Biology subjects

Neiman, M.

Publications and source records attributed to Neiman, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Preprint solicitation as a natural experiment in scholarly publishing

Preprinting is a growing and increasingly recognized mechanism for scientific communication and productivity and a way to facilitate global access to science. The interplay of preprinting practices with formal peer-reviewed publication is an open question that is now tractable to targeted analysis. Here, we take advantage of nearly a decade of preprint solicitation at Proceedings B to address this question, which offers a quasi-experimental setting for comparing outcomes for solicited preprints and traditionally submitted manuscripts. We used submission records from 15,368 manuscripts from 2018-2024 to assess whether preprint solicitation affects acceptance rates, journal scope, author geographic diversity, and post-publication uptake. Solicited manuscripts were accepted at nearly twice the rate of traditional submissions and received more downloads and citations after publication. Submission topics were broadly similar between the two routes, though solicited manuscripts showed marginally greater subject diversity. Geographic disparities favoring the Global North persisted, but acceptance rates for solicited manuscripts converged across regions, narrowing the gap seen in traditional submissions. These findings extend earlier work on this initiative and indicate that editor-driven solicitation can identify high-quality preprints, broaden geographic representation, and increase research visibility, offering a replicable model for journals seeking to diversify authorship while maintaining editorial standards.

scientific communication and education↗

bioRxiv2026

Triploid asexual freshwater snails grow faster than sexual diploid conspecifics regardless of dietary phosphorus availability

The number of chromosome sets per nucleus is a fundamental trait, but why this number is nearly always two for multicellular eukaryotes remains unclear. Chromosomes are made of nucleic acids, which possess abundant phosphorus (P). Therefore, producing new chromosomes, as well as generating new cells and organismal growth, demands substantial phosphorus. Yet, because P is often limiting in nature, P availability could influence the prevalence of diploidy versus polyploidy. Here, we compare growth rates of diploid and triploid Potamopyrgus antipodarum, a freshwater snail, relative to P availability. Because diploid P. antipodarum are obligately sexual while obligately asexual individuals are polyploid, costs associated with sensitivity to P limitation in polyploids could also help explain the maintenance of sexual P. antipodarum. We raised juvenile diploid and triploid snails on either P-adequate or P-deficient diets and found that independent of P availability, juvenile triploid asexual snails grew faster and harbored higher P content as adults than sexual diploid conspecifics. Together, these results suggest life-history advantages of polyploidy or asexual reproduction that exacerbate rather than ameliorate the cost of sex. These outcomes suggest that P availability is unlikely to be a main driver of ploidy polymorphism or the maintenance of sex in P. antipodarum.

evolutionary biology↗

bioRxiv2026

Intraspecific genetic variation modulates immune responses to acute heat exposure in an aquatic ectotherm

Climate change-induced heatwaves threaten ectotherms, whose physiology is tightly coupled to ambient temperature. Vulnerability assessments often rely on data from one or a few populations, implicitly assuming uniform thermal sensitivity across species genetic diversity. Quantifying such variation is especially important for traits with wider ecological consequences; our focus here is on immune function, which shapes disease dynamics. We addressed this knowledge gap using ten clonal lineages of the New Zealand snail Potamopyrgus antipodarum exposed to ambient (17{degrees}C) or heatwave conditions (27{degrees}C) for 4 or 8 days. We measured two complementary innate immune traits: general phenoloxidase-like (PO-like) activity, which integrates the activity of multiple phenoloxidase enzymes, and laccase activity, which targets a specific PO enzyme subclass important in mollusc immunity. Heat exposure suppressed both traits, but patterns differed across clones. While PO-like activity declined uniformly, laccase activity showed substantial among-clone variation in heatwave responses at day 4, though these differences converged by day 8. Heat-induced immune suppression is thus trait-specific, depends on genetic background, and varies with exposure duration. Together, these results demonstrate that studies limited to a single genotype, population, or timepoint risk miscalculating species-level vulnerability.

physiology↗

bioRxiv2026

Ploidy reorganizes ionomic composition across metabolically active and mineralized tissues.

