Biology subjects

Graham, M. R.

Publications and source records attributed to Graham, M. R..

6 recordsLinked to original sources

bioRxiv2026

Comparative genomics of the unusual arachnid order Solifugae spotlight the molecular and genetic basis for adaptations to arid habitats

The evolutionary transition to terrestrial life required overcoming several physiological hurdles; however, such challenges were amplified in desert environments. While several xeric-adapted arachnids utilize permanent burrows or "sit-and-wait" foraging strategies as possible energy conservation adaptations in harsh habitats, camel spiders exhibit a counterintuitive, high-energy lifestyle. To investigate the molecular underpinnings distinguishing Solifugae within Chelicerata, we utilized a comparative genomics framework that incorporates a newly sequenced, previously unpublished solifuge genome. We identified lineage-specific expanded orthogroups and evaluated selective pressures acting upon paralogous sequences within our ingroup solifuge species. Additionally, we also focused on fatty acid-associated proteins and heat shock proteins to elucidate how Solifugae may have evolved such anomalous behaviors compared to their arachnid relatives. Our analyses revealed significant signatures of positive selection within key gene families across the solifuge lineage. Notably, paralogs within the cytochrome P450 and biotinidase families showed consistent evidence of selection across all three taxa, suggesting specialized metabolic or detoxification requirements. Furthermore, we identified candidate loci implicated in axonal guidance and lipid metabolism, and a specialized fatty acid enzyme repertoire. While subsequent research is required to determine whether some of the genomic signatures unveiled here are shared across a broader phylogenetic distribution within Solifugae, we establish a critical baseline for future functional validation.

evolutionary biology↗

bioRxiv2025

Microbiota discovered in scorpion venom

With low nutrient availability and presence of numerous antimicrobial peptides, animal venoms have been traditionally considered to be harsh sterile environments that lack bacteria. Contrary to this assumption, recent studies of animal venom and venom-producing tissues have revealed the presence of diverse microbial communities, warranting further studies of potential microbiota in other venomous animals. In this study we used 16S rRNA amplicon sequencing to elucidate whether scorpion venom contained bacteria, to characterize the bacterial communities, and determine if venom microbiomes differed across geologically complex geographic locations. Our study compares the venom microbiome of two scorpion species, sampled from sites between the Mojave and Great Basin deserts, Paruoctonus becki (family of Vaejovidae) and Anuroctonus phaiodactylus (family of Anuroctonidae), and represents the first assessment of microbial diversity ever conducted using the venom secretion itself, rather than the venom-producing organ and its surrounding tissues.

microbiology↗

bioRxiv2024

Unveiling the genetic blueprint of a desert scorpion: A chromosome-level genome of Hadrurus arizonensis provides the first reference for Parvorder Iurida

Over 400 million years old, scorpions represent an ancient group of arachnids and one of the first animals to adapt to life on land. Presently, the lack of available genomes within scorpions hinders research on their evolution. This study leverages ultra-long nanopore sequencing and Pore-C to generate the first chromosome level assembly and annotation for the desert hairy scorpion, Hadrurus arizonensis. The assembled genome is 2.23 Gb in size with an N50 of 280 Mb. Pore-C scaffolding re-oriented 99.6% of bases into nine chromosomes and BUSCO identified 998 (98.6%) complete arthropod single copy orthologs. Repetitive elements represent 54.69% of the assembled bases, including 872,874 (29.39%) LINE elements. A total of 18,996 protein-coding genes and 75,256 transcripts were predicted, and extracted protein sequences yielded a BUSCO score of 97.2%. This is the first genome assembled and annotated within the family Hadruridae, representing a crucial resource for closing gaps in genomic knowledge of scorpions, resolving arachnid phylogeny, and advancing studies in comparative and functional genomics. SignificanceGenomic resources for the study of arachnids are limited. To date, only four scorpion genomes have been published; none of these are chromosome-level assemblies, and all four belong to a single family, Buthidae. In this study, we assembled the first chromosome-level, annotated genome for a non-buthid species (Hadrurus arizonensis). This high quality reference will provide a critical resource for comparative and functional genomics and contribute to the understanding of arachnid evolution.

genomics↗

bioRxiv2022

Neglected no longer: Phylogenomic resolution of higher-level relationships in Solifugae

