Global assessment of effective population sizes: Consistent taxonomic differences in meeting the 50/500 rule.

Effective population size (Ne) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum Ne of 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between Ne and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced Ne estimates from 3829 populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal and amphibian populations had a <54% probability of reaching N ̂ e = 50 and a <9% probability of reaching N ̂ e = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller median N ̂ e than unlisted populations, and this was consistent across all taxonomic groups. N ̂ e was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation of N ̂ e in wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on Ne and help prioritise assessment of populations from taxa most at risk of failing to meet conservation thresholds.

INHABIT: A web-based decision support tool for invasive plant species habitat visualization and assessment across the contiguous United States.

Narrowing the communication and knowledge gap between producers and users of scientific data is a longstanding problem in ecological conservation and land management. Decision support tools (DSTs), including websites or interactive web applications, provide platforms that can help bridge this gap. DSTs can most effectively disseminate and translate research results when producers and users collaboratively and iteratively design content and features. One data resource seldom incorporated into DSTs are species distribution models (SDMs), which can produce spatial predictions of habitat suitability. Outputs from SDMs can inform management decisions, but their complexity and inaccessibility can limit their use by resource managers or policy makers. To overcome these limitations, we present the Invasive Species Habitat Tool (INHABIT), a novel, web-based DST built with R Shiny to display spatial predictions and tabular summaries of habitat suitability from SDMs for invasive plants across the contiguous United States. INHABIT provides actionable science to support the prevention and management of invasive species. Two case studies demonstrate the important role of end user feedback in confirming INHABIT's credibility, utility, and relevance.

Universal scaling of robustness of ecosystem services to species loss.

Ensuring reliable supply of services from nature is key to the sustainable development and well-being of human societies. Varied and frequently complex relationships between biodiversity and ecosystem services have, however, frustrated our capacity to quantify and predict the vulnerability of those services to species extinctions. Here, we use a qualitative Boolean modelling framework to identify universal drivers of the robustness of ecosystem service supply to species loss. These drivers comprise simple features of the networks that link species to the functions they perform that, in turn, underpin a service. Together, they define what we call network fragility. Using data from >250 real ecological networks representing services such as pollination and seed-dispersal, we demonstrate that network fragility predicts remarkably well the robustness of empirical ecosystem services. We then show how to quantify contributions of individual species to ecosystem service robustness, enabling quantification of how vulnerability scales from species to services. Our findings provide general insights into the way species, functional traits, and the links between them together determine the vulnerability of ecosystem service supply to biodiversity loss.

Above- and belowground biodiversity jointly tighten the P cycle in agricultural grasslands.

Experiments showed that biodiversity increases grassland productivity and nutrient exploitation, potentially reducing fertiliser needs. Enhancing biodiversity could improve P-use efficiency of grasslands, which is beneficial given that rock-derived P fertilisers are expected to become scarce in the future. Here, we show in a biodiversity experiment that more diverse plant communities were able to exploit P resources more completely than less diverse ones. In the agricultural grasslands that we studied, management effects either overruled or modified the driving role of plant diversity observed in the biodiversity experiment. Nevertheless, we show that greater above- (plants) and belowground (mycorrhizal fungi) biodiversity contributed to tightening the P cycle in agricultural grasslands, as reduced management intensity and the associated increased biodiversity fostered the exploitation of P resources. Our results demonstrate that promoting a high above- and belowground biodiversity has ecological (biodiversity protection) and economical (fertiliser savings) benefits. Such win-win situations for farmers and biodiversity are crucial to convince farmers of the benefits of biodiversity and thus counteract global biodiversity loss.

NAMS webserver: coding potential assessment and functional annotation of plant transcripts.

Recent advances in transcriptomics have uncovered lots of novel transcripts in plants. To annotate such transcripts, dissecting their coding potential is a critical step. Computational approaches have been proven fruitful in this task; however, most current tools are designed/optimized for mammals and only a few of them have been tested on a limited number of plant species. In this work, we present NAMS webserver, which contains a novel coding potential classifier, NAMS, specifically optimized for plants. We have evaluated the performance of NAMS using a comprehensive dataset containing more than 3 million transcripts from various plant species, where NAMS demonstrates high accuracy and remarkable performance improvements over state-of-the-art software. Moreover, our webserver also furnishes functional annotations, aiming to provide users informative clues to the functions of their transcripts. Considering that most plant species are poorly characterized, our NAMS webserver could serve as a valuable resource to facilitate the transcriptomic studies. The webserver with testing dataset is freely available at http://sunlab.cpy.cuhk.edu.hk/NAMS/.

