Biology subjects

Jones, F. A.

Publications and source records attributed to Jones, F. A..

4 recordsLinked to original sources

bioRxiv2025

Diverging drivers of alpha and beta diversity across management types in Swedish boreal forests

O_LIManaging multifunctional forest landscapes requires a better understanding of how biodiversity dimensions respond to habitat structures and management regimes. While species richness is commonly used to assess conservation value, it may not capture compositional differences critical for maintaining regional biodiversity. C_LIO_LIWe examined how local species richness (alpha diversity) and community turnover (beta diversity) relates to forest structure and management in Swedish boreal forests. We surveyed lichens, bryophytes, and polypore fungi, representing three sessile taxo-ecological groups across 120 sites.. The sites were distributed between three management types: young production forests, retention patches (trees left during harvest to support mature forest species in production forests), and unmanaged set-asides. We used generalised linear models and generalised dissimilarity modelling to assess how habitat structures (deadwood and living tree metrics) and spatial distance explained patterns of richness and turnover across taxa and management types. C_LIO_LIFor all taxa, species richness increase with lying deadwood volume. Lichen species richness also increased with living tree volume, and decreased with tree density in retention patches. Lichens had higher species richness in retention patches and set-asides, whereas only set-asides had statistically higher bryophyte richness, and there were no differences for polypore richness. In contrast, beta diversity was more often associated with geographic distance, with only limited influence of deadwood volume. The relationships between lichen beta diversity and habitat structures were not consistent between retention patches and set-asides, suggesting that retention patches may have limitations in conserving mature forest species despite supporting similar lichen species richness. C_LIO_LISynthesis and applications. Our results demonstrate that alpha and beta diversity can be driven by different ecological processes and management contexts, and that while tree retention can support higher biodiversity than young production forests in some taxa, it cannot replace the value of conserving mature forests. Effective conservation therefore needs to combine habitat quality and spatial complementarity when planning conservation initiatives to maintain diversity patterns across managed landscapes. C_LI

ecology↗

bioRxiv2025

Host specificity of fungal functional groups covaries with elevation: implications for intraspecific plant interactions

Plants of the same species can harbor shared enemies, resulting in indirect, intraspecific competition. When this competition is strong, there are fitness costs associated with growing near a same-species individual, termed Conspecific Negative Density Dependence (CNDD). Host-specific microbial pathogens are known mediators of this type of indirect, intraspecific plant competition, yet how these plant-microbe interactions vary with environmental context is less explored. Further, microbial pathogens and mutualists may jointly contribute to the relative strength of intraspecific competition, yet most studies focus only on pathogens. We use ITS metabarcoding to characterize soil and foliar fungal functional groups associated with individual trees of three dominant conifers in forests where the strength of CNDD is known to be greater at lower elevations relative to higher elevations. We hypothesize that plants found in the mesic low elevation forests accumulate more host-specific fungal pathogens compared to plants found in the more xeric high elevation forests. Conversely, we hypothesize that plants found in the high elevation forests accumulate more host-specific mutualists compared to those found at low elevations. We test these hypotheses by evaluating three metrics of plant-associated fungal functional groups - alpha diversity, relative abundance, and host specificity - that together address the degree to which a plant recruits particular groups. We find the diversity, relative abundance and host specificity of soil fungal pathogens to decrease with elevation. In contrast, we find ectomycorrhizal fungal host specificity, but not diversity or relative abundance, to increase with elevation. Aboveground, we find a key foliar pathogen Nothophaeocryptocus gaeumanii to support our hypotheses as a dominant, and highly host specific pathogen that is enriched at low elevation sites. Our results indicate that across a climate gradient known to negatively covary with CNDD strength, soil pathogens recruitment is most prevalent in the mesic climates and, to a lesser extent, ectomycorrhizal recruitment is most prevalent in the xeric climates. Together these findings suggest that both pathogenic and mutualistic fungal symbionts could contribute to landscape level variation in competitive, intraspecific plant interactions.

