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bioRxiv2014

A Distance Method to Reconstruct Species Trees In the Presence of Gene Flow

One of the central tasks in evolutionary biology is to reconstruct the evolutionary relationships among species from sequence data, particularly from multilocus data. In the last ten years, many methods have been proposed to use the variance in the gene histories to estimate species trees by explicitly modeling deep coalescence. However, gene flow, another process that may produce gene history variance, has been less studied. In this paper, we propose a simple yet innovative method for species trees estimation in the presence of gene flow. Our method, called STEST (Species Tree Estimation from Speciation Times), constructs species tree estimates from pairwise speciation time or species divergence time estimates. By using methods that estimate speciation times in the presence of gene flow, (for example, M1 (Yang 2010) or SIM3s (Zhu and Yang 2012)), STEST is able to estimate species trees from data subject to gene flow. We develop two methods, called STEST (M1) and STEST (SIM3s), for this purpose. Additionally, we consider the method STEST (M0), which instead uses the M0 method (Yang 2002), a coalescent-based method that does not assume gene flow, to estimate speciation times. It is therefore devised to estimate species trees in the absence of gene flow. Our simulation studies show that STEST (M0) outperforms STEST(M1), STEST (SIM3s) and STEM in terms of estimation accuracy and outperfroms *BEAST in terms of running time when the degree of gene flow is small. STEST (M1) outperforms STEST (M0), STEST (SIM3s), STEM and *BEAST in term of estimation accuracy when the degree of gene flow is large. An empirical data set analyzed by these methods gives species tree estimates that are consistent with the previous results.

Evolutionary Biology↗

bioRxiv2017

Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible lineages

A major goal of evolutionary biology is to identify key evolutionary transitions that correspond with shifts in speciation and extinction rates. Stochastic character mapping has become the primary method used to infer the timing, nature, and number of character state transitions along the branches of a phylogeny. The method is widely employed for standard substitution models of character evolution. However, current approaches cannot be used for models that specifically test the association of character state transitions with shifts in diversification rates such as state-dependent speciation and extinction (SSE) models. Here we introduce a new stochastic character mapping algorithm that overcomes these limitations, and apply it to study mating system evolution over a time-calibrated phylogeny of the plant family Onagraceae. Utilizing a hidden state SSE model we tested the association of the loss of self-incompatibility with shifts in diversification rates. We found that self-compatible lineages have higher extinction rates and lower net-diversification rates compared to self-incompatible lineages. Furthermore, these results provide empirical evidence for the \"senescing\" diversification rates predicted in highly selfing lineages: our mapped character histories show that the loss of self-incompatibility is followed by a short-term spike in speciation rates, which declines after a time lag of several million years resulting in negative net-diversification. Lineages that have long been self-compatible, such as Fuchsia and Clarkia, are in a previously unrecognized and ongoing evolutionary decline. Our results demonstrate that stochastic character mapping of SSE models is a powerful tool for examining the timing and nature of both character state transitions and shifts in diversification rates over the phylogeny.

evolutionary biology↗

bioRxiv2018

Genome-wide disruption of DNA methylation by 5-aza-2’-deoxycytidine in the parasitioid wasp Nasonia vitripennis

