Biology subjects

Ovaskainen, O.

Publications and source records attributed to Ovaskainen, O..

24 records · Page 2Linked to original sources

bioRxiv2019

Maternal effects and environmental filtering shape seed fungal communities in oak trees

O_LITrees, as foundation species, play a pivotal role in the species interaction networks that constitute forest ecosystems. From the seed stage, they interact with microbial communities that affect their growth, health and fitness. Despite their eco-evolutionary importance, the processes shaping seed microbial communities in natural forests have received little attention.\nC_LIO_LITo unravel these processes, we analyzed the microbial communities of seeds collected in populations of sessile oak (Quercus petraea) growing along elevation gradients. We focused on the fungal communities as this group includes seed pathogens. Ecological processes shaping the communities were quantified using joint species distribution models.\nC_LIO_LIFungi were present in all seed tissues, including the embryo. Fungal communities differed significantly among oak populations along the elevation gradients, and among mother trees within the same population. These maternal effects remained significant after seed fall, despite colonization by fungal species on the ground. Associations between tree pathogens and their antagonists were detected in the seeds.\nC_LIO_LIOur results demonstrate that both maternal effects and environmental filtering shape seed microbial communities of sessile oak. They provide a starting point for future research aimed at identifying the seed extended phenotypic traits that influence seed dispersal and germination, and seedling survival and growth across environments.\nC_LI

ecology↗

bioRxiv2019

Joint species distribution modelling with HMSC-R

O_LIJoint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analyzing data in community ecology. JSDM allow the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships, and the spatio-temporal context of the study, providing predictive insights into community assembly processes from non-manipulative observational data of species communities. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs, yet its full range of functionality has remained restricted to Matlab users only.\nC_LIO_LITo make HMSC accessible to the wider community of ecologists, we introduce HMSC-R 3.0, a user-friendly R implementation of the framework described in Ovaskainen et al (Ecology Letters, 20 (5), 561-576, 2017) and further extended in several later publications.\nC_LIO_LIWe illustrate the use of the package by providing a series of five vignettes that apply HMSC-R 3.0 to simulated and real data. HMSC-R applications to simulated data involve single-species models, models of small communities, and models of large species communities. They demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. They further demonstrate how HMSC-R can be applied to normally distributed data, count data, and presence-absence data. The real data consist of bird counts in a spatio-temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. The vignettes demonstrate how to construct and fit many kinds of models, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates, and how to make predictions.\nC_LIO_LIThe package, along with the extended vignettes, makes JSDM fitting and post-processing easily accessible to ecologists familiar with R.\nC_LI

ecology↗

bioRxiv2019

SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and abundances using DNA barcodes or mitogenomes

The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community description and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (1) a percent-coverage threshold to filter out false positives, (2) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (3) technical replicates to correct for stochasticity across sequencing runs. This pipeline achieves a strikingly high accuracy of intraspecific abundance estimates from samples of known composition (mapping to barcodes R2=0.93, mitogenomes R2=0.95) and a high repeatability across environmental-sample replicates (barcodes R2=0.94, mitogenomes R2=0.93). As proof of concept, we sequence arthropod samples from the High Arctic systematically collected over 17 years, detecting changes in species richness, abundance, and phenology using either barcodes or mitogenomes. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities, with direct application to environmental biomonitoring. Statement of authorshipNMS has been involved in running the BioBasis sampling program for more than twenty years. TR, NMS, DWY, and OO conceived the study and its design. TH led the work in generating all the DNA samples and YJ led the work in assembling and annotating the mitogenomes for the mitochondrial genome reference database. TH led the work in generating the mock communities and bulk samples, with contributions from YJ and JW. YJ and DWY developed the molecular and bioinformatic methods. OO led the modelling of the data. TR and OO wrote the first draft of the manuscript, and all authors contributed substantially to its further improvement. Data accessibility statementShould the manuscript be accepted, the data supporting the results will be archived in an appropriate public repository (Dryad), and the data DOI will be included at the end of the article. The bioinformatic and R scripts and associated data tables will also be made available on github.com.

ecology↗

bioRxiv2019

Variation in Melitaea cinxia gut microbiota is phylogenetically highly structured but only mildly driven by host plant microbiota, sex or parasitism.

