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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2022

Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress

Understanding the interplay between phenotypic plasticity and genetic adaptation is a long-standing focus of evolutionary biology. In bacteria, the oxidative stress response limits the formation of mutagenic reactive oxygen species (ROS) under diverse stress conditions. This suggests that the dynamics of the oxidative stress response are closely tied to the timing of the mutation supply that fuels genetic adaptation to stress. Here, we explored how mutation rates change in real-time in Escherichia coli cells during continuous hydrogen peroxide treatment in microfluidic channels. By visualising nascent DNA replication errors, we uncovered that sudden oxidative stress causes a burst of mutations. We developed a range of single-molecule and single-cell microscopy assays to determine how these mutation dynamics arise from phenotypic adaptation mechanisms. Signalling of peroxide stress by the transcription factor OxyR rapidly induces ROS scavenging enzymes. However, an adaptation delay leaves cells vulnerable to the mutagenic and toxic effects of hydroxyl radicals generated by the Fenton reaction. Resulting DNA damage is counteracted by a spike in DNA repair activities during the adaptation delay. Prior stress exposure or constitutive OxyR induction allowed cells to avoid the burst of mutations. Similar observations for alkylation stress show that mutation bursts are a general phenomenon associated with adaptation delays.

microbiology↗
bioRxiv2022

Survival of mineral-bound peptides into the Miocene

The oldest authenticated peptide sequences to date were reported in 2016 from 3.8 Ma old ostrich eggshell (OES) from the site of Laetoli, Tanzania (Demarchi et al., 2016). Here we demonstrate survival of the same sequences in 6.5-9 Ma OES recovered from a palaeosteppe setting in northwestern China. The eggshell is thicker than those observed in extant species and consistent with the Liushu Struthio sp. ootaxon. These findings push the preservation of ancient proteins back to the Miocene and highlight their potential for paleontology, paleoecology and evolutionary biology.

paleontology↗
bioRxiv2022

Integrating gene annotation with orthology inference at scale

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA, a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared to state-of-the-art methods, and handles even highly-fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. Together, TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

genomics↗
bioRxiv2022

Metadata preservation and stewardship for genomic data is possible, but must happen now

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic diversity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a "distributed datathon" to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 561 contained samples from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 78% of these 561 datasets (N = 440 BioProjects comprising 45,105 individuals or BioSamples from 762 species in 17 phyla). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the samples were taken was the most easily found; information about sampling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.

bioinformatics↗
bioRxiv2022

Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter

The Zrt-/Irt-like protein (ZIP) family consists of ubiquitously expressed divalent metal transporters critically involved in maintaining systemic and cellular homeostasis of zinc, iron, and manganese. Here, we present a study on a prokaryotic ZIP from Bordetella bronchiseptica (BbZIP) by combining structural biology, evolutionary covariance, computational modeling, and a variety of biochemical assays to tackle the issue of the transport mechanism which has not been established for the ZIP family. The apo state structure in an inward-facing conformation revealed a disassembled transport site, altered inter-helical interactions, and importantly, a rigid body movement of a 4-transmembrane helix (TM) bundle relative to the other TMs. The computationally generated and biochemically validated outward-facing conformation model revealed a slide of the 4-TM bundle, which carries the transport site(s), by approximately 8 [A] toward the extracellular side against the static TMs which mediate dimerization. These findings allowed us to conclude that BbZIP is an elevator-type transporter.

biochemistry↗
bioRxiv2022

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul

Pallass cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manuls zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17,097 bp mitogenome for O. manul. The primary nuclear assembly had 56x sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; sixty-one differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.

genomics↗
bioRxiv2022

Infer global, predict local: quantity-quality trade-off in protein fitness predictions from sequence data