DNA methylation of cytosine residues across the genome influences how genes and phenotypes are regulated in a wide range of organisms. As such, understanding the role of DNA methylation and other epigenetic mechanisms has become very much a part of mapping genotype to phenotype, a major question in evolutionary biology. Ideally, we would like to manipulate DNA methylation patterns on a genome-wide scale, to help us to elucidate the role that epigenetic modifications play in phenotypic expression. Recently, the demethylating agent 5-aza-2-deoxycytidine (5-aza-dC; commonly used in the epigenetic treatment of certain cancers), has been deployed to explore the epigenetic regulation of a number of traits of interest to evolutionary ecologists, including facultative sex allocation in the parasitoid wasp Nasonia vitripennis. In a recent study, we showed that treatment with 5-aza-dC did not ablate the facultative sex allocation response in Nasonia, but shifted the patterns of sex allocation in a way predicted by genomic conflict theory. This was the first (albeit indirect) experimental evidence for genomic conflict over sex allocation facilitated by DNA methylation. However, that work lacked direct evidence of the effects of 5-aza-dC on DNA methylation, and indeed the effect of the chemical has since been questioned in Nasonia. Here, using whole-genome bisulphite sequencing of more than 4 million CpGs, across more than 11,000 genes, we demonstrate unequivocally that 5-aza-dC disrupts methylation on a large scale across the Nasonia vitripennis genome. We show that the disruption can lead to both hypo- and hyper-methylation, may vary across tissues and time of sampling, and that the effects of 5-aza-dC are context- and sequence specific. We conclude that 5-aza-dC does indeed have the potential to be repurposed as a tool for studying the role of DNA methylation in evolutionary ecology, whilst many details of its action remain to be discovered. Author SummaryShedding light on the mechanistic basis of phenotypes is a major aim in the field of evolutionary biology. If we understand how phenotypes are controlled at the molecular level, we can begin to understand how evolution has shaped that phenotype and conversely, how genetic architecture may constrain trait evolution. Epigenetic markers (such as DNA methylation) also influence phenotypic expression by regulating how and when genes are expressed. Recently, 5-aza-2-deoxycytidine (5-aza-dC), a hypomethylating agent used in the treatment of certain cancers, has been used to explore the epigenetic regulation of traits of interest to evolutionary ecologists. Previously, we used 5-aza-dC to validate a role for DNA methylation in facultative sex allocation behaviour in the parasitoid wasp Nasonia vitripennis. However, the direct effects of the chemical were not examined at that point and its efficacy in insects was questioned. Here, we demonstrate that 5-aza-dC disrupts DNA methylation on a genome-wide scale in a context- and sequence-specific manner and results in both hypo- and hyper-methylation. Our work demonstrates that 5-aza-dC has the potential to be repurposed as a tool for studying the role of DNA methylation in phenotypic expression.

evolutionary biology↗

bioRxiv2019

Slow recovery from inbreeding depression generated by the complex genetic architecture of segregating deleterious mutations

The deleterious effects of inbreeding have been of extreme importance to evolutionary biology, but it has been difficult to characterize the complex interactions between genetic constraints and selection that lead to fitness loss and recovery after inbreeding. Viruses, bacteria, and the selfing nematode Caenorhabditis elegans have been shown to be capable of rapid recovery from the fixation of novel deleterious mutation, however the potential for fitness recovery from fixation of segregating variation under inbreeding in outcrossing organisms is poorly understood. C. remanei is an outcrossing relative of C. elegans with high polymorphic variation and extreme inbreeding depression. Here we sought to characterize changes C. remanei in patterns of genomic diversity after [~]30 generations of inbreeding via brother-sister mating followed by several hundred generations of recovery at large population size. As expected, inbreeding led to a large decline in reproductive fitness, but unlike results from mutation accumulation experiments, recovery from inbreeding at large populations sizes generated only very moderate recovery in fitness after 300 generations. At the genomic level, we found that while 66% of ancestral segregating SNPs were fixed in the inbred population, this was far fewer than expected under neutral processes. Under recovery, 36 SNPs across 30 genes involved in alimentary, muscular, nervous and reproductive systems changed reproducibly across all replicates, indicating that strong selection for fitness recovery does exist but is likely mutationally limited due to the large number of potential targets. Our results indicate that recovery from inbreeding depression via new compensatory mutations is likely to be constrained by the large number of segregating deleterious variants present in natural populations, limiting the capacity for rapid evolutionary rescue of small populations. Impact SummaryInbreeding is defined as mating between close relatives and can have a large effect on the genetic diversity and fitness of populations. This has been recognized for over 100 years of study in evolutionary biology, but the specific genomic changes that accompany inbreeding and the loss of fitness are still not known. Evolutionary theory predicts that inbred populations lose fitness through the fixation of many deleterious alleles and it is not known if populations can recover fitness after prolonged periods of inbreeding and deleterious fixations, or how long recovery may take. These questions are particularly important for wild populations experiencing declines. In this study we use laboratory populations of the nematode worm Caenorhabditis remanei to analyze the loss of fitness and genomic changes that accompany inbreeding via brother-sister mating, and to track the populations as they recover from inbreeding at large population size over 300 generations. We find that: O_LITotal progeny decreased by 65% after inbreeding C_LIO_LIThere were many nucleotides in the genome that remained heterozygous after inbreeding C_LIO_LIThere was an excess of inbreeding-resistant nucleotides on the X chromosome C_LIO_LIThe number of progeny remained low after 300 generations of recovery from inbreeding C_LIO_LI30 genes changed significant in allele frequency during recovery, including genes involved in the alimentary, muscular, nervous and reproductive systems C_LI Together, our results demonstrate that recovery from inbreeding is difficult, likely due to the fixation of numerous deleterious alleles throughout the genome.

