Estimates Of Diversity Research Articles

Deep learning with citizen science data enables estimation of species diversity and composition at continental extents.

Effective solutions to conserve biodiversity require accurate community- and species-level information at relevant, actionable scales and across entire species' distributions. However, data and methodological constraints have limited our ability to provide such information in robust ways. Herein we employ a Deep-Reasoning Network implementation of the Deep Multivariate Probit Model (DMVP-DRNets), an end-to-end deep neural network framework, to exploit large observational and environmental data sets together and estimate landscape-scale species diversity and composition at continental extents. We present results from a novel year-round analysis of North American avifauna using data from over nine million eBird checklists and 72 environmental covariates. We highlight the utility of our information by identifying critical areas of high species diversity for a single group of conservation concern, the North American wood warblers, while capturing spatiotemporal variation in species' environmental associations and interspecific interactions. In so doing, we demonstrate the type of accurate, high-resolution information on biodiversity that deep learning approaches such as DMVP-DRNets can provide and that is needed to inform ecological research and conservation decision-making at multiple scales.

Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake

Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation, yet this widely used approach has recently been questioned in the genomics era. Here, we leverage a chromosome-level genome assembly of an endangered rattlesnake (Sistrurus catenatus) combined with whole genome resequencing data (N = 110 individuals) to evaluate the relationship between levels of genome-wide neutral and functional diversity over historical and future timescales. As predicted, we found positive correlations between genome-wide estimates of neutral genetic diversity (π) and inferred levels of adaptive variation and an estimate of inbreeding mutation load, and a negative relationship between neutral diversity and an estimate of drift mutation load. However, these correlations were half as strong for projected future levels of neutral diversity based on contemporary effective population sizes. Broadly, our results confirm that estimates of neutral genetic diversity provide an accurate measure of genetic erosion in populations of a threatened vertebrate. They also provide nuance to the neutral-functional diversity controversy by suggesting that while these correlations exist, anthropogenetic impacts may have weakened these associations in the recent past and into the future.

Multi-taxon biodiversity responses to the 2019-2020 Australian megafires.

Conditions conducive to fires are becoming increasingly common and widespread under climate change. Recent fire events across the globe have occurred over unprecedented scales, affecting a diverse array of species and habitats. Understanding biodiversity responses to such fires is critical for conservation. Quantifying post-fire recovery is problematic across taxa, from insects to plants to vertebrates, especially at large geographic scales. Novel datasets can address this challenge. We use presence-only citizen science data from iNaturalist, collected before and after the 2019-2020 megafires in burnt and unburnt regions of eastern Australia, to quantify the effect of post-fire diversity responses, up to 18 months post-fire. The geographic, temporal, and taxonomic sampling of this dataset was large, but sampling effort and species discoverability were unevenly spread. We used rarefaction and prediction (iNEXT) with which we controlled sampling completeness among treatments, to estimate diversity indices (Hill numbers: q = 0-2) among nine broad taxon groupings and seven habitats, including 3885 species. We estimated an increase in species diversity up to 18 months after the 2019-2020 Australian megafires in regions which were burnt, compared to before the fires in burnt and unburnt regions. Diversity estimates in dry sclerophyll forest matched and likely drove this overall increase post-fire, while no taxon groupings showed clear increases inconsistent with both control treatments post-fire. Compared to unburnt regions, overall diversity across all taxon groupings and habitats greatly decreased in areas exposed to extreme fire severity. Post-fire life histories are complex and species detectability is an important consideration in all post-fire sampling. We demonstrate how fire characteristics, distinct taxa, and habitat influence biodiversity, as seen in local-scale datasets. Further integration of large-scale datasets with small-scale studies will lead to a more robust understanding of fire recovery.

Toward a common set of functional traits for soil protists

Protists are major actors of soil communities and play key roles in shaping food webs, community assembly, and ecosystem processes, yet their functional diversity is understudied. High-throughput sequencing data have revealed their ubiquity and diversity, but lack of standardized traits has hampered the integration of functional information, limiting our understanding of soil ecosystems. Here, we propose a functional framework for soil protists, identify a set of common traits to characterize their functional diversity, and apply the framework on a broad-scale, real-world dataset. We reviewed studies on soil protists to identify the traits used in the literature, and define a framework based on 10 key traits that satisfy two criteria: availability of information, and applicability to most taxa. The framework was tested on a dataset of environmental DNA metabarcoding data from 1123 soil samples collected in 48 glacier forelands worldwide. Traits were assigned to the 570 Molecular Operational Taxonomic Units (MOTUs) detected in our dataset, leading to the production of a global trait-based dataset from glacier forelands. We estimated the functional space of protist communities and evaluated if the selected traits were effective in describing protist diversity. The functional space of protist communities showed that the MOTUs are clustered in three regions, mainly reflecting different nutritional and habitat preferences. The proposed framework is appropriate for multiple applications, including estimation of functional diversity and food web analyses, and provides a basis for ecological studies on soil protists, enabling the functional characterization of this essential but often neglected component of soil biodiversity.