Genome size, defined as total nuclear DNA content, varies widely within species and can influence cell size, metabolic scaling, and organismal performance. Yet the mechanisms linking genome architecture to phenotype remain unresolved, especially in animals. Because organisms are far-from-equilibrium systems built from interacting chemical elements, genome size variation should reorganize elemental allocation across tissues rather than shift single-element requirements in isolation. We tested this hypothesis in the New Zealand mudsnail (Potamopyrgus antipodarum), which includes co-occurring diploid, triploid, and tetraploid individuals and exhibits strong compartmentalization between metabolically active soft tissue and mineralized shell. We quantified multielemental composition of both tissues and analyzed allocation using additive log-ratios anchored to the measured elemental pool. Tissue type explained most multielemental variance, confirming distinct ionomic regimes for shell and soft tissue. Across tissues, ploidy was associated with significant redistribution of relative elemental allocation despite weak single-element effects. Ploidy-associated imbalances were more pronounced in shell than soft tissue, consistent with long-term integration of elemental fluxes in inert structures and buffering in active tissues. Genome size variation therefore reshapes organismal chemistry through coordinated multielemental redistribution, linking genome architecture to system-level chemical organization.

evolutionary biology↗

bioRxiv2025

Whole-genome sequence of Potamopyrgus antipodarum: a model system for the maintenance of sexual reproduction reveals a recent whole-genome duplication

Key unanswered questions in biology center on the causes, consequences, and maintenance of sexual reproduction ("sex"). Genome-driven processes are central to the evolutionary and genetic mechanisms inherent to sex, making genomic resources a fundamental part of answering these questions. We present the first genome assembly for a species that is uniquely well-suited for the study of (a)sex in nature, Potamopyrgus antipodarum. This New Zealand snail is unusual in featuring multiple separate transitions from obligately sexual to obligately asexual reproduction, leading to the coexistence of phenotypically similar sexual and asexual forms, a feature that is required to directly study the maintenance of sex. These separately derived asexual lineages constitute separate evolutionary experiments, providing a powerful means of characterizing how the absence of sex affects genome evolution. Our genome assembly provides critical steps towards understanding causes and consequences of sex in this system and important resources for the rapidly growing P. antipodarum and molluscan genomics research community. In characterizing this genome, we uncovered unexpected evidence for a recent whole-genome duplication (WGD) in P. antipodarum. This discovery sets the stage for using P. antipodarum to evaluate processes of rediploidization following WGD and assess whether WGD might drive transitions to asexuality.

genomics↗

bioRxiv2025

Characterization of nuclear genome size and variation in a freshwater snail model system featuring a recent whole-genome duplication

Species are defined by unique nuclear genome characteristics like nucleotide composition, genomic structure, and genome size. These fundamental aspects of the nuclear genome can themselves be the object of natural selection. We here provide the first high-quality direct measurements of nuclear genome DNA content in a representative diverse sample of Potamopyrgus antipodarum, an Aotearoa New Zealand freshwater snail that is a textbook example of the maintenance of sexual reproduction in nature and is invasive worldwide. We used propidium-iodide-based flow cytometry to characterize nuclear DNA content, and its variation, in nearly 100 P. antipodarum from multiple populations representing both sexual and asexual individuals. We also estimated nuclear DNA content in multiple P. estuarinus, a closely related obligately sexual species. These data confirmed and extended earlier lines of evidence for polyploidy and variable genome size within asexual P. antipodarum and provided the first direct evidence for distinctly higher nuclear genome content in diploid (sexual) P. antipodarum relative to diploid sexual P. estuarinus. These data are consistent with genomic evidence for a recent whole-genome duplication (WGD) and subsequent and in-process rediploidization in P. antipodarum, setting the stage for use of Potamopyrgus as a model for WGD and its consequences.

