Biology subjects

Alverson, A. J.

Publications and source records attributed to Alverson, A. J..

15 recordsLinked to original sources

bioRxiv2026

Gene loss under constant cold reveals "natural knockout" loci in Antarctic notothenioid fishes

BackgroundGene loss is a major but often underappreciated mode of genome evolution. Genes loss can reflect relaxed selective constraint, neutral decay, compensation, or adaptive change; once fixed, however, they alter the inherited gene complement and can shape the evolutionary trajectories available to descendant lineages. Shared losses near the base of a radiation may therefore become part of the genomic background on which later specialization occurs. The Antarctic notothenioid (cryonotothenioid) radiation provides a powerful system for studying gene loss in an extreme polar environment: it diversified in the thermally stable Southern Ocean, and outgroups outside the clade allow ancestral gene presence to be inferred. ResultsUsing whole-genome alignments and orthology-aware comparative analyses across 11 cryonotothenioids and four non-Antarctic notothenioid outgroups, we systematically identified gene-inactivating mutations and reconstructed their phylogenetic distribution. After applying stringent filters to reduce reference bias, mitigate assembly and annotation artifacts, and exclude loci with detectable transcriptomic support, we identified 30 high-confidence single-copy orthologs with loss of coding potential across sampled cryonotothenioids but intact coding sequences in outgroups. These clade-wide losses affect genes associated with lipid and amino acid metabolism, water transport, renal glucose reabsorption, skeletal mineralization, circadian regulation, and tRNA modification pathways. We also identified 12 additional single-copy orthologs lost across examined icefishes but retained in red-blooded notothenioids and outgroups, including genes associated with oxygen transport, iron handling, erythroid biology, and vesicular trafficking. ConclusionsOur study provides a genome-wide catalog of coding-gene losses shared across sampled cryonotothenioids, together with additional lineage-specific losses in icefishes. Many of these losses occur in conserved genes associated with disease-relevant phenotypes in humans or model vertebrates, suggesting that Antarctic notothenioids offer a natural comparative system for studying how loss-of-function variants can persist in viable wild populations. These candidate natural knockouts provide testable hypotheses for how environmental buffering, paralog compensation, and pathway rewiring may shape vertebrate physiology under chronic cold.

genomics↗

bioRxiv2024

The divergent responses of salinity generalists to hyposaline stress provide insights into the colonization of freshwaters by diatoms

Environmental transitions, such as the salinity divide separating marine and fresh waters, shape biodiversity over both shallow and deep timescales, opening up new niches and creating opportunities for accelerated speciation and adaptive radiation. Understanding the evolutionary genetic underpinnings behind habitat transitions is therefore a central question in evolutionary biology. We used time-resolved transcriptomics to contrast the hyposalinity stress responses of two ecologically important diatoms: Skeletonema marinoi has a deep marine ancestry but recently invaded brackish waters, whereas Cyclotella cryptica has deep freshwater ancestry and can withstand a much broader salinity range. S. marinoi is less adept at mitigating even mild salinity stress compared to C. cryptica, which has distinct mechanisms for rapid mitigation of hyposaline stress and long-term growth in low salinity. We show that the cellular mechanisms underlying low salinity tolerance, which has allowed diversification across freshwater habitats worldwide, includes elements that are both conserved and variable across the diatom lineage. The balance between ancestral and lineage-specific environmental responses in phytoplankton have likely shaped marine-freshwater transitions on evolutionary timescales and, on contemporary timescales, will likely determine which lineages survive and adapt to changing ocean conditions.

evolutionary biology↗

bioRxiv2023

The nitrogenase cofactor biogenesis enzyme NifB is essential for the viability of methanogens

