Phylogenetic Metrics Research Articles

Meta-analysis of ecological and phylogenetic biomass maturity metrics

Although a wide variety of biomass sources have been subjected to 16S rRNA gene sequencing, ecological and phylogenetic signatures of maturity have not been identified quantitatively. In this meta-analysis we reanalyzed data from the only published study with publicly available 16S and temperature data (Zhou et al., 2018), and then applied the Zhou results to 705 samples from 13 additional studies. Using the Zhou data, we found that Faith’s alpha diversity index correlated inversely with compost temperature and positively with maturity. We also noted a dramatic shift in the ratios of Bacilliota to Acidobacteriota, Planctomycetota, and Pseudomonadota, as samples cooled below 44 °C (p < 0.001). A negative correlation between Bacillota and Pseudomonadota was also observed in all 705 samples that included compost, sugarcane mill mud, anerobic digestates, and vermicompost. Even in the absence of temperature data for the majority of samples, our meta-analysis shows that microbiomes of diverse residuals converged on similar communities that resemble those of soil, regardless of the starting material or residual management process. We propose that approximately < 0.4 log(Bacillota:Pseudomonadota) and > 43 Faith’s phylogenetic diversity indices are indicative of maturity of diverse biomass materials destined for land application.

Hot node limitations and impact of taxonomic resolution on phylogenetic divergence patterns: A case study on Ecuadorian ethnomedicinal flora

SummarySocietal Impact StatementNovel phylogenetic approaches have emerged in recent years to study traditional medicinal plants, aiming to identify potential sources of new drugs. This line of research holds considerable promise yet remains in its early stages. Here, we examine the prevalent methods employed in the field, revealing the impact of methodological choices that have often been made arbitrarily. We also highlight a widespread misconception regarding ‘hot node analysis’, a tool gaining popularity for identifying plants with high bioactive potential. Our findings should advance future research aimed at guiding the selection of promising candidates for bioprospection.Summary Advances in phylogenetics offer a ground‐breaking approach to analysing ethnobotanical data. This line of research typically involves calculating the degree of phylogenetic clustering (i.e. phylogenetic divergence) of a set of medicinal plants and identifying clades with a significant overabundance of these plants, known as hot nodes, which are purportedly responsible for the clustering patterns. However, despite showing great promise, the adequacy of this procedure remains to be tested, and the results have so far been inconclusive and, at times, contradictory. Here, we examine two key elements through a case study of Ecuadorian medicinal flora: the impact of taxonomic resolution (species‐ and genus‐level data) on phylogenetic divergence metrics (Mean Pairwise Distance; MPD, and Mean Nearest Taxon Distance; MNTD), and the efficacy of the hot node analysis in identifying clades that significantly influence these metrics. To identify clades with a significant impact on MPD and MNTD, we implemented a jackknifing procedure and compared outcomes with the hot nodes. Phylogenetic divergence was strongly dependent on the taxonomic resolution, with clustering mainly revealed by MPD at the genus level. Further, the hot nodes incompletely matched those with significant influence on MPD and MNTD according to the jackknifing analysis. We highlight the impact of taxonomic resolution on commonly used phylogenetic divergence metrics and the limitations of hot nodes in identifying influential clades, stressing the potential of alternative jackknifing techniques. We recommend the use of the most resolved tree possible and combining jackknifing with hot node analyses as complementary sources to pinpoint clades for bioprospection.

