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Results for “Evolutionary Biology”

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bioRxiv2025

Analysis of duplication and possible sub-functionalization of wing gene network components in pea aphids

A fundamental focus of evolutionary-developmental biology is uncovering the genetic mechanisms responsible for the gain and loss of characters. One approach to this question is to investigate changes in the coordinated expression of a group of genes important for the development of a character of interest (a gene regulatory network). Here we consider the possibility that modifications to the wing gene regulatory network (wGRN), as defined by work primarily done in Drosophila melanogaster, were involved in the evolution of wing dimorphisms of the pea aphid (Acyrthosiphon pisum). We hypothesize that this may have occurred via changes in expression levels or duplication followed by sub-functionalization of wGRN components. To test this, we annotated members of the wGRN in the pea aphid genome and assessed their expression levels in first and third nymphal instars of winged and wingless morphs of males and asexual females. We find that only two of the 32 assessed genes exhibit morph-biased expression. We also find that three wing genes (apterous (ap), warts (wts), and decapentaplegic (dpp)) have undergone gene duplication. In each case, the resulting paralogs show signs of functional divergence, exhibiting either sex-, morph-, or stage-specific expression. Two gene duplicates, wts2 and dpp3, are of particular interest with respect to wing dimorphism, as they exhibit a wingless male-specific isoform and wingless male-biased expression, respectively. These results supplement our understanding of trends in developmental gene network evolution, such as side-stepping pleiotropic constraint via duplication and sub-functionalization, underlying the emergence of novel phenotypes.

evolutionary biology↗

bioRxiv2021

BMP signaling underlies the craniofacial heterochrony in phyllostomid bats, a hyperdiverse mammal group

The potential for variation and the capacity to evolve in response to ecological opportunity are important aspects of an adaptive radiation. Identifying the origin of phenotypic variation, in which natural selection might act upon, is a major goal of evolutionary developmental biology. The New World leaf-nosed bats (phyllostomids) are a textbook example of an adaptive radiation. Their cranial morphology is diverse along relative facial length, which is related to their diets. We previously used geometric morphometrics to reveal peramorphosis, a type of heterochrony, in the cranial evolution among phyllostomid bats. We then demonstrated that the mechanism of peramorphic diversity in phyllostomid rostrum length resulted from altered cellular proliferation. Here, we investigate the progenitors of the face, the cranial neural crest, and a key signaling pathway related to their proliferation and differentiation into mature tissues: the bone morphogenetic protein (BMP). With geometric morphometrics, immunofluorescence, and confocal imaging--in three phyllostomid species and one outgroup bat species--we show the molecular patterns that underlie the adaptive and innovative traits seen in phyllostomid bats. Then, with mouse genetics, we mimic the BMP molecular pattern observed in nectar feeding bats and recapitulate the elongated morphological variation in mice. Surprisingly, we also observe an expansion in the nose-tip of mice, akin to the expanding leaf-nose tissue in phyllostomid bats. These data, combined with the mouse genetics literature on BMP signaling, suggest the BMP developmental pathway plays a central role in shaping the craniofacial variation necessary for adaptation in bats. Further, we speculate that the BMP signaling pathway could underlie other bizarre facial phenotypes in mammals that are derived from frontonasal mesenchyme, such as the proboscis. Overall, this study combines a comparative framework to developmental data, with a genetic approach, to directly investigate the role of development on complex morphology.

evolutionary biology↗

bioRxiv2022

Why is the average collateral effect of synonymous mutations so similar across alternative reading frames?

The standard genetic code has been shown to have multiple interesting properties which impact on molecular biology and the evolutionary process. One facet of molecular biology where code structure is particularly important is the origin and evolution of overlapping genes. We have previously reported that the structure of the standard genetic code ensures that synonymous mutations in a protein coding gene will lead to a remarkably similar average "collateral" mutation effect size in at least four out of the five alternative reading frames. Here we show that only 0.26% of alternative codes with the block structure of the standard genetic code perform at least as well as the standard code in this property. Considering this finding within a code optimality framework suggests that this consistent effect size across the different frames may be adaptive. Here we give context for this finding and present a simple model where a trade-off between evolvability and robustness leads to an average mutation effect size which maximises population fitness. This supports the intuition that similar mutation effects across the different alternative reading frames may be an adaptive property of the standard genetic code which facilitates evolvability through the use of alternative reading frames.

