Biology subjects

DeNardo, D. F.

Publications and source records attributed to DeNardo, D. F..

4 recordsLinked to original sources

bioRxiv2024

Strong signatures of selection on genes underlying core reinforcement mechanisms in speciating desert tortoises

Genomic reinforcement and differential ecological adaptation are thought to be fundamental mechanisms of speciation. In this study we investigate the genomic basis of adaptation and reinforcement between two desert tortoise species of North America that occupy desert habitats with differing seasonal rainfall patterns and have considerable behavioral and reproductive differences yet maintain a narrow hybrid zone. We generated a chromosome-scale reference genome for Gopherus morafkai and performed analysis of synteny, genes under positive selection, and environmental niche modeling. Results show extensive positive selection (422 genes) including related to eye development and function that may relate to environmental differences, as well as prezygotic isolation mechanisms such as sperm-egg recognition, and postzygotic reinforcement mechanisms such as the spindle assembly checkpoint, and sister chromatid pairing. Together, results offer strong genetic support for the role of these classic processes in shaping reproductive isolation and lineage divergence of speciating tortoises.

evolutionary biology↗

bioRxiv2023

Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly

Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z-chromosome scaffolds. These putative Z-chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.

evolutionary biology↗

bioRxiv2022

Early transition in foraging mode promoted greater reproductive effort in widely foraging lizards

Life-history theory suggests that the optimal reproductive effort of an organism is affected by factors such as energy acquisition and predation risk. The observation that some organisms actively search for their prey and others ambush them creates the expectation of different energy needs and predation risk associated with each foraging behavior, the so-called "foraging-mode paradigm". Although this paradigm has been around for decades, the empirical evidence consists of conflicting results derived from competing models based on different mechanisms. For instance, models within the foraging-mode paradigm suggest that widely-foraging females have evolved low reproductive effort, because a heavy reproductive load decreases their ability to escape from predators. By contrast, a long-standing prediction of evolutionary theory indicates that organisms subject to high extrinsic mortality, should invest more in reproduction. Here, we present the first partial evidence that widely-foraging species have evolved greater reproductive effort than have sit-and-wait species, which we attribute to a larger body size and greater mortality among mobile foragers. According to our findings, we propose a theoretical model that could explain the observed pattern in lizards, suggesting ways for evolutionary ecologists to test mechanistic hypotheses at the intraspecific level.

evolutionary biology↗

bioRxiv2021

A novel lineage of polyomaviruses identified in bark scorpions

Polyomaviruses are non-enveloped viruses with circular double-stranded DNA genomes that range in size from [~]4-7 kilobasepairs. Initially identified in mammals, polyomaviruses have now been identified in birds and a few fish species. Although fragmentary polyomavirus-like sequences have been detected as apparent hitchhikers in shotgun genomics datasets for various arthropods, the possible diversity of these viruses in invertebrates remains unclear. In general, polyomaviruses are host-specific, showing strong evidence of host-virus co-evolution. Identification of polyomaviruses in a broader range of animals could shed useful light on the evolutionary history of this medically important group of viruses. Scorpions are predatory arachnids that are among the oldest terrestrial animals. Thus far, viromes of arachnids have been under-sampled and understudied. Here, high-throughput sequencing and traditional molecular techniques were used to explore the diversity of circular DNA viruses associated with bark scorpions (Centruroides sculpturatus) from the greater Phoenix area, Arizona, USA. The complete genomes of eight novel polyomaviruses were identified. Analysis of Centruroides transcriptomic datasets elucidated the splicing of the viral late gene array, which is more complex than that of vertebrate polyomaviruses. Phylogenetic analysis provides further evidence of co-divergence of polyomaviruses with their hosts, suggesting that at least one ancestral species of polyomaviruses was circulating amongst the primitive common ancestors of arthropods and chordates.

microbiology↗