Biology subjects

Stephens, J.

Publications and source records attributed to Stephens, J..

9 recordsLinked to original sources

bioRxiv2025

Genomic and microbiome data support a hypothesis of hybrid speciation in endangered brown lemurs

The gut microbiome is shaped by host ecology and evolution, but the relative influences of each remain unresolved in natural hybrid zones where species boundaries are permeable. We investigated these dynamics using a hybrid zone formed between two species of brown lemur in southeastern Madagascar, Eulemur rufifrons and E. cinereiceps. These hybrids occupy a novel ecological niche and were previously proposed as a hybrid species, though this had never been tested with genome-wide data. Here, we combined low-coverage host genomes derived from fecal DNA with 16S rRNA gut microbiome profiles across a 180-kilometer transect. Population genomic analyses recovered two population clusters connected by a hybrid zone biased towards E. rufifrons ancestry. Though our data did not support a hypothesis of hybrid speciation, the hybrid zone was dominated by later-generation crosses. Hybrid microbiomes were compositionally intermediate between parental species, but more closely resembled E. rufifrons, mirroring patterns of genomic ancestry. Microbiome beta diversity was significantly correlated with host genomic distance after accounting for geography and ecology. In contrast, predicted microbial functional profiles were broadly conserved across host taxa. Together, these findings demonstrate that phylosymbiosis can emerge in the face of interspecific gene flow, providing new insight into host-microbiome dynamics during the early stages of speciation.

evolutionary biology↗

bioRxiv2025

The origins and adaptive consequences of polyploidy in a dominant prairie grass

Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hypotheses have been proposed including polyploid abundance is proportional to the opportunity for whole genome duplication (WGD), and WGD alters phenotypes that may increase fitness. We tested these two hypotheses together in the mixed-ploidy species Andropogon gerardi, a dominant grass species in endangered North American tallgrass prairies. Leveraging a novel, phased allopolyploid reference genome, we found the A. gerardi hexaploid arose after the C4 grassland expansion in the early Pleistocene, when glacial cycles likely increased secondary contact between the diploid progenitors. We sequenced A. gerardi from 25 popula-tions and examined cytotype performance and morphology in a controlled environment to investigate the consequences of the contemporary mixed-ploidy populations. We found the 9x A. gerardi cytotype is a neopolyploid and a result of recurrent WGD events. Further, we demonstrate the 9x neopolyploids have greater growth and a decreased stomatal pore index, which is adaptive in xeric climates where the 9x cy-totype is most common. Together, our results support both hypotheses for polyploid abundance in North America: WGD is a product of opportunity and can have immediate fitness consequences. Although the changes to fitness may provide an advantage to 9x A. gerardi, the establishment of 9x may lower overall population fitness due to the lower reproductive viability of 9x individuals. Significance statementPolyploid species are abundant in North American prairies and make up many of the dominant species in the ecosystem. This prominence could be a result of whole genome duplication conferring an advantage that increases the frequency of polyploids or could simply indicate that the opportunity for whole genome duplication is higher in this ecosystem, or both. Through examining three polyploidization events in A. gerardi, the dominant species in endangered tallgrass North American prairies, we found whole genome duplication is both surprisingly common and confers traits that are beneficial in some environments.

plant biology↗

bioRxiv2023

Evaluation of resampling-based inference for topological features of neuroimages

Many recent studies have demonstrated the inflated type 1 error rate of the original Gaussian random field (GRF) methods for inference of neuroimages and identified resampling (permutation and bootstrapping) methods that have better performance. There has been no evaluation of resampling procedures when using robust (sandwich) statistical images with different topological features (TF) used for neuroimaging inference. Here, we consider estimation of distributions TFs of a statistical image and evaluate resampling procedures that can be used when exchangeability is violated. We compare the methods using realistic simulations and study sex differences in life-span age-related changes in gray matter volume in the Nathan Kline Institute Rockland sample. We find that our proposed wild bootstrap and the commonly used permutation procedure perform well in sample sizes above 50 under realistic simulations with heteroskedasticity. The Rademacher wild bootstrap has fewer assumptions than the permutation and performs similarly in samples of 100 or more, so is valid in a broader range of conditions. We also evaluate the GRF-based pTFCE method and show that it has inflated error rates in samples less than 200. Our R package, pbj, is available on Github and allows the user to reproducibly implement various resampling-based group level neuroimage analyses.

neuroscience↗

bioRxiv2020

Long-read sequencing resolves structural variants in SERPINC1 causing antithrombin deficiency and identifies a complex rearrangement and a retrotransposon insertion not characterized by routine diagnostic methods

