.6%) of the CWR species as 'high priority', 36 as 'medium priority' and nine as 'low priority' for further ex-situ and in situ conservation actions. New areas of high PD and richness with large ex-situ gap collections were identified mainly in the northern part of the Andes of Colombia. We found that 56% of the grid cells with the highest PD values were unprotected. These baseline data could be used to create a comprehensive national strategy of CWR conservation in Colombia.

The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change

Research relating gut microbiome composition to autism spectrum disorders (ASD) has produced inconsistent results, indicative of the disorder’s complexity and the need for more sophisticated experimental designs. We address this need by (i) comparing gut microbiome composition between individuals with ASD and neurotypical controls in Arizona and Colorado using standardized DNA extraction and sequencing methods at both locations and (ii) longitudinally evaluating the gut microbiome’s relationship to autism behavioral severity, diet, and gastrointestinal symptoms. Gut microbiome composition differed between individuals in Arizona and individuals in Colorado, and gastrointestinal symptoms were significantly higher in ASD individuals than in neurotypical individuals in Arizona but not in Colorado. Gut microbiome composition was significantly associated with ASD while controlling for study-site location but not when controlling for gastrointestinal symptoms. This suggests that non-ASD-related study site differences in gut microbiome composition and different degrees of gastrointestinal symptoms involvement with ASD between sites may contribute to inconsistent results in the literature regarding the association between gut microbiome composition and ASD. In the longitudinal analysis, we found that difference in levels of lethargy/social withdrawal measured in individuals at different time points correlated with the degree of change in gut microbiome composition and that a worsening of inappropriate speech between time points was associated with decreased gut microbiome diversity. This relationship between changes in the gut microbiome composition within individuals and ASD behavioral severity metrics indicates that longitudinal study designs may be useful for exploring microbial drivers of ASD severity when substantial variability exists in baseline microbiome compositions across individuals and geographical regions.

IMPORTANCE Autism spectrum disorder (ASD) is a brain developmental disorder with varying behavioral symptom severity both across individuals and within individuals over time. There have been promising but also inconsistent literature results regarding how the gut microbiota (microbiome) may be involved. We found that the gut microbiome in individuals with ASD is affected by study-site location as well as gastrointestinal symptom severity. When we sampled some individuals with ASD at several different time points, we found that some behaviors, such as lethargy/social withdrawal and inappropriate speech, changed along with changes in the gut microbiota composition. This is the first study to relate severity of behavior symptoms to gut microbiome composition within individuals over time and suggests a dynamic relationship between ASD-associated symptoms and gut microbes. Longitudinal study designs as well as collaborative efforts across multiple centers are needed to fully characterize the relationship between ASD and gut microbes.

Urban areas as hotspots for bees and pollination but not a panacea for all insects

Urbanisation is an important global driver of biodiversity change, negatively impacting some species groups whilst providing opportunities for others. Yet its impact on ecosystem services is poorly investigated. Here, using a replicated experimental design, we test how Central European cities impact flying insects and the ecosystem service of pollination. City sites have lower insect species richness, particularly of Diptera and Lepidoptera, than neighbouring rural sites. In contrast, Hymenoptera, especially bees, show higher species richness and flower visitation rates in cities, where our experimentally derived measure of pollination is correspondingly higher. As well as revealing facets of biodiversity (e.g. phylogenetic diversity) that correlate well with pollination, we also find that ecotones in insect-friendly green cover surrounding both urban and rural sites boost pollination. Appropriately managed cities could enhance the conservation of Hymenoptera and thereby act as hotspots for pollination services that bees provide to wild flowers and crops grown in urban settings.

Should biodiversity and nature have to earn their keep? What it really means to bring environmental goods into the marketplace

Pursuit of economic gain has sponsored much of our planet's despoliation. Yet conservation increasingly operates as an economic sector that markets biodiversity, ecosystems, and nature as natural capital, service provider, or option value. This essay first elucidates what basic moral theory says about the principle that the goodness of biodiversity and nature is largely economic. It explains why economic valuations may be morally unimportant, inapt for environmental goods, and subversive of more important ideals. It also shows why neither econometric notions of option value nor Daniel Faith's qualitative one credibly applies. The essay then turns to what an economic conception of goodness implies for conservation practice. It refers to two prominent conservation organizations, whose conservation principles match the market-based ones of the World Business Council on Sustainable Development's. The environmental record of the latter organization's practices according to these principles predicts what their adoption for conservation entails.

Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis

The purpose of this review is to present the most common and emerging DNA-based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA-based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can "scale up" by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands-on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad-scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science-based decision-making, and provide a greater socio-economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.