evolutionary biology↗

bioRxiv2024

Phthalate exposure influences mating behavior and sperm morphology in an aquatic ecotoxicology model system

Phthalates are a group of chemicals used to make plastics more durable, found in applications from cosmetics, lubricating oils, and flooring to soap, shampoo, and hairspray (CDC, 2021). Phthalates are also now known to be endocrine disruptors with connections to adverse reproductive outcomes in animals, including humans. Here, we evaluate the potential effects of a widely used phthalate ester, dimethyl phthalate (DMP), on male reproduction in a freshwater snail. DMP is found in industrial applications like solid rocket propellant as well as consumer products such as insect repellents and plastics. While there is some evidence that DMP negatively affects reproduction, especially in females, we still know very little about potential DMP effects on males. We addressed this important knowledge gap by testing the effects of DMP on Potamopyrgus antipodarum, a prosobranch snail native to New Zealand. These snails are very sensitive to water conditions and environmental chemicals, including endocrine-disrupting compounds, and are thus rising in prominence as water-quality sentinels and ecotoxicology models. We exposed experimental groups of male P. antipodarum to one of three different concentrations of DMP and characterized mating behavior and sperm morphology as a function of DMP exposure. Differences in these traits were primarily observed between the males in the control versus the High (10-6 M) DMP concentration group. As DMP exposure levels increased, we found that mating frequency ultimately decreased by more than 69% and that sperm morphology was increasingly altered relative to control males. Altogether, study outcomes suggest DMP exposure in male animals could have negative effects on reproduction, with particular relevance in aquatic and marine environments that are especially likely to harbor leached endocrine-disrupting chemicals.

ecology↗

bioRxiv2023

Genome evolution and introgression in the New Zealand mud snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa

We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species P. antipodarum--a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness--and thus provide key evolutionary context for understanding its unusual biology. The P. estuarinus and P. kaitunuparaoa genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of P. antipodarum--a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that P. kaitunuparaoa is likely the closest relative to P. antipodarum. We nevertheless show that there has been considerable introgression between P. estuarinus and P. kaitunuparaoa. That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between P. estuarinus and P. kaitunuparaoa. Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of non-introgression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species. Significance StatementNo whole-nuclear genome sequences are currently available for snails of the genus Potamopyrgus, best known for Potamopyrgus antipodarum, an invasive species of rivers and lakes worldwide, and a famous model for the study of the evolution of sex. We have sequenced and analyzed the genome of sexual P. estuarinus and P. kaitunuparaoa, the closest known relatives of P. antipodarum. We show that 1) the genomes are very similar in gene content and size, 2) P. kaitunuparaoa is the closest relative to P. antipodarum, 3) significant introgression has occurred between P. estuarinus and P. kaitunuparaoa; these genomes set the stage for powerful direct analyses of the genomic features, e.g., sex to asexual transitions and invasive success, that make P. antipodarum unique.

evolutionary biology↗

bioRxiv2023

Mitochondrial-nuclear variation for metabolic plasticity with potential consequences for invasion success in New Zealand mud snails

Metabolic rate is an emergent organismal trait that integrates energetic costs of living and influences species distributions and response to climate change. For ectotherms, metabolic rate is likely shaped by interactions between mitochondrial and nuclear genomes and environmental temperature. Variation in reproductive mode (e.g., asexual vs. sexual reproduction) can enhance or interfere with cross-generational transmission of these interactions, with implications for evolutionary responses to selection on standing genetic variation for metabolism-related traits. We leveraged known patterns of mitochondrial-nuclear discordance in a global invader, the snail Potamopyrgus antipodarum, to measure thermal plasticity of metabolic rate in invasive vs. native asexual lineages that combined multiple mitochondrial haplotypes with nuclear genomic variation from distinct lake populations. Native lineages harbored significant mitochondrial-nuclear variation for metabolic plasticity, with some genotypes maintaining low metabolic rates at high temperature. Invasive lineages contained only a small subset of this variation, with non-plastic and lower metabolic rates relative to native lineages at high temperature. Together, these data indicate that mitochondrial-nuclear-environment interactions contribute to variation in the metabolic rate of asexual lineages. Our results also demonstrate that invasive lineages have metabolic phenotypes that could facilitate successful colonization of aquatic habitats via decreased maintenance metabolism under high temperatures.

