Biology subjects

Tice, A. K.

Publications and source records attributed to Tice, A. K..

10 recordsLinked to original sources

bioRxiv2026

Integrative morphology and phylogenetics of Arcellidae (Amoebozoa:Arcellinida), with redescription of Arcella leidyana and Arcella artocrea and description of Galeripora purdoni sp. nov.

Arcellidae is a family of testate amoebae within Arcellinida (Amoebozoa), comprising three recognized genera: Arcella, Galeripora, and Antarcella. Although species in the family have been studied for nearly two centuries, many historically described taxa and major morphological groups remain unsampled at the molecular level. Here, we provide a comprehensive review of Arcellidae and generate new cytochrome c oxidase subunit I (COI) sequences for arcellid species from Canadian peatlands, focusing on tall-shelled Arcella historically classified in section Altae sensu Deflandre. COI phylogenetic analyses recover a strongly supported monophyletic clade corresponding to North American representatives of Altae, providing the first molecular corroboration of this morphologically defined group. Within this clade, we redescribe Arcella leidyana based on modern material from Eeyou Istchee (Quebec). We further describe Galeripora purdoni sp. nov. from a calcareous fen in eastern Ontario, representing a novel terrestrial lineage within the genus, and redescribe Galeripora artocrea, which we transfer to Arcella based on congruent molecular and morphological evidence. Phylogenomic analyses of Arcellidae isolates from the Protist 10,000 Genomes Project reveal an additional deep lineage basal to Arcella and Galeripora. Together, these results highlight hidden diversity and demonstrate the importance of integrative approaches for resolving arcellid systematics and refining its classification.

evolutionary biology↗

bioRxiv2026

Evaluating the potential role and contribution of transposable elements to the evolution of microbial multicellularity across the tree of eukaryotes

Multicellularity has evolved multiple times across the eukaryotic tree of life, including among protist lineages. Because transposable elements (TEs) strongly influence genome architecture and gene regulation, understanding their potential impact on genome structure and their relationship with gene expression may provide insight into the evolution of multicellularity. Here, we generated a new genome assembly for the facultatively multicellular amoeba Acrasis kona and performed comparative analyses of TE composition, TE diversity, and TE-density organization across diverse protist lineages. Comparative analyses included unicellular and multicellular representatives from across the tree of eukaryotes, (Heterolobosea, Filasterea, Cristidiscoidea, and Chlorophyceae), including Naegleria spp., Tetramitus jugosus, Capsaspora owczarzaki, Pigoraptor spp., Fonticula alba, Parvularia atlantis, Volvox carteri, and Chlamydomonas reinhardtii. To examine relationships between TEs and gene regulation, we integrated transcriptomic datasets from A. kona, Capsaspora owczarzaki, and Volvox carteri with genome-wide TE-density analyses of differentially expressed genes. TE abundance and composition varied substantially among lineages, with species that exhibit more complex developmental or cellular organization generally containing higher TE proportions than closely related unicellular taxa. Patterns of TE-density organization near up-regulated, down-regulated, and non-differentially expressed genes also differed among systems, ranging from strong TE depletion in A. kona to weaker or cell-type-specific patterns in Capsaspora and Volvox. Together, these findings suggest that transposable elements are associated with multicellularity across diverse protist lineages, although the specific roles they play appear to be complex, lineage-specific, and not yet fully understood.

genetics↗

bioRxiv2025

Pyrumthecina Infraorder Nov.: Revisiting the morphological diversity and identifying the phylogenetic home of Argynnia within Arcellinida (Tubulinea:Amoebozoa)

