Biology subjects

Edwards, C.

Publications and source records attributed to Edwards, C..

18 recordsLinked to original sources

bioRxiv2026

Scalable spatial DNA sequencing from archival tissue maps copy number subclones

Spatially resolved DNA sequencing holds promise due to its potential utility in understanding cancer intra-tumour heterogeneity and tumour evolution in relation to tissue architecture. However, it has so far been used to a limited extent due to technical challenges and high cost of existing methods. Hence we aimed to develop a high throughput spatial genomic assay to obtain copy number alteration (CNA) information at user-defined spatial resolution. We derived CNA profiles from ultra-low coverage whole genome sequencing at sub-millimetre resolution from archival samples using a novel method called Adaptive Resolution Multiscale Spatial DNA sequencing (ARMS DNAseq). We used it to profile CNAs from more than 766 regions (tiles) from 3 patients, covering a total area of over 300 mm2, with 1.2-2.6 million mapped reads per tile and tile sizes of 0.1-0.99mm2. Using ARMS DNAseq, we delineate tumour evolution in a spatial context, and identify more tumour subclones that were obscured or incompletely represented in bulk multi-region whole genome sequencing. Next, we show associations between tumour subclones and morphology, and prediction of subclone identity from deep learning-derived image representations. Finally, we demonstrate multi-omic integration by alignment with spatial transcriptomic data, showing subclone-specific immune cell co-occurrence as well as transcriptional programmes cutting across subclone boundaries. ARMS DNAseq converts low-throughput, region-by-region profiling into a scalable and adaptable workflow for direct spatial copy number profiling from archival tissue sections.

genomics↗

bioRxiv2026

Large phenological advances and delays over 124 years of climate change alter co-flowering among North American Viola

Shifts in flowering phenology are one of the most well studied plant responses to global climate change. Many studies have documented these shifts and their drivers, including some that describe altered patterns of co-flowering among taxonomically diverse species within communities. In comparison, few analyses have examined systematic changes in co-flowering between closely related, interfertile species, where co-flowering can have unique evolutionary consequences. To address such shifts in co-flowering among close relatives, we investigate phenological responses to climate change and its effect on patterns of co-flowering over the past 124 years in 52 species of North America violets (Viola). This genus has many co-occurring species that reproductively interact via shared pollinators and hybridization. We use [~]14,000 herbarium records along with environmental and species trait data to model the magnitude of recent flowering phenology shifts, environmental variables and/or species traits associated with these shifts, and resulting changes in co-flowering among species. While both the magnitude and direction of phenological shifts varied among Viola species, nearly half (25/52) show significant changes in flowering day. Regardless of whether flowering was advanced or delayed, flowering date was most consistently associated with local mean temperature. Of six species-level traits, geographical region also significantly predicted flowering shifts, consistent with environment and geography together explaining broad phenological responses across this group. These shifts have produced significant changes to pairwise patterns of co-flowering among species--ranging from a 59 day increase in co-flowering to complete loss of co-flowering overlap. Sympatric pairs specifically have experienced both increases and decreases in co-flowering, within a significant geographic pattern of increased co-flowering mainly in eastern US and decreased co-flowering common in western US. Because Viola species are generalist pollinated and already known to hybridize, these new co-flowering patterns could further undermine reproductive barriers among species in this genus.

evolutionary biology↗

bioRxiv2026

Epithelial function of the circadian clock gene, Bmal1, in regulating the mucosa.

Circadian rhythms, 24-hour repeating oscillations in daily physiology, are implicated in maintaining intestinal homeostasis. These rhythms are driven by the circadian clock, a molecular timekeeper found throughout cells of the body, including those of the intestinal epithelium. Loss of clock function has been found to worsen colitis; however, it is not clear how the clock impacts regeneration which enables a tissue to return to its homeostatic set point following an injury. To investigate these questions, we used a conditional knockout of the core clock gene, Bmal1, in mouse colon epithelial cells. Our data show that prior to injury Bmal1 promotes colon mucus production, which increases in thickness and within goblet cells when mice are active and begin feeding. Bmal1 loss lowers mucus production but does not drive an apparent tissue phenotype until the system is injured and regenerates itself. In this context, Bmal1 epithelial loss drives a male-specific colitis phenotype and a delay in the ability of colon epithelial cells of both male and female mice to resolve injury to return to their homeostatic set point. Our data suggest that epithelial sex-specific clock rhythms are needed for optimal colon barrier homeostasis.

