Biology subjects

Clark, A. T.

Publications and source records attributed to Clark, A. T..

12 recordsLinked to original sources

bioRxiv2025

Joint profiling of 5mC, 5hmC, and the transcriptome in single cells identifies factors responsible for genome-wide DNA methylation erasure in human primordial germ cell maturation

Reprogramming of DNA methylation plays a vital role in the establishment of cell identity during early mammalian development. To gain deeper mechanistic insights into this process requires capturing the entire dynamics of DNA methylation - both 5-methylcytosine (5mC) and its downstream oxidation product 5-hydroxymethylcytosine (5hmC) - in individual cells. Therefore, in this work, we report a new single-cell genome-wide strand-specific sequencing method, scMHT-seq, to jointly profile 5mC, 5hmC, and the transcriptome from individual cells. Using human embryonic stem cells (hESCs), we first show that scMHT-seq can accurately detect both 5mC and 5hmC from the same cell with minimal crosstalk in quantifying these two DNA modifications, and that the multi-modal measurements are in close agreement with individual measurements of 5mC and 5hmC in single cells. After establishing the method, we next applied scMHT-seq to gain insights into human primordial germ cell (hPGC) development. After specification, hPGCs undergo rapid global demethylation as they mature, and this reprogramming is critical for normal development of gametes. However, it has not been possible to fully overcome this key epigenetic barrier in culture, thereby limiting our ability to generate mature hPGC-like cells (hPGCLCs) and accomplish in vitro gametogenesis. To gain deeper understanding of the molecular factors involved in germ cell maturation, we applied scMHT-seq to an extended in vitro culture system for generating hPGCLCs and observed partial and heterogeneous erasure of the methylome across single cells that is mechanistically predominantly driven by passive demethylation due to reduced DNMT1-mediated maintenance methylation activity. Notably, we discover that hPGCLCs in extended culture can be transcriptionally classified into two distinct states, with one population enriched with more mature hPGCLCs exhibiting genome-wide loss of DNA methylation. Moreover, analysis of these two cell states identifies DND1 and SOX15 as two factors that are potentially key drivers of hPGCLC demethylation and maturation. Overall, we demonstrate that scMHT-seq is a robust and high-throughput technology that can provide insights into the mechanisms driving DNA methylation dynamics and their effect on cell states.

genomics↗

bioRxiv2024

demres: An R package to study time-varying demographic resilience

1- Quantifying the resilience of populations to disturbances is essential to assess how threatened populations are. Demographic resilience has been defined as the ability of populations to resist and recover from alterations in their demographic structures. Resilience metrics are typically obtained by applying transient analyses to matrix population models. Until now, the questions of how demographic resilience can change over time, how to quantify such temporal variation and when it is important to account for it have not yet been studied. However, since demographic rates fluctuate over time, it is essential to evaluate whether and under what conditions the assumption of time-constant demographic resilience remains appropriate. 2- In this study we introduce demres - an R package that offers functions to quantify time-varying and time-constant demographic resilience metrics, including time to convergence, damping ratio, inertia, maximum amplification, maximum attenuation and reactivity. The package also allows the comparison of these two approaches, both visually and by means of distance metrics. 3- We use a case study to illustrate the versatility of demres and demonstrate how this tool can be readily used by conservation biologists, managers and others to assess the time-varying resilience of wildlife populations using long-term demographic data. Our framework facilitates standardised comparisons of demographic resilience metrics, for example by means of comparative studies across populations and species.

ecology↗

bioRxiv2024

Climate change shapes richness-evenness relationships in a subalpine grassland experiment

Grasslands face an uncertain future due to climate change. Although there is increased interest in the interdependencies of different biodiversity components, the effects of climate change on these relationships remain understudied. One of these is the richness-evenness relationship (RER), which is sensitive to altered species abundances in relation to richness. This relationship may be important as evenness and richness jointly shape diverse ecosystem functions, such as stability and productivity. As evenness affects productivity differently in low and high richness communities, the richness-evenness relationship is important to investigate, especially under climate change. Here, we assess the effects of increased CO2 concentrations, temperature, and drought on the RER in a subalpine long-term (2010 - ongoing) grassland climate change experiment, and test whether these effects can be buffered by reseeding. We provide evidence that climate change alters the RER in our experiment, and that these changes occur independently of changes in richness and evenness separately. Reseeding erases the differences in RER between treatments and controls but fails to restore the negative RER initially found in controls. Further, we show that the dominant grass species in our system (Arrhenatherum elatius) responds differently to each climate change factor, with opposite effects in high vs. low richness plots, thereby largely determining the direction of the RER. These results suggest that the RER can reveal additional insights on community responses to climate change and represents a different signal than evenness or richness alone. A more nuanced approach integrating evenness and maximizing richness in seed mixtures could be an important step forward to better match restoration treatments to particular community types and global change drivers.

ecology↗

bioRxiv2024

A Novel Mutation in LXRalpha Uncovers a Role for Cholesterol Sensing in Limiting Metabolic Dysfunction-Associated Steatohepatitis (MASH).