Arcellinida is a diverse lineage of testate amoebae within Amoebozoa, whose evolutionary history has been clarified through phylogenomics. These efforts have led to a stable classification of the group into suborders and infraorders. However, several taxa, such as the genus Argynnia, remain unplaced due to ambiguous morphology and unresolved positions in single-gene phylogenies. In this study, we explore the diversity of Argynnia by presenting new records of species sampled across Brazil. To address its longstanding taxonomic uncertainty, we performed a phylogenomic analysis incorporating transcriptomic data from the Protist 10,000 Genomes isolate P10K-MW-000941 (P10K941). Through single-gene phylogenies, this isolate was shown to be closely related to Argynnia, which previously lacked genomic-level data. Here, we further confirm this relationship and present a 227-gene phylogenomic reconstruction that identifies the placement of P10K941 within Arcellinida, thereby resolving the phylogenetic placement of Argynnia. We obtained a curated, contaminant-free phylogenomic dataset for Arcellinida, including the P10K941, through the PhyloFisher workflow. Our analysis recovers P10K941 as a well-supported long-branch, sister to the infraorder Longithecina. Given this phylogenomic placement, along with Argynnias characteristic morphology and the consistent results of single-marker analyses placing it outside existing infraorders, we propose the Pyrumthecina infraorder novum and the family Argynniidae family novum to accommodate the P10K941 isolate and all Argynnia species. These findings resolve the phylogenetic position of Argynnia and allow for interpreting shell evolution and deep diversification patterns within Arcellinida. The recognition of Pyrumthecina also highlights the likely existence of deeply branching lineages among arcellinid taxa currently classified as incertae sedis.

evolutionary biology↗

bioRxiv2025

Phylogenetic placement and contamination screening of Amoebozoa genomic data from the Protist 10,000 Genomes (P10K) Database

BackgroundGenomic data are essential for uncovering the evolutionary history, ecological roles, and diversity of life. Yet, diverse microbial eukaryotes, predominantly unicellular and traditionally referred to as protists, remain critically underrepresented in genomic repositories, limiting our ability to address fundamental questions in eukaryotic evolution. The Protist 10,000 Genomes (P10K) initiative seeks to fill this gap by generating and compiling genomic and transcriptomic data for a wide range of microbial eukaryotes. However, large-scale sequencing efforts face persistent challenges, including contamination and imprecise taxonomic identification, particularly for poorly studied taxa that require specialized taxonomic expertise. To ensure the reliability of these resources, robust and scalable approaches for taxonomic identification and contamination screening are essential. ResultsWe developed CSI-SSU (https://github.com/AlexTiceLab/CSI-SSU), a command-line tool for Contaminant Sequence Investigation (CSI) that uses small subunit ribosomal RNA (SSU) sequences, chimeric sequence detection, and phylogenetic placement to rapidly identify, retrieve, and classify SSU sequences from eukaryotic genomic-level assemblies. CSI-SSU incorporates a curated SSU reference dataset representing the major known eukaryotic supergroups, with sequences and taxonomic nomenclature derived from the Protist Ribosomal Reference (PR2) database. In addition to detecting contaminant sequences, CSI-SSU enables approximate taxonomic assignment of the target lineage in each assembly, with resolution constrained by the current diversity represented in PR2. To further assess potential bacterial contamination, CSI-SSU employs bacterial BUSCO searches as a proxy. We demonstrate CSI-SSU utility and performance by screening 2,960 genomic-level assemblies spanning a broad diversity of eukaryotes from P10K. CSI-SSU efficiently detected non-target eukaryotic SSU sequences, revealing cross-group contamination. Classifications also corroborated or refined the original taxonomic assignments, with resolution depending on PR2 representation. Bacterial BUSCO searches indicated bacterial contamination. Independent SSU and COI phylogenies of Amoebozoa supported CSI-SSU classifications, highlighting its accuracy and sensitivity. ConclusionCSI-SSU provides a scalable and reproducible framework for phylogenetically informed contamination screening and taxonomic validation of genomic and transcriptomic data. Coupling phylogenetic placement with contamination detection enabled us to distinguish high-quality P10K datasets from those requiring decontamination or additional sequencing before downstream use. These findings serve as a reference for future analyses and guide further sequencing efforts to expand the taxonomic diversity of microbial eukaryotes at the genomic level. Addressing imprecise taxonomic assignments, contamination, and reproducibility in genomic-level datasets will enhance the value of these resources and facilitate studies illuminating the evolution and diversification of eukaryotic life.

genomics↗

bioRxiv2024

Validating the genus Pocheina (Acrasidae, Heterolobosea, Excavata) leads to the recognition of three major lineages within Acrasidae

