Biology subjects

Stoeckel, S.

Publications and source records attributed to Stoeckel, S..

14 recordsLinked to original sources

bioRxiv2026

A mosaic of genomic architectures underpins parasitism loss in a jawless vertebrate

Lampreys are the only ancestrally parasitic vertebrate lineage, yet parasitism has been repeatedly lost alongside a suite of life-history changes, such as loss of migration and juvenile feeding and accelerated maturation. Combining whole-genome resequencing, haplotype-resolved assemblies, hybrid-zone genotyping, multi-tissue transcriptomics, and sperm phenotyping, we map this life-history syndrome in European Lampetra to six chromosomes spanning a mosaic of genomic architectures: a [~]20 Mb low-recombination region on chromosome 1 lacking chromosomal rearrangements within Lampetra but involving inter-specific rearrangements across deep lamprey lineages; a translocated inversion with ecotype-dependent sperm-velocity effects; and ecotype-divergent deletions overlapping genes crucial for nervous system (CNTNAP2) and reproductive development (FSHR). However, this genomic basis is not shared with a convergent sister lineage, pointing to independent routes to a recurring life-history transition in lampreys.

evolutionary biology↗

bioRxiv2026

Genotype frequency dynamics in finite-sized, partially clonal population with mutation

Most eukaryotes reproduce using partial clonality, for which appropriate population genetic models remain limited. This gap constrains our ability to accurately reconstruct past population dynamics, predict future trajectories, and infer the evolutionary processes involved. We present a Wright-Fisher-like model tailored for tracking the mean and the variance of genotype frequencies over generations at one locus with multiple alleles in a same finite-sized population with mutation. Different initial conditions and rates of clonality generate unique mean trajectories of genotype frequencies. Partially clonal populations converge to the same unique stable equilibrium as exclusively sexual populations, that only depends on the reciprocal mutation rates between alleles. The dynamics unfold in two phases: First, genotype frequencies move towards Hardy-Weinberg proportions; Then iterate along the Hardy-Weinberg proportions until reaching the stable equilibrium. Mean allele frequencies and gene diversity remain unchanged by different rates of clonality along the trajectories. Instead, clonality influences the speed at which populations return to Hardy-Weinberg proportions and thus shapes the temporal sequence of genotype frequency distributions over generations. Variance around each mean trajectory depends only on parental genotype frequency distributions and population size, not on clonality. Taken together, these explain why both negative and positive Fis values are expected in partially clonal populations, and why variance of Fis across loci is a reliable proxy for inferring clonal rates. Our model will enable the analysis and prediction of changes in genotype frequencies within monitored populations, and will support future inference methods relying on time-series genotyping data from a target population. HighlightsO_LIOut of equilibrium, sexual and clonal populations share the same two-step dynamics. C_LIO_LIFirst, return to Hardy-Weinberg parabola impacted by rates of clonality; Then, iteration along this parabola until reaching equilibrium that only depends on mutation rates C_LIO_LIIncreasing clonality change the speed and direction of mean dynamics out of Hardy-Weinberg parabola without affecting mean allele frequencies C_LIO_LIVariance around mean dynamics depends on parental genotype frequencies and population size but not affected by clonality C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/717696v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@1207e9dorg.highwire.dtl.DTLVardef@587d2dorg.highwire.dtl.DTLVardef@18224eborg.highwire.dtl.DTLVardef@145e2ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

Behind the shadow play: Shedding light on the population genetics of partially clonal organisms through clone age distributions

Partial clonality is widespread in natural populations; however, the distributions of clone ages under different rates of clonality and their effects on genetic diversity remain unexplored. To fill this gap, we simulated partially clonal populations over 10,000 generations across a range of clonality and mutation rates. Using a forward-in-time individual-based model, we evaluated genetic and genotypic indices alongside measures of clone age distribution to examine how different clonality rates influence clone age distributions, and how these distributions impact population structure and genetic diversity over time. Our results reveal two distinct trajectories: (i) at low to moderate rates of clonality evolution is driven by sharp and predictable patterns of rapid clone turnovers, resulting in predominantly young clones which relative abundances well align with genotypic indices ; (ii) at extreme rates of clonality, demographic stochasticity generates very variable clone age distributions which mirror the high variance of mean and variance of FIS that summarize gene reshuffling between individuals. Interestingly, a portion of the variability of these indices can be explained by differences in clone age distribution that occur by chance. Our results, therefore, complement previous theoretical studies on the population genetics of partial clonality by providing biological insights into how clonal turnover dynamics shape the temporal evolution and variability of highly clonal populations. These results have practical implications for inferring evolutionary trajectories and managing partially clonal species.

