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Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18 S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.

Complexity is well accepted as one of the primary drivers of biodiversity, however, empirical support for such positive associations is often confounded with surface area and undermined by other potential explanatory factors, especially the type of structural component (e.g., pits, crevices, overhangs, etc.). In the present study, sample units (artificial substrates) of equal surface area (±0.2%) were used to simultaneously examine the independent effects of complexity and different structural component types on species richness (S), abundance (N), and community composition. We created simple and complex concrete substrates of four different geometric designs using novel software. The substrates (n = 8) were mounted onto granite seawalls (at two tidal heights) on two islands south of Singapore Island. After 13 months of colonization, all 384 tiles were collected and their assemblages compared. A total of 53 744 individuals of 70 species/morphospecies were collected and identified. Our results show that greater complexity can support greater species richness and different communities that are independent of surface area. Furthermore, the type of structure (e.g., \"pits,\" \"grooves,\" \"towers\") can have an effect on richness and community composition that is independent of complexity.

Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding small-subunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.

Pocillopora corals, the dominant reef-builders in the Eastern Tropical Pacific, exhibit a high level of phenotypic plasticity, making the interpretation of morphological variation and the identification of species challenging. To test the hypothesis that different coral morphospecies represent phenotypes that develop in different flow conditions, we compared branch characters in three Pocillopora morphospecies (P. damicornis, P. verrucosa, and P. meandrina) from two communities in the Gulf of California exposed to contrasting flow conditions. Morphological variation and branch modularity (i.e., the tendency of different sets of branch traits to vary in a coordinated way) were assessed in colonies classified as Pocillopora type 1 according to two mitochondrial regions. Our results can be summarized as follows. (1) Pocillopora type 1 morphospecies corresponded to a pattern of morphological variation in the Gulf of California. Overall, P. damicornis had the thinnest branches and its colonies the highest branch density, followed by P. verrucosa, and then by P. meandrina, which had the thickest branches and its colonies the lowest branch density. (2) The differentiation among morphospecies was promoted by different levels of modularity of traits. P. verrucosa had the highest coordination of traits, followed by P. damicornis, and P. meandrina. (3) The variation and modularity of branch traits were related to water flow condition. Morphology under the high-flow condition was more similar among morphospecies than under the low-flow condition and seemed to be related to mechanisms for coping with these conditions. Our results provide the first evidence that in scleractinian corals different levels of modularity can be promoted by different environmental conditions.

Ants, an ecologically successful and numerically dominant group of animals, play key ecological roles as soil engineers, predators, nutrient recyclers, and regulators of plant growth and reproduction in most terrestrial ecosystems. Further, ants are widely used as bioindicators of the ecological impact of land use. We gathered information of ant species in the Atlantic Forest of South America. The ATLANTIC ANTS data set, which is part of the ATLANTIC SERIES data papers, is a compilation of ant records from collections (18,713 records), unpublished data (29,651 records), and published sources (106,910 records; 1,059 references), including papers, theses, dissertations, and book chapters published from 1886 to 2020. In total, the data set contains 153,818 ant records from 7,636 study locations in the Atlantic Forest, representing 10 subfamilies, 99 genera, 1,114 ant species identified with updated taxonomic certainty, and 2,235 morphospecies codes. Our data set reflects the heterogeneity in ant records, which include ants sampled at the beginning of the taxonomic history of myrmecology (the 19th and 20th centuries) and more recent ant surveys designed to address specific questions in ecology and biology. The data set can be used by researchers to develop strategies to deal with different macroecological and region-wide questions, focusing on assemblages, species occurrences, and distribution patterns. Furthermore, the data can be used to assess the consequences of changes in land use in the Atlantic Forest on different ecological processes. No copyright restrictions apply to the use of this data set, but we request that authors cite this data paper when using these data in publications or teaching events.

Background The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants ( Camellia sect. Thea ) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group. Results Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea , while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters. Conclusion This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.

Constructing ecological networks has become an indispensable approach in understanding how different taxa interact. However, the methods used to generate data in network research vary widely among studies, potentially limiting our ability to compare results meaningfully. In particular, methods of classifying nodes vary in their precision, likely altering the architecture of the network studied. For example, rather than being classified as Linnaean species, taxa are regularly assigned to morphospecies in observational studies, or to molecular operational taxonomic units (MOTUs) in molecular studies, with the latter defined based on an arbitrary threshold of sequence similarity. Although the use of MOTUs in ecological networks holds great potential, especially for allowing rapid construction of large data sets of interactions, it is unclear how the choice of clustering threshold can influence the conclusions obtained. To test the impact of taxonomic precision on network architecture, we obtained and analyzed 16 data sets of ecological interactions, inferred from metabarcoding and observations. Our comparisons of networks constructed under a range of sequence thresholds for assigning taxa demonstrate that even small changes in node resolution can cause wide variation in almost all key metric values. Moreover, relative values of commonly used metrics such as robustness were seen to fluctuate continuously with node resolution, thereby potentially causing error in conclusions drawn when comparing multiple networks. In observational networks, we found that changing node resolution could, in some cases, lead to substantial changes to measurements of network topology. Overall, our findings highlight the importance of classifying nodes to the greatest precision possible, and demonstrate the need for caution when comparing networks that differ with respect to node resolution, even where taxonomic groups and interaction types are similar. In such cases, we recommend that comparisons of networks should focus on relative differences rather than absolute values between the networks studied.

