Biology subjects

Thom, G.

Publications and source records attributed to Thom, G..

12 recordsLinked to original sources

bioRxiv2026

Incipient speciation, rapid expansion and repeated introgressive hybridization in an African Giant Shrew (Crocidura olivieri)

The African giant shrew (Crocidura olivieri) is one of the most widespread native small mammals in sub-Saharan Africa, occupying habitats ranging from humid tropical forests to arid Savanna. Its broad distribution, ecological diversity, and unresolved evolutionary relationships suggest a history of rapid diversification, yet the roles of hybridization and demographic expansion remain poorly understood. We combined genome-wide ddRAD and mitochondrial data from populations sampled across sub-Saharan Africa to reconstruct the evolutionary history of African giant shrews. We reveal extensive mitonuclear discordance across the clade and show that it reflects a complex history of repeated introgressive hybridization rather than a single evolutionary event. Genomic analyses resolve three major evolutionary lineages and identify four introgression events, including extensive bidirectional genome-wide introgression between the ancestors of the C. olivieri and arid adapted species followed by later unidirectional introgression associated with range expansion. Within the C. olivieri group, we identify five geographically structured lineages connected by ongoing gene flow, representing different stages of incipient speciation. Demographic analyses further reveal repeated population expansion during the Late Pleistocene and Early Holocene, with lineage-specific timing consistent with climatic fluctuations and a possible contribution of increasing human association. Our results identify repeated range expansion and hybridization as major drivers of diversification in African giant shrews and establish this system as a powerful model for studying the genomic processes underlying early speciation.

evolutionary biology↗

bioRxiv2025

Artemis Regulates Homology-Independent Prime Editing (PRINS) for Enhanced Genomic Insertions

Nuclease-based prime editing (PEn) offers enhanced genomic insertion efficiency compared to nickase-based prime editors, but its reliance on double-strand break (DSB) repair leads to complex and often unpredictable on-target indel distributions. PRINS editing, a PEn variant utilizing springRNAs, uniquely relies on non-homologous end joining (NHEJ) for insertions, providing an insertion-only strategy ideal for functional protein tagging or serine integrase landing pad insertions, yet it suffers from inherent imprecision. Here, we identify the DNA repair factor Artemis (DCLRE1C) as a key regulator of PEn-generated indel profiles, particularly in springRNA-mediated PRINS editing. Through a targeted genetic screen, we show that the absence of Artemis significantly shifts indel distributions away from deletions and shorter truncations towards longer, functionally acceptable insertions. Our data indicates that Artemis cleaves PEn-generated 3-overhangs in a length-dependent manner, with its impact increasing for longer reverse-transcribed overhangs. This understanding reveals that regulating Artemis activity can improve insertion frequency specifically for PRINS. We develop and validate robust epigenetic (CRISPRoff) and antisense oligonucleotide (ASO) strategies to effectively silence/knockdown Artemis expression, successfully recapitulating the beneficial PRINS editing outcomes observed in Artemis-deficient cells. Leveraging these insights, we show that Artemis modulation can enhance endogenous protein tagging in cells, including challenging hiPSC-derived non-dividing cardiomyocytes. Our findings support Artemis as a key regulator of PRINS editing outcomes and present a tunable strategy to optimize insertion efficiency for diverse genomic engineering and therapeutic applications.

molecular biology↗

bioRxiv2025

The genomic landscape of asymmetric introgression tracks chromosomal characteristics in tinamous (Aves: Tinamidae)

We use single genomes from seven tinamou species (Palaeognathae: Tinamidae) and apply a genome-architecture-aware phylogenomic approach to (1) quantify the landscape of introgression, (2) discriminate among conflicting genealogical signals in the genome, and (3) reconstruct evolutionary history. Using summary statistics and full likelihood, we detect pervasive asymmetric introgression between two sympatric Amazonian species clouding phylogenetic relationships in this group. However, these introgression results are sensitive to the assumed species tree. When assuming the Z-chromosome phylogeny as the species tree, the landscape of introgression is non-random; introgression is negatively associated with chromosome length, elevated at macrochromosome ends, and near zero for the Z-chromosome (the avian sex chromosome). A pseudo-autosomal region on the Z-chromosome, which recombines homologously with that of the W-chromosome, shows elevated introgression comparable to that of autosomes. Our results resolve the species tree of tinamous and imply a history of linked selection purging migrant alleles that are deleterious in the hybrid genome. This selection is countered in regions of the genome expected to experience elevated recombination, allowing introgressed alleles to accumulate across >20% of the genome. This work demonstrates a genome-architecture-aware approach to resolving the species tree in the face of introgression. As chromosome-level reference genomes spanning the tree of life become increasingly available, phylogenomic studies would benefit from the adoption of genome-architecture-aware approaches like ours. This is because the genomic landscapes of introgression and genealogy are largely predicted by chromosomal characteristics.