The identification and characterization of structural variants (SVs) in clinical genetics have remained historically challenging as routine genetic diagnostic techniques have limited ability to evaluate repetitive regions and SVs. Long-read whole-genome sequencing (LR-WGS) has emerged as a powerful approach to resolve SVs. Here, we used LR-WGS to study 19 unrelated cases with type I Antithrombin Deficiency (ATD), the most severe thrombophilia, where routine molecular tests were either negative, ambiguous, or not fully characterized. We developed an analysis workflow to identify disease-associated SVs and resolved 10 cases. For the first time, we identified a germline complex rearrangement involved in ATD previously misclassified as a deletion. Additionally, we provided molecular diagnoses for two unresolved individuals that harbored a novel SINE-VNTR-Alu retroelement insertion that we fully characterized by de novo assembly and confirmed by PCR amplification in all affected relatives. Finally, the nucleotide-level resolution achieved for all the SVs allowed breakpoint analysis, which revealed a replication-based mechanism for most of the cases. Our study underscores the utility of LR-WGS as a complementary diagnostic method to identify, characterize, and unveil the molecular mechanism of formation of disease-causing SVs, and facilitates decision making about long-term thromboprophylaxis in ATD patients.

genomics↗

bioRxiv2020

Targeted mutation of barley (1,3;1,4)-β-glucan synthases reveals complex relationships between the storage and cell wall polysaccharide content

Barley (Hordeum vulgare L) grain is comparatively rich in (1,3;1,4)-{beta}-glucan, a source of fermentable dietary fibre that protects against various human health conditions. However, low grain (1,3;1,4)-{beta}-glucan content is preferred for brewing and distilling. We took a reverse genetics approach, using CRISPR/Cas9 to generate mutations in members of the Cellulose synthase-like (Csl) gene superfamily that encode known (HvCslF6 and HvCslH1) and putative (HvCslF3 and HvCslF9) (1,3;1,4)-{beta}-glucan synthases. Resultant mutations ranged from single amino acid (aa) substitutions to frameshift mutations causing premature stop codons, and led to specific differences in grain morphology, composition and (1,3;1,4)-{beta}-glucan content. (1,3;1,4)-{beta}-Glucan was absent in the grain of cslf6 knock-out lines whereas cslf9 knock-out lines had similar (1,3;1,4)-{beta}-glucan content to WT. However, cslf9 mutants showed changes in the abundance of other cell wall-related monosaccharides compared to WT. Thousand grain weight (TGW), grain length, width and surface area were altered in cslf6 knock-outs and to a lesser extent TGW in cslf9 knock-outs. cslf3 and cslh1 mutants had no effect on grain (1,3;1,4)-{beta}-glucan content. Our data indicate that multiple members of the CslF/H family fulfil important functions during grain development but, with the exception of HvCslF6, do not impact the abundance of (1,3;1,4)-{beta}-glucan in mature grain.

plant biology↗

bioRxiv2019

A cereal aphid effector promotes barley susceptibility in a species-specific manner through suppression of defence gene expression.

Aphids secrete diverse repertoires of effectors into their hosts to promote the infestation process. While \"omics\"-approaches facilitated the identification and comparison of effector repertoires from a number of aphid species, the functional characterization of these proteins has been limited to dicot (model) plants. The bird cherry-oat aphid Rhopalosiphum padi is a pest of cereal crops, including barley. Here, we extended efforts to characterize aphid effectors with regards to their role in promoting susceptibility to the R. padi-barley interaction. We selected 3 R. padi effectors based on sequences similarity to previously characterized M. persicae effectors and assessed their subcellular localisation, expression, and role in promoting plant susceptibility. Expression of R. padi effectors RpC002 and Rp1 in transgenic barley lines enhanced plant susceptibility to R. padi but not M. persicae, for which barley is a poor host. Characterization of Rp1 transgenic barley lines revealed reduced gene expression of plant hormone signalling genes relevant to plant-aphid interactions, indicating this effector enhances susceptibility by suppressing plant defences in barley. Our data suggests that some aphid effectors specifically function when expressed in host species, and feature activities that benefit their corresponding aphid species.

plant biology↗

bioRxiv2018

Whole Genome Sequencing of Primary Immunodeficiency reveals a role for common and rare variants in coding and non-coding sequences