Pocheina and Acrasis are two genera of heterolobosean sorocarpic amoebae within Acrasidae that have historically been considered close relatives. The two genera were differentiated based on their differing fruiting body morphologies. The validity of this taxonomic distinction was challenged when a SSU rRNA phylogenetic study placed an isolate morphologically identified as Pocheina rosea within a clade of Acrasis rosea isolates. The authors speculated that pocheinoid fruiting body morphology might be the result of aberrant A. rosea fruiting body development, which if true, would nullify this taxonomic distinction between genera. To clarify Acrasidae systematics, we analyzed SSU rRNA and ITS region sequences from multiple isolates of Pocheina, Acrasis, and Allovahlkampfia generated by PCR and transcriptomics. We demonstrate that the initial SSU sequence attributed to P. rosea originated from an A. rosea DNA contamination in its amplification reaction. Our analyses, based on morphology, SSU and 5.8S rRNA genes phylogenies, as well as comparative analyses of ITS1 and ITS2 sequences, resolve Acrasidae into three major lineages; Allovahlkampfia and the strongly supported clades comprising Pocheina and Acrasis. We confirm that the latter two genera can be identified by their fruiting body morphologies.

evolutionary biology↗

bioRxiv2023

A PhyloFisher utility for nucleotide-based phylogenomic matrix construction; nucl_matrix_constructor.py

Phylogenies built from multiple genes have become a common component of evolutionary biology studies. Molecular phylogenomic matrices used to build multi-gene phylogenies can be built from either nucleotide or protein matrices. Nucleotide-based analyses are often more appropriate for addressing phylogenetic questions in evolutionarily shallow timescales (i.e., less than 100 million years) while protein-based analyses are often more appropriate for addressing deep phylogenetic questions. PhyloFisher is a phylogenomic software package written in Python3. The manually curated PhyloFisher database contains 240 protein-coding genes from 304 eukaryotic taxa. Here we present nucl_matrix_constructor.py, an expansion of the PhyloFisher starting database, and an update to PhyloFisher that maintains DNA sequences. This combination will allow users the ability to easily build nucleotide phylogenomic matrices while retaining the benefits of protein-based pre-processing used to identify contaminants and paralogy.

bioinformatics↗

bioRxiv2023

Amoebozoan testate amoebae illuminate the diversity of heterotrophs and the complexity of ecosystems throughout geological time

Heterotrophic protists are vital in Earths ecosystems, influencing carbon and nutrient cycles and occupying key positions in food webs as microbial predators. Fossils and molecular data suggest the emergence of predatory microeukaryotes and the transition to a eukaryote-rich marine environment by 800 million years ago (Ma). Neoproterozoic vase-shaped microfossils (VSMs) linked to Arcellinida testate amoebae represent the oldest evidence of heterotrophic microeukaryotes. This study explores the phylogenetic relationship and divergence times of modern Arcellinida and related taxa using a relaxed molecular clock approach. We estimate the origin of nodes leading to extant members of the Arcellinida Order to have happened during the latest Mesoproterozoic and Neoproterozoic (1054 - 661 Ma), while the divergence of extant infraorders postdates the Silurian. Our results demonstrate that at least one major heterotrophic eukaryote lineage originated during the Neoproterozoic. A putative radiation of eukaryotic groups (e.g. Arcellinida) during the early-Neoproterozoic sustained by favorable ecological and environmental conditions may have contributed to eukaryotic life endurance during the Cryogenian severe ice ages. Moreover, we infer that Arcellinida most likely already inhabited terrestrial habitats during the Neoproterozoic, coexisting with terrestrial Fungi and green algae, before land plant radiation. The most recent extant Arcellinida groups diverged during the Silurian Period, alongside other taxa within Fungi and flowering plants. These findings shed light on heterotrophic microeukaryotes evolutionary history and ecological significance in Earths ecosystems, using testate amoebae as a proxy. Significance StatementArcellinida shelled amoebae are heterotrophic microbial eukaryotes with an extensive Neoproterozoic fossil record represented by the vase-shaped microfossils (VSMs), a diverse group that is abundant and widespread in late Tonian rocks (VSMs). Here we combined phylogenomic sampling and the fossil record to generate time-calibrated trees. Our results illuminate key events in the history of life, including: i) the Tonian origin of extant microbial eukaryote lineages; ii) a speculative proposed radiation of eukaryotes before the Cryogenian, "Tonian revolution"; iii) the establishment of complex terrestrial habitats before the Cryogenian; iv) a post-Silurian divergence of modern Arcellinida sub-clades in terrestrial (including freshwater) habitats. Our results provide valuable insights into the evolution of life throughout geological time and are congruent with recent discoveries regarding the early diversification of eukaryotes, including the Precambrian history of eukaryotic protosteroids.

