Biology subjects

Walden, K. K. O.

Publications and source records attributed to Walden, K. K. O..

8 recordsLinked to original sources

bioRxiv2026

Large-scale genomic rearrangements are a potential explanation for reproductive isolation in the Pogonomyrmex dependent-lineage system

Genetic variation is the raw material for evolution. One source of variation is chromosomal rearrangements, which can bring genes together and form genetic linkage. Rearrangements can also suppress recombination and gene flow, as in the case of sex chromosome evolution. We conducted the first population genomic study of the red harvester ant Pogonomyrmex barbatus to investigate genomic rearrangements that differentiate the lineages J1 and J2 in the "dependent-lineage system" (also known as "social hybridogenesis"). In this unusual reproductive system, males and females from different lineages mate to create hybrids, yet these hybrids develop into sterile offspring (workers), and so the two lineages remain reproductively isolated. We sequenced high-quality reference genomes for the two lineages to search for a potential explanation of the suppression of gene flow between them. Comparison of the two genome assemblies revealed multiple large-scale genomic rearrangements, all of which occurred in the J1 lineage. The rearrangements formed some of the largest J1 chromosomes, including the largest scaffold in the assembly that was formed by at least two translocation events and additional intra-chromosomal rearrangements. The translocations brought together 118 odorant receptor (OR) genes on this rearranged chromosome, 44 of which are 9-exon ORs, which are implicated in chemical communication in ants. We also identified an enrichment of transposable elements in a large synteny gap between the translocated segments. The discovery of multiple translocations that formed large rearranged chromosomes provides a potential explanation for the reproductive isolation between the pair of dependent lineages in this system, and opens the way for the study of the molecular genetic basis of an intriguing evolutionary phenomenon in these and in other ant lineages.

evolutionary biology↗

bioRxiv2026

A phylogenomic framework for avian feather lice (Phthiraptera: Ischnocera)

Comprehensive phylogenies serve as foundations for taxonomic, comparative, and coevolutionary studies. Avian feather lice comprise the most diverse Parvorder (Ischnocera) of parasitic lice (Phthiraptera). Convergence and reduction of morphological features in this group have made past attempts at understanding the evolutionary relationships of feather lice challenging. Several recent phylogenomic studies have begun shedding light on the broader scale evolutionary tree of this group. However, additional taxonomic sampling is needed for a more complete understanding of the phylogeny and for higher statistical power in comparative studies. Here we investigate the higher-level relationships of feather lice based on the most comprehensive taxon sample to date. We leverage genome sequences of 260 samples of feather lice and 25 outgroup taxa to reconstruct a phylogenomic tree based on 2,395 target nuclear ortholog genes, using both concatenated and coalescent methods. These trees provide high support across nearly all branches of the topology, resolving backbone relationships as well as more detailed relationships within major groups. These phylogenies provide a framework for future comparative studies of feather lice, including comparisons with avian phylogeny and investigating patterns of diversification.

evolutionary biology↗

bioRxiv2025

An improved gray whale assembly highlights how allospecific reference-genome choice can affect genomic diversity estimates

Gray whales (Eschrichtius robustus) are unique as bottom feeding baleen whales and they have long been a conservation concern on both sides of the Pacific, in part because they migrate and disperse farther than any other species on earth. They experienced drastic population size declines due to environmental changes and commercial whaling. Here, we present an improved genome assembly for the gray whale. This genome assembly covers 2.4 Gb divided across 2689 contigs with an N50 of 15Mb. From the new assembly, we identify 75Mb sex-linked contigs and a identify 94.6% of searched genes based on Benchmarking Universal Single-Copy Ortholog score. We use the gray whale assembly to explore the effects of mapping to conspecific vs allospecific reference genomes when estimating genome-wide heterozygosity (H) and runs of homozygosity (ROH). The use of allospecific genomes significantly underestimate both H and ROH burden regardless of genomic distance and assembly quality. Our analyses highlight the importance of using contiguous conspecific assemblies in whale genomics and conservation. SignificanceGray whales are unique in their behavior, morphology and ecology. The novel and contiguous genome assembly presented here will serve as a valuable resource for studies of their population and comparative genomics, as well as for identifying key adaptations that have evolved in this clade. Finally, our results demonstrate that biases can arise when using allopatric assemblies to evaluate diversity metrics, so they should be used and interpreted with caution.