evolutionary biology↗

bioRxiv2024

Comprehensive analysis of 111 Pleuronectiformes mitochondrial genomes: insights into structure, conservation, variation and evolution

Pleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, is limited. In this study, we analyzed the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstructed the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species. Our analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes across species. The mitochondrial genomes of most flatfish were conservative, while obvious gene rearrangements were found in several species, especially for the whole region rearrangement of nad5-nad6-cytb in Samaridae family and the swapping rearrangement of nad6 and cytb gene in Bothidae family, suggesting a unique evolutionary history or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, with Samaridae family forming a distinct outgroup when the first approach was used. The identification of simple sequence repeats and various long repetitive sequences (forward, reverse, palindromic and complementary repeats) provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices. In summary, this study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into the conservation biology, evolutionary biology and functional usages of variations.

genomics↗

bioRxiv2020

Epigenetic clock and DNA methylation studies of roe deer in the wild

DNA methylation-based biomarkers of aging (epigenetic clocks) promise to lead to new insights in the evolutionary biology of ageing. Relatively little is known about how the natural environment affects epigenetic aging effects in wild species. In this study, we took advantage of a unique long-term (>40 years) longitudinal monitoring of individual roe deer (Capreolus capreolus) living in two wild populations (Chize and Trois Fontaines, France) facing different ecological contexts to investigate the relationship between chronological age and levels of DNA methylation (DNAm). We generated novel DNA methylation data from n=90 blood samples using a custom methylation array (HorvathMammalMethylChip40). We present three DNA methylation-based estimators of age (DNAm or epigenetic age), which were trained in males, females, and both sexes combined. We investigated how sex differences influenced the relationship between DNAm age and chronological age through the use of sex-specific epigenetic clocks. Our results highlight that both populations and sex influence the epigenetic age, with the bias toward a stronger male average age acceleration (i.e. differences between epigenetic age and chronological ages) particularly pronounced in the population facing harsh environmental conditions. Further, we identify the main sites of epigenetic alteration that have distinct aging patterns across the two sexes. These findings open the door to promising avenues of research at the crossroad of evolutionary biology and biogerontology.

evolutionary biology↗

bioRxiv2023

Selection leads to false inferences of introgression using popular methods

Detecting introgression between closely related populations or species is a fundamental objective in evolutionary biology. Existing methods for detecting migration and inferring migration rates from population genetic data often assume a neutral model of evolution. Growing evidence of the pervasive impact of selection on large portions of the genome across diverse taxa suggests that this assumption is unrealistic in most empirical systems. Further, ignoring selection has previously been shown to negatively impact demographic inferences (e.g., of population size histories). However, the impacts of biologically realistic selection on inferences of migration remain poorly explored. Here, we simulate data under models of background selection, selective sweeps, balancing selection, and adaptive introgression. We show that ignoring selection sometimes leads to false inferences of migration in popularly used methods that rely on the site frequency spectrum (SFS). Specifically, balancing selection and some models of background selection result in the rejection of isolation-only models in favor of isolation-with-migration models and lead to elevated estimates of migration rates. BPP, a method that analyzes sequence data directly, showed false positives for all conditions at recent divergence times, but balancing selection also led to false positives at medium divergence times. Our results suggest that such methods may be unreliable in some empirical systems, such that new methods that are robust to selection need to be developed. Article SummaryDetecting migration between closely related populations is a central objective in many evolutionary biology studies. However, popular methods for detecting migration assume a simplified model of evolution. Here, we evaluate the impacts of biologically realistic natural selection, recombination, and mutation on three methods for detecting migration. We find that biological complexity leads to false inferences of migration, suggesting that results should be interpreted with caution and that new methods are needed to make robust inferences of migration across empirical systems.

