Biology subjects

Bird, K.

Publications and source records attributed to Bird, K..

6 recordsLinked to original sources

bioRxiv2025

Convergence and constraint in glucosinolate evolution across the Brassicaceae

Diversity in plant specialized metabolites plays critical roles in plant-environment interactions. In longer evolutionary scales, e.g. between families or orders, this diversity arises from whole-genome and tandem duplication events. Less is known about the evolutionary patterns shaping chemical diversity at shorter scales, e.g. within a family. Utilizing the aliphatic glucosinolate pathway we explored how the terminal structural modification enzyme GSL-OH evolved across the Brassicaceae and the genomic processes that control presence-absence variation of its products (R)-2-hydroxy-but-3-enyl and (S)-2-hydroxy-but-3-enyl. We implemented a phylo-functional approach where we functionally validated GSL-OH orthologs across the Brassicaceae and used that information to map the genomic origin and trajectory of the loci. This uncovered a complex mechanism involving at least three ancestral loci with extensive gene loss across all species creating unequal retention across the phylogenetic relationships. Convergent evolution in enantiomeric specificity was observed where several independent species had tandem duplicates diverged towards producing the R or S enantiomers. To explore potential biological differences between the enantiomers, we performed Trichoplusia ni insect assays and Botrytis cinerea detached leaf assays. We found that plants with the S enantiomer were more susceptible to B. cinerea infection while plants with the R enantiomer seemed more susceptible to T. ni herbivory. This variation in activity between the precursor and different enantiomeric products may shape the recurrent evolution of their production.

plant biology↗

bioRxiv2024

Evolutionary and biological mechanisms underpinning chitin degradation in aquatic fungi

Fungal biology underpins major processes in ecosystems. The Chytridiomycota (chytrids) is a group of early-diverging fungi, many of which function in ecosystems as saprotrophs processing high molecular weight biopolymers, however the mechanisms underpinning chytrid saprotrophy are poorly understood. Genome sequences from representatives across the group and the use of model chytrids offers the potential to determine new insights into their evolution. In this study, we focused on the biology underpinning chitin saprotrophy, a common ecosystem function of aquatic chytrids. The genomes of chitinophilic chytrids have expanded inventories of glycoside hydrolase genes responsible for chitin processing, complemented with bacteria-like chitin-binding modules (CBMs) that are absent in other chytrids. In the model chitinophilic saprotroph Rhizoclosmatium globosum JEL800, the expanded repertoire of chitinase genes is diverse and almost half were detected as proteins in the secretome when grown with chitin. Predicted models of the secreted chitinases indicate a range of active site sizes and domain configurations. We propose that increased diversity of secreted chitinases is an adaptive strategy that facilitates chitin degradation in the complex heterologous organic matrix of the arthropod exoskeleton. Free swimming R. globosum JEL800 zoospores are chemotactic to the chitin monomer N-acetylglucosamine and accelerate zoospore development when grown with chitin. Our study sheds light on the underpinning biology and evolutionary mechanisms that have supported the saprotrophic niche expansion of some chytrids to utilise lucrative chitin-rich particles in aquatic ecosystems and is a demonstration of the adaptive capability of this successful fungal group.

evolutionary biology↗

bioRxiv2023

Between-group heritability and the status of hereditarianism as an evolutionary science

Hereditarianism is a school of thought that contends there are substantial evolved cognitive and behavioral differences among groups of humans which are both resistant to environmental intervention and are a root cause of differential social outcomes across groups. The relationship of betweengroup heritability [Formula] to within-group heritability [Formula] is one of the key theoretical components of hereditarianism and forms one of the bases for its claim to be an evolutionary science. Here, we examine the relationship between [Formula]and [Formula] and its application to problems in the hereditarian literature from an evolutionary genetic perspective. We demonstrate that the formulation of the relationship between [Formula] and [Formula]used in the hereditarian literature has no evolutionary content. By re-writing the relationship between [Formula] and[Formula] in a novel evolutionary framework, we demonstrate that there is no way to predict[Formula] using[Formula] without considerable additional theory that is absent from the hereditarian literature. Furthermore, we demonstrate that the hereditarian technique that uses[Formula] and [Formula] as a means of judging whether a given difference between groups may be plausibly ameliorated through environmental intervention is mathematically flawed. Lastly, we fill a gap in the hereditarian literature by writing out a means of using [Formula] to predict the absolute difference between groups under a neutral evolutionary model and find that it is much smaller than claimed by hereditarians. In conclusion, we propose a path forward for the study of human variation that moves us past the ill-conceived nature vs. nurture question and allows us to focus on more productive issues.

