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Results for “Evolutionary Biology”

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bioRxiv2023

Improving the accuracy of bulk fitness assays by correcting barcode processing biases

Measuring the fitnesses of genetic variants is a fundamental objective in evolutionary biology. A standard approach for measuring microbial fitnesses in bulk involves labeling a library of genetic variants with unique sequence barcodes, competing the labeled strains in batch culture, and using deep sequencing to track changes in the barcode abundances over time. However, idiosyncratic properties of barcodes (e.g., GC content) can induce non-uniform amplification or uneven sequencing coverage that cause some barcodes to be over-or under-represented in samples. This systematic bias can result in erroneous read count trajectories and misestimates of fitness. Here we develop a computational method for inferring the effects of processing bias by leveraging the structure of systematic deviations in the data. We illustrate this approach by applying it to fitness assay data collected for a large library of yeast variants, and show that this method estimates and corrects for bias more accurately than standard proxies, such as GC-based corrections. Our method mitigates bias and improves fitness estimates in high-throughput assays with-out introducing additional complexity to the experimental protocols, with potential value in a range of experimental evolution and mutation screening contexts.

evolutionary biology↗

bioRxiv2018

Evolution of dispersal can rescue populations from expansion load

Understanding the causes and consequences of range expansions or range shifts has a long history in evolutionary biology. Recent theoretical, experimental, and empirical work has identified two particularly interesting phenomena in the context of species range expansions: (i) gene surfing and the relaxation of natural selection, and (ii) spatial sorting. The former can lead to an accumulation of deleterious mutations at range edges, causing an expansion load and slowing down expansion. The latter can create gradients in dispersal-related traits along the expansion axis and cause an acceleration of expansion. We present a theoretical framework that treats spatial sorting and gene surfing as spatial versions of natural selection and genetic drift, respectively. This model allows us to study analytically how gene surfing and spatial sorting interact, and to derive the probability of fixation of pleiotropic mutations at the expansion front. We use our results to predict the co-evolution of mean fitness and dispersal rates, taking into account the effects of random genetic drift, natural selection and spatial sorting, as well as correlations between fitnessand dispersal-related traits. We identify a \"rescue effect\" of spatial sorting, where the evolution of higher dispersal rates at the leading edge rescues the population from incurring expansion load.

evolutionary biology↗

bioRxiv2026

Regional connectivity and viability selection in a range-expanding marine species

Identifying spatial and temporal patterns of connectivity among populations is fundamental to marine ecology, evolutionary biology, and fisheries management. Yet, due to large population sizes and low genetic differentiation among populations, empirical quantification of population connectivity across a species entire range has not been achieved for an open-coast marine organism. Here, we leverage experimental transcriptomics to develop a genotyping-in-thousands by sequencing (GT-seq) panel to support assignment of recruits of the kelp forest gastropod, Kellets whelk (Kelletia kelletii), collected across the species biogeographic range. Over a three-year period, we identified high self-recruitment in the historical range (100%) and low self-recruitment in the expanded range (10.53 - 13.73%). Additionally, self-recruitment within the expanded range generally increased with recruit age, from 27.14% at 0.93 years to 43.40% at 1.93 years, indicating that the locally spawned individuals were more likely to survive to older ages than migrants from the historical range. Together, these results reveal limited self-recruitment in the expanded range and suggest that a post-settlement selective filter contributes to differential survival in a high gene flow marine system.

evolutionary biology↗

bioRxiv2023

Characterizing the impact and maintenance of specialized toxin tolerance in a generalist species

Understanding how plant-herbivore interactions can drive coevolution is a central goal of ecology and evolutionary biology. Of particular interest are the defenses produced by host plants/fungi and their impact on herbivore feeding strategies. In the immigrans-tripunctata radiation of Drosophila, mushroom-feeding species are classified as generalists, but their acceptable hosts include deadly Amanita species. In this study, we used behavioral assays to assess whether the mushroom-feeding species Drosophila guttifera is becoming a specialist and to characterize the impact of competition on host usage. We conducted feeding assays to confirm the presence of cyclopeptide toxin tolerance. We then completed host preference assays in female flies and larvae and did not find a preference for toxic mushrooms in either. Finally, we assessed the effect of competition on oviposition preference. We found that the presence of a competitors eggs on the preferred host was associated with the flies increasing the number of eggs laid on the toxic mushrooms. Our results suggest that an adaptation associated with specialized feeding behavior is not altering host usage and that competition plays a role in maintaining this trait. More broadly our work highlights how access to a low competition host resource helps to maintain adaptations with fitness costs.

