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At least 19 recordsLinked to original sources
bioRxiv2026

Assessing the Efficacy of Computational Workshops and Participatory Live Coding in Evolutionary Biology

Computational workshops are common in evolutionary biology and are used to share discipline-specific tools and skills with researchers. Despite the perceived importance of these workshops, there is no common set of criteria for workshop success, and there are few peer-reviewed studies investigating the efficacy of workshops or assessing the value of particular instructional techniques in this context. Here, we focused on one key element of a successful workshop: its ability to increase participants motivation to use the methods and tools presented during the workshop. We analyzed the goals, perceptions, and future plans of research practitioners engaging in a workshop on phylogenetic methods of historical biogeography using pre- and post-workshop surveys. Overall, the workshop was successful at motivating participants, and survey responses provided insights into participants perceptions of different activities, including "participatory live coding". Apart from this case study, we aim to highlight the importance of developing a common set of workshop goals in collaboration with other workshop stakeholders and the need for specialized, validated tools for assessing the efficacy of computational workshops for researchers.

evolutionary biology↗
bioRxiv2015

The State of Software in Evolutionary Biology

With Next Generation Sequencing Data (NGS) coming off age and being routinely used, evolutionary biology is transforming into a data-driven science.\n\nAs a consequence, researchers have to rely on a growing number of increasingly complex software. All widely used tools in our field have grown considerably, in terms of the number of features as well as lines of code. In addition, analysis pipelines now include substantially more components than 5-10 years ago.\n\nA topic that has received little attention in this context is the code quality of widely used codes. Unfortunately, the majority of users tend to blindly trust software and the results it produces. To this end, we assessed the code quality of 15 highly cited tools (e.g., MrBayes, MAFFT, SweepFinder etc.) from the broader area of evolutionary biology that are used in current data analysis pipelines.\n\nWe also discuss widely unknown problems associated with floating point arithmetics for representing real numbers on computer systems. Since, the software quality of the tools we analyzed is rather mediocre, we provide a list of best practices for improving the quality of existing tools, but also list techniques that can be deployed for developing reliable, high quality scientific software from scratch.\n\nFinally, we also discuss journal and science policy as well as funding issues that need to be addressed for improving software quality as well as ensuring support for developing new and maintaining existing software.\n\nOur intention is to raise the awareness of the community regarding software quality issues and to emphasize the substantial lack of funding for scientific software development.

Evolutionary Biology↗
bioRxiv2021

EcoEvoApps: Interactive Apps for Teaching Theoretical Models in Ecology and Evolutionary Biology

O_LIThe integration of theory and data drives progress in science, but a persistent barrier to such integration in ecology and evolutionary biology (EEB) is that theory is often developed and expressed in the form of mathematical models that can feel daunting and inaccessible for students and empiricists with variable quantitative training and attitudes towards math. C_LIO_LIA promising way to make mathematical models more approachable is to embed them into interactive tools with which one can visually evaluate model structures and directly explore model outcomes through simulation. C_LIO_LITo promote such interactive learning of quantitative models, we developed EcoEvoApps, a collection of free, open-source (R/Shiny) apps that include model overviews, interactive model simulations, and code to implement these models directly in R. The package currently focuses on canonical models of population dynamics, species interaction, and landscape ecology. We also outline a vision and approach for growing the collection to include more models from across EEB. C_LIO_LIThese apps help illustrate fundamental results from theoretical ecology and can serve as valuable teaching tools in classroom settings. We present data from student surveys which show that students rate these apps as useful learning tools, and that using interactive apps leads to substantial gains in students interest and confidence in mathematical models. This points to the potential for interactive activities to make theoretical models more accessible to a wider audience, and thus facilitate the feedback between theory and data across ecology and evolutionary biology. C_LI

scientific communication and education↗
bioRxiv2022

Increased academic performance and prolonged career duration among Taiwanese academic faculty in ecology and evolutionary biology

