Biology subjects

Keen, E.

Publications and source records attributed to Keen, E..

5 recordsLinked to original sources

bioRxiv2026

Breath to genome: Whole genome sequencing of large whales from blow sampling

Preserving biodiversity requires the genetic monitoring of wild populations, but traditional invasive sampling techniques can impact animal welfare. For cetaceans, a promising non-invasive approach is the collection of exhaled respiratory vapour, or blow, to generate individual genetic profiles. Here, we demonstrate the feasibility of generating whole genomes from the blow of humpback whales with data of sufficient quality for population genomics. A total of 58 blow samples from 26 Northeast Pacific humpback whales (Megaptera novaeangliae) were collected in Gitgaat First Nation territory using a commercially available drone. The high endogenous content at 84% on average allowed us to generate low-coverage nuclear genomes (mean 2.3x, range 0.2x-3.5x) and high coverage mitochondrial genomes (mean 94x, range 7.7x-151.3x) for inference of population structure, diversity and phylogenomics. The reliability of the blow-derived genomes was demonstrated by direct comparison between replicate blow samples, as well as paired tissue samples from a subset of individuals.

genomics↗

bioRxiv2024

The diffusion of cooperative and solo bubble net feeding in Canadian Pacific humpback whales

Cooperative foraging, a mutualistic resource acquisition behaviour observed across diverse taxa, can drive social network structure, as it typically involves high rates of interactions between individuals. Understanding the mechanisms and distribution of such behaviours is important to elucidate the drivers of social organisation. Bubble net feeding ( bubble netting) is a specialised foraging technique practised by certain humpback whale (Megaptera novaeangliae) populations globally. Over 20 years of study in the northern Canadian Pacific, we observed the diffusion of two morphs of this behaviour: social cooperative and independent, or solo, bubble netting. Network-based diffusion analyses - a tool developed to test for social learning - find strong evidence for the social learning of bubble netting when a static social network is used, even after accounting for individual-level traits such as site fidelity and sex (10.6 x103 to 35.4x103 times more support for social versus asocial learning; p < 0.0001). However, we could not completely exclude homophily due to the inherent sociality of this cooperative foraging behaviour. Nonetheless, it is clear that the rapid diffusion of bubble netting throughout this population has significant consequences for its social structure, which should be information considered by those planning the conservation of this threatened population.

animal behavior and cognition↗

bioRxiv2023

Optimizing CRE and PhiC31 mediated recombination in Aedes aegypti

Genetic manipulation of Aedes aegypti is key to developing a deeper understanding of this insects biology, vector-virus interactions and makes future genetic control strategies possible. Despite some advances, this process remains laborious and requires highly skilled researchers and specialist equipment. Here we present two improved methods for genetic manipulation in this species. Use of transgenic lines which express Cre recombinase allowed, by simple crossing schemes, germline or somatic recombination of transgenes, which could be utilized for numerous genetic manipulations. PhiC31 integrase based methods for site-specific integration of genetic elements was also improved, by developing a plasmid which expresses PhiC31 when injected into early embryos, eliminating the need to use costly and unstable mRNA as is the current standard.

bioengineering↗

bioRxiv2022

Swapped genetic code blocks viral infections and gene transfer

Removing cellular transfer RNAs (tRNAs), making their cognate codons unreadable, creates a genetic firewall that prevents viral replication and horizontal gene transfer. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus, including tRNAs, potentially rendering a genetic-code-based firewall ineffective. In this paper, we show that such horizontally transferred tRNA genes can enable viral replication in Escherichia coli cells despite the genome-wide lack of three codons and the previously essential cognate tRNAs and release factor 1. By repurposing viral tRNAs, we then develop recoded cells bearing an amino-acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino-acid-swapped genetic code renders cells completely resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. Finally, we also repurpose the third free codon to biocontain this virus-resistant host via dependence on an amino acid not found in nature.

synthetic biology↗

bioRxiv2020

Social survival: humpback whales (Megaptera novaeangliae) use social structure to partition ecological niches within proposed critical habitat

Animal culture and social bonds are relevant to wildlife conservation because they influence patterns of geography, behavior, and strategies of survival. Numerous examples of socially-driven habitat partitioning and ecological-niche specialization can be found among vertebrates, including toothed whales. But such social-ecological dynamics, described here as social niche partitioning, are not known among baleen whales, whose societies -- particularly on foraging grounds -- are largely perceived as unstructured and incidental to matters of habitat use and conservation. However, through 16 years of behavioral and photo-identification observations of humpback whales (Megaptera novaeangliae) feeding within a fjord system in British Columbia, Canada, we have documented long-term pair bonds (lasting up to 12 years) as well as a complex societal structure, which corresponds closely to persistent patterns in feeding strategy, long-term site fidelity (extended seasonal occupancy and annual rate of return up to 75%), specific geographic preferences within the fjord system, and other forms of habitat use. Randomization tests of network congruency and clustering algorithms were used to test for overlap in patterns of social structure and habitat use, which confirmed the occurrence of social niche partitioning on the feeding grounds of this baleen whale. In addition, we document the extensive practice of group bubble net feeding in Pacific Canada. This coordinated feeding behavior was found to strongly mediate the social structure and habitat use within this humpback whale society. Additionally, during our 2004 - 2019 study, we observed a shift in social network structure in 2010 - 2012, which corresponded with environmental and demographic shifts including a sudden decline in the populations calving rate. Our findings indicate that the social lives of humpback whales, and perhaps baleen whales generally, are more complex than previously supposed and should be a primary consideration in the assessment of potential impacts to important habitat.

animal behavior and cognition↗