Soil pH determines fungal diversity along an elevation gradient in Southwestern China

Fungi play important roles in ecosystem processes, and the elevational pattern of fungal diversity is still unclear. Here, we examined the diversity of fungi along a 1,000 m elevation gradient on Mount Nadu, Southwestern China. We used MiSeq sequencing to obtain fungal sequences that were clustered into operational taxonomic units (OTUs) and to measure the fungal composition and diversity. Though the species richness and phylogenetic diversity of the fungal community did not exhibit significant trends with increasing altitude, they were significantly lower at mid-altitudinal sites than at the base. The Bray-Curtis distance clustering also showed that the fungal communities varied significantly with altitude. A distance-based linear model multivariate analysis (DistLM) identified that soil pH dominated the explanatory power of the species richness (23.72%), phylogenetic diversity (24.25%) and beta diversity (28.10%) of the fungal community. Moreover, the species richness and phylogenetic diversity of the fungal community increased linearly with increasing soil pH (P<0.05). Our study provides evidence that pH is an important predictor of soil fungal diversity along elevation gradients in Southwestern China.

Dimensions of biodiversity loss: Spatial mismatch in land-use impacts on species, functional and phylogenetic diversity of European bees

Aim

Agricultural intensification and urbanization are important drivers of biodiversity change in Europe. Different aspects of bee community diversity vary in their sensitivity to these pressures, as well as independently influencing ecosystem service provision (pollination). To obtain a more comprehensive understanding of human impacts on bee diversity across Europe, we assess multiple, complementary indices of diversity.

Location

One Thousand four hundred and forty six sites across Europe.

Methods

We collated data on bee occurrence and abundance from the published literature and supplemented them with the PREDICTS database. Using Rao's Quadratic Entropy, we assessed how species, functional and phylogenetic diversity of 1,446 bee communities respond to land‐use characteristics including land‐use class, cropland intensity, human population density and distance to roads. We combined these models with statistically downscaled estimates of land use in 2005 to estimate and map—at a scale of approximately 1 km²—the losses in diversity relative to semi‐natural/natural baseline (the predicted diversity of an uninhabited grid square, consisting only of semi‐natural/natural vegetation).

Results

We show that—relative to the predicted local diversity in uninhabited semi‐natural/natural habitat—half of all EU27 countries have lost over 10% of their average local species diversity and two‐thirds of countries have lost over 5% of their average local functional and phylogenetic diversity. All diversity measures were generally lower in pasture and higher‐intensity cropland than in semi‐natural/natural vegetation, but facets of diversity showed less consistent responses to human population density. These differences have led to marked spatial mismatches in losses: losses in phylogenetic diversity were in some areas almost 20 percentage points (pp.) more severe than losses in species diversity, but in other areas losses were almost 40 pp. less severe.

Main conclusions

These results highlight the importance of exploring multiple measures of diversity when prioritizing and evaluating conservation actions, as species‐diverse assemblages may be phylogenetically and functionally impoverished, potentially threatening pollination service provision.

Fixism and conservation science

The field of biodiversity conservation has recently been criticized as relying on a fixist view of the living world in which existing species constitute at the same time targets of conservation efforts and static states of reference, which is in apparent disagreement with evolutionary dynamics. We reviewed the prominent role of species as conservation units and the common benchmark approach to conservation that aims to use past biodiversity as a reference to conserve current biodiversity. We found that the species approach is justified by the discrepancy between the time scales of macroevolution and human influence and that biodiversity benchmarks are based on reference processes rather than fixed reference states. Overall, we argue that the ethical and theoretical frameworks underlying conservation research are based on macroevolutionary processes, such as extinction dynamics. Current species, phylogenetic, community, and functional conservation approaches constitute short-term responses to short-term human effects on these reference processes, and these approaches are consistent with evolutionary principles.

The pattern of GPI-80 expression is a useful marker for unusual myeloid maturation in peripheral blood

Myeloid-derived suppressor cells (MDSCs) have a wide spectrum of immunosuppressive activity; control of these cells is a new target for improving clinical outcomes in cancer patients. MDSCs originate from unusual differentiation of neutrophils or monocytes induced by inflammatory cytokines, including granulocyte-colony stimulating factor (G-CSF) and granulocyte-macrophage (GM)-CSF. However, MDSCs are difficult to detect in neutrophil or monocyte populations because they are not uniform cells, resembling both neutrophils and monocytes; thus, they exist in a heterogeneous population. In this study, we investigated GPI-80, a known regulator of Mac-1 (CD11b/CD18) and associated closely with neutrophil maturation, to clarify this unusual differentiation. First, we demonstrated that the mean fluorescence intensity (MFI) of GPI-80 and coefficient of variation (CV) of GPI-80 were increased by treatment with G-CSF and GM-CSF, respectively, using a human promyelocytic leukaemia (HL60) cell differentiation model. To confirm the value of GPI-80 as a marker of unusual differentiation, we measured GPI-80 expression and MDSC functions using peripheral blood cells from metastatic renal cell carcinoma patients. The GPI-80 CV was augmented significantly in the CD16^hi neutrophil cell population, and GPI-80 MFI was increased significantly in the CD33^hi monocyte cell population. Furthermore, the GPI-80 CV in the CD16^hi population was correlated inversely with the proliferative ability of T cells and the GPI-80 MFI of the CD33^hi population was correlated with reactive oxygen species production. These results led us to propose that the pattern of GPI-80 expression in these populations is a simple and useful marker for unusual differentiation, which is related to MDSC functions.