Assessing phylogenetic diversity metrics in terrestrial ecological restoration: global trends and gaps

Phylogenetic diversity (PD) metrics estimate community diversity through evolutionary relationships, yet their potential in restoration ecology remains underutilized. This study reviews the literature on ecological restoration of terrestrial vegetation to evaluate the use of PD metrics, focusing on their application, global trends, and existing research gaps. Most studies were conducted in the United States, China, and Brazil, primarily in temperate broadleaf mixed forests (36.36%) and tropical and subtropical moist broadleaf forests (33.33%). Half of the papers were based on observational studies of restorations, and the other half were experimental studies. Plant PD was the primary focus in 90.09% of papers, with grasses and trees being the most studied life forms. Standardized effect size of the mean pairwise distance and mean nearest taxonomic distance metrics were the most commonly used metrics. The majority of studies used PD as a response variable and restoration indicators (e.g. age, initial seed/seedling mixture, and restoration impact) as explanatory variables. Research bias toward grassland and limited studies in Africa and Oceania were noted. Future studies should broaden geographic coverage in restoration to provide a more comprehensive understanding of PD dynamics globally. Also, efforts should be made to expand the taxonomic scope beyond to capture the full spectrum of biodiversity in restoration assessments.

Phylogenetic structure and turnover between lowland and montane subtropical forests indicate differential community assembly processes, affected by successional stage and spatial gradients

Secondary forests represent an increasing proportion of global forest cover and offer a range of ecosystem services that are integral to environmental policy targets. Highly disturbed landscapes with temporal records of forest plant community composition offer key insights into the processes that shape plant communities as forests undergo secondary succession. We investigated patterns of plant community phylogenetic structure and phylogenetic beta diversity. Mean pairwise distance (MPD) and Mean Nearest Taxon Distance (MNTD) metrics were determined between co-occurring species within plant communities, in addition to phylogenetic beta diversity metrics relative to null models of random phylogenetic assembly. MPD and MNTD were compared between elevational and successional classes and modelled as products of intercommunity distance (metres) and forest community age (years). Phylogenetic nonmetric multidimensional scaling explored phylogenetic community structure between lowland and montane forest type in Hong Kong. We found that plant communities in secondary forests in Hong Kong exhibited patterns of increased basal phylogenetic clustering with increasing community elevation, while phylogenetic turnover was influenced by spatial and successional factors in lowland and montane forest. Our findings indicate differential community assembly in lowland compared to montane forest type in Hong Kong, as well as evidence for barriers to plant dispersal in secondary forest communities due to patterns of spatial phylogenetic clustering. Plant communities in montane forests were found to be phylogenetically distinct from lowland forest plant communities. Patterns of spatial phylogenetic clustering may suggest significant dispersal or post-dispersal processes causing the clustering of related species at fine spatial scales, while phylogenetic turnover with increasing successional age may indicate compositional changes during the process of passive forest regeneration. Collectively, these results emphasize the need to investigate active pathways for rewilding dispersal limited late successional forest tree species in Hong Kong.

A multifaceted approach to expanding conservation efforts in the Pan-Himalayan landscape

The Pan-Himalayan biogeographic domain is a significant region for biodiversity conservation and climate resilience. This region has both tropical and extratropical flora and holds ecological, cultural, and socio-economic importance. However, knowledge about the spatial distribution and threats to threatened plant species in the study area is still poorly known. In this study we evaluate the phylogenetic diversity and phylogenetic endemism of threatened flora in the region, and also examine the effect of rapid land cover transformation and landscape fragmentation between 2000 and 2020 on the preservation of distinct evolutionary lineages. Phylogenetic metrics provide a better understanding of ecological, historical, and evolutionary factors that shape plant communities in highly biodiverse regions. Our result show that current protected areas are insufficient for preserving Pan-Himalayan biodiversity, and also reveal a significant gap in conservation efforts within these areas. We highlight conservation priorities areas in the western Himalayan belt encompassing 2.43 million km2 and covering 26.73% of the total area. However, a large conservation gap encompassed 22.67% (2.06 million km2) hotspots of total study area, whereas non-hotspot priorities covered 67.62% (0.77 million km2) of the total protected area, revealing a mismatch between biodiversity hotspots and protected areas. In addition, biodiversity priority areas have been threatened by rapid land cover transformation and landscape fragmentation between 2000 and 2020. There were 6.93% increase in cropland area and 172.64% increase in impervious surface, while an increase in landscape fragmentation and a decrease in landscape cohesion in different hotspots within protected areas. The biodiversity hotspot regions emphasize the need to conserve unique evolutionary lineages and high species occurrence areas with targeted conservation strategies. Mountainous, but cross-border international cooperation is highly recommended for effective preservation strategies. Our study has implications for advancing biodiversity preservation and sustainable ecosystem management not only in the Pan-Himalayan but also in similar regions, as well as for achieving the 2030 protection goal.

