Biology subjects

Michael T Monaghan

Publications and source records attributed to Michael T Monaghan.

4 recordsLinked to original sources

bioRxiv2016

Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

The study of processes driving diversification requires a fully sampled and well resolved phylogeny. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (Canaries, Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.

Evolutionary Biology↗

bioRxiv2016

Universal metabarcoding of pico- to mesoplankton reveals seasonal dynamics and a bacterial bloom

Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. We tested whether DNA-metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. We found significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a three-month period in spring. Patterns followed the same trend as plankton estimates using traditional microscopic methods. We characterized the bloom of a conditionally rare bacterial taxon belonging to Arcicella, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. Our data demonstrate the potential of universal DNA-metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.

Ecology↗

bioRxiv2016

Large shifts among eukaryotes, bacteria, and archaea define the vertical organization of a lake sediment

Sediments are depositional areas where particles sink from water columns, but they are also microbial hotspots that play an important role in biogeochemical cycles. Unfortunately, the importance of both processes in structuring microbial community composition has not been assessed. We surveyed all organismic signals of the last ca. 170 years of sediment by metabarcoding, identifying global trends for eukaryotes, bacteria, archaea, and monitored 40 sediment parameters. We linked the microbial community structure to ongoing and historical environmental parameters and defined three distinct sediment horizons. This not only expands our knowledge of freshwater sediments, but also has profound implications for understanding the microbial community structure and function of sediment communities in relation to future, present, and past environmental changes.

Ecology↗

bioRxiv2016

High habitat-specificity in fungal communities of an oligo-mesotrophic, temperate lake

Freshwater fungi are a poorly studied paraphyletic group that include a high diversity of phyla. Most studies of aquatic fungal diversity have focussed on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in meso-oligotrophic, temperate Lake Stechlin in northern Germany, including the pelagic and littoral water column, sediments, and biotic substrates. We pyrosequenced with an universal eukaryotic marker within the ribosomal large subunit (LSU) in order to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1024 fungal OTUs (97% criterion). Diversity was highest in the sediment, biofilms, and benthic samples (293-428 OTUs), intermediate in water and reed samples (36-64 OTUs), and lowest in plankton (8 OTUs) samples. NMDS clustering clearly grouped the eight studied habitats into six clusters, indicating that total diversity was strongly influenced by turnover among habitats. Fungal communities exhibited pronounced changes at the levels of phylum and order along a gradient from littoral to pelagic habitats. The large majority of OTUs could not be classified below the order level due to the lack of aquatic fungal entries in taxonomic databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat-specificity to total fungal diversity. This remarkable diversity is probably an underestimate, because most lakes undergo seasonal changes and previous studies have uncovered differences in fungal communities among lakes.

Ecology↗