Considerable progress has been achieved in resolving higher-level relationships of Arthropoda in the past two decades, largely precipitated by advances in sequencing technology. Yet, dark branches persist in the arthropod tree of life, principally among groups that are difficult to collect, occur in cryptic habitats, or are characterized by minute body size. Among chelicerates, the mesodiverse order Solifugae (commonly called camel spiders or sun spiders) is one of the last orders of Arachnida that lacks a higher-level phylogeny altogether and has long been characterized as one of the "neglected cousins", a lineage of arachnid orders that are comparatively poorly studied with respect to evolutionary relationships. Though renowned for their aggression, remarkable running speed, and adaptation to arid habitats, inferring solifuge relationships has been hindered by inaccessibility of diagnostic characters in most ontogenetic stages for morphological datasets, whereas molecular investigations to date have been limited to one of the 12 recognized families. In this study we generated a phylogenomic dataset via capture of ultraconserved elements (UCEs) and sampled all extant families. We recovered a well-resolved phylogeny of solifuge families, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. To provide a temporal context to solifuge diversification, we estimated molecular divergence times using fossil calibrations within a least-squares framework. Solifugae were inferred to have radiated by the Permian, with divergences of most families dating to the post Paleogene-Cretaceous extinction. These results accord with a diversification history largely driven by vicariance as a result of continental breakup.

evolutionary biology↗

bioRxiv2019

Brain BOLD MRI O2 and CO2 stress testing: Implications for perioperative neurocognitive disorder following surgery

Respiratory end-tidal (ET) gas control is fundamental to anaesthetic management. The range of ET O2 and CO2 during the conduct of anaesthesia can significantly deviate from values in the awake state. Recent work shows ET CO2 influences the incidence of perioperative neurocognitive disorder (POND). We examine the effects of controlled alterations in both ET O2 and CO2 on cerebral blood flow (CBF) in awake adults using BOLD MRI. Twelve healthy adults had BOLD and CBF responses measured to alterations in ET CO2 and O2 in various combinations commonly observed under anaesthesia. Dynamic alterations in regional BOLD and CBF were seen in all subjects with expected and inverse responses to both stimuli. These effects were incremental and rapid (within seconds). The most dramatic effects were seen with combined hyperoxia and hypocapnia. Inverse responses increased with age. Here we show that human brain CBF responds dramatically to alterations in ET respiratory gas tensions commonly seen during anaesthesia. Such alterations may impact the observed incidence of POND following surgery and intensive care, and is an important area for further investigation.

neuroscience↗

bioRxiv2018

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

Whole genome sequencing (WGS) is a powerful tool for public health infectious disease investigations owing to its higher resolution, greater efficiency, and cost-effectiveness over traditional genotyping methods. Implementation of WGS in routine public health microbiology laboratories is impeded by a lack of user-friendly automated and semi-automated pipelines, restrictive jurisdictional data sharing policies, and the proliferation of non-interoperable analytical and reporting systems. To address these issues, we developed the Integrated Rapid Infectious Disease Analysis (IRIDA) platform (irida.ca), a user-friendly, decentralized, open-source bioinformatics and analytical web platform to support real-time infectious disease outbreak investigations using WGS data. Instances can be independently installed on local high-performance computing infrastructure, enabling private and secure data management and analyses according to organizational policies and governance. IRIDAs data management capabilities enable secure upload, storage and sharing of all WGS data and metadata. The core platform currently includes pipelines for quality control, assembly, annotation, variant detection, phylogenetic analysis, in silico serotyping, multi-locus sequence typing, and genome distance calculation. Analysis pipeline results can be visualized within the platform through dynamic line lists and integrated phylogenomic clustering for research and discovery, and for enhancing decision-making support and hypothesis generation in epidemiological investigations. Communication and data exchange between instances are provided through customizable access controls. IRIDA complements centralized systems, empowering local analytics and visualizations for genomics-based microbial pathogen investigations. IRIDA is currently transforming the Canadian public health ecosystem and is freely available at https://github.com/phac-nml/irida and www.irida.ca.\n\nImpact StatementWhole genome sequencing (WGS) is revolutionizing infectious disease analysis and surveillance due to its cost effectiveness, utility, and improved analytical power. To date, no \"one-size-fits-all\" genomics platform has been universally adopted, owing to differences in national (and regional) health information systems, data sharing policies, computational infrastructures, lack of interoperability and prohibitive costs. The Integrated Rapid Infectious Disease Analysis (IRIDA) platform is a user-friendly, decentralized, open-source bioinformatics and analytical web platform developed to support real-time infectious disease outbreak investigations using WGS data. IRIDA empowers public health, regulatory and clinical microbiology laboratory personnel to better incorporate WGS technology into routine operations by shielding them from the computational and analytical complexities of big data genomics. IRIDA is now routinely used as part of a validated suite of tools to support outbreak investigations in Canada. While IRIDA was designed to serve the needs of the Canadian public health system, it is generally applicable to any public health and multi-jurisdictional environment. IRIDA enables localized analyses but provides mechanisms and standard outputs to enable data sharing. This approach can help overcome pervasive challenges in real-time global infectious disease surveillance, investigation and control, resulting in faster responses, and ultimately, better public health outcomes.\n\nDATA SUMMARYO_LIData used to generate some of the figures in this manuscript can be found in the NCBI BioProject PRJNA305824.\nC_LI

bioinformatics↗