Plant phylogenetic diversity along the urban–rural gradient and its association with urbanization degree in Shanghai, China

ContextThe spatial distribution of plant diversity in urban areas is fundamental to understanding the relationship between urbanization and biodiversity. Previous research has primarily focused on taxonomic levels to assess species richness. In contrast, investigations into the spatial patterns of phylogenetic diversity in urban plants remain limited.ObjectivesThis study aims to investigate the spatial patterns of plant phylogenetic diversity along an urban–rural gradient and quantify how phylogenetic diversity and the degree of urbanization are related.MethodsA survey of vascular plants was conducted at 134 randomly selected sample plots along four urban–rural transects in Shanghai, China. Three phylogenetic diversity metrics were calculated: Faith’s phylogenetic diversity (PD), net relatedness index (NRI), and net nearest taxon index (NTI), along with the urbanization degree index (UDI). Regression analysis was employed to quantify the spatial patterns of plant phylogenetic diversity across different taxa along the urban–rural gradients and their relationships with UDI.ResultsThe study observed seven distinct patterns of plant phylogenetic diversity along the urban–rural gradients in different taxa, which support the previous hypotheses that biological distribution patterns at the species level also hold true at the phylogenetic level. Faith’s phylogenetic diversity (PD) showed a linear increase with increasing UDI for total, woody, perennial, and cultivated plant assemblages. The UDI explained 3–36% of the variation in PD for these taxa. In contrast, PD for annual and spontaneous plants exhibited a linear decrease with increasing UDI, which explained 25% and 3% variation in PD for annual and spontaneous plants, respectively. The net relatedness index (NRI) for woody, perennial, and cultivated plants, as well as the net nearest taxon index (NTI) for perennial and cultivated plants, linearly increases with UDI, whereas the NRI for total, annual, and spontaneous plants, as well as NTI for total, woody, annual, and spontaneous plants linearly decrease with UDI. However, some of these trends were only marginally significant.ConclusionsThe spatial patterns of plant phylogenetic diversity varied along the urban-to-rural gradients, indicating that urban environmental filtering has an impact on plant phylogenetic diversity. Urbanization increased the phylogenetic richness of different plant taxa in Shanghai but resulted in more clustering and relatedness of species within plant assemblages. Phylogenetic richness exhibited a linear increase with UDI, while the phylogenetic divergence decreased with UDI. The UDI is a useful predictor for examining variations in plant phylogeny due to urbanization. Our findings provide insights into how urbanization impacts plant phylogenetic diversity, helping urban plant diversity conservation.

Avian phylogenetic and functional diversity are better conserved by land‐sparing than land‐sharing farming in lowland tropical forests

Abstract The transformation of natural habitats for farming is a major driver of tropical biodiversity loss. To mitigate impacts, two alternatives are promoted: intensifying agriculture to offset protected areas (land sparing) or integrating wildlife‐friendly habitats within farmland (land sharing). In the montane and dry tropics, phylogenetic and functional diversity, which underpin evolutionary values and the provision of ecosystem functioning and services, are best protected by land sparing. A key question is how these components of biodiversity are best conserved in the more stable environments of lowland moist tropical forests. Focusing on cattle farming within the Colombian Amazon, we investigated how the occupancy of 280 bird species varies between forest and pasture spanning gradients of wildlife‐friendly features. We then simulated scenarios of land‐sparing and land‐sharing farming to predict impacts on phylogenetic and functional diversity metrics. Predicted metrics differed marginally between forest and pasture. However, community assembly varied significantly. Wildlife‐friendly pastures were inadequate for most forest‐dependent species, while phylogenetic and functional diversity indices showed minimal variation across gradients of wildlife‐friendly features. Land sparing consistently retained higher levels of Faith's phylogenetic diversity (~30%), functional richness (~20%) and evolutionarily distinct lineages (~40%) than land sharing, and did so across a range of landscape sizes. Securing forest protection through land‐sparing practices remains superior for conserving overall community phylogenetic and functional diversity than land sharing. Synthesis and applications: To minimise the loss of avian phylogenetic diversity and functional traits from farming in the Amazon, it is imperative to protect large blocks of undisturbed and regenerating forests. The intensification required within existing farmlands to make space for spared lands while meeting agricultural demand needs to be sustainable, avoiding long‐term negative impacts on soil quality and other ecosystem services. Policies need to secure the delivery of both actions simultaneously.

Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric

Background: The phylogenetic bootstrap, first proposed by Felsenstein in 1985, is a critically important statistical method in assessing the robusticity of phylogenetic datasets. Core to its concept was the use of pseudo sampling - assessing the data by generating new replicates derived from the initial dataset that was used to generate the phylogeny. In this way, phylogenetic support metrics could overcome the lack of perfect, infinite data. With infinite data, however, it is possible to sample smaller replicates directly from the data to obtain both the phylogeny and its statistical robusticity in the same analysis. Due to the growth of whole genome sequencing, the depth and breadth of our datasets have greatly expanded and are set to only expand further. With genome-scale datasets comprising thousands of genes, we can now obtain a proxy for infinite data. Accordingly, we can potentially abandon the notion of pseudo sampling and instead randomly sample small subsets of genes from the thousands of genes in our analyses. Methods: We introduce Scoutknife, a jackknife-style subsampling implementation that generates 100 datasets by randomly sampling a small number of genes from an initial large-gene dataset to jointly establish both a phylogenetic hypothesis and assess its robusticity. We assess its effectiveness by using 18 previously published datasets and 100 simulation studies. Results: We show that Scoutknife is conservative and informative as to conflicts and incongruence across the whole genome, without the need for subsampling based on traditional model selection criteria. Conclusions: Scoutknife reliably achieves comparable results to selecting the best genes on both real and simulation datasets, while being resistant to the potential biases caused by selecting for model fit. As the amount of genome data grows, it becomes an even more exciting option to assess the robusticity of phylogenetic hypotheses.

Soil flooding filters evolutionary lineages of tree communities in Amazonian riparian forests.

Inundations in Amazonian black-water river floodplain result in the selection of different tree lineages, thus promoting coexistence between species. We investigated whether Amazonian tree communities are phylogenetically structured and distributed along a flooding gradient from irregularly flooded forests along streams embedded within upland (terra-firme) forest to seasonally flooded floodplains of large rivers (igapós). Floristic inventories and hydrological monitoring were performed along the Falsino River, a black-water river in the eastern Amazon within the Amapá National Forest. We constructed a presence-and-absence matrix and generated a phylogeny using the vascular plant database available in GenBank. We calculated the standardized values of the metrics of phylogenetic diversity (ses.PD), average phylogenetic distance (ses.MPD), and average nearest-neighbor distance (ses.MNTD) to test whether the history of relationships between species in the community is influenced by inundation. We used the phylogenetic endemism (PE) metric to verify the existence of taxa with restricted distribution. Linear regressions were used to test whether phylogenetic metrics have a significant relationship with the variables: maximum flood height, maximum water table depth, and maximum flood amplitude. The results show that forests subject to prolonged seasonal flooding have reduced taxon richness, low phylogenetic diversity, and random distribution of lineages within communities. On the other hand, terra-firme riparian forests showed higher rates of taxon richness, diversity, and phylogenetic dispersion, in addition to greater phylogenetic endemism. These results indicate that seasonal and predictable soil flooding filters tree lineages along the hydrographic gradient. Different adaptations to root waterlogging are likely requirements for colonization in these environments and may represent an important factor in the diversification of tree lineages in the Amazon biome.

