Biology subjects

Michalak, P.

Publications and source records attributed to Michalak, P..

13 recordsLinked to original sources

bioRxiv2026

Interspecies variation of 45S ribosomal DNA in vertebrates

Ribosomal DNA (rDNA) remains one of the least resolved components of complex genomes despite its central role in cellular function and evolutionary inference. Using chromosome-scale assemblies from the Vertebrate Genomes Project, we present a comparative analysis of the 45S rDNA locus across vertebrates. rDNA organization varies widely among clades, with lineage-specific differences in chromosomal distribution, copy number, and positional bias. Mammals and birds typically restrict rDNA to few, often terminal loci, whereas amphibians and several fish lineages exhibit highly dispersed architectures, including extreme cases spanning dozens of chromosomes. Copy number varies by more than an order of magnitude and does not scale simply with repeat-unit size or predicted functional demand, consistent with rDNA functioning as a flexible genomic reservoir rather than a direct proxy for ribosome production. At the sequence level, the 45S unit resolves into distinct evolutionary regimes. Genes encoding rRNAs (18S, 5.8S, 28S) remain highly conserved and retain strong phylogenetic signal, whereas internal transcribed spacers show rapid divergence, lineage-specific expansion, and pronounced asymmetry between intergenic spacers ITS1 and ITS2. Sequence-structure analyses reveal a gradient of constraint across the locus, from tightly coupled evolution in rRNA-encoding regions to increasingly permissive regimes in spacers. Structure-informed phylogenetic inference yields modest but consistent improvements under high divergence, highlighting its value when sequence signal degrades. Together, these results establish the 45S rDNA locus as a multi-layered evolutionary system integrating deep conservation with structural plasticity across vertebrates.

genomics↗

bioRxiv2026

Genome-wide architecture of prolonged starvation adaptation in experimentally evolved Drosophila and comparative enrichment in human orthologs

Long-term starvation stress represents a strong evolutionary constraint across taxa, yet the genetic architecture underlying adaptation to sustained nutrient deprivation remains poorly resolved. We experimentally evolved Drosophila melanogaster under starvation stress for 60 generations, maintaining four starvation-selected populations and four matched controls, and then performed whole-genome resequencing. Starvation-selected populations exhibited extended survival and pronounced genome-wide restructuring, including the expansion of low-heterozygosity regions, reduced nucleotide diversity, and recurrent sweep signatures across replicates. Drift-aware allele-frequency modeling identified 3,578 single-nucleotide polymorphisms (SNPs) whose shifts exceeded neutral expectations, indicating widespread, parallel responses to sustained starvation. Mitochondrial pathways emerged as prominent targets: nuclear-encoded mitochondrial genes were significantly enriched among low-diversity, sweep-associated, and drift-exceeding loci, and the mitochondrial origin of replication harbored a sharply differentiated variant, suggesting a mito-nuclear component of starvation adaptation. Comparative analyses further showed that human orthologs of starvation-responsive fly genes were enriched for highly differentiated variants in selected 1000 Genomes populations, with regulators of TOR/S6K signaling recurring among loci in the extreme tails of population differentiation. Together, these results define a replicate-convergent and functionally coherent genomic response to prolonged starvation in Drosophila, comprising regional signatures of linked selection and distributed allele-frequency shifts exceeding neutral expectations, and connect laboratory selection in flies to population differentiation in human orthologs.

evolutionary biology↗

bioRxiv2026

Seminal fluid proteins can mitigate sexual conflict: the case of remating in insects

Males during mating never transfer just sperm; to the best of our knowledge, they always deliver a rich seminal fluid as well. The proteins in the seminal fluid have an important sperm supporting role, but they also cause changes in the female physiology and can impose a mating cost. The associated costs and delay in the time of remating, lead to the view that those proteins evolved primarily due to sexual conflict and delay female remating beyond the optimal rate. To examine the role of seminal fluid proteins in sexual conflict we use a mathematical model of reproductive physiology, informed by the accumulated knowledge on Drosophila melanogaster. In accordance with the theory, we find that males always benefit from inducing longer remating intervals in females. But, we also find that this conflict is reduced when female reproduction is regulated by the male proteins. Without seminal fluid proteins females have a single, well-defined, optimal remating rate. However, when seminal proteins are used to regulate females reproduction, females can reach the same offspring production for a range of mating intervals. This wider range of possible remating times could provide females with a buffer against uncertain mating opportunity. It could also allow females to be more selective on male quality, by reducing the cost associated with delaying remating. Our results suggest that, while there is a conflict over the remating rate, seminal fluid proteins reduce its intensity, highlighting their role in aligning the interests of both sexes.