ecology↗

bioRxiv2022

Single-molecule sequencing of animal mitochondrial genomes reveals chloroplast-like architecture and repeat-mediated recombination

Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of mitochondrial genome architecture and landscapes of recombination. We used PacBio sequencing to re-assemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a [~]1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by assembly of short sequencing reads and likely corresponding to a large non-coding region commonly present in mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy region (LSC) and a small single-copy region (SSC) separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of "flip-flop" recombination, apparently mediated by the IRs. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive inter-molecular recombination between SNPs in the LSC region. Together, these observations suggest that mitochondrial inheritance is not strictly maternal in these snails. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of such architecture, whether and how recombination mediates mitochondrial genome evolution, and the role of genome architecture in driving cytoplasmic genome biology and the maintenance of cytoplasmic genomes.

evolutionary biology↗

bioRxiv2021

Asexual freshwater snails make poor mate choice decisions

Once-useful traits that no longer contribute to fitness tend to decay over time. Here, we address whether the expression of mating-related traits that increase the fitness of sexually reproducing individuals but are likely less useful or even costly to asexual counterparts seems to exhibit decay in the latter. Potamopyrgus antipodarum is a New Zealand freshwater snail characterized by repeated transitions from sexual to asexual reproduction. The frequent coexistence of sexual and asexual lineages makes P. antipodarum an excellent model for the study of mating-related trait loss. We used a mating choice assay including sexual and asexual P. antipodarum females and conspecific (presumed better choice) vs. heterospecific (presumed worse choice) males to evaluate the loss of behavioral traits related to sexual reproduction. We found that sexual females engaged in mating behaviors with conspecific mating partners more frequently and for a greater duration than with heterospecific mating partners. By contrast, asexual females mated at similar frequency and duration as sexual females, but did not mate more often or for longer duration with conspecific vs. heterospecific males. These results are consistent with a scenario where selection acting to maintain mate choice in asexual P. antipodarum is weak or ineffective relative to sexual females and, thus, where asexual reproduction contributes to the evolutionary decay of mating-related traits in this system.

evolutionary biology↗

bioRxiv2020

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health

In order to explore opportunities for personalized and predictive health care, we collected serial clinical measurements, health surveys and multiomics profiles (genomics, proteomics, autoantibodies, metabolomics and gut microbiome) from 96 individuals. The participants underwent data-driven health coaching over a 16-month period with continuous digital monitoring of activity and sleep. Multiomics factor analysis resulted in an unsupervised, data-driven and integrated view of human health, revealing distinct and independent molecular factors linked to obesity, diabetes, liver function, cardiovascular disease, inflammation, immunity, exercise, diet and hormonal effects. The data revealed novel and previously uncovered associations between risk factors, molecular pathways, and quantitative lifestyle parameters. For example, ethinyl estradiol use had a distinct impact on metabolites, proteins and physiology. Multidimensional molecular and digital health signatures uncovered biological variability between people and quantitative effects of lifestyle changes, hence illustrating the value of the combined use of molecular and digital monitoring of human health.

systems biology↗

bioRxiv2020

Matching a snail's pace: Successful use of environmental DNA techniques to detect early stages of invasion by the destructive New Zealand mud snail

