Biology subjects

Evans, B. J.

Publications and source records attributed to Evans, B. J..

5 recordsLinked to original sources

bioRxiv2026

Reconstructing 50 million years of Xenopus borealis evolution: three temporal strata of DNA rearrangements and persistent sex chromosome homomorphism

Genomic rearrangements are fundamental drivers of biodiversity, yet dynamics of structural evolution following polyploidization remain poorly understood. Genus Xenopus provides a valuable tool to study these phenomena. Utilizing the diploid X. tropicalis as a reference, we employed cytogenetic and genomic mapping to track the structural evolution of the allotetraploids X. borealis and X. laevis across a 50-million-year timeline. Based on chromosome morphometrics and C-banding patterns, we characterized the X. borealis pseudotetraploid karyotype (2n = 4x = 36), localizing the nucleolus organizer region (NOR) to chromosome 5L, U1 and U2 small nuclear DNAs to 1S and 8L, and 5S rDNA to nearly all chromosomes. Our analysis revealed 17 genomic rearrangements distributed within three temporal strata: ancestral (50-35 Mya), intermediate (35-15 Mya), and recent (< 15 Mya). Although we categorized chromosome 9/10 fusion as an ancestral rearrangement, the 2/9 translocation previously identified in X. mellotropicalis was absent in both studied allotetraploids. Furthermore, we tested for sex-specific structural polymorphism on the X. borealis W chromosome. Despite a large region of recombination suppression between the W and Z, no inversions were detected, indicating persistent sex chromosome homomorphism. Results are consistent with the expectation that tandem repeats such as NORs follow an asymmetric trajectory driven by a jumping mechanism and biased deletion, whereas small nuclear DNA loci are governed by copy number reduction-expansion dynamics. These findings indicate that structural rearrangements in Xenopus were not limited to punctuated bursts immediately following whole-genome duplication; rather, they accumulated over a prolonged evolutionary history, affecting the entire polyploid complement.

evolutionary biology↗

bioRxiv2022

Large scale functional screen identifies genetic variants with splicing effects in modern and archaic humans

Humans co-existed and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,224 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 969 exonic splicing mutations (ESMs) that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than in Neanderthals. Adaptively introgressed variants were enriched for moderate effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a novel tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a novel Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide novel insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.

genomics↗

bioRxiv2022

Population genomics of Xenopus laevis in southern Africa

Allotetraploid genomes have two distinct genomic compartments called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog - the African clawed frog (Xenopus laevis) - over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of the southern Africa.

genetics↗

bioRxiv2020

The bear bones: mosaic ancestry of Macaca arctoides explains divergent baculum morphology

Genital divergence is thought to contribute to reproductive barriers by establishing a "lock- and-key" mechanism for reproductive compatibility. One such example, Macaca arctoides, the bear macaque, has compensatory changes in both male and female genital morphology as compared to close relatives. Macaca arctoides also has a complex evolutionary history, having extensive introgression between the fascicularis and sinica macaque species groups. Here, phylogenetic relationships were analyzed via whole genome sequences from five species, including M. arctoides, and two species each from the putative parental species groups. This analysis revealed [~]3x more genomic regions supported placement in the sinica species group as compared to the fascicularis species group. Additionally, introgression analysis of the M. arctoides genome revealed it is a mosaic of recent polymorphisms shared with both species groups. To examine the evolution of their unique genital morphology further, the prevalence of candidate genes involved in genital morphology were compared against genome-wide outliers in various population genetic metrics, while accounting for background variation in recombination rate. This analysis identified 66 outlier genes, including several genes that influence baculum morphology in mice, which were of interest since the bear macaque has the longest primate baculum. The mean of several metrics was statistically different in the candidate genes as compared to the rest of the genome, suggesting that genes involved in genital morphology have increased divergence and decreased diversity beyond expectations. These results highlight how extensive introgression may have contributed to reproductive isolation and shaped the unique genital morphology in the bear macaque.

evolutionary biology↗

bioRxiv2019

ODORANT RECEPTOR INHIBITION IS FUNDAMENTAL TO ODOR ENCODING

Most natural odors are complex mixtures of many volatile components, competing to bind odorant receptors (ORs) expressed in olfactory sensory neurons (OSNs) of the nose. To date surprisingly little is known about how OR antagonism shapes neuronal representations in the periphery of the olfactory system. Here, we investigated its prevalence, the degree to which it disrupts OR ensemble activity, and its conservation across related ORs. Calcium imaging microscopy of dissociated OSNs revealed significant inhibition, often complete attenuation, of responses to indole, a commonly occurring volatile associated with both floral and fecal odors, by a set of 36 tested odorants. To confirm an OR mechanism for the observed inhibition, we performed single-cell transcriptomics on OSNs that exhibited specific response profiles to a diagnostic panel of odorants and identified the receptor Olfr743 which, when tested in vitro, recapitulated ex vivo responses. We screened ten ORs from the Olfr743 clade with 800 perfumery-related odorants spanning a range of chemical scaffolds and functional groups, over half of which (430) antagonized at least one of the ten ORs. Furthermore, OR activity outcomes were divergent rather than redundant, even for the most closely related paralogs. OR activity fitted a mathematical model of competitive receptor binding and suggests that normalization of OSN ensemble responses to odorant mixtures is the rule rather than the exception. In summary, we observed OR antagonism, inverse agonism and partial agonism occurring frequently and in a combinatorial manner. Thus, extensive receptor-mediated computation of mixture information appears to occur in the olfactory epithelium prior to transmission of odor information to the olfactory bulb.

neuroscience↗