ecology↗

bioRxiv2021

A new oomycete metabarcoding method using the rps10 gene

Oomycetes are a group of eukaryotes related to brown algae and diatoms, many of which cause diseases in plants and animals. Improved methods are needed for rapid and accurate characterization of oomycete communities using DNA metabarcoding. We have identified the mitochondrial 40S ribosomal protein S10 gene (rps10) as a locus useful for oomycete metabarcoding and provide primers predicted to amplify all oomycetes based on available reference sequences from a wide range of taxa. We evaluated its utility relative to a popular barcode, the internal transcribed spacer 1 (ITS1), by sequencing environmental samples and a mock community using Illumina MiSeq. Amplified sequence variants (ASVs) and operational taxonomic units (OTUs) were identified per community. Both the sequence and predicted taxonomy of ASVs and OTUs were compared to the known composition of the mock community. Both rps10 and ITS yielded ASVs with sequences matching 21 of the 24 species in the mock community and matching all 24 when allowing for a 1 bp difference. Taxonomic classifications of ASVs included 23 members of the mock community for rps10 and 17 for ITS1. Sequencing results for the environmental samples suggest the proposed rps10 locus results in substantially less amplification of non-target organisms than the ITS1 method. The amplified rps10 region also has higher taxonomic resolution than ITS1, allowing for greater discrimination of closely related species. We present a new website with a searchable rps10 reference database for species identification and all protocols needed for oomycete metabarcoding. The rps10 barcode and methods described herein provide an effective tool for metabarcoding oomycetes using short-read sequencing. Interpretive summaryOomycetes are a group of eukaryotes related to brown algae and diatoms, many of which cause diseases in plants and animals. Improved methods are needed to rapidly characterize the diversity of oomycete species found in environmental samples. We have identified the mitochondrial 40S ribosomal protein S10 gene (rps10) as being useful for oomycete community sequencing. We evaluated its utility relative to a popular barcode, the internal transcribed spacer 1 (ITS1), by sequencing environmental samples and a community we synthesized in the laboratory. The amplified rps10 region is predicted to have a higher taxonomic resolution than ITS1, allowing for greater discrimination of closely related species. We present a new website with a searchable rps10 reference database for species identification and all protocols needed for oomycete community sequencing. The rps10 barcode and methods described herein provide an effective tool for characterizing oomycetes using environmental DNA sequencing.

microbiology↗

bioRxiv2021

Testing for pollinator recognition in multiple species of Heliconia

Many plants have evolved floral traits that, in effect, filter pollinator communities and promote pollination by efficient pollinators. Most documented pollinator filter traits act to deter or reduce visitation rates by a subsect of the community of floral visitors. However, a recently described pollinator filter termed pollinator recognition (PR) acts at a stage after a pollinator visit. PR was first documented experimentally in Heliconia tortuosa whereby pollen tube germination - a proxy for reproduction - was enhanced following visits from morphologically specialized pollinators, but not generalists. This is thought to promote outcrossing among plants by preferentially investing in reproduction following visits by long-ranging hummingbirds with specialized bill shapes. To date, this plant behavior has only been described in H. tortuosa, but, if widespread, could have important ecological implications; given declines in abundances of specialist pollinators, visits by generalists would not buffer the loss of pollination services to plants with PR. We therefore tested for PR in four taxa spread widely across the Heliconiaceae. We corroborated previous results that visits by long-billed, but not short-billed hummingbirds increased pollen tubes in H. tortuosa with aviary experiments that standardized pollen quality and minimized variation in pollen quantity. Across species, we found great variation in pollen tube responses to experimental treatments. For one species (H. rostrata), we found increased numbers of pollen tubes in those visited by hummingbirds compared to hand pollination alone, regardless of the visiting birds bill morphology, indicating recognition of hummingbirds in general. In other cases, hummingbird visits decreased pollen tube counts compared to hand pollinations alone. Furthermore, our results could not substantiate any specific mechanism for pollinator recognition and highlight the need for further work on the complexities of and variability in reproductive strategies across plant taxa.

ecology↗