evolutionary biology↗

bioRxiv2016

Uplift and erosion of genomic islands with standing genetic variation

Details of the processes that generate biological diversity have long been of interest to evolutionary biologists. A common theme in nature is diversification via divergent selection with gene flow. Empirical studies on this topic find variable genetic differentiation throughout the genome, that genetic differentiation is non-randomly distributed, and that loci of adaptive significance are often found clustered together within \"genomic islands of divergence\". Theoretical models based on new mutations show how these genomic islands can arise and grow as a result of a complex interaction of various evolutionary and genic processes. In the current study, I ask if such genomic islands can alternatively arise from divergent selection from standing genetic variation and I tested this using a simple two locus model of selection. There are numerous ways in which standing genetic variation can be partitioned (e.g., between alleles, between loci, and between populations) and I tested which of these scenarios can give rise to an island pattern compared to no genomic differentiation or complete genomic differentiation. I found that divergent selection, even without reciprocal gene exchange between populations, following a bout of admixture can relatively quickly produce an island pattern. Moreover, I found two pathways in which islands can form from divergence from standing variation: 1) through the build up of islands and 2) through the breakdown of larger, genome-wide differentiation. Lastly, similar to new mutation theory, I found that the frequency of recombination is an important determinant of island formation from standing genetic variation such that mating behavior of a species (e.g., facultative or obligate sexual) can impact the likelihood of island formation.

Evolutionary Biology↗

bioRxiv2017

TreeTime: maximum likelihood phylodynamic analysis

Mutations that accumulate in the genome of replicating biological organisms can be used to infer their evolutionary history. In the case of measurably evolving organisms genomes often reveal their detailed spatiotemporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly evolving viral pathogens. The number of genome sequences available for different pathogens, however, has increased dramatically over the last couple of years and traditional methods for phylodynamic analysis scale poorly with growing data sets. Here, we present TreeTime, a Python based framework for phylodynamic analysis using an approximate Maximum Likelihood approach. TreeTime can estimate ancestral states, infer evolution models, reroot trees to maximize temporal signals, estimate molecular clock phylogenies and population size histories. The run time of TreeTime scales linearly with data set size.

evolutionary biology↗

bioRxiv2020

Were ancestral proteins less specific?

Some have hypothesized that ancestral proteins were, on average, less specific than their descendants. If true, this would provide a universal axis along which to organize protein evolution and suggests that reconstructed ancestral proteins may be uniquely powerful tools for protein engineering. Ancestral sequence reconstruction studies are one line of evidence used to support this hypothesis. Previously, we performed such a study, investigating the evolution of peptide binding specificity for the paralogs S100A5 and S100A6. The modern proteins appeared more specific than their last common ancestor (ancA5/A6), as each paralog bound a subset of the peptides bound by ancA5/A6. In the current study, we revisit this transition, using quantitative phage display to measure the interactions of 19,194 random peptides with human S100A5, S100A6, and ancA5/A6. This unbiased screen reveals a different picture. While S100A5 and S100A6 do indeed bind to a subset of the peptides recognized by ancA5/A6, they also acquired new peptide partners outside of the set recognized by ancA5/A6. Our previous work showed that ancA5/A6 had lower specificity than its descendants when measured against biological targets; our new work shows that ancA5/A6 has similar specificity to the modern proteins when measured against a random set of peptide targets. This demonstrates that altered biological specificity does not necessarily indicate altered intrinsic specificity, and sounds a cautionary note for using ancestral reconstruction studies with biological targets as a means to infer global evolutionary trends in specificity.

evolutionary biology↗

bioRxiv2022

Pervasive gene duplications as a major evolutionary driver of coral biology

Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to these ecosystems, providing habitat and food to a great diversity of species. In the frame of the Tara Pacific expedition, we generated two coral genomes, Porites lobata and Pocillopora meandrina with vastly improved contiguity that allowed us to study the functional organisation of these genomes. We annotated their gene catalog and report a relatively higher gene number (43,000 and 32,000 genes respectively) than that found in other public coral genome sequences. This finding is explained by a high number of tandemly duplicated genes (almost a third of the predicted genes). We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to immune system and disease-resistance, which we suggest to be functionally linked to coral host resilience. At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

genomics↗

bioRxiv2022

Morphological evolution of bird wings follows a mechanical sensitivity gradient determined by the aerodynamics of flapping flight