Predicting the effects of mutations on protein function is an important issue in evolutionary biology and biomedical applications. Computational approaches, ranging from graphical models to deep-learning architectures, can capture the statistical properties of sequence data and predict the outcome of high-throughput mutagenesis experiments probing the fitness landscape around some wild-type protein. However, how the complexity of the models and the characteristics of the data combine to determine the predictive performance remains unclear. Here, based on a theoretical analysis of the prediction error, we propose descriptors of the sequence data, characterizing their quantity and quality relative to the model. Our theoretical framework identifies a trade-off between these two quantities, and determines the optimal subset of data for the prediction task, showing that simple models can outperform complex ones when inferred from adequately-selected sequences. We also show how repeated subsampling of the sequence data allows for assessing how much epistasis in the fitness landscape is not captured by the computational model. Our approach is illustrated on several protein families, as well as on in silico solvable protein models. Significance StatementIs more data always better? Or should one prefer fewer data, but of higher quality? Here, we investigate this question in the context of the prediction of fitness effects resulting from mutations to a wild-type protein. We show, based on theory and data analysis, that simple models trained on a small subset of carefully chosen sequence data can perform better than complex ones trained on all available data. Furthermore, we explain how comparing the simple local models obtained with different subsets of training data reveals how much of the epistatic interactions shaping the fitness landscape are left unmodeled.

biophysics↗
bioRxiv2023

Spatial exclusion leads to tug-of-war ecological dynamics between competing species within microchannels

Competition is ubiquitous in microbial communities, shaping both their spatial and temporal structure and composition. Many classic minimal models, such as the Moran model, have been employed in ecology and evolutionary biology to understand the role of fixation and invasion in the maintenance of a population. Informed by recent experimental studies of cellular competition in confined spaces, we extend the Moran model to explicitly incorporate spatial exclusion through mechanical interactions among cells within a one-dimensional, open microchannel. The results of our spatial exclusion model differ significantly from those of its classical counterpart. The fixation/extinction probability of a species sharply depends on the species initial relative abundance, and the mean time to fixation is greatly accelerated, scaling logarithmically, rather than algebraically, with the system size. In non-neutral cases, spatial exclusion tends to attenuate the effects of fitness differences on the probability of fixation, and the fixation times increase as the relative fitness differences between species increase. Successful fixation by invasive species, whether through mutation or immigration, are also less probable on average than in the Moran model. Surprisingly, in the spatial exclusion model, successful fixations occur on average more rapidly in longer channels. The mean time to fixation heuristically arises from the boundary between populations performing either quasi-neutral diffusion, near a semi-stable fixed point, or quasi-deterministic avalanche dynamics away from the fixed point. These results, which can be tested in microfluidic monolayer devices, have implications for the maintenance of species diversity in dense bacterial ecosystems where spatial exclusion is central to the competition, such as in organized biofilms or intestinal crypts. The results may be broadly applied to any system displaying tug-of-war type dynamics with a region of quasi-neutral diffusion centered around regions of deterministic population collapse. Author summaryCompetition for territory between different species has far reaching consequences for the diversity and fate of bacterial communities. In this study, we theoretically and computationally study the competitive dynamics of two bacterial populations competing for space in confined environments. The model we develop extends classical models that have served as paradigms for understanding competitive dynamics but did not explicitly include spatial exclusion. We find that spatial effects drastically change the probability of one species successfully outcompeting the other and accelerates the mean time it takes for a species to exclude the other from the environment. In comparison to the predictions of population models that neglect spatial exclusion, species with higher selective advantages are less heavily favoured to outcompete their rival species. Moreover, spatial exclusion influences the success of an invasive species taking over a densely populated community. Compared to classical well-mixed models, there is a reduction in the effectiveness of an invaders fitness advantage at improving the chances of taking over the population. Our results show that spatial exclusion has rich and unexpected repercussions on species dominance and the long-time composition of populations. These must be considered when trying to understand complex bacterial ecosystems such as biofilms and intestinal flora.

ecology↗
bioRxiv2023

The evolution of parthenogen fertilization rates in switching environments: from facultative cell-fusion to oogamy