Academic job markets have become increasingly challenging worldwide, yet it remains poorly characterized how competitively-successful candidates should be and what the underlying determinants of their success are. Focusing on the field of ecology and evolutionary biology, we analyzed the academic performance (measured as h-index) as well as the duration before recruitment as a new faculty member and promotion to full professor of 145 principal investigators (PI) over the past 34 years in Taiwan. We found that PIs had higher performance and longer duration before recruitment more recently. Performance before promotion remained stable, whereas the duration increased over time. The origin and prestige of doctorate had no effect on the performance or duration either before recruitment or before promotion. We also found that the difference in performance before and after recruitment ("After" performance -- "Before" performance) decreased in recent years, with PIs recruited in earlier years maintaining their performance after recruitment while those recruited in later years exhibiting a performance drop. While PIs performed equally well before and after recruitment irrespective of doctorate origin, those with domestic PhD degrees showed a decrease in performance after promotion compared to their counterparts with foreign degrees. Taken together, our findings reveal a prolonged career duration for researchers as a result of intensifying competition in academia, and highlight the increasingly crucial role of academic performance, rather than PhD degree itself, in determining academic success.

scientific communication and education↗
bioRxiv2019

DNA energy constraints shape biological evolutionary trajectories

Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetrate themselves. Thus, the biological information contained within a dsDNA molecule, in terms of a linear sequence of nucleotides, has been considered the main target of the evolution. However, in this information-centred perspective, certain DNA sequence symmetries are difficult to explain. Here we show that these patterns can emerge from the physical peculiarities of the dsDNA molecule itself and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. Our predictions are valid for both prokaryotes and eukaryotes, and also inform the interpretation of observed codon biases and context-dependent mutation patterns in human populations. Our results suggest that the double helix energy constraints and, more generally, the physical properties of the dsDNA are the hard drivers of the overall DNA sequence architecture, whereas the biological selective processes act as soft drivers, which only under extraordinary circumstances overtake the overall entropy content of the genome.

molecular biology↗
bioRxiv2020

Chromosome-level genome assembly of the common chaffinch (Aves: Fringilla coelebs): a valuable resource for evolutionary biology

The common chaffinch, Fringilla coelebs, is one of the most common, widespread and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87 Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian dataset. Around 7.8 % of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian and vertebrate evolution.

evolutionary biology↗
bioRxiv2019

EvolvingSTEM: A microbial evolution-in-action curriculum that enhances learning of evolutionary biology and increases interest in STEM

Evolution is a central, unifying theory for all of life science, yet the subject is poorly represented in most secondary-school biology courses, especially in the United States. One challenge to learning evolution is that it is taught as a conceptual, retrospective subject with few tangible outcomes for students. These typical passive learning strategies lead to student disengagement with the material and misunderstanding of evolutionary concepts. To promote greater investment and comprehension, we developed EvolvingSTEM, an inquiry-based laboratory curriculum that demonstrates concepts of natural selection, heredity, and ecological diversity through experimental evolution of a benign bacterium. Students transfer populations of Pseudomonas fluorescens growing on plastic beads, which selects for biofilm formation and mutants with new, conspicuous phenotypes. We introduced our curriculum to four introductory high school biology classes alongside their standard curriculum materials and found that students who learned evolution through EvolvingSTEM scored significantly better on a common assessment targeted to Next Generation Science Standards than students taught only the standard curriculum. This latter group subsequently achieved similar scores once they too completed our curriculum. Our work demonstrates that inquiry-based, hands-on experiences with evolving bacterial populations can greatly enhance student learning of evolutionary concepts.

evolutionary biology↗
bioRxiv2021

Morphological integration during postnatal ontogeny: implications for evolutionary biology