Occurrence-based diversity estimation reveals macroecological and conservation knowledge gaps for global woody plants.

Incomplete sampling of species' geographic distributions has challenged biogeographers for many years to precisely quantify global-scale biodiversity patterns. After correcting for the spatial inequality of sample completeness, we generated a global species diversity map for woody angiosperms (82,974 species, 13,959,780 occurrence records). The standardized diversity estimated more pronounced latitudinal and longitudinal diversity gradients than the raw data and improved the spatial prediction of diversity based on environmental factors. We identified areas with potentially high species richness and rarity that are poorly explored, unprotected, and threatened by increasing human pressure: They are distributed mostly at low latitudes across central South America, Central Africa, subtropical China, and Indomalayan islands. These priority areas for botanical exploration can help to efficiently fill spatial knowledge gaps for better describing the status of biodiversity and improve the effectiveness of the protected area network for global woody plant conservation.

Estimation of genetic diversity in Cenchrus ciliaris accessions introduced in the Brazilian semi-arid region

Estimation of genetic diversity in Cenchrus ciliaris accessions introduced in the Brazilian semi-arid region

DNA barcodes provide insights into the diversity and biogeography of the non-biting midge Polypedilum (Diptera, Chironomidae) in South America.

South America, particularly within its tropical belt, is renowned for its unparalleled high levels of species richness, surpassing other major biomes. Certain neotropical areas harbor fragmented knowledge of insect diversity and face imminent threats from biodiversity loss and climate change. Hence, there is an urgent need for rapid estimation methods to complement slower traditional taxonomic approaches. A variety of algorithms for delimiting species through single-locus DNA barcodes have been developed and applied for rapid species diversity estimates across diverse taxa. However, tree-based and distance-based methods may yield different group assignments, leading to potential overestimation or underestimation of putative species. Here, we investigate the performance of different DNA-based species delimitation approaches to rapidly estimate the diversity of Polypedilum (Chironomidae, Diptera) in South America. Additionally, we test the hypothesis that significant differences exist in the community structure of Polypedilum fauna between South America and its neighboring regions, particularly the Nearctic. Our analysis encompasses a dataset of 1492 specimens from 598 locations worldwide, with a specific focus on South America. Within this region, we analyzed a subset of 247 specimens reported from 37 locations. Using various methods including the Barcode Index Number (BIN), Bayesian Poisson tree processes (bPTP), multi-rate Poisson tree processes (mPTP), single-rate Poisson tree processes (sPTP), and generalized mixed Yule coalescent (sGMYC), we identify molecular operational taxonomic units (MOTUs) ranging from 267 to 520. Our results indicate that the sGMYC method is the most suitable for estimating putative species in our dataset, resulting in the identification of 75 species in the Neotropical region, particularly in South America. Notably, this region exhibited higher species richness in comparison to the Palearctic and Oriental realms. Additionally, our findings suggest potential differences in species composition of Polypedilum fauna between the Neotropical and the adjacent Nearctic realms, highlighting high levels of endemism and species richness in the first. These results support our hypothesis that there are substantial differences exist in species composition between the Polypedilum fauna in South America and the neighboring regions.

