Guillaume Lavanchy

University of Lausanne

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Tanja Schwander

University of Lausanne

Christophe Dufresnes

École Pratique des Hautes Études

Zoé Dumas

University of Lausanne

Karim Ghali

University of Lausanne

Marjorie Labédan

Quadram Institute

Roberto Sermier

University of Lausanne

Alan Brelsford

University of California, Riverside

Anne Freitag

Natural History Museum of Geneva

Susana Freitas

University of Lausanne

Andrea Luchetti

University of Bologna

Cooperative Institutions

University of Lausanne

Centre National de la Recherche Scientifique

University of Bern

University of Sheffield

University of Helsinki

Musée cantonal de zoologie de Lausanne

Institut de Biologia Evolutiva

École Pratique des Hautes Études

University of Bologna

University of Queensland

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Facultative parthenogenesis: a transient state in transitions between sex and obligate asexuality in stick insects?

bioRxiv (Cold Spring Harbor Laboratory) (2022)

Chloé Larose Guillaume Lavanchy Susana Freitas Darren J. Parker Tanja Schwander

Abstract Transitions from obligate sex to obligate parthenogenesis have occurred repeatedly across the tree of life. Whether these transitions occur abruptly or via a transient phase of facultative parthenogenesis is rarely known. We discovered and characterised facultatively parthenogenetic populations of the North American stick insect Timema douglasi , a species in which only obligately parthenogenetic populations were known so far. These populations comprised three genetic lineages. Females from all lineages were capable of parthenogenesis (with variable efficiency) but their propensity to reproduce sexually after mating varied extensively. In all three lineages, parthenogenesis resulted in the complete loss of heterozygosity in a single generation. Obligately parthenogenetic Timema have also lost all heterozygosity, suggesting that the transition to obligate parthenogenesis did not require a modification of the proximate mechanism, but rather involved a gradual increase in frequency. We speculate that facultative parthenogenesis may often be transient and be replaced by obligate strategies (either sex or parthenogenesis) because of a trade-off between the efficiency of the two reproductive modes. Such a trade-off could help explain why facultative parthenogenesis is rare among animals, despite its potential to combine the known benefits of sex and parthenogenesis.

Parthenogenesis

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Facultative

Asexuality

10.1101/2022.03.25.485836

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Citations (2)

Decontaminating genomic data for accurate species delineation and hybrid detection in the Lasius ant genus

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Kristine Jecha Guillaume Lavanchy Tanja Schwander

Species identification and delineation by molecular methods has become a widely used technique and has revealed hybrids between species previously believed to be completely reproductively isolated. However, the application of molecular methods is associated with a risk of DNA contamination, which can result in the identification of false hybrids and generate inaccurate conclusions about the species' identities and characteristics. Here, we generate and analyze a dataset of nuclear SNP data and mitochondrial DNA sequences from over 1,000 Lasius ants to accurately investigate the species delineation and hybridization proclivity within the genus. We describe an approach, based on a combination of competitive mapping and allelic depth ratio analysis, that allows us to identify DNA contaminations and filter them from large-scale datasets. By applying this approach to the Lasius ants, we are able to remove interspecific contamination, and to clearly delineate each species genetically as well as identify a hybrid individual between L. emarginatus and L. platythorax.

Lasius

10.1101/2024.11.27.625433

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Investigating Fine‐Scale Breeding Habitat Use by Amphibians in a Continuous Wetland Using Environmental DNA

Environmental DNA (2025)

Julie Morgane Guenat Antoine Gander Luca Fumagalli Guillaume Lavanchy

ABSTRACT Designing effective conservation plans to protect species from extinction requires a comprehensive understanding of their ecology. Conventional methods used to investigate habitat use are time‐consuming, and the detectability of cryptic species is often insufficient. Environmental DNA (eDNA)‐based approaches provide a complementary tool to traditional monitoring methods for ecosystem monitoring and assessment. Nevertheless, to our knowledge, such methods have rarely been applied to investigate habitat use at a fine scale in a continuous wetland environment. Here, we used an eDNA metabarcoding approach to characterize the breeding habitat use of local amphibian species in a wet meadow expanse along the southern shore of Lake Neuchâtel, Switzerland. We retrieved DNA from six out of the seven species expected to be present. We tested the influence of six abiotic environmental variables on overall species assemblages and individual species occurrences. We showed that the main factor structuring species assemblages was water temperature and that the distribution of three amphibian species was associated with several environmental variables. Our results indicate that the eDNA detection approaches are promising tools to study species' ecology at a small scale in continuous wetland habitats.