Dinitrogen (N2) is only bioavailable to select bacteria and archaea that possess the metalloenzyme nitrogenase, which reduces N2 to NH3 in a process called nitrogen fixation or diazotrophy. A long-term goal is to engineer diazotrophy into plants to decrease the use of nitrogen fertilizers, saving billions of dollars annually and greatly reducing nutrient pollution. This goal has not been realized, in part due to the inability to produce the nitrogenase metallocofactor within plants. Biogenesis of the cofactor requires NifB, a radical S-adenosy-L-methionine (SAM) enzyme that generates a precursor [8Fe-9S-C] cluster that matures into the final metallocofactor. Although maturation of nitrogenase is the only known function of NifB in bacteria, bioinformatic analyses reveal that NifB is conserved across methanogens, including those lacking nitrogenase, which suggests NifB functions outside of nitrogenase maturation. Indeed, several lines of evidence show that NifB is essential for viability of the model diazotroph, Methanosarcina acetivorans. First, CRISPRi repression was unable to abolish NifB production, whereas CRISPRi repression abolishes non-essential nitrogenase production. Second, unlike nitrogenase production, NifB production is not controlled by fixed nitrogen availability. Finally, nifB could not be deleted from M. acetivorans unless complemented in trans with nifB from other methanogens, including Methanothrix thermoacetophila, a species that lacks nitrogenase. Notably, M. thermoacetophila NifB supported diazotrophy in M. acetivorans, demonstrating that NifB from a non-diazotrophic methanogen produces the [8Fe-9S-C] cluster. Overall, these results link the metallocofactor biogenesis function of NifB to nitrogen fixation and methanogenesis, two processes of global importance. SIGNIFICANCEMethanogens directly impact life on Earth since they produce methane, a potent greenhouse gas, and are the principal archaea capable of nitrogen fixation, a process that requires nitrogenase. In this study, we demonstrate that NifB, an enzyme required to produce the metallocofactor in non-essential nitrogenase, is essential to the viability of methanogens. This identifies NifB as a new potential target in the goal of inhibiting methanogens to reduce methane emissions. The discovery that NifB functions outside of nitrogenase maturation will also aid efforts to engineer nitrogen fixation in plants, since NifB is a key factor to achieve this goal. Realization of these goals would have immense economic, environmental, and societal benefits.

microbiology↗

bioRxiv2023

Local adaptation of a marine diatom is governed by genome-wide changes in diverse metabolic processes

Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics data with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experiment that has played out over the past 8,000 years in one of the worlds largest brackish water bodies: the colonization of the Baltic Sea by the marine diatom Skeletonema marinoi. To this end, we used a novel approach for protist population genomics, combining target capture of the entire nuclear genome with pooled sequencing, and showed that the method performs well on both cultures and single cells. Genotype-environment association analyses identified >3,000 genes with signals of selection in response to major environmental gradients in the Baltic Sea, which apart from salinity, include marked differences in temperature and nutrient availability. Locally adapted genes were related to diverse metabolic processes, including signal transduction, cell cycle, DNA methylation, and maintenance of homeostasis. The locally adapted genes showed significant overlap with salinity-responsive genes identified in a laboratory common garden experiment, suggesting the Baltic salinity gradient is a major factor driving local adaptation of S. marinoi. Altogether, our data show that local adaptation of phytoplankton to complex coastal environments, which are characterized by a multitude of environmental gradients, is driven by intricate changes in diverse metabolic pathways and functions.

microbiology↗

bioRxiv2023

Cooperative Motility, Force Generation and Mechanosensing in a Foraging Non-Photosynthetic Diatom

Diatoms are ancestrally photosynthetic microalgae. However, some underwent a major evolutionary transition, losing photosynthesis to become obligate heterotrophs. The molecular and physiological basis for this transition is unclear. Here, we isolate and characterize new strains of non-photosynthetic diatoms from the coastal waters of Singapore. These diatoms occupy diverse ecological niches and display glucose-mediated catabolite repression, a classical feature of bacterial and fungal heterotrophs. Live-cell imaging reveals deposition of secreted extracellular polymeric substance (EPS). Diatoms moving on pre-existing EPS trails (runners) move faster than those laying new trails (blazers). This leads to cell-to-cell coupling where runners can push blazers to make them move faster. Calibrated micropipettes measure substantial single cell pushing forces, which are consistent with high-order myosin motor cooperativity. Collisions that impede forward motion induce reversal, revealing navigation-related force sensing. Together, these data identify aspects of metabolism and motility that are likely to promote and underpin diatom heterotrophy.

cell biology↗

bioRxiv2022

Resolving marine-freshwater transitions by diatoms through a fog of gene tree discordance and hemiplasy

Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic dataset of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a small set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.

evolutionary biology↗

bioRxiv2022

The dynamic response to hypoosmotic stress reveals distinct stages of freshwater acclimation by a euryhaline diatom