evolutionary biology↗

bioRxiv2018

Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds

The relative roles of regulatory and protein evolution in the origin and loss of convergent phenotypic traits is a core question in evolutionary biology. Here we combine phylogenomic, epigenomic and developmental data to show that convergent evolution of regulatory regions, but not protein-coding genes, is associated with flightlessness in palaeognathous birds, a classic example of a convergent phenotype. Eleven new genomes, including a draft genome from an extinct moa, resolve palaeognath phylogeny and show that the incidence of independent, convergent accelerations among 284,000 conserved non-exonic elements is significantly more frequent in ratites than other bird lineages. Ratite-specific acceleration of conserved regions and measures of open chromatin across eight tissues in the developing chick identify candidate regulatory regions that may have modified or lost function in ratites. Enhancer activity assays conducted in the early developing chicken forelimb confirm that volant versions of a conserved element in the first intron of the TEAD1 gene display conserved enhancer activity, whereas an accelerated flightless version fails to drive reporter gene expression. Our results show that convergent molecular changes associated with loss of flight are largely regulatory in nature.

evolutionary biology↗

bioRxiv2023

Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages

Understanding genetic incompatibilities and genetic introgression between incipient species are major goals in evolutionary biology. Mitochondrial genes evolve rapidly and exist in dense gene networks with coevolved nuclear genes, suggesting that mitochondrial respiration may be particularly susceptible to disruption in hybrid organisms. Mitonuclear interactions have been demonstrated to contribute to hybrid disfunction between deeply divergent taxa crossed in the laboratory, but there are few empirical examples of mitonuclear interactions between younger lineages that naturally hybridise. Here we use experimental crosses and high resolution respirometry to provide the first evidence in a bird that inter-lineage mitonuclear interactions impact mitochondrial aerobic metabolism. Specifically, respiration capacity of the two paternal backcrosses (with mismatched mito-nuclear combinations) differ from one another, although they do not differ to the parental groups or maternal backcrosses as we would expect of mitonuclear disruptions. In the wild hybrid zone between these subspecies the mitochondrial cline centre is shifted west of the nuclear cline centre, which is consistent with the direction of our experimental results. Our results therefore demonstrate asymmetric mitonuclear interactions that impact the capacity of cellular mitochondrial respiration and may help to explain the geographic discordance between mitochondrial and nuclear genomes observed in the wild.

evolutionary biology↗

bioRxiv2019

Allopatric speciation is more prevalent than parapatric ecological divergence in tropical montane systems (Asteraceae: Piofontia)

Elucidating how species accumulate in diversity hotspots is an ongoing debate in evolutionary biology. The paramo, in the Northern Andes, has remarkably high indices of plant diversity, endemicity, and diversification rates. A hypothesis for explaining such indices is that allopatric speciation is high in the paramo given its island-like distribution; an alternative hypothesis is that the altitudinal gradient of the Andean topography provides a variety of niches that drive vertical parapatric ecological speciation. A formal test for evaluating the relative roles of allopatric speciation and parapatric ecological divergence is lacking. The main aim of our study is to test which kind of speciation is more common in an endemic paramo genus. We developed a framework incorporating phylogenetics, species distributions, and a morpho-ecological trait (leaf area) to compare sister species and infer whether allopatric or parapatric ecological divergence caused their speciation. We applied our framework to the species-rich genus Linochilus (63 spp.) and found that the majority of recent speciation events in it (12, 80%) have been driven by allopatric speciation, while a smaller fraction (1, 6.6%) is attributed to parapatric ecological divergence; two pairs produced inconclusive results (13.3%). We conclude that paramo autochthonous diversification is primarily driven by allopatric speciation.