evolutionary biology↗

bioRxiv2018

Genotypic context modulates fitness landscapes: Effects onthe speed and direction of evolution for antimicrobialresistance

Understanding the forces that drive the dynamics of adaptive evolution is a goal of many subfields within evolutionary biology. The fitness landscape analogy has served as a useful abstraction for addressing these topics across many systems, and recent treatments have revealed how different environments can frame the particulars of adaptive evolution by changing the topography of fitness landscapes. In this study, we examine how the larger, ambient genotypic context in which the fitness landscape being modeled is embedded affects fitness landscape topography and subsequent evolution. Using simulations on empirical fitness landscapes, we discover that genotypic context, defined by genetic variability in regions outside of the locus under study (in this case, an essential bacterial enzyme target of antibiotics), influences the speed and direction of evolution in several surprising ways. These findings have implications for how we study the evolution of drug resistance in nature, and for presumptions about how biological evolution might be expected to occur in genetically-modified organisms. More generally, the findings speak to theory surrounding how \"difference can beget difference\" in adaptive evolution: that small genetic differences between organisms can greatly alter the specifics of how evolution occurs, which can rapidly drive even slightly diverged populations further apart.\n\nAuthor summaryTechnological advances enable scientists to engineer individual mutations at specific sites within an organisms genome with increasing ease. These breakthroughs have provided scientists with tools to study how different engineered mutations affect the function of a given gene or protein, yielding useful insight into genotype-phenotype mapping and evolution. In this study, we use engineered strains of bacteria to show how the dynamics (speed and direction) of evolution of drug resistance in an enzyme depends on the species-type of that bacterial enzyme, and on the presence/absence of mutations in other genes in the bacterial genome. These findings have broad implications for public health, genetic engineering, and theories of speciation. In the context of public health and biomedicine, our results suggest that future efforts in managing antimicrobial resistance must consider genetic makeup of different pathogen populations before predicting how resistance will occur, rather than assuming that the same resistance pathways will appear in different pathogen populations. With regard to broader theory in evolutionary biology, our results show how even small genetic differences between organisms can alter how future evolution occurs, potentially causing closely-related populations to quickly diverge.

evolutionary biology↗

bioRxiv2018

Reproduction and longevity A Mendelian randomization study of gonadotropin-releasing hormone and ischemic heart disease

BackgroundAccording to well-established evolutionary biology theory reproduction trades-off against longevity, implying that upregulating the reproductive axis might drive major diseases. We assessed whether the central driver of reproduction gonadotropin-releasing hormone 1 (GnRH1) had a causal effect on the leading cause of global morbidity and mortality, i.e. ischemic heart disease (IHD). As a contrast we similarly examined the role of GnRH2 because it is more a driver of female sexual behavior.\n\nMethodsWe applied strong (p-value <5x10-6) and independent genetic predictors of GnRH1 and GnRH2 to an extensively genotyped IHD case (n=76,014) - control (n=264,785) study using multiplicative random effects inverse variance weighted (IVW), weighted median, MR-Egger and MR-PRESSO estimates.\n\nResultsGnRH1, predicted by 11 genetic variants, was positively associated with IHD (IVW odds ratio (OR) 1.04 per effect size, 95% confidence interval (CI) 1.01 to 1.08), but GnRH2, predicted by 15 genetic variants, was not (IVW OR 0.98, 95% CI 0.95 to 1.02).\n\nConclusionsGnRH1 is a potential IHD genetic target. Apart from demonstrating a central tenet of evolutionary biology in humans, our study suggests that existing treatments and environmental factors targeting GnRH1, its drivers or consequences could be re-purposed to prevent and treat IHD. Given, the importance of reproduction to the human species, many such exposures likely exist.

