Suitable habitat shifts and ecological niche overlay assessments among benthic Oplegnathus species in response to climate change.

Climate change has had a significant impact on many marine organisms. To investigate the effects of environmental changes on deep-water benthic fishes, we selected the genus Oplegnathus and applied species distribution modeling and ecological niche modeling. From the last glacial maximum to the present, the three Oplegnathus species (O. conwayi, O. robinsoni, and O. peaolopesi) distributed in the Cape of Good Hope region of southern Africa experienced fitness zone fluctuations of 39.9%, 13%, and 5.7%, respectively. In contrast, O. fasciatus and O. punctatus, which were primarily distributed in the western Pacific Ocean, had fitness zone fluctuations of -6.5% and 11.7%, respectively. Neither the O. insignis nor the O. woodward varied by more than 5% over the period. Under future environmental conditions, the range of variation in fitness zones for the three southern African Oplegnathus species was expected to be between -30.8% and -26.5%, while the range of variation in fitness zones for the two western Pacific stonefish species was expected to remain below 13%. In addition, the range of variation in the fitness zones of the O. insignis was projected to be between -2.3% and 7.1%, and the range of variation in the fitness zones of the O. woodward is projected to be between -5.7% and -2%. The results indicated that O. fasciatus and O. punctatus had a wide distribution and high expansion potential, while Oplegnathus species might have originated in western Pacific waters. Our results showed that benthic fishes were highly adaptable to extreme environments, such as the last glacial maximum. The high ecological niche overlap between Oplegnathus species in the same region suggested that they competed with each other. Future research could explore the impacts of environmental change on marine organisms and make conservation and management recommendations.

Prediction of suitable habitat shifts and assessment of ecological niche overlaps for three Tridentiger species with intertidal and subtidal characteristics under future climate changes.

To show how dramatic global climate change affects marine ecosystem species in different habitats. We used a joint species distribution model (SDM) and an ecological niche model (ENM) to investigate the suitable habitat shifts and ecological niche overlaps of the Tridentiger fishes. In the present study, the SDM results showed that 5 hotspots were identified for T. trigonocephalus and T. barbatus, and 4 hotspots for T. bifasciatus. The study on center-of-mass transfer revealed notable reductions in the habitual range of the three Tridentiger species with future climate change and no significant bipolar shifts in the center of mass. The ENM results indicated that T. trigonocephalus and T. barbatus exhibited the greatest ecological niche overlap with Schoener's D (D) and Hellinger-based I (I) values of 0.4719 and 0.7690, respectively. Both SDM and ENM results have suggested that T. trigonocephalus occupied a wider distribution and greater adaptability to future climate change. This study sought to measure the variations in the effects of global climate change on marine species in different habitats. Our study first found that intertidal species with specific life histories may be more resilient to environmental change.

Chromosome-level genome assembly of the silver pomfret Pampus argenteus.

Pampus argenteus (Euphrasen, 1788) is one of the major fishery species in coastal China. Pampus argenteus has a highly specialized morphology, and its declining fishery resources have encouraged massive research efforts on its aquacultural biology. In this study, we reported the first high-quality chromosome-level genome of P. argenteus obtained by integrating Illumina, PacBio HiFi, and Hi-C sequencing techniques. The final size of the genome was 518.06 Mb, with contig and scaffold N50 values of 20.47 and 22.86 Mb, respectively. The sequences were anchored and oriented onto 24 pseudochromosomes based on Hi-C data corresponding to the 24-chromatid karyotype of P. argenteus. A colinear relationship was observed between the P. argenteus genome and that of a closely related species (Scomber japonicus). A total of 24,696 protein-coding genes were identified from the genome, 98.9% of which were complete BUSCOs. This report represents the first case of high-quality chromosome-level genome assembly for P. argenteus and can provide valuable information for future evolutionary, conservation, and aquacultural research.

Chromosome-Level Genome Reveals the Origin of Neo-Y Chromosome in the Male Barred Knifejaw Oplegnathus fasciatus.

The barred knifejaw, Oplegnathus fasciatus, is characterized by an X1X2Y system with a neo-Y chromosome for males. Here, a chromosome-level genome was assembled to investigate the origin of neo-Y chromosome to the male O. fasciatus. Twenty-three chromosomes corresponding to the male karyotypes were scaffolded to 762-Mb genome with a contig N50 length of 2.18 Mb. A large neo-Y chromosome (Ch9) in the male O. fasciatus genome was also assembled and exhibited high identity to those of the female chromosomes Ch8 and Ch10. Chromosome rearrangements events were detected in the neo-chromosome Ch9. Our results suggested that a centric fusion of acrocentric chromosomes Ch8 and Ch10 should be responsible for the formation of the X1X2Y system. The high-quality genome will not only provide a solid foundation for further sex-determining mechanism research in the X1X2Y system but also facilitate the artificial breeding aiming to improve the yield and disease resistance for Oplegnathus.

