Biology subjects

Hime, P. M.

Publications and source records attributed to Hime, P. M..

3 recordsLinked to original sources

bioRxiv2024

Waves of Colonization and Gene Flow in a Great Speciator

Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones--where reproductive isolation can further develop via reinforcement or phenotypic displacement--or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayrs foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.

evolutionary biology↗

bioRxiv2023

Pathogenic Morphological Signatures of Perturbations in Mitochondrial-Related Genes Revealed by Pooled Imaging Assay

Mutations in mitochondrial-related genes underlie numerous neurodegenerative diseases, yet the significance of most variants remains uncertain concerning disease phenotypes. Several thousand genes have been shown to regulate mitochondria in eukaryotic cells, but which of these genes are necessary for proper mitochondrial dynamics? We investigated the degree of morphological disruptions in mitochondrial gene-silenced cells to understand the magnitude of genetic contribution to properly functioning mitochondria and to identify pathogenic variants. We analyzed 5,835 gRNAs in a high dimensional phenotypic dataset produced by the image-based pooled analysis platform Raft-Seq. Using the MFN2-mutant cell phenotype, we identified several genes, including TMEM11, TIMM8A, and three NADH Ubiquinone proteins, as crucial for normal mitochondrial morphology in human U2OS cells. Additionally, we found several missense and UTR variants within the genes SLC25A19 and ATAD3A as drivers of mitochondrial aggregation. By examining multiple features instead of a single readout, this analysis was powered to detect genes which had morphological signatures aligned with MFN2-mutant phenotypes. Reanalysis with anomaly detection revealed other critical genes, including APOOL, MCEE, NIT, PHB, and SLC16A7, which perturb mitochondrial network morphology in a manner divergent from MFN2. These studies offer insights into the molecular basis for mitochondrial dysfunction, setting the stage for new genomic diagnostics and therapeutic discovery.

genetics↗

bioRxiv2023

A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)

The Notomicrus traili species group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this group, with multiple distinct clades sharing overlapping distributions and lineages attributed to N. traili and the closely related N. gracilipes recovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within the N. traili group. First, we use short-read whole genome sequencing of four noterid genera to design a noterid-specific UCE probe set (Noteridae 3.4Kv1) targeting over 3,400 unique loci. Using this probe set, we capture UCE data from population-level sampling of 44 traili group specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putative N. traili group populations overlap. We subject the resulting data matrix to various trimming and data completeness treatments and reconstruct the phylogeny with both concatenated maximum likelihood and coalescent congruent methods. We recover robust phylogenetic estimates that identify several phylogenetically distinct clades within the traili group that share overlapping distributions. To test for the genetic distinctiveness of populations, we extract single nucleotide polymorphism (SNP) data from UCE alignments and examine patterns of genetic clustering using principal component analyses (PCAs) and STRUCTURE. Population genetic results are highly concordant with recovered phylogenetic structure, revealing a high degree of co-ancestry shared within identified clades, contrasting with limited ancestry sharing between clades. We recover a pattern consistent with repeated diversification and dispersal of the traili group in the Neotropics, highlighting the efficacy of a tailored UCE approach for facilitating shallow-scale phylogenetic reconstructions and population genetic analyses, which can reveal novel aspects of coleopteran phylogeography.

evolutionary biology↗