Early detection of invasive species allows for a more rapid and effective response. Restoration of the native ecosystem after an invasive population has established is expensive and difficult but more likely to succeed when invasions are detected early in the invasion process. Containment efforts to prevent the spread of known invasions also benefit from earlier knowledge of invaded sites. Environmental DNA (eDNA) techniques have emerged as a tool that can identify invasive species at a distinctly earlier time point than traditional methods of detection. Due to expected range expansion in eastern North America, we focus on the destructive New Zealand Mud Snail Potamopyrgus antipodarum (NZMS) invasion. We collected water samples from eight sites that prior evidence indicated were not yet invaded by the NZMS. After filtering these samples to collect eDNA, we used a species-specific probe with qPCR to identify NZMS eDNA. We found evidence for NZMS invasion at five of the eight sites, with later physical confirmation of mud snails at one of these sites. This study is the first example of successful detection of a previously unidentified invasive population of NZMS, setting the stage for further monitoring of at-risk sites to detect and control new invasions of this destructive snail. This study also shows potential opportunities for invasion monitoring offered by using low-cost efforts and methods that are adaptable for citizen science.

ecology↗

bioRxiv2020

Invasive freshwater snails form novel microbial symbioses

Resident microbes (microbiota) can shape host organismal function and adaptation in the face of environmental change. Invasion of new habitats exposes hosts to novel selection pressures, but little is known about the impact of invasion on microbiota and the host-microbiome relationship after this transition (e.g., how rapidly symbioses are formed, whether microbes influence invasion success). We used high-throughput 16S rRNA sequencing of New Zealand (native) and European (invasive) populations of the freshwater snail Potamopyrgus antipodarum and found that while invaders do carry over some core microbial taxa from New Zealand, most of their microbial community is distinct. This finding highlights that invasions can result in the formation of novel symbioses. We further show that the native microbiome is composed of fewer core microbes than the microbiome of invasive snails, suggesting that the microbiota is streamlined to essential members. Together, our findings demonstrate that microbiota comparisons across native and invasive populations can reveal the impact of a long coevolutionary history and specialization of microbes in the native host range, as well as new associations occurring after invasion. We lay essential groundwork for understanding how microbial relationships affect invasion success and how microbes may be utilized in the control of invasive hosts.

evolutionary biology↗

bioRxiv2019

Male evolution under relaxed selection: Evidence for degeneration in sperm produced by male snails from asexual lineages

How drastic changes in selective regimes affect trait evolution is an important open biological question. We take advantage of naturally occurring and repeated transitions from sexual to asexual reproduction in a New Zealand freshwater snail species to address how relaxed selection on male-specific traits influences sperm morphology. The occasional production of male offspring by the otherwise all-female asexual lineages allows a unique and powerful opportunity to assess the fate of sperm traits in a context where males are unnecessary. These comparisons revealed that the sperm produced by "asexual" males are markedly distinct from sexual counterparts. In particular, the asexual male sperm harbored markedly higher phenotypic variation and was much more likely to be morphologically abnormal. Together, these data suggest that transitions to asexual reproduction might be irreversible at least in part because male function is likely to be compromised. More broadly, our results are consistent with a scenario where relaxed selection translates into rapid trait degeneration.

evolutionary biology↗

bioRxiv2017

Sex in the wild: why field-based studies play a critical role in resolving the problem of sex

Why and how sexual reproduction is maintained in natural populations, the so-called \"queen of problems\", is a key unanswered question in evolutionary biology. Recent efforts to solve the problem of sex have often emphasized results generated from laboratory settings. Here, we use a survey of representative \"sex in the wild\" literature to review and synthesize the outcomes of empirical studies focused on natural populations. Especially notable results included relatively strong support for mechanisms involving niche differentiation and a near absence of attention to adaptive evolution. Support for a major role of parasites is largely confined to a single study system, and only three systems contribute most of the support for mutation accumulation hypotheses. This evidence for taxon specificity suggests that outcomes of particular studies should not be more broadly extrapolated without extreme caution. We conclude by suggesting steps forward, highlighting tests of niche differentiation mechanisms in both lab and nature and empirical evaluation of adaptive evolution-focused hypotheses in the wild. We also emphasize the value of leveraging the growing body of genomic resources for non-model taxa to address whether the clearance of harmful mutations and spread of beneficial variants in natural populations proceeds as expected under various hypotheses for sex.\n\nAuthor contributionsSM and MN conceived the paper idea, SM, PM, MN, and TS designed the review strategy, reviewed and analysed the literature, and wrote the manuscript. All authors gave final approval for publication.\n\nData archival locationThe results of our literature survey are provided as electronic supplementary material.