Organisms with external fertilisation exhibit a broad range of reproductive modes, from simple parthenogenesis to sexual reproduction encompassing isogamy, anisogamy, and oogamy, and including environmentally-mediated facultative sex. Here we develop a unifying mathematical model which explains the emergence of these modes via the coevolution of fertilization rate and cell size. Using a minimal assumption that survival is dependent on cell mass, and by carefully accounting for biological and evolutionary time scales, we find two distinct evolutionary outcomes: high fertilization rate (obligate sexuality) is selected when costs to cell fusion are low, while zero fertilization rate (obligate asexuality) is selected for when these costs are high. Surprisingy, in high fertilization rate scenarios evolving populations can transition from isogamy to anisogamy and oogamy via evolutionary branching. Furthermore, in variable environments we show that, without phenotypic plasticity, intermediate fertilization rates and isogamy can be maintained through bet-hedging. Allowing phenotypic plasticity can give rise to facultative sex; sexual reproduction in harsh environmental conditions, and asexuality in more benign conditions. These results parsimoniously explain a large range of empirically observed parthenogen reproduction strategies, and offer an hypothesis for the origin of binary cell fusion, a key step in the evolution of syngamy and sexual reproduction itself.

evolutionary biology↗
bioRxiv2023

Leveraging genomic redundancy to improve inference and alignment of orthologous proteins

Identifying protein sequences with common ancestry is a core task in bioinformatics and evolutionary biology. However, methods for inferring and aligning such sequences in annotated genomes have not kept pace with the increasing scale and complexity of the available data. Thus, in this work we implemented several improvements to the traditional methodology that more fully leverage the redundancy of closely related genomes and the organization of their annotations. Two highlights include the application of the more flexible k-clique percolation algorithm for identifying clusters of orthologous proteins and the development of a novel technique for removing poorly supported regions of alignments with a phylogenetic HMM. In making the latter, we also wrote a fully documented Python package Homomorph that implements standard HMM algorithms and created a set of tutorials to promote its use by a wide audience. We applied the resulting pipeline to a set of 33 annotated Drosophila genomes, generating 22,813 orthologous groups and 8,566 high-quality alignments.

bioinformatics↗
bioRxiv2023

The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction

AO_SCPLOWBSTRACTC_SCPLOWJust as a phylogeny encodes the evolutionary relationships among a group of organisms, a cophylogeny represents the coevolutionary relationships among symbiotic partners. Both are widely used to investigate a range of topics in evolutionary biology and beyond. Both are also primarily reconstructed using computational analysis of biomolecular sequence data as well as other biological character data. The most widely used cophylogenetic reconstruction methods utilize an important simplifying assumption: species phylogenies for each set of coevolved taxa are required as input and assumed to be correct. Many theoretical and experimental studies have shown that this assumption is rarely - if ever - satisfied, and the consequences for cophylogenetic studies are poorly understood. To address this gap, we conduct a comprehensive performance study that quantifies the relationship between species tree estimation error and downstream cophylogenetic estimation accuracy. The study includes performance benchmarking using in silico model-based simulations. Our investigation also includes assessments of cophylogenetic reproducibility using genomic sequence datasets sampled from two important models of symbiosis: soil-associated fungi and their endosymbiotic bacteria, and bobtail squid and their bioluminescent bacterial symbionts. Our findings conclusively demonstrate the major impact that upstream phylogenetic estimation error has on downstream cophylogenetic reconstruction quality.

bioinformatics↗
bioRxiv2023

Swimming, Feeding and Inversion of Multicellular Choanoflagellate Sheets

The recent discovery of the striking sheet-like multicellular choanoflagellate species Choanoeca flexa that dynamically interconverts between two hemispherical forms of opposite orientation raises fundamental questions in cell and evolutionary biology, as choanoflagellates are the closest living relatives of animals. It similarly motivates questions in fluid and solid mechanics concerning the differential swimming speeds in the two states and the mechanism of curvature inversion triggered by changes in the geometry of microvilli emanating from each cell. Here we develop fluid dynamical and mechanical models to address these observations and show that they capture the main features of the swimming, feeding, and inversion of C. flexa colonies.

