Biology subjects

Goodall, J.

Publications and source records attributed to Goodall, J..

4 recordsLinked to original sources

bioRxiv2025

Adaptive introgression from Pacific herring to Atlantic herring in the brackish Baltic Sea

The genomic era has revealed that interspecific gene flow can play an important role in adaptive evolution. Here, we report a striking case of adaptive introgression from Pacific into Atlantic herring following the colonization of the brackish Baltic Sea. Gene flow likely occurred in the Arctic, where the distributions of the two species overlap. Although introgression affected only 0.29% of the genome, these regions encompass about 10% of the loci showing strong differentiation between Atlantic and Baltic herring, indicating that natural selection has favored introgressed alleles in functionally important parts of the genome. Adaptive introgression may have been facilitated by shared spawning depths and salinity preferences between Pacific and Baltic herring, in contrast to Atlantic herring, which spawn in deeper, fully marine waters. Introgressed genes such as THRB and SEC16B may have enhanced visual acuity and lipid metabolism, respectively, promoting adaptation to the brackish Baltic environment.

evolutionary biology↗

bioRxiv2024

Evolution of fast-growing piscivorous herring in the young Baltic Sea

The circumstances under which species diversify to genetically distinct lineages is a fundamental question in biology1. Atlantic herring is an extremely abundant zooplanktivorous species that is subdivided into multiple ecotypes that differ regarding spawning time and genetic adaption to local environmental conditions such as temperature, salinity, and light conditions2,3. Here we show using whole genome analysis that multiple populations of piscivorous (fish-eating) herring have evolved sympatrically after the colonization of the brackish Baltic Sea within the last 8,000 years postglaciation. The piscivorous ecotype grows faster, and is much larger and less abundant than the zooplanktivorous Baltic herring. Lesions of the gill rakers in the piscivorous ecotype indicated incomplete adaptation to a fish diet. This niche expansion of herring in the young Baltic Sea with its paucity of piscivorous species suggests that empty niche space is more important than geographic isolation for the evolution of biodiversity.

evolutionary biology↗

bioRxiv2024

Fast and robust objective EEG audiometry

The current gold standard of audiometry relies on subjective behavioral responses, which is impractical and unreliable for certain groups such as children, individuals with severe disabilities, or the disabled elderly. This study presents a novel electroencephalography (EEG) system that is easy to setup and estimates audiometric thresholds quickly. Air-conduction audiometric thresholds at 250, 500, 1000, 2000, 4000, and 8000 Hz and 5 dB resolution were estimated from ten elderly patients with asymmetric sensorineural hearing loss and five normal hearing young adults using three different systems: the novel EEG system, conventional pure-tone audiometry (PTA), and an automated behavioral test with the same stimulus properties as in the EEG test. EEG data was collected for 15 minutes from 32 semi-dry EEG electrodes. Later, the EEG system was trimmed to 8 electrodes and 7.5 minutes of data with satisfactory results. Correlation and regression analysis validated the hearing thresholds derived from both EEG configurations relative to the behavioral hearing thresholds-Pearsons correlation of 0.82 between PTA and 8-electrode 7.5-minute EEG data. The results of this study open the door to fast and objective hearing threshold estimation with EEG.

neuroscience↗

bioRxiv2018

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome

The black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally. However, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date. The assembly was carried out in multiple assemblers using 2x125 bp HiSeq data from PolyA selected, ribo-depleted RNA extracted from nine adult tissues and eight early life-history stages. In total, approximately 700 million high-quality sequence reads were obtained and assembled into 236,388 clusters. These were then further segregated into 99,203 adult tissue specific clusters, and 58,678 early life-history stage specific clusters. The final transcriptome had a high TransRate score of 0.37, with 88% of all reads successfully mapping back to the transcriptome. BUSCO statistics showed the assembly to be highly complete with low fragmentation, few genes missing, but higher redundancy or transcript duplication (Complete: 98.2% (Duplicated: 51.3%), Fragmented: 0.8%, Missing: 1.0%), and to greatly exceed the completeness of existing P. monodon transcriptomes. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. To help address the lack of annotation, transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. Additionally, transcripts of shrimp viruses previously not known to occur in Australia were also discovered. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.

molecular biology↗