evolutionary biology↗

bioRxiv2017

Comparative transcriptomics reveals lineage specific evolution of cold response in Pooideae

BackgroundUnderstanding how complex traits evolve through adaptive changes in gene regulation remains a major challenge in evolutionary biology. Over the last ~50 million years, Earth has experienced climate cooling and ancestrally tropical plants have adapted to expanding temperate environments. The grass subfamily Pooideae dominates the grass flora of the temperate regions, but the role of cold-response gene regulation in the transitioning from tropical to temperate climate remains unexplored.\n\nResultsTo establish if molecular responses to cold are conserved throughout the phylogeny, we assembled the transcriptomes of five Pooideae species spanning early to later diverging lineages, and compared short- and long-term cold responsive genes using 8633 high confidence ortholog groups with resolved gene tree topologies. We found that a majority of cold responsive genes were specific to one or two lineages, an observation that we deem incompatible with a cold adapted Pooideae ancestor. However, all five species shared short-term cold response in a small set of general stress genes as well as the ability to down-regulate the photosynthetic machinery during cold temperatures.\n\nConclusionsOur observations indicate that the different Pooideae lineages have assembled cold response programs in parallel by taking advantage of a common potential for cold adaptation.

evolutionary biology↗

bioRxiv2021

Fluctuating environments maintain genetic diversity through neutral fitness effects and balancing selection

Genetic variation is the raw material upon which selection acts. The majority of environmental conditions change over time and therefore may result in variable selective effects. How temporally fluctuating environments impact the distribution of fitness effects and in turn population diversity is an unresolved question in evolutionary biology. Here, we employed continuous culturing using chemostats to establish environments that switch periodically between different nutrient limitations and compared the dynamics of selection to static conditions. We used the pooled Saccharomyces cerevisiae haploid gene deletion collection as a synthetic model for populations comprising thousands of unique genotypes. Using barcode sequencing (barseq), we find that static environments are uniquely characterized by a small number of high fitness genotypes that rapidly dominate the population leading to dramatic decreases in genetic diversity. By contrast, fluctuating environments are enriched in genotypes with neutral fitness effects and an absence of extreme fitness genotypes contributing to the maintenance of genetic diversity. We also identified a unique class of genotypes whose frequencies oscillate sinusoidally with a period matching the environmental fluctuation. Oscillatory behavior corresponds to large differences in short term fitness that are not observed across long timescales pointing to the importance of balancing selection in maintaining genetic diversity in fluctuating environments. Our results are consistent with a high degree of environmental specificity in the distribution of fitness effects and the combined effects of reduced and balancing selection in maintaining genetic diversity in the presence of variable selection.

evolutionary biology↗

bioRxiv2023

Hybridization and its impact on the ontogenetic allometry of skulls in macaques

The role of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite the accumulated knowledge on adult hybrid variation, how hybridization affects ontogenetic allometry is less well understood. Here, we investigated the effects of hybridization on postnatal ontogenetic allometry in the skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (M. fuscata). Genomic analyses indicated that the population consisted of individuals with varying degrees of admixture, formed by male migration from Japanese to Taiwanese macaques. For overall skull shape, ontogenetic trajectories were shifted by hybridization in a nearly additive manner, with moderate transgressive variation observed throughout development. In contrast, for the maxillary sinus (hollow space in the face), hybrids grew as fast as Taiwanese macaques, diverging from Japanese macaques, which showed slow growth. Consequently, adult hybrids showed a mosaic pattern, i.e., the maxillary sinus is as large as that of Taiwanese macaques, while the overall skull shape is intermediate. Our findings suggest that the transgressive variation can be caused by prenatal shape modification and non-additive inheritance on regional growth rates, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.

evolutionary biology↗

bioRxiv2026

The phylogenetic signal in primate ontogenies, with special attention to dental development