physiology↗

bioRxiv2025

Non-human primate LIBRA-Seq accelerates neutralizing antibody discovery in RM vaccinated against HIV-1

Broadly neutralizing antibodies (bNAbs) exhibit protective efficacy against HIV-1 infection making them an ideal archetype for HIV-1 vaccine design. Presently, no vaccine candidate has induced antibody responses capable of meaningful protection against the swathe of circulating, difficult to neutralize tier 2 HIV-1 viruses. However, the development of stabilized, native-like envelope (Env) trimers such as BG505.SOSIP.664.T332N (BG505 SOSIP) has marked a significant advancement in vaccine design, due to their ability to elicit NAbs that neutralize tier 2 viruses in rhesus macaques (RM). NAb development following envelope trimer immunization in RM remains poorly understood, with hypothesized contributions from genetic variation at the IG loci, naive B cell repertoire, and differential gene expression in B cell lineages. To address these knowledge gaps, we have developed a set of BG505 SOSIP probes capable of recovering paired clonotype identity, antigen specificity, and gene expression of B cells in a high throughput fashion. These probes were constructed by conjugating biotinylated BG505 SOSIP to streptavidin covalently linked to both sc-RNA-Seq compatible DNA oligonucleotides and flow cytometry compatible fluorophores. Using these reagents, we isolated and sequenced BG505 SOSIP specific memory B cells from the PBMCs of an RM that developed high titers of neutralizing antibodies. To benchmark the accuracy of our technology, we compared our recovered heavy and light chain sequences to those identified from the same animal using conventional methodology and recovered 100% of previously identified NAbs. We then applied this technology to recover BG505 SOSIP specific memory B cells from five additional vaccinated RMs, cloned 34 antibodies for functional characterization, and identified ten antibodies with autologous neutralizing activity. Author SummaryUnderstanding how effective antibodies arise after HIV vaccination is essential for developing a protective vaccine, yet studying these responses in non-human primates has been limited by low- throughput methods. In this study, we adapted a high-throughput single-cell sequencing approach to identify HIV envelope-specific antibodies from vaccinated rhesus macaques. This method allowed us to recover paired antibody sequences together with their antigen specificity from thousands of individual B cells. We successfully identified known neutralizing antibodies and discovered additional antibodies capable of neutralizing HIV across multiple animals. Our analysis revealed that vaccine-elicited antibody responses were dominated by a small number of expanded lineages, with shared genetic features among animals with stronger neutralization. These findings demonstrate that this approach can efficiently define the antibody repertoires generated by HIV vaccines and provide a powerful tool for evaluating and improving immunogens in preclinical vaccine studies.

immunology↗

bioRxiv2024

Genomic insights into red squirrels in Scotland reveals loss of heterozygosity associated with extreme founder effects

Remnant populations of endangered species often have complex demographic histories associated with human impact. This can present challenges for conservation as the genetic status of these populations are often a-typical of natural populations, and may require bespoke management. The Eurasian red squirrel, Sciurus vulgaris (L., 1758), is endangered in the UK. Scotland represents a key stronghold, but Scottish populations have been subjected to intense anthropogenic influence, including wide-spread extirpations, reintroductions and competition from an invasive species. This study examined the genetic legacy of these events through whole genome resequencing of 106 red squirrels. Using SNP and genotype likelihood datasets, previously undetected population structure and patterns of gene-flow were uncovered. One off-shore island, three mainland Scottish populations, and a key east-coast migration corridor were observed. An abrupt historical population bottleneck related to extreme founder effects has led to a severe and prolonged depression in genome-wide heterozygosity, which is amongst the lowest reported for any species. Current designated red squirrel conservation stronghold locations do not encompass all existing diversity. These findings highlight the genetic legacies of past anthropogenic influence on long-term diversity in endangered taxa. Continuing management interventions and regular genetic monitoring are recommended to safeguard and improve future diversity.