Primary immunodeficiency (PID) is characterised by recurrent and often life-threatening infections, autoimmunity and cancer, and it presents major diagnostic and therapeutic challenges. Although the most severe forms present in early childhood, the majority of patients present in adulthood, typically with no apparent family history and a variable clinical phenotype of widespread immune dysregulation: about 25% of patients have autoimmune disease, allergy is prevalent, and up to 10% develop lymphoid malignancies1-3. Consequently, in sporadic PID genetic diagnosis is difficult and the role of genetics is not well defined. We addressed these challenges by performing whole genome sequencing (WGS) of a large PID cohort of 1,318 participants. Analysis of coding regions of 886 index cases found disease-causing mutations in known monogenic PID genes in 10.3%, while a Bayesian approach (BeviMed4) identified multiple potential new candidate genes, including IVNS1ABP. Exploration of the non-coding genome revealed deletions in regulatory regions which contribute to disease causation. Finally, a genome-wide association study (GWAS) identified PID-associated loci and uncovered evidence for co-localisation of, and interplay between, novel high penetrance monogenic variants and common variants (at the PTPN2 and SOCS1 loci). This begins to explain the contribution of common variants to variable penetrance and phenotypic complexity in PID. Thus, a cohort-based WGS approach to PID diagnosis can increase diagnostic yield while deepening our understanding of the key pathways influencing human immune responsiveness.

immunology↗

bioRxiv2018

Diagnostic high-throughput sequencing of 2,390 patients with bleeding, thrombotic and platelet disorders

A targeted high-throughput sequencing (HTS) panel test for clinical diagnostics requires careful consideration of the inclusion of appropriate diagnostic-grade genes, the ability to detect multiple types of genomic variation with high levels of analytic sensitivity and reproducibility, and variant interpretation by a multi-disciplinary team (MDT) in the context of the clinical phenotype. We have sequenced 2,390 index patients using the ThromboGenomics HTS panel test of diagnostic-grade genes known to harbour variants associated with rare bleeding, thrombotic or platelet disorders (BPD). The diagnostic rate was determined by the clinical phenotype, with an overall rate of 50.4% for all thrombotic, coagulation, platelet count and function disorder patients and a rate of 6.2% for patients with unexplained bleeding disorders characterized by normal hemostasis test results. The MDT classified 756 unique variants, including copy number and intronic variants, as Pathogenic, Likely Pathogenic or Variants of Uncertain Significance. Almost half (49.7%) of these variants are novel and 41 unique variants were identified in 7 genes recently found to be implicated in BPD. Inspection of canonical hemostasis pathways identified 29 patients with evidence of oligogenic inheritance. A molecular diagnosis has been reported for 897 index patients providing evidence that introducing a HTS genetic test for BPD patients is meeting an important unmet clinical need.\n\nKey pointsO_LIHigh-throughput sequencing (HTS) test reveals a molecular diagnosis for 38% of 2,390 patients with bleeding, thrombotic and platelet disorders.\nC_LIO_LIThromboGenomics HTS test validates recent gene discoveries and detects copy number and intronic variants.\nC_LI

genetics↗

bioRxiv2018

Complex Structural Variants Resolved by Short-Read and Long-Read Whole Genome Sequencing in Mendelian Disorders

Complex structural variants (cxSVs) are genomic rearrangements comprising multiple structural variants, typically involving three or more breakpoint junctions. They contribute to human genomic variation and can cause Mendelian disease, however they are not typically considered during genetic testing. Here, we investigate the role of cxSVs in Mendelian disease using short-read whole genome sequencing (WGS) data from 1,324 individuals with neurodevelopmental or retinal disorders from the NIHR BioResource project. We present four cases of individuals with a cxSV affecting Mendelian disease-associated genes. Three of the cxSVs are pathogenic: a de novo duplication-inversion-inversion-deletion affecting ARID1B in an individual with Coffin-Siris syndrome, a deletion-inversion-duplication affecting HNRNPU in an individual with intellectual disability and seizures, and a homozygous deletion-inversion-deletion affecting CEP78 in an individual with cone-rod dystrophy. Additionally, we identified a de novo duplication-inversion-duplication overlapping CDKL5 in an individual with neonatal hypoxic-ischaemic encephalopathy. Long-read sequencing technology used to resolve the breakpoints demonstrated the presence of both a disrupted and an intact copy of CDKL5 on the same allele; therefore, it was classified as a variant of uncertain significance. Analysis of sequence flanking all breakpoint junctions in all the cxSVs revealed both microhomology and longer repetitive sequences, suggesting both replication and homology based processes. Accurate resolution of cxSVs is essential for clinical interpretation, and here we demonstrate that long-read WGS is a powerful technology by which to achieve this. Our results show cxSVs are an important although rare cause of Mendelian disease, and we therefore recommend their consideration during research and clinical investigations.

genomics↗