Functional diversity metrics can perform well with highly incomplete data sets

Abstract Characterising changes in functional diversity at large spatial scales provides insight into the impact of human activity on ecosystem structure and function. However, the approach is often based on trait data sets that are incomplete and unrepresentative, with uncertain impacts on functional diversity estimates. To address this knowledge gap, we simulated random and biased removal of data from three empirical trait data sets: an avian data set (9579 species), a plant data set (2185 species) and a crocodilian data set (25 species). For these data sets, we assessed whether functional diversity metrics were robust to data incompleteness with and without using imputation to fill data gaps. We compared two metrics each calculated with two methods: functional richness (calculated with convex hulls and trait probabilities densities) and functional divergence (calculated with distance‐based Rao and trait probability densities). Without imputation, estimates of functional diversity (richness and divergence) for birds and plants were robust when 20%–70% of species had missing data for four out of 11 and two out of six continuous traits, respectively, depending on the severity of bias and method used. However, when missing traits were imputed, functional diversity metrics consistently remained representative of the true value when 70% of bird species were missing data for four out of 11 traits and when 50% of plant species were missing data for two out of six traits. Trait probability densities and distance‐based Rao were particularly robust to missingness and bias when combined with imputation. Convex hull‐based estimations of functional richness were less reliable. When applied to a smaller data set (crocodilians, 25 species), all functional diversity metrics were much more sensitive to missing data. Expanding global morphometric data sets to represent more taxa and traits, and to quantify intraspecific variation, remains a priority. In the meantime, our results show that widely used methods can successfully quantify large‐scale functional diversity even when data are missing for half of species, provided that missing traits are estimated using imputation. We recommend the use of trait probability densities or distance‐based Rao when working with large incomplete data sets and filling data gaps with imputation.

Diversity and species richness of land snails inhabiting an impacted macro-zone-Mfamosing limestone hill in Sub-Saharan Region

The land snail diversity and abundance and some ecological aspects of the fauna in a threatened limestone hill in Mfamosing, Cross Rivers state, Nigeria was investigated between May 2017 and June 2018. Twelve plots of 10 m x 10 m each using a combination of leaf litter in the forest floor (litter and topsoil in a total of ninety sample bags) were sampled from which shells were extracted by handpicking. A total of 289 (two hundred and eighty-nine) specimens representing twenty-three species in seven molluscan families were recorded. The carnivorous Streptaxidae family dominated the fauna regarding species richness while the family Urocyclidae dominated species abundance. The families Eucolinidae and Aillyidae accounted for the least dominant species. The family Streptaxidae with seven species accounted for over 30% of the mollusk abundance, while Urocyclidae had the highest number of individual specimens. True estimates of diversity using Chao2 and second-order Jack-Knife estimators yielded 25 and 24 species respectively. The Land Snail diversity in Mfamosing limestone hill when compared with those from other parts of Nigeria (Okomu in Edo State) and some other parts of the world (Sabah, Malaysia) is relatively high, with moderate levels of species abundance, showing relatively high differentiation, local dominance and endemism by few species. This reveals that Mfamosing limestone hill is one of the biodiversity hotspots for terrestrial mollusks and requires urgent conservation measures, given the current rate of Limestone quarrying in the region.

Genomic DNA extraction from honey bee (Apis mellifera) queen spermathecal content

Genetic analysis of the honey bee spermathecal content can be particularly useful to provide an estimate of the genetic diversity and purity of the surrounding populations. Here we compared the concentration and quality of DNA extracted from queen spermatheca using four commercial kits to determine the best method to obtain DNA suitable for single nucleotide polymorphism genotyping by next-generation sequencing. The four kits were tested with different adjustments in the lysis incubation time, use of RNA-carrier, elution conditions and number of re-elutions. Only the use of QIAamp DNA Microkit with 3 h of lysis incubation, the addition of RNA-carrier and multiple re-elutions produced a DNA concentration over the required threshold.

Adapting a multiscale approach to assess the compositional diversity of landscapes

ContextThe role of landscape diversity and structure is crucial for maintaining biodiversity. Both landscape diversity and structure have often been analysed on one thematic layer, focusing on Shannon diversity. The application of compositional diversity, however, has received little attention yet.ObjectivesOur main goal was to introduce a novel framework to assess both landscape compositional diversity and structure in one coherent framework. Moreover, we intended to demonstrate the significance of the use of a neutral model for landscape assessments.MethodsBoth entire Hungary and nine of its regions were used as study areas. Juhász-Nagy’s information theory-based functions, i.e. “compositional diversity” and “associatum”, were introduced and applied in landscape context. Potential and actual landscape characteristics were compared by analysing a probabilistic representation of potential natural vegetation (multiple PNV, MPNV) and actual vegetation (AV), treating MPNV as a neutral model.ResultsA significant difference was found between the MPNV- and AV-based, maximal compositional diversity estimates. MPNV-based maximal compositional diversity was higher and the maximum appeared at a finer spatial scale. The differences were more prominent in human-modified regions. Associatum implied the spatial aggregation of both MPNV and AV. Fragmentation of AV was indicated by larger units carrying maximal compositional diversity and maximal associatum values.ConclusionsApplying the multiscale Juhász-Nagy’s functions to landscape composition allowed more precise characterization of the landscape state than traditional Shannon diversity. Our results underline, that increasingly transformed landscapes host decreasing complexity of vegetation type combinations and increasing grain that carries the richest information on landscape vegetation patterns.