The physical principles that govern the function of biological structures also mediate their evolution, but the evolutionary drivers of morphological traits within complex structures can be difficult to predict. We used morphological traits measured from 1096 3-dimensional bird wing scans from 178 species to test how two frameworks for relating morphology to evolution interact. We examined whether the modular organization of the wing into handwing and armwing regions, or the relationship between trait morphology and functional output (i.e. mechanical sensitivity, driven here by flapping flight aerodynamics) dominate evolutionary rate ({sigma}2) and mode. Our results support discretization of the armwing and handwing as morphological modules, but morphological disparity and{sigma} 2 varied continuously with the mechanical sensitivity gradient and were not modular. Thus, mechanical sensitivity should be considered an independent driver of evolutionary dynamics, distinct from morphological modularity. TeaserMechanical sensitivity drives wing shape evolution in birds and may be fundamental to the evolution of biomechanical systems.

evolutionary biology↗

bioRxiv2022

Exploring the distribution of phylogenetic networks generated under a birth-death-hybridization process

Gene-flow processes such as hybridization and introgression play important roles in shaping diversity across the tree of life. Recent studies extending birth-death models have made it possible to investigate patterns of reticulation in a macroevolutionary context. These models allow for different macroevolutionary patterns of gene flow events that can either add, maintain, or remove lineages--with the gene flow itself possibly being dependent on the relatedness between species--thus creating complex diversification scenarios. Further, many reticulate phylogenetic inference methods assume specific reticulation structures or phylogenies belonging to certain network classes. However, the distributions of phylogenetic networks under reticulate birth-death processes are poorly characterized, and it is unknown whether they violate common methodological assumptions. We use simulation techniques to explore phylogenetic network space under a birth-death-hybridization process where the hybridization rate can have a linear dependence on genetic distance. Specifically, we measured the number of lineages through time and role of hybridization in diversification along with the proportion of phylogenetic networks that belong to commonly used network classes (e.g., tree-child, tree-based, or level-1 networks). We find that the growth of phylogenetic networks and class membership are largely affected by assumptions about macroevolutionary patterns of gene flow. In accordance with previous studies, a lower proportion of networks belonged to these classes based on type and density of reticulate events. However, under a birth-death-hybridization process, these factors form an antagonistic relationship; the type of reticulation events that cause high membership proportions also lead to the highest reticulation density, consequently lowering the overall proportion of phylogenies in some classes. Further, we observed that genetic distance-dependent gene flow and incomplete sampling increase the proportion of class membership, primarily due to having fewer reticulate events. Our results can inform studies if their biological expectations of gene flow are associated with evolutionary histories that satisfy the assumptions of current methodology and aid in finding phylogenetic classes that are relevant for methods development.

evolutionary biology↗

bioRxiv2024

Discordance between phylogenomic datasets in aphids: who is telling the truth?

Aphids (Hemiptera: Aphididae) are intensively studied due to their significance as pests and their captivating biological traits. Despite this considerable research interest, the evolutionary history of this insect family is poorly understood. Recent phylogenomic analyses have produced conflicting topologies, particularly at deep nodes, complicating our understanding of aphid trait evolution. In this work, we aimed to produce new data to unravel the backbone phylogeny of aphids. We sequenced partial and whole mitochondrial genomes from 87 species that were added to 31 published mitochondria. We additionally sequenced 42 nuclear loci across 95 aphid species and sourced 146 genes from 12 new and 61 published genomes from the primary aphid obligate endosymbiont, Buchnera aphidicola. We obtain data from these three sources for a subset of 51 aphid species, facilitating a comparative analysis of their phylogenetic signals. Our analyses confirm the monophyly of subfamilies, validating current taxonomic classifications, except for Eriosomatinae and Calaphidinae. However, relationships between subfamilies remain contentious in both mitochondrial and nuclear phylogenies. The topologies obtained with Buchnera appear fully resolved but exhibit some discordance with host phylogenies at deep evolutionary scales and conflict with views on the evolution of aphid morphology. We discuss alternative hypotheses for these discrepancies. Finally, the paucity of phylogenetic information at deep phylogenetic scales may stem from an initial rapid radiation. Though challenging to establish, this scenario may inherently hinder resolution in aphid phylogenetics.

evolutionary biology↗

bioRxiv2025

Sizing up phylogenetic testing in geometric morphometrics: A case study of allometry