Turnover of bird species along the Nullarbor Plain: Insights from taxonomic, phylogenetic, and functional beta diversity

AbstractThe Nullarbor Plain constitutes one of the main biogeographic barriers of Australia, and it has been suggested to have played a key role in the disjunct distribution of numerous southern Australian species. Although previous research has shown that the origin of this barrier coincides with the timing of the speciation events in some plant lineages, it is not clear whether the uplift of this barrier promoted divergence events in vertebrates. We addressed the role of the Nullarbor barrier and its fringing semiarid habitats as drivers of beta diversity in bird assemblages. Specifically, we determined the effect of distance from the Nullarbor barrier, environmental conditions, and isolation by distance on the composition of local communities on both sides of the plain. We measured beta diversity using taxonomic, phylogenetic, and functional metrics of composition. The influence of precipitation, geographic distance, and distance to the Nullarbor barrier on these metrics was addressed using generalized dissimilarity models and a moving‐window approach. We also tested for differences in local extinction, dispersal and speciation rates, and lineage diversity between two regions, southeastern (SE) and southwestern (SW) Australia. Geological and orogenetic dynamics linked to the appearance of the Nullarbor Plain may have spurred speciation events in SE. However, evidence suggests that subsequent periods in which this region was wetter and forested favored dispersal, mainly from SE to SW. Accordingly, observed dissimilarity in species composition was lower than expected at random, suggesting the existence of considerable turnover between regions. Our results suggest that precipitation deficit (and the xeric vegetation that it promotes) was the most important predictor of beta diversity, whereas the distance to the barrier explained some variation in terms of phylogenetic composition. This study shows that the uplift of the Nullarbor barrier played a minor role in shaping present‐day bird diversity in southern Australia. Recent speciation events coupled with historical connectivity can explain the observed patterns.

Drug resistance and epidemiological success of modern Mycobacterium tuberculosis lineages in western India.

Transmission is contributing to the slow decline of tuberculosis (TB) incidence globally. Drivers of TB transmission in India, the country estimated to carry a quarter of the World's burden, are not well studied. We conducted a genomic epidemiology study to compare epidemiological success, host factors and drug resistance (DR) among the four major Mycobacterium tuberculosis (Mtb) lineages (L1-4) circulating in Pune, India. We performed whole-genome sequencing (WGS) of Mtb sputum culture-positive isolates from participants in two prospective cohort studies and predicted genotypic susceptibility using a validated random forest model. We used maximum likelihood estimation to build phylogenies. We compared lineage specific phylogenetic and time-scaled metrics to assess epidemiological success. Of the 642 isolates that underwent WGS, 612 met sequence quality criteria. Most isolates belonged to L3 (44.6%). The majority (61.1%) of multidrug-resistant isolates belonged to L2 (P < 0.001). In molecular dating, L2 demonstrated a higher rate and more recent resistance acquisition. We measured higher clustering, and time-scaled haplotypic density (THD) for L4 and L2 compared to L3 and/or L1 suggesting higher epidemiological success. L4 demonstrated higher THD and clustering (OR 5.1 (95% CI 2.3-12.3) in multivariate models controlling for host factors and DR. L2 shows a higher frequency of DR and both L2 and L4 demonstrate evidence of higher epidemiological success than L3 or L1 in the study setting. Our findings highlight the need for contact tracing around TB cases, and heightened surveillance of TB DR in India.

Spatial patterns and climatic drivers of phylogenetic structure of regional liverwort assemblages in China.

