Biology subjects

Richter, D. J.

Publications and source records attributed to Richter, D. J..

16 recordsLinked to original sources

bioRxiv2026

Inverse relationship between mitochondrial and non-coding nuclear DNA content in free-living kinetoplastids

The evolution of genome size and eukaryotic genome organisation has puzzled evolutionary biologists for decades. Are differences in DNA content and protein-coding capacity of eukaryotic genomes a result of natural selection, or neutral processes? If they were shaped by natural selection, which features might be connected with these differences: cell volume, ecological strategy, availability of nutrients, etc.? Kinetoplastids are protists with compact nuclear genomes that almost entirely lack introns, but whose mitochondrial DNA content (kDNA) can rival that of their nuclei. We hypothesised that the reduction in non-protein coding nuclear DNA content during the evolution of kinetoplastids is connected with an increase in kDNA content: species with larger fractions of total cellular DNA that is allocated to kDNA will have concomitantly smaller fractions of non-coding DNA in the nuclear genome. We developed a framework for estimation of DNA content in both the mitochondria and nuclei from quantitative fluorescence microscopy data, and inferred the fraction of non-coding DNA in nuclear genomes based on the combination of transcriptomic and fluorescence imaging data. Across 10 genetically distant isolates from diverse free-living kinetoplastid lineages, there is indeed a trend towards a lower proportion of non-protein-coding nuclear DNA when kDNA proportion is higher relative to the total DNA in the cell. This observation is consistent with the hypothesis that in free-living kinetoplastids, mitochondrial and nuclear genomes might co-evolve in terms of their DNA content. This finding raises the possibility that natural selection acts on genome size evolution in kinetoplastids, and contributes evidence and methodology to address this question more broadly in eukaryotes.

evolutionary biology↗

bioRxiv2025

OligoN-design: A simple and versatile tool to design specific probes and primers from large heterogeneous datasets

High-throughput environmental DNA sequencing has ushered ecological and evolutionary studies into the big data era. With thousands to millions of DNA sequences, designing taxon-specific oligonucleotides is a current bottleneck of molecular studies that rely on primers for Polymerase Chain Reactions (PCRs) or probes for Fluorescence in situ Hybridization (FISH). No software currently exists to design specific oligonucleotides starting from a custom set of sequences. Existing tools rely on specific databases, alignments or phylogenetic trees, or cannot accommodate increasingly large molecular environmental datasets. Here we present oligoN-design, a versatile tool to design oligonucleotides specific to a set of target sequences while minimizing predicted binding to non-target sequences. OligoN-design is simple, reproducible, and adaptable to high-throughput sequencing data analyses. It requires only two fasta files as input, one containing target taxa and the other containing non-target taxa. Using standard bioinformatic formats, it integrates easily with other tools such as BLAST, VSEARCH or MAFFT. OligoN-design allows a range of strategies that we present in detail, from an unsupervised end-to-end usage all the way to a detailed and thorough expert usage. Starting with large, comprehensive ribosomal databases that are widely used by the community (i.e., PR2, SILVA) and the unsupervised function, we were able to replicate known taxa-specific oligonucleotides in under 30 minutes and up to 6 Gb of RAM on a personal laptop. OligoN-design v1, available at github.com/MiguelMSandin/oligoN-design under GNU General Public License version 3.0, is easily installed via bioconda bioconda.github.io/recipes/oligon-design/README.html.

bioinformatics↗

bioRxiv2025

Phylogenomics of free-living neobodonids reveals they are a paraphyletic group from which all other metakinetoplastids are descended

