Biology subjects

Farmer, T.

Publications and source records attributed to Farmer, T..

3 recordsLinked to original sources

bioRxiv2026

Pooled progeny sequencing effectively estimates polyandry in species with large families

Polyandry, multiple mating by females, both benefits females by increases genetic variation within families and provides an opportunity for sexual selection through sperm competition and cryptic female choice. Estimating polyandry in species with large clutches is challenging because genotyping all progeny individually can be impractical. We present a likelihood-based framework for estimating the number of sires and their relative contributions from the maternal genotype and pooled sequencing of entire progeny pools. The method evaluates the probability of observed pooled offspring read counts under alternative paternal genotype mixtures, accounting for Mendelian segregation and sampling variation from finite sequencing depth. We implement this framework for both biallelic SNPs and short-read mini-haplotype markers constructed from closely linked SNPs, which provide multi-allelic information comparable to traditional microsatellite markers. Simulations show that this approach accurately recovers sire number and sire contributions across a range of conditions. We then applied the method to 275 wild-caught Drosophila melanogaster females and their offspring from a Kansas population using 3,053 biallelic SNPs and 239 four-allele mini-haplotype markers. Estimates from the two marker sets were highly concordant, and combined analyses indicate that 57% of families were sired by a single male. These results demonstrate that pooled progeny sequencing provides an efficient genomic approach for estimating polyandry in species with large families.

genomics↗

bioRxiv2024

Genomic insights into the successful invasion of the avian vampire fly (Philornis downsi) in the Galapagos Islands

Invasive species disrupt island ecosystems, posing significant threats to native species. The avian vampire fly (Philornis downsi), introduced into the Galapagos Islands, has become a major threat to endemic birds including Darwins finches, yet the genetic mechanisms of its invasion remain unclear. This study used whole-genome sequencing of P. downsi populations from Galapagos and its native range in mainland Ecuador, revealing reduced genetic diversity in Galapagos, indicative of a recent bottleneck. We found evidence of ongoing gene flow among island populations and identified regions under positive selection near genes related to neural signaling, muscle development, and metabolic processes, which may have contributed to the flys invasion success in Galapagos. These findings highlight the importance of genomic research for mitigating the impact of P. downsi on Galapagos biodiversity.

evolutionary biology↗

bioRxiv2022

The Novel Role of Midbody-Associated mRNAs in Regulating Abscission

Midbodies (MBs) have been shown to function during telophase as a recruiting hub, especially for ESCRT-III complex subunits, to regulate the abscission step of cytokinesis. However, the molecular machinery governing specific protein targeting and activation at the MB remains poorly understood. Until recently, it was thought that abscission regulating proteins, such as ESCRT-III complex subunits, accumulate at the MB by directly or indirectly binding to the MB resident protein, CEP55. However, recent studies have shown that depletion of CEP55 does not fully block ESCRT-III targeting to the MB, and cells in CEP55 knock-out mice divide normally. Additionally, since MBs are microtubule-rich, proteinaceous structures, it is conceptually hard to imagine how large protein complexes, such as the ESCRT-III complex, can successfully diffuse into the MB from the cytosol in a rapid and highly regulated manner. Here, we show that MBs contain mRNAs and that these MB-associated mRNAs can be locally translated, resulting in the accumulation of abscission-regulating proteins. We also demonstrate that localized MB-associated translation of CHMP4B is required for its targeting to the abscission site and that 3' UTR-dependent CHMP4B mRNA targeting to the MB is required for successful completion of cytokinesis. Finally, we identify regulatory cis-elements within RNAs that are necessary and sufficient for mRNA trafficking to the MB. Based on all this data, we propose a novel method of regulating cytokinesis and abscission by MB-associated targeting and localized translation of selective mRNAs.

cell biology↗