Biology subjects

Holmes, V. R.

Publications and source records attributed to Holmes, V. R..

3 recordsLinked to original sources

bioRxiv2024

Varroa mites escape the evolutionary trap of haplodiploidy

Genetic diversity is essential for populations adapting to environmental-changes. Following genetic bottlenecks, invasive species often have reduced diversity, yet must rapidly adapt to novel environments. This paradox is especially pronounced in parasites, which face repeated transmission bottlenecks and anthropogenic countermeasures. The challenge of maintaining diversity in the short-term intensifies in haplodiploid species, where males inherit and transmit only half of their mothers genome, limiting effective population size. To examine how such species may maintain adaptability, we studied inheritance in Varroa mites (Varroa destructor), globally invasive honey bee parasite. Using three-generation pedigrees, we found that Varroa is not haplodiploid, as previously thought. Rather, females produce diploid sons who transmit either maternal allele to daughters. This system slows reduced heterozygosity loss under sib-mating, compared to ancestral haplodiploidy, increasing effective population size and adaptability. Our findings reveal a rare reversion from haplodiploidy, long considered an evolutionary end state, and suggest reproductive plasticity underlies the resilience of invasive parasites like Varroa.

evolutionary biology↗

bioRxiv2022

The genomic basis of evolutionary novelties in a leafhopper

Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the Glassy-Winged Sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS, then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory.

genomics↗

bioRxiv2019

Measuring genome sizes using read-depth, k-mers, and flow cytometry: methodological comparisons in beetles (Coleoptera)

Measuring genome size across different species can yield important insights into evolution of the genome and allow for more informed decisions when designing next-generation genomic sequencing projects. New techniques for estimating genome size using shallow genomic sequence data have emerged which have the potential to augment our knowledge of genome sizes, yet these methods have only been used in a limited number of empirical studies. In this project, we compare estimation methods using next-generation sequencing (k-mer methods and average read depth of single-copy genes) to measurements from flow cytometry, the gold standard for genome size measures, using ground beetles (Carabidae) and other members of the beetle suborder Adephaga as our test system. We also present a new protocol for using read-depth of single-copy genes to estimate genome size. Additionally, we report flow cytometry measurements for five previously unmeasured carabid species, as well as 21 new draft genomes and six new draft transcriptomes across eight species of adephagan beetles. No single sequence-based method performed well on all species, and all tended to underestimate the genome sizes, although only slightly in most samples. For one species, Bembidion haplogonum, most sequence-based methods yielded estimates half the size suggested by flow cytometry. This discrepancy for k-mer methods can be explained by a large number of repetitive sequences, but we have no explanation for why read-depth methods yielded results that were also strikingly low.

genomics↗