Biology subjects

Medeiros, M. J.

Publications and source records attributed to Medeiros, M. J..

3 recordsLinked to original sources

bioRxiv2025

Abiotic factors are the primary determinants of endemic Hawaiian Drosophila microbiome assembly

The Hawaiian Drosophila radiation exemplifies rapid adaptation and species diversification. Many factors have been attributed to these phenomena, including allopatry, sexual selection, and ecological specialization. In recent years, the microbiome has come to the forefront as an important driver of adaptation that is capable of facilitating host survivorship, enhancing resilience to local environmental challenges, and enabling the use of different dietary resources. To determine how microbial communities assemble in natural populations and potentially contribute to the rapid adaptation of Hawaiian drosophilids, we conducted a survey of bacterial and fungal communities from over 500 wild flies collected from across six islands of the Hawaiian archipelago. These samples represent a breadth of host plant specializations, habitats, lifestyles, and endemicity. Our findings reveal that microbiome assembly is largely driven by abiotic factors including elevation, temperature, rainfall, and evapotranspiration, but is not strongly constrained by phylogenetic relatedness. Identical species inhabiting two separate locations exhibited different microbiomes. By contrast, distantly related species inhabiting the same site had more similar microbiomes. The microbiomes of native species also differ from recently introduced, non-native Drosophila in terms of diversity, composition, and function. Given the myriad roles of the microbiome in nutrition, reproduction, and mate choice, these results support a role for the microbiome in the remarkable ecological divergence of Hawaiian Drosophila.

ecology↗

bioRxiv2023

Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

evolutionary biology↗

bioRxiv2023

Bacterial and fungal components of the gut microbiome have distinct, sex-specific roles in Hawaiian Drosophila reproduction

Gut microbiomes provide numerous physiological benefits for host animals. The role of bacterial members of microbiomes in host physiology is well-documented. However, much less is known about the contributions and interactions of fungal members of the microbiome even though fungi are significant components of many microbiomes, including those of humans and insects. Here, we used antibacterial and antifungal drugs to manipulate the gut microbiome of a Hawaiian picture-wing Drosophila species, D. grimshawi, and identified distinct, sex-specific roles for the bacteria and fungi in microbiome community stability and reproduction. Female oogenesis, fecundity and mating drive were significantly diminished when fungal communities were suppressed. By contrast, male fecundity was more strongly affected by bacterial but not fungal populations. For males and females, suppression of both bacteria and fungi severely reduced fecundity and altered fatty acid levels and composition, implicating the importance of interkingdom interactions on reproduction and lipid metabolism. Overall, our results reveal that bacteria and fungi have distinct, sexually-dimorphic effects on host physiology and interkingdom dynamics in the gut help to maintain microbiome community stability and enhance reproduction.

microbiology↗