Biology subjects

Gillingham, M.

Publications and source records attributed to Gillingham, M..

3 recordsLinked to original sources

bioRxiv2025

Host filtering and biogeography structure island bird gut microbiomes

Gut microbiomes are central to host ecology and evolution, yet the mechanisms driv-ing their diversification remain elusive, partly because host evolution and biogeography are often confounded. The recent radiation of chaffinches in Macaronesia, coupled with their broadly similar ecologies across islands, makes them an ideal replicated natural experiment to separate spatial from host-driven effects on microbiome structure. Us-ing long-read 16S rRNA gene sequencing, diet metabarcoding, and whole-genome host data, we show that gut microbiome diversity aligns with predictions of island biogeog-raphy theory rather than host colonization history, revealing that microbial dispersal limitation independent of the host is a dominant mechanism of community assembly. Geography and diet primarily explain bacterial presence-absence patterns, whereas host genetic differentiation and heterozygosity influence abundant, potentially resident taxa. Challenging previous assumptions about birds, we detect clear signals of phylosymbiosis (i.e. similar microbiome composition among closely related hosts), however phylogenetic reconciliation reveals these associations result from convergent host filtering of environ-mentally acquired bacteria, likely via shared diets or physiological traits, rather than de-tectable co-diversification. Our study reframes our understanding of avian host-microbe relationships, revealing that birds maintain host-specific microbiome associations within biogeographic constraints, but these arise from ecological filtering processes rather than co-evolutionary partnerships.

evolutionary biology↗

bioRxiv2019

Relationship between early body condition, energetic reserves and fitness in an iteroparous insect

O_LIInsects are core actors for the balance of many earth ecosystems, as well as an alternative source of food and feed with a low ecological footprint. A comprehensive understanding of their life history requires reliable tools. Body condition constitutes the amount of energy reserves available to a fitness trait after maintenance costs have been accounted for. Body condition is standardly estimated using Body Condition Indexes (BCIs) in vertebrates. In insects the relevance of BCIs is frequently questioned on the basis that they might not accurately reflect neither energy reserves nor fitness.. However, to date no study has tested whether the very concept of body condition is relevant in insects, i.e. whether BCIs accurately reflect the relative energy reserves allocated to fitness traits. C_LIO_LIWe propose that the relevance of using BCIs in insects depends on whether their structural size has a fitness cost. If on the contrary insects only benefit from a larger body size, a simple measurement of body size or mass will predict fitness, but not a BCI. We experimentally manipulated food availability at the larval and adult stage and used total fecundity of females as a fitness proxy of Tenebrio molitor, an important model in physiology, ecology and evolution, and one of the first insects to be considered as a source of food and feed. C_LIO_LIOur results support three key assumptions of the relevance of BCIs in insects: (i) a valid BCI correlated with energy reserves corrected for a given size (i.e. relative energy reserves) and not with absolute measures of energy reserves; (ii) both structural size and body condition positively predict different components of fitness; and, (iii) the effect of body condition was dependent on resource availability, whereby its effect was only apparent and large when food was unrestricted at the larval stage and restricted at the adult stage. C_LIO_LIOverall we demonstrate the relevance of using BCIs in insects. Their use should be generalized to improve fitness readouts in evolution, ecological and physiological studies, as well as improve their husbandry for commercial purposes. C_LI

ecology↗

bioRxiv2019

A novel workflow to improve multi-locus genotyping of wildlife species: an experimental set-up with a known model system

AO_SCPCAPBSTRACTC_SCPCAPGenotyping novel complex multigene systems is particularly challenging in non-model organisms. Target primers frequently amplify simultaneously multiple loci leading to high PCR and sequencing artefacts such as chimeras and allele amplification bias. Most next-generation sequencing genotyping pipelines have been validated in non-model systems whereby the real genotype is unknown and the generation of artefacts may be highly repeatable. Further hindering accurate genotyping, the relationship between artefacts and copy number variation (CNV) within a PCR remains poorly described. Here we investigate the latter by experimentally combining multiple known major histocompatibility complex (MHC) haplotypes of a model organism (chicken, Gallus gallus, 43 artificial genotypes with 2-13 alleles per amplicon). In addition to well defined "optimal" primers, we simulated a non-model species situation by designing "naive" primers, with sequence data from closely related Galliform species. We applied a novel open-source genotyping pipeline (ACACIA) to the data, and compared its performance with another, previously published, pipeline. ACACIA yielded very high allele calling accuracy (>98%). Non-chimeric artefacts increased linearly with increasing CNV but chimeric artefacts leveled when amplifying more than 4-6 alleles. As expected, we found heterogeneous amplification efficiency of allelic variants when co-amplifying multiple loci. Using our validated ACACIA pipeline and the example data of this study, we discuss in detail the pitfalls researchers should avoid in order to reliably genotype complex multigene systems. ACACIA and the datasets used in this study are publicly available at GitLab and FigShare (https://gitlab.com/psc_santos/ACACIA and https://figshare.com/projects/ACACIA/66485).

molecular biology↗