evolutionary biology↗

bioRxiv2017

Variation in physiological function across source populations of a New Zealand freshwater snail

Mitochondrial function is critical for energy homeostasis and should shape how genetic variation in metabolism is transmitted through levels of biological organization to generate stability in organismal performance. Mitochondrial function is encoded by genes in two distinct and separately inherited genomes - the mitochondrial genome and the nuclear genome - and selection is expected to maintain functional mito-nuclear interactions. Nevertheless, high levels of polymorphism in genes involved in these mito-nuclear interactions and variation for mitochondrial function are nevertheless frequently observed, demanding an explanation for how and why variability in such a fundamental trait is maintained. Potamopyrgus antipodarum is a New Zealand freshwater snail with coexisting sexual and asexual individuals and, accordingly, contrasting systems of separate vs. co-inheritance of nuclear and mitochondrial genomes. As such, this snail provides a powerful means to dissect the evolutionary and functional consequences of mito-nuclear variation. The lakes inhabited by P. antipodarum span wide environmental gradients, with substantial across-lake genetic structure and mito-nuclear discordance. This situation allows us to use comparisons across reproductive modes and lakes to partition variation in cellular respiration across genetic and environmental axes. Here, we integrated cellular, physiological, and behavioral approaches to quantify variation in mitochondrial function across a diverse set of wild P. antipodarum lineages. We found extensive across-lake variation in organismal oxygen consumption, mitochondrial membrane potential, and behavioral response to heat stress, but few global effects of reproductive mode or sex. Taken together, our data set the stage for applying this important model system for sexual reproduction and polyploidy to dissecting the complex relationships between mito-nuclear variation, performance, plasticity, and fitness in natural populations.

evolutionary biology↗

bioRxiv2017

Comparative transcriptome profiling of the human and mouse dorsal root ganglia: An RNA-seq-based resource for pain and sensory neuroscience research

Molecular neurobiological insight into human nervous tissues is needed to generate next generation therapeutics for neurological disorders like chronic pain. We obtained human Dorsal Root Ganglia (DRG) samples from organ donors and performed RNA-sequencing (RNA-seq) to study the human DRG (hDRG) transcriptional landscape, systematically comparing it with publicly available data from a variety of human and orthologous mouse tissues, including mouse DRG (mDRG). We characterized the hDRG transcriptional profile in terms of tissue-restricted gene co-expression patterns and putative transcriptional regulators, and formulated an information-theoretic framework to quantify DRG enrichment. Our analyses reveal an hDRG-enriched protein-coding gene set (~140), some of which have not been described in the context of DRG or pain signaling. A majority of these show conserved enrichment in mDRG, and were mined for known drug - gene product interactions. Comparison of hDRG and tibial nerve transcriptomes suggest pervasive mRNA transport of sensory neuronal genes to axons in adult hDRG, with potential implications for mechanistic insight into chronic pain in patients. Relevant gene families and pathways were also analyzed, including transcription factors (TFs), g-protein coupled receptors (GCPRs) and ion channels. We present our work as an online, searchable repository (http://www.utdallas.edu/bbs/painneurosciencelab/DRGtranscriptome), creating a valuable resource for the community. Our analyses provide insight into DRG biology for guiding development of novel therapeutics, and a blueprint for cross-species transcriptomic analyses.\n\nSummaryWe generated RNA sequencing data from human DRG samples and comprehensively compared this transcriptome to other human tissues and a matching panel of mouse tissues. Our analysis uncovered functionally enriched genes in the human and mouse DRG with important implications for understanding sensory biology and pain drug discovery.

neuroscience↗