Despite the fundamental role of centromeres two different types are observed across plants and animals. Monocentric chromosomes possess a single region that function as the centromere while in holocentric chromosomes centromere activity is spread across the entire chromosome. Proper segregation may fail in species with monocentric chromosomes after a fusion or fission, which may lead to chromosomes with no centromere or multiple centromeres. In contrast, species with holocentric chromosomes should still be able to safely segregate chromosomes after fusion or fission. This along with the observation of high chromosome number in some holocentric clades has led to the hypothesis that holocentricity leads to higher rates of chromosome number evolution. To test for differences in rates of chromosome number evolution between these systems, we analyzed data from 4,393 species of insects in a phylogenetic framework. We found that insect orders exhibit striking differences in rates of fissions, fusions, and polyploidy. However, across all insects we found no evidence that holocentric clades have higher rates of fissions, fusions, or polyploidy than monocentric clades. Our results suggest that holocentricity alone does not lead to higher rates of chromosome number changes. Instead, we suggest that other co-evolving traits must explain striking differences between clades. One of the most basic features of the genome is its division into chromosomes. When we look across clades, we find a striking pattern where almost all species in some groups exhibit the same number of chromosomes, while in other groups, there is great variation in chromosome number even between closely related species. One possible explanation for these differences is the type of centromeres that a clade possesses. Monocentric chromosomes must have a single region that functions as the centromere, while in holocentric chromosomes, centromere activity is present across the entire chromosome. For this reason, it has been hypothesized that holocentric species should tolerate structural changes in chromosomes (fusions, fission, etc.) better than monocentric species. To test this hypothesis, we estimated the rate of fusion, fission, and polyploidy using data from 4,393 species of insects spanning 22 orders. We found that insect orders exhibit striking differences in rates of chromosome evolution. However, across all insects, we found no evidence that holocentric orders have higher rates of fissions, fusions, or polyploidy than monocentric orders. Our results suggest that holocentricity alone does not lead to higher rates of chromosome number changes.

Single-cell sequencing technologies have led to a revolution in our knowledge of the diversity of cell types, connections between biological levels of organization, and relationships between genotype and phenotype. These advances have mainly come from using model organisms; however, using single-cell sequencing in non-model organisms could enable investigations of questions inaccessible with typical model organisms. This primer describes a general workflow for single-cell sequencing studies and considerations for using non-model organisms (limited to multicellular animals). Importantly, single-cell sequencing, when further applied in non-model organisms, will allow for a deeper understanding of the mechanisms between genotype and phenotype and the basis for biological variation.

Despite advancement of neural progenitor cell transplantation to spinal cord injury clinical trials, there remains a lack of understanding of how biological sex of transplanted cells influences outcomes after transplantation. To address this, we transplanted GFP-expressing sex-matched, sex-mismatched, or mixed donor cells into sites of spinal cord injury in adult male and female mice. Biological sex of the donor cells does not influence graft neuron density, glial differentiation, formation of the reactive glial cell border, or graft axon outgrowth. However, male grafts in female hosts feature extensive hypervascularization accompanied by increased vascular diameter and perivascular cell density. We show greater T-cell infiltration within male-to-female grafts than other graft types. Together, these findings indicate a biological sex-specific immune response of female mice to male donor cells. Our work suggests that biological sex should be considered in the design of future clinical trials for cell transplantation in human injury.

Chromosomal mutations such as fusions and fissions are often thought to be deleterious, especially in heterozygotes (underdominant), and consequently are unlikely to become fixed. Yet, many models of chromosomal speciation ascribe an important role to chromosomal mutations. When the effective population size (N_e) is small, the efficacy of selection is weakened, and the likelihood of fixing underdominant mutations by genetic drift is greater. Thus, it is possible that ecological and phenotypic transitions that modulate N_e facilitate the fixation of chromosome changes, increasing the rate of karyotype evolution. We synthesize all available chromosome number data in Coleoptera and estimate the impact of traits expected to change N_e on the rate of karyotype evolution in the family Carabidae and 12 disparate clades from across Coleoptera. Our analysis indicates that in Carabidae, wingless clades have faster rates of chromosome number increase. Additionally, our analysis indicates clades exhibiting multiple traits expected to reduce N_e, including strict inbreeding, oligophagy, winglessness, and island endemism, have high rates of karyotype evolution. Our results suggest that chromosome number changes are likely fixed by genetic drift despite an initial fitness cost and that chromosomal speciation models may be important to consider in clades with very small N_e.

Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge, we performed comparative analyses of 304 available insect genomes. We investigated the impact of sequence assembly methods and assembly quality on the inference of microsatellite content, and we explored the influence of chromosome type and number on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet. Diploid chromosome number had no impact on the rate of microsatellite evolution or the amount of microsatellite content in genomes. We found that centromere type (holocentric or monocentric) is not associated with a difference in the amount of microsatellite content; however, in those species with monocentric chromosomes, microsatellite content tends to evolve faster than in species with holocentric chromosomes.

Microsatellites are repetitive DNA sequences usually found in non-coding regions of the genome. Their quantification and analysis have applications in fields from population genetics to evolutionary biology. As genome assemblies become commonplace, the need for software that can facilitate analyses has never been greater. In particular, R packages that can analyze genomic data are particularly important since this is one of the most popular software environments for biologists. We created an R package, micRocounter, to quantify microsatellites. We have optimized our package for speed, accessibility, and portability, making the automated analysis of large genomic data sets feasible. Computationally intensive algorithms were built in C++ to increase speed. Tests using benchmark datasets show a 200-fold improvement in speed over existing software. A moderately sized genome of 500 Mb can be processed in under 50 sec. Results are output as an object in R increasing accessibility and flexibility for practitioners.