Biology subjects

Geneva, A. J.

Publications and source records attributed to Geneva, A. J..

4 recordsLinked to original sources

bioRxiv2026

Whole-Genome Sequencing and Phylogenetic Analysis of Anolis adenovirus 2 Reveals Conserved Genome Organization and Gene-Specific Evolutionary Patterns

Adenoviruses, which infect vertebrates, have a rich history of evolution that includes both host switching and coevolution, particularly within Barthadenovirus, a genus that infects squamate reptiles, birds, and mammals. Potential host-switching events can be identified by comparing the evolutionary histories between viruses and their hosts; however, many Barthadenovirus phylogenies have been inferred based on a limited number of easily-amplifiable gene segments. Whole-genome sequencing novel strains of Barthadenovirus can provide greater phylogenetic confidence, and therefore more accurately identify host-switching when it occurs. Here, we present the whole-genome sequence, annotation, reconciled species tree, and molecular evolution analyses of two isolates of Anolis adenovirus 2, a member of Barthadenovirus. Our two isolates of Anolis adenovirus 2 are sister lineages with very high sequence similarity. Our results support existing hypotheses regarding the ancestral hosts of Barthadenovirus (squamate reptiles), and proposed host switching events within and between squamate reptiles and other vertebrate classes. We leverage our novel genome annotations to perform comparative synteny analyses, identifying a set of shared genes across Barthadenovirus whose gene order is largely conserved within the genus. Finally, our molecular evolution analyses highlight trends in evolutionary pressures on individual genes: Genes associated with viral replication and structure have experienced slower rates of evolution than those encoding proteins involved in host interaction. Our two sequenced isolates of Anolis adenovirus 2 add to an expanding number of Adenovirus genomic resources and facilitate future investigations into the patterns and processes shaping adenovirus diversification.

evolutionary biology↗

bioRxiv2025

Intrinsic Reproductive Isolation among Ecologically Divergent Anolis Lizards

The evolution of reproductive isolation lies at the core of our modern concept of species. Despite this central importance, study of the evolution of reproductive isolation is largely limited to a set of laboratory amenable species. When shallowly divergent populations are associated with different habitats, extrinsic isolation is often assumed to play a major role. Because this type of isolation is environmentally mediated it can be ephemeral, for instance, if habitats change in response to climate. In contrast, intrinsic isolation is heritable and therefore loss of this type of isolation requires genetic changes in one or both populations. We performed a hybridization and backcross experiment to test for and characterize intrinsic reproductive isolation between two recently diverged, ecologically differentiated populations of Anolis lizards. We find evidence of substantial intrinsic isolation that appears to operate at the postmating, prezygotic phase. Our findings suggest that intrinsic isolation may play a substantial role in the maintenance of shallow, yet ecologically divergent, lineages.

evolutionary biology↗

bioRxiv2025

Chromosomal Fusions and Evolutionary Forces: Exploring theNeo-Sex Chromosome System of Anolis distichus

The evolutionary dynamics of sex chromosomes differ from autosomes due to their unique pattern of in-heritance and regions of hemizygosity in non-recombining areas. However, the study of sex chromosomes and sex-linked gene evolution has been limited by the rarity of truly novel sex chromosome complements in model systems. Recent advances in next-generation sequencing have enabled the identification of neo-sex chromosomes, created by the fission or fusion of autosomes with sex chromosomes, providing a new avenue to investigate the dynamics of sex chromosome evolution. Squamate reptiles, particularly Anolis lizards, are an excellent system for studying the consequences of sex-linkage due to their frequent sex chromosome-autosome fusions. The Hispaniolan Bark Anole, Anolis distichus, has experienced two sex chromosome and autosome fusions that led to a multiple sex chromosome system (X1X2Y). We present a high-quality whole-genome assembly and annotation of a male A. distichus (X1X2Y), enabling a detailed analysis of all three of its neo-sex chromosomes. We identify scaffolds associated with X1, X2, and Y chromosomes using an integra-tive approach and estimate degeneration and selection strength. Our results support long-held theories of differential evolutionary pressures in sex chromosomes, such as the Fast X effect and Y degeneration. Additionally, we find that chromosome 12 has become sex-linked independently in two different Anolis species, suggesting that some autosomes may be more likely to become sex-linked. Altogether, our genome adds to the diversity of available taxa sequenced and enables novel comparative analyses in a variety of fields, including speciation, chromosomal synteny, and sex chromosome evolution.

genomics↗

bioRxiv2021

Chromosome-scale genome assembly of the brown anole (Anolis sagrei), a model species for evolution and ecology

Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a new, highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei - a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue.

genomics↗