Biology subjects

Blackmon, H.

Publications and source records attributed to Blackmon, H..

7 recordsLinked to original sources

bioRxiv2026

Dismantling Chromosomal Stasis Across the Eukaryotic Tree of Life

Chromosome number shapes genome organization, recombination, and speciation, yet how fast it evolves across the tree of life has never been measured. We analyzed 63,682 karyotypes across 55 eukaryotic clades and found that dysploidy rates vary by 844-fold, from approximately 0.0008 to 0.7 events per million years. This variation does not follow kingdom boundaries or deep phylogeny; intraclade variance exceeds interclade differences by more than an order of magnitude. Even birds, the textbook example of chromosomal stasis, exceed the global median rate once microchromosome dynamics are resolved. Contrasting the stasis of Odonata with the volatility of Orchidaceae reveals that life history and population structure, rather than deep phylogenetic constraints, govern the tempo of karyotypic change.

evolutionary biology↗

bioRxiv2025

Functional synaptic connectivity of engrafted spinal cord neurons with locomotor circuitry in the injured spinal cord

Spinal cord injury (SCI) results in significant neurological deficits, with no currently available curative therapies. Neural progenitor cell (NPC) transplantation has emerged as a promising approach for neural repair, as graft-derived neurons (GDNs) can integrate into the host spinal cord and support axon regeneration. However, the mechanisms underlying functional recovery remain poorly understood. In this study, we investigate the synaptic integration of NPC-derived neurons into locomotor circuits, the projection patterns of distinct neuronal subtypes, and their potential to modulate motor circuit activity. Using transsynaptic tracing in a mouse thoracic contusion SCI model, we found that NPC-derived neurons form synaptic connections with host locomotor circuits, albeit at low frequencies. Furthermore, we mapped the axon projections of V0C and V2a interneurons, revealing distinct termination patterns within host spinal cord laminae. To assess functional integration, we employed chemogenetic activation of GDNs, which induced muscle activity in a subset of transplanted animals. However, NPC transplantation alone did not significantly improve locomotor recovery, highlighting a key challenge in the field. Our findings suggest that while GDNs can integrate into host circuits and modulate motor activity, synaptic connectivity remains a limiting factor in functional recovery. Future studies should focus on enhancing graft-host connectivity and optimizing transplantation strategies to maximize therapeutic benefits for SCI.

neuroscience↗

bioRxiv2024

From Micro to Macro: Avian Chromosome Evolution is Dominated by Natural Selection

Birds display striking variation in chromosome number, defying the traditional view of highly conserved avian karyotypes. However, the evolutionary drivers of this variability remain unclear. To address this, we fit probabilistic models of chromosome number evolution across birds, enabling us to estimate rates of evolution for total chromosome number and the number of microchromosomes and macrochromosomes while simultaneously accounting for the impact of other evolving traits. Our analyses revealed higher rates of chromosome fusion than fission across all bird lineages. Notably, much of this signal was driven by Passeriformes, where migratory species showed a particularly strong bias towards fusions compared to sedentary counterparts. Furthermore, a robust correlation between the rearrangement rates of microchromosomes and macrochromosomes suggests that genome-wide processes drive rates of structural evolution. Additionally, we found that lineages with larger population sizes exhibited higher rates of both fusion and fission, indicating that positive selection plays a dominant role in driving divergence in chromosome number. Our findings illuminate the evolutionary dynamics of avian karyotypes and highlight that, while the fitness effects of random structural mutations are often deleterious, beneficial mutations may dominate karyotype divergence in some clades.

evolutionary biology↗

bioRxiv2024

Genome assembly of the southern pine beetle (Dendroctonus frontalis Zimmerman) reveal the origins of gene content reduction in Dendroctonus

Dendroctonus frontalis, also known as southern pine beetle (SPB), represents the most damaging forest pest in the southeastern United States. Strategies to predict, monitor and suppress SPB outbreaks have had limited success. Genomic data are critical to inform on pest biology and to identify molecular targets to develop improved management approaches. Here, we produced a chromosome-level genome assembly of SPB using long-read sequencing data. Synteny analyses confirmed the conservation of the core coleopteran Stevens elements and validated the bona fide SPB X chromosome. Transcriptomic data were used to obtain 39,588 transcripts corresponding to 13,354 putative protein-coding loci. Comparative analyses of gene content across 14 beetle and 3 other insects revealed several losses of conserved genes in the Dendroctonus clade and gene gains in SPB and Dendroctonus that were enriched for loci encoding membrane proteins and extracellular matrix proteins. While lineage-specific gene losses contributed to the gene content reduction observed in Dendroctonus, we also showed that widespread misannotation of transposable elements represents a major cause of the apparent gene expansion in several non-Dendroctonus species. Our findings uncovered distinctive features of the SPB gene complement and disentangled the role of biological and annotation-related factors contributing to gene content variation across beetles.

genomics↗

bioRxiv2021

CaveCrawler: An interactive analysis suite for cavefish bioinformatics

The growing use of genomics data in diverse animal models provides the basis for identifying genomic and transcriptional differences across species and contexts. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but are lacking for most emerging models of evolution. There is a rapidly expanding use of genomic, transcriptional, and functional genetic approaches to study diverse traits of the Mexican tetra, Astyanax mexicanus. This species exists as two morphs, eyed surface populations and at least 30 blind cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results can be processed with other analysis platforms including Gene Ontology (GO) to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built A. mexicanus can readily applied to other emerging model systems.

bioinformatics↗

bioRxiv2020

The Probability of Fusions Joining Sex Chromosomes and Autosomes

Chromosome fusion and fission are primary mechanisms of karyotype evolution. In particular, the fusion of a sex chromosome and an autosome has been proposed as a mechanism to resolve intralocus sexual antagonism. If sexual antagonism is common throughout the genome, we should expect to see an excess of fusions that join sex chromosomes and autosomes. Here, we present a null model that provides the probability of a sex chromosome autosome fusion, assuming all chromosomes have an equal probability of being involved in a fusion. This closed-form expression is applicable to both male and female heterogametic sex chromosome systems and can accommodate unequal proportions of fusions originating in males and females.

evolutionary biology↗

bioRxiv2020

Ghosts of a structured past: Impacts of ancestral isolation by distance on divergence time estimation

Isolation by distance is a widespread pattern in nature that describes the reduction of genetic correlation between subpopulations with increased geographic distance. In the population ancestral to modern sister species, this pattern may hypothetically inflate population divergence time estimation due to the potential for allele frequency differences in subpopulations at the ends of the ancestral population. In this study, we analyze the relationship between the time to the most recent common ancestor and the population divergence time when the ancestral population model is a linear stepping-stone. Using coalescent simulations, we compare the coalescent time to the population divergence time for various ratios of the divergence time over the product of the population size and the deme number. Next, we simulate whole genomes to obtain SNPs, and use the Bayesian coalescent program SNAPP to estimate divergence times. We find that as the rate of migration between neighboring demes decreases, the coalescent time becomes significantly greater than the population divergence time when sampled from end demes. Divergence-time overestimation in SNAPP becomes severe when the divergence-to-population size ratio < 10 and migration is low. We conclude that studies estimating divergence times be cognizant of the potential ancestral population structure in an explicitly spatial context or risk dramatically overestimating the timing of population splits.

evolutionary biology↗