Biology subjects

Duchen, P.

Publications and source records attributed to Duchen, P..

15 recordsLinked to original sources

bioRxiv2026

Niche differentiation confers coexistence prior to the species boundary in an aquatic plant

Despite the prevailing view that ecological divergence drives speciation, we know little about when or how nascent lineages evolve the ecological differences needed to coexist upon secondary contact. Here, we apply ecological coexistence theory to quantify the potential for coexistence among 126 allopatric lineages of the globally distributed duckweed Spirodela polyrhiza. Using competition experiments simulating secondary contact, we found that rapid accumulation of niche differences stabilized coexistence to permit sympatry among potentially interbreeding lineages. Competition against sister-species Spirodela intermedia further showed that niche differences accumulate more slowly post-speciation, revealing that niche differences enabling coexistence evolve well before timescales at which speciation is complete. Our findings suggest that rapid coexistence may thus contribute to time-lags in speciation, shaping both the origin and maintenance of biodiversity.

ecology↗

bioRxiv2025

Environmental fluctuations trigger faster evolution and turnover

Biodiversity patterns and species communities emerge from the interactions between organisms and their environment and from processes spanning across different spatial and temporal scales. Understanding the dynamics of these interactions remains difficult as it requires mapping how microevolutionary processes scale up to macroevolutionary outcomes. Here, we use an individual-based simulation framework to model how populations respond to environmental fluctuations in a spatially explicit context. Our approach tracks evolutionary processes over thousands of generations to quantify the emerging macroevolutionary patterns under varying degrees of environmental instability modeled as shifting environmental gradients. We found that increased instability across time and space leads to elevated rates of species-level extinctions leading to homogenization of species communities, while promoting high rates of phenotypic evolution. Emerging extinction patterns indicate a selective process where species with low migration ability, narrow environmental tolerance, and limited evolvability are disproportionally affected by phases of rapid environmental change. Understanding the impact of environmental variation on organisms and species evolution remains challenging but can be explored through simulations to generate expectations and testable hypotheses about evolutionary processes across different scales.

evolutionary biology↗

bioRxiv2025

Bulk segregant analysis reveals genomic regions associated with imidacloprid resistance in the Colorado potato beetle

Given the increased accessibility of genomic techniques, the speed of evolution of resistance, and the large number of genes involved in resistance, investigations into the genetic basis of resistance in more species are pertinent. Despite being an important agricultural pest, only a limited number of genetic mapping studies based on crossed populations have been performed to identify genes involved in resistance in the Colorado potato beetle (Leptinotarsa decemlineata, CPB). Here, we performed bulk segregant analysis on a mapping population generated by creating advanced intercross lines from five European strains of CPB. We identified eight peaks across chromosomes 1,8,10, and 16 involved in resistance against the neonicotinoid, imidacloprid. We identified 337 genes within these peaks and shortlisted three candidates based on gene expression and functional annotation. Among the three candidates thus identified, we found that an ABC transporter and a galactosyl transferase are expressed in relatively higher amounts in a relatively more susceptible strain than in a resistant strain. We attempted to validate the role of these two genes in insecticide resistance by knocking them down in a resistant strain using RNA interference (RNAi) and performing toxicity experiments. Surprisingly, our results showed that the activation of RNAi machinery reduced imidacloprid resistance and the effect is not specific to the tested candidate genes, which raised a concern on the suitability of using RNAi for validating insecticide resistance mechanisms in CPB.

genetics↗

bioRxiv2024

Advances and applications of the closest-tree algorithm and Hadamard conjugation in phylogenetic inference

In phylogenetic inference Hadamard methods and the closest-tree algorithm have been a promising alternative to likelihood-based methods. However, applications to actual biological problems have been limited so far. In the early nineties, Hendy and Penny (1993) developed the two-state closest-tree algorithm for estimating the optimal branch lengths of a phylogenetic tree, whose parameters correspond to the Cavenders molecular evolution model (CFN). Steel et al. (1992) then developed the four-state version of this method, whose parameters correspond to the Kimura 3STs molecular evolution model (K3ST). In both cases, formulas for solving the optimization problems were provided. Here, we do not only contribute with proofs for these formulas, but we also adapt this methodology to the orchid genus Lophiarella, whose phylogenetic relationships remain unclear. With this biological application, we show the efficacy of the closest-tree algorithm coupled with Hadamard conjugation, phylogenetic invariants and edge-parameter inequalities (in Fourier coordinates) in jointly inferring the tree topology and the molecular evolution model that best explains the data. Finally, we reconcile this phylogeny with biogeographical and morphological aspects within this genus.