Originality-Significance StatementThe factors contributing to the assembly of microbiota in animals are extremely complex, and thus a comprehensive understanding of the mechanisms shaping host-associated microbial communities in natural ecosystems requires extensive ecological studies and appropriate statistical methods. In this study, we investigated the bacterial microbiota associated with the caterpillars of the Glanville fritillary (Melitaea cinxia), which is a long-term-studied ecological model system. We assessed the structure of variation in both occurrence and abundance of gut microbial communities of individuals collected in the wild with joint-species modelling, with the aim to relate the microbial community structure with multiple potentially impacting covariates: host plant microbiota and metabolites, hosts sex, potential parasitoid infection, and family structure. These covariates exhibited substantial correlation with multiple microbial taxas occurrences, which correlations were consistent for phylogenetically related groups of taxa, but varied across the whole microbial community; on the contrary, only few correlations were found with taxas abundances. The dominating co-occurrence pattern of microbiota assembly, which effectively split caterpillar individuals into two distinct groups, was, however, unrelated to any of the considered covariates.\n\nSummaryUnderstanding of what ecological factors shape intraspecific variation of insect microbiota is still relatively poor. In Lepidopteran caterpillars, microbiota is assumed to be mainly composed of transient bacterial symbionts acquired from the host plant. We sampled Glanville fritillary (Melitaea cinxia) caterpillars from natural populations to describe the microbiome and to identify potential factors that determine the structure of the microbial community, including the sex of the host, the impact of parasitoid infection, and the possible link between host plant and caterpillar microbiota. Our results demonstrate high variability of microbiota composition even among caterpillars that shared the same host plant individual. The observed variation in microbiota composition is partially attributed to the measured properties of the host or its plant microbial and chemical composition, and is aligned with microbial phylogenetic structure, with related taxa exhibiting similar patterns. However, the prevailing part of the observed variation was not associated with any of the assessed characteristics, although it followed a pronounced segregation structure: in some caterpillars the microbial communities were dominated by several related Enterobacteriaceae taxa, while in others these taxa were absent. Our results challenge previous findings that the host plant properties are the major drivers of microbiota communities of insect herbivores.

ecology↗

bioRxiv2018

Habitat fragmentation and species diversity in competitive species communities

Abstract.Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. On the other hand, different empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness.\n\nTo explain this apparent disparity, we devise a stochastic, spatially-explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have a non-monotone and non-linear effect on the species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity.

ecology↗

bioRxiv2018

Adaptation to local climate in size, growth and phenology across 19 silver fir (Abies alba Mill.) populations from Switzerland

Attempts to identify and understand selection pressures responsible for local adaptation are central to evolutionary research. We tested whether populations of silver fir (Abies alba Mill.), sampled across a heterogeneous environment, have more strongly diverged at quantitative traits than expected from genetic drift. We genotyped 387 trees from 19 Swiss populations at 374 single-nucleotide polymorphisms (SNPs) to estimate their demographic distances, and used these to generate a null expectation for divergence in a multi-trait space including morphology and life-history traits obtained from a published common garden trial. Local soil and historical climate data were used to identify the selective environment of the source populations. Our results revealed a strong selection on height driven by temperature: trees from warm sites evolved to become taller than those from cooler sites. The evolution of growth rate, growth duration and bud break were correlated, and populations evolved towards two extreme strategies, \"start early and grow slow\" or \"start late and grow fast\", driven by precipitation seasonality. We conclude that local climate has shaped the morphology and life-history of silver fir populations since they recolonized the Alps. Our methodology provides a show-case for empirical evaluation of adaptive evolutionary strategies combining genetic data and common gardens.

evolutionary biology↗