The salinity gradient separating marine and freshwater environments is a major ecological divide, and the mechanisms by which most organisms adapt to new salinity environments are poorly understood. Diatoms are a lineage of ancestrally marine microalgae that have repeatedly colonized and diversified in freshwaters. Cyclotella cryptica is a euryhaline diatom that naturally tolerates a broad range of salinities, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. To understand how diatoms mitigate acute hypoosmotic stress, we abruptly shifted C. cryptica from seawater to freshwater and performed transcriptional profiling during the first 10 hours. Freshwater shock dramatically remodeled the transcriptome, with ~50% of the genome differentially expressed in at least one time point. The peak response occurred within 1 hour, with strong repression of genes involved in cell growth and osmolyte production, and strong induction of specific stress defense genes. Transcripts largely returned to baseline levels within 4-10 hours, with growth resuming shortly thereafter, suggesting that gene expression dynamics may be useful for predicting acclimation. Moreover, comparison to a transcriptomics study of C. cryptica following months-long acclimation to freshwater revealed little overlap between the genes and processes differentially expressed in cells exposed to acute stress versus fully acclimated conditions. Altogether, this study highlights the power of time-resolved transcriptomics to reveal fundamental insights into how cells dynamically respond to an acute environmental shift and provides new insights into how diatoms mitigate natural salinity fluctuations and have successfully diversified across freshwater habitats worldwide.

genomics↗

bioRxiv2022

Phylotranscriptomics Reveals the Reticulate Evolutionary History of a Widespread Diatom Species Complex

In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea, a widespread species complex with several morphologically based taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear-lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Subsequent gene-tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies and a resulting putative recent hybrid. Our study shows that phylogenomic analyses of many unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes.

genomics↗

bioRxiv2021

Genotype-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline

The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of S. marinoi grown in a common garden. Our experiment included eight genotypes from source populations spanning the Baltic Sea salinity cline. Changes in gene expression revealed a shared response to salinity across genotypes, where low salinities induced profound changes in cellular metabolism, including upregulation of carbon fixation and storage compound biosynthesis, and increased nutrient demand and oxidative stress. Nevertheless, the genotype effect overshadowed the salinity effect, as genotypes differed significantly in their response, both in the magnitude and direction of gene expression. Intraspecific differences included regulation of transcription and translation, nitrogen metabolism, cell signaling, and aerobic respiration. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond and adapt to environmental change.

microbiology↗

bioRxiv2021

The dynamic trophic architecture of open-ocean protist communities revealed through machine- guided metatranscriptomics

Intricate networks of single-celled eukaryotes (protists) dominate carbon flow in the ocean. Their growth, demise, and interactions with other microorganisms drive the fluxes of biogeochemical elements through marine ecosystems. Mixotrophic protists are capable of both photosynthesis and ingestion of prey and are dominant components of open-ocean planktonic communities. Yet, the role of mixotrophs in elemental cycling is obscured by their capacity to act as primary producers or heterotrophic consumers depending on factors that remain largely uncharacterized. Here we introduce a machine learning model that can predict the in situ nutritional mode of aquatic protists based on their patterns of gene expression. This approach leverages a public collection of protist transcriptomes as a training set to identify a subset of gene families whose transcriptional profiles predict trophic status. We applied our model to nearly 100 metatranscriptomes obtained during two oceanographic cruises in the North Pacific and found community-level and population-specific evidence that abundant open-ocean mixotrophic populations shift their predominant mode of nutrient and carbon acquisition in response to natural gradients in nutrient supply and sea surface temperature. In addition, metatranscriptomic data from ship-board incubation experiments revealed that abundant mixotrophic prymnesiophytes from the oligotrophic North Pacific subtropical gyre rapidly remodelled their transcriptome to enhance photosynthesis when supplied with limiting nutrients. Coupling the technique introduced here with experiments designed to reveal the mechanisms driving mixotroph physiology is a promising approach for understanding the ecology of mixotrophic populations in the natural environment. Significance statementMixotrophy is a ubiquitous nutritional strategy in marine ecosystems. Although our understanding of the distribution and abundance of mixotrophic plankton has improved significantly, the functional roles of mixotrophs are difficult to pinpoint, as mixotroph nutritional strategies are flexible and form a continuum between heterotrophy and phototrophy. We employ a machine learning-driven metatranscriptomic technique to assess the nutritional strategies of abundant planktonic populations in situ and demonstrate that mixotrophic populations play varying functional roles along physico-chemical gradients in the North Pacific Ocean, revealing a degree of physiological plasticity unique to aquatic mixotrophs. Our results highlight mechanisms that may dictate the flow of biogeochemical elements and the ecology of the North Pacific Ocean, one of the largest biogeographical provinces on Earth.

ecology↗

bioRxiv2020

The genome of the nonphotosynthetic diatom, Nitzschia sp.: Insights into the metabolic shift to heterotrophy and the rarity of loss of photosynthesis in diatoms