evolutionary biology↗

bioRxiv2024

Comparative and population genomics analyses of the regulatory Transcription Factor (TF)-DNA interaction

Natural selection heavily influences the evolutionary trajectories of species by impacting their genotype to phenotype transitions. On the molecular level, these genotype to phenotype transitions are shaped by the regulatory sequences (RSs). In this study, we employed a combination of population and comparative genomics to investigate how natural selection affects specific RS classes involved in the regulatory transcription factor (TF)-DNA interactions. These interactions consist of two motifs, namely: TF-binding domains (TF-BDs) and TF-binding sites (TF-BSs). Using publicly available annotation data, we constructed the species-specific lists of the TF-BD and TF-BS regions. We also constructed a non-synonymous equivalent class for the TF-BS regions for making comparative analyses across the coding and non-coding regions. On applying some of the commonly used summary statistics, we found a consistent signal of purifying selection acting on TF-BDs, consistent with their functional importance. Interestingly, we also observed that non-coding TF-BS regions showed similar levels of constraint to that of coding regions for populations with large Ne. Concerning positive selection, we showed that the regulatory motifs of large Ne species are, overall, subject to an increased intensity of positive selection. We found an overall positive correlation between the intensity of purifying and positive selection and the species-specific Ne, which is expected under drift-selection equilibrium. Finally, we contrasted the signal of positive selection in H. sapiens and D. melanogaster (outcrossing species) with A. thaliana (selfing species) and noted that selfing plays a key role in influencing the action of positive selection.

evolutionary biology↗

bioRxiv2024

Sex-biased migration and demographic history of the big European firefly Lampyris noctiluca

Differential dispersion between the sexes can impact population structure and connectivity between populations, which in turn, can have an effect on the evolvability capability of a species. Here we explored the demographic history of the big European firefly, Lampyris noctiluca, which exhibits female neoteny. L. noctiluca distribution extends throughout Europe, but nothing is known on how its colonization processes. To investigate this, we produced the first Lampyris genome (653Mb), including an IsoSeq annotation and the identification of the X chromosome. We collected 115 individuals from six populations of L. noctiluca (Finland to Italy) and generated whole genome re-sequencing for each individual. We inferred several population expansions and bottlenecks throughout the Pleistocene that correlate with glaciation events. Surprisingly, we uncovered strong population structure and low gene-flow. We reject a stepwise, south to north, colonization history scenario and instead uncovered a complex demographic history with a putative eastern European origin. Analyzing the evolutionary history of the mitochondrial genome as well as X-linked and autosomal loci, we found evidence of a maternal colonialization of Germany, putatively from a western European population, followed by male-only migration from south of the Alps (Italy). Overall, investigating the demographic history and colonization patterns of a species should form part of an integrative approach of biodiversity research. Our results provide evidence of sex-biased migration which is important to consider for demographic, biogeographic and species delimitation studies.

evolutionary biology↗

bioRxiv2023

Phylogenetic modeling provides evidence for sudden shifts in expression after small-scale duplication in vertebrates and strong support for the ortholog conjecture

Gene duplication is a potential source of innovation, but the evolutionary dynamics of functional change are still poorly understood. Under the debated "ortholog conjecture", most functional change and innovation is assumed to follow duplication. Testing the ortholog conjecture allows to better understand and characterize the way in which gene function evolves. Most models of functional evolution assume continuous change, an assumption which we challenge here. We have applied a Levy model of evolutionary trait jumps to the evolution of gene expression in vertebrates, with a special focus on duplication in teleost fishes. We show for the first time that trait jumps strongly affects paralogs, in addition to other modes of functional evolution. We find that at least 25% of teleost fish small-scale duplicates follow a rapid evolutionary rate shift model for both expression level and tissue-specificity, much more than after speciations. However, genome-wide duplicates (ohnologs) do not support such a trait jump model, and thus follow a different evolutionary dynamic. While there is some evidence for more positive selection at the protein-coding level after duplication, it is not strongly linked to jumps in expression. Finally, both small-scale paralogs and ohnologs strongly support the ortholog conjecture by contrasting speciation branches pre- and post-duplication to the duplication branches themselves, with trait jumps explaining much of the higher phylogenetic independent contrasts between small-scale paralogs. Significance statementThe debate on the ortholog conjecture, i.e. that gene function changes little between orthologs but changes frequently between paralogs, provides a framework to understand better the evolution of gene function. Here we add two pieces to the puzzle: a novel way to use phylogenetic contrasts to test the ortholog conjecture, by comparing not only duplication to speciation, but speciation according to whether they were preceded by a duplication; and a model of jumps rather than continuous change of gene function. We tested these on vertebrates, with emphasis on teleost fishes, distinguishing small-scale duplications and whole-genome duplication; in all cases we support strongly the ortholog conjecture. We find that trait jumps strongly affect small-scale paralogs but not genome duplication paralogs, providing an exciting new model for gene function evolution.