evolutionary biology↗

bioRxiv2024

Genetic differentiation is constrained to chromosomal inversions and putative centromeres in locally adapted populations with higher gene flow

The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes in shaping genetic diversity across genomes and among populations. This is particularly relevant when local adaptation occurs despite gene flow, where clustering of differentiated loci can maintain locally adapted variants by reducing recombination between them. However, the limited genomic resources for non-model species, including reference genomes and recombination maps, has constrained our understanding of these patterns. In this study, we leverage the Atlantic silverside--a non-model fish with extensive local adaptation across a steep latitudinal gradient--as an ideal system to explore how genome structure influences adaptation under varying levels of gene flow, using a newly available reference genome and multiple recombination maps. Analyzing 168 genomes from four populations, we found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. With increasing gene flow, the number and clustering of FST outlier loci also increased, with differentiated loci tightly clustered in large haploblocks harboring inversions and smaller peaks overlapping putative centromeres. Notably, sequence divergence was only evident in inversions, supporting their role in adaptive divergence with gene flow, whereas centromeres appeared differentiated because of low recombination and reduced diversity, with no indication of elevated sequence divergence. Our results support the hypothesis that clustered genomic architectures evolve with high gene flow and enhance our understanding of how inversions and centromeres are linked to different evolutionary processes. Significance StatementHow populations preserve favorable combinations of genes adapted to their local environment despite reproducing with populations adapted to different conditions is a longstanding question in evolutionary biology. By analyzing the genomes of 168 Atlantic silverside fish from four populations, we found that when populations adapted to different environments frequently interbreed, genetic differences concentrate in specific parts of the genome, particularly in chromosomal inversions--where segments of DNA are flipped. These inversions help preserve locally adapted gene combinations, enabling populations to maintain differences essential for survival in their habitats. This research enhances our understanding of genomic adaptation, a fundamental evolutionary question with increasing relevance as environmental changes pose new challenges globally.

evolutionary biology↗

bioRxiv2026

Direct selection under resource allocation trade-offs enables the evolution of obligate and facultative sexuality

Sexual reproduction is considered to incur multiple costs relative to asexual reproduction. Although previous research has identified indirect selective advantages that help explain the widespread occurrence of sex, the emergence and maintenance of high rates of sexual reproduction remain a central puzzle in evolutionary biology, because indirect selection favoring sex becomes weak when the sexual rate is high. Using a modifier framework that allows the simultaneous evolution of sexual rate and sex allocation, I investigate the evolution of sex via direct selection by incorporating resource allocation trade-offs between sexual and asexual reproduction. The results show that such trade-offs can substantially facilitate the invasion of sex. Crucially, the evolutionarily stable sexual rate depends on the return exponents of female fertility and asexual fertility with respect to resource investment, as well as on the initial allocation to female function within sexual reproduction. Obligate sexuality is evolutionarily stable when asexual fertility exhibits linear or accelerating returns on investment and when both the initial sexual rate and female function allocation within sexual reproduction exceed certain levels. In contrast, facultative sexuality will be evolutionarily stable when female fertility within sexual reproduction and/or asexual fertility exhibit diminishing returns. Contrary to previous theoretical predictions, self-fertilization often inhibits the evolution of sex or reduces the evolutionarily stable sexual rate. This study provides insights into the prevalence of high sexual rates, as well as the continuous spectrum of sexual rates in some groups, highlighting the importance of key parameters in reproductive ecology in shaping the evolution of sex. Significance statementWhy sexual reproduction is so common despite its substantial costs remains a longstanding puzzle in evolutionary biology. Most previous explanations focus on indirect genetic benefits of sex, which generally become weaker as the rate of sexual reproduction increases, and therefore cannot explain the prevalence of intermediate to high sexual rates in nature. This study shows that with resource allocation trade-offs between sexual and asexual reproduction, obligate or facultative sexuality can evolve and be stably maintained via direct selection alone, depending on the marginal returns of asexual and female fertility, as well as the initial allocation to female function. These results highlight the underappreciated role of reproductive ecology in shaping the evolution of sex in nature.