genomics↗

bioRxiv2024

Onco-Circuit Addiction and Onco-Nutrient mTORC1 Signaling Vulnerability in a Model of Aggressive T Cell Malignancy

How genetic lesions drive cell transformation and whether they can be circumvented without compromising function of non-transformed cells are enduring questions in oncology. Here we show that in mature T cells--in which physiologic clonal proliferation is a cardinal feature-- constitutive MYC transcription and Tsc1 loss in mice modeled aggressive human malignancy by reinforcing each others oncogenic programs. This cooperation was supported by MYC-induced large neutral amino acid transporter chaperone SLC3A2 and dietary leucine, which in synergy with Tsc1 deletion overstimulated mTORC1 to promote mitochondrial fitness and MYC protein overexpression in a positive feedback circuit. A low leucine diet was therapeutic even in late-stage disease but did not hinder T cell immunity to infectious challenge, nor impede T cell transformation driven by constitutive nutrient mTORC1 signaling via Depdc5 loss. Thus, mTORC1 signaling hypersensitivity to leucine as an onco-nutrient enables an onco-circuit, decoupling pathologic from physiologic utilization of nutrient acquisition pathways.

cancer biology↗

bioRxiv2024

Prolonged airway explant culture enables study of health, disease, and viral pathogenesis

In vitro models play a major role in studying airway physiology and disease. However, the native lungs complex tissue architecture and non-epithelial cell lineages are not preserved in these models. Ex vivo tissue models could overcome in vitro limitations, but methods for long-term maintenance of ex vivo tissue has not been established. We describe methods to culture human large airway explants, small airway explants, and precision-cut lung slices for at least 14 days. Human airway explants recapitulate genotype-specific electrophysiology, characteristic epithelial, endothelial, stromal and immune cell populations, and model viral infection after 14 days in culture. These methods also maintain mouse, rabbit, and pig tracheal explants. Notably, intact airway tissue can be cryopreserved, thawed, and used to generate explants with recovery of function 14 days post-thaw. These studies highlight the broad applications of airway tissue explants and their use as translational intermediates between in vitro and in vivo studies.

bioengineering↗

bioRxiv2023

Glucose-stimulated KIF5B-driven microtubule sliding organizes microtubule networks in pancreatic beta cells

In pancreatic islet {beta} cells, molecular motors use cytoskeletal polymers microtubules as tracks for intracellular transport of insulin secretory granules. The {beta}-cell microtubule network has a complex architecture and is non-directional, which provides insulin granules at the cell periphery for rapid secretion response, yet to avoid over-secretion and subsequent hypoglycemia. We have previously characterized a peripheral sub-membrane microtubule array, which is critical for the withdrawal of excessive insulin granules from the secretion sites. Microtubules in {beta} cells originate at the Golgi in the cell interior, and how the peripheral array is formed is unknown. Using real-time imaging and photo-kinetics approaches in clonal mouse pancreatic {beta} cells MIN6, we now demonstrate that kinesin KIF5B, a motor protein with a capacity to transport microtubules as cargos, slides existing microtubules to the cell periphery and aligns them to each other along the plasma membrane. Moreover, like many physiological {beta}-cell features, microtubule sliding is facilitated by a high glucose stimulus. These new data, together with our previous report that in high glucose sub-membrane MT array is destabilized to allow for robust secretion, indicate that MT sliding is another integral part of glucose-triggered microtubule remodeling, likely replacing destabilized peripheral microtubules to prevent their loss over time and {beta}-cell malfunction.

cell biology↗

bioRxiv2023

CViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets

We have developed CViewer, a java-based framework to consolidate, visualize, and explore enormous amount of information recovered from shotgun sequencing experiments. This information includes and integrates all levels of gene products, mRNA, protein, metabolites, as well as their interactions in a single platform. The software provides a single platform to give statistical inference, and employs algorithms, some borrowed from numerical ecology literature to allow exploratory as well as hypothesis driven analyses. The end product is a highly interactive toolkit with multiple document interface, that makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant hypotheses. As a proof-of-concept, we have used CViewer to explore two distinct metagenomics datasets: a dietary intervention study to understand Crohns disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean.