evolutionary biology↗

bioRxiv2023

Population genomics and epigenomics provide insights into the evolution of facultative asexuality in plants

Many organisms, particularly plants, are facultatively asexual. Because asexual reproduction is beneficial for the short term but costly for the long term, during the range expansion, natural selection should act on the genetic controls of asexuality in these facultatively asexual organisms. However, the genomic evidence of natural selection driving asexuality remains scarce, and the evolutionary consequences of facultatively asexuality on the genomic and epigenomic diversity remain controversial. Here, by analyzing population genomes and epigenomes of Spirodela polyrhiza (L.) Schleid., a facultatively asexual plant that flowers rarely, we show that this plant has the lowest genomic diversity and DNA methylation levels among all studied multicellular eukaryotes. Within species, demographic history and the frequency of asexual reproduction jointly determined intra-specific variations of genomic diversity and DNA methylation levels. Genome-wide scans revealed that multiple genes involved in flowering and embryogenesis were under positive selection, consistent with the hypothesis that natural selection drove the evolution of asexuality during the recent habitat expansions in this plant. Together, these results provide new insights into the evolution of plant reproductive systems and suggest that natural selection can drive the evolutionary changes of asexuality, which in turn alters the levels of genomic and epigenomic diversity.

evolutionary biology↗

bioRxiv2022

Evidence of active oviposition avoidance to systemically applied imidacloprid in the Colorado Potato Beetle (Leptinotarsa decemlineata)

Agricultural pests can develop behavioral resistance to insecticides via choosing to feed or oviposit on non-toxic hosts. As young larvae have relatively low mobility, oviposition preferences from female adults may play a critical role in shaping the evolutionary trajectory of pest populations. While oviposition avoidance of toxic hosts was found in different agriculture pests, it remains unclear whether such preferences can be learned from female adults. To address this question, we investigated feeding and oviposition preferences to imidacloprid in the Colorado Potato Beetle (CPB, Leptinotarsa decemlineata), a major potato pest. We first identified two CPB strains that have different levels of resistance to imidacloprid. Then, we performed choice assays in the two strains and found that both strains did not have an innate feeding avoidance to systemically applied imidacloprid at both larval and adult stages. Further oviposition choice assays showed that the susceptible strain preferred to lay eggs on insecticide-free plants while the resistant strain did not. Analysing moving patterns of the two strains suggested that the oviposition preference is likely due to active learning by the female adults. Together, these results indicate that CPB can have active oviposition avoidance, which might have contributed to the rapid global invasion of this agricultural pest.

animal behavior and cognition↗

bioRxiv2021

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

Fireflies (Coleoptera: Lampyridae) consist of over 2,000 described extant species. A well-resolved phylogeny of fireflies is important for the study of their population genetics, bioluminescence, evolution, and conservation. We used a recently published anchored hybrid enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10 outgroup species) and state-of-the-art statistical methods (the fossilized birth-death-range process implemented in a Bayesian framework) to estimate a time-calibrated phylogeny of Lampyridae. Unfortunately, estimating calibrated phylogenies using AHE and the latest and most robust time-calibration strategies is not possible because of computational constraints. As a solution, we subset the full dataset by applying three different strategies: (i) using the most complete loci, (ii) using the most homogeneous loci, and (iii) using the loci with the highest accuracy to infer the well established Photinus clade. The estimated topology using the three data subsets agreed on almost all major clades and only showed minor discordance within less supported nodes. The estimated divergence times overlapped for all nodes that are shared between the topologies. Thus, divergence time estimation is robust as long as the topology inference is robust and any well selected data subset suffices. Additionally, we observed an un-expected amount of gene tree discordance between the 436 AHE loci. Our assessment of model adequacy showed that standard phylogenetic substitution models are not adequate for any of the 436 AHE loci which is likely to bias phylogenetic inferences. We performed a simulation study to explore the impact of (a) incomplete lineage sorting, (b) uniformly distributed and systematic missing data, and (c) systematic bias in the position of highly variable and conserved sites. For our simulated data, we observed less gene tree variation which shows that the empirically observed amount of gene tree discordance for the AHE dataset is unexpected and needs further investigation.