Influence of tree shape and evolutionary time-scale on phylogenetic diversity metrics

During the last decades, describing, analysing and understanding the phylogenetic structure of species assemblages has been a central theme in both community ecology and macro-ecology. Among the wide variety of phylogenetic structure metrics, three have been predominant in the literature: Faith's phylogenetic diversity (PDFaith), which represents the sum of the branch lengths of the phylogenetic tree linking all species of a particular assemblage, the mean pairwise distance between all species in an assemblage (MPD) and the pairwise distance between the closest relatives in an assemblage (MNTD). Comparisons between studies using one or several of these metrics are difficult because there has been no comprehensive evaluation of the phylogenetic properties each metric captures. In particular it is unknown how PDFaith relates to MDP and MNTD. Consequently, it is possible that apparently opposing patterns in different studies might simply reflect differences in metric properties. Here, we aim to fill this gap by comparing these metrics using simulations and empirical data. We first used simulation experiments to test the influence of community structure and size on the mismatch between metrics whilst varying the shape and size of the phylogenetic tree of the species pool. Second we investigated the mismatch between metrics for two empirical datasets (gut microbes and global carnivoran assemblages). We show that MNTD and PDFaith provide similar information on phylogenetic structure, and respond similarly to variation in species richness and assemblage structure. However, MPD demonstrate a very different behaviour, and is highly sensitive to deep branching structure. We suggest that by combining complementary metrics that are sensitive to processes operating at different phylogenetic depths (i.e. MPD and MNTD or PDFaith) we can obtain a better understanding of assemblage structure.

Seed plant phylogenetic diversity and species richness in conservation planning within a global biodiversity hotspot in eastern Asia

One of the main goals of conservation biology is to understand the factors shaping variation in biodiversity across the planet. This understanding is critical for conservation planners to be able to develop effective conservation strategies. Although many studies have focused on species richness and the protection of rare and endemic species, less attention has been paid to the protection of the phylogenetic dimension of biodiversity. We explored how phylogenetic diversity, species richness, and phylogenetic community structure vary in seed plant communities along an elevational gradient in a relatively understudied high mountain region, the Dulong Valley, in southeastern Tibet, China. As expected, phylogenetic diversity was well correlated with species richness among the elevational bands and among communities. At the community level, evergreen broad-leaved forests had the highest levels of species richness and phylogenetic diversity. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region. Evergreen broad-leaved forests were phylogenetically overdispersed, whereas other vegetation types tended to be phylogenetically clustered. We suggest that communities with high species richness or overdispersed phylogenetic structure should be a focus for biodiversity conservation within the Dulong Valley because these areas may help maximize the potential of this flora to respond to future global change. In biodiversity hotspots worldwide, we suggest that the phylogenetic structure of a community may serve as a useful measure of phylogenetic diversity in the context of conservation planning.

Predicting loss of evolutionary history: Where are we?

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical, and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG) in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream, and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.

Mapping biodiversity and setting conservation priorities for SE Queensland's rainforests using DNA barcoding

Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.

Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses

The phylogenetic diversity measure, ('PD'), measures the relative feature diversity of different subsets of taxa from a phylogeny. At the level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of lineages and features include those integrating probabilities of extinction, providing estimates of expected PD. This approach has known advantages over the evolutionarily distinct and globally endangered (EDGE) methods. Expected PD methods also have limitations. An alternative notion of expected diversity, expected functional trait diversity, relies on an alternative non-phylogenetic model and allows inferences of diversity at the level of functional traits. Expected PD also faces challenges in helping to address phylogenetic tipping points and worst-case PD losses. Expected PD may not choose conservation options that best avoid worst-case losses of long branches from the tree of life. We can expand the range of useful calculations based on expected PD, including methods for identifying phylogenetic key biodiversity areas.

Mapping biodiversity and setting conservation priorities for SE Queensland's rainforests using DNA barcoding

Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.

Darwinian shortfalls in biodiversity conservation

If we were to describe all the species on Earth and determine their distributions, we would solve the popularly termed 'Linnean' and 'Wallacean' shortfalls in biodiversity conservation. Even so, we would still be hindered by a 'Darwinian shortfall', that is, the lack of relevant phylogenetic information for most organisms. Overall, there are too few comprehensive phylogenies, large uncertainties in the estimation of divergence times, and, most critically, unknown evolutionary models linking phylogenies to relevant ecological traits and life history variation. Here, we discuss these issues and offer suggestions for further research to support evolutionary-based conservation planning.