Biology subjects

Kovacs, T. G. L.

Publications and source records attributed to Kovacs, T. G. L..

4 recordsLinked to original sources

bioRxiv2025

GHIST 2024: The 1st Genomic History Inference Strategies Tournament

Evaluating population genetic inference methods is challenging due to the complexity of evolutionary histories, potential model misspecification, and unconscious biases in self-assessment. The Genomic History Inference Strategies Tournament (GHIST) is a community-driven competition designed to evaluate methods for inferring evolutionary history from population genomic data. The inaugural GHIST competition ran from July to November 2024 and featured four demographic history inference challenges of varying complexity: a bottleneck model, a split with isolation model, a secondary contact model with demographic complexity, and an archaic admixture model. Data were provided as error-free VCF files, and participants submitted numerical parameter estimates that were scored by relative root mean squared error. Approximately 60 participants competed, using diverse approaches. Results revealed the current dominance of methods based on site frequency spectra, while highlighting the advantages of flexible model-building approaches for complex demographic histories. We discuss insights regarding the competition and outline the next iteration, which is ongoing with expanded challenge diversity. By providing standardized benchmarks and highlighting areas for improvement, GHIST represents a substantial step toward more reliable inference of evolutionary history from genomic data.

evolutionary biology↗

bioRxiv2025

Mutation rate estimate and population genomic analysis reveals decline of koalas prior to human arrival

The koala (Phascolarctos cinereus), an iconic Australian marsupial, has experienced substantial historical and contemporary population declines. Identifying the drivers of these declines has been hindered by limited genomic data and by uncertainty regarding the koala mutation rate. Here, we provide the first direct estimate of the koala mutation rate, based on four parent-offspring trios, yielding a mean of 6.12x10{square}{square} mutations per base pair per generation (95% confidence interval: 5.03-7.45x10{square}{square}). Using this estimate of the rate, we reconstructed the demographic history of koalas using 458 whole-genome sequences sampled across their entire range. Our results refine the estimated timing of past changes in population size, suggesting a large decline beginning [~]100 kya, before the arrival of modern humans in Australia. The koala population then split into five genetic populations 6-30 kya, which are now spread across >3500 km on the east coast of Australia. We also use the koala mutation rate to infer recombination maps for each population, confirming lower recombination rates in marsupials than in eutherian mammals. These findings provide critical insights into the evolutionary history of koalas, while highlighting the impact of using species-specific evolutionary rates in the inference of demographic histories and recombination landscapes. Our estimates of the genome-wide mutation rate and population-specific recombination maps for koalas provide valuable resources for future evolutionary and conservation analyses of marsupials.

evolutionary biology↗

bioRxiv2023

Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life

Microbial symbioses have had profound impacts on the evolution of animals. Conversely, changes in host biology may impact the evolutionary trajectory of symbionts themselves. Blattabacterium cuenoti is present in almost all cockroach species and enables hosts to subsist on a nutrient-poor diet. To investigate if host biology has impacted Blattabacterium at the genomic level, we sequenced and analysed 25 genomes from Australian soil-burrowing cockroaches (Blaberidae: Panesthiinae) which have undergone at least seven independent subterranean transitions from above-ground, wood-feeding ancestors. We find at least three independent instances of genome erosion have occurred in Blattabacterium strains exclusive to Australian soil-burrowing cockroaches. Such shrinkages have involved the repeated inactivation of genes involved in amino acid biosynthesis and nitrogen recycling, the core role of Blattabacterium in the host-symbiont relationship. The most drastic of these erosions have occurred in hosts thought to have transitioned underground the earliest relative to other lineages. As Blattabacterium is unable to fulfil its core function in such host groups, our findings suggest soil-burrowing cockroaches must acquire these nutrients from novel sources. Our study represents one of the first cases, to our knowledge, of parallel host adaptations leading to concomitant parallelism in their mutualistic symbionts, further underscoring the intimate relationship between these two partners.

genomics↗

bioRxiv2023

Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analysed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by phylogenetic analyses of mitochondrial genomes and UCE loci. Furthermore, Bayesian dating analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all ten major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated [~]115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.

evolutionary biology↗