Latitudinal diversity gradients have been intimately linked to the tropical niche conservatism hypothesis, which posits that there has been a strong filter due to the challenges faced by ancestral tropical lineages to adapt to low temperatures and colonize extra-tropical regions. In liverworts, species richness is higher towards the tropics, but the centres of diversity of the basal lineages are distributed across extra-tropical regions, pointing to the colonization of tropical regions by phylogenetically clustered assemblages of species of temperate origin. Here, we test this hypothesis through analyses of the relationship between macroclimatic variation and phylogenetic diversity in Chinese liverworts. Phylogenetic diversity metrics and their standardized effect sizes for liverworts in each of the 28 regional floras at the province level in China were related to latitude and six climate variables using regression analysis. We conducted variation partitioning analyses to determine the relative importance of each group of climatic variables. We find that the number of species decreases with latitude, whereas phylogenetic diversity shows the reverse pattern, and that phylogenetic diversity is more strongly correlated with temperature-related variables compared with precipitation-related variables. We interpret the opposite patterns observed in phylogenetic diversity and species richness in terms of a more recent origin of tropical diversity coupled with higher extinctions in temperate regions.

The curious case of small mammal community in a rice-Pantanal agroecosystem of Brazil: A tale of multiple diversity metrics

To understand how certain types of agroecosystem management provide resources for biodiversity and conservation opportunities beyond protected areas, it is necessary to consider the cumulative effects on a local scale. Our study focuses on a rice-Pantanal wetland agricultural system within Brazil, where our goals were: i) to quantify the impact of rice paddies on taxonomic, functional, and phylogenetic diversity metrics of small mammals as biodiversity indicators, ii) to compare diversity indices based on incidence and abundance data. We carried out a thorough assessment to sample small mammal species in both the rice paddy and the adjacent legal reserve by employing a multiple diversity metrics approach. We captured the small mammals until reaching saturation on the species accumulation curve over 12,774 trap nights, resulting in 447 individuals, 10 species, including seven rodents and three marsupial species. Abundance-based beta-diversity between rice-paddy and forest reserve were higher (0.95) than incidence-based estimate (0.33). The species composition differed between the legal reserve (8 spp.) and the rice paddy (7 spp.), with the reserve exhibiting higher taxonomic diversity values compared to the rice paddy. In terms of functional and phylogenetic diversity, overall, the rice paddy exhibited higher values for the incidence-based metrics and the abundance-based metrics indicated that the reserve was more diverse. We conclude that Neotropical Pantanal rice fields retain substantial functional and phylogenetic diversities, providing suitable habitats for species thriving in open and semi-aquatic environments. Simultaneously, the legal reserve retains an essential aspect of functional diversity, when considering abundance, needed to maintain ecosystem resilience and stability. Proper abundance estimation is thus a key parameter for accurately evaluating the role of agricultural landscapes as biodiversity conservation opportunities beyond protected areas. Abundance-based indices should be used to correctly evaluate the contribution of each habitat to agroecosystem sustainability, especially in seasonal or extreme event-prone environments.

The geographic and phylogenetic structure of public DNA barcode databases: an assessment using Chrysomelidae (leaf beetles)

IntroductionDNA barcoding in insects has progressed rapidly, with the ultimate goal of a complete inventory of the world’s species. However, the barcoding effort to date has been driven by a few national campaigns and leaves much of the world unsampled. This study investigates to what degree the current barcode data cover the species diversity across the globe, using the leaf beetle family Chrysomelidae as an example.MethodsA recent version (June 2023) of the Barcode-of-Life database was subjected to test of sampling completeness using the barcode-to-BIN ratio and sampling coverage (SC) metric. All barcodes were placed in a phylogenetic tree of ~600 mitochondrial genomes, applying phylogenetic diversity (PD) and metrics of community phylogenetics to national barcode sets to test for sampling completeness at clade level and reveal the global structure of species diversity.ResultsThe database included 73342 barcodes, grouped into 5310 BINs (species proxies) from 101 countries. Costa Rica contributed nearly half of all barcode sequences, while nearly 50 countries were represented by less than ten barcodes. Only five countries, Costa Rica, Canada, South Africa, Germany, and Spain, had a high sampling completeness, although collectively the barcode database covers most major taxonomic and biogeographically confined lineages. PD showed moderate saturation as more species diversity is added in a country, and community phylogenetics indicated clustering of national faunas. However, at the species level the inventory remained incomplete even in the most intensely sampled countries, and the sampling was insufficient for assessment of global species richness patterns.DiscussionThe sequence-based inventory in Chrysomelidae needs to be greatly expanded to include more areas and deeper local sampling before reaching a knowledge base similar to the existing Linnaean taxonomy. However, placing the barcodes into a backbone phylogenetic tree from mitochondrial genomes, a taxonomically and biogeographically highly structured pattern of global diversity emerges into which all species can be integrated via their barcodes.

