INVESTIGATING CROSS CONGRUENCE BETWEEN BUTTERFLY TAXA AND ECOLOGICAL COMMUNITY WITHIN THE FRAMEWORK OF SYSTEMATIC CONSERVATION PLANNING: A CASE STUDY FROM LESSER CAUCASUS ECOREGION OF TURKEY

Cross taxa congruence was investigated between butterfly taxa and ecological community for fine spatial scale (10 × 10 km² UTM grids) in north-eastern part of Turkey. The study area was evaluated within the scope of systematic conservation planning, and analyses were performed for sets of priority protected areas composed using complementarity-based site selection software Marxan. Cross taxa congruence was subsequently examined both in species richness and ecologic complementarity. Accordingly, it has been observed that the cross-taxon congruence between butterfly taxa and ecological community was relatively better than the results of previous studies. Another remarkable finding is that ecological community was a more robust surrogate than butterfly taxa. Although the results are valuable for conservation studies, they highlight the fact that a simple surrogate-based site selection would be inadequate to represent overall biodiversity. The weakness of congruence patterns among surrogates would also lead to gaps in biodiversity conservation. These findings therefore draw attention to the necessities of incorporating surrogates of distinct ecology or some other surrogates like environmental parameters into conservation planning. Otherwise, there may be mistakes regarding species representation and the vast majority of species may be misrepresented in protected areas and protected area plans. At this point, it should be emphasized that understating cross taxa congruence and/or relationships is a key component for efficient biodiversity conservation.

Poplar box woodlands of Eastern Australia: an assessment of a threatened ecological community within the IVC framework

Aims: Ecosystems nationally at risk in Australia are listed under the Environmental Protection and Biodiversity Act (EPBC Act), and many cross State jurisdictional boundaries. The determination of these ecosystems across the State boundaries are based on expert knowledge. The International Vegetation Classification has the potential to be useful as a cross-jurisdictional hierarchy which also gives global perspective to ecosystems. Study Area: All bioregions that include Eucalyptus populnea as a dominant or major component of woodlands across the species known distribution. Methods: We use plot-based data (455 plots) from two states (Queensland and New South Wales) in eastern Australia and quantitative classification methods to assess the definition and description for the Poplar Box Woodland ecosystem type (hereafter “ecological community” or “community”) that is listed as endangered under the EPBC Act. Analyses were conducted using kR-CLUSTER methods to generate alliances. Within these alliances, analyses were undertaken to define associations using agglomerative hierarchical clustering and similarity profile testing (SIMPROF). We then explore how assigning this community into the IVC hierarchy may provide a mechanism for linking Australian communities, defined at the association and alliance levels, to international communities at risk. Results: We define three alliances and 23 associations based on the results of floristic analysis. Using the standard rule-set of the IVC system, we found that the IVC hierarchy was a useful instrument in correlating ecological communities across jurisdictional boundaries where different classification systems are used. It is potentially important in giving a broader understanding of communities that may be at risk continentally and globally. Conclusions: We conclude that the IVC hierarchy can incorporate Australian communities at the association level into useful units at higher levels, and provides a useful classification tool for Australian ecosystems. Taxonomic reference: PlantNET (http://plantnet/10rbgsyd.nsw.gov.au/) [accessed June 2019]. Abbreviations: EPBC Act = Environmental Protection and Biodiversity Act; IVC = International Vegetation Classification; NMDS = non-metric multidimensional scaling; NSW = New South Wales; PCT = Plant Community Type; QLD = Queensland; RE = Regional Vegetation Community; SIMPER = similarity percentage analysis; SIMPROF = Similarity profile analysis.

Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan

Micro-evolutionary processes acting in populations and communities ultimately produce macro-evolutionary patterns. However, current models of species life histories -- including processes of speciation, persistence, hybridization, and eventual extinction -- rarely connect these two time scales. This leaves us with a limited theoretical understanding of the subtleties of diversification, such as the relationship between species abundance in an ecological community and species longevity over evolutionary time, or the impact of selection on patterns of speciation and extinction when structuring an ecological community. Here we present a model for evolution in spatially extended populations with a focus on selection for mito-nuclear compatibility. We find that mito-nuclear selection acting at the individual level decreases genetic variability among species in a radiation, reducing the total number of species and skewing species abundances distributions towards mono-dominance. Also, intraspecific diversity increases as species become more abundant, leading to frequent evolutionary branching that reduces species lifetimes. The equilibrium of such communities is characterized by high rates of speciation, extinction, and hybridization, i.e., high turnover rate. These theoretical results are in concordance with empirical patterns of diversity across latitudinal gradients. Model predictions in the absence of mito-nuclear selection resemble the tropics, with high biodiversity, old species, and low speciation and extinction rates. Whereas model predictions under strong selection, which we expect in the harsh environments of temperate zones, produce fewer species and elevated recent speciation rates.

ecocomDP: A data design pattern and R package to facilitate FAIR biodiversity data for ecological synthesis