genomics↗

bioRxiv2025

STAMPS: Signal-peptide Transformer for Augmenting Mammalian Protein Secretion

While secretion plays a key role in the diverse applications of cell engineering, to date only a handful of mammalian signal peptides have been characterised in depth and systematic efforts to build novel variants remain sporadic. We present STAMPS (Signal-peptide Transformer for Augmenting Mammalian Protein Secretion), a generative, autoregressive transformer fine-tuned on [~]6,000 mammalian signal peptides to design de novo sequences that modulate and enhance secretion across proteins and hosts. We show that STAMPS can be used to identify candidate signal peptides that outperform the widely used IgG {kappa} light-chain leader (IgKL) when used to secrete EGFP in HEK293T and CHO cells, and hEPO in HEK293T cells. When incorporated in an industrial cell line development framework, STAMPS leads to the generation of signal peptides that yield [~]2.3-fold gain in secretion of a VHH-Fc compared to the internal industrial benchmark in CHO G22 cells, with the same candidates ranking highly in both CHO and HEK293T hosts. Sequence-to-function analysis highlights a longer, strongly hydrophobic core and a tightly positioned cleavage site as drivers of this strong performance. Together, these results establish data-driven, generative design of mammalian signal peptides as a practical route to tune and improve secretion for bioproduction and cell engineering applications.

synthetic biology↗

bioRxiv2025

Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life

The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data, presenting a unique opportunity to build macrophylogenies (phylogenies sampling > 1,000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting datasets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture datasets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the "fast" maximum likelihood (ML) methods, (2) filtering datasets to reduce heterogeneity, (3) supertree estimation based on published phylogenomic trees, and (4) a "divide-and-conquer" strategy, wherein smaller ML trees were estimated and subsequently combined using a supertree approach. Additionally, we examined the impact of these methods on divergence time estimation using a dataset that includes newly vetted fossil calibrations for the Avian Tree of Life. Our findings highlight that recently developed fast tree search approaches offer a reasonable compromise between computational efficiency and phylogenetic accuracy, facilitating inference of macrophylogenies.

evolutionary biology↗

bioRxiv2024

Improved nuclease-based prime editing by DNA repair modulation and pegRNA engineering

Prime editing is a genome engineering tool that allows installation of small edits with high precision. However, prime editing efficiency and purity can vary widely across different edits, genomic targets, and cell types. Prime editing nuclease (PEn) utilizes a fully active Cas9 instead of the nickase employed in conventional prime editors. PEn is capable of editing sites resistant to nickase-based prime editors but induces more undesired editing events. In this work, we introduce two strategies to enhance PEn precision and efficiency. First, we apply a small molecule approach, selectively modulating DNA repair pathways, to improve PEn precision up to 9.8-fold and reduce off-target editing by 90%. Second, through pegRNA engineering, we devise a strategy that mitigates unintended pegRNA scaffold integration, which is a common prime editing by-product, enhancing precision up to 3.5-fold. We apply this approach to a specific type of PEn editing mediated through non-homologous end joining and use it to achieve efficient and precise prime editing in multiple human cell lines, primary human hepatocytes, and mouse embryos. Together, this work presents two general strategies to improve prime editing, overcomes the limitations of current PEn editors, and provides reliable and precise genome editing outcomes, a pivotal requirement for therapeutic applications.

bioengineering↗

bioRxiv2023

Geo-genomic predictors of genetree heterogeneity in an Amazonian bird (Thamnophilus aethiops)

Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of four populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 kya, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered two primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence, and was recovered for the Z chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length, and found that smaller chromosomes experienced higher gene flow. Given that (1) gene-trees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future biogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification.