evolutionary biology↗

bioRxiv2020

The integrin-mediated adhesome complex, essential to multicellularity, is present in the most recent common ancestor of animals, fungi, and amoebae

Integrins are transmembrane receptor proteins that activate signal transduction pathways upon extracellular matrix binding. The Integrin Mediated Adhesion Complex (IMAC), mediates various cell physiological process. The IMAC was thought to be an animal specific machinery until over the last decade these complexes were discovered in Obazoa, the group containing animals, fungi, and several microbial eukaryote lineages. Amoebozoa is the eukaryotic supergroup sister to Obazoa. Even though Amoebozoa represents the closest outgroup to Obazoa, little genomic-level data and attention to gene inventories has been given to the supergroup. To examine the evolutionary history of the IMAC, we examine gene inventories of deeply sampled set of 100+ Amoebozoa taxa, including new data from several taxa. From these robust data sampled from the entire breadth of known amoebozoan clades, we show the presence of an ancestral complex of integrin adhesion proteins that predate the evolution of the Amoebozoa. Our results highlight that many of these proteins appear to have evolved earlier in eukaryote evolution than previously thought. Co-option of an ancient protein complex was key to the emergence of animal type multicellularity. The role of the IMAC in a unicellular context is unknown but must also play a critical role for at least some unicellular organisms.

evolutionary biology↗

bioRxiv2019

An efficient single-cell transcriptomics workflow to assess protist diversity and lifestyle

Most diversity in the eukaryotic tree of life are represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcriptomes give a biased view of the actual diversity. This biased view is partly caused by the scientific community, which has prioritized certain microbes of biomedical and agricultural importance. Additionally, it is challenging to establish protist cultures, which further influence what has been studied. It is now possible to bypass the time-consuming process of cultivation and directly analyze the gene content of single protist cells. Single-cell genomics was used in the first experiments where individual protists cells were genomically explored. Unfortunately, single-cell genomics for protists are often associated with low genome recovery and the assembly process can be complicated because of repetitive intergenic regions. Sequencing repetitive sequences can be avoided if single-cell transcriptomics is used, which only targets the part of the genome that is transcribed. In this study we test different modifications of Smart-seq2, a single-cell RNA sequencing protocol originally developed for mammalian cells, to establish a robust and more cost-efficient workflow for protists. The diplomonad Giardia intestinalis was used in all experiments and the available genome for this species allowed us to benchmark our results. We could observe increased transcript recovery when freeze-thaw cycles were added as an extra step to the Smart-seq2 protocol. Further we tried reducing the reaction volume and purifying with alternative beads to test different cost-reducing changes of Smart-seq2. Neither improved the procedure, and cutting the volumes by half actually led to significantly fewer genes detected. We also added a 5 biotin modification to our primers and reduced the concentration of oligo-dT, to potentially reduce generation of artifacts. Except adding freeze-thaw cycles and reducing the volume, no other modifications lead to a significant change in gene detection. Therefore, we suggest adding freeze-thaw cycles to Smart-seq2 when working with protists and further consider our other modification described to improve cost and time-efficiency.

genomics↗

bioRxiv2017

Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group

Recent phylogenetic analyses position certain orphan protist lineages deep in the tree of eukaryotic life, but their exact placements are poorly resolved. We conducted phylogenomic analyses that incorporate deeply sequenced transcriptomes from representatives of collodictyonids (diphylleids), rigifilids, Mantamonas and ancyromonads (planomonads). Analyses of 351 genes, using site-heterogeneous mixture models, strongly support a novel supergroup-level clade that includes collodictyonids, rigifilids and Mantamonas, which we name CRuMs. Further, they robustly place CRuMs as the closest branch to Amorphea (including animals and fungi). Ancyromonads are strongly inferred to be more distantly related to Amorphea than are CRuMs. They emerge either as sister to malawimonads, or as a separate deeper branch. CRuMs and ancyromonads represent two distinct major groups that branch deeply on the lineage that includes animals, near the most commonly inferred root of the eukaryote tree. This makes both groups crucial in examinations of the deepest-level history of extant eukaryotes.

evolutionary biology↗