AbstractAccounting for phylogenetic relatedness in the analysis of shape has become a common practice, deemed necessary to factor in the non-independence between species because of common ancestry. However, when adjusting error distributions to account for relatedness, the phylogenetic-generalised-least-squares (PGLS) test can obscure an important component of variation called conservative trait correlation (CTC). This is the amount of variation in a response variable that is both attributable to a predictor variable and phylogenetically structured. If CTC represents a large amount of correlated variation, true biological associations with strong phylogenetic signal (from unrepeated evolutionary events for example) might not be supported using a PGLS. We demonstrate this effect using geometric morphometric shape analysis on 370 crania from the speciose Australian rock- wallabies (genus Petrogale). In this clade, well-recognised allometric patterns such as scaling of the braincase (Hallers rule) and snout length (craniofacial evolutionary allometry) are supported using ordinary least squares (OLS) regression, but not PGLS, indicating that important between-species shape variation is lost. We then apply two methods capable of quantifying aspects of the missing variation: variation partitioning (VARPART), which estimates the proportion of variation shared between the predictor and phylogeny, and multi- response phylogenetic mixed models (MR-PMM), which identify the strength of correlation within the phylogenetic component of trait variance. Both methods show that CTC dominates the allometric shape variation in our sample, highlighting its importance in assessing phylogenetically informed models. We suggest approaches that can consider CTC become more widely used to better understand morphology and its predictors.

evolutionary biology↗

bioRxiv2019

Within-host Mycobacterium tuberculosis evolution: a population genetics perspective

The within-host evolutionary dynamics of TB remain unclear, and underlying biological characteristics render standard population genetic approaches based upon the Wright-Fisher model largely inappropriate. In addition, the compact genome combined with an absence of recombination is expected to result in strong purifying selection effects. Thus, it is imperative to establish a biologically-relevant evolutionary framework incorporating these factors in order to enable an accurate study of this important human pathogen. Further, such a model is critical for inferring fundamental evolutionary parameters related to patient treatment, including mutation rates and the severity of infection bottlenecks. We here implement such a model and infer the underlying evolutionary parameters governing within-patient evolutionary dynamics. Results demonstrate that the progeny skew associated with the clonal nature of TB severely reduces genetic diversity and that the neglect of this parameter in previous studies has led to significant mis-inference of mutation rates. As such, our results suggest an underlying de novo mutation rate that is considerably faster than previously inferred, and a progeny distribution differing significantly from Wright-Fisher assumptions. This inference largely reconciles the seemingly contradictory observations of both rapid drug-resistance evolution but extremely low levels of genetic variation in both resistant and non-resistant populations.

genetics↗

bioRxiv2026

Signatures of selection in pleiotropic genes involved in insect neuronal and immune systems

Pleiotropy, where a single gene contributes to multiple biological functions, plays a central role in shaping evolutionary constraints. The nervous and immune systems are tightly integrated both functionally and genetically, but it is not clear whether pleiotropy constrains adaptation in each system or contributes to disease. Building on evidence that genes that are pleiotropic between development and immunity in Drosophila melanogaster evolve slower than immune-specific genes, we tested whether pleiotropic neuro-immune genes likewise exhibit reduced evolutionary rates compared to genes functioning solely in neuronal or immune processes, and whether such evolutionary constraint is associated with human neurological disease. We identified immune, neuronal, and neuro-immune genes in D. melanogaster using Gene Ontology annotations, estimated their evolutionary rates across 12 Drosophila species, and investigated the breadth of their expression across developmental stages as a complementary proxy for pleiotropy. We further curated associations between the human orthologs for these genes and neurological disease and tested whether their evolutionary rates and pleiotropic status predicted disease involvement. We found that pleiotropic genes exhibited significantly lower dN/dS values and were less stage-specific than non-pleiotropic immune genes. Slower-evolving genes were more likely to be associated with human neurological diseases but this pattern was strongest for non-pleiotropic neuronal genes, suggesting that pleiotropy alone is not the strongest predictor of disease. Our results therefore indicate that dN/dS could be a stronger predictor of disease association than pleiotropy, raising new questions about the maintenance of pleiotropy in evolutionarily dynamic physiological systems.

evolutionary biology↗

bioRxiv2020

Genome editing enables reverse genetics of multicellular development in the choanoflagellate Salpingoeca rosetta

In a previous study, we established a forward genetic screen to identify genes required for multicellular development in the choanoflagellate, Salpingoeca rosetta (Levin et al., 2014). Yet, the paucity of reverse genetic tools for choanoflagellates has hampered direct tests of gene function and impeded the establishment of choanoflagellates as a model for reconstructing the origin of their closest living relatives, the animals. Here we establish CRISPR/Cas9-mediated genome editing in S. rosetta by engineering a selectable marker to enrich for edited cells. We then use genome editing to disrupt the coding sequence of a S. rosetta C-type lectin gene, rosetteless, and thereby demonstrate its necessity for multicellular rosette development. This work advances S. rosetta as a model system in which to investigate how genes identified from genetic screens and genomic surveys function in choanoflagellates and evolved as critical regulators of animal biology.

