Biology subjects

Cain, K. E.

Publications and source records attributed to Cain, K. E..

3 recordsLinked to original sources

bioRxiv2025

Threatened bat species reduce their activity in presence of traffic noise playback, and may shout louder

Anthropogenic sound is a prevalent pollutant with broad effects on wildlife. As human populations grow, exposure of natural environments to anthropogenic noise will increase. Automobile traffic is a notably pervasive source of noise pollution; transportation networks often cross otherwise relatively undisturbed habitats and the sound they produce is typically chronic and of high intensity. How this noise interferes with the production and reception of animal acoustic signals for communication and navigation remains largely unknown. In particular, bats (order Chiroptera) have received limited attention in anthropogenic noise studies, despite being the second most diverse mammalian group and relying strongly on acoustic signals. We used a phantom road paradigm to experimentally isolate and assess the effect of traffic sound playback on the behaviour of the two extant bat species in Aotearoa New Zealand. To begin to understand how bats might behaviourally respond to a noisy environment, we also investigated whether bats call sequence and structure differed with and without sound playback. We found an approximate 50% reduction in the mean number of sequences per night of both bat species during sound playback, suggesting bats avoid noisy areas. We also found that calls from the bats that were present were emitted at higher frequencies and increased intensities (loudness) during playback. As avoidance of areas reduces the amount of quality habitat accessible and call modulation can impose metabolic costs, chronic noise may impose fitness costs on declining populations of native bats. With increasing areas of natural habitat exposed to anthropogenic noise, untangling the effects of high sound levels is crucial for conservation of bats and the ecosystem services they provide.

ecology↗

bioRxiv2025

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

Bird genomes are among the most stable in terms of synteny and gene content across vertebrates. However, germline-restricted chromosomes (GRCs) represent a striking exception where programmed DNA elimination confines large-scale genomic changes to the germline. GRCs are known to occur in songbirds (oscines), but have been studied only in a few species of Passerides such as the zebra finch, the key model for passerine genomics. Their presence and evolutionary dynamics in most major passerine lineages remain largely unexplored, with suboscines entirely unexamined by cytogenetic or genomic methods. Here, we present the most comprehensive comparative analysis of GRCs to date, spanning 44 million years of passerine evolution. By generating the first germline reference genomes of an oscine and a suboscine, 22 novel germline draft genomes spanning nearly all major passerine lineages and a germline draft genome of a parrot outgroup, we show that the GRC is likely present in 6,700 passerine species. Our results reveal that the GRC evolves rapidly and distinctly from the standard A chromosomes (autosomes and sex chromosomes), yet retains functionally important, selectively maintained genes. We observed gene and repeat turnover occuring orders of magnitude faster than on the A chromosomes. Some GRC genes, such as cpeb1 and pim1, are widespread from an ancient duplication. In contrast, other GRC genes, like mfsd2b and bmp15, have been independently duplicated onto the GRC multiple times, suggesting adaptive constraints. The discovery of zglp1 on the zebra finch GRC, initially copied from chromosome 30 and subsequently lost from it, indicates functional replacement, where the GRC permits gene loss from the standard genome. As the GRC harbors the only zglp1 copy in most of the [~]4000 Passerides species, GRC loss would compromise essential germline functions. Our findings establish the GRC as a genomic innovator driving rapid germline evolution. This fact highlights its evolutionary significance for passerine diversification and suggests that programmed DNA elimination may be an overlooked yet phylogenetically widespread mechanism in many understudied animal lineages.

genomics↗

bioRxiv2022

Host Phylogeny Shapes Viral Transmission Networks in an Island Ecosystem

Viral transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator-prey relationships, may govern cross-species virus transmission and zoonotic risk, although their relative impact is unknown. By characterising the virome of a relatively isolated island ecological community linked through a food web we show that phylogenetic barriers result in distantly related host species sharing fewer viruses. Host ecology had a much smaller influence on overall virome composition. Network analysis revealed that hosts with a high diversity of viruses were more likely to gain new viruses, and that generalist viruses were more likely to infect new hosts. Such a highly connected ecological community heightens the risk of disease emergence, particularly among closely related species. One-Sentence SummarySequencing of an entire island virome reveals that closely related hosts have highly connected virus communities, increasing emergence risk.

microbiology↗