Biology subjects

Baldwin-Brown, J. G.

Publications and source records attributed to Baldwin-Brown, J. G..

7 recordsLinked to original sources

bioRxiv2026

Determinants of dicentric chromosome breakage in Drosophila

Eukaryotic genomes often have fragile sites where chromosomes are particularly prone to break. In Drosophila, when dicentric ring chromosomes try to segregate, they break at nonrandom hotspots. Here, we precisely map breakage hotspots produced by dicentric ring chromosomes in Drosophila. Our study provides three key results about the nature of dicentric chromosome breakage. First, duplications produced by dicentric ring chromosome breakage are surprisingly complex and involve many structural rearrangements, indicating that healing of these breaks is not a simple process. Second, characterization of one particular hotspot showed that new termini all occurred within a single intron of a large testis-expressed gene, suggesting that replication-transcription conflict may be a key determinant of chromosome fragile sites. Third, the new ends are often located near preexisting transposons, suggesting that transposon insertions may contribute to fragility or participate in stabilization of broken ends.

genetics↗

bioRxiv2026

Signatures of sex ratio distortion in humans

Segregation distortion, the disproportionate inheritance of selfish genetic elements, is an important evolutionary force. While many species carry distorters, it is not clear if humans do. Major limitations for detecting human distortion are the small size of human families and the lack of genetic markers in most subjects. Here, we present evidence of strong distortion in a large human pedigree. We analyzed pedigrees from the Utah Population Database and identified lineages with a high chance of carrying a distorter. In particular, we identified a family that preferentially produced male offspring at a 2:1 ratio. This pattern is consistent with a distorting Y-chromosome, a rarity in species with degenerate Y-chromosomes. The detection of such non-Mendelian inheritance patterns suggests that human genomes may harbor segregation distorters.

genetics↗

bioRxiv2024

Genomics of experimental adaptive radiation in the cryptic coloration of feather lice

1A major challenge faced by living organisms is adaptation to novel environments. This process is poorly understood because monitoring genetic changes in natural populations is difficult. One way to simplify the task is to focus on organisms that can be studied in captivity under conditions that remain largely natural. Feather lice (Insecta, Phthiraptera, Ischnocera) are host-specific parasites of birds that live, feed, and breed solely on feathers. Birds defend themselves against lice, which damage feathers, by killing them with their beaks during bouts of preening. In response, feather lice have evolved background-matching cryptic coloration to help them avoid preening. We experimentally manipulated the color backgrounds of host-specific pigeon lice (Columbicola columbae) by confining them to different colored breeds of rock pigeon (Columba livia) over a period of four years (ca. 60 louse generations). Over the course of the experiment, we sampled lice from pigeons every six months for genomic resequencing, and then calculated allele frequency differences and trajectories to identify putative genomic sites under selection. We documented many loci that changed in response to selection for color. Most loci putatively under selection were unshared among replicate populations of lice, indicating that independent adaptation of distinct lineages to the same novel environment resulted in similar phenotypes driven by different genotypes.

evolutionary biology↗

bioRxiv2024

Decoding chromosome organization using CheC-PLS: chromosome conformation by proximity labeling and long-read sequencing

Genomic approaches have provided detailed insight into chromosome architecture. However, commonly deployed techniques do not preserve connectivity-based information, leaving large-scale genome organization poorly characterized. Here, we developed CheC-PLS: a proximity-labeling technique that indelibly marks, and then decodes, protein-associated sites. CheC-PLS tethers dam methyltransferase to a protein of interest, followed by Nanopore sequencing to identify methylated bases - indicative of in vivo proximity - along reads >100kb. As proof-of-concept we analyzed, in budding yeast, a cohesin-based meiotic backbone that organizes chromatin into an array of loops. Our data recapitulates previously obtained association patterns, and, importantly, exposes variability between cells. Single read data reveals cohesin translocation on DNA and, by anchoring reads onto unique regions, we define the internal organization of the ribosomal DNA locus. Our versatile technique, which we also deployed on isolated nuclei with nanobodies, promises to illuminate diverse chromosomal processes by describing the in vivo conformations of single chromosomes.

genomics↗

bioRxiv2020

The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite

The pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low-cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.

genomics↗

bioRxiv2017

A new standard for crustacean genomes: the highly contiguous, annotated genome assembly of the clam shrimp Eulimnadia texana reveals HOX gene order and identifies the sex chromosome

Vernal pool clam shrimp (Eulimnadia texana) are a promising model system due to their ease of lab culture, short generation time, modest sized genome, a somewhat rare stable androdioecious sex determination system, and a requirement to reproduce via desiccated diapaused eggs. We generated a highly contiguous genome assembly using 46X of PacBio long read data and 216X of Illumina short reads, and annotated using Illumina RNAseq obtained from adult males or hermaphrodites. 85% of the 120Mb genome is contained in the largest 8 contigs, the smallest of which is 4.6Mb. The assembly contains 98% of transcripts predicted via RNAseq. This assembly is qualitatively different from scaffolded Illumina assemblies: it is produced from long reads that contain sequence data along their entire length, and is thus gap free. The contiguity of the assembly allows us to order the HOX genes within the genome, identifying two loci that contain HOX gene orthologs, and which approximately maintain the order observed in other arthropods. We identified a partial duplication of the Antennapedia gene adjacent to the few genes homologous to the Bithorax locus. Because the sex chromosome of an androdioecious species is of special interest, we used existing allozyme and microsatellite markers to identify the E. texana sex chromosome, and find that it comprises nearly half of the genome of this species. Linkage patterns indicate that recombination is extremely rare and perhaps absent in hermaphrodites, and as a result the location of the sex determining locus will be difficult to refine using recombination mapping.

genomics↗

bioRxiv2017

Pooled population resequencing of clam shrimp (Eulimnadia texana) from different vernal pools reveals signatures of local adaptation

Vernal pool clam shrimp (Eulimnadia texana) are a promising model due to ease of culturing, short generation time, modest genome size, and obligate desiccated diapaused eggs. We collected Illumina data (Poolseq) from eleven pooled wild vernal pool clam shrimp populations. We hypothesized that restricted gene flow between vernal pools, separated by distances of 0.36 to 253 km, in concert with Poolseq data from each population, could be used to identify genes important in local adaptation. We adapted Bayenv2 to genome-wide Poolseq data and detected thirteen genomic regions showing a strong excess of population subdivision relative to a genome-wide background. We identified a set of regions that appear to be significantly diverged in allele frequency, above what is expected based on the relationships amongst the populations. Regions identified as significant were on average 9.5 kb in size and harbored 3.8 genes. We attempted to identify correlations between allele frequencies at each genomic region and environmental variables that may influence local adaptation in the sequences populations, but found that there were too many confounding environmental variables to draw strong conclusions. One such genomic region harbored an ortholog of Drosophila melanogaster CG10413, a gene predicted to have sodium/potassium/chloride activity. Finally, we demonstrate that the identified regions could not have been found with less powerful statistics, i.e. FST, or with a less contiguous genome assembly.

evolutionary biology↗