The acquisition of P and N from soil and their exchange for fixed C are key functions of mycorrhizal fungi in their symbiotic relationship with host plants. Additional contribution to plant nutrition is possible when hyphae proliferate into soil space not directly accessible to plant roots or when they locate nutrient-rich patches more effectively than plant roots. We performed a field-based experiment in a seminatural grassland. Community composition, diversity, and root colonisation intensity of mycorrhizal fungi was compared across different types of substrate patches (enriched or not with inorganic N, P or both), between two exposure times, and with unmanipulated soil and patches enriched with plant biomass. Beside evaluating the response of the communities of arbuscular mycorrhizal fungi (G-AMF) and fine root endophytes (M-FRE), we estimated foraging speed and precision of multiple taxa within these two groups. We compared the relative abundance of both groups using molecular barcoding. While G-AMF responded in community composition and diversity to inorganic and organic N enrichment, M-FRE did not discriminate among diferentially nutrient-enriched patches. Individual taxa varied in foraging response, but G-AMF were slower and possibly more discriminatory than M-FRE in occupying patches differing in N and/or P-enrichment. Particularly two virtual taxa of the Rhizophagus irregularis morphospecies of the G-AMF grew preferentially into the N-enriched patches. We thus conclude that there exist important differences in the strategies of soil exploration for nutrients within both fungal groups.

Plant growth responses following colonization with different isolates of a single species of an arbuscular mycorrhizal (AM) fungus can range from highly beneficial to detrimental, but the reasons for this high within-species diversity are currently unknown. To examine whether differences in growth and nutritional benefits are related to the phosphate (P) metabolism of the fungal symbiont, the effect of 31 different isolates from 10 AM fungal morphospecies on the P and nitrogen (N) nutrition of Medicago sativa and the P allocation among different P pools was examined. Based on differences in the mycorrhizal growth response, high, medium, and low performance isolates were distinguished. Plant growth benefit was positively correlated to the mycorrhizal effect on P and N nutrition. High performance isolates increased plant biomass by more than 170 % and contributed substantially to both P and N nutrition, whereas the effect of medium performance isolates particularly on the N nutrition of the host was significantly lower. Roots colonized by high performance isolates were characterized by relatively low tissue concentrations of inorganic P and short-chain polyphosphates and a high ratio between long- to short-chain polyphosphates. The high performance isolates belonged to different morphospecies and genera, indicating that the ability to contribute to P and N nutrition is widespread within the Glomeromycota and that differences in symbiotic performance and P metabolism are not specific for individual fungal morphospecies.

Oxytrigona tataira Smith (Trans Ent Soc Lond 11:497–512, 1863) was considered by different taxonomists to be a species with complex taxonomy, a dubious status and in need of taxonomic reevaluation. Furthermore, it has Oxytrigona cagafogo Müller (Nature 10:31–32, 1874) as its junior synonym, although there is no evidence to support such a decision. In this study, we used an integrative approach combining morphological data, geometric morphometric analysis of wings, and ecological niche overlap analysis to elucidate the true identity of O. tataira. For the morphological study, 923 specimens and the lectotype of Trigona tataira (= O. tataira) were examined, 470 wings were used for geometric morphometry, and 106 unique occurrence records were used for niche overlap analysis. In the morphological study, three species/morphospecies were identified: morphospecies 1 (morphologically corresponding to O. tataira), morphospecies 2 (morphologically corresponding to O. cagafogo), and morphospecies 3 (a new species for the genus). The geometric morphometry of the wings corroborated the results of the morphological study. The ecological niche overlap analysis, despite indicating a small niche overlap between O. tataira and O. cagafogo, also corroborated the results of the morphological and morphometric studies. Thus, our results confirmed the hypothesis that O. tataira and O. cagafogo are distinct taxonomic entities; therefore, we propose the revalidation of the taxonomic status of O. cagafogo Müller (Nature 10:31–32, 1874) status nov. Furthermore, it was still possible to identify and delimit a new species for Oxytrigona, which has already been described and will soon be formally published.