Momtazi, F. | bioRxiv Science

bioRxiv2026

How will climate change affect global amphipod species distributions by the end of the century?

Concern about how climate change affects marine ecosystems is growing, despite international commitments to reduce CO2 emissions. Predicting amphipod species responses to ocean warming is critical due to their high abundance and key ecological role in marine ecosystems. We selected 35 widespread benthic amphipod species with at least 30 unique occurrence records after thinning from two or more biogeographical regions and classified them according to depth and feeding strategy. Following spatial thinning, 17 species retained sufficient occurrence records for Maximum Entropy (MaxEnt) modelling, of which 15 met the model evaluation criteria by having a Partial ROC value below 1 or a 5% omission rate exceeding 0.2. We projected species distributions under the low emission RCP 2.6 and high emission RCP 8.5 scenarios for 2050 and 2100. To compare species responses among feeding groups, we used linear mixed effects models with feeding type, scenario_time combination, and their interaction as fixed effects and species identity as a random effect. Species were also classified by depth, but statistical comparisons among depth groups were not performed because of limited species representation. Projected distributions showed substantial species-specific distribution shifts, including both gains and losses of suitable habitat and changes in areas of high species richness. Linear mixed effects models showed that potential future changes in suitable habitat area did not differ significantly among feeding groups, whereas centroid shifts were significantly influenced by the interaction between feeding type and scenario-time combinations. This indicates that trophic strategy influences the spatial response of amphipods to future climate change. These findings highlight that climate change may dramatically alter the functional composition of benthic communities and their ecological roles, beyond simple changes in species distributions. Incorporating trophic identity and functional roles into climate impact assessments will be essential for predicting ecosystem responses and informing conservation strategies that safeguard marine ecosystems functioning under future climate change. This approach will improve predictions of ecosystem responses and strengthen conservation and management strategies aimed at maintaining ecosystem functioning in a rapidly changing ocean.

ecology↗

bioRxiv2026

Genome-wide discovery of cis-regulatory elements in a large genome

Identifying non-coding regulatory elements in the genome poses a challenge in most organisms. Classical methods rely on trial and error to test the regulatory activities of DNA fragments using reporter constructs. In large eukaryotic genomes, where cis-regulatory elements can spread over long distances, separated by large stretches of non-functional DNA, this trial and error approach is particularly challenging. Here, we generate two types of resources that can be used to narrow the search for such cis-regulatory elements in the 3.6 Gbp genome of Parhyale hawaiensis (comparable in size to the human genome). First, we use bulk ATAC-seq to uncover genome-wide patterns of chromatin accessibility in embryonic and adult tissues of Parhyale (whole embryos and legs), and single-nucleus ATAC-seq to identify regions of open chromatin in diverse cell types recovered from adult legs, including epidermal, neuronal, muscle and blood cells. Second, by sequencing the genomes of three congeneric species of Parhyale hawaiensis - P. darvishi, P. aquilina and P. plumicornis - we identify islands of sequence conservation across the genome, corresponding to DNA elements that are functionally constrained during evolution. We present an approach by which low-coverage (10-15x) short-read genome sequencing, without genome assembly, is sufficient to provide reliable maps of sequence conservation. This approach cuts the cost and labour required to generate these maps, making the identification of cis-regulatory elements more widely accessible. We demonstrate the utility of these resources by identifying cis-regulatory elements that drive robust expression of fluorescent reporters ubiquitously and in specific cell types.

developmental biology↗