Rapid cryptic divergence of the Anastrepha fraterculus complex in the Late Pleistocene: a phylogeographical–ecological approach

Abstract The Anastrepha fraterculus complex (AF complex) is a complex of fruit fly species consisting of eight morphotypes distributed across the Americas. In this study, landscape genetics, phylogeographical inferences and coalescence simulations were used to unveil the evolutionary history of the AF complex. Nuclear ribosomal ITS1 sequences from 331 samples distributed in 10 American countries throughout 32 ecoregions and seven biomes were analysed. Results showed high levels of diversity, intraspecific divergence and structuring associated with the different morphotypes of the complex. The analysis of gene flow and genetic diversity showed a clear geographical and environmental pattern. The morphotype–environment association suggested that the cryptic divergence process has involved local adaptation as a mechanism to withstand harsh, novel or variable conditions. The analysis showed a rapid divergence between morphotypes. Haplotypes have been diverging for ~27 000 years before the present, probably enhanced by environmental changes during the Last Glacial Maximum. Diversity estimators and neutrality tests revealed that populations have been experiencing a recent linear growth, starting in the Early Holocene (~11 500 years before the present). The Bayesian phylogeographical and ecological clustering approach detected five spatially separated and ecologically differentiated clusters. Additionally, equatorial Amazonia was indicated to be the most probable ancestral centre of origin for the AF complex.

Microbial diversity and authigenic siderite mediation in sediments surrounding the Kedr-1 mud volcano, Lake Baikal.

The gas hydrate-bearing structure-mud volcano Kedr-1 (Lake Baikal, southern basin)-is located near the coal-bearing sediments of the Tankhoy formation of Oligocene-Miocene age and can be an ideal source of gas-saturated fluid. A significant amount of siderite minerals (FeCO3 ) were collected from sediments at depths ranging from 0.5 to 327 cm below the lake floor (cmblf). An important feature of these carbonate minerals is the extremely strong enrichment in the heavy 13 C isotope, reaching values of +33.3‰ VPDB. The δ13 C of the siderite minerals, as well as their morphology and elemental composition, and the δ13 CDIC of the co-existing pore water, differed across layers of the core, which implies at least two generations of siderite formation. Here, we leverage mineralogical and geochemical data with 16S rRNA data from the microbial communities in sediments surrounding layers containing siderite minerals. Statistical data reveal the formation of three clusters of microbial communities based on taxonomical composition, key taxa among bacteria and archaea, and environmental parameters. Diversity and richness estimators decrease with sediment depth, with several similar prevailing clades located at the bottom of the core. Most of the taxa in the deep sediments could be associated with putative metabolisms involving organotrophic fermentation (Bathyarchaeia, Caldatribacteriota, and Chloroflexota). Various groups of methanogens (Methanoregulaceae, Methanosaetaceae, and Methanomassiliicoccales) and methanotrophic (Methanoperedenaceae) archaea are present in the sediment at variable relative abundances throughout the sampled depth. Based on the physicochemical characteristics of the sediment, carbon isotope analysis of carbonate minerals and DIC, and phylogenetic analysis of individual taxa and their metabolic potential, we present several models for subsurface siderite precipitation in Lake Baikal sediments.

Deciphering the mandibular shape variation in a group of Malagasy primates using Fourier outline analysis.

Among living Malagasy primates, the family Lemuridae has previously been recognized as presenting a higher mandibular morphological variation than other families. We conducted a quantitative analysis of mandibular size and shape within the five genera (Lemur, Eulemur, Hapalemur, Prolemur, and Varecia) associated with a set of covariables that could explain this variation. We used Fourier outline analysis on the left hemimandible of 182 specimens covering the Lemuridae family. The influence of the phylogeny but also seven covariables (genus, diet, sex, sexual behavior, mating system, ecoregion, and forest type) on mandibular variation was examined using multivariate statistics and model selection. Our results indicate that the high level of morphological variation within the family, associated with a phylogenetic effect and differences in diet, is due to a strong distinction between the genera Prolemur and Hapalemur and the other genera of the family. A second analysis, correcting this strong effect, indicates that mandibular shape variation is influenced not only by the phylogeny and the diet but by a combination of all the covariables. The analysis of morphological variation is a powerful tool with major applications, both for the estimation of biological diversity and for the understanding of the fundamental parameters of species' ecology. Our work indicates that, if mandibular shape variation is mainly driven by dietary adaptation, other variables describing ecology and habitat should be considered and taken into account for an integrative understanding of species resources and the establishment of conservation measures.