evolutionary biology↗

bioRxiv2025

THE CONSEQUENCES OF PARTIAL CLONALITY ON THE SPATIOTEMPORAL GENETIC STRUCTURE OF THE RED ALGA CHONDRIA TUMULOSA (CERAMIALES, RHODOPHYTA)

The relative rates of sexual versus clonal reproduction partition genetic diversity but the quantification of these rates remains limited in natural populations. This knowledge gap is particularly acute among tropical macroalgae. Chondria tumulosa is a red macroalga that has been documented at high abundance in the three northernmost atolls in the Papah[a]naumoku[a]kea Marine National Monument. We sampled thalli at Manawai in 2021 and 2023, at Kuaihelani in 2022 and 2023, and at H[o]lanik[u] in 2023 to characterize the reproductive mode and patterns of gene flow. Tetrasporophytes overwhelmingly dominated at all sites, atolls, and years, although eight cystocarpic female gametophytes (<1%) were documented for the first time. We observed evidence of very high clonal rates, accompanied by an increase in homozygosity. Surprisingly, our temporal analyses suggested site-specific trends in the predominance of selfing, outcrossing, or clonality. A very small haploid proportion combined with high genetic drift likely rendered temporal analyses of genotypic frequencies challenging to implement and interpret whereby point estimates were a better reflection of reproductive mode variation. Genetic differentiation increased with geographic distance, with strong temporal and spatial structure. The patterns of genetic diversity and structure combined with the dominance of tetrasporophytes suggest that C. tumulosa thalli were introduced to this region, possibly via marine debris. Future studies should focus on identifying the native range to document the ecological and evolutionary shifts that have facilitated the rapid increase and spread of C. tumulosa and its potential similarities to other invasive haploid-diploid algae.

evolutionary biology↗

bioRxiv2025

A CLONAL LEGACY? REPRODUCTIVE MODE VARIATION IN HARD AND SOFT BOTTOM GRACILARIA VERMICULOPHYLLA POPULATIONS

The red macroalga Gracilaria vermiculophylla invasion provides an opportunity to investigate the evolution of biphasic life cycles and of reproductive modes by understanding how they structure and contribute colonizing new environments in natural conditions. In hard bottom habitats, we find gametophytes and tetrasporophytes fixed by holdfasts to hard substrates, whereas in soft bottom habitats, we find free-living tetrasporophytes either drifting or anchored by tube-building polychaetes. We collected thalli from hard and soft bottom habitats along the Eastern Shore of Virginia and Maryland to investigate the role of substrate on life cycle and reproductive mode dynamics. We determined the phase and sex using observable reproductive structures and a sex-linked PCR assay, followed by genotyping all thalli using nine microsatellite loci. Sexual reproduction prevailed in hard bottom sites, whereas clonal (asexual) reproduction dominated soft bottom sites and was accompanied by tetrasporophytic dominance. There was site-specific variation in selfing and clonal rates that are supported by observations of physiological stress and local extirpation, such as at Ape Hole Creek and Fowling Point, respectively. We found evidence of isolation by distance and the structuring of genetic diversity by habitat type, then site, and finally by year. While broad patterns have been described across the extant range, we clarify population genetic patterns in hard versus soft bottom habitats that are not confounded by the invasion history comparing native and non-native thalli. These results have implications for the on-going spread of this alga and contribute to our understanding of the population genetics of partially clonal taxa.

evolutionary biology↗

bioRxiv2025

Increased clonality, decreased allele diversity and high genetic structure in tetraploid sea anemone Aulactinia stella populations from North Pacific to Atlantic across the Arctic Ocean