Two programs that provide high-quality long-term ecological data, the Environmental Data Initiative (EDI) and the National Ecological Observatory Network (NEON), have recently teamed up with data users interested in synthesizing biodiversity data, such as ecological synthesis working groups supported by the US Long Term Ecological Research (LTER) Network Office, to make their data more Findable, Interoperable, Accessible, and Reusable (FAIR). To this end: we have developed a flexible intermediate data design pattern for ecological community data (L1 formatted data in Fig. 1, see Fig. 2 for design details) called "ecocomDP" (O'Brien et al. 2021), and we provide tools to work with data packages in which this design pattern has been implemented. we have developed a flexible intermediate data design pattern for ecological community data (L1 formatted data in Fig. 1, see Fig. 2 for design details) called "ecocomDP" (O'Brien et al. 2021), and we provide tools to work with data packages in which this design pattern has been implemented. The ecocomDP format provides a data pattern commonly used for reporting community level data, such as repeated observations of species-level measures of biomass, abundance, percent cover, or density across multiple locations. The ecocomDP library for R includes tools to search for data packages, download or import data packages into an R (programming language) session in a standard format, and visualization tools for data exploration steps that are recommended for data users prior to any cross-study synthesis work. To date, EDI has created 70 ecocomDP data packages derived from their holdings, which include data from the US Long Term Ecological Research (US LTER) program, Long Term Research in Environmental Biology (LTREB) program, and other projects, which are now discoverable and accessible using the ecocomDP library. Similarly, NEON data products for 12 taxonomic groups are discoverable using the ecocomDP search tool. Input from data users provided guidance for the ecocomDP developers in mapping the NEON data products to the ecocomDP format to facilitate interoperability with the ecocomDP data packages available from the EDI repository. The standardized data design pattern allows common data visualizations across data packages, and has the potential to facilitate the development of new tools and workflows for biodiversity synthesis. The broader impacts of this collaboration are intended to lower the barriers for researchers in ecology and the environmental sciences to access and work with long-term biodiversity data and provide a hub around which data providers and data users can develop best practices that will build a diverse and inclusive community of practice.

Standardized NEON organismal data for biodiversity research

Understanding patterns and drivers of species distributions and abundances, and thus biodiversity, is a core goal of ecology. Despite advances in recent decades, research into these patterns and processes is currently limited by a lack of standardized, high-quality, empirical data that spans large spatial scales and long time periods. The National Ecological Observatory Network (NEON) fills this gap by providing freely available observational data that are: generated during robust and consistent organismal sampling of several sentinel taxonomic groups within 81 sites distributed across the United States; and will be collected for at least 30 years. The breadth and scope of these data provides a unique resource for advancing biodiversity research. To maximize the potential of this opportunity, however, it is critical that NEON data be maximally accessible and easily integrated into investigators’ workflows and analyses. To facilitate its use for biodiversity research and synthesis, we created a workflow to process and format NEON organismal data into the ecocomDP (ecological community data design pattern) format, and available through the `ecocomDP` R package; we then provided the standardized data as an R data package (`neonDivData`). We briefly summarize sampling designs and data wrangling decisions for the major taxonomic groups included in this effort. Our workflows are open-source so the biodiversity community may: add additional taxonomic groups; modify the workflow to produce datasets appropriate for their own analytical needs; and regularly update the data packages as more observations become available. Finally, we provide two simple examples of how the standardized data may be used for biodiversity research. By providing a standardized data package, we hope to enhance the utility of NEON organismal data in advancing biodiversity research.

Herbaceous perennial ornamental plants can support complex pollinator communities

Human-designed landscapes can host diverse pollinator communities, and the availability of floral resources is central to supporting insect biodiversity in highly modified environments. However, some urban landscapes have relatively few pollinator-attractive plant species and management in urban environments rarely considers the function of these plants in generating and supporting a stable ecological community. Evaluations of 25 cultivars within five commercially popular herbaceous perennial ornamental plant genera (Agastache, Echinacea, Nepeta, Rudbeckia, and Salvia) revealed variation in the total and proportional abundance of visitors attracted. These varieties supported multiple pollinator functional groups, however bees were the primary visitors to in this system. Cultivars were assessed according to their function within a plant–pollinator network. Comparisons of artificial networks created with the six most attractive and six least attractive cultivars demonstrated that a planting scheme using the most attractive cultivars would attract nearly four times as many bee species, including several specialists and rare species. Plant diversity in the landscape was correlated with abundance and diversity of pollinator visitors, demonstrating that community context shapes a plant’s relative attractiveness to pollinators. We conclude that herbaceous perennial cultivars can support an abundance and diversity of pollinator visitors, however, planting schemes should take into consideration the effects of cultivar, landscape plant diversity, floral phenology, floral area, and contribution to a stable ecological community.

Transposable element diversity remains high in gigantic genomes

ABSTRACTTransposable elements (TEs) are repetitive sequences of DNA that replicate and proliferate throughout genomes. Taken together, all the TEs in a genome form a diverse community of sequences, which can be studied to draw conclusions about genome evolution. TE diversity can be measured using models for ecological community diversity that consider species richness and evenness. Several models predict TE diversity decreasing as genomes expand because of selection against ectopic recombination and/or competition among TEs to garner host replicative machinery and evade host silencing mechanisms. Salamanders have some of the largest vertebrate genomes and highest TE loads. Salamanders of the genus Plethodon, in particular, have genomes that range in size from 20 to 70 Gb. Here, we use Oxford Nanopore sequencing to generate low-coverage genomic sequences for four species of Plethodon that encompass two independent genome expansion events, one in the eastern clade (P. cinereus, 29.3 Gb vs. P. glutinosus, 38.9 Gb) and one in the western clade (P. vehiculum, 46.4 Gb vs P. idahoensis, 67.0 Gb). We classified the TEs in these genomes and found ~52 TE superfamilies, accounting for 27-32% of the genomes. We calculated Simpson’s and Shannon’s diversity indices to quantify overall TE diversity. In both pairwise comparisons, the diversity index values for the smaller and larger genome were almost identical. This result indicates that, when genomes reach extremely large sizes, they maintain high levels of TE diversity at the superfamily level, in contrast to predictions made by previous studies on smaller genomes.