An excavate root for the eukaryote tree of life

Science Advances, Journal Year: 2023, Volume and Issue: 9(17)

Published: April 28, 2023

Much of the higher-order phylogeny eukaryotes is well resolved, but root remains elusive. We assembled a dataset 183 eukaryotic proteins archaeal ancestry to test this root. The resulting identifies four lineages currently classified as "Excavata" branching separately at base tree. Thus, Parabasalia appear first major branch followed sequentially by Fornicata, Preaxostyla, and Discoba. All excavate points receive full statistical support from analyses with commonly used evolutionary models, protein structure partition model that we introduce here, various controls for deep artifacts. absence aerobic mitochondria in Parabasalia, Preaxostyla suggests modern arose under anoxic conditions, probably much earlier than expected, without benefit mitochondrial respiration.

Language: Английский

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Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(4), P. 671 - 682

Published: May 16, 2023

Abstract Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems informing policy decision‐making, especially in an era massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at forefront technological advances monitoring, last few years have seen major progress solutions to technical challenges from laboratory bioinformatics. Water eDNA has been shown allow fast efficient recovery signals, but rapid pace development meant that some important principles regarding sampling design, which well established traditional inventories, neglected. Using a spatially explicit river flow model, we illustrate how must be adjusted size watercourse increase quality signal recovered. We additionally investigate effect parameters (volume, number sites, sequencing depth) detection probability empirical data set. Based principles, propose aquatic replication volume scaled match organisms' ecosystems' properties provide reliable estimates. present generalizable conceptual equation describing features as function ecosystem monitored, abundance target organisms, procedure. The aim this formalization enhance standardization critical steps design inventory studies using eDNA. More robust standards will generate more eDNA, necessary method's long‐term plausibility comparability.

Language: Английский

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The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2024, Volume and Issue: 99(4), P. 1218 - 1241

Published: Feb. 13, 2024

ABSTRACT The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, discovery many new species remarkably uniform unstructured pelagic environment appeared to challenge concept ecological niches. Later, it became obvious that only fraction had been formally described, because assemblages are dominated by understudied eukaryotic lineages with small size lack clearly distinguishable morphological features. high confirmed comprehensive metabarcoding surveys, but interpretation underlying molecular taxonomies is hindered insufficient integration genetic taxonomy observations. Here we use planktonic foraminifera as study model reveal full their investigate geographical patterns distribution. To this end, assembled global data set ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established robust taxonomic framework observed diversity, used query covering ~1700 samples ~2.48 billion reads. This allowed us extract assign 1 million reads, enabling characterisation structure group across ~1100 oceanic stations worldwide. Our sampling revealed existence of, at most, 94 distinct operational units (MOTUs) level divergence indicative biological species. doubles number described identified Furthermore, allocation morphospecies uneven. Only 16 disguise evolutionarily significant proportion show increases poleward. Finally, observe MOTUs have narrower geographic distribution than some cases belonging same (cryptic species) different environmental preferences. Overall, our analysis reveals even light sampling, modest finite. However, cryptic diversification decoupled diversification, hinting mechanisms acting levels divergence.

Language: Английский

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Geographic characteristics and environmental variables determine the diversities and assembly of the algal communities in interconnected river-lake system

Water Research, Journal Year: 2023, Volume and Issue: 233, P. 119792 - 119792

Published: March 1, 2023

Language: Английский

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Sedimentary ancient DNA: a new paleogenomic tool for reconstructing the history of marine ecosystems

Frontiers in Marine Science, Journal Year: 2023, Volume and Issue: 10

Published: June 9, 2023

Sedimentary ancient DNA ( seda DNA) offers a novel retrospective approach to reconstructing the history of marine ecosystems over geological timescales. Until now, biological proxies used reconstruct paleoceanographic and paleoecological conditions were limited organisms whose remains are preserved in fossil record. The development analysis techniques substantially expands range studied taxa, providing holistic overview past biodiversity. Future research is expected dramatically improve our understanding how biota responded changing environmental conditions. However, as an emerging approach, holds many challenges, its ability recover reliable biodiversity information needs be carefully assessed. This review aims highlight current advances discuss potential methodological pitfalls limitations.

