Biology subjects

Doan, K.

Publications and source records attributed to Doan, K..

2 recordsLinked to original sources

bioRxiv2026

Domestic dog introgression in Australian dingoes: environmental drivers and evolutionary consequences

Introgressive hybridization between wild and domestic animals is a widespread phenomenon with important implications for genetic diversity, local adaptation, and conservation management. The causes and consequences of this process are poorly understood. In Australia, hybridization between dingoes and domestic dogs presents a dual conservation challenge, threatening the genetic integrity of dingoes while allowing potential adaptive introgression. To investigate the environmental drivers of this process, we analyzed high-density SNP array data in 390 dingoes and 396 domestic dogs. Dingo populations showed regional genetic structure and were clearly differentiated from domestic dogs. Using local ancestry inference and genome-environment association analyses, we found low levels of dog introgression in dingoes from remote areas in Central and Western Australia, and moderate levels in Eastern and Southern populations. Climatic variables (maximum temperature of the warmest month, mean temperature of the driest quarter) and the Human Footprint Index (reflecting density of human populations and environmental modifications) were significant predictors of introgression. We identified four genomic regions with overrepresented dog ancestry, including a large introgressed block on chromosome 27, which contained an olfactory receptor gene showing signatures of positive selection, suggesting adaptive introgression. In addition, a chromosomal inversion previously described in dogs and absent in dingoes was initially identified as an introgressed block. We also detected eight genomic regions nearly free of dog ancestry, suggesting purifying selection against maladaptive variants. Together, these results highlight the complex interplay between introgression, human influence, and local adaptation in dingoes, offering valuable insights for conserving the evolutionary potential of this apex predator in increasingly modified landscapes.

evolutionary biology↗

bioRxiv2023

Inferring patterns of recombination and divergence with ancient and modern treponemal genomes

BackgroundTreponemal diseases pose significant global health risks, presenting severe challenges to public health due to their serious health impacts if left untreated. Despite numerous genomic studies on Treponema pallidum and the known possible biases introduced by the choice of the reference genome used for mapping, few investigations have addressed how these biases affect phylogenetic and evolutionary analysis of these bacteria. In this study, we assessed the impact of selecting an appropriate genomic reference on phylogenetic and evolutionary analyses of T. pallidum. ResultsWe designed a multiple-reference-based (MRB) mapping strategy using four different reference genomes and compared it to traditional single-reference mapping. To conduct this comparison, we created a genomic dataset comprising 77 modern and ancient genomes from the three subspecies of T. pallidum, including a newly sequenced 17th-century genome (35X coverage) of a syphilis-causing strain (designated as W86). Our findings show that recombination detection was consistent across different references, but the choice of reference significantly affected ancient genome reconstruction and phylogenetic inferences. The high-coverage W86 genome obtained here also provided a new calibration point for Bayesian molecular clock dating, improving the reconstruction of the evolutionary history of treponemal diseases. Additionally, we identified novel recombination events, positive selection targets, and refined dating estimates for key events in the species history. ConclusionsThis study highlights the importance of considering methodological implications and reference genome bias in High-Throughput Sequencing-based whole-genome analysis of T. pallidum, especially of ancient or low-coverage samples, contributing to a deeper understanding of this pathogen and its subspecies.

microbiology↗