Population dynamics of an invasive bird parasite, Philornis downsi (Diptera: Muscidae), in the Galapagos Islands.

The invasive parasitic fly, Philornis downsi (Muscidae), is one of the greatest threats to the avifauna of the Galapagos Islands. The larvae of this fly feed on the blood and tissues of developing nestlings of at least 18 endemic and native birds. The aim of the current study was to investigate biotic and abiotic factors that may influence the population dynamics of this invasive parasite. To study the influence of vegetation zone and related climatic factors on fly numbers, a bi-weekly monitoring program using papaya-baited traps was carried out at a dry, lowland site and at a humid, highland site on Santa Cruz Island between 2012-2014. Female flies, a large proportion of which were inseminated and gravid, were collected throughout the year at both sites, indicating females were active during and between the bird breeding seasons. This is the first evidence that female flies are able to persist even when hosts are scarce. On the other hand, catch rates of male flies declined between bird breeding seasons. Overall, catch rates of P. downsi were higher in the drier, lowland habitat, which may be a consequence of host or resource availability. Time was a stronger predictor of adult fly numbers than climate, further suggesting that P. downsi does not appear to be limited by its environment, but rather by host availability. Seasonal catch rates suggested that populations in both habitats were continuous and multivoltine. Numbers of adult female flies appeared to be regulated chiefly by simple direct density dependence, and may be governed by availability of bird nests with nestlings. Nevertheless, confounding factors such as the existence of reservoir hosts that perpetuate fly populations and changes in behavior of P. downsi may increase the vulnerability of bird hosts that are already IUCN red-listed or in decline.

A novel host-adapted strain of Salmonella Typhimurium causes renal disease in olive ridley turtles (Lepidochelys olivacea) in the Pacific.

Salmonella spp. are frequently shed by wildlife including turtles, but S. enterica subsp. enterica serovar Typhimurium or lesions associated with Salmonella are rare in turtles. Between 1996 and 2016, we necropsied 127 apparently healthy pelagic olive ridley turtles (Lepidochelys olivacea) that died from drowning bycatch in fisheries and 44 live or freshly dead stranded turtles from the west coast of North and Central America and Hawaii. Seven percent (9/127) of pelagic and 47% (21/44) of stranded turtles had renal granulomas associated with S. Typhimurium. Stranded animals were 12 times more likely than pelagic animals to have Salmonella-induced nephritis suggesting that Salmonella may have been a contributing cause of stranding. S. Typhimurium was the only Salmonella serovar detected in L. olivacea, and phylogenetic analysis from whole genome sequencing showed that the isolates from L. olivacea formed a single clade distinct from other S. Typhimurium. Molecular clock analysis revealed that this novel clade may have originated as recently as a few decades ago. The phylogenetic lineage leading to this group is enriched for non-synonymous changes within the genomic area of Salmonella pathogenicity island 1 suggesting that these genes are important for host adaptation.

Invasive parasites, habitat change and heavy rainfall reduce breeding success in Darwin's finches.

Invasive alien parasites and pathogens are a growing threat to biodiversity worldwide, which can contribute to the extinction of endemic species. On the Galápagos Islands, the invasive parasitic fly Philornis downsi poses a major threat to the endemic avifauna. Here, we investigated the influence of this parasite on the breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea) and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island in 2010 and 2012. While the population of the small tree finch appeared to be stable, the warbler finch has experienced a dramatic decline in population size on Santa Cruz Island since 1997. We aimed to identify whether warbler finches are particularly vulnerable during different stages of the breeding cycle. Contrary to our prediction, breeding success was lower in the small tree finch than in the warbler finch. In both species P. downsi had a strong negative impact on breeding success and our data suggest that heavy rain events also lowered the fledging success. On the one hand parents might be less efficient in compensating their chicks' energy loss due to parasitism as they might be less efficient in foraging on days of heavy rain. On the other hand, intense rainfalls might lead to increased humidity and more rapid cooling of the nests. In the case of the warbler finch we found that the control of invasive plant species with herbicides had a significant additive negative impact on the breeding success. It is very likely that the availability of insects (i.e. food abundance)is lower in such controlled areas, as herbicide usage led to the removal of the entire understory. Predation seems to be a minor factor in brood loss.