Liver x receptor alpha (LXR, Nr1h3) functions as an important intracellular cholesterol sensor that regulates fat and cholesterol metabolism at the transcriptional level in response to the direct binding of cholesterol derivatives. We have generated mice with a mutation in LXR that reduces activity in response to endogenous cholesterol derived LXR ligands while still allowing transcriptional activation by synthetic agonists. The mutant LXR functions as a dominant negative that shuts down cholesterol sensing. When fed a high fat, high cholesterol diet LXR mutant mice rapidly develop pathologies associated with Metabolic Dysfunction-Associated Steatohepatitis (MASH) including ballooning hepatocytes, liver inflammation, and fibrosis. Strikingly LXR mutant mice have decreased liver triglycerides but increased liver cholesterol. Therefore, MASH-like phenotypes can arise in the absence of large increases in triglycerides. Reengaging LXR signaling by treatment with synthetic agonist reverses MASH suggesting that LXR normally functions to impede the development of liver disease.

physiology↗

bioRxiv2024

Should regional species loss be faster, or slower, than local loss? It depends on density-dependent rate of death

1Assessment of the rate of species loss, which we also label extinction, is an urgent task. However, the rate depends on spatial grain (average area A) over which it is assessed--local species loss can be on average faster, or slower, than regional or global loss. Ecological mechanisms behind this discrepancy are unclear. We propose that the relationship between extinction rate and A is driven by two classical ecological phenomena: the Allee effect and the Janzen-Connell effect. Specifically, we hypothesize that (i) when per-individual probability of death (Pdeath) decreases with population density N (as in Allee effects), per-species extinction rate (Px) should be high at regional grains, and low locally. (ii) In contrast, when Pdeath increases with N (as in Janzen-Connell effects), Px should be low regionally, but high locally. (iii) Total counts of extinct species (Ex) should follow a more complex relationship with A, as they also depend on drivers of the species-area relationship (SAR) prior to extinctions, such as intraspecific aggregation, species pools, and species-abundance distributions. We tested these hypotheses using simulation experiments, the first based on point patterns, the second on a system of generalized Lotka-Volterra equations. In both experiments, we used a single continuous parameter that moved between the Allee effect, no relationship between Pdeath and N, and the Janzen-Connell effect. We found support for our hypotheses, but only when regional species-abundance distributions were uneven enough to provide sufficiently rare or common species for Allee or Janzen-Connell to act on. In all, we have theoretically demonstrated a mechanism behind different rates of biodiversity change at different spatial grains which has been observed in empirical data.

ecology↗

bioRxiv2023

Influence of functional and phylogenetic dissimilarity on exotic plant invasion depends on spatial scale

O_LIDarwins theory of natural selection provides two seemingly contradictory hypotheses for explaining the success of introduced species: 1) the pre-adaptation hypothesis posits that introduced species that are closely related to native species will be more likely to succeed than distantly related invaders because they already possess relevant characteristics; 2) the limiting-similarity hypothesis posits that invaders that are more similar to resident species will be less likely to succeed due to competitive exclusion. Previous studies assessing this conundrum show mixed results, possibly stemming from variation in study spatial scales and lack of both functional and phylogenetic information. C_LIO_LIWe used species abundances compiled in a 33-year grassland successional survey based at Cedar Creek Ecosystem Science Reserve (USA) to assess the support for the pre-adaptation and limiting similarity hypotheses at two different spatial scales (neighbourhood scale of 0.5m2, site scale of ~40m2). We combined compositional surveys of 303 vascular plant taxa (256 native, 47 introduced) taken across 2700 plots in a chronosequence of abandonment from agriculture with species functional dissimilarities, phylogenetic distances, environmental covariates and information on species origin. C_LIO_LIOur results consistently supported the pre-adaptation hypothesis at the site scale but diverged at neighbourhood scale, with functional dissimilarity supporting the limiting similarity hypothesis and phylogenetic distance supporting the pre-adaptation hypothesis. Introduced species with low leaf dry matter content (LDMC), low height and high seed mass tended to be most abundant than rest of species, while relationships between species abundance and specific leaf area (SLA) varied with scale. Introduced species were more abundant than natives at higher concentrations of soil N but were less abundant than natives over time. C_LIO_LISynthesis: Our study highlights the importance of environmental filtering on grassland community assembly at the scale of a site - here 40 m2, a spatial resolution that is usually considered "local". This influence of environmental filtering might mask effects of limiting similarity at small "local" scales. Our results demonstrate the importance of accounting for both phylogenetic and functional dissimilarity when examining the complex interaction between species biogeographic origin, functional strategies and evolutionary history as considering one alone can lead to different conclusions. C_LI

ecology↗

bioRxiv2022

Beyond variance: simple random distributions are not a good proxy for intraspecific variability in systems with environmental structure