evolutionary biology↗

bioRxiv2025

The role of fecundity dynamics and time of injury for femalereproductive fitness

Animals have a wide range of reproductive strategies and change how they produce offspring as a function of their age, environment, risk of predation or starvation, and as a result of trade-offs with other life history traits. In turn, these temporal patterns of reproduction, or fecundity dynamics, will determine how vulnerable the animal is to many of the same factors that shaped the dynamics in the first place. In this study, we tested how individual fecundity dynamics influence vulnerability of female fecundity to the deleterious environmental factors. We injured Drosophila melanogaster females at various moments during periods before and after mating. Injuries are prevalent in nature and provide a punctuated stimulus, making them particularly well suited to study their connection with the dynamics of reproduction. Our aim was to determine periods of vulnerability and impact of wounds on female fitness resulting from the change. The observed fecundity dynamics exhibited a high early peak in offspring production, suggesting that early after mating females might be particularly vulnerable to environmental conditions. However, females produced the same number of offspring, regardless of the time of injury, suggesting that fitness of female Drosophila is robust to wounds inflicted under laboratory conditions.

evolutionary biology↗

bioRxiv2024

Can seminal fluid proteins be honest signals of sperm availability?

Seminal fluid proteins (Sfps) are produced by males, yet they have significant effects on female physiology and behaviour. Sfps are often viewed as a mechanism for males to manipulate female reproductive behaviours, but despite many studies identifying their varied effects and their molecular underpinnings, the ways males and females use Sfps remain unclear. In the most studied case of Drosophila melanogaster particular peptides within the seminal fluid have been identified to guide female reproduction: sex peptide (SP, Acp70A) is known to induce changes in egg production, oviposition and remating and is attached to sperm and continuously supplied for days after mating, while ovulation inducing peptide, ovulin (Acp26Aa), is a free peptide with only short term effects after mating. Using a biologically informed model we show how these peptides can synchronize sperm and egg release, hence reducing the number of unfertilized eggs a female lays. We further show that the exhaustion of SP might be the key signal of this synchronization. Finally, we demonstrate that sexual conflict over the regulation of female reproductive physiology by Sfps should be limited, with the primary conflict probably centring around the regulation of remating behaviour.

evolutionary biology↗

bioRxiv2023

Humoral and T-cell-mediated responses to a pre-clinical Zika vaccine candidate that utilizes a unique insect-specific flavivirus platform

Vaccination is critical for the control and prevention of viral outbreaks, yet conventional vaccine platforms may involve trade-offs between immunogenicity and safety. Insect-specific viruses have emerged as a novel vaccine platform to overcome this challenge. Detailed studies of humoral and T-cell responses induced by new insect-specific flavivirus (ISFV)-based vaccine platforms are needed to better understand correlates of protection and improve vaccine efficacy. Previously, we used a novel ISFV called Aripo virus (ARPV) to create a Zika virus (ZIKV) vaccine candidate (designated ARPV/ZIKV). ARPV/ZIKV demonstrated exceptional safety and single-dose efficacy, completely protecting mice from a lethal ZIKV challenge. Here, we explore the development of immune responses induced by ARPV/ZIKV immunization and evaluate its correlates of protection. Passive transfer of ARPV/ZIKV-induced immune sera to naive mice prior to challenge emphasized the importance of neutralizing antibodies as a correlate of protection. Depletion of T-cells in vaccinated mice and adoptive transfer of ARPV/ZIKV-primed T-cells to naive mice prior to challenge indicated that ARPV/ZIKV-induced CD4+ and CD8+ T-cell responses contribute to the observed protection but may not be essential for protection during ZIKV challenge. However, vaccination of Rag1 KO, Tcra KO, and muMt- mice demonstrated the critical role for ARPV/ZIKV-induced T-cells in developing protective immune responses following vaccination. Overall, both humoral and T-cell-mediated responses induced by ISFV-based vaccines are important for comprehensive immunity, and ISFV platforms continue to be a promising method for future vaccine development.

microbiology↗

bioRxiv2022

The E2 glycoprotein holds key residues for Mayaro virus adaptation to the urban Aedes aegypti mosquito