bioinformatics↗

bioRxiv2022

STING activation promotes autologous type I interferon-dependent development of type 1 regulatory T cells during malaria

The development of highly effective malaria vaccines and improving drug treatment protocols to boost anti-parasitic immunity is critical for malaria elimination. However, these efforts are hampered by parasite-specific immunoregulatory networks that are rapidly established following exposure to malaria parasites. Here, we identify stimulator of interferon genes (STING) as a critical mediator of type I interferon production by CD4+ T cells during blood-stage Plasmodium falciparum infection. STING activation by cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) stimulated IFNB gene transcription that promoted development of IL-10 and IFN{gamma} co-producing CD4+ T (type I regulatory; Tr1) cells. CD4+ T cell sensitivity to STING phosphorylation increased in healthy volunteers following P. falciparum infection, particularly in Tr1 cells. Finally, we found the JAK1/2 inhibitor ruxolitinib modulated this innate signalling axis in CD4+ T cells to increase parasite-specific Th1 and diminish Tr1 cell responses. These findings identify STING as a critical mediator of Tr1 cell development during malaria.

immunology↗

bioRxiv2022

Scanning ion-conductance microscopy for studying β-amyloid aggregate formation on living cell surface

Alzheimers disease (AD) is the most common form of dementia, a progressive neurological disorder characterized by short and long-term memory loss, including cognitive and functional impairment, which is refractory to current therapy. It is suggested that the aggregation of {beta}-amyloid (A{beta}) peptide on neuronal cell surface leads to various deviations of its vital function due to myriad pathways defined by internalization of calcium ions, apoptosis promotion, reduction of membrane potential, synaptic activity loss etc. These are associated with structural reorganizations and pathologies of the cell cytoskeleton mainly involving actin filaments and microtubules, and consequently - alterations of cell mechanical properties. Thus, the effect of amyloid oligomers on cells Youngs modulus has been observed in a variety of studies. However, the precise connection between the formation of amyloid aggregates on cell membranes and their effects on local mechanical properties of living cells is still unresolved. In this work, we have used correlative scanning ion-conductance microscopy (SICM) to study cell topography, Youngs modulus mapping and confocal imaging of A{beta} aggregates formation on living cell surfaces with subsequent assessment of the reactive oxygen species levels inside single cells using platinum nanoelectrodes. We showed that correlative SICM technique, in conjunction with topography mapping and confocal imaging, can be used for Patch-Clamp recordings from living cells with evidently formed FAM-labeled A{beta} aggregates on its surface. As we demonstrated, SICM can be successfully applied to studying cytotoxicity mechanisms of A{beta} aggregates on living cell surface.

cell biology↗

bioRxiv2021

Cell-extrinsic autophagy in mature adipocytes regulates anti-inflammatory response to intestinal tissue injury through lipid mobilization

Lipids play a major role in inflammatory diseases by altering inflammatory cell functions, through their use as energy substrates or as lipid mediators such as oxylipins. Autophagy, a lysosomal degradation pathway that limits inflammation, is known to impact on lipid availability, however whether this controls inflammation remains unexplored. We found that upon intestinal inflammation visceral adipocytes upregulate autophagy and that adipocyte-specific loss of the autophagy gene Atg7 exacerbates inflammation. While autophagy decreased lipolytic release of free fatty acids, loss of the major lipolytic enzyme Pnpla2/Atgl in adipocytes did not alter intestinal inflammation, ruling out free fatty acids as anti- inflammatory energy substrates. Instead, Atg7-deficient adipose tissues exhibited an altered oxylipin balance, driven through an NRF2-mediated upregulation of Ephx1. This was accompanied by a shift in adipose tissue macrophage polarization with reduced secretion of IL-10, leading to lower circulating levels of IL-10. These results suggest an underappreciated fat-gut crosstalk through an autophagy- dependent regulation of anti-inflammatory oxylipins, indicating a protective effect of adipose tissues for distant inflammation.

immunology↗

bioRxiv2021

The glycosphingolipid inhibitor eliglustat inhibits autophagy in osteoclasts to increase bone mass and reduce myeloma bone disease