Economic use of plants is key to their naturalization success.

Humans cultivate thousands of economic plants (i.e. plants with economic value) outside their native ranges. To analyze how this contributes to naturalization success, we combine global databases on economic uses and naturalization success of the world's seed plants. Here we show that naturalization likelihood is 18 times higher for economic than non-economic plants. Naturalization success is highest for plants grown as animal food or for environmental uses (e.g. ornamentals), and increases with number of uses. Taxa from the Northern Hemisphere are disproportionately over-represented among economic plants, and economic plants from Asia have the greatest naturalization success. In regional naturalized floras, the percentage of economic plants exceeds the global percentage and increases towards the equator. Phylogenetic patterns in the naturalized flora partly result from phylogenetic patterns in the plants we cultivate. Our study illustrates that accounting for the intentional introduction of economic plants is key to unravelling drivers of plant naturalization.

Spatial and temporal variation of the vegetation of the semiarid Puna in a pastoral system in the Pozuelos Biosphere Reserve.

This study aimed to analyze the spatial and temporal variation of the vegetation in the northern Argentine Puna, utilizing both field sampling and remote-sensing tools. The study was performed within the Pozuelos Biosphere Reserve (Jujuy province, Argentina), which aims to generate socio-economic development compatible with biodiversity conservation. Our study was designed to analyze the dynamics of the Puna vegetation at local scale and assess and monitor the seasonal (dry and wet seasons), interannual, and spatial variation of the vegetation cover, biomass, dominant species, and vegetation indices. Ten vegetation units (with differences in composition, cover, and high and low stratum biomass) were identified at our study site. The diversity of these vegetation units correlated with geomorphology and soil type. In the dry season, the vegetation unit with greatest vegetation cover and biomass was the Festuca chrysophylla grassland, whereas in the wet season, the units with greatest cover and biomass were vegas (peatlands) and short grasslands. The Festuca chrysophylla grasslands and short grasslands were located in areas with clay soils, except peatlands, associated with valleys and coarse-texture soils. The vegetation indices used (NDVI, SAVI, and MSAVI2) were able to differentiate functional types of vegetation and showed a good statistical fit with cover values. Our results suggest that the integrated utilization of remote-sensing tools and field surveys improves the assessment of the Puna vegetation and would allow a periodic monitoring at production unit scale taking into account its spatial and temporal variation.

The 2011 National Wetland Condition Assessment: overview and an invitation.

The first National Wetland Condition Assessment (NWCA) was conducted in 2011 by the US Environmental Protection Agency (USEPA) and its federal and state partners, using a survey design that allowed inference of results to national and regional scales. Vegetation, algae, soil, water chemistry, and hydrologic data were collected at each of 1138 locations across the conterminous United States (US). Ecological condition was assessed in relation to a disturbance gradient anchored by least disturbed (reference) and most disturbed sites identified using chemical, physical, and biological disturbance indices based on site-level data. A vegetation multimetric index (VMMI) was developed as an indicator of condition, and included four metrics: a floristic quality assessment index, relative importance of native plants, number of disturbance-tolerant plant species, and relative cover of native monocots. Potential stressors to wetland condition were identified and incorporated into two indicators of vegetation alteration, four indicators of hydrologic alteration, a soil heavy metal index, and a nonnative plant indicator and were used to quantify national and regional stressor extent, and the associated relative and attributable risk. Approximately 48 ± 6% of the national wetland area was found to be in good condition and 32 ± 6% in poor condition as defined by the VMMI. Across the conterminous US, approximately 20% of wetland area had high or very high stressor levels related to nonnative plants. Vegetation removal, hardening, and ditching stressors had the greatest extent of wetland area with high stressor levels, affecting 23-27% of the wetland area in the NWCA sampled population. The results from the 2016 NWCA will build on those from the 2011 assessment and initiate the ability to report on trends in addition to status. The data and tools produced by the NWCA can be used by others to further our knowledge of wetlands in the conterminous US.