Adaptation to mosquito vectors suited for transmission in urban settings is a major driver in the emergence of arboviruses. To better anticipate future emergence events, it is crucial to assess their potential to adapt to new vector hosts. In this work, we used two different experimental evolution approaches to study the adaptation process of an emerging alphavirus, Mayaro virus (MAYV), to Aedes aegypti, an urban mosquito vector of many arboviruses. We identified E2-T179N as a key mutation increasing MAYV replication in insect cells and enhancing transmission by live Aedes aegypti. In contrast, this mutation decreased viral replication and binding in human fibroblasts, a primary cellular target of MAYV in humans. We also showed that MAYV E2-T179N was attenuated in vivo in a mouse model. We then used structural and experimental analyses to show that MAYV E2-T179N bound less efficiently to human cells, though the decrease in replication or binding was not mediated through interaction with one of the host receptors, Mxra8. When this mutation was introduced in the closely related chikungunya virus, which has caused major outbreaks globally in the past two decades, we observed increased replication in both human and insect cells, suggesting E2 position 179 is an important determinant of alphavirus host-adaptation, although in a virus-specific manner. Collectively, these results indicate that adaptation at the T179 residue in MAYV E2 may result in increased vector competence - but coming at the cost of optimal replication in humans - and may represent a first step towards a future emergence event. Author SummaryMosquito-borne viruses must replicate in both mosquito and vertebrate hosts to be maintained in nature successfully. When viruses that are typically transmitted by forest dwelling mosquitoes enter urban environments due to deforestation or travel, they must adapt to urban mosquito vectors to transmit effectively. For mosquito-borne viruses, the need to also replicate in a vertebrate host like humans constrains this adaptation process. Towards understanding how the emerging alphavirus, Mayaro virus, might adapt to transmission by the urban mosquito vector, Aedes aegypti, we used natural evolution approaches to identify several viral mutations that impacted replication in both mosquito and vertebrate hosts. We show that a single mutation in the receptor binding protein increased transmission by Aedes aegypti but simultaneously reduced replication and disease in a mouse model, suggesting that this mutation alone is unlikely to be maintained in a natural transmission cycle between mosquitoes and humans. Understanding the adaptive potential of emerging viruses is critical to preventing future pandemics.

microbiology↗

bioRxiv2021

The mating system affects the temperature sensitivity of male and female fertility

O_LITo mitigate effects of climate change it is important to understand species responses to increasing temperatures. This has often been done by studying survival or activity at temperature extremes. Before such extremes are reached, however, effects on fertility may already be apparent. C_LIO_LISex differences in the thermal sensitivity of fertility (TSF) could impact species persistence under climate warming because female fertility is typically more limiting to population growth than male fertility. However, little is known about sex differences in TSF. C_LIO_LIHere we first demonstrate that the mating system can strongly influence TSF using the seed beetle Callosobruchus maculatus. We exposed populations carrying artificially induced mutations to two generations of short-term experimental evolution under alternative mating systems, manipulating the opportunity for natural and sexual selection on the mutations. We then measured TSF in males and females subjected to juvenile or adult heat stress. C_LIO_LIPopulations kept under natural and sexual selection had higher fitness, but similar TSF, compared to control populations kept under relaxed selection. However, females had higher TSF than males, and strikingly, this sex difference had increased over only two generations in populations evolving under sexual selection. C_LIO_LIWe hypothesized that an increase in male-induced harm to females during mating had played a central role in driving this evolved sex difference, and indeed, remating under conditions limiting male harassment of females reduced both male and female TSF. Moreover, we show that manipulation of mating system parameters in C. maculatus generates intraspecific variation in the sex difference in TSF equal to that found among a diverse set of studies on insects. C_LIO_LIOur study provides a causal link between the mating system and TSF. Sexual conflict, (re)mating rates, and genetic responses to sexual selection differ among ecological settings, mating systems and species. Our study therefore also provides mechanistic understanding for the variability in previously reported TSFs which can inform future experimental assays and predictions of species responses to climate warming. C_LI

ecology↗

bioRxiv2021

Co-Infection of cattle in Virginia with Theileria orientalis ikeda genotype and Anaplasma marginale

Theileria orientalis ikeda is a newly identified agent of bovine infectious anemia in the United States. Although it is transmitted by separate tick hosts than Anaplasma marginale - a bacterial etiology of bovine infectious anemia -the geographic distributions of these two infectious organisms overlap, with co-infection reported in some cattle. Only anaplasmosis has approved effective treatment in the United States. To provide rapid diagnostic information for producers with anemic animals, we developed a duplex qPCR for A. marginale and T. orientalis. With a cut-off of 38 cycles, the duplex assay has a sensitivity of 96.97% and a specificity of 100% for A. marginale; with a cut-off of 45 cycles, the duplex assay has a sensitivity and a specificity of 100% for T. orientalis. In addition to providing a tool for improved clinical decision-making for veterinarians and producers, this qPCR facilitates the study of co-infection rate of cattle in Virginia. Of 1,359 blood samples analyzed, 174 were positive for the presence of T. orientalis, 125 were positive for the presence of A. marginale, and 12 samples were positive for both T. orientalis and A. marginale. This indicated that co-infection of both of these etiologies of bovine infectious anemia does occur within the state of Virginia. It is likely that this pattern of infection will be seen in regions where T. orientalis and A. marginale are endemic, despite the difference in tick vectors.