genetics↗

bioRxiv2022

Predicting yield traits of individual field-grown Brassica napus plants from rosette-stage leaf gene expression

BackgroundIn the plant sciences, results of laboratory studies often do not translate well to the field because lab growth conditions are very different from field conditions. To help close this lab-field gap, we developed a new strategy for studying the wiring of plant traits directly in the field, based on molecular profiling and phenotyping of individual plants of the same genetic background grown in the same field. This single-plant omics strategy leverages uncontrolled micro-environmental variation across the field and stochastic variation among the individual plants as information sources, rather than controlled perturbations. Here, we use single-plant omics on winter-type Brassica napus (rapeseed) plants to investigate to what extent rosette-stage gene expression profiles can be linked to the early and late phenotypes of individual field-grown plants. ResultsWe find that rosette leaf gene expression in autumn has substantial predictive power for both autumnal leaf phenotypes and final yield in spring. Many of the top predictor genes are linked to developmental processes known to occur in autumn in winter-type B. napus accessions, such as the juvenile-to-adult and vegetative-to-reproductive phase transitions, indicating that the yield potential of winter-type B. napus is influenced by autumnal development. ConclusionsOur results show that profiling individual plants under uncontrolled field conditions is a valid strategy for identifying genes and processes influencing crop yield in the field.

systems biology↗

bioRxiv2021

A cellular and molecular atlas reveals the basis of chytrid development.

The chytrids (phylum Chytridiomycota) are a major early-diverging fungal lineage of ecological and evolutionary importance. Despite their importance, many fundamental aspects of chytrid developmental and cell biology remain poorly understood. To address these knowledge gaps, we combined quantitative volume electron microscopy and comparative transcriptome profiling to create an atlas of the cellular and molecular basis of the chytrid life cycle, using the model chytrid Rhizoclosmatium globosum. From our developmental atlas, we show that zoospores exhibit a specialised biological repertoire dominated by inactive ribosome aggregates, and that lipid processing is complex and dynamic throughout the cell cycle. We demonstrate that the chytrid apophysis is a distinct subcellular structure characterised by high intracellular trafficking, providing evidence for division of labour in the chytrid cell plan, and show that zoosporogenesis includes animal like amoeboid cell morphologies resulting from endocytotic cargo transport from the interstitial maternal cytoplasm. Taken together, our results reveal insights into chytrid developmental biology and provide a basis for future investigations into early-diverging fungal cell biology.

developmental biology↗

bioRxiv2021

Brassica rapa domestication: untangling wild and feral forms and convergence of crop morphotypes

The study of domestication contributes to our knowledge of evolution and crop genetic resources. Human selection has shaped wild Brassica rapa into diverse turnip, leafy, and oilseed crops. Despite its worldwide economic importance and potential as a model for understanding diversification under domestication, insights into the number of domestication events and initial crop(s) domesticated in B. rapa have been limited due to a lack of clarity about the wild or feral status of conspecific non-crop relatives. To address this gap and reconstruct the domestication history of B. rapa, we analyzed 68,468 genotyping-by-sequencing-derived SNPs for 416 samples in the largest diversity panel of domesticated and weedy B. rapa to date. To further understand the center of origin, we modeled the potential range of wild B. rapa during the mid-Holocene. Our analyses of genetic diversity across B. rapa morphotypes suggest that non-crop samples from the Caucasus, Siberia, and Italy may be truly wild, while those occurring in the Americas and much of Europe are feral. Clustering, tree-based analyses, and parameterized demographic inference further indicate that turnips were likely the first crop type domesticated, from which leafy types in East Asia and Europe were selected from distinct lineages. These findings clarify the domestication history and nature of wild crop genetic resources for B. rapa, which provides the first step toward investigating cases of possible parallel selection, the domestication and feralization syndrome, and novel germplasm for Brassica crop improvement.

evolutionary biology↗