Reproductive mode is a key factor shaping genetic diversity, evolutionary potential, and the processes of dispersal and colonization. Clonality is particularly common in harsh environments and at the margins of species ranges, where it supports persistence, enables rapid growth, and promotes the maintenance of locally adapted genotypes. In the rapidly changing Arctic, increasing ecological connectivity is eroding historical barriers for sessile species. Evaluating genetic diversity in this context, before global change further alters Arctic ocean, is essential for understanding evolutionary dynamics during range expansion and for informing conservation strategies. Aulactinia stella is a circumpolar sea anemone with physiological characteristics in laboratory conditions suggesting a potential for clonal reproduction. In this study, we investigated its reproductive modes in natural populations across the Arctic ocean, from the northern Pacific to the Atlantic, and examined how genetic diversity is structured between adults and juveniles at five sampled sites. Across all study sites, we observed only females or individuals lacking gonads, with the exception of Kamchatka, where males were also present. Genetic indices and changes in genotype frequencies between adults and juveniles confirmed that this species reproduces partially by parthenogenesis. Populations on the Atlantic side were highly clonal with clonal rates (c) estimated at 80-99%, whereas populations on the Pacific side reproduced more sexually (c around 50%). Allelic diversity was twice as high in Kamchatka and Kuril populations, suggesting North Pacific coasts being the main last glacial refugia of A. stella. We found a stepping-stone pattern of genetic structure from Kamchatka to Atlantic populations, consistent with contemporary ocean currents and melted summer sea ice. Only a subset of the juvenile genetic diversity, mostly of local origin, was found in the established adults, while juveniles exhibited lower levels of genetic differentiation across the Arctic Ocean. Our findings underscore the need for further ecological and behavioral investigations to elucidate the mechanisms allowing the current possibilities of dispersal of this species across the Arctic Ocean. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/650399v4_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@b395e6org.highwire.dtl.DTLVardef@364804org.highwire.dtl.DTLVardef@1b22eeeorg.highwire.dtl.DTLVardef@1272ae6_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract (photo: Ekaterina Bocharova)

evolutionary biology↗

bioRxiv2025

Long-lasting coexistence of multiple asexual lineages alongside their sexual counterparts in a fungal plant pathogen

Sexual-to-asexual transitions within species are crucial for understanding reproductive evolution, yet the coexistence of both modes of fungal species in the same environment is poorly documented. Here, we report this transition in a plant pathogen species that coexists within the same geographical environment. Our biological model is the poplar rust fungus Melampsora larici-populina, which displays a complex life cycle typical of rust fungi (Pucciniales). It alternates between two unrelated hosts to complete an obligate sexual life cycle once a year. We conducted a comprehensive population genetic analysis, using 21 microsatellite markers and data from 2,122 individuals gathered over 30 years from various locations in France. Our results demonstrate the existence of many distinct lineages that reproduce asexually through the years, skipping the sexual phase. Clustering analysis identified a group of multilocus lineages that displayed all hallmarks of the genetic consequences of asexual reproduction, including highly negative and large variance among loci of the inbreeding coefficient (FIS). This indirect evidence for asexual reproduction was confirmed by the direct observation of these asexual lineages being repeatedly sampled across multiple years. This result demonstrates the coexistence of these lineages with their sexual counterparts in the same ecological niche, challenging conventional assumptions about geographical sorting of reproductive modes. These considerations are of paramount importance for understanding the contemporary evolution of major pathogen species. This switch from sexual to asexual reproduction has contributed to devastating epidemics worldwide.

evolutionary biology↗

bioRxiv2024

Seasonality and inter-annual stability in the population genetic structure of Batrachospermum gelatinosum (Rhodophyta)

Temporal population genetic studies have investigated evolutionary processes, but few have characterized the temporal patterns of reproductive system variation. Yet, temporal sampling may improve our understanding of reproductive system evolution through assessing the relative rates of selfing, outcrossing, and clonality. In this study, we focus on the monoicous, haploid-diploid freshwater red alga Batrachospermum gelatinosum. This species has a perennial, microscopic diploid phase (chantransia) that produces an ephemeral, macroscopic haploid phase (gametophyte). Recent work focusing on single time point genotyping suggested high rates of intragametophytic selfing, though there was variation among sites. We expand on this work by genotyping 191 gametophytes from four sites with reproductive system variation at multiple time points within and among years. Intra-annual data suggest shifts in gametophytic genotypes present throughout the gametophytic season. We hypothesize this pattern is likely due to the seasonality of the life cycle and the timing of meiosis among the chantransia. Inter-annual patterns were characterized by consistent genotypic and genetic composition, indicating stability in the prevailing reproductive system through time. Yet, our study identified limits to which available theoretical predictions and analytical tools can resolve reproductive system variation using haploid data. There is a need to develop better tools to understand the evolution of sex by expanding our ability to characterize the spatiotemporal variation in reproductive systems across diverse life cycles.

