Biology subjects

Bentz, B.

Publications and source records attributed to Bentz, B..

3 recordsLinked to original sources

bioRxiv2026

The tortured past of young polymorphic sex chromosomes revealed through multiple de novo genome assemblies of the mountain pine beetle

Neo-sex chromosomes provide a powerful system for studying the early stages of sex chromosome evolution and the genomic mechanisms that may contribute to reproductive isolation. Using PacBio long-read HiFi sequencing, Hi-C scaffolding, and sex-specific transcriptomic data, we generated six chromosome-level assemblies (male and female from three populations) of the mountain pine beetle (Dendroctonus ponderosae), a species known to harbor three partially reproductively isolated neo-Y haplogroups. These assemblies reveal that the large neo-X and neo-Y chromosomes formed through sequential fusions of the ancestral X with three autosomes, with recombination cessation occurring at [~]8.6, [~]6.3, and [~]4.3 MYA for each event. Comparative analyses show that while neo-X chromosomes remain largely collinear across populations, neo-Ys exhibit dramatic structural divergence, with 900-1,200 inverted segments per haplogroup and only [~]65% of sequence able to be aligned to the neo-X. Repeat analyses demonstrate moderate TE accumulation on the neo-Y, particularly LTR elements, and gene mapping analyses reveal extensive degeneration: [~]62% of neo-Y genes exhibit gene loss, fragmentation, or disruptive mutations. All populations retain a single pseudoautosomal region (PAR), though PAR size and gene content vary due to neo-Y specific rearrangements. Across neo-Ys, 27 genes are uniquely missing in the Western haplogroup, including previously identified candidates implicated in hybrid male sterility. Broader comparisons among neo-Ys show widespread structural variation, population specific patterns of degeneration, and limited gene family expansions. Together, these results provide the first full characterization of neo-sex chromosome evolution in D. ponderosae, revealing rapid, lineage specific neo-Y degeneration and highlighting the potential for sex chromosome divergence to contribute to emerging reproductive incompatibilities within a single species.

genomics↗

bioRxiv2025

QTL identification and characterization of the recombination landscape of the mountain pine beetle (Dendroctonus ponderosae)

Insect pests can rapidly accumulate in number and thrive in diverse environments, making them valuable models for studying phenotypic plasticity and the genetic basis of local adaptation. The mountain pine beetle (Dendroctonus ponderosae) is a major forest pest and adult body size and generation time are two traits that vary among populations and directly influence reproductive success and outbreak dynamics. To identify regions of the genome linked to these two traits, we generated ddRAD sequencing data from an F2 intercross, using populations from two Y haplogroups with phenotypic and genetic differences in these traits. A high-density linkage map was generated and QTL analyses performed. We identified a single large effect QTL for generation time, associated with an adult diapause. The QTL spans the entire X chromosome, peaking over the evolutionarily conserved portion of the X. We were unable to detect a significant QTL for body size. Our linkage map identified putative inversions shared by parents that are absent in the published reference genome, with three putative inversions on chromosomes 2, 3, and the X. We also detected extensive regions of low recombination that were associated with low gene density, indicative of large pericentromeric regions. Surprisingly, we found that in our cross, F2 males inherited X chromosomes with significantly fewer crossover events than F2 females. Our findings provide information about the recombination landscape, the sex-biased inheritance of recombined Xs, and the genomic location of a key trait in a major forest pest.

genetics↗

bioRxiv2021

Lignin accumulation in phloem and outer bark is not associated with resistance to mountain pine beetle in high elevation pines

A key component in understanding plant-insect interactions is the nature of host defenses. Research on defense traits among Pinus species has focused on specialized metabolites and axial resin ducts, but the role of lignin in defense within diverse systems is unclear. We investigated lignin levels in the outer bark and phloem of P. longaeva, P. balfouriana, and P. flexilis; high elevation species in the western United States known to differ in susceptibility to mountain pine beetle (Dendroctonus ponderosae; MPB). Relative to P. flexilis, P. longaeva and P. balfouriana are attacked by MPB less frequently, and MPB brood production in P. longaeva is limited. Because greater lignification of feeding tissues has been shown to provide defense against bark beetles in related genera, such as Picea, we hypothesized that P. longaeva and P. balfouriana would have greater lignin concentrations than P. flexilis. Contrary to expectations, we found that the more MPB-susceptible P. flexilis had greater phloem lignin levels than the less susceptible P. longaeva and P. balfouriana. No differences in outer bark lignin levels among the species were found. We conclude that lignification in Pinus phloem and outer bark is likely not adaptive as a physical defense against MPB.

ecology↗