Arkhipkin, A. | Search bioRxiv

bioRxiv2025

A non-invasive method to genotype cephalopod sex by quantitative PCR

Coleoid cephalopods (cuttlefish, octopus, and squid) are emerging model organisms in neuroscience, development, and evolutionary biology, and are of major economic importance in global fisheries. However, they are notoriously difficult and expensive to culture. The ability to determine sex early in development would enable more efficient and sustainable population management in both laboratory and wild settings. Here, we present a non-invasive method to genotype the sex of dwarf cuttlefish (Ascarosepion bandense) as young as three hours post-hatching using a skin swab and quantitative PCR assay, which detects a two-fold dosage difference between ZZ and Z0 sex chromosomes of males and females, respectively. Furthermore, we designed and validated primers for four additional cephalopod research species with assembled genomes (Octopus bimaculoides, Sepia officinalis, Euprymna berryi, Doryteuthis pealeii), and for a wild-caught species of economic value (Illex illecebrosus) using low-coverage whole genome sequencing data. This method enables accurate sex determination from hatchlings to adults across cephalopods, independent of genome quality or availability. HighlightsO_LIThe Z sex chromosome was identified in multiple cuttlefish, squid, and octopus species. C_LIO_LIA sensitive quantitative PCR assay can genotype ZZ/Z0 sex in each species. C_LIO_LILow-coverage short-read sequencing data is sufficient to design effective primers. C_LIO_LIqPCR on non-invasive skin swabs enables genotyping of living animals. C_LI

genetics↗

bioRxiv2020

Are we ready to track climate-driven shifts in marine species across international boundaries? - A global survey of scientific bottom trawl data

Marine biota is redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of data availability, and mismatch between data and real species distributions. To assess the extent of this challenge, we review the global status and accessibility of ongoing scientific bottom trawl surveys. In total, we gathered metadata for 283,925 samples from 95 surveys conducted regularly from 2001 to 2019. 59% of the metadata collected are not publicly available, highlighting that the availability of data is the most important challenge to assess species redistributions under global climate change. We further found that single surveys do not cover the full range of the main commercial demersal fish species and that an average of 18 surveys is needed to cover at least 50% of species ranges, demonstrating the importance of combining multiple surveys to evaluate species range shifts. We assess the potential for combining surveys to track transboundary species redistributions and show that differences in sampling schemes and inconsistency in sampling can be overcome with vector autoregressive spatio-temporal modeling to follow species density redistributions. In light of our global assessment, we establish a framework for improving the management and conservation of transboundary and migrating marine demersal species. We provide directions to improve data availability and encourage countries to share survey data, to assess species vulnerabilities, and to support management adaptation in a time of climate-driven ocean changes.

ecology↗