evolutionary biology↗

bioRxiv2020

The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs. autosomes

Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.

evolutionary biology↗

bioRxiv2021

The adaptive potential of non-heritable somatic mutations

Non-heritable somatic mutations are typically associated with deleterious effects such as in cancer and senescence, so their role in adaptive evolution has received little attention. However, most somatic mutations are harmless and some even confer a fitness advantage to the organism carrying them. We hypothesized that heritable, germline genotypes that are likely to express an advantageous phenotype via non-heritable somatic mutation will have a selective advantage over other germline genotypes, and this advantage will channel evolving populations toward more fit germline genotypes, thus promoting adaptation. We tested this hypothesis by simulating evolving populations of developing organisms with an impermeable germline-soma separation navigating a minimal fitness landscape. The simulations revealed the conditions under which non-heritable somatic mutations promote adaptation. Specifically, this can occur when the somatic mutation supply is high, when only very few cells with the advantageous somatic mutation are required to increase organismal fitness, and when the somatic mutation also confers a selective advantage to cells with that mutation. We therefore provide proof-of-principle that non-heritable somatic mutations can promote adaptive evolution via a process we call somatic genotypic exploration. We discuss the biological plausibility of this phenomenon, as well as its evolutionary implications. SignificanceThe immensity of non-heritable genetic diversity arising in the soma has been largely disregarded in evolutionary theory as a source of adaptation. Here, we introduce a model in which non-heritable somatic mutations arising during development confer an organismal fitness advantage. Analysis of this model shows how such mutations channel evolving populations toward adaptive germline genotypes. This is most likely to occur when somatic mutations confer a fitness benefit at both the cellular and organismal levels, evoking a synergistic form of multi-level selection that contrasts with the antagonistic forms typically associated with somatic mutations in cancer and senescence. As such, our study invites a new view of somatic genetic diversity in evolutionary theory as a potential source of adaptation.

evolutionary biology↗

bioRxiv2022

Invasion genetics of the longhorn crazy ant: the global expansion of a double-clonal reproduction system

Reproduction mode represents a key determinant for success of biological invasion as it influences the genetic variation and evolutionary potential of introduced populations. The worlds most widespread invasive ant, Paratrechina longicornis, was found to display an unusual double-clonal reproduction system, whereby both males and queens were produced clonally, while workers are produced sexually. Despite its worldwide distribution, the origin of this ant species and the prevalence of the double-clonal reproductive system across the ants geographic range remain unknown. To retrace the evolutionary history of this global invasive species and its reproductive system, we examined genetic variation and characterized the mode of reproduction of P. longicornis sampled worldwide using both microsatellite genotyping and mitochondrial DNA sequencing approaches. Analyses of global genetic variations indicate that the Indian subcontinent is a genetic diversity hotspot of this species, suggesting that this geographic area is at least part of its native range. Our analyses revealed that inferred native and introduced populations both exhibit double-clonal reproduction. Remarkably, queens and males worldwide belong to two separate, non-recombining clonal lineages. Workers are highly heterozygous and first-generation inter- lineage hybrids, a pattern strongly supportive of a strict worldwide prevalence of double clonality. By maintaining heterozygosity in the worker force, this unusual genetic system allows P. longicornis to avoid inbreeding during colonization bottlenecks and may have acted as an adaptive trait linked to the species invasion success.

evolutionary biology↗

bioRxiv2022

Resolving deleterious and near-neutral effects requires different pooled fitness assay designs

Pooled sequencing-based fitness assays are a powerful and widely used approach to quantifying fitness of thousands of genetic variants in parallel. Despite the throughput of such assays, they are prone to biases in fitness estimates, and errors in measurements are typically larger for deleterious fitness effects, relative to neutral effects. In practice, designing pooled fitness assays involves tradeoffs between the number of timepoints, the sequencing depth, and other parameters to gain as much information as possible within a feasible experiment. Here, we combined theory, simulations, and reanalysis of an existing experimental dataset to explore how assay parameters impact measurements of near-neutral and deleterious fitness effects. We found that sequencing multiple timepoints at relatively modest depth improved estimates of near-neutral fitness effects, but systematically biased measurements of deleterious effects. We identified a theoretical lower bound for estimates from bulk fitness assays, and showed that increasing sequencing depth, and reducing number of timepoints improved resolution of deleterious fitness effects. Our results highlight a tradeoff between measurement of deleterious and near-neutral effect sizes for a fixed amount of data and suggest that fitness assay design should be tuned for fitness effects that are relevant to the specific biological question.

evolutionary biology↗