How covariance patterns of phenotypes change during development is fundamental for a broader understanding of evolution. There is compelling evidence that mammalian skull covariance patterns change during ontogeny. However, it is unclear to what extent variation in covariance patterns during ontogeny can impact the response to selection. To tackle this question we explored: i) the extent to which covariance patterns change during postnatal ontogeny; ii) in which ontogenetic stages covariance patterns differ the most, and iii) the extent to which the phenotypic covariance pattern at different ontogenetic stages can be explained by the same processes determining additive genetic covariance. We sampled postnatal ontogenetic series for both marsupials, and placentals. Within each ontogenetic series, we compared covariance matrices (P-matrices) at different ontogenetic stages. Furthermore, we compared these P-matrices to two target matrices [adult P-matrix and an additive genetic covariance matrix (G-matrix)]. Our results show that for all ontogenetic series, covariance patterns from weaning onward are conserved and probably shaped by the same processes determining the G-matrix. We conclude that irrespective of eventual differences in how selection operates during most of postnatal ontogeny, the net response to such pressures will probably not be affected by ontogenetic differences in the covariance pattern.

developmental biology↗
bioRxiv2023

Identification of genome safe harbor loci for human gene therapy based on evolutionary biology and comparative genomics

Gene transfer into CD34+ hematopoietic stem and progenitor cells (HSPCs) involving integrating viral vectors has unpredictable outcomes including potential adverse events like leukemogenesis, resulting from insertional mutagenesis. Therefore, identifying and characterizing genome safe harbor (GSH) sites where exogenous gene material can be safely integrated into adult progenitor and stem cells is critically important for therapeutic gene addition. Here, we present a novel approach to identify new GSH sites based on a proven system of stable transgene insertion: the evolutionarily conserved integration of parvovirus DNA into the germlines of host species. From a dataset of 199 unique endogenous parvovirus (EPV) integration events identified in host species genomes, 102 loci were mapped to the human genome with 17 being experimentally evaluated as GSHs in primary human CD34+ HSPCs. Nine promising GSHs resulted in cells edited using nucleofection alone or in combination with rAAV transduction. Of the nine GSH sites, six edited loci displayed sustained transgene expression in both erythroid and immune phenotypes while three clearly exhibited immune branch specific-regulation. Following this approach, additional GSH sites are likely to emerge from the remaining mapped loci for gene addition in hematopoietic stem and progenitor cells. Since it is unlikely that the GSH-lineage-restricted transgene expression is exclusive to hematopoietic stem cells, this approach extends the options for gene knock-ins while reducing the risks of insertional mutagenesis, unpredictable expression profiles, effects on differentiation, and increasing therapeutic effects.

genetics↗
bioRxiv2019

Beyond parallel evolution: when several species colonize the same environmental gradient

Genomic signatures associated with population divergence, speciation and the evolutionary mechanisms responsible for these are key research topics in evolutionary biology. Evolutionary radiations and parallel evolution have offered opportunities to study the role of the environment by providing replicates of ecologically driven speciation. Here, we apply an extension of the parallel evolution framework to study replicates of ecological speciation where multiple species went through a process of population divergence during the colonization of a common environmental gradient. We used the conditions offered by the North Sea - Baltic Sea environmental transition zone and found clear evidence of population structure linked to the Baltic Sea salinity gradient in four flatfish species. We found highly heterogeneous signatures of population divergence within and between species, and no evidence of parallel genomic architecture across species associated with the divergence. Analyses of demographic history suggest that Baltic Sea lineages are older than the age of the Baltic Sea itself. In most cases, divergence appears to involve reticulated demography through secondary contact, and our analyses revealed that genomic patterns of divergence were likely the result of a combination of effects from past isolation and subsequent adaptation to a new environment. In one case, we identified two large structural variants associated with the environmental gradient, where populations were inferred to have diverged in the presence of gene flow. Our results highlight the heterogeneous genomic effects associated with complex interplays of evolutionary forces, and stress the importance of genomic background for studies of parallel evolution.

evolutionary biology↗
bioRxiv2014

The disruption of trace element homeostasis due to aneuploidy as a unifying theme in the etiology of cancer