microbiology↗

bioRxiv2021

A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation

SummaryWhile SARS-CoV-2 likely has animal origins1, the viral genetic changes necessary to adapt this animal-derived ancestral virus to humans are largely unknown, mostly due to low levels of sequence polymorphism and the notorious difficulties in experimental manipulations of coronavirus genomes. We scanned more than 182,000 SARS-CoV-2 genomes for selective sweep signatures and found that a distinct footprint of positive selection is located around a non-synonymous change (A1114G; T372A) within the Receptor-Binding Domain of the Spike protein, which likely played a critical role in overcoming species barriers and accomplishing interspecies transmission from animals to humans. Structural analysis indicated that the substitution of threonine with an alanine in SARS-CoV-2 concomitantly removes a predicted glycosylation site at N370, resulting in more favorable binding predictions to human ACE2, the cellular receptor. Using a novel bacteria-free cloning system for manipulating RNA virus genomes, we experimentally validated that this SARS-CoV-2-unique substitution significantly increases replication in human cells relative to its putative ancestral variant. Notably, this mutations impact on virus replication in human cells was much greater than that of the Spike D614G mutant, which has been widely reported to have been selected for during human-to-human transmission2,3.

microbiology↗

bioRxiv2020

Seasonal changes in recombination rate, crossover interference, and their response to desiccation stress in a natural population of Drosophila melanogaster from India

Environmental seasonality is a potent evolutionary force, capable to maintain polymorphism, promote phenotypic plasticity, and cause bet-hedging. In Drosophila, it has been reported to affect life-history traits, tolerance to abiotic stressors, and immunity. Oscillations in frequencies of alleles underlying fitness-related traits were also documented alongside SNP alleles across genome. Here, we test for seasonal changes in recombination in a natural D. melanogaster population from India using morphological markers of the three major chromosomes. We show that winter flies (collected after the dry season) have significantly higher desiccation tolerance than their autumn counterparts. This difference proved to hold also for hybrids with three independent marker stocks, suggesting its genetic rather than plastic nature. Significant segment-specific changes are documented for recombination rate (in five of 13 intervals) and crossover interference (in five of 16 studied pairs of intervals); both single- and double-crossover rates tended to increase in the winter cohort. The winter flies also display weaker plasticity of recombination characteristics to desiccation. We ascribe the observed differences to indirect selection on recombination caused by directional selection on desiccation tolerance. Our findings suggest that changes in recombination can arise even after a short period of seasonal adaptation (~8-10 generations).

evolutionary biology↗

bioRxiv2019

The tuatara genome: insights into vertebrate evolutionfrom the sole survivor of an ancient reptilian order

The tuatara (Sphenodon punctatus), the only living member of the archaic reptilian order Rhynchocephalia (Sphenodontia) once widespread across Gondwana, is an iconic and enigmatic terrestrial vertebrate endemic to New Zealand. A key link to the now extinct stem reptiles from which dinosaurs, modern reptiles, birds and mammals evolved, the tuatara provides exclusive insights into the ancestral amniotes. The tuatara genome, at [~]5 Gbp, is among the largest vertebrate genomes assembled. Analysis of this genome and comparisons to other vertebrates reinforces the uniqueness of the tuatara. Phylogenetic analyses indicate tuatara diverged from the snakes and lizards [~]250 MYA. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Genome sequence analysis identifies expansions of protein, non-protein-coding RNA families, and repeat elements, the latter of which show an extraordinary amalgam of reptilian and mammalian features. Sequencing of this genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. It also provides important insights into both the technical challenges and the cultural obligations associated with genome sequencing.

genomics↗

bioRxiv2018

Desiccation-induced changes in recombination rate and interference in fruit flies: an evidence for fitness-dependent plasticity

Meiotic recombination is evolutionarily ambiguous, giving both benefits and costs to its bearers, with the resultant depending on a variety of conditions. The existing theoretical models explain why recombination does exist while the existence of its essential features remains underexplored. Here we test whether recombination plasticity and interference plasticity are fitness dependent. We compare effects of desiccation on recombination and interference in chromosome 3 in desiccation-sensitive and desiccation-tolerant Drosophila lines. We show that in desiccation-sensitive genotypes the treatment causes significant segment-specific increase in single- and double-crossover frequencies while in desiccation-tolerant genotypes changes are less pronounced, if seen at all. These results indicate that desiccation is a recombinogenic factor, and that desiccation-induced changes in both recombination and interference are fitness dependent, with a negative-feedback pattern implying the tendency of less fitted individuals to produce more variable progeny. Such dependence may play an important role in regulation of genetic variation in population experiencing environmental challenges.

genetics↗