The role of intraspecific variability (IV) in shaping community dynamics and species coexistence has been intensively discussed over the past decade and modelling studies have played an important role in that respect. However, these studies often implicitly assume that IV can be represented by independent random draws around speciesspecific mean parameters. This major assumption has largely remained undiscussed, although a great part of observed IV is structured in space or time, in particular when environmental dimensions that influence individual performance are imperfectly characterised or unobserved in the field. To test the impact of this strong assumption on the outcome of community dynamics models, we designed a simulation experiment where we varied the level of knowledge of the environment in virtual communities, resulting in different relative importance of explained vs unexplained spatial individual variation in performance. We used a community dynamics simulator to generate communities where the unexplained individual variation is, or is not, added as an unstructured random noise. Communities simulated with unstructured IV never reached the community diversity and composition of those where all the variation was explained and structured (perfect knowledge model). This highlights that incorporating unstructured IV (i.e. a random noise) to account for unexplained (but structured) variation can lead to incorrect simulations of community dynamics. In addition, the effects of unstructured IV on community diversity and composition depended on the relative importance of structured vs unstructured IV, i.e. on the level of knowledge of the environment, which may partly explain the contrasting results of previous studies on the effect of IV on species coexistence. In particular, the effect of unstructured IV on community diversity was positive when the proportion of structured IV vs unstructured IV in the model was low, but negative when this proportion was high. This is because unstructured random noise can either limit the competitive exclusion of inferior competitors in low dimensions or destabilise tight niche partitioning in high dimension. Our study suggests that it is crucial to account for the sources and structure of observed IV in real communities to better understand its effect on community assembly and properly include it in community dynamics models.

ecology↗

bioRxiv2022

The recovery of biodiversity and species composition after agricultural abandonment across spatial scales

O_LIHuman impacts have led to dramatic biodiversity change which can be highly scale-dependent across space and time. A primary means to manage these changes is via passive (here, the removal of disturbance) or active (management interventions) ecological restoration. The recovery of biodiversity, following the removal of disturbance is often incomplete relative to some kind of reference target. The magnitude of recovery of ecological systems following disturbance depend on the landscape matrix, as well as the temporal and spatial scales at which biodiversity is measured. C_LIO_LIWe measured the recovery of biodiversity and species composition over 27 years in 17 temperate grasslands abandoned after agriculture at different points in time, collectively forming a chronosequence since abandonment from one to eighty years. We compare these abandoned sites with known agricultural land-use histories to never-disturbed sites as relative benchmarks. We specifically measured aspects of diversity at the local plot-scale (-scale, 0.5m2) and site-scale ({gamma}-scale, 10m2), as well as the within-site heterogeneity ({beta}-diversity) and among-site variation in species composition (turnover and nestedness). C_LIO_LIAt our -scale, sites recovering after agricultural abandonment only had 70% of the plant species richness (and [~]30% of the evenness), compared to never-ploughed sites. Within-site {beta}-diversity recovered following agricultural abandonment to around 90% after 80 years. This effect, however, was not enough to lead to recovery at our {gamma}-scale. Richness in recovering sites was [~]65% of that in remnant never-ploughed sites. The presence of species characteristic of the never disturbed sites increased in the recovering sites through time. Forb and legume cover declines in years since abandonment, relative to graminoid cover across sites. C_LIO_LISynthesis. We found that, during the 80 years after agricultural abandonment, old-fields did not recover to the level of biodiversity in remnant never-ploughed sites at any scale. {beta}-diversity recovered more than -scale or {gamma}-scales. Plant species composition recovered, but not completely, over time, and some species groups increased their cover more than others. Patterns of ecological recovery in degraded ecosystems across space and long time-scales can inform effective, targeted active restoration interventions and perhaps, lead to better outcomes. C_LI