Although most of the tens of thousands of diatom species are obligate photoautotrophs, many mixotrophic species can also use extracellular organic carbon for growth, and a small number of obligate heterotrophs have lost photosynthesis entirely. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia sp. strain Nitz4, to determine how carbon metabolism was altered in the wake of this rare and radical trophic shift in diatoms. Like other groups that have lost photosynthesis, the genomic consequences were most evident in the plastid genome, which is exceptionally AT-rich and missing photosynthesis-related genes. The relatively small (27 Mb) nuclear genome did not differ dramatically from photosynthetic diatoms in gene or intron density. Genome-based models suggest that central carbon metabolism, including a central role for the plastid, remains relatively intact in the absence of photosynthesis. All diatom plastids lack an oxidative pentose phosphate pathway (PPP), leaving photosynthesis as the main source of plastid NADPH. Consequently, nonphotosynthetic diatoms lack the primary source of NADPH required for essential biosynthetic pathways that remain in the plastid. Genomic models highlighted similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids. The ancestral absence of a plastid PPP might constrain loss of photosynthesis in diatoms compared to Archaeplastida, whose plastid PPP continues to produce reducing cofactors following loss of photosynthesis. Finally, Nitzschia possesses a complete {beta}-ketoadipate pathway. Previously known only from fungi and bacteria, this pathway may allow mixotrophic and heterotrophic diatoms to obtain energy through the degradation of abundant plant-derived aromatic compounds.

genomics↗

bioRxiv2020

Improved reference genome for Cyclotella cryptica CCMP332, a model for cell wall morphogenesis, salinity adaptation, and lipid production in diatoms (Bacillariophyta)

The diatom, Cyclotella cryptica, is a well-established experimental model for physiological studies and, more recently, biotechnology applications of diatoms. To further facilitate its use as a model diatom species, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms. Data available fromNCBI BioProjects PRJNA628076 and PRJNA589195

genomics↗

bioRxiv2018

Freshwater diatoms diversify faster than marine in both planktonic and benthic habitats

Many clades that span the marine-freshwater boundary are disproportionately more diverse in the younger, shorter-lived, and scarcer freshwater environments than they are in the marine realm. This disparity is thought to be related to differences in diversification rates between marine and freshwater lineages. However, marine and freshwaters are not ecologically homogeneous, so the study of diversification across the salinity divide should also account for other potentially interacting variables. In diatoms, freshwater and substrate-associated (benthic) lineages are several-fold more diverse than their marine and suspended (planktonic) counterparts. These imbalances provide an excellent system to understand whether these variables interact with diversification. Using multistate hidden-state speciation and extinction models we found that freshwater lineages diversify faster than marine lineages regardless of whether they inhabit the plankton or the benthos. Freshwater lineages also had higher turnover rates (speciation + extinction), suggesting that habitat transitions impact speciation and extinction rates jointly. The plankton-benthos contrast was also consistent with state-dependent diversification, but with modest differences in diversification and turnover rates. Asymmetric, and bidirectional transitions rejected hypotheses about the plankton and freshwaters as absorbing, inescapable habitats. Our results further suggest that the high turnover rate of freshwater diatoms is related to high turnover of freshwater systems themselves.

evolutionary biology↗

bioRxiv2018

A single loss of photosynthesis in diatoms

Loss of photosynthesis is a common and often repeated trajectory in nearly all major groups of photosynthetic eukaryotes. One small subset of apochloritic diatoms in the genus Nitzschia have lost their ability to photosynthesize and require extracellular carbon for growth. Similar to other secondarily nonphotosynthetic taxa, apochloritic diatoms maintain colorless plastids with highly reduced plastid genomes. Although the narrow taxonomic breadth of apochloritic diatoms suggests a single loss of photosynthesis in the common ancestor of these species, previous phylogenetic analyses suggested that photosynthesis was lost multiple times. We sequenced additional phylogenetic markers from the nuclear and mitochondrial genomes for a larger set of taxa and found that the best trees for datasets representing all three genetic compartments provided low to moderate support for monophyly of apochloritic Nitzschia, consistent with a single loss of photosynthesis in diatoms. We sequenced the plastid genome of one apochloritic species and found that it was highly similar in all respects to the plastid genome of another apochloritic Nitzschia species, indicating that streamlining of the plastid genome had completed prior to the split of these two species. Finally, it is increasingly clear that some locales host relatively large numbers apochloritic Nitzschia species that span the phylogenetic diversity of the group, indicating that these species co-exist because of resource abundance or resource partitioning in ecologically favorable habitats. A better understanding of the phylogeny and ecology of this group, together with emerging genomic resources, will help identify the factors that have driven and maintained the loss of photosynthesis in this group, a rare event in diatoms.

evolutionary biology↗

bioRxiv2017

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

Premise of the studyDiatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.\n\nMethodsWe used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.\n\nKey resultsSeveral methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.\n\nConclusionsWhole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.

evolutionary biology↗