Environmental DNA

10.1002/edn3.70063

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Evolution of alternative reproductive systems inBacillusstick insects

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Guillaume Lavanchy Alexander Brandt Marc Bastardot Zoé Dumas Marjorie Labédan

Abstract Reproduction is a key feature of all organisms, yet the way in which it is achieved varies greatly across the tree of life. One striking example of this variation is the stick insect genus Bacillus , in which five different reproductive modes have been described: sex, facultative and obligate parthenogenesis, and two highly unusual reproductive modes: hybridogenesis and androgenesis. Under hybridogenesis, the entire genome from the paternal species is eliminated, and replaced each generation by mating with the corresponding species. Under androgenesis, an egg is fertilized but the developing diploid offspring bear two paternal genomes, and no maternal genome, as a consequence of unknown mechanisms. Here, we re-evaluate previous descriptions of Bacillus lineages and the proposed F 1 hybrid ancestries of the hybridogenetic and obligately parthenogenetic lineages (based on allozymes and karyotypes) from Sicily, where all these reproductive modes are found. We generate a chromosome-level genome assembly for a facultative parthenogenetic species ( B. rossius ) and combine extensive field sampling with RADseq and mtDNA data. We identify and genetically corroborate all previously described species and confirm the ancestry of hybrid lineages. All hybrid lineages have fully retained their F1 hybrid constitution throughout the genome, indicating that the elimination of the paternal genome in hybridogens is always complete and that obligate parthenogenesis in Bacillus hybrid species is not associated with an erosion of heterozygosity as known in other hybrid asexuals. Our results provide a stepping stone towards understanding the transitions between reproductive modes and the proximate mechanisms of genome elimination.

10.1101/2023.07.31.550487

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Facultative parthenogenesis: a transient state in transitions between sex and obligate asexuality in stick insects?

Peer Community Journal (2023)

Chloé Larose Guillaume Lavanchy Susana Freitas Darren J. Parker Tanja Schwander

Transitions from obligate sex to obligate parthenogenesis have occurred repeatedly across the tree of life. Whether these transitions occur abruptly or via a transient phase of facultative parthenogenesis is rarely known. We discovered and characterised facultatively parthenogenetic populations of the North American stick insect Timema douglasi, a species in which only obligately parthenogenetic populations were known so far. These populations comprised three genetic lineages. Females from all lineages were capable of parthenogenesis (with variable efficiency) but their propensity to reproduce sexually after mating varied extensively. In all three lineages, parthenogenesis resulted in the complete loss of heterozygosity in a single generation. Obligately parthenogenetic Timema have also lost all heterozygosity, suggesting that the transition to obligate parthenogenesis did not require a modification of the proximate mechanism, but rather involved a gradual increase in frequency. We speculate that facultative parthenogenesis may often be transient and be replaced by obligate strategies (either sex or parthenogenesis) because of a trade-off between the efficiency of the two reproductive modes. Such a trade-off could help explain why facultative parthenogenesis is rare among animals, despite its potential to combine the known benefits of sex and parthenogenesis.

Parthenogenesis

Obligate

Facultative

Asexuality

10.24072/pcjournal.283

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Citations (8)

A rapid rate of sex-chromosome turnover and non-random transitions in true frogs

Nature Communications (2018)

Daniel L. Jeffries Guillaume Lavanchy Roberto Sermier Michael J. Sredl Ikuo Miura

Abstract The canonical model of sex-chromosome evolution predicts that, as recombination is suppressed along sex chromosomes, gametologs will progressively differentiate, eventually becoming heteromorphic. However, there are numerous examples of homomorphic sex chromosomes across the tree of life. This homomorphy has been suggested to result from frequent sex-chromosome turnovers, yet we know little about which forces drive them. Here, we describe an extremely fast rate of turnover among 28 species of Ranidae. Transitions are not random, but converge on several chromosomes, potentially due to genes they harbour. Transitions also preserve the ancestral pattern of male heterogamety, in line with the ‘hot-potato’ model of sex-chromosome transitions, suggesting a key role for mutation-load accumulation in non-recombining genomic regions. The importance of mutation-load selection in frogs might result from the extreme heterochiasmy they exhibit, making frog sex chromosomes differentiate immediately from emergence and across their entire length.

Sex linkage

10.1038/s41467-018-06517-2

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Citations (187)

Hybridogenesis

Current Biology (2019)

Guillaume Lavanchy Tanja Schwander

Spelling

10.1016/j.cub.2019.01.020

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Citations (5)

Investigating fine-scale breeding habitat use by amphibians in a continuous wetland using environmental DNA

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Julie Morgane Guenat Antoine Gander Luca Fumagalli Guillaume Lavanchy

ABSTRACT Designing effective conservation plans to protect species from extinction requires a better understanding of their ecology. Conventional methods used to investigate habitat use are time consuming, and detectability of cryptic species is often insufficient. Environmental DNA (eDNA)-based approaches now provide an alternative for ecosystems monitoring and assessment. Nevertheless, to our knowledge, such methods have never been applied to investigate habitat use at a fine scale in a continuous wetland environment. Here, we used an eDNA metabarcoding approach to characterize the breeding habitat use of local amphibian species in a wet meadow expanse along the southern shore of Lake Neuchâtel, Switzerland. We retrieved DNA from six out of the seven species expected to be present. We tested the influence of six abiotic environmental variables on overall species communities as well as individual species occurrences. We showed that the main factor structuring species communities was water temperature, and that the distribution of three amphibian species was associated with several environmental variables. Our results indicate that the eDNA approach is a promising tool to study species’ ecology at a small scale in continuous wetland habitats.

Environmental DNA

Extinction (optical mineralogy)

10.1101/2023.02.27.530201

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Citations (0)

LEVERAGING CITIZEN SCIENCE TO ASSESS RICHNESS, DIVERSITY, AND ABUNDANCE IN ANT COMMUNITIES

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Tim M. Szewczyk Guillaume Lavanchy Anne Freitag Aline Dépraz Amaury Avril

A bstract Citizen science is a key resource in overcoming the logistical challenges of monitoring biodiversity. While datasets collected by groups of volunteers typically have biases, recent methodological and technological advances provide approaches for accounting for such biases, particularly in the context of modelling species distributions and diversity. Specifically, data integration techniques allow for the combination of scientifically collected datasets with haphazardly sampled presence-only datasets created by most citizen science initiatives. Here, we use a hierarchical Bayesian framework to integrate a set of ant presences collected by citizen scientists in the Vaud canton (Switzerland) with ant colony density data collected concurrently in the same region following a scientific sampling design. The community-level Poisson point process model included species-specific responses to the local (1.2 m 2 ) and regional (1 km 2 ) environment, with the presence-only samples incorporated at the regional scale to predict local and regional ant communities. At the regional scale, species richness followed a hump-shaped pattern and peaked near 1000 m while abundance increased with elevation. Low elevation and montane ant communities were composed of distinct species assemblages. At the local scale, the link between elevation and richness, diversity, and abundance was weak. At low elevations, local plots varied both in total abundance and species composition, while at higher elevations, the species composition was less variable. The citizen science dataset showed a general tendency toward under-representation of certain species, and heavy spatial sampling bias. Nonetheless, the inclusion of the citizen science data improved predictions of local communities, and also reduced susceptibility to over-fitting. Additionally, the citizen science dataset included many rare species not detected in the structured abundance dataset. The model described here illustrates a framework for capitalizing on the efforts of citizen scientists to better understand the patterns and distribution of biodiversity.

Citizen Science

10.1101/2024.06.11.598431

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Citations (0)

Hybridogenesis

Current Biology (2019)

Guillaume Lavanchy Tanja Schwander

Sexual reproduction

10.1016/j.cub.2018.11.046

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Citations (31)