Comparative studies in evolutionary biology must account for trait non-independence arising from shared ancestry. While the phylogenetic signal of adult traits has been extensively studied, little is known about how conserved developmental trajectories are across species. Here, I quantify the phylogenetic signal (K) in the ontogeny of 35 traits across 157 primate species, spanning motor, cognitive, life-history, and dental development. Using Blombergs K statistic and a species-level mammalian phylogeny, I test two predictions: (i) that morphological (dental) traits exhibit the strongest phylogenetic signal, and (ii) that earlier-developing traits are more conserved. Results show that life-history traits are the most phylogenetically labile, while dental development is the most conserved (K = 0.7-2.6), with the eruption of the mandibular canine showing the highest signal (K = 2.6). Contrary to expectations, later-developing traits, particularly permanent teeth, display stronger phylogenetic conservation than earlier-developing deciduous teeth. These findings suggest that even within a single developmental system, the strength of phylogenetic constraint varies markedly with timing. The results provide an empirical foundation for identifying reliable temporal anchors in comparative primate ontogeny and have implications for interpreting maturational patterns in human evolution and the fossil record.

evolutionary biology↗

bioRxiv2026

Multiple host species maintain genetic diversity in herbivore populations

How natural populations maintain genetic variation for fitness remains a central problem in evolutionary biology. Theory predicts that opposing selective pressures across environments can preserve fitness-associated polymorphism, but how interactions among species contribute to this process remains poorly understood. Here we show that host diversity preserves standing genetic variation within sexual populations of the leafmining fly Scaptomyza flava. We evolved twelve populations for ten generations on either of two naturally co-occurring host plants or on both, pooling survivors from the two hosts before mating. Single-host populations evolved reciprocal fitness trade-offs, whereas two-host populations maintained relatively even performance across hosts. Whole-genome time series dynamics identified a linked region in which alleles increased on one host and decreased on the other, while showing little net change under two-host conditions. Wild flies reared from the two hosts showed corresponding allele-frequency differences within this region. Across the genome, two-host populations retained more rare variants than populations evolving on either host alone. These findings show that selection imposed by different host species in sympatry can maintain standing genetic diversity within an herbivore population.

evolutionary biology↗

bioRxiv2014

An amino acid polymorphism in the Drosophila insulin receptor demonstrates pleiotropic and adaptive function in life history traits

Finding the specific nucleotides that underlie adaptive variation is a major goal in evolutionary biology, but polygenic traits pose a challenge because the complex genotype-phenotype relationship can obscure the effects of individual alleles. However, natural selection working in large wild populations can shift allele frequencies and indicate functional regions of the genome. Previously, we showed that the two most common alleles of a complex amino acid insertion-deletion polymorphism in the Drosophila insulin receptor show independent, parallel clines in frequency across the North American and Australian continents. Here, we report that the cline is stable over at least a five-year period and that the polymorphism also demonstrates temporal shifts in allele frequency concurrent with seasonal change. We tested the alleles for effects on levels of insulin signaling, fecundity, development time, body size, stress tolerance, and lifespan. We find that the alleles are associated with predictable differences in these traits, consistent with patterns of Drosophila life history variation across geography that likely reflect adaptation to the heterogeneous climatic environment. These results implicate insulin signaling as a major mediator of life history adaptation in Drosophila, and suggest that life history tradeoffs can be explained by extensive pleiotropy at a single locus.

Evolutionary Biology↗

bioRxiv2023

Evolutionary dynamics and ecological influences on Felidae

In the field of evolutionary biology, researchers have long been interested in comprehending the patterns of diversification and elucidating the mechanisms responsible for the impressive variety of lifeforms observed within taxonomic groups. Based on the fossil records of Felidae, and using a Bayesian framework, we assess here how speciation and extinction rates vary across the last 25 Myr, and how it can potentially be associated with changes in two major ecomorphological traits of Felidae, body mass and carnassial teeth, over such time span. We found two coupled independent increases in both traits along Felidae evolution, one in Machairodontinae, which gradually increases over the last 15 Myr, and the second in Panthera, which rapidly increases within 5 million years. Furthermore, gradual reductions in body mass and carnassial teeth were also observed for some genera such as Leopardus, Lynx, and Felis. Diversification rates showed a gradual reduction throughout the Miocene and Pliocene, with significant rate shifts occurring around 9 and 2 Myr. We suggest that felids were influenced by major environmental changes over the last 17 Myr that probably shaped both traits studied here in order to hunt larger herbivores, but also to explore new niches that became available.