Multiple myeloma (MM) is a fatal hematological malignancy, where the majority of patients are diagnosed with, or develop, destructive and debilitating osteolytic bone lesions. Current treatments for MM bone disease such as the bisphosphonate zoledronic acid can result in deleterious side effects at high doses. In this study, eliglustat, an FDA approved glycosphingolipid inhibitor, was shown to reduce MM bone disease in preclinical models of MM. Mechanistically, eliglustat alters the lipid composition and plasma membrane fluidity and acts as an autophagy flux inhibitor in bone-resorbing osteoclasts (OC). Autophagic degradation of the signaling molecule TRAF3 is key step in OC differentiation; this was prevented by eliglustat in OC precursors. In addition, eliglustat works depend on TRAF3 in vivo. Furthermore, the combination of eliglustat and zoledronic acid was found to have an additive effect to reduce MM bone disease, suggesting the potential for combination therapies that would allow for drug dose reductions. Taken together, this project identifies a novel mechanism in which glycosphingolipid inhibition reduces osteoclastogenesis via autophagy and highlights the translational potential of eliglustat for the treatment of bone loss disorders such as MM. One Sentence SummaryTranslational use of eliglustat as an autophagy inhibitor to limit bone lesions in multiple myeloma.

cell biology↗

bioRxiv2021

An increase in atypical petal numbers during a shift to autogamy in a coastal sand verbena and potential evolutionary mechanisms

PremiseIn plants, meristic traits, such as petal and sepal numbers, are usually considered invariant within taxa, yet certain species consistently exhibit great variability in these traits. The factors contributing to "atypical" counts are not well-known, published hypotheses include relaxation of pollinator selection, inbreeding, and hybridization, among others. The sand verbenas, Abronia (Nyctaginaceae), usually have five perianth lobes ( petals), yet certain taxa exhibit marked departures from this norm. MethodsHere we integrate an analysis of images from community science data (iNaturalist) and common garden experiments to evaluate a comprehensive set of adaptive and nonadaptive explanations for the production of these atypical flowers across an evolutionary transition from xenogamy (outcrossing) to autogamy (selfing) in the coastal sand verbena Abronia umbellata. Key resultsThe shift to autogamy in this lineage correlated with a higher frequency of atypical flowers from ~7% to ~20% and a significant reduction in mean petal number per inflorescence. Autogamous success did not change with petal number, and neither hybridization or up to three generations of inbreeding consistently increased production of atypical flowers or decreased mean petal number, all in contrast to previously-published hypotheses. In contrast, intra-inflorescence, inter-plant (intra-population), inter-population, and inter-variety comparisons demonstrated a correlation of reduced floral size with reduced petal number, suggesting correlated evolution due to a well-established relation between organ number and meristem size. ConclusionsThe reduction in petal number was probably a consequence of selection for smaller flowers associated with increased selfing. While we could not completely eliminate several alternative hypotheses, including a long-term history of inbreeding or relaxed selection on petal number constancy, those are less likely to explain the observed changes, though they may have contributed to the trend. In general, we develop a framework of hypotheses for evolutionary investigations of meristic variation in floral organs.

evolutionary biology↗

bioRxiv2019

Syndecan-1 facilitates breast cancer metastasis to the brain

PurposeAlthough survival rates for patients with localized breast cancer have increased, patients with metastatic breast cancer still have poor prognosis. Understanding key factors involved in promoting breast cancer metastasis is imperative for better treatments. In this study, we investigated the role of syndecan-1 (Sdc1) in breast cancer metastasis. MethodsTo assess the role of Sdc1 in breast cancer metastasis, we silenced Sdc1 expression in the triple-negative breast cancer human MDA-MB-231 cell line and overexpressed it in the mouse mammary carcinoma 4T1 cell line. Intracardiac injections were performed in an experimental mouse metastasis model using both cell lines. In vitro transwell blood-brain barrier (BBB) and brain section adhesion assays were utilized to specifically investigate how Sdc1 promotes brain metastasis. A cytokine array was performed to evaluate differences in the breast cancer cell secretome when Sdc1 was silenced. ResultsSilencing expression of Sdc1 in breast cancer cells significantly reduced metastasis to the brain. Conversely, overexpression of Sdc1 increased metastasis to the brain. We found that the reduction in brain metastases with Sdc1 knockdown was likely due to reduced breast cancer cell migration across the BBB and adhesion to the perivascular regions of the brain. However, there was no change in attachment to brain endothelial cells or astrocytes. Loss of Sdc1 also led to changes in breast cancer cell-secreted cytokines, which may influence the BBB. ConclusionsTaken together, our study demonstrates a role for Sdc1 in promoting breast cancer metastasis to the brain. These findings suggest that Sdc1 supports breast cancer cell migration across the BBB through regulation of cytokines, which may modulate the BBB. Further elucidating this mechanism will allow for the development of therapeutic strategies to combat brain metastasis.