biophysics↗
bioRxiv2023

Genetic and Environmental interactions contribute to immune variation in rewilded mice

The relative and synergistic contributions of genetics and environment to inter-individual immune response variation remain unclear, despite its implications for understanding both evolutionary biology and medicine. Here, we quantify interactive effects of genotype and environment on immune traits by investigating three inbred mouse strains rewilded in an outdoor enclosure and infected with the parasite, Trichuris muris. Whereas cytokine response heterogeneity was primarily driven by genotype, cellular composition heterogeneity was shaped by interactions between genotype and environment. Notably, genetic differences under laboratory conditions can be decreased following rewilding, and variation in T cell markers are more driven by genetics, whereas B cell markers are driven more by environment. Importantly, variation in worm burden is associated with measures of immune variation, as well as genetics and environment. These results indicate that nonheritable influences interact with genetic factors to shape immune variation, with synergistic impacts on the deployment and evolution of defense mechanisms.

immunology↗
bioRxiv2023

The amino acid composition of a protein influences its expression

The quantity of each protein in a cell only is only partially correlated with its gene transcription rate. Independent influences on protein synthesis levels include mRNA sequence motifs, amino acyl-tRNA synthesis levels, elongation factor action, and protein susceptibility to degradation. Here we report two novel forms of interaction between the amino acid composition of a protein and its expression level. In animals, the differing origins of amino acids define a nutritional classification system and indicate their potential for scarcity - essential amino acids (EAA) are solely obtained from dietary supply, non-essential amino acids (NEAA) from biosynthetic supply, and conditionally essential amino acids (CEAA) from both. Accessing public proteomic datasets, we demonstrate that CEAA sequence composition is inversely correlated with expression - a rule of supply that is further magnified by rapid cellular proliferation. Similarly, proteins with the most extreme compositions of EAA are reduced in abundance. Homeostatic responses to malnutrition may result from the reductions in expression of extreme composition proteins participating in biological systems such as taste and food-seeking behaviour, oxidative phosphorylation, and chemokine function. The rule can also influence general human phenotypes and disease susceptibility: stature proteins are enriched in CEAAs, and a curated dataset of over 700 cancer proteins is significantly under-represented in EAAs. A second rule, whereby individual amino acids influence protein expression is also described. This rule is shared across all kingdoms of life and rooted in the immutable structural and encoding parameters of each amino acid. Species-specific environmental survival pathways are shown to be enriched in proteins with amino acid compositions favouring higher expression according to this rule. These two rules of protein expression regulation promise new insights into systems biology, evolutionary studies, experimental research design, and public health intervention.

biochemistry↗
bioRxiv2023

Telling mutualistic and antagonistic ecological networks apart by learning their multiscale structure

O_LICharacterizing and understanding the processes that shape the structure of ecological networks, which represent who interacts with whom in a community, has many implications in ecology, evolutionary biology, and conservation. A highly debated question is whether and how the structure of a bipartite ecological network differs between antagonistic (e.g., herbivory) and mutualistic (e.g., pollination) interaction types. C_LIO_LIHere, we tackle this question by using a multiscale characterization of network structure, machine learning tools, and a large database of empirical and simulated bipartite networks. C_LIO_LIContrary to previous studies focusing on global structural metrics, such as nestedness and modularity, which concluded that antagonistic and mutualistic networks cannot be told apart from only their structure, we find that they can be told apart by combining a meso-scale characterization of their structure and supervised machine learning. Motif frequencies appear particularly informative, with an over-representation of densely connected motifs in antagonistic networks and of motifs with asymmetrical specialization in mutualistic networks. These characteristics can be used to predict interaction types with relatively good confidence. Beyond this classical mutualism/antagonism dichotomy, we also find significant structural uniqueness linked to specific ecologies (e.g., pollination, parasitism). C_LIO_LIOur results clarify structural differences between antagonistic and mutualistic networks and suggest the investigation of the structural uniqueness of specific ecologies as a promising approach for characterizing interactions beyond the coarse antagonistic/mutualistic dichotomy. C_LI