Evolutionary causes of global patterns of species richness in regional fern floras across the world

AbstractAimGlobally, biodiversity is unevenly distributed, as a result of varying environmental conditions and regionally different historical processes. The influence of the latter on current diversity patterns is poorly understood. We explore geographic patterns of matches and mismatches between phylogenetic relatedness metrics measuring different depths of evolutionary history and investigate the effects of evolutionary legacy at different evolutionary depths on species density of ferns.MethodsWe divided the globe into 392 geographic regions on land, and collated species lists of ferns for each geographic region. We related species richness to phylogenetic metrics reflecting different depths of evolutionary history (standardized effect sizes of mean nearest taxon distance and mean pairwise distance, MNTDses and MPDses, respectively) for ferns in regional floras across the world.LocationGlobal.Time PeriodCurrent.TaxonFerns.ResultsWe show that different centers of fern diversity have strikingly different phylogenetic composition. We find that overall fern species diversity is negatively correlated with both MNTDses and MPDses, so that regions with high species diversity tend to have clustered species assemblages, whereas species‐poor regions tend to have overdispersed species assemblages. At the global extent, MNTDses and MPDses together explained 62.2%, 19.3%, and 65.7% of the variation in species diversity for all ferns as a whole, non‐polypod ferns, and polypods, respectively.Main ConclusionsOur study suggests that current geographic patterns of fern species richness are driven, at least in part, by evolutionary history of ferns, which varies among biogeographic regions.

Conserving diversity, distinctiveness and connectivity in the Sunshine Coast heathlands, Queensland, Australia

AbstractAustralia is committed to global area‐based conservation targets whilst ensuring its National Reserve system is representative of ecosystem types. However, concern remains for the increasing habitat loss and fragmentation, and the possible impacts of loss of connectivity between remnant vegetation. This study uses a range of diversity metrics to examine the biodiversity conservation status of the Sunshine Coast heathlands, in the South Eastern Queensland bioregion. The pre‐clearing and remnant extent, and the protection status of the nine heath Regional Ecosystems were calculated. Fragmentation and connectivity were examined by comparing heath patch sizes, and by calculating the distance between patches, from pre‐clearing estimates, until 2019. Diversity metrics for the Regional Ecosystems, including phylogenetic metrics, were tested for correlation with habitat extent, patch size, patch number and distance between patches. Of the pre‐clearing extent, 62% of Sunshine Coast heathlands remain and 46% is protected in National Parks. Levels of protection in National Parks vary across the Local Government Areas, and between Regional Ecosystems, and the priority Regional Ecosystems for further protection were identified. There has been habitat loss resulting in reduced patch sizes, and fragmentation due to urbanization, but the number of patches of heath remains intact, and connectivity in terms of distance between patches remains stable. Phylogenetic dispersion, but not diversity, was correlated with the extent of heath and the number of patches. This highlights the opportunity to maintain biodiversity in these heathlands, with the value of small patches of heath identified as key to maintaining connectivity in the coastal lowlands, distinctiveness in the montane heaths and dunes, and overall phylogenetic dispersion. This study has shown how a variety of diversity metrics and landscape analyses can inform on priority areas for biodiversity conservation in the heathlands of an increasingly urbanized region.

Do phylogenetic community metrics reveal the South African quartz fields as terrestrial-habitat islands?