Kinetoplastea is a major taxon of microbial eukaryotes that includes the well-known trypanosomatid parasites, species of which cause diseases in humans, animals and plants. Free-living kinetoplastids are greatly understudied compared to their parasitic relatives, but are ecologically important microbivores, and collectively comprise the great majority of kinetoplastid diversity. For two decades kinetoplastids have been divided into prokinetoplastids and metakinetoplastids, with the latter further split into four orders, the most diverse of which is Neobodonida. However, the position of the root of the metakinetoplastids and whether neobodonids are a clade has remained unclear due to very limited multi-gene data from free-living kinetoplastids, particularly neobodonids. Here, we present transcriptomic data for eleven newly or recently cultivated free-living neobodonid kinetoplastids. Phylogenomic analyses of a de novo generated data set of 444 inferred orthologs and 49 taxa robustly resolve the kinetoplastid tree, including the position of the root of metakinetoplastids. This divides metakinetoplastids such that Trypanosomatida, Eubodonida, Parabodonida, Allobodonidae (formerly neobodonid clade 1E) and neobodonid clade 1D fall on one side, while neobodonid clades Nd6, 1B (Rhynchomonadidae) and 1C fall on the other. Neobodonids are thus inferred to be a paraphyletic group from which all other metakinetoplastids descend. This analysis is the most thorough examination of metakinetoplastid phylogeny thus far, and forms a new basis for tracing the evolutionary history of the entire kinetoplastid group. Significance statementThis study provides transcriptomic data for 11 novel free-living kinetoplastid species, allowing the most accurate phylogeny of metakinetoplastids to date, revealing that neobodonids are paraphyletic and that eubodonids, parabodonids and trypanosomatids emerged within neobodonids. This new framework is essential for understanding the evolution of this major group of parasites and ecologically important free-living heterotrophs.

evolutionary biology↗

bioRxiv2025

Looks can be deceiving: discordances in phylogeny and morphology within loricate choanoflagellates

Choanoflagellates are heterotrophic holozoans that are classified into two groups based on their morphology: loricates, which possess a silica-based extracellular structure, and craspedids, which do not. Although the craspedid versus loricate morphological separation is currently supported by their phylogenetic relationship, recent evidence has suggested inconsistencies between morphology and phylogeny within each group. Loricate choanoflagellate taxonomy has historically been based on selected aspects of their lorica morphology, and on their mode of cell division, in which tectiform daughter cells emerge into a lorica synthesized by their mother cell following division, and nudiform daughter cells do not. Here, we characterize two new loricate strains that display unexpected morphological features when compared to their nearest genetic relatives. The strain BEAP0094 very closely matched the 18S ribosomal gene of the tectiform Pseudostephanoeca paucicostata, but its morphology clearly differed, due to the absence of the characteristic anterior ring found in all Stephanoeca species. Instead, its features resembled more closely those of the Acanthocorbis genus, raising the possibility of the existence of either multiple lorica morphologies within the same or very closely related species, or multiple morphological species sharing the same 18S ribosomal gene. The second strain we investigated, BEAP0360, presented a morphological match to Stephanoeca cauliculata, but its 18S ribosomal sequence did not, suggesting that different species could share the same lorica architecture. BEAP0360, here described as Cepoeca plumata (n. gen. n. sp.), possesses a key phylogenetic placement, potentially as the earliest branching member within nudiform loricates, which would be informative for investigating the evolution of the nudiform lifestyle. Our findings are inconsistent with a strict classification based on currently defined aspects of lorica morphology and support the usage of genetic data as primary criterion for genus-level taxonomic assignment.

evolutionary biology↗

bioRxiv2025

Description of a new Telonemia genus and species with novel observations providing insights into its hidden diversity

Telonemia is a fascinating and understudied group of microbial eukaryotes known to have a vast diversity that is still uncharacterized. In fact, although they are thought to be the closest relatives of the eukaryotic supergroup SAR (Stramenopiles, Alveolata and Rhizaria), their diversity and biology are largely unexplored: to date, there are only seven described species in three genera, although there are estimated to be hundreds more unknown lineages. Here, we describe the isolation and characterization of two new strains, including a new genus (Hyaliora molinica gen. et sp. nov.) and a new species (Telonema blandense sp. nov.), and the re-isolation of a previously characterized telonemid, Telonema subtile, accompanied by new behavioral observations. We present morphological measurements highlighting differences among the isolates and a phylogenetic tree incorporating their 18S rRNA gene sequences. Furthermore, key aspects of their cell biology and structure are highlighted to provide insights into the evolution of TSAR. Since they are relevant not only phylogenetically, but also play a crucial role in food webs with some very abundant representatives in aquatic ecosystems, the findings of this study provide a further sampling and culturing of Telonemia to increase the knowledge of the hidden diversity and evolution of this mysterious group.

evolutionary biology↗

bioRxiv2025

The evolution of gene functional repertoire in Amorphea: Divergent strategies across Amoebozoa, Fungi, and Metazoa.

