Biology subjects

Culham, A.

Publications and source records attributed to Culham, A..

5 recordsLinked to original sources

bioRxiv2025

CactEcoDB: Trait, spatial, environmental, phylogenetic and diversification data for the cactus family

Integrated datasets linking traits, spatial distributions, environmental variables and phylogenies are essential for comparative research, but remain limited for many plant taxa, including those which are most threatened. Cactaceae are a morphologically and ecologically diverse succulent family that are iconic components of ecosystems across the Americas, and face high extinction risk. To support future comparative research, we present CactEcoDB (The Cactus Ecological Database), an Open Access dataset of curated spatial, ecological, trait, phylogenetic, and diversification data for over 1,000 cactus species. CactEcoDB includes species-level trait data, geographic occurrence records, environmental variables, range size estimates, speciation rates, and the largest time-calibrated phylogeny of cacti to date. By integrating these diverse data in a single platform, CactEcoDB enables analyses of trait evolution, trait-environment interactions, biogeography, climatic niche evolution, and macroevolutionary dynamics in one of the most celebrated and threatened plant families.

evolutionary biology↗

bioRxiv2021

Comparative plastomics of Amaryllidaceae: Inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq.

Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution.

plant biology↗

bioRxiv2020

Apples before the fall: does shape stability coincide with maturity?

Fruit shape is the result of the interaction between genetic, epigenetic, environmental factors, and stochastic processes. As a core biological descriptor both for taxonomy and horticulture, the point at which shape stability is reached becomes paramount in apple cultivar identification, and authentication in commerce. Twelve apple cultivars were sampled at regular intervals from anthesis to harvest over two growing seasons. Linear and geometric morphometrics were analyzed to establish if and when shape stabilized and whether fruit asymmetry influenced this. Shape stability was detected in seven cultivars, four asymmetric and three symmetric. The remaining five did not stabilize. Shape stability, as defined here, is cultivar-dependent, and when it occurs, it is late in the growing season. Geometric morphometrics detected stability more readily than linear, especially in symmetric cultivars. Key shape features are important in apple marketing, giving the distinctness and apparent uniformity between cultivars expected at point of sale.

plant biology↗

bioRxiv2020

When do apples stop growing, and why does it matter?

Background Apples in the commercial food chain are harvested up to two weeks before maturity. We explore apple fruit development through the growing season to establish the point at which the features differentiating those cultivars become evident. This is relevant both for the understanding of the growing process and to ensure that any identification and classification tools can be used both on ripened-on-tree and stored fruit. Current literature presents some contradictory findings on apple development, we explored the size development of 12 apple cultivars in the Brogdale National Fruit Collection, UK over two growing seasons.Methods Fruit were sampled at regular time points throughout the growing season and four morphometrics (maximum length, maximum diameter, weight, and centroid size) were collected. These were regressed against growing degree days in order to appropriately describe the growth pattern observed.Results All four morphometrics were adequately described using log-log linear regressions, with adjusted R2 estimates ranging from 78.3% (maximum length) to 86.7% (weight). For all four morphometrics, a 10% increase in growing degree days was associated with a 1% increase in the morphometric measurement.Discussion Our findings refine previous work presenting rapid early growth followed by a plateau in later stages of development and are in disagreement with published expo-linear models. We established that apples harvested for commercial storage purposes, two weeks prior to maturity, showed only a modest decrease in size, demonstrating that size morphometric approaches are appropriate for classification of apples, both ripened-on-tree and stored.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2018

Can you make morphometrics work when you know the right answer? Pick and mix approaches for apple identification.

Morphological classification of living things has challenged science for several centuries and has led to a wide range of objective morphometric approaches in data gathering and analysis. In this paper we explore those methods using apple cultivars, a model biological system in which discrete groups are pre-defined but in which there is a high level of overall morphological similarity. The effectiveness of morphometric techniques in discovering the groups is evaluated using statistical learning tools. No one technique proved optimal in classification on every occasion, linear morphometric techniques slightly out-performing geometric (72.6% accuracy on test set versus 66.7%). The combined use of these techniques with post-hoc knowledge of their individual successes with particular cultivars achieves a notably higher classification accuracy (77.8%). From this we conclude that even with pre-determined discrete categories, a range of approaches is needed where those categories are intrinsically similar to each other, and we raise the question of whether in studies where potentially continuous natural variation is being categorised the level of match between categories is routinely set too high.

plant biology↗