ecology↗

bioRxiv2022

Rethinking the role of intraspecific variability in species coexistence

ContextIntraspecific variability (IV) has been proposed to explain species coexistence in diverse communities. Assuming, sometimes implicitly, that conspecific individuals can perform differently in the same environment and that IV blurs species differences, previous studies have found contrasting results regarding the effect of IV on species coexistence. ObjectiveWe aim at showing that the large IV observed in data does not mean that conspecific individuals are necessarily different in their response to the environment and that the role of high-dimensional environmental variation in determining IV has been largely underestimated in forest plant communities. Methods and ResultsWe first used a simulation experiment where an individual attribute is derived from a high-dimensional model, representing "perfect knowledge" of individual response to the environment, to illustrate how a large observed IV can result from "imperfect knowledge" of the environment. Second, using growth data from clonal Eucalyptus plantations in Brazil, we estimated a major contribution of the environment in determining individual growth. Third, using tree growth data from long-term tropical forest inventories in French Guiana, Panama and India, we showed that tree growth in tropical forests is structured spatially and that despite a large observed IV at the population level, conspecific individuals perform more similarly locally than compared with heterospecific individuals. SynthesisAs the number of environmental dimensions that are typically quantified is generally much lower than the actual number of environmental dimensions influencing individual attributes, a great part of observed IV might be misinterpreted as random variation across individuals when in fact it is environmentally-driven. This mis-representation has important consequences for inference about community dynamics. We emphasize that observed IV does not necessarily impact species coexistence per se but can reveal species response to high-dimensional environment, which is consistent with niche theory and the observation of the many differences between species in nature.

ecology↗

bioRxiv2020

gauseR: Simple methods for fitting Lotka-Volterra models describing Gause's "Struggle for Existence"

The ecological models of Alfred J. Lotka and Vito Volterra have had an enormous impact on ecology over the past century. Some of the earliest - and clearest - experimental tests of these models were famously conducted by Georgy Gause in the 1930s. Although well known, the data from these experiments are not widely available, and are often difficult to analyze using standard statistical and computational tools. Here, we introduce the gauseR package, a collection of tools for fitting Lotka-Volterra models to time series data of one or more species. The package includes several methods for parameter estimation and optimization, and includes 42 datasets from Gauses species interaction experiments and related work. Additionally, we include with this paper a short blog post discussing the historical importance of these data and models, and an R vignette with a walk-through introducing the package methods. The package is available for download at github.com/adamtclark/gauseR. To demonstrate the package, we apply it to several classic experimental studies from Gause, as well as two other well-known datasets on multi-trophic dynamics on Isle Royale, and in spatially structured mite populations. In almost all cases, models fit observations closely, and fitted parameter values make ecological sense. Taken together, we hope that the methods, data, and analyses that we present here provide a simple and user-friendly way to interact with complex ecological data. We are optimistic that these methods will be especially useful to students and educators who are studying ecological dynamics, as well as researchers who would like a fast tool for basic analyses.

ecology↗

bioRxiv2019

TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids

Telencephalic organoids generated from human pluripotent stem cells (hPSCs) are emerging as an effective system to study the distinct features of the developing human brain and the underlying causes of many neurological disorders. While progress in organoid technology has been steadily advancing, many challenges remain including rampant batch-to-batch and cell line-to-cell line variability and irreproducibility. Here, we demonstrate that a major contributor to successful cortical organoid production is the manner in which hPSCs are maintained prior to differentiation. Optimal results were achieved using fibroblast-feeder-supported hPSCs compared to feeder-independent cells, related to differences in their transcriptomic states. Feeder-supported hPSCs display elevated activation of diverse TGF{beta} superfamily signaling pathways and increased expression of genes associated with naive pluripotency. We further identify combinations of TGF{beta}-related growth factors that are necessary and together sufficient to impart broad telencephalic organoid competency to feeder-free hPSCs and enable reproducible formation of brain structures suitable for disease modeling. HIGHLIGHTSO_LIhPSC maintenance conditions influence outcomes in cortical organoid formation C_LIO_LIIdentification of an intermediate pluripotency state optimal for cortical organoids C_LIO_LIFeeder support involves activation of diverse TGF{beta} signaling pathways C_LIO_LIThe organoid-promoting effects of feeders can be mimicked by a TGF{beta} factor mixture C_LI

developmental biology↗

bioRxiv2017

Differentiation of primate primordial germ cell-like cells following transplantation into the adult gonadal niche

A major challenge in stem cell differentiation validation is the availability of bioassays to prove cell types generated in vitro are equivalent to cells in vivo. In the mouse model, differentiation of primordial germ cell-like cells (PGCLCs) from pluripotent cells was validated by transplantation, leading to the generation of spermatogenesis and to the birth of offspring. Here we report the use of xenotransplantation (monkey to mouse) and homologous transplantation (monkey to monkey) to validate our in vitro protocol for differentiating male rhesus macaque PGCLCs (rPGCLCs) from rhesus macaque induced pluripotent stem cells (riPSCs). Specifically, transplantation of aggregates containing rPGCLCs into mouse and nonhuman primate testicles overcomes a major bottleneck in rPGCLC differentiation with the expression of VASA and MAGEA4, but not ENO2. These findings suggest that immature rPGCLCs once transplanted into an adult gonadal niche commit to differentiate towards late PGCs and spermatogonia-like cells but do not complete the conversion into ENO2-positive spermatogonia.

developmental biology↗