Data_Sheet_1_Dynamics of Gut Microbiota Diversity During the Early Development of an Avian Host: Evidence From a Cross-Foster Experiment.docx

Despite the increasing knowledge on the processes involved in the acquisition and development of the gut microbiota in model organisms, the factors influencing early microbiota successions in natural populations remain poorly understood. In particular, little is known on the role of the rearing environment in the establishment of the gut microbiota in wild birds. Here, we examined the influence of the nesting environment on the gut microbiota of Great tits (Parus major) by performing a partial cross-fostering experiment during the intermediate stage of nestling development. We found that the cloacal microbiota of great tit nestlings underwent substantial changes between 8 and 15 days of age, with a strong decrease in diversity, an increase in the relative abundance of Firmicutes and a shift in the functional features of the community. Second, the nesting environment significantly influenced community composition, with a divergence among separated true siblings and a convergence among foster siblings. Third, larger shifts in both microbiota diversity and composition correlated with lower nestling body condition. Our results shed new light on the dynamics of microbial diversity during the ontogeny of avian hosts, indicating that the nest environment continues to shape the gut microbiota during the later stages of nestling development and that the increase in gut diversity between hatching and adulthood may not be as linear as previously suspected. Lastly, the microbiota changes incurred during this period may have implications for nestling body condition which can lead to long-term consequences for host fitness.</p

Source code and data

The package provides Matlab code for the individual based model and approximate Bayesian computation based inference introduced in article "Assessing the dynamics of natural populations by fitting individual based models with approximate Bayesian computation" by Jukka Sirén, Luc Lens, Laurence Cousseau and Otso Ovaskainen accepted for publication in Methods in Ecology and Evolution. The package includes also the White-starred robin data analyzed in the article

Dryad Greenbulls - Vangestel Carl

Microsatellite data (10 loci) of 362 birds (Phyllastrephus cabanisi) sampled in the Taita Hills, Kenya during 2 periods (first period (1996-2000), second period (2006-2010))

Map of the study area with the location of three large (MB, CH, NG) and two small (FU, ND) indigenous forest fragments that hold breeding populations of cabanis’s greenbul (<i>Phyllastrephus</i><i>cabanisi</i>).

<p>Analyses were performed along linear transects at two different geographical scales: a local (within-fragment) scale in fragment MB (A), and a landscape (among-fragment) scale including fragments CH, NG, FU and ND (B).</p

Data_Sheet_3_Dynamics of Gut Microbiota Diversity During the Early Development of an Avian Host: Evidence From a Cross-Foster Experiment.XLSX

<p>Despite the increasing knowledge on the processes involved in the acquisition and development of the gut microbiota in model organisms, the factors influencing early microbiota successions in natural populations remain poorly understood. In particular, little is known on the role of the rearing environment in the establishment of the gut microbiota in wild birds. Here, we examined the influence of the nesting environment on the gut microbiota of Great tits (Parus major) by performing a partial cross-fostering experiment during the intermediate stage of nestling development. We found that the cloacal microbiota of great tit nestlings underwent substantial changes between 8 and 15 days of age, with a strong decrease in diversity, an increase in the relative abundance of Firmicutes and a shift in the functional features of the community. Second, the nesting environment significantly influenced community composition, with a divergence among separated true siblings and a convergence among foster siblings. Third, larger shifts in both microbiota diversity and composition correlated with lower nestling body condition. Our results shed new light on the dynamics of microbial diversity during the ontogeny of avian hosts, indicating that the nest environment continues to shape the gut microbiota during the later stages of nestling development and that the increase in gut diversity between hatching and adulthood may not be as linear as previously suspected. Lastly, the microbiota changes incurred during this period may have implications for nestling body condition which can lead to long-term consequences for host fitness.</p

Multiple distance class plots illustrating the gradual decay of positive genetic structure with increasing geographical distance.

<p>Plots are shown for each sex at various spatio-temporal scales: at a regional scale for period 1 (a), period 2 (b) and both sexes lumped (c); at a local scale (within Mbololo) for period 2 (d). Error bars indicate 95% CI as determined by 9999 bootstraps.</p

Data_Sheet_2_Dynamics of Gut Microbiota Diversity During the Early Development of an Avian Host: Evidence From a Cross-Foster Experiment.XLSX

<p>Despite the increasing knowledge on the processes involved in the acquisition and development of the gut microbiota in model organisms, the factors influencing early microbiota successions in natural populations remain poorly understood. In particular, little is known on the role of the rearing environment in the establishment of the gut microbiota in wild birds. Here, we examined the influence of the nesting environment on the gut microbiota of Great tits (Parus major) by performing a partial cross-fostering experiment during the intermediate stage of nestling development. We found that the cloacal microbiota of great tit nestlings underwent substantial changes between 8 and 15 days of age, with a strong decrease in diversity, an increase in the relative abundance of Firmicutes and a shift in the functional features of the community. Second, the nesting environment significantly influenced community composition, with a divergence among separated true siblings and a convergence among foster siblings. Third, larger shifts in both microbiota diversity and composition correlated with lower nestling body condition. Our results shed new light on the dynamics of microbial diversity during the ontogeny of avian hosts, indicating that the nest environment continues to shape the gut microbiota during the later stages of nestling development and that the increase in gut diversity between hatching and adulthood may not be as linear as previously suspected. Lastly, the microbiota changes incurred during this period may have implications for nestling body condition which can lead to long-term consequences for host fitness.</p

Levels of admixture provided by Bayesian clustering analyses (STRUCTURE) for each period separately (left panel: period 1/right panel: period 2).

<p>Following the procedure outlined in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071624#B56" target="_blank">56</a>], optimal cluster sizes of K=2 and K=4 were assigned to period 1 and period 2, respectively.</p

Distribution of maximum post-fledging recapture distances of <i>P</i><i>. cabanisi</i> fledglings during their first year and over multiple years.

<p>Data were collected between 2007–2012, sample sizes are indicated above each vertical bar.</p

Distribution of randomized statistics under the null hypothesis of equal dispersal rates in both sexes.

<p>Permuted test statistics are ‘male mAI_c-female mAIc’ (left) and ‘vAI_c female/vAI_c male’ (right). Observed statistics are indicated by vertical dashed line and extreme positive values indicate female-biased dispersal. Upper panel: regional - period 1; middle panel: regional - period 2; lower panel: local - period 2.</p