Biology subjects

Gable, S. M.

Publications and source records attributed to Gable, S. M..

5 recordsLinked to original sources

bioRxiv2026

Disagreement among Genomic Markers Profoundly Influences Phylogenetic Inference in Squamates

Phylogenomic-scale studies of the same clades using different markers and methods often support highly confident yet different species trees, obscuring many phylogenetic relationships and hampering comparative studies. Among reptiles, the >11,000 extant species of squamates (Order Squamata: lizards, snakes, and amphisbaenians) comprise a highly diverse and well-studied clade, yet many unresolved questions about squamate origins remain, including the root of the squamate phylogeny and the relationships of snakes to other toxicoferans. To understand biological, molecular, and methodological sources of phylogenomic heterogeneity in squamates, we analyzed four genome-scale marker datasets, including thousands of protein-coding genes, anchored hybrid enrichment loci, and ultra-conserved elements. We applied standardized alignment, filtering, and tree-building methods across marker sets, analyzed patterns in substitutional saturation and codon positions, and measured gene tree-species tree discordance across all data partitions. We found that many contentious relationships in squamate phylogenetics are driven by conflicts stemming from input data quality, incorrect model fit, and sampling bias, and that biological drivers of heterogeneity include both incomplete lineage sorting and introgression. We account for these sources of heterogeneity and strengthen resolution of the squamate phylogeny. Using a simulation approach, we find that current ultra-conserved element datasets for squamates deviate the most from phylogenetic expectations among marker types. Our work demonstrates that identifying sources of phylogenomic heterogeneity while accounting for input data limitations can resolve phylogenetic conflicts.

genomics↗

bioRxiv2025

Sex chromosome identification and genome curation, at scale, from a single individual with SCINKD

In most animal species, the sex determining pathway is typically initiated by the presence/absence of a primary genetic cue at a critical point during development. This primary genetic cue is often located on a single locus--referred to as sex chromosomes--and can be limited to females (in a ZZ/ZW system) or males (in an XX/XY system). One trademark of sex chromosomes is a restriction or cessation of recombination surrounding the sex-limited region (to prevent its inheritance in the homogametic sex). This may lead to--through a variety of mechanisms--higher amounts of genetic divergence within this region, i.e. between the X/Z and Y/W chromosomes, especially when compared to their autosomal counterparts. Recent advances in genome sequencing and computation have brought with them the ability to resolve haplotypes within a diploid individual, permitting assembly of previously challenging genomic regions like sex chromosomes. Leveraging these advances, we identified replicable diagnostic characteristics between typical autosomes and sex chromosomes (within a single genome assembly). Under this framework, we can use this information to identify putative sex chromosome linkage groups across divergent vertebrate taxa and simultaneously curate misassembled regions on autosomes. Here, we present this conceptual framework and associated tool for identifying candidate sex chromosome linkage groups from a single, diploid individual dubbed Sex Chromosome Identification by Negating Kmer Densities, or SCINKD.

genomics↗

bioRxiv2024

Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; [~]11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

genomics↗

bioRxiv2023

Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)

There is increasing interest in the African spiny mouse (Acomys cahirinus) as a model organism because of its ability for regeneration of tissue after injury in skin, muscle, and internal organs such as the kidneys. A high-quality reference genome is needed to better understand these regenerative properties at the molecular level. Here, we present an improved reference genome for A. cahirinus generated from long Nanopore sequencing reads. We confirm the quality of our annotations using RNA sequencing data from four different tissues. Our genome is of higher contiguity and quality than previously reported genomes from this species and will facilitate ongoing efforts to better understand the regenerative properties of this organism.

genomics↗

bioRxiv2021

A Genomic Perspective on the Evolutionary Diversification of Turtles

To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies based on annotated regions from the western painted turtle (Chrysemys picta bellii) genome (coding regions, introns, untranslated regions, intergenic, and others). We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for temporal patterns in phylogenomic conflict across turtle evolution. We found strong and consistent support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa. Our results suggest that gene tree-species tree discordance in these datasets is likely driven by population-level processes such as incomplete lineage sorting. We found very little effect of substitutional saturation on species tree topologies, and no clear phylogenetic patterns in codon usage bias and compositional heterogeneity. There was no correlation between gene and site concordance, node age, and DNA substitution rate across most annotated genomic regions. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible in order to obtain accurate phylogenies for assessing conservation priorities in turtles.

evolutionary biology↗