Language: Английский

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Diplonemids – A Review on "New" Flagellates on the Oceanic Block

Protist, Journal Year: 2022, Volume and Issue: 173(2), P. 125868 - 125868

Published: March 3, 2022

Language: Английский

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Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: March 14, 2023

Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They ubiquitous, represent most the genetic and functional diversity among eukaryotes, play essential roles in nutrient energy cycling. Yet, protists remain black box marine sedimentary ecosystems like intertidal mudflats Bay Fundy. The harsh conditions zone high nature tides Fundy provide an ideal system for gaining insights into major food web players, patterns potential structuring influences protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations vertical stratification communities mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms abundance, richness, prevalence), drove overall community dynamics formed core microbiome Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), Dinophyceae (dominated by toxigenic, bloom-forming species). Consumers trophic comprised mostly eukaryvorous bacterivorous Cercozoa, omnivorous Ciliophora, while phototrophs dominated Bacillariophyta. codominance Apicomplexa (invertebrate parasites) Syndiniales (protist parasite assemblages, coupled with broader patterns, highlighted combined terrestrial on microbial inhabiting findings, comprehensive hypertidal system, suggest that synergistic interactions both local regional processes (notably benthic-pelagic coupling) may drive heterogenous distribution high-energy coastal systems.

Language: Английский

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Global beta diversity patterns of microbial communities in the surface and deep ocean

Global Ecology and Biogeography, Journal Year: 2022, Volume and Issue: 31(11), P. 2323 - 2336

Published: Aug. 11, 2022

Abstract Aim Dispersal and environmental gradients shape marine microbial communities, yet the relative importance of these factors across taxa with distinct sizes dispersal capacity in different ocean layers is unknown. Here, we report a comparative analysis surface deep beta diversity examine how patterns are tied to oceanic distance gradients. Location Tropical subtropical oceans (30°N–40°S). Time period 2010–2011. Major studied Prokaryotes picoeukaryotes (eukaryotes between 0.2 3 μm). Methods Beta was calculated from metabarcoding data on prokaryotic picoeukaryotic microbes collected during Malaspina expedition tropical oceans. Mantel correlations were used determine contribution environment driving community diversity. Results Mean similarity all sites for prokaryotes 38.9% 51.4% ocean, compared mean 25.8 12.1% respectively, picoeukaryotes. Higher rates smaller body likely contributed significantly higher The ecological mechanisms determining biogeography varied depth. In differences space more important factor distribution distance, defined as shortest path two avoiding land. picoeukaryote communities slightly structured by while shaped combined action filtering. Main conclusions Horizontal assembly differed depths, did shaping them. played significant roles spatial distribution, influence stronger than distance.

Language: Английский

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Discovering marine biodiversity in the 21st century

Advances in marine biology, Journal Year: 2022, Volume and Issue: unknown, P. 23 - 115

Published: Jan. 1, 2022

Language: Английский

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Multiple parallel origins of parasitic Marine Alveolates

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 3, 2023

Microbial eukaryotes are important components of marine ecosystems, and the Marine Alveolates (MALVs) consistently both abundant diverse in global environmental sequencing surveys. MALVs dinoflagellates that thought to be parasites other protists animals, but lack data beyond ribosomal RNA gene sequences from all a few described species means much their biology evolution remain unknown. Using single-cell transcriptomes several free-living relatives, we show evolved independently two distinct, ancestors parasitism parallel. Phylogenomics shows one subgroup (MALV-II -IV, or Syndiniales) is related novel lineage free-living, eukaryovorous predators, eleftherids, while (MALV-I, Ichthyodinida) predator Oxyrrhis retains proteins targeted non-photosynthetic plastid. Reconstructing photosynthesis, plastids, early-diverging number parallels with apicomplexan sisters. In groups, similar forms multiple times photosynthesis was lost many times. By contrast, complete loss plastid organelle infrequent and, when this does happen, leaves no residual genes.

Language: Английский

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