evolutionary biology↗

bioRxiv2017

A Non-Classical Phase Diagram for Virus-Bacterial Co-Evolution Mediated by CRISPR

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The conditions for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape the recognition by CRISPR. When bacteria have a small rate of deleting spacers, a new parameter region in which bacteria and viruses can coexist arises, and it leads to a more complex coexistence patten for bacteria and viruses. For example, when the virus mutation rate is low, the virus extinction probability changes non-montonically with the bacterial exposure rate. The virus and bacteria co-evolution not only alters the virus extinction probability, but also changes the bacterial population structure. Additionally, we show that recombination is a successful strategy for viruses to escape from CRISPR recognition when viruses have multiple proto-spacers, providing support for a recombination-mediated escape mechanism suggested experimentally. Finally, we suggest that the reentrant phase diagram, in which phages can progress through three phases of extinction and two phases of abundance at low spacer deletion rates as a function of exposure rate to bacteria, is an experimentally testable phenomenon.

evolutionary biology↗

bioRxiv2026

Temporal genomics reveals rapid parallel adaptation in experimental populations of Trinidadian guppies (Poecilia reticulata)

Understanding the genomic basis of early adaptation is a central question in evolutionary biology. Although there is ongoing debate about whether early adaptation is more likely to be driven by polygenic responses or by loci of large effect, few studies of natural populations have been able to address this problem. Furthermore, early adaptation to a novel environment often coincides with founding events, making it difficult to disentangle neutral effects from adaptive genomic changes. Here we take advantage of the unique in situ guppy experimental system, in which we established replicate populations by translocating guppies from a high predation locality to four low predation localities. We present whole genome sequencing from the source population and the four experimental populations, sampled after [~]8-10 generations (first period), and again at [~]18-22 generations (second period). We find signatures of inbreeding only in the first period, despite documented population crashes in the second period. We show genome-wide dynamics of selection as well as selective change at single loci and uncover new targets of selection. Overall, we found signatures of selection at all levels; genome-wide, chromosome, and individual windows are more repeatable among replicates in the first period than in the second period.

evolutionary biology↗

bioRxiv2017

The demographic history and mutational load of African hunter-gatherers and farmers

The distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains unclear. Here, we report high-coverage exome sequencing data from various populations of rainforest hunter-gatherers and farmers from central Africa. We find that the recent demographic histories of hunter-gatherers and farmers differed considerably, with population collapses for hunter-gatherers and expansions for farmers, accompanied by increased gene flow. We show that purifying selection against deleterious alleles is of similar efficiency across African populations, in contrast with Europeans where we detect weaker purifying selection. Furthermore, the per-individual mutation load of rainforest hunter-gatherers is similar to that of farmers, under both additive and recessive models. Our results indicate that differences in the cultural practices and demographic regimes of African populations have not resulted in large differences in mutational burden, and highlight the beneficial role of gene flow in reshaping the distribution of deleterious genetic variation across human populations.

evolutionary biology↗

bioRxiv2022

Comprehensive analysis of gene regulatory dynamics, fitness landscape, and population evolution during sexual reproduction

The fitness landscape is a critical concept in evolutionary biology and genetics that depicts fitness in the genotype space and visualizes the relationship between genotype and fitness. However, the fitness landscape is challenging to characterize because the quantitative relationships between genotype and phenotype and their association to fitness has not been comprehensively well described. To address this challenge, we adopted gene regulatory networks to determine gene expression dynamics. We analyzed how phenotype and fitness are shaped by the genotype in two-gene networks. A two-by-two matrix provided the two-gene regulatory network in which a vector with two angle values ({Theta}) was introduced to characterize the genotype. Mapping from this angle vector to phenotypes allowed for the classification of steady-state expression patterns of genes into seven types. We then studied all possible fitness functions given by the Boolean output from the on/off expression of the two genes. The possible fitness landscapes were obtained as a function of the genetic parameters {Theta}. Finally, the evolution of the population distribution under sexual reproduction was investigated in the obtained landscape. We found that the distribution was restricted to a convex region within the landscape, resulting in the branching of population distribution, including the speciation process.

evolutionary biology↗