evolutionary biology↗

bioRxiv2014

Bridging the Genotype and the Phenotype: Towards An Epigenetic Landscape Approach to Evolutionary Systems Biology

Understanding the mapping of genotypes into phenotypes is a central challenge of current biological research. Such mapping, conceptually represents a developmental mechanism through which phenotypic variation can be generated. Given the nongenetic character of developmental dynamics, phenotypic variation to a great extent has been neglected in the study of evolution. What is the relevance of considering this generative process in the study of evolution? How can we study its evolutionary consequences? Despite an historical systematic bias towards linear causation schemes in biology; in the post-genomic era, a systems-view to biology based on nonlinear (network) thinking is increasingly being adopted. Within this view, evolutionary dynamics can be studied using simple dynamical models of gene regulatory networks (GRNs). Through the study of GRN dynamics, genotypes and phenotypes can be unambiguously defined. The orchestrating role of GRNs constitutes an operational non-linear genotype-phenotype map. Further extension of these GRN models in order to explore and characterize an associated Epigenetic Landscape enables the study of the evolutionary consequences of both genetic and non-genetic sources of phenotypic variation within the same coherent theoretical framework. The merging of conceptually clear theories, computational/mathematical tools, and molecular/genomic data into coherent frameworks could be the basis for a transformation of biological research from mainly a descriptive exercise into a truly mechanistic, explanatory endeavor.

Systems Biology↗

bioRxiv2024

Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation

A major question in evolutionary biology is what drives the diversification of lineages. Rapid, recent radiations are ideal systems for addressing how new species arise because they still show key morphological and ecological adaptations associated with speciation. While most studied recent radiations have evolved in an insular environment, less research has been carried out on continental radiations with complex species interactions. Melinaea and Mechanitis butterflies (Nymphalidae: Ithomiini) have rapidly radiated in the Neotropics. They are classical models for Amazonian biogeography and colour pattern mimicry and have been proposed as biodiversity indicators. We generated reference genomes for five species of each genus, and whole-genome resequencing data of most species and subspecies covering a wide geographic range to assess phylogeographic relationships, patterns of hybridisation and chromosomal rearrangements. Our data help resolve the classification of these taxonomically challenging butterflies and reveal very high diversification rates. We find rampant evidence of historical hybridisation and putative hybrid species in both radiations, which may have facilitated their rapid diversification. Moreover, dozens of chromosomal fusions and fissions were identified between congeneric species, and even some within species. We conclude that interactions between geography, hybridisation and chromosomal rearrangements have contributed to these two rapid radiations in the highly diverse Neotropical region. We suggest that rapid radiations may be spurred by repeated periods of geographic isolation during Pleistocene climate oscillations, combined with lineage-specific rapid accumulation of incompatibilities during allopatric phases, followed by secondary contact with some gene exchange. Significance StatementUnderstanding factors contributing to rapid speciation is a key aim of evolutionary biology. Here we focus on two rapid radiations of Neotropical butterflies. Our genomic data with broad taxonomic and geographic coverage reveal rampant hybridisation and chromosomal rearrangements, each likely contributing to the high diversification rates. Our study highlights the use of genomic data to resolve taxonomically challenging species groups and elucidate drivers of diversification in rapid radiations. We show that for biodiversity hotspots with recent radiations, barcoding is insufficient to characterise species richness due to gene flow and recent speciation. The taxonomic implications of both introgression and karyotype diversity for species delimitation are important to consider during monitoring and management of biodiversity in these vulnerable habitats.

evolutionary biology↗

bioRxiv2025

Selection inference in a complex genomic landscape: the role of inversions in the spruce bark beetle