Metazoa and Fungi have been extensively studied to reconstruct the trajectory of Opisthokont evolution. Their sister group, Amoebozoa, provides additional potential to generate valuable insights into the origins of Opisthokont lineages. Amoebozoa represent a diverse group of amoeboid organisms, which have adapted to a wide range of environments and ecological niches. Studying Amoebozoa not only helps to illuminate Opisthokont evolution but also reveals the mechanisms that have driven their ecological success. Here we report the discovery of Apostamoeba explorator strain BEAP0066, representing a novel lineage within Amoebozoa with intriguing behaviors like the "double-amoeba", a behavior characterized by the bipolarization of a cell into two poles that coexist and act as two semi-independent cells; and the "colonizing rings", the generation of a front of amoebae advancing together and grazing on bacterial mats. By analyzing the gene content of A. explorator and diverse amoebozoans with ancestral gene content reconstructions, correspondence analyses of Clusters of Orthologous Groups (COG) category composition and Pfam clan clustering, we revealed distinct evolutionary trajectories for Amoebozoa, Metazoa, and Fungi. Amoebozoa retained an ancestral Amorphea-like state, characterized by an enrichment of genes related to motility, phagocytosis, and environmental adaptability; while Metazoa specialized in multicellularity-related genes and Fungi in metabolism and transport. These findings suggest that retention of gene function composition, rather than gene loss, played a key role in shaping Amoebozoa evolution. SIGNIFICANCE STATEMENTAmoebae are cells with no defined shape that move by extending temporary cell membrane projections, usually composed of actin, called pseudopodia. Amoeboid cells are present in all major eukaryotic lineages, from the well-known Amoeba proteus in Amoebozoa to human macrophages in Metazoa, Salpingoeca rosetta in Choanoflagellatea, Vampyrella lateritia in Rhizaria, and other examples such as Naegleria fowleri in Heterolobosea. The prevalence of this lifestyle highlights the evolutionary success of the amoeboid form and its ability to adapt to diverse environmental conditions and ecological roles. The study of amoebae and amoeboid cell types is crucial for advancing research in medicine, ecology, and evolution. Understanding the phylogeny of Amoebozoa remains a key focus in phylogenomics, as deep divergences within the group complicate the taxonomic placement of certain taxa and have implications for character evolution. Thus, the discovery, identification, and characterization of new Amoebozoa species can help resolve current uncertainties. Recent studies have identified divergent trajectories in gene content composition within one lineage of Amorphea, the Opisthokonts. Fungi evolved through an expansion of metabolic genes, whereas Metazoa accumulated genes associated with multicellularity. Inspired by these findings, we analyzed the proteomes of Amoebozoa, Metazoa, and Fungi. Using correspondence analysis of the relative composition of Clusters of Orthologous Groups (COG), ancestral reconstruction and the analysis of Pfam domain clan presence in supergroup-specific gene clusters, we aimed to determine whether the three supergroups within Amorphea exhibit distinct clustering patterns. Our results provide evidence of divergent functional evolution in Amoebozoa, Fungi, and Metazoa. Amoebozoa retained an ancestral Amorphea-like state, characterized by an enrichment of genes related to motility, phagocytosis, and environmental adaptability; while Metazoa specialized in multicellularity-related genes and Fungi in metabolism and transport. These findings suggest that retention of gene function composition, rather than gene loss, played a key role in shaping Amoebozoa evolution.

evolutionary biology↗

bioRxiv2025

The morphology and small subunit rDNA gene phylogeny of the novel goniomonad genus Ebisugoniomonas and two novel Poseidogoniomonas species

