Biology subjects

Vision, T. J.

Publications and source records attributed to Vision, T. J..

3 recordsLinked to original sources

bioRxiv2022

Local exclusion and regional decline of an endemic Galapagos tree species (Psidium galapageium) by an invasive relative (P. guajava)

Invasive species can interact with native relatives in a variety of ways which may jeopardize their long-term coexistence. Here we show that interactions with an invasive species of guava (Psidium guajava) appear to be driving the local exclusion and regional decline of guayabillo (Psidium galapageium), a tree species endemic to the Galapagos archipelago. We find evidence consistent with recent historic exclusion of guayabillo from the highlands of San Cristobal Island, signatures of ongoing demographic decline in sympatric populations at lower elevations, and evidence suggesting that the four coinhabited islands represent points along a time series of regional decline, with the extent of guayabillo decline depending on the date that guava was introduced to each island. Based on these results, we then use the percentage of guava cover surrounding guayabillo populations to target populations that are at imminent risk of exclusion to aid in prioritizing management targets.

ecology↗

bioRxiv2019

Genetic architecture influences when and how hybridization contributes to colonization

The role of genetic architecture in adaptation to novel environments has received considerable attention when the source of adaptation variation is de novo mutation. Relatively less is known when the source of adaptive variation is inter- or intraspecific hybridization. We model hybridization between divergent source populations and subsequent colonization of an unoccupied novel environment using individual-based simulations in order to understand the influence of genetic architecture on the timing of colonization and the mode of adaptation. We find that two distinct categories of genetic architecture facilitate rapid colonization but that they do so in qualitatively different ways. For few and/or tightly linked loci, the mode of adaptation is via the recovery of adaptive parental genotypes. With many unlinked loci, the mode of adaptation is via the generation of novel hybrid genotypes. The first category results in the shortest colonization lag phases across the widest range of parameter space, but further adaptation is mutation limited. The second category takes longer and is more sensitive to genetic variance and dispersal rate, but can facilitate adaptation to environmental conditions which exceed the tolerance of parental populations. These findings have implications for understanding the origins of biological invasions and the success of hybrid populations.

evolutionary biology↗

bioRxiv2016

Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles

In phenotype annotations curated from the biological and medical literature, considerable human effort must be invested to select ontological classes that capture the expressivity of the original natural language descriptions, and finer annotation granularity can also entail higher computational costs for particular reasoning tasks. Do coarse annotations suffice for certain applications? Here, we measure how annotation granularity affects the statistical behavior of semantic similarity metrics. We use a randomized dataset of phenotype profiles drawn from 57,051 taxon-phenotype annotations in the Phenoscape Knowledgebase. We compared query profiles having variable proportions of matching phenotypes to subject database profiles using both pairwise and groupwise Jaccard (edge-based) and Resnik (node-based) semantic similarity metrics, and compared statistical performance for three different levels of annotation granularity: entities alone, entities plus attributes, and entities plus qualities (with implicit attributes). All four metrics examined showed more extreme values than expected by chance when approximately half the annotations matched between the query and subject profiles, with a more sudden decline for pairwise statistics and a more gradual one for the groupwise statistics. Annotation granularity had a negligible effect on the position of the threshold at which matches could be discriminated from noise. These results suggest that coarse annotations of phenotypes, at the level of entities with or without attributes, may be sufficient to identify phenotype profiles with statistically significant semantic similarity.

bioinformatics↗