#### #### ABSTRACT FOR SCIENTISTS: While decades of cancer research have firmly established multiple hallmarks of cancer 1,2, cancers genomic landscape remains to be fully understood. Particularly, the phenomenon of aneuploidy gains and losses of large genomic regions, i.e. whole chromosomes or chromosome arms and why most cancer cells are aneuploid remains enigmatic 3. Another frequent observation in many different types of cancer is the deregulation of the homeostasis of the trace elements copper, zinc and iron. Concentrations of copper are markedly increased in cancer tissue and the blood plasma of cancer patients, while zinc levels are typically decreased 49. Here we discuss the hypothesis that the disruption of trace element homeostasis and the phenomenon of aneuploidy might be linked. Our tentative analysis of genomic data from diverse tumor types mainly from The Cancer Genome Atlas (TCGA) project suggests that gains and losses of metal transporter genes occur frequently and correlate well with transporter gene expression levels. Hereby they may confer a cancer-driving selective growth advantage at early and possibly also later stages during cancer development. This idea is consistent with recent observations in yeast, which suggest that through chromosomal gains and losses cells can adapt quickly to new carbon sources 10, nutrient starvation 11 as well as to copper toxicity 12. In human cancer development, candidate driving events may include, among others, the gains of zinc transporter genes SLC39A1 and SLC39A4 on chromosome arms 1q and 8q, respectively, and the losses of zinc transporter genes SLC30A5, SLC39A14 and SLC39A6 on 5q, 8p and 18q. The recurrent gain of 3q might be associated with the iron transporter gene TFRC and the loss of 13q with the copper transporter gene ATP7B. By altering cellular trace element homeostasis such events might contribute to the initiation of the malignant transformation. Intriguingly, attenuation or overexpression of several of these metal transporter genes has been shown to lead to malignant cellular behavior in vitro. Consistently, it has been shown that zinc affects a number of the observed hallmarks of cancer characteristics including DNA repair, inflammation and apoptosis, e.g. through its effects on NF-kappa B signaling. We term this model the aneuploidy metal transporter cancer (AMTC) hypothesis and find it compatible with the cancer-promoting role of point mutations and focal copy number alterations in established tumor suppressor genes and oncogenes (e.g. MYC, MYCN, TP53, PIK3CA, BRCA1, ERBB2). We suggest a number of approaches for how this hypothesis could be tested experimentally and briefly touch on possible implications for cancer etiology, metastasis, drug resistance and therapy. #### #### ABSTRACT FOR KIDS: We humans are made up of many very small building blocks, which are called cells. These cells can be seen with a microscope and they know how to grow and what to do from the information on the DNA of their chromosomes. Sometimes, if this information is messed up, a cell can go crazy and start to grow without control, even in places of the body where it should not. This process is called cancer, a terrible disease that makes people very sick. Scientists do not understand exactly what causes cells to go crazy, so it would be good to find out. Many years ago, scientists observed that chromosomes in these cancer cells are missing or doubled but could not find an explanation for it. More recently, scientists have detected that precious metals to our bodies, which are not gold and silver, but zinc, iron and copper, are not found in the right amounts in these crazy cancer cells. There seems to be not enough zinc and iron but too much copper, and again, scientists do not really understand why. So there are many unanswered questions about these crazy cancer cells and in this article, we describe a pretty simple idea on how chromosome numbers and the metals might be connected: we think that the missing or doubled chromosomes produce less or more transporters of zinc, iron and copper. As a result, cancer cells end up with little zinc and too much copper and these changes contribute to their out-of-control growth. If this idea were true, many people would be excited about it. But first this idea needs to be investigated more deeply in the laboratory, on the computer and in the hospitals. Therefore, we put it out on the internet so that other people can also think about and work on our idea. Now there are plenty of ways to do exciting experiments and with the results, we will hopefully understand much better why cancer cells go crazy and how doctors could improve their therapies to help patients in the future. #### #### ABSTRACT FOR ADULTS: One hundred years ago, it was suggested that cancer is a disease of the chromosomes, based on the observations that whole chromosomes or chromosome arms are missing or duplicated in the genomes of cells in a tumor. This phenomenon is called aneuploidy and is observed in most types of cancer, including breast, lung, prostate, brain and other cancers. However, it is not clear which genes could be responsible for this observation or if this phenomenon is only a side effect of cancer without importance, so it is important to find out. A second observation from basic research is that concentrations of several micronutrients, especially of the trace elements zinc, copper and iron are changed in tumor cells. In this article, we speculate that aneuploidy is the reason for these changes and that together, these two phenomena are responsible for some of the famous hallmarks or characteristics that are known from cancer cells: fast growth, escape from destruction by the immune system and poor DNA repair. This idea is new and has not been tested yet. We name it the aneuploidy metal transporter cancer (AMTC) hypothesis. To test our idea we used a wealth of information that was shared by international projects such as the Human Genome Project or the Cancer Genome Atlas Project. Indeed, we find that many zinc, iron and copper transporter genes in the genome are affected by aneuploidy. While a healthy cell has two copies of each gene, some tumor cells have only one or three copies of these genes. Furthermore, the amounts of protein and the activities of these metal transporters seem to correlate with these gene copy numbers, at least we see that the intermediate molecules and protein precursors called messenger RNA correlate well. Hence, we found that the public data is compatible with our suggested link between metal transporters and cancer. Furthermore, we identified hundreds of studies on zinc biology, evolutionary biology, genome and cancer research that also seem compatible. For example, cancer risk increases in the elderly population as well as in obese people, it also increases after certain bacterial or viral infections and through alcohol consumption. Consistent with the AMTC hypothesis and in particular, the idea that external changes in zinc concentrations in an organ or tissue may kick off the earliest steps of tumor development, all of these risk factors have been correlated with changes in zinc or other trace elements. However, since additional experiments to test the AMTC hypothesis have not yet been performed, direct evidence for our hypothesis is still missing. We hope, however, that our idea will promote further research with the goal to better understand cancer as a first step towards its prevention and the development of improved anti-cancer therapies in the future.