cancer biology↗

bioRxiv2018

Intracellular mechanisms of fungal space searching in microenvironments

The underlying intracellular mechanisms involved in the fungal growth received considerable attention, but the experimental and theoretical work did not take into account the modulation of these processes by constraining microenvironments similar to many natural fungal habitats. To fill this gap in the scientific knowledge, we used time-lapse live-cell imaging of Neurospora crassa growth in custom-built confining microfluidics environments. We show that the position and dynamics of the Spitzenkorper-microtubules system in constraining environments differs markedly from that associated with unconstrained growth. First, when hyphae encounter an obstacle at shallow angles, the Spitzenkorper moves from its central position in the apical dome off-axis towards a contact with the obstacle, thus functioning as a compass preserving the directional memory of the initial growth. The trajectory of Spitzenkorper is also followed by microtubules, resulting in a cutting corners pattern of the cytoskeleton in constrained geometries. Second, when an obstacle blocks a hypha at nearnormal incidence, the Spitzenkorper-microtubule system temporarily disintegrates, followed by the formation of two equivalent systems in the proto-hyphae - the basis of obstacle-induced branching. Third, a hypha, passing a lateral opening along a wall, continues to grow largely unperturbed while a lateral proto-hypha gradually branches into the opening, which starts forming its own Spitzenkorper-microtubule system. These observations suggest that the Spitzenkorper-microtubules system conserves the directional memory of the hyphae when they navigate around obstacles, but in the absence of the Spitzenkorper-microtubule system during constrainment-induced apical splitting and lateral branching, the probable driving force of obstacle-induced branching is the isotropic turgor pressure.

cell biology↗

bioRxiv2018

Relevance of coral geometry in the outcomes of the coral-algal benthic war

Corals have built reefs on the benthos for millennia, becoming an essential element in marine ecosystems. Climate change and human impact, however, are favoring the invasion of non-calcifying benthic algae and reducing coral coverage. Corals rely on energy derived from photosynthesis and heterotrophic feeding, which depends on their surface area, to defend their outer perimeter. But the relation between geometric properties of corals and the outcome of competitive coral-algal interactions is not well known. To address this, 50 coral colonies interacting with algae were sampled in the Caribbean island of Curacao. 3D and 2D digital models of corals were reconstructed to measure their surface area, perimeter, and polyp sizes. A box counting algorithm was applied to calculate their fractal dimension. The perimeter and surface dimensions were statistically non-fractal, but differences in the mean surface fractal dimension captured relevant features in the structure of corals. The mean fractal dimension and surface area were negatively correlated with the percentage of losing perimeter and positively correlated with the percentage of winning perimeter. The combination of coral perimeter, mean surface fractal dimension, and coral species explained 19% of the variability of losing regions, while the surface area, perimeter, and perimeter-to-surface area ratio explained 27% of the variability of winning regions. Corals with surface fractal dimensions smaller than two and small perimeters displayed the highest percentage of losing perimeter, while corals with large surface areas and low perimeter-to-surface ratios displayed the largest percentage of winning perimeter. This study confirms the importance of fractal surface dimension, surface area, and perimeter of corals in coral-algal interactions. In combination with non-geometrical measurements such as microbial composition, this approach could facilitate environmental conservation and restoration efforts on coral reefs.

ecology↗

bioRxiv2018

Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments

Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae of Madagascar, and high altitude Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examine potential correlates between molecular evolution within this clade and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we presented detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and identified a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche and did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and while these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.

evolutionary biology↗