Cross species/genera transferability of simple sequence repeat markers, genetic diversity and population structure analysis in gladiolus (Gladiolus × grandiflorus L.) genotypes.

Genetic analysis of gladiolus germplasm using simple sequence repeat (SSR) markers is largely missing due to scarce genomic information. Hence, microsatellites identified for related genera or species may be utilized to understand the genetic diversity and assess genetic relationships among cultivated gladiolus varieties. In the present investigation, we screened 26 genomic SSRs (Gladiolus palustris, Crocus sativus, Herbertia zebrina, Sysirinchium micranthum), 14 chloroplast SSRs (Gladiolus spp., chloroplast DNA regions) and 25 Iris Expressed Sequence Tags (ESTs) derived SSRs across the 84 gladiolus (Gladiolus × grandiflorus L.) genotypes. Polymorphic markers detected from amplified SSRs were used to calculate genetic diversity estimates, analyze population structure, cluster analysis and principal coordinate analysis (PCoA). A total of 41 SSRs showed reproducible amplification pattern among the selected gladiolus cultivars. Among these, 17 highly polymorphic SSRs revealed a total of 58 polymorphic alleles ranging from two to six with an average of 3.41 alleles per marker. Polymorphic information content (PIC) values ranged from 0.11 to 0.71 with an average value of 0.48. A total of 4 SSRs were selectively neutral based on the Ewens-Watterson test. Hence, 66.66% of Gladiolus palustris, 48% of Iris spp. EST, 71.42% of Crocus sativus SSRs showed cross-transferability among the gladiolus genotypes. Analysis of genetic structure of 84 gladiolus genotypes revealed two subpopulations; 35 genotypes were assigned to subpopulation 1, 37 to subpopulation 2 and the remaining 12 genotypes could not be attributed to either subpopulation. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations, whereas 36.55% of variation among individuals within the total population. The least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation between two subpopulations was observed. The grouping pattern of population structure was consistent with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on simple matching dissimilarity coefficient and PCoA. SSR markers from the present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement. Genetic relationships assessed among the genotypes of respective clusters may assist the breeders in selecting desirable parents for crossing.

Environmental DNA reveals the genetic diversity and population structure of an invasive species in the Laurentian Great Lakes

Environmental DNA (eDNA) has been established as a noninvasive and efficient approach to sample genetic material from aquatic environments. Although most commonly used to determine species presence and measure biodiversity, eDNA approaches also hold great potential to obtain population-level genetic information from water samples. In this study, we sequenced a panel of multiallelic microsatellite markers from filtered water and fish tissue samples to uncover patterns of intraspecific diversity in the freshwater Round Goby (Neogobius melanostomus) across their invaded range in the Laurentian Great Lakes region. Although we found that the concentration of nuclear eDNA is lower than mitochondrial eDNA, we nonetheless detected over two-thirds of all nuclear alleles identified from genotyped tissues in our eDNA samples, with the greatest recovery of common alleles in the population. Estimates of allele frequencies and genetic variability within and between populations were detected from eDNA in patterns that were consistent with individual tissue-based estimates of genetic diversity and differentiation. The strongest genetic differentiation in both eDNA and tissues exists in an isolation by distance pattern. Our study demonstrates the potential for eDNA-based approaches to characterize key population parameters required to effectively monitor, manage, or sustain aquatic species.

Modeling β Diversity and Simpson’s Index Using Hyperion Reflectance in Vansda National Park, Gujarat

Global biodiversity is under threat due to increasing anthropogenic activities. Pressure on biodiversity is immense especially in rapidly developing countries like India. In the present study, an attempt has been made to establish accurate relationships between Hyperion (EO1) reflectance spectra and measured β diversity index and Simpson’s index of the tropical moist deciduous forest of the study area. Developed accurate models can help in mapping and assessment of diversity at larger spatial scales. The efficiency of statistical modeling techniques including Partial Least Square (PLS) regression and Multiple Linear Regression (MLR), is demonstrated in this study (with maximum R2 of 0.74 and 0.73 for PLS and MLR respectively). A vegetation index (SR 1457/933) is introduced for β diversity estimation, yielding exceptional accuracy in model development and validation (with a maximum R2 of 0.63).