Cancer Biology↗
bioRxiv2022

Statistical analysis of number of genes and chromosome lengths of different microbial species

Genome architecture concerns the organisation of genes on a chromosome, and has important implications to the fidelity in which genes are encoded on the chromosome, and how the information is read by DNA polymerase and RNA polymerase. This facet of genomics did receive attention in the early epoch of genomics, but it has received less attention in contemporary genomics as attention shifts to structural and functional genomics with the goal of annotating the function of each gene in the genome. This work sought to uncover relationships between number of genes and chromosome length in a variety of bacteria and archaea species as a preamble to understanding the prevalence and importance of repetitive sequences in the genome of prokaryotic species. Aggregate results with the ensemble of prokaryotic species profiled revealed a positive linear correlation between number of genes and chromosome length. Upon dissection into the Bacteria and Archaea domains, the linear relationship described above still stands for Bacteria but starts to break down in Archaea. This suggests that repetitive sequences are more important to Archaea species, which generally have a smaller genome (1.8 to 2.8 Mbp) and fewer genes (1500 to 2400) compared to bacterial species. In comparison, the bacterial genome is larger (4 to 5.6 Mbp), and encodes more genes (3600 to 5100). Overall, the results highlight that bacterial genome are efficiently encoded with few repetitive sequences. This, however, is not true for archaeal genome, which provides another line of evidence supporting the notion that archaea are ancestral eukaryotic cells, which like the archaea also houses large repetitive sequences. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/503871v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1632506org.highwire.dtl.DTLVardef@13e91forg.highwire.dtl.DTLVardef@12e1316org.highwire.dtl.DTLVardef@1e7381e_HPS_FORMAT_FIGEXP M_FIG C_FIG Short descriptionStatistical analysis across an ensemble of 59 microbial species revealed a strong linear correlation between number of genes and chromosome length. This suggests that prokaryotic genomes are highly compact with genes, and do not carry significant amounts of repeats unlike the case in eukaryotic organisms. The result holds significant implications for our understanding of genome evolution and compaction in prokaryotic organisms, and what drove their accession as foundational species of many ecosystems. Subject areasgenomics, molecular biology, evolutionary biology, bioinformatics, systems biology,

genomics↗
bioRxiv2024

Evolutionary and biological mechanisms underpinning chitin degradation in aquatic fungi