evolutionary biology↗

bioRxiv2020

A cautionary note on the use of haplotype callers in Phylogenomics

Next-generation-sequencing haplotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional haplotype callers such as the one from GATK, is that they are optimized for variant calling at the population level, but not at the phylogenetic level. Thus, the consequences for downstream analyses can be substantial. Here, through simulations, we compare the performance between the haplotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show how the haplotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also quantified the level at which the accuracy of heterozygote calls declines with increasing distance to the reference genome. Such decrease is very sharp in GATK, while ATLAS maintains a high accuracy in variant calling, even at moderately-divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies.

evolutionary biology↗

bioRxiv2019

On the inference of a southern origin of the North American firefly Photinus pyralis

The firefly Photinus pyralis inhabits a wide range of latitudinal and ecological niches, with populations living from temperate to tropical habitats. Its ample geographic distribution makes this species an ideal system for the study of local adaptation and demographic inference of wild populations. Therefore, in this study we modelled and inferred different demographic scenarios for North American populations of P. pyralis, collected from Texas to New Jersey. To do this, we used a combination of ABC techniques (for multi-population/colonization analyses), and likelihood inference (dadi) for single-population demographic inference, which proved useful with our RAD data.We uncovered that the most ancestral North American population lays in Texas, which further colonized the Central region of the US and more recently the North Eastern coast. Our study confidently rejects a demographic scenario where the North Eastern populations colonized more southern populations until reaching Texas. Our results suggest that P. pyralis originated in Central- or South America, followed by migration events that populated northern latitudes. Finally, modelling the demographic history of North American P. pyralis serves as a null model of nucleotide diversity patterns, which will inform future studies of adaptation, not only in P. pyralis, but also in other North American taxa.

evolutionary biology↗

bioRxiv2019

On the effect of asymmetrical trait inheritance on models of trait evolution

Current phylogenetic comparative methods modeling quantitative trait evolution generally assume that, during speciation, phenotypes are inherited identically between the two daughter species. This, however, neglects the fact that species consist of a set of individuals, each bearing its own trait value. Indeed, because descendent populations after speciation are samples of a parent population, we can expect their mean phenotypes to randomly differ from one another potentially generating a "jump" of mean phenotypes due to asymmetrical trait inheritance at cladogenesis. Here, we aim to clarify the effect of asymmetrical trait inheritance at speciation on macroevolutionary analyses, focusing on model testing and parameter estimation using some of the most common models of quantitative trait evolution. We developed an individual-based simulation framework in which the evolution of species phenotypes is determined by trait changes at the individual level accumulating across generations and cladogenesis occurs then by separation of subsets of the individuals into new lineages. Through simulations, we assess the magnitude of phenotypic jumps at cladogenesis under different modes of trait inheritance at speciation. We show that even small jumps can strongly alter both the results of model selection and parameter estimations, potentially affecting the biological interpretation of the estimated mode of evolution of a trait. Our results call for caution when interpreting analyses of trait evolution, while highlighting the importance of testing a wide range of alternative models. In the light of our findings, we propose that future methodological advances in comparative methods should more explicitly model the intra-specific variability around species mean phenotypes and how it is inherited at speciation.

evolutionary biology↗

bioRxiv2018

Linking micro and macroevolution in the presence of migration

1. The process of speciation is of key importance in evolutionary biology because it shapes macroevolutionary patterns. This process starts at the microevolutionary level, for instance, when two subpopulations evolve towards different phenotypic optima. The speed at which these optima are reached is controlled by the degree of stabilising selection, which pushes a mean trait towards an optimum within subpopulations, and ongoing migration that pulls the mean phenotype away from that optimum. Traditionally, macro phenotypic evolution with selection has been modelled by Ornstein-Uhlenbeck (OU) processes, but these models have ignored the role of migration within species.\n\n2. Here, our goal is to reconcile the processes of micro and macroevolution by modelling migration during speciation. More precisely, we introduce an OU model where migration happens between two subpopulations within a branch of a phylogeny and this migration decreases over time as it happens during speciation. We then use this model to study the evolution of trait means along a phylogeny, as well as the way phenotypic disparity between species changes with successive epochs.\n\n3. We show that ignoring the effect of migration in sampled time-series data leads to a significant underestimation of the selective forces acting upon it. We also show that migration decreases the expected phenotypic disparity between species and we show the effect of migration in the particular case of niche filling. We further introduce a method to jointly estimate selection and migration from time-series data.\n\n4. Our model extends standard results of interactions selection-migration in a microevolutionary time frame across multiple speciation events at a macroevolutionary scale. Our results further proof that not accounting for gene flow has important consequences in inferences at both the micro and macroevolutionary scale.

evolutionary biology↗

bioRxiv2016

Inference of evolutionary jumps in large phylogenies using Levy processes

While it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriini parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis.

evolutionary biology↗