USA-scale patterns in wetland water quality as determined from the 2011 National Wetland Condition Assessment.

Water quality is a central component of ecological assessments but less well characterized in wetlands than other waterbody types. The 2011 National Wetland Condition Assessment, spanning freshwater and brackish wetlands across the conterminous USA, provided an unprecedented opportunity to examine water quality patterns across broad wetland types and geographic scales. Surface water samples were obtained from 634 (56%) of sites visited. Total nitrogen (TN), total phosphorus (TP), planktonic chlorophyll (CHLA), and specific conductance (SPCOND) ranged 4 orders of magnitude across sites and were inter-correlated. Woody versus herbaceous vegetation type was an important classifier, with herbaceous sites having standing water more often and generally higher pH, nutrients, and CHLA. Nutrient ratios spanned a range from P-limited to N-limited in most biogeographic regions, and increasing TP was associated with decreasing TN:TP ratios. Compared to national-scale data for other waterbody types (lakes, streams, marine nearshore), wetlands had generally higher TN and TP but not higher CHLA. Differences among biogeographic regions in water quality were concordant between inland wetlands and lakes, and between marine-coast wetlands and the marine nearshore. Associations of TN, TP, and CHLA to percent agriculture or natural land were stronger for the watershed scale than for smaller concentric buffer scales, suggesting that wetlands are influenced by landuse some distance away. SPCOND was related to landuse in inland wetlands but reflected seawater influence in marine-coast wetlands. Water quality exhibits the same general patterns and responses across wetlands as across other waterbody types and thus can provide a basis for ecological classification and condition assessment.

Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials.

Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown "barcode" sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.

Comparative Analysis of Plant Demographic Traits Across Species of Different Conservation Concern: Implications for Pesticide Risk Assessment.

Pesticide risk assessment for "listed" (threatened and endangered) plant species is hampered by a lack of quantitative demographic information. Demographic information for nonlisted plant species could provide risk-assessment data and inform recovery plans for listed species; however, it is unclear how representative demography of the former would be for the latter. We performed a comparison of plant demographic traits and elasticity metrics to explore how similar these are between listed and nonlisted species. We used transition matrices from the COMPADRE Plant Matrix Database to calculate population growth rate (λ), net reproductive rate (Ro ), generation time (Tg ), damping ratio (ρ), and summed elasticities for survival (stasis), growth, fertility (reproduction), and evenness of elasticity (EE). We compared these across species varying in conservation status and population trend. Phylogenetic generalized least squares (PGLS) models were used to evaluate differences between listed and nonlisted plants. Overall, demographic traits were largely overlapping for listed and nonlisted species. Population trends had a significant impact on most demographic traits and elasticity patterns. The influence of Tg on elasticity metrics was consistent across all data groupings. In contrast, the influence of λ on elasticity metrics was highly variable, and correlated in opposite directions in growing and declining populations. Our results suggested that population models developed for nonlisted plant species may be useful for assessing the risks of pesticides to listed species. Environ Toxicol Chem 2019;38:2043-2052. © 2019 SETAC.

Multi-driver and multi-scale assessment of vine community structure and composition across a complex tropical environmental matrix.

Ecological communities are structured by multiple processes operating at multiple scales yet understanding the scale-dependency of these processes remains an open challenge. This might be particularly true for parasites, for which biotic rather than abiotic processes may play a primary role in structuring communities. Focusing on vines, a group of structural parasites that gain access to the canopy using different climbing mechanisms, we examined the influence of abiotic factors in tandem with host-parasite and parasite-parasite interactions in the assembly of tropical vine communities. Two synthetic variables, namely Climate1 and landscape Variety, were consistently important in explaining variation in species richness and diversity, as well as species composition, but their importance varied with scale. Whereas Climate1 summarizes the largest variability among climatic variables, landscape Variety expresses landscape heterogeneity within a neighborhood. Significant patterns of species co-occurrences suggest that vine-vine interactions also contribute to vine community assembly. Our results may be critical to understand vine proliferation and help design management strategies for their control.