Fungal biology underpins major processes in ecosystems. The Chytridiomycota (chytrids) is a group of early-diverging fungi, many of which function in ecosystems as saprotrophs processing high molecular weight biopolymers, however the mechanisms underpinning chytrid saprotrophy are poorly understood. Genome sequences from representatives across the group and the use of model chytrids offers the potential to determine new insights into their evolution. In this study, we focused on the biology underpinning chitin saprotrophy, a common ecosystem function of aquatic chytrids. The genomes of chitinophilic chytrids have expanded inventories of glycoside hydrolase genes responsible for chitin processing, complemented with bacteria-like chitin-binding modules (CBMs) that are absent in other chytrids. In the model chitinophilic saprotroph Rhizoclosmatium globosum JEL800, the expanded repertoire of chitinase genes is diverse and almost half were detected as proteins in the secretome when grown with chitin. Predicted models of the secreted chitinases indicate a range of active site sizes and domain configurations. We propose that increased diversity of secreted chitinases is an adaptive strategy that facilitates chitin degradation in the complex heterologous organic matrix of the arthropod exoskeleton. Free swimming R. globosum JEL800 zoospores are chemotactic to the chitin monomer N-acetylglucosamine and accelerate zoospore development when grown with chitin. Our study sheds light on the underpinning biology and evolutionary mechanisms that have supported the saprotrophic niche expansion of some chytrids to utilise lucrative chitin-rich particles in aquatic ecosystems and is a demonstration of the adaptive capability of this successful fungal group.

evolutionary biology↗
bioRxiv2017

Genomic regression of claw keratin, taste receptor and light-associated genes inform biology and evolutionary origins of snakes

Regressive evolution of anatomical traits corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The origin of snakes coincided with the regression of a number of anatomical traits, including limbs, taste buds and the visual system. By studying the genomes of snakes, I was able to test three hypotheses associated with the regression of these features. The first concerns two keratins that are putatively specific to claws. Both genes that encode these keratins were pseudogenized/deleted in snake genomes, providing additional evidence of claw- specificity. The second hypothesis is whether snakes lack taste buds, an issue complicated by unequivocal, conflicting results in the literature. I found evidence that different snakes have lost one or more taste receptors, but all snakes examined retained at least some capacity for taste. The final hypothesis I addressed is that the earliest snakes were adapted to a dim light niche. I found evidence of deleted and pseudogenized genes with light- associated functions in snakes, demonstrating a pattern of gene loss similar to other historically nocturnal clades. Together these data also provide some bearing on the ecological origins of snakes, including molecular dating estimates that suggest dim light adaptation preceded the loss of limbs.

evolutionary biology↗
bioRxiv2025

Applications of Wedderburn's Theorem in Modelling Non-Commutative Biological and Evolutionary Systems

A wide range of biological and evolutionary processes is determined not merely by the occurrence of specific events, but by the exact order in which those events unfold. Gene regulation, developmental pathways, metabolic cascades and genetic evolution often display non-commutative behaviour, in which reversing the sequence of events results in functionally distinct outcomes. Conventional modelling approaches often fail to account for such directionality and sequence dependence, thereby limiting their capacity to capture the complexity of regulatory logic. We represent ordered sequences of biological operations--such as transcription factor binding or mutational trajectories--as elements of a non-commutative algebra designed to encode the functional logic of systems where the order of events is critically determinant. Subsequently, we apply Wedderburns Theorem to decompose the algebra into a direct sum of matrix modules, each capturing an irreducible and functionally distinct component of the underlying sequence-dependent system. We provide examples from gene expression regulation and evolutionary dynamics, focusing on scenarios where trait development is determined by the specific order of underlying molecular or mutational events. Our results demonstrate that the algebraic framework effectively maps intricate biological processes onto smaller, linear components, facilitating clearer interpretation and analysis. Simplifying non-commutative biological systems into interpretable submodules, Wedderburn-style decomposition may clarify gene regulatory logic, capture behavioural outcomes, reduce computational burden and uncover pathway redundancies and structural symmetries. Overall, by unifying diverse biological processes within a coherent algebraic structure, our method may improve the tractability of complex, order-dependent systems.