evolutionary biology↗

bioRxiv2024

CLONALITY AND POLYPLOIDY CONTRIBUTE TO THE SPREAD OF AVRAINVILLEA LACERATA (BRYOPSIDALES, CHLOROPHYTA) IN HAWAI'I

The relative rates of sexual versus asexual reproduction influence the partitioning of genetic diversity within and among populations. During range expansions, uniparental reproduction often facilitates colonization and establishment. The arrival of the green alga Avrainvillea lacerata has caused shifts in habitat structure and community assemblages since its discovery in 1981 offshore of west Oahu, Hawai i. Field observations suggest this species is spreading via vegetative reproduction. To characterize the reproductive system of A. lacerata in Hawai i, we developed seven microsatellite loci and genotyped 321 blades collected between 2018 and 2023 from two intertidal sites at Maunalua Bay and Ewa Beach. We found one to four alleles at multiple loci, suggesting A. lacerata is tetraploid. Each site was characterized by high genotypic richness (R > 0.8). However, clonal rates were also high at both sites, suggesting vegetative spread of A. lacerata plays a significant role. The importance of clonal reproduction for the persistence of A. lacerata in Hawai i is consistent with the ecological data collected for this species, and observations of other abundant macroalgal invaders in Hawaii and other regions of the world. These data demonstrate the necessity for implementing appropriate population genetic methods and provide insights into the biology of this alga that will contribute to future studies on effective management strategies incorporating its reproductive system. This study represents one of the few investigating green algal population genetic patterns and contributes to our understanding of algal reproductive system evolution.

evolutionary biology↗

bioRxiv2022

Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population

Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering the full trajectory compared to few time samples. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetics changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.

evolutionary biology↗

bioRxiv2022

Interplay between demography and selection: a forward model illuminates the temporal genetic signatures of rapid adaptation in plant pathogens

Pathogen species are experiencing strong joint demographic and selective events, especially when they adapt to a new host, for example through overcoming plant resistance. Stochasticity in the founding event and the associated demographic variations hinder our understanding of the expected evolutionary trajectories and the genetic structure emerging at both neutral and selected loci. What would be the typical genetic signatures of such a rapid adaptation event is not elucidated. Here, we build a demogenetic model to monitor pathogen population dynamics and genetic evolution on two host compartments (susceptible and resistant). We design our model to fit two plant pathogen life cycles, with and without host alternation. Our aim is to draw a typology of eco-evolutionary dynamics. Using time-series clustering, we identify three main scenarios: 1) small variations in the pathogen population size and small changes in genetic structure, 2) a strong founder event on the resistant host that in turn leads to the emergence of genetic structure on the susceptible host, and 3) evolutionary rescue that results in a strong founder event on the resistant host, preceded by a bottleneck on the susceptible host. We pinpoint differences between life cycles with notably more evolutionary rescue with host alternation. Beyond the selective event itself, the demographic trajectory imposes specific changes in the genetic structure of the pathogen population. Most of these genetic changes are transient, with a signature of resistance overcoming that vanishes within a few years only. Considering time-series is therefore of utmost importance to accurately decipher pathogen evolution.

evolutionary biology↗

bioRxiv2021

Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heterostylous invasive populations of Ludwigia grandiflora subsp. hexapetala