Understanding the genetic basis of adaptation is a key objective in evolutionary biology. Although advances in genomic selection scans have greatly improved our ability to detect signatures of adaptation, distinguishing true signals from false positives remains challenging. This task is particularly difficult in regions of reduced recombination, such as polymorphic inversions. In this study, we examine the genome-wide landscape of selection in the European spruce bark beetle (Ips typographus), Europes most destructive forest pest, which has one of the most complex inversion-associated recombination landscapes known. Using simulation-based analyses and whole-genome resequencing data from 312 individuals across 23 populations, we applied two complementary selection scan methods (nSL and {Lambda}) to assess how inversions influence the detection of adaptive signals. Simulations revealed that the two selection scan methods differ in their susceptibility to false-positive signals within inversions and that partitioning data by inversion genotype (i.e., homozygote classes) can substantially reduce these errors. Consistent with the results of our simulations, our empirical data showed that inversions are highly enriched for selection signals when all inversion genotypes are analyzed but are depleted when only homozygotes are considered. This demonstrates that focusing on homozygote genotypes allows for a more precise identification of putative selection targets and haplotype-specific signals, as it overcomes the confounding effects of suppressed recombination in heterokaryotypic individuals. In contrast, the detection of selection in collinear regions was largely unaffected by the presence of inversions. Our findings highlight that inversions may play an important role in shaping adaptation, underscoring the need to account for species-specific genomic architecture when interpreting signals from selection scans. Author summaryDetecting the genetic basis of adaptation is one of the main goals in evolutionary biology. However, it is often difficult to tell whether selection signals identified by genome scans truly reflect natural selection signatures or are simply artefacts of genome structure. In this study, we examined how polymorphic inversions affect the detection of selection in the European spruce bark beetle, one of Europes most destructive forest pests. First, we assessed two selection scan methods using simulation approach. Second, we tested the influence of polymorphic inversion on the selection inference using genome-wide data from 23 beetle populations. We showed that inversions can create false signals of selection when all individuals are analyzed together but by separating individuals according to their inversion genotypes, we were able to distinguish potential adaptive regions from false positives. Our results demonstrate that accounting for genomic architecture is crucial for identifying selection signatures and provide practical guidelines for studying species with inversion-rich genomes.

evolutionary biology↗

bioRxiv2024

Chromosome Numbers and Reproductive Life Cycles in Green Plants: A Genomic Perspective

The strong correlation between reproductive life cycle type and chromosome numbers in green plants has been a long-standing mystery in evolutionary biology. Within green plants, the derived condition of heterosporous reproduction has emerged from the ancestral condition of homospory in disparate locations on the phylogenetic tree at least 11 times, of which 3 lineages are extant. In all green plant lineages where heterospory has emerged, there has been a significant downsizing in chromosome numbers (refer to figure 1). This dynamic has been investigated without clear answers for many decades. In this study, we combine known ideas from existing literature with novel methods, tools, and data to generate fresh insights into an old question. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/604804v3_fig1.gif" ALT="Figure 1"> View larger version (8K): org.highwire.dtl.DTLVardef@fcc574org.highwire.dtl.DTLVardef@10759bforg.highwire.dtl.DTLVardef@1950e33org.highwire.dtl.DTLVardef@d7718d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:-C_FLOATNO A simplified phylogeny of green plants/Embryophytes with the respective group and their average chromosome numbers in each group. Heterosporous lineages highlighted in green. C_FIG Using gene family evolution models and selection analyses, we identified gene families that have undergone significant expansion, contraction, or selection in heterosporous lineages. Our results reveal both shared and lineage-specific genomic changes associated with the evolution of heterospory. We found expansions in gene families related to developmental regulation, signaling pathways, and stress responses across heterosporous groups. Notably, the MATE efflux family showed consistent expansion and evidence of selection in heterosporous lineages, suggesting a potentially conserved role in heterospory evolution. These findings highlight novel insights that may underpin the association between heterospory and reduced chromosome numbers. The general importance of chromosome numbers, structure, and sizes in cellular biology notwithstanding, the association between the emergence of heterosporous reproduction and chromosome number reduction/genome downsizing is not fully understood. It remains unclear why there exists an association between aspects of biology at such disparate levels as reproductive life-cycles and chromosome numbers/genome size. Exploring and answering this conundrum of evolutionary biology can add to our broader understanding of life sciences and of biology at different levels. Applying the novel tools and methods emerging from ongoing progress in biotechnology and computational sciences presents an opportunity to make new inroads into this long-standing question.