evolutionary biology↗

bioRxiv2025

Independent and repeated acquisition of endosymbiotic bacteria across the diversification of feather lice

Many parasitic insects, including lice, form close relationships with endosymbiotic bacteria that are crucial for their survival. In this study, we used genomic sequencing to investigate the distribution and evolutionary history of the bacterial genus Sodalis across a broad range of feather louse species spanning 156 genera. Phylogenomic analysis revealed significant diversity among Sodalis lineages in feather lice, and robust evidence for their independent and repeated acquisition by different louse clades throughout their radiation. Among the 1,020 louse genomes analyzed, at least 22% contained Sodalis, distributed across 57 louse genera. Cophylogenetic analyses between the Sodalis and feather louse phylogenies indicated considerable mismatch. This phylogenetic incongruence between lice and Sodalis, along with the presence of distantly related Sodalis lineages in otherwise closely related louse species, strongly indicates repeated independent acquisition of this endosymbiont. Additionally, evidence of cospeciation among a few closely related louse species, coupled with frequent acquisition of these endosymbionts from free-living bacteria, further highlights the diverse evolutionary processes shaping Sodalis endosymbiosis in feather lice.

evolutionary biology↗

bioRxiv2023

De novo genome assembly of four Andean potato weevil species (Premnotrypes,Rhigopsidius), the primary agricultural pest of the potato in South America

The Andean potato weevil complex are the most widespread and serious insect pests to potato crops in the Andes. More broadly, genomic assemblies of insect pests are currently lacking in agricultural research, especially those from the order Coleoptera. These genome data are essential for identifying potential underlying mechanisms important to biological control strategies and food security in the highlands. Here, we present the de novo genome assemblies for four species of the Andean potato weevil complex: Premnotrypes vorax, P. suturicallus, P. latithorax, and Rhigopsidius piercei. Genome assemblies exceeded the average size of those from the order Coleoptera and were highly repetitive: for P. vorax (1.33 Gb, 71.51% repetitive), P. latithorax (623 Mb, 59.03% repetitive), P. suturicallus (1.23 Gb, 70.19% repetitive), and R. piercei (1.55 Gb, 71.91% repetitive). We examined genomic regions related to metabolic potato plant detoxification and insecticide resistance using the available Colorado potato beetle (Leptinotarsa decemlineata) genome annotations as a guide. Our analysis of these weevil genomes identified chemosensory receptors and odorant binding proteins that could be related to detecting their hosts, the potato plant (Solanum tuberosum), as well as many genomic regions involved in subverting pesticide resistance. We have generated the first whole-genome assemblies of the Andean potato weevil complex that will be foundational for future agricultural pest management and entomological research in South America. Author SummaryWithin the South American Andean mountains the Andean potato weevil insects are the most widespread and serious pests to potatoes, destroying around 89% of potato harvests a year when insecticides are not used. Here, we collected and performed whole-genome sequencing for the first time for four Andean potato weevil species: Premnotrypes vorax, P. suturicallus, P. latithorax, and Rhigopsidius piercei. After analysis of these genome assemblies, we found that they were large and highly repetitive compared to other published beetle genome data in the order Coleoptera. After further examination of these genome assemblies, we found regions related to metabolic potato plant detoxification, insecticide resistance, and chemosensory and odorant binding protein receptors that could be related to detecting potato plants. These genomic identifications provide novel molecular insight into regions associated with insecticide resistance, metabolic abilities, and environmental receptors, and can serve as a future valuable resource in classifying phylogenetic relationships as well as identifying regions of interest for improved pest management for potato farmers.

genomics↗

bioRxiv2021

High-quality reference genome for an arid-adapted mammal, the banner-tailed kangaroo rat (Dipodomys spectabilis)

Kangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semi-arid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered. The precarious state of many Dipodomys populations, including those occupying extreme environments, make species of this genus valuable subjects for studying the impacts of habitat degradation and fragmentation on population genomic patterns and for characterizing the genomic bases of adaptation to harsh conditions. To facilitate exploration of such questions, we assembled and annotated a reference genome for the banner-tailed kangaroo rat (D. spectabilis) using PacBio HiFi sequencing reads, providing a more contiguous genomic resource than two previously assembled Dipodomys genomes. Using the HiFi data for D. spectabilis and publicly available sequencing data for two other Dipodomys species (D. ordii and D. stephensi), we demonstrate the utility of this new assembly for studies of congeners by conducting inference of historic effective population sizes (Ne) and linking these patterns to the species current extinction risk statuses. The genome assembly presented here will serve as a valuable resource for population and conservation genomic studies of Dipodomys species, comparative genomic research within mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes. Significance statementKangaroo rats in the genus Dipodomys occur in a wide variety of habitat types, ranging from scrublands to arid deserts, and are increasingly impacted by habitat fragmentation with populations of many species in strong decline. To facilitate population and conservation genomic studies of Dipodomys species, we generated the first reference genome assembly for the extensively studied banner-tailed kangaroo rat (D. spectabilis) from long read PacBio sequencing data. The genome assembly presented here will serve as a valuable resource for studies of Dipodomys species--which have long served as ecological and physiological models for the study of osmoregulation--comparative genomic surveys of mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes.

genomics↗

bioRxiv2021

Genome size evolution in the beetle genus Diabrotica

Diabrocite corn rootworms are one of the most economically significant pests of maize in the United States and Europe and an emerging model for insect-plant interactions. Genome sizes of several species in the genus Diabrotica were estimated using flow cytometry along with that of Acalymma vittatum as an outgroup. Genome sizes ranged between 1.56 - 1.64 gigabase pairs (Gb) and between 2.26-2.59 Gb, respectively, for the Diabrotica subgroups fucata and virgifera; the Acalymma vittatum genome size was around 1.65 Gb. This result indicated that a substantial increase in genome size occurred in the ancestor of the virgifera group. Further analysis of fucata group and virgifera group genome sequencing reads indicated that the genome size difference between the Diabrotica subgroups could be attributed to a higher content of transposable elements, mostly miniature inverted-transposable elements (MITEs) and gypsy-like long terminal repeat (LTR) retroelements.

genomics↗

bioRxiv2019

Selective sweeps in a nutshell; the genomic footprint of rapid insecticide resistance evolution in a major insect pest of tree nuts

Relatively few genome-wide population studies of field-acquired insecticide resistance have been carried out on agricultural pests. Recently acquired bifenthrin resistance in a population of the navel orangeworm (Amyelois transitella), the main insect pest of almond orchards in California, provided an opportunity to examine the short- and long-term effects of heavy insecticide usage in the population genomic landscape of this species. We re-sequenced the genomes of three contemporary A. transitella natural populations differing in bifenthrin resistance status and characterized their population genetics parameters, in the process we detected an exceptionally large selective sweep in all populations. This sweep has virtually no polymorphisms and extends up to 1.3 Mb (spanning 43 genes) in the resistant population. We analyzed the possible causes of this unusually strong population genetic signature, and found genes in the sweep that are associated with DDT and pyrethroid resistance including a cluster of cytochrome P450 coding genes and the gene coding for the small conductance sodium channel "para". Moreover, we found that the sequence along the sweep is nearly identical in the genome assembled from a strain founded in 1966, suggesting that the underpinning for insecticide resistance may have been laid a half-century ago when the California Central Valley experienced massive area-wide applications of DDT for pest control. Our findings are consistent with a scenario whereby insecticide resistance in this species evolved as a stacking of selective pressures that started decades ago and that effectively reduced variation in a region of the genome containing several genes associated with resistance to insecticides with a shared target site and mechanism of action.

genomics↗