Biology subjects

Landis, J.

Publications and source records attributed to Landis, J..

4 recordsLinked to original sources

bioRxiv2026

Canalized gene regulatory networks stabilize floral polymorphism and enable modular transgressive expression

O_LIFloral polymorphisms frequently persist across heterogeneous environments despite ongoing gene flow, yet the regulatory mechanisms maintaining discrete phenotypes remain unclear. We tested whether alternative flower-colour morphs in Stellera chamaejasme L. are maintained by canalized gene regulatory architectures that stabilize expression around morph-specific optima. C_LIO_LIWe used a pan-transcriptomic and eco-evolutionary framework integrating genome-wide gene expression profiling, co-expression network analysis, functional enrichment, ortholog-based phylogenomics, and variance-based modeling of regulatory canalization and transgressive expression to quantify regulatory variation across morphs. C_LIO_LITranscriptomic variation was structured primarily by morph identity rather than geography, indicating consistent morph-associated regulatory programs. Parental morphs showed reduced within-morph variance in gene co-expression modules, consistent with strong regulatory constraint at the network level. In contrast, a naturally occurring mosaic morph exhibited extensive non-additive and predominantly transgressive expression, with most genes falling outside the parental range. This transgressive signal was modular, with most networks remaining stable while a subset showed elevated variance and disrupted inheritance. Functional analyses further reveal that floral pigmentation is embedded within broader metabolic and stress-response pathways, linking color polymorphism to coordinated physiological states and ecological differentiation. C_LI

plant biology↗

bioRxiv2026

The dynamics of introgression across an adaptive radiation: examining hybrid speciation and parallel adaptation in North American Vitis

Hybridization between species can contribute to parallel adaptive events and, in some cases, speciation. However, the prevalence of introgression is rarely measured across multiple species, meaning that it is rarely integrated with landscape-scale processes or connected to adaptive repeatability. Here, we analyzed whole-genome resequencing data from 639 accessions representing 48 Vitis species. Vitis is notable for the domesticated grapevine (V. vinifera), multiple economically important North American species, and as an example of a temperate adaptive radiation. Our dataset included population-level sampling for 19 species, from which we reconstructed individual- and species-level phylogenetic frameworks for the genus. The analyses uncovered widespread evidence of introgression, comprising [~]14% of the average Vitis genome. Introgression was associated with geographic distribution between species, and highly admixed individuals were more frequently found near ecological niche margins. Genetic analyses further indicated that previously recognized hybrid taxa, V. x doaniana and V. x champinii, likely represent hybrid swarms rather than distinct species. We also assessed patterns of adaptive repeatability across eight species with denser population sampling. For six of the eight species, most of the detected sweeps overlapped with sweeps in other species; on average, more recently diverged species shared more overlapping sweeps. Parallel sweep events were driven mostly by introgression, although a substantial fraction ([~]40%) was attributed to selection on ancestral standing variation. By integrating population genomic data across many species, this study highlights the central role of shared genetic variation across an adaptive radiation.

evolutionary biology↗

bioRxiv2025

The power to resolve relationships: identifying incongruence and precision of reduced representation and genome-wide data in phylogenomics and population genomics

Target capture of ultraconserved elements (UCEs) and taxon-specific probes are widely used reduced-representation methods in phylogenomics and, increasingly, in population genomics for their ability to retrieve hundreds to thousands of homologous loci across divergent taxa. Meanwhile, declining costs and improved computational methods have made genome resequencing more accessible for non-model species, enabling the generation of datasets that can address evolutionary and ecological questions from micro- to macroevolutionary scales. Whether target capture approaches to likewise generate datasets that can address questions across broad hierarchical scales remains unclear. Here, we assess the efficacy of data collection (i.e., single nucleotide polymorphism (SNP) retention), predicted genetic variation across samples (i.e., heterozygosity), and phylogenetic congruence between data generated using reduced-representation methods and genome resequencing, leveraging publicly available datasets from plants and animals. We found that SNP retention varied by locus type, with genome-wide datasets retaining the highest proportion of SNPs and UCEs the lowest proportion. Heterozygosity also differed, with Benchmarking Universal Single-Copy Orthologs (BUSCOs) producing the lowest estimates, followed by UCEs; the inclusion of supercontig flanking regions raised heterozygosity values moderately. Across all phylogenetic trees, UCE datasets had the lowest bootstrap support, followed by BUSCOs and single copy orthologous genes. Population structure analyses frequently underestimated the number of ancestral populations in reduced-representation datasets, often identifying fewer populations than genome-wide datasets and assigning samples to different clusters. These discrepancies underscore the challenges of relying solely on reduced-representation methods for robust inferences of genetic diversity, phylogenetic relationships, and population structure.

evolutionary biology↗

bioRxiv2024

The topography of gene tree topology space in a plant genus with a legacy of recent polyploidy and introgression

The eukaryotic genome has been described as a collection of different histories; for any set of taxa one of these histories is the record of cladogenic events that together comprise the species tree. Among the other histories expected to occur are those attributable to deep coalescence/lineage sorting; to biological causes such as introgression and horizontal transfer; or to pseudo-orthology, long branch attraction, and other technical issues. Gene tree topology space is the portion of tree space occupied by the gene trees reconstructed for a particular dataset of sampled genetic loci. Because coalescent theory predicts that the species tree topology will generally be the most frequent among gene trees, a reasonable expectation is that there will be a peak in gene tree topology space at the species tree topology, with secondary peaks present due to trees tracking other histories. Gene tree topology space in the small ([~]30 species, including the cultivated soybean) legume genus, Glycine should not only have signals from the species tree and from lineage sorting, but also from a likely introgression event that created incongruence between the plastid and nuclear genomes. Additionally, Glycine is the product of a relatively recent (<13 million years) whole genome duplication, raising the possibility of pseudo-orthology. We explored this space using a set of 2389 nuclear genes and representative accessions from a 570-taxon concatenation tree, reconstructing gene trees for all nuclear loci and from complete plastid genomes and partial mitochondrial genomes. Species trees (ASTRAL) and maximum likelihood (ML) concatenation trees were congruent for a 61-taxon dataset but were incongruent with organellar genome trees. Gene tree topology space was flat: No topology was represented by more than one gene tree. This was also true for a reduced dataset of 27 taxa; only when the dataset was reduced to six ingroup taxa were multiple gene trees having the species tree topology observed, along with a topology congruent with the chloroplast genome topology, presumably representing nuclear loci introgressed along with the plastome. Clustering failed to identify any regional differentiation of gene tree topology space populated by loci with similar topologies. Pseudo-orthology did not contribute meaningfully to incongruence, in agreement with recent modeling work that minimizes concerns about this phenomenon. Clearly, different genes have different historical signals, but these signals are complex and exist at the level of clades within trees rather than as entire gene trees.

evolutionary biology↗