ecology↗
bioRxiv2023

Migration in uncertain times

Understanding the conditions that promote the evolution of migration is important in ecology and evolution. When environments are fixed and there is one most favorable site, migration to other sites lowers overall growth rate and is not favored. Here we ask, can environmental variability favor migration when there is one best site on average? Previous work suggests that the answer is yes, but a general and precise answer remained elusive. Here we establish new, rigorous inequalities to show (and use simulations to illustrate) how stochastic growth rate can increase with migration when fitness (dis)advantages fluctuate over time across sites. The effect of migration between sites on the overall stochastic growth rate depends on the difference in expected growth rates and the variance of the fluctuating difference in growth rates. When fluctuations (variance) are large, a population can benefit from bursts of higher growth in sites that are worse on average. Such bursts become more probable as the between-site variance increases. Our results apply to many ([≥] 2) sites, and reveal an interplay between the length of paths between sites, the average differences in site-specific growth rates, and the size of fluctuations. Our findings have implications for evolutionary biology as they provide conditions for departure from the reduction principle, and for ecological dynamics: even when there are superior sites in a sea of poor habitats, variability and habitat quality across space determine the importance of migration.

ecology↗
bioRxiv2023

Temporal variation in introgressed segments' length statistics sheds light on past admixture pulses

AbstractHybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remains a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomics data for a two-population system and described temporal neutral introgression patterns under a single- and two-pulse admixture model. We computed three summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within-genomes, as well as genome-wide introgression proportions. The first two statistics can confidently be used to infer inter-lineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions provided more limited insights. We then computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse with Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of genomes.

genomics↗
bioRxiv2023

Extreme genome scrambling in cryptic Oikopleura dioica species

Genes are not randomly distributed throughout chromosomes. How gene order evolves and how selective constraints act to preserve or vary gene order, both at the macrosyntenic level of whole chromosomes or microsyntenic level of gene blocks, are central questions of evolutionary biology and genomics that remain largely unsolved. Here, after sequencing several genomes of the appendicularian tunicate Oikopleura dioica from different locations around the globe, we show an unprecedented amount of genome scrambling in animals with no obvious morphological differences, consistent with cryptic speciation. Our assemblies suggest that all members of this clade possess a common 3-chromosome karyotype, and that different species largely preserve gene content, despite the presence of thousands of rearrangements in gene order. The movements of genes are largely restricted to chromosome arms and sex-specific regions, which appear to be the primary unit of macrosynteny conservation, and examples of these within-arm movements can be seen in the Hox and Fgf gene families. Our approach employing whole-genome alignments demonstrates that segments containing protein-coding elements tend to be preserved at the microsyntenic scale, consistent with strong purifying selection, with appreciably less preservation of non-coding elements. Unexpectedly, scrambling did not preserve operon structure across species, suggesting an absence of selective pressure to maintain operon structure. As well, genome scrambling does not occur uniformly across all chromosomes, as short chromosome arms possess shorter genes, smaller operons, more breakpoints, and elevated dN/dS values compared to long chromosome arms. Estimation of divergence times among the cryptic O. dioica lineages yielded an estimated breakpoint accumulation rate of 6 to 25 breakpoints per megabase per million years, which is an order of magnitude higher than the rates for other ascidian tunicates or Drosophila species. Therefore, O. dioica appears to be an attractive animal system to unravel the mechanisms that underlie gene order and synteny conservation, as well as exploring the limits of genome scrambling without an apparent impact on phenotypic evolution.

genomics↗