Drift drives the evolution of chromosome number II: The impact of range size on genome evolution in Carnivora.

Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations.

A reference quality genome assembly for the Jewel scarab Chrysina gloriosa.

The jewel scarab Chrysina gloriosa is one of the most charismatic beetles in the United States and is found from the mountains of West Texas to the Southeastern Arizona sky islands. This species is highly sought by professional and amateur collectors worldwide due to its gleaming metallic coloration. However, the impact of the large-scale collection of this beetle on its populations is unknown, and there is a limited amount of genetic information available to make informed decisions about its conservation. As a first step, we present the genome of C. gloriosa, which we reconstructed using a single female specimen sampled from our ongoing effort to document population connectivity and the demographic history of this beetle. Using a combination of long-read sequencing and Omni-C data, we reconstructed the C. gloriosa genome at a near-chromosome level. Our genome assembly consisted of 454 scaffolds spanning 642 MB, with the ten largest scaffolds capturing 98% of the genome. The scaffold N50 was 72 MB, and the BUSCO score was 95.5%. This genome assembly will be an essential tool to accelerate understanding C. gloriosa biology and help make informed decisions for the conservation of Chrysina and other species with similar distributions in this region. This genome assembly will further serve as a community resource for comparative genomic analysis.

Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short-read data.

Highly polymorphic markers, such as microsatellites, are invaluable for the study of natural populations. However, contemporary methods for genotyping highly polymorphic variants have serious drawbacks that impede their efficiency. We created Polly, an R package with C++ source code that uses Illumina short-read data to genotype microsatellites, detect highly polymorphic variants and identify clusters of highly polymorphic SNPs, indels and microsatellites. We tested Polly on short-read data from Xiphophorus birchmanni (Teleostei: Poeciliidae) and Arabidopsis thaliana, finding it to be efficient and accurate both for microsatellite genotyping and polymorphic marker detection. This program can be applied to any diploid population for which there exists short-read data and at least one scaffolded reference genome.

Wright was right: leveraging old data and new methods to illustrate the critical role of epistasis in genetics and evolution.

Much of evolutionary theory is predicated on assumptions about the relative importance of simple additive versus complex epistatic genetic architectures. Previous work suggests traits strongly associated with fitness will lack additive genetic variation, whereas traits less strongly associated with fitness are expected to exhibit more additive genetic variation. We use a quantitative genetics method, line cross analysis, to infer genetic architectures that contribute to trait divergence. By parsing over 1,600 datasets by trait type, clade, and cross divergence, we estimated the relative importance of epistasis across the tree of life. In our comparison between life-history traits and morphological traits, we found greater epistatic contributions to life-history traits. Our comparison between plants and animals showed that animals have more epistatic contribution to trait divergence than plants. In our comparison of within-species versus between-species crosses, we found that only animals exhibit a greater epistatic contribution to trait divergence as divergence increases. While many scientists have argued that epistasis is ultimately of little importance, our results show that epistasis underlies much of trait divergence and must be accounted for in theory and practical applications like domestication, conservation breeding design, and understanding complex diseases.

Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera.

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 (Ne) 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 Ne 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 Ne 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 Ne, 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 Ne.

Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes).

Some species are able to hybridize despite being exceptionally diverged. The causes of this variation in accumulation of reproductive isolation remain poorly understood, and domestication as an impetus or hindrance to reproductive isolation remains to be characterized. In this study, we investigated the role of divergence time, domestication, and mismatches in morphology, habitat, and clutch size among hybridizing species on reproductive isolation in the bird order Galliformes. We compiled and analyzed hybridization occurrences from literature and recorded measures of postzygotic reproductive isolation. We used a text-mining approach leveraging a historical aviculture magazine to quantify the degree of domestication across species. We obtained divergence time, morphology, habitat, and clutch size data from open sources. We found 123 species pairs (involving 77 species) with known offspring fertility (sterile, only males fertile, or both sexes fertile). We found that divergence time and clutch size were significant predictors of reproductive isolation (McFadden's Pseudo-R2 = 0.59), but not habitat or morphological mismatch. Perhaps most interesting, we found a significant relationship between domestication and reproductive compatibility after correcting for phylogeny, removing extreme values, and addressing potential biases (F1,74 = 5.43, R2 = 0.06, P-value = 0.02). We speculate that the genetic architecture and disruption in selective reproductive regimes associated with domestication may impact reproductive isolation, causing domesticated species to be more reproductively labile.

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.

BACKGROUND: The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. METHODS: We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. RESULTS: We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference. CONCLUSIONS: We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.

Tempo and Mode of Genome Structure Evolution in Insects.

The division of the genome into discrete chromosomes is a fundamental characteristic of eukaryotic life. Insect taxonomists' early adoption of cytogenetics has led to an incredible amount of data describing genome structure across insects. In this article, we synthesize data from thousands of species and use biologically realistic models to infer the tempo and mode of chromosome evolution among insect orders. Our results show that orders vary dramatically in the overall rate of chromosome number evolution (a proxy of genome structural stability) and the pattern of evolution (e.g., the balance between fusions and fissions). These findings have important implications for our understanding of likely modes of speciation and offer insight into the most informative clades for future genome sequencing.

Genomic investigation refutes record of most diverged avian hybrid.

The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the "record" of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.

Diptera and Drosophila Karyotype Databases: A Useful Dataset to Guide Evolutionary and Genomic Studies.