Goniomonads are heterotrophic representatives of Cryptista, sister lineage to the phototrophic Cryptists. Goniomonads are morphologically and genetically diverse, comprising nine genera described so far. Besides morphologically described genera, SSU rDNA sequencing data has revealed the existence of at least one more monophyletic genus-level lineage within goniomonads, as well as more novel species within the described genera. Furthermore, the diversity of SSU rDNA sequences within goniomonads is not fully investigated, and addition of novel sequences can be crucial for understanding the evolution and diversity of goniomonads and for providing a basis for taxonomic descriptions. The morphological data record available for goniomonads is relatively limited: many cellular features remain undescribed, or described only for a few isolates. In this study, we describe the new genus and species Ebisugoniomonas hispanica n. gen. n. sp., and two novel species within Poseidogoniomonas: P. posteriocircus n. sp. and P. zopfkaesiformis n. sp. We report a range of observations on the cellular features of goniomonads: periplast plate arrangement pattern and intracellular structures. We also update the SSU rDNA phylogeny of goniomonads by adding sequences from novel isolates and environmental DNA studies. Several sequences recovered from novel isolates and environmental DNA datasets likely represent highly divergent lineages of goniomonads in the SSU rDNA phylogeny.

microbiology↗

bioRxiv2024

A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analyses

Metabarcoding has emerged as a robust method for understanding biodiversity patterns by retrieving environmental DNA (eDNA) directly from ecosystems. Its low cost and accessibility have extended its use across biological topics, from symbiosis to biogeography, and ecology. A successful metabarcoding application depends on accurate and comprehensive reference databases for proper taxonomic assignment. The 18S rRNA gene is the primary genetic marker used for general/broad eukaryotic metabarcoding due to its combination of conserved and hypervariable regions, and the availability of extensive taxonomically-informed reference databases like PR2 and SILVA. Despite its advantages, 18S rRNA has certain limitations at lower taxonomic levels, depending on the lineage. Alternative fast-evolving molecular markers, such as the mitochondrial cytochrome oxidase subunit I (COI) gene, have been adopted as widely used "barcoding genes" for eukaryotes due to their resolution to the species level. However, the COI gene lacks a curated taxonomically-informed database covering all eukaryotes, including protists, comparable to those available for 18S rRNA. To address this gap, we introduce eKOI, a curated COI gene database aimed at enhancing the taxonomic annotation and primer design for COI-based metabarcoding at the community level. This database integrates COI gene data from GenBank and mitochondrial genomes that are publicly available, followed by rigorous manual curation to eliminate redundancies and contaminants and to correct taxonomic annotations. We validate using the eKOI database for taxonomic annotation of protists by re-annotating several COI-based metabarcoding studies, revealing previously unidentified biodiversity. Phylogenetic analyses confirmed the accuracy of the taxonomic annotations, highlighting the potential of eKOI to uncover new biodiversity in various eukaryotic lineages.

ecology↗

bioRxiv2023

Dollo parsimony overestimates ancestral gene content reconstructions

Ancestral reconstruction is a widely-used technique that has been applied to understand the history of gain and loss of gene families over evolutionary time scales, and to produce hypotheses on how these gains and losses may have influenced the evolutionary trajectories of extant organisms. Ancestral gene content can be reconstructed via different phylogenetic methods, such as maximum likelihood or Bayesian inference, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character can only be gained once in evolutionary history. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence (including random sequence similarity and parallel gene gains), non-orthologous homology or lateral gene transfer. The aim of this study is to test Dollo parsimonys suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach which allows a gene family to be gained more than once within a tree. In order to test our hypothesis, we first compared the performance of the two approaches on a series of artificial datasets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, which were more pronounced at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.

evolutionary biology↗

bioRxiv2023

On the relationship between protist metabarcoding and protist metagenome-assembled genomes