An integrated phenotypic trait-network in thermo-Mediterranean vegetation describing alternative, coexisting resource-use strategies.

Vascular plants have been found to align along globally-recognised resource-allocation trade-offs among specific functional traits. Genetic constrains and environmental pressures limit the spectrum of viable resource-use strategies employed by plant species. While conspecific plants have often been described as identical, intraspecific variation facilitates species coexistence and evolutionary potential. This study attempts to link an individual's phenotype to its environmental tolerance and ecosystem function. We hypothesised that: (1) seasonal variation in water availability has selected for tight phenotypic integration patterns that shape Mediterranean vegetation; however, (2) coexisting species employ alternative resource-use strategies to avoid competitive exclusion; specifically (3) species with smaller climatic niches (i.e. potential distributions) display higher functional diversity. We examined the interdependence among and the sources of variation within 11 functional traits, reflecting whole-plant economics (e.g. construction costs, hydraulics, defences, water storage capacity), from nine dominant, thermo-Mediterranean species measured across a wide environmental and geographic gradient. Furthermore, we delineated the phenotypic and climatic hypervolumes of each studied species to test for climatic niche overlap and functional distinctiveness. By adopting this multidimensional trait-based approach we detected fundamental phenotypic integration patterns that define thermo-Mediterranean species regardless of life history strategy. The studied traits emerged intercorrelated shaping a resource-allocation spectrum. Significant intraspecific variability in most measured traits allowed for functional distinctiveness among the measured species. Higher functional diversity was observed in species restricted within narrower climatic niches. Our results support our initial hypotheses. The studied functional traits collectively formed an integrated space of viable phenotypic expressions; however, phenotypic plasticity enables functionally distinctive species to succeed complementary in a given set of environmental conditions. Functional variability among coexisting individuals defined species' climatic niches within the trait-spectrum permitted by Mediterranean conditions. Ultimately, a species establishment in a locality depends on the extent that it can shift its trait values.

Topological assessment of metabolic networks reveals evolutionary information.

Evolutionary information was inferred from the topology of metabolic networks corresponding to 17 plant species belonging to major plant lineages Chlorophytes, Bryophytes, Lycophytes and Angiosperms. The plant metabolic networks were built using the substrate-product network modeling based on the metabolic reactions available on the PlantCyc database (version 9.5), from which their local topological properties such as degree, in-degree, out-degree, clustering coefficient, hub-score, authority-score, local efficiency, betweenness and eigencentrality were measured. The topological measurements corresponding to each metabolite within the networks were considered as a set of metabolic characters to compound a feature vector representing each plant. Our results revealed that some local topological characters are able to discern among plant kinships, since similar phylogenies were found when comparing dendrograms obtained by topological metrics to the one obtained by DNA sequences of chloroplast genes. Furthermore, we also found that even a smaller number of metabolic characters is able to separate among major clades with high bootstrap support (BS > 95), while for some suborders a bigger content has been required.

DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists.

DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two-week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.

HeLM: a macrophyte-based method for monitoring and assessment of Greek lakes.

The Water Framework Directive (WFD) requires Member States to develop appropriate assessment methods for the classification of the ecological status of their surface waters. Mediterranean region has lagged behind in this task, so we propose here the first developed method for Greek lakes, Hellenic Lake Macrophyte (HeLM) assessment method. This method is based on two metrics, a modified trophic index and maximum colonization depth Cmax that quantify the degree of changes in lake macrophytic vegetation, as a response to eutrophication and general degradation pressures. The method was developed on the basis of a data set sampled from 272 monitoring transects in 16 Greek lakes. Sites from three lakes were selected as potential reference sites by using a screening process. Ecological quality ratios were calculated for each metric and for each lake, and ecological status class boundaries were defined. For the evaluation of effectiveness of the method, the correlations between individual metrics and final HeLM values and common pressure indicators, such as total phosphorus, chlorophyll a and Secchi depth, were tested and found highly significant and relatively strong. In addition, the ability of HeLM values and its individual metrics to distinguish between different macrophytic communities' structure was checked using aquatic plant life-forms and found satisfactory. The HeLM method gave a reliable assessment of the macrophytic vegetation's condition in Greek lakes and may constitute a useful tool for the classification of ecological status of other Mediterranean lakes.