Updated estimates of biotic diversity and endemism for Madagascar—revisited after 20 years – CORRIGENDUM

Updated estimates of biotic diversity and endemism for Madagascar—revisited after 20 years – CORRIGENDUM

Choice of bead-beater instrument can result in significant differences in the outcome of host-associated microbiome studies

Background: Accurate assessment of the abundance and composition of microbial assemblages in a complex environmental sample depends on the successful lysis of microbial cells, for which bead-beating is typically used. In this study, we compared two commonly used bead beaters, FastPrep and the Bead Ruptor Elite, for their ability to lyse the eastern-oyster-associated bacterial communities over three different time points. Methods: Genomic DNA was extracted from homogenized oyster samples using two different lysis equipment: the MSP FastPrep and the Bead Ruptor Elite. The V4-V5 variable regions of microbial small subunit ribosomal RNA (16S rRNA) genes were PCR-amplified and sequenced using Illumina Miseq, obtained sequences were bioinformatically processed using QIIME2 and the MicrobiomeAnalyst pipeline. Results: We found that the oyster samples were mostly populated by Proteobacteria phyla, regardless of lysis method. Additionally, the samples isolated by the FastPrep lysis method also harbored Firmicutes and Bacteroidota, which were not identified in the samples treated with the Bead Ruptor Elite lysis equipment. Differences were more obvious at the genus level, such that Delftia genus dominated at 80-85% when the lysis was performed using the FastPrep method. Conversely, 80-90% of the microbial abundances in the Bead Ruptor Elite-treated samples belonged to Burkholderia spp. Diversity and evenness estimates revealed that the FastPrep-treated samples were 40% more diverse and 70% more evenly distributed relative to the Bead Ruptor Elite method. Furthermore, principal component analysis (PCA) led to a distinct separation of the bacterial communities retrieved from the two lysis methods. Conclusions: Overall, this study shows that two different lysis protocols can yield significantly different microbial taxa from the same sample; thus, researchers need to be cognizant of DNA extraction process being followed for metagenomics studies, especially those that involve host tissues containing high amounts of mucous and other PCR inhibitory materials.

High‐throughput metabarcoding of SAR11 assemblages from the southwest Atlantic shelf and arid Patagonia: richness and associated rank abundance distributions

The SAR11 clade is likely the most abundant microbial lineage on earth. Here, we provide detailed analyses of the group’s richness and AD in poorly studied Southern microbiomes. This requires whole community composition analyses to be performed, which are also provided in conjunction with the SAR11‐specific studies. In this way, the work describes unknown aspects of the diversity of an outstanding bacterial lineage and novel data on remote and relatively little‐studied microbial communities.BackgroundMassively parallel sequencing of environmental DNA allows microbiological studies to be performed in greater detail than was possible with first‐generation sequencing. For example, it facilitates the use of approaches hitherto largely applied to flora and fauna, such as rank abundance distribution (RAD) analyses.MethodsHere, we set out to advance the knowledge on Ca. Pelagibacterales (SAR11) communities from southern South America using environmental sequences from the open ocean in the Argentine sea, the uncharted Engaño Bay, as well as a river and an oligohaline shallow lake from the Patagonian Steppe ecoregion. The structures of the SAR11 assemblages present in these ecosystems were dissected by direct and rarefaction‐based estimates of species richness, and evaluations of the corresponding abundance distributions (ADs), which was addressed by RAD analyses.ResultsMicrobial community composition analyses revealed that the studied SAR11 assemblages coexist with 27 bacterial phyla. SAR11 richness was in general very high, but ADs turned out to be highly uneven. The results were compatible with prior knowledge, and similar to that derived from point estimates of diversity. However, our comprehensive dissection allowed for more detailed quantitative comparisons to be made between the environments surveyed, and revealed differences regarding both richness and the underlying ADs.ConclusionsDespite SAR11 assemblages being extremely rich, their ADs are very uneven. Richness and ADs can vary, not only between fresh and salt water, but also between oceanic and coastal marine environments. The obtained results provide insights on general topics such as adaptation and the contrast between marine and freshwater radiations.