AO_SCPLOWBSTRACTC_SCPLOWThe two most commonly used approaches to study the composition of environmental protist communities are marker gene metabarcoding and whole genome analysis through metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches have been developed to assemble metagenomic sequence reads into metagenome-assembled genomes (MAGs). Understanding the correspondence between the data produced by these two approaches can help to integrate information between the datasets and to explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent. Due to the nature of their construction, MAGs do not contain the most commonly used barcoding loci, meaning that sequence homology approaches cannot be used to match OTUs and MAGs. We made an attempt to match V9 metabarcoding OTUs from the 18S rRNA gene (V9 OTUs) and MAGs from the Tara Oceans expedition (2009-2013) based on the correspondence of their relative abundances across the same set of samples. We evaluated the performance of several methods for detecting correspondence between features in these two compositional datasets and developed a series of controls to filter artefacts of data structure and processing. After selecting the best-performing correspondence metrics, ranking the V9 OTU/MAG matches by their proportionality/correlation coefficients and applying a set of selection criteria, we identified candidate matches between V9 OTUs and MAGs. In a subset of cases, V9 OTUs and MAGs could be successfully matched with one another with a one-to-one correspondence, implying that they likely represent the same underlying biological entity. More generally, matches we observed could be classified into 4 scenarios: Scenario I - one V9 OTU matches more than one MAG; Scenario II - more than one V9 OTU matches more than one MAG; Scenario III - more than one V9 OTU matches one MAG; Scenario IV - one V9 OTU matches one MAG. These diverse scenarios for V9 OTU-MAG matches illustrate the complex nature of the OTU/MAG relationship. Notably, we found some instances in which different OTU-MAG matches from the same taxonomic group were not classified in the same scenario, with all four scenarios possible even within the same taxonomic group, illustrating that factors beyond taxonomic lineage influence the relationship between OTUs and MAGs. Overall, each scenario produces a different interpretation of V9 OTUs, MAGs and how they compare in terms of the genomic and ecological diversity that they represent.

bioinformatics↗

bioRxiv2022

EukRibo: a manually curated eukaryotic 18S rDNA reference database to facilitate identification of new diversity

EukRibo is a manually curated, public reference database of small-subunit ribosomal RNA gene (18S rDNA) sequences of eukaryotes, specifically aimed at taxonomic annotation of high-throughput metabarcoding datasets. Unlike other reference databases of ribosomal genes, it is not meant to exhaustively capture all publicly available 18S rDNA sequences from the INSDC repositories, but to represent a subset of highly trustable sequences covering the whole known diversity of eukaryotes. EukRibo strives to include only sequences with verified, up-to-date taxonomic identifications, with a strong focus on protists, and relatively low genetic redundancy, to keep the database compact yet comprehensive. Environmental clone sequences representing previously identified novel diversity are accepted as reference sequences only if they have a precise lineage designation, useful for taxonomic annotation. EukRibo is part of a suite of public resources generated by the UniEuk project, which all follow a common taxonomic framework for maximal interoperability. The high level of taxonomic accuracy of EukRibo allows higher confidence in the taxonomic annotation of environmental metabarcodes, and should facilitate identification of new eukaryotic diversity at various taxonomic levels. The database is currently in version 2, and all versions are permanently stored and made available via the FAIR open platform Zenodo. It is our hope that EukRibo will help ongoing curation efforts of other 18S rDNA reference databases, and we welcome suggestions of corrections and new features to be included in subsequent versions.

bioinformatics↗

bioRxiv2022

Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding

Microbial eukaryotes are diverse and ecologically important organisms, yet sampling constraints have hindered the understanding of their distribution and diversity in freshwater ecosystems. Metabarcoding has provided a powerful complement to traditional limnological studies, revealing an unprecedented diversity of protists in freshwater environments. Here, we aim to expand our knowledge of the ecology and diversity of protists in lacustrine ecosystems by targeting the V4 hypervariable region of the 18S rRNA gene in water column, sediment and biofilm samples collected from Sanabria Lake (Spain) and surrounding freshwater ecosystems. Sanabria is a temperate lake, which are relatively understudied by metabarcoding in comparison to alpine and polar lakes. The phylogenetic diversity of microbial eukaryotes detected in Sanabria span all currently recognized eukaryotic supergroups, with Stramenopiles being the most abundant and diverse supergroup in all sampling sites. Parasitic microeukaryotes account for 21% of the total protist ASVs identified in our study and were dominated by Chytridiomycota, both in terms of richness and abundance in all sampling sites. Sediments, biofilms and water column samples harbour distinct microbial communities. Phylogenetic placement of poorly assigned and abundant ASVs indicates molecular novelty inside Rhodophyta, Bigyra, early-branching Nucletmycea and Apusomonadida. In addition, we report the first freshwater incidence of the previously exclusively marine genera Abeoforma and Sphaeroforma. Our results contribute to a deeper understanding of microeukaryotic communities in freshwater ecosystems, and provide the first molecular reference for future biomonitoring surveys in Sanabria Lake.