evolutionary biology↗
bioRxiv2021

Fitness landscape analysis reveals that the wild type allele is sub-optimal and mutationally robust

Fitness landscape mapping and the prediction of evolutionary trajectories on these landscapes are major tasks in evolutionary biology research. Evolutionary dynamics is tightly linked to the landscape topography, but this relation is not straightforward. Here, we analyze a fitness landscape of a yeast tRNA gene, previously measured under four different conditions. We find that the wild type allele is sub-optimal, and 8%-10% of its variants are fitter. We rule out the possibilities that the wild type is fittest on average on multiple conditions or located on a local fitness maximum. Instead, we find that the wild type is mutationally robust ( flat), while more fit variants are typically mutationally fragile. Similar observations of mutational robustness or flatness have been so far made in very few cases, predominantly in viral genomes.

evolutionary biology↗
bioRxiv2025

Admixture mapping reveals evidence for multiple mitonuclear incompatibilities in swordtail fish hybrids

How barriers to gene flow arise between closely related species is one of the oldest questions in evolutionary biology. Classic models in evolutionary biology predict that negative epistatic interactions between variants in the genomes of diverged lineages, known as hybrid incompatibilities, will reduce viability or fertility in hybrids. The genetic architecture of these interactions and the evolutionary paths through which they arise have profound implications for the efficacy of hybrid incompatibilities as barriers to gene flow between species. While these questions have been studied using theoretical approaches for several decades, only recently has it become possible to genetically map larger numbers of hybrid incompatibilities. Here, we use admixture mapping in natural hybrid populations of swordtail fish (Xiphophorus) to identify hybrid incompatibilities involving genetic interactions between the mitochondrial and nuclear genomes. We find that at least nine regions of the genome are involved in mitonuclear incompatibilities. These incompatibilities involve interactions between the nuclear genome and the X. malinche mitochondria, the X. birchmanni mitochondria, or both. Moreover, they vary in the strength of selection they experience, and the degree to which they limit gene flow in natural hybrid populations. Our results build a deeper understanding of the complex architecture of selection against incompatibilities in naturally hybridizing species and highlight an important role of mitonuclear interactions in the evolution of reproductive barriers between closely related species.

evolutionary biology↗
bioRxiv2017

A phylogenomic framework and timescale for comparative genomics and evolutionary developmental biology of tunicates

BackgroundTunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species.\n\nResultsPhylogenetic analyses using site-heterogeneous CAT mixture models of amino acid sequence evolution resulted in a strongly supported tree topology resolving the relationships among four major tunicate clades: 1) Appendicularia, 2) Thaliacea + Phlebobranchia + Aplousobranchia, 3) Molgulidae, and 4) Styelidae + Pyuridae. Notably, the morphologically derived Thaliacea are confirmed as the sister-group of the clade uniting Phlebobranchia + Aplousobranchia within which the precise position of the model ascidian genus Ciona remains uncertain. Relaxed molecular clock analyses accommodating the accelerated evolutionary rate of tunicates reveal ancient diversification (~450-350 million years ago) among the major groups and allow comparing their evolutionary age with respect to the major vertebrate model lineages.\n\nConclusionsOur study represents the most comprehensive phylogenomic dataset for the main tunicate lineages. It offers a reference phylogenetic framework and first tentative timescale for tunicates, allowing the direct comparison with vertebrate model species in comparative genomics and evolutionary developmental biology studies.

evolutionary biology↗