Karyotypes and chromosome data have been widely used in many subfields of biology over the last century. Unfortunately, this data is largely scattered among hundreds of articles, books, and theses, many of which are only available behind paywalls. This creates a barrier to new researchers wishing to use this data, especially those from smaller institutions or in countries lacking institutional access to much of the scientific literature. We solved this problem by building two datasets for true flies (Order: Diptera and one specific to Drosophila), These datasets are available via a public interactive database that allows users to explore, visualize and download all data. The Diptera karyotype databases currently contain a total of 3,474 karyotype records from 538 publications. Synthesizing this data, we show several groups are of particular interest for future investigations by whole genome sequencing.

Effects of biological sex mismatch on neural progenitor cell transplantation for spinal cord injury in mice.

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.

CaveCrawler: an interactive analysis suite for cavefish bioinformatics.

The growing use of genomics in diverse organisms provides the basis for identifying genomic and transcriptional differences across species and experimental conditions. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but most emerging models lack such databases. The Mexican tetra, Astyanax mexicanus exists as 2 morphs: surface-dwelling and cave-dwelling. There exist at least 30 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 of diverse studies can be analyzed in conjunction with other genetic data (e.g. Gene Ontology information), to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built for A. mexicanus can be adapted for other emerging model systems.

Phylogenetics in space: How continuous spatial structure impacts tree inference.

The tendency to discretize biology permeates taxonomy and systematics, leading to models that simplify the often continuous nature of populations. Even when the assumption of panmixia is relaxed, most models still assume some degree of discrete structure. The multispecies coalescent has emerged as a powerful model in phylogenetics, but in its common implementation is entirely space-independent - what we call the "missing z-axis". In this article, we review the many lines of evidence for how continuous spatial structure can impact phylogenetic inference. We illustrate and expand on these by using complex continuous-space demographic models that include distinct modes of speciation. We find that the impact of spatial structure permeates all aspects of phylogenetic inference, including gene tree stoichiometry, topological and branch-length variance, network estimation, and species delimitation. We conclude by utilizing our results to suggest how researchers can identify spatial structure in phylogenetic datasets.

Retrogene survival is not impacted by linkage relationships.

In retrogene evolution, the out-of-the-X pattern is the retroduplication of X-linked housekeeping genes to autosomes, hypothesized to be driven by meiotic sex chromosome inactivation during spermatogenesis. This pattern suggests that some retrogene survival is driven by selection on X-linkage. We asked if selection on linkage constitutes an important evolutionary force in retrogene survival, including for autosomal parents. Specifically, is there a correlation between retrogene survival and changes in linkage with parental gene networks? To answer this question, we compiled data on retrogenes in both Homo sapiens and Drosophila melanogaster and using Monte Carlo methods, we tested whether retrogenes exhibit significantly different linkage relationships than expected under a null assumption of uniform distribution in the genome. Overall, after excluding genes involved in the out-of-the-X pattern, no general pattern was found associating genetic linkage and retrogene survival. This demonstrates that selection on linkage may not represent an overarching force in retrogene survival. However, it remains possible that this type of selection still influences the survival of specific retrogenes.

A Primer for Single-Cell Sequencing in Non-Model Organisms.

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.

Simulation Tests of Methods in Evolution, Ecology, and Systematics: Pitfalls, Progress, and Principles.

Complex statistical methods are continuously developed across the fields of ecology, evolution, and systematics (EES). These fields, however, lack standardized principles for evaluating methods, which has led to high variability in the rigor with which methods are tested, a lack of clarity regarding their limitations, and the potential for misapplication. In this review, we illustrate the common pitfalls of method evaluations in EES, the advantages of testing methods with simulated data, and best practices for method evaluations. We highlight the difference between method evaluation and validation and review how simulations, when appropriately designed, can refine the domain in which a method can be reliably applied. We also discuss the strengths and limitations of different evaluation metrics. The potential for misapplication of methods would be greatly reduced if funding agencies, reviewers, and journals required principled method evaluation.

Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data.

Stochastic models of character trait evolution have become a cornerstone of evolutionary biology in an array of contexts. While probabilistic models have been used extensively for statistical inference, they have largely been ignored for the purpose of measuring distances between phylogeny-aware models. Recent contributions to the problem of phylogenetic distance computation have highlighted the importance of explicitly considering evolutionary model parameters and their impacts on molecular sequence data when quantifying dissimilarity between trees. By comparing two phylogenies in terms of their induced probability distributions that are functions of many model parameters, these distances can be more informative than traditional approaches that rely strictly on differences in topology or branch lengths alone. Currently, however, these approaches are designed for comparing models of nucleotide substitution and gene tree distributions, and thus, are unable to address other classes of traits and associated models that may be of interest to evolutionary biologists. Here, we expand the principles of probabilistic phylogenetic distances to compute tree distances under models of continuous trait evolution along a phylogeny. By explicitly considering both the degree of relatedness among species and the evolutionary processes that collectively give rise to character traits, these distances provide a foundation for comparing models and their predictions, and for quantifying the impacts of assuming one phylogenetic background over another while studying the evolution of a particular trait. We demonstrate the properties of these approaches using theory, simulations, and several empirical data sets that highlight potential uses of probabilistic distances in many scenarios. We also introduce an open-source R package named PRDATR for easy application by the scientific community for computing phylogenetic distances under models of character trait evolution.[Brownian motion; comparative methods; phylogeny; quantitative traits.].

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. We find that over 25% of all chromosomal fusions are expected to join a sex chromosome and an autosome whenever the diploid autosome count is fewer than 16, regardless of the sex chromosome system. We also demonstrate the utility of our model by analysing two contrasting empirical datasets: one from Drosophila and one from the jumping spider genus Habronattus. We find that in the case of Habronattus, there is a significant excess of sex chromosome autosome fusions but that in Drosophila there are far fewer sex chromosome autosome fusions than would be expected under our null model.