DNA barcoding of invasive plants in China: A resource for identifying invasive plants.

Invasive plants have aroused attention globally for causing ecological damage and having a negative impact on the economy and human health. However, it can be extremely challenging to rapidly and accurately identify invasive plants based on morphology because they are an assemblage of many different families and many plant materials lack sufficient diagnostic characteristics during border inspections. It is therefore urgent to evaluate candidate loci and build a reliable genetic library to prevent invasive plants from entering China. In this study, five common single markers (ITS, ITS2, matK, rbcL and trnH-psbA) were evaluated using 634 species (including 469 invasive plant species in China, 10 new records to China, 16 potentially invasive plant species around the world but not introduced into China yet and 139 plant species native to China) based on three different methods. Our results indicated that ITS2 displayed largest intra- and interspecific divergence (1.72% and 91.46%). Based on NJ tree method, ITS2, ITS, matK, rbcL and trnH-psbA provided 76.84%, 76.5%, 63.21%, 52.86% and 50.68% discrimination rates, respectively. The combination of ITS + matK performed best and provided 91.03% discriminatory power, followed by ITS2 + matK (85.78%). For identifying unknown individuals, ITS + matK had 100% correct identification rate based on our database, followed by ITS/ITS2 (both 93.33%) and ITS2 + matK (91.67%). Thus, we propose ITS/ITS2 + matK as the most suitable barcode for invasive plants in China. This study also demonstrated that DNA barcoding is an efficient tool for identifying invasive species.

Preliminary results of water quality assessment using phytoplankton and physicochemical approaches in the Huai River Basin, China.

Water pollution has been a significant issue in the Huai River Basin (HRB) of China since the late 1970s. In July and December 2013, two field investigations were carried out at 10 sites along the main streams of the basin. The monitoring indices contained both physicochemical variables and the structure and composition of phytoplankton communities. The correlations between communities and physicochemical variables were analyzed using cluster analysis and redundancy analysis. Moreover, water quality was evaluated using the comprehensive nutrition state index (TLI) and Shannon-Wiener diversity index (H). Results indicated that more phytoplankton species were present in December than in July, but total density was less in December. Phytoplankton communities in the midstream of the Shaying River were affected by the same physicochemical factors throughout the year, but ammonia nitrogen and total phosphorus had the greatest influence on these sites in July and December, respectively. The water pollution status of the sampling sites was much greater in the Shaying River midstream than at other sites. TLI was more suitable than H for assessing water quality in the study area. These results provide valuable information for policy makers and stakeholders in water quality assessment, water ecosystem restoration, and sustainable basin management in the HRB.

Using worldwide edaphic data to model plant species niches: An assessment at a continental extent.

Ecological niche modeling (ENM) is a broadly used tool in different fields of plant ecology. Despite the importance of edaphic conditions in determining the niche of terrestrial plant species, edaphic data have rarely been included in ENMs of plant species perhaps because such data are not available for many regions. Recently, edaphic data has been made available at a global scale allowing its potential inclusion and evaluation on ENM performance for plant species. Here, we take advantage of such data and address the following main questions: What is the influence of distinct predictor variables (e.g. climatic vs edaphic) on different ENM algorithms? and what is the relationship between the performance of different predictors and geographic characteristics of species? We used 125 plant species distributed over the Neotropical region to explore the effect on ENMs of using edaphic data available from the SoilGrids database and its combination with climatic data from the CHELSA database. In addition, we related these different predictor variables to geographic characteristics of the target species and different ENM algorithms. The use of different predictors (climatic, edaphic, and both) significantly affected model performance and spatial complexity of the predictions. We showed that the use of global edaphic plus climatic variables generates ENMs with similar or better accuracy compared to those constructed only with climate variables. Moreover, the performance of models considering these different predictors, separately or jointly, was related to geographic properties of species records, such as number and distribution range. The large geographic extent, the variability of environments and the different species' geographical characteristics considered here allowed us to demonstrate that global edaphic data adds useful information for plant ENMs. This is particularly valuable for studies of species that are distributed in regions where more detailed information on soil properties is poor or does not even exist.

Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo).

DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses.