Biology subjects

Anstett, J.

Publications and source records attributed to Anstett, J..

4 recordsLinked to original sources

bioRxiv2024

Evolutionary rescue during extreme drought

Populations declining due to climate change may need to evolve to persist. While evolutionary rescue has been demonstrated in theory and the lab, its relevance to natural populations facing climate change remains unknown. Here we link rapid evolution and population dynamics in scarlet monkeyflower, Mimulus cardinalis, during an exceptional drought. We leverage whole-genome sequencing across 55 populations to identify climate-associated loci. Simultaneously we track demography and allele frequency change throughout the drought. We establish range-wide population decline during the drought, geographically variable rapid evolution, and variable population recovery that is predictable by standing genetic variation in and rapid evolution at climate-associated loci. These findings demonstrate evolutionary rescue in the wild, showing that genetic variation at adaptive, but not neutral loci, predicts population recovery.

evolutionary biology↗

bioRxiv2024

Structural variants underlie parallel adaptation following global invasion

Rapid adaptation during invasion has historically been considered limited and unpredictable. We leverage whole-genome sequencing of >2600 plants across six continents to investigate the relative roles of colonization history and adaptation during the worldwide invasion of Trifolium repens. Introduced populations contain high levels of genetic variation with independent colonization histories evident on different continents. Five large structural variants on three chromosomes exist as standing genetic variation within the native range, and exhibit strong signatures of parallel climate-associated adaptation across continents. Common gardens in the native and introduced ranges demonstrate that three structural variants exhibit patterns of selection consistent with local adaptation across each range. Our results provide strong evidence that rapid and parallel adaptation during invasion is caused by large-effect structural variants introduced throughout the world. Significance StatementBiological invasions occur over short timescales and introductions are often hypothesized to include limited genetic diversity, making the role of adaptation in invasion success controversial. We demonstrate that the invasion of a human-commensal species, Trifolium repens, likely stems from multiple, diverse introductions with significant evidence of climate-associated adaptation following introduction. The genetic basis of adaptation is most strongly linked to five chromosomal rearrangements that each span hundreds of genes - matching theoretical predictions that large-effect variants are key to the initial stages of adaptation to novel environments. Chromosomal rearrangements have remarkably parallel signatures of adaptation across different introductions despite initial colonization from different areas of Europe. Our study highlights the impact of globalization and rapid adaptation for the invasion success of human commensal species.

evolutionary biology↗

bioRxiv2024

MetaPathways v3.5: Modularity and Scalability Improvements for Pathway Inference from Environmental Genomes

Over the past decade MO_SCPLOWETAC_SCPLOWPO_SCPLOWATHWAYSC_SCPLOW has advanced as a modular pipeline for constructing environmental pathway genome databases (ePGDBs), increasing our understanding of microbial metabolism at the individual, population and community levels of biological organization. With this release, we have addressed several user experience issues related to installation, module integration, and database management. With a refactored code base, MO_SCPLOWETAC_SCPLOWPO_SCPLOWATHWAYSC_SCPLOW v3.5 enhances the user experience through streamlined installation via package indexes or containers, refined modules, and interface upgrades. It boasts updated algorithm support for sequence feature prediction, annotation, metabolic inference, and coverage metrics including genome resolved metagenomes. Tested and refined on synthetic datasets, MO_SCPLOWETAC_SCPLOWPO_SCPLOWATHWAYSC_SCPLOW v3.5 demonstrates improved performance and usability; facilitating more in-depth exploration of microbial interactions and metabolic functions in environmental genomes that scales with con-temporary sequencing throughput. Availability and ImplementationMO_SCPLOWETAC_SCPLOWPO_SCPLOWATHWAYSC_SCPLOW v3.5 is available via AO_SCPLOWNACONDAC_SCPLOW, DO_SCPLOWOCKERC_SCPLOW, and AO_SCPLOWPPTAINERC_SCPLOW. The source code is available on BO_SCPLOWITC_SCPLOWBO_SCPLOWUCKETC_SCPLOW:https://bitbucket.org/BCB2/metapathways/ The documentation is available via RO_SCPLOWEADC_SCPLOWTO_SCPLOWHEC_SCPLOWDO_SCPLOWOCSC_SCPLOW:https://metapathways.readthedocs.io Contactshallam@mail.ubc.ca

bioinformatics↗

bioRxiv2023

Does urbanization lead to parallel demographic shifts across the world in a cosmopolitan plant?

Urbanization is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the "urban facilitation model" suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the Global Urban Evolution project (GLUE), to study the effects of urbanization on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of a reduction in Ne linked to urbanization. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides one of the largest comprehensive tests of demographic effects of urbanization and our results contrast the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.

evolutionary biology↗