evolutionary biology↗

bioRxiv2021

Genomic architecture controls spatial structuring in Amazonian birds

Large rivers are ubiquitously invoked to explain the distributional limits and speciation of the Amazon Basins mega-diversity. However, inferences on the spatial and temporal origins of Amazonian species have narrowly focused on evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known to produce heterogeneity in differentiation across the genome. To test how genomic architecture impacts our ability to reconstruct patterns of spatial diversification across multiple taxa, we sequenced whole genomes for populations of bird species that co-occur in southeastern Amazonian. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with the species tree topology weight. Gene flow was less pervasive in regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection skewing genome-wide estimates of effective population sizes and gene flow between populations towards lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from the neutral processes to elucidate how speciation hypotheses and biogeographic patterns are sensitive to genomic architecture.

genomics↗

bioRxiv2021

River network rearrangements promote speciation in lowland Amazonian birds

Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river-barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate histories of divergence and introgression in six Amazonian avian species-complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river dynamics promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates in part from fine-scale barrier displacement processes -including river dynamics- which allow small populations to differentiate and disperse into secondary contact.

evolutionary biology↗

bioRxiv2021

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

AimWe tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. LocationSolimoes River, Western Amazon, South America TaxonMyrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis Methods: We analyzed thousands of UltraConserved Elements to explore spatial patterns of genetic diversity and connectivity between individuals. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species in order to test if the occupation of dynamic habitats could predict spatial patterns of genetic diversity. ResultsOur study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusionsOur results suggest that demographic expansions along the Solimoes River might be linked to geographic homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

evolutionary biology↗

bioRxiv2021

Systemic antibody-oligonucleotide delivery to the central nervous system ameliorates mouse models of spinal muscular atrophy

Antisense oligonucleotides (ASOs) have emerged as one of the most innovative new genetic drug modalities, however, the high molecular weight limits their bioavailability for otherwise treatable neurological disorders. We investigated conjugation of ASOs to an antibody against the murine transferrin receptor (TfR), 8D3130, and evaluated it via systemic administration in mouse models of the neurodegenerative disease, spinal muscular atrophy (SMA). SMA like several other neurological and neuromuscular diseases, is treatable with single-stranded ASOs, inducing splice modulation of the survival motor neuron 2 (SMN2) gene. Administration of 8D3130-ASO conjugate resulted in bioavailability of 2.7% of the injected dose in brain. Additionally, 8D3130-ASO yielded therapeutically high levels of SMN2 splicing in the central nervous system of mildly affected adult SMA mice and resulted in extended survival of severe SMA mice. Systemic delivery of nucleic acid therapies with brain targeting antibodies offers powerful translational potential for future treatments of neuromuscular and neurodegenerative diseases.

molecular biology↗

bioRxiv2018

Climate explains recent population divergence, introgression and persistence in tropical mountains: phylogenomic evidence from Atlantic Forest warbling finches

Taxa with disjunct distributions are common in montane biotas and offer excellent opportunities to investigate historical processes underlying genetic and phenotypic divergence. In this context, subgenomic datasets offer novel opportunities to explore historical demography in detail, which is key to better understand the origins and maintenance of diversity in montane regions. Here we used a large ultraconserved elements dataset to get insights into the main biogeographic processes driving the evolution of the Montane Atlantic Forest biota. Specifically, we studied two species of warbling finches disjunctly distributed across a region of complex geological and environmental history. We found that a scenario of three genetically differentiated populations is best supported by genomic clustering methods. Also, demographic simulations support simultaneous isolation of these populations at ~10 kya, relatively stable population sizes over recent time, and recent gene flow. Our results suggest a dual role of climate: population divergence, mediated by isolation in mountain tops during warm periods, as well as population maintenance - allowing persistence mediated by shifts in elevation distribution during periods of climate change, with episodic bouts contact and gene flow. Additional support for the role of climate comes from evidence of their contact in a recent past. We propose that two major gaps, which we call Sao Paulo and Caparao subtropical gaps, have been historically important in the divergence of cold adapted organisms in the Atlantic Forest, and could be associated to cryptic diversity. Finally, our results suggest that shallow divergence and past gene flow may be common in montane organisms, but complex demographic histories may be detectable only when using subgenomic or genomic datasets.

evolutionary biology↗