bioinformatics↗

bioRxiv2021

The role of migration in mutant evolution in fragmented populations

Mutant evolution in fragmented populations has been studied extensively in evolutionary biology. With an increased focus on evolutionary dynamics in medical research, quantification of mutant load in fragmented populations with varying levels of migration has become especially important. Examples of fragmented populations are hematopoietic stem cell niches in the bone marrow where cells can re-circulate between niches through the blood, or colonic crypts where movement of cells across different crypts is not thought to be common. Here we use a combination of experiments and theory to investigate the role of migration in mutant distribution. In the case of neutral mutants, the experiments confirmed that while the mean number of mutants is not influenced by migration, the probability distribution is, which manifested itself in a change in the skewedness of the distribution of the mutant numbers in the demes. In the case of disadvantageous mutants, we investigated the phenomenon of the increase in the expected number of mutants compared to that of the selection-mutation balance. In a single deme, this increase is observed when the deme size is lower than the critical size, Nc. In a fragmented system that consists of connected demes with a probability of migration, the increase in mutant numbers above the selection-mutation balance can be maintained in small (N < Nc) demes as long as the migration rate is sufficiently small. The migration rate above which the mutants approach the selection-mutation balance decays exponentially with N/Nc. These findings are relevant in the context of the complex and poorly understood processes that may lead to changes in the clonal composition in tissues and tumors.

evolutionary biology↗

bioRxiv2018

Evolutionary rate coevolution between mitochondria and mitochondria-associated nuclear-encoded proteins in insects

The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. How these two genomes coevolve is a long-standing question in evolutionary biology. Here we initially investigate the evolutionary rates of mitochondrial components (oxidative phosphorylation (OXPHOS) proteins and ribosomal RNAs) and nuclear-encoded proteins associated with mitochondria, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondria and mitochondria-associated nuclear-encoded proteins, which is likely driven by different rates of mitochondrial sequence evolution and compensatory changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for nuclear-encoded OXPHOS proteins in contact with mitochondrial-encoded OXPHOS proteins and nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNA. Mitochondrial-associated proteins show apparent rate acceleration over evolutionary time, but we suspect this pattern to be due to artifacts (e.g. rate estimation or calibration bias). We find that ERC between mitochondrial and nuclear proteins is a strong predictor of nuclear proteins known to interact with mitochondria, and therefore ERCs can be used to predict new candidate nuclear proteins with mitochondrial function. Using this approach, we detect proteins with high ERCs but not with known mitochondrial function based on gene ontology (GO). Manual screening of the literature revealed potential mitochondrial function for some of these proteins in humans or yeast. Their holometabolous ERCs therefore indicate these proteins may have phylogenetically conserved mitochondrial function. Twenty three additional candidates warrant further study for mitochondrial function based on this approach, including ERC evidence that proteins in the minichromosome maintenance helicase (MCM) complex interact with mitochondria. We conclude that the ERC method shows promise for identifying new candidate proteins with mitochondrial function.

evolutionary biology↗

bioRxiv2026

The hypercubic Mk model in reduced state space for the coupled, reversible coevolution of multiple binary characters

Many scientific questions involve the coevolution of coupled, binary features over time - from phenotypes in evolutionary biology to mutations in cancer development. Evolutionary accumulation models (EvAMs) often neglect reversibility in these systems, uncertainty in observations, and/or phylogenetic connections between observations. By contrast, the Mk model from phylogenetic comparative methods supports reversibility, uncertainty, and relatedness, but compute time scales like O(4L) in number of features L, making it challenging to apply to more than about six coupled, coevolving binary characters. Here, we introduce HyperMk2, a method using output from a Fitch-like parsimony algorithm to reduce the state space associated with many coevolving characters while retaining flexibility, reversibility, and phylogenetic information. This approach, while approximate, scales linearly in the number of distinct observations rather than exponentially in the number of characters, supporting the investigation of much larger systems than previously possible. We demonstrate how this method allows the inference of evolutionary dynamics of anti-microbial resistance in bacteria, including the identification of potential influences between characters, and discuss its broader application.

evolutionary biology↗