AO_SCPLOWBSTRACTC_SCPLOWBreeding system influences local population genetic structure, effective size, offspring fitness and functional variation. Determining the respective importance of self- and cross-fertilization in hermaphroditic flowering plants is thus important to understand their ecology and evolution. The worldwide invasive species, Ludwigia grandiflora subsp. hexapetala (Lgh) presents two floral morphs: one self-compatible short-styled morph (S-morph) and one self-incompatible long-styled morph (L-morph). In this study, we identified the breeding systems of western European experimental and natural populations of Lgh by comparing structural characteristics of pollen and style, by studying self- and cross-pollen tube elongations and the viability of the resulting seeds and seedlings in both floral morphs. Our results showed no differences in pollen shape and stigma surfaces no matter the floral morph. In the self-incompatible L-morph flowers, self-pollen tubes were stopped tardily, in the ovarian area, and were unable to fertilize the ovules. This first formal identification of a late-acting, prezygotic self-incompatible system (LSI) in Ludwigia genus contributes a case of LSI in an additional family within the Myrtales order. In the self-compatible S-morph flowers, self-pollen always succeeded to self-fertilize the ovules that nearly all developed into viable seedlings. However, cross-pollen tubes always elongated faster than self-pollen tubes in both morphs. S-morph individuals may thus advantage preferential allogamy over selfing when cross-pollen is available despite its self-compatibility. As expected in late-acting self-incompatible systems, L-morph flowers authorised 0.2{per thousand} of selfed seeds during the uppermost flowering season, that increased to 1{per thousand} at the end of the flowering season. Such delayed selfing resulted in a significant quantity of viable floating seeds. They may contribute to the local regeneration, seed bank and propagation of the L-morph, which may contribute to explain its invasion success worldwide. Management plans of Lgh would gain to consider the breeding systems we identified.

ecology↗

bioRxiv2020

Untangling structural factors and evolutionary drivers in nascent polyploids

O_LIAllopolyploids have globally higher fitness than their diploid progenitors however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success. C_LIO_LIUsing the Brassica model, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploid B. napus and systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors and polyploid formation type. We evaluated the evolution of meiotic behavior, fertility and identified rearrangements in S1 to S9 lineages, to explore the positive consequences of euploid selection on B. napus genome stability. C_LIO_LIRecurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a quasi disappearance of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number strongly depended on the genetic background and cytoplasm donor. C_LIO_LIThe combined use of both self-fertilisation and outcrossing as well as recurrent euploid selection, allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explain B. napus speciation success. C_LI

evolutionary biology↗

bioRxiv2020

Self-incompatibility limits sexual reproduction rather than environmental conditions in an invasive aquatic plant

SummaryFruitfulness and fertility are important components of sexual reproductive success in plants, and often depends on environmental conditions and reproductive systems. For invasive plants, fruitfulness and fertility control their ecological success and adaptation in invaded ecosystems. We studied which factors bring about fruitfulness and fertility in invasive populations of the aquatic plant Ludwigia grandiflora subsp. hexapetala.We analysed fruitfulness and fertility of 37 populations growing under variable climatic conditions in Western Europe, and sub-sampled fruitful and fruitless populations grown in common controlled conditions. We carried out self- and cross-pollinations and measured their floral biometrics.Environmental conditions, and temperature in particular, did not affect fruitfulness and fertility in-situ or in common controlled environments. Hand-pollinations resulted in fruit production by individuals sampled from fruitless populations when pollen came from fruitful populations, and by individuals sampled from fruitful populations whatever the origin of pollen. Floral biometrics evidenced the existence of two floral morphs that overlapped with fruitfulness, and individual incompatibility.Our results rebutted the hypothesis that environmental conditions control fruitfulness and fertility in these invasive populations. We instead found that fruit and seed production were controlled by a reproductive system involving a self-incompatible approach herkogamous morph and a self-compatible reverse herkogamous morph. We assessed the floral morphs distribution worldwide of fruitless and fruitful native and invasive populations that matched our results at larger scale. Our results may constitute the first evidence of a possible heteromorphic self-incompatible system in Ludwigia populations and in Onagraceae phylogeny. It calls for further investigations on reproductive systems in this plant family. Finally, the observation that the self-incompatible morph seemed to be the world most invasive morph in this species tackles our understanding of biological and ecological conditions for invasiveness.Synthesis. Our study showed that fruitfulness and fertility in the aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala depend on a self-incompatibility system coinciding with two floral morphs, rather than environmental conditions and limitations. These new explanations on the sexual success of Ludwigia invasive populations will help defining new predictions about its worldwide spreads and ecological success, and will help reappraising future management plans.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