ecology↗

bioRxiv2021

Colonial choanoflagellate isolated from Mono Lake harbors a microbiome

Choanoflagellates offer key insights into bacterial influences on the origin and early evolution of animals. Here we report the isolation and characterization of a new colonial choanoflagellate species, Barroeca monosierra, that, unlike previously characterized species, harbors a microbiome. B. monosierra was isolated from Mono Lake, California and forms large spherical colonies that are more than an order of magnitude larger than those formed by the closely related Salpingoeca rosetta. By designing fluorescence in situ hybridization probes from metagenomic sequences, we found that B. monosierra colonies are colonized by members of the halotolerant and closely related Saccharospirillaceae and Oceanospirillaceae, as well as purple sulfur bacteria (Ectothiorhodospiraceae) and non-sulfur Rhodobacteraceae. This relatively simple microbiome in a close relative of animals presents a new experimental model for investigating the evolution of stable interactions among eukaryotes and bacteria. IMPORTANCEThe animals and bacteria of Mono Lake (California) have evolved diverse strategies for surviving the hypersaline, alkaline, arsenic-rich environment. We sought to investigate whether the closest living relatives of animals, the choanoflagellates, exist among the relatively limited diversity of organisms in Mono Lake. We repeatedly isolated members of a single species of choanoflagellate, which we have named Barroeca monosierra, suggesting that it is a stable and abundant part of the ecosystem. Characterization of B. monosierra revealed that it forms large spherical colonies that each contain a microbiome, providing an opportunity to investigate the evolution of stable physical associations between eukaryotes and bacteria.

microbiology↗

bioRxiv2020

EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotic life

AO_SCPLOWBSTRACTC_SCPLOWEukProt is a database of published and publicly available predicted protein sets selected to represent the breadth of eukaryotic diversity, currently including 993 species from all major supergroups as well as orphan taxa. The goal of the database is to provide a single, convenient resource for gene-based research across the spectrum of eukaryotic life, such as phylogenomics and gene family evolution. Each species is placed within the UniEuk taxonomic framework in order to facilitate downstream analyses, and each data set is associated with a unique, persistent identifier to facilitate comparison and replication among analyses. The database is regularly updated, and all versions will be permanently stored and made available via FigShare. The current version has a number of updates, notably The Comparative Set (TCS), a reduced taxonomic set with high estimated completeness while maintaining a substantial phylogenetic breadth, which comprises 196 predicted proteomes. A BLAST web server and graphical displays of data set completeness are available at http://evocellbio.com/eukprot/. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, with the goal of building a collaborative resource that will promote research to understand eukaryotic diversity and diversification.

evolutionary biology↗

bioRxiv2019

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical and physical context of the ocean (the seascape) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

ecology↗

bioRxiv2017

Transcriptome sequencing and delimitation of cryptic Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA.

The homoscleromorph sponge Oscarella carmela, first described from central California, USA is shown to represent two morphologically similar but phylogenetically distant species that are co-distributed. We here describe a new species as Oscarella pearsei, sp. nov. and redescribe Oscarella carmela; the original description was based upon material from both species. Further, we correct the identification of published genomic/transcriptomic resources that were originally attributed to O. carmela, and present new Illumina-sequenced transcriptome assemblies for each of these species, and the mitochondrial genome sequence for O. pearsei sp. nov. Using SSU and LSU ribosomal DNA and the mitochondrial genome, we report the phylogenetic relationships of these species relative to other Oscarella species, and find strong support for placement of O. pearsei sp. nov. in a clade defined by the presence of spherulous cells that contain paracrystalline inclusions; O. carmela lacks this cell type and is most closely related to the Western Pacific species, O. malakhovi. Oscarella pearsei sp. nov and O. carmela can be tentatively distinguished based upon gross morphological differences such as color, surface texture and extent of mucus production, but can be more reliably identified using mitochondrial and nuclear barcode sequencing, ultrastructural characteristics of cells in the mesohyl, and the morphology of the follicle epithelium which surrounds the developing embryo in reproductively active individuals. Usually, cryptic species are very closely related to each other, but in this case and in sponges generally, cryptic species may be very distantly related because sponges can be difficult to identify based upon gross morphological characteristics.

evolutionary biology↗