The quartz fields of the Greater Cape Floristic Region (GCFR) are arid and island-like special habitats, hosting ~142 habitat-specialized plant species, of which 81 % are local endemics, characterized by a rapid turnover of species between and among sites. We use several phylogenetic community metrics: (1) to examine species diversity and phylogenetic structure within and among quartz fields; (2) to investigate whether quartz field specialists are evolutionarily drawn from local species pools, whereas the alternative hypothesis posits that there is no significant evolutionary connection between quartz field specialists and the local species pools; and (3) to determine whether there is an association between certain traits and the presence of species in quartz fields. We sampled and developed dated phylogenies for six species-rich angiosperm families (Aizoaceae, Asteraceae, Crassulaceae, Cyperaceae, Fabaceae and Santalaceae) represented in the quartz field floras of southern Africa. Specifically, we focused on the flora of three quartz field regions in South Africa (Knersvlakte, Little Karoo and Overberg) and their surrounding species pools to address our research questions by scoring traits associated with harsh environments. We found that the Overberg and Little Karoo had the highest level of species overlap for families Aizoaceae and Fabaceae, whereas the Knersvlakte and the Overberg had the highest species overlap for families Asteraceae, Crassulaceae and Santalaceae. Although our phylogenetic community structure and trait analyses showed no clear patterns, relatively low pairwise phylogenetic distances between specialists and their local species pools for Aizoaceae suggest that quartz species could be drawn evolutionarily from their surrounding areas. We also found that families Aizoaceae and Crassulaceae in Knersvlakte and Little Karoo were phylogenetically even. Despite their proximity to one another within the GCFR, the studied areas differ in their species pools and the phylogenetic structure of their specialists. Our work provides further justification for increased conservation focus on these unique habitats under future scenarios of global change.

Effects of climate and environmental heterogeneity on the phylogenetic structure of regional angiosperm floras worldwide

The tendency of species to retain ancestral ecological distributions (phylogenetic niche conservatism) is thought to influence which species from a species pool can persist in a particular environment. Thus, investigating the relationships between measures of phylogenetic structure and environmental variables at a global scale can help understand the variation in species richness and phylogenetic structure in biological assemblages across the world. Here, we analyze a comprehensive data set including 341,846 species in 391 angiosperm floras worldwide to explore the relationships between measures of phylogenetic structure and environmental variables for angiosperms in regional floras across the world and for each of individual continental (biogeographic) regions. We find that the global phylogenetic structure of angiosperms shows clear and meaningful relationships with environmental factors. Current climatic variables have the highest predictive power, especially on phylogenetic metrics reflecting recent evolutionary relationships that are also related to current environmental heterogeneity, presumably because this favors plant speciation in various ways. We also find evidence that past climatic conditions, and particularly refugial conditions, play an important role in determining the phylogenetic structure of regional floras. The relationships between environmental conditions and phylogenetic metrics differ between continents, reflecting the different evolutionary histories of their floras.

Multiple dimensions of phylogenetic diversity are needed to explain the complex aboveground–belowground diversity relationships

The complex relationship between aboveground and belowground diversity and whether they act as surrogates for one another remains unresolved. Increasing evidence suggests that investigating phylogenetic diversity could provide valuable insights into the interplay between plants and soil microbes, but the proliferation of phylogenetic diversity metrics has hindered comparative studies and the identification of general patterns. To overcome this challenge, we implemented a multi‐dimensional framework that classifies phylogenetic diversity metrics into three dimensions: richness, divergence, and regularity, each of which captures different ecological aspects of species differences. Then we applied this framework to investigate the relationship between above and belowground diversity in a subtropical forest in eastern China. We found that phylogenetic diversity of plant and soil microbes, including bacteria and fungi, were more strongly correlated at the richness and regularity dimensions compared with divergence dimension. Further analyses revealed that these observed correlation patterns align with variations in soil total phosphorus content, a key factor influencing both plant and microbial phylogenetic diversity at richness and regularity dimensions. Together, our study demonstrated the necessity of using a multi‐dimensional approach to advance our understanding of the complex relationships between plant and soil microbial biodiversity.

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.