An official website of the United States government
ABSTRACT ObjectiveApex-predator-initiated trophic cascades occur in many nearshore marine habitats that simultaneously serve as critical habitat and food sources for commercially and ecologically important species, including juvenile Pacific salmon Oncorhynchus spp. Yet the potential relationships among apex predators (e.g., sea otters Enhydra lutris), submerged aquatic vegetation, and juvenile salmonids are not well understood. In Southeast Alaska, we investigated (1) juvenile salmonid abundance in eelgrass Zostera marina meadows and understory kelp beds and (2) potential drivers of juvenile Chum Salmon Oncorhynchus keta and Pink Salmon O. gorbuscha abundance in eelgrass meadows. MethodsWe analyzed historic (1998–2007) beach seine surveys to compare juvenile salmonid abundance in nearshore habitats. We then employed the same survey (2017, 2019) in eelgrass to quantify juvenile salmonid abundance alongside the influence of sea otter density (number/km2), distance from anadromous stream (km), seasonality, sediment categorization, and aboveground eelgrass biomass (g/m2). ResultsWe found greater abundance of Chum Salmon in understory kelp compared with eelgrass, whereas Pink Salmon abundance was similar between habitats. In eelgrass, Chum Salmon abundance peaked in June and was positively associated with sea otter density. Pink Salmon abundance varied seasonally, peaking in May. We found increased Pink Salmon abundance with increasing sea otter density and distance from anadromous stream and decreased abundance with increased eelgrass biomass. ConclusionGrowth and survival while juvenile salmonids are out-migrating from streams and relying on nearshore vegetated habitats can determine if they recruit to fisheries as adults. Here, we highlight the use of multiple habitats, eelgrass and understory kelp, indicating that both should be explored as critical nursery habitat. We present evidence of indirect effects of sea otters influencing the abundance of juvenile salmonids, with potential further implications as sea otter populations expand. Apex predators, quality of vegetated habitats, and their structuring roles in the nearshore are critical for informing adaptive coastal fisheries management.
more »
« less
An EvoDevo Study of Salmonid Visual Opsin Dynamics and Photopigment Spectral Sensitivity
Salmonids are ideal models as many species follow a distinct developmental program from demersal eggs and a large yolk sac to hatching at an advanced developmental stage. Further, these economically important teleosts inhabit both marine- and freshwaters and experience diverse light environments during their life histories. At a genome level, salmonids have undergone a salmonid-specific fourth whole genome duplication event (Ss4R) compared to other teleosts that are already more genetically diverse compared to many non-teleost vertebrates. Thus, salmonids display phenotypically plastic visual systems that appear to be closely related to their anadromous migration patterns. This is most likely due to a complex interplay between their larger, more gene-rich genomes and broad spectrally enriched habitats; however, the molecular basis and functional consequences for such diversity is not fully understood. This study used advances in genome sequencing to identify the repertoire and genome organization of visual opsin genes (those primarily expressed in retinal photoreceptors) from six different salmonids [Atlantic salmon ( Salmo salar ), brown trout ( Salmo trutta ), Chinook salmon ( Oncorhynchus tshawytcha ), coho salmon ( Oncorhynchus kisutch ), rainbow trout ( Oncorhynchus mykiss ), and sockeye salmon ( Oncorhynchus nerka )] compared to the northern pike ( Esox lucius ), a closely related non-salmonid species. Results identified multiple orthologues for all five visual opsin classes, except for presence of a single short-wavelength-sensitive-2 opsin gene. Several visual opsin genes were not retained after the Ss4R duplication event, which is consistent with the concept of salmonid rediploidization. Developmentally, transcriptomic analyzes of Atlantic salmon revealed differential expression within each opsin class, with two of the long-wavelength-sensitive opsins not being expressed before first feeding. Also, early opsin expression in the retina was located centrally, expanding dorsally and ventrally as eye development progressed, with rod opsin being the dominant visual opsin post-hatching. Modeling by spectral tuning analysis and atomistic molecular simulation, predicted the greatest variation in the spectral peak of absorbance to be within the Rh2 class, with a ∼40 nm difference in λ max values between the four medium-wavelength-sensitive photopigments. Overall, it appears that opsin duplication and expression, and their respective spectral tuning profiles, evolved to maximize specialist color vision throughout an anadromous lifecycle, with some visual opsin genes being lost to tailor marine-based vision.
more »
« less
- Award ID(s):
- 1638567
- PAR ID:
- 10378285
- Date Published:
- Journal Name:
- Frontiers in Neuroanatomy
- Volume:
- 16
- ISSN:
- 1662-5129
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Salmonid fishes have emerged as a tractable model to study whole‐genome duplications (WGDs) as this group has undergone four rounds of WGDs. While most of the salmonid genome has returned to a diploid state, a significant proportion of genes are maintained as duplicates and are referred to as ohnologs. The fact that much of the modern salmonid gene repertoire is comprised of ohnologs, while other genes have returned to their singleton state creates complications for genetic studies by obscuring homology relationships. The difficulty this creates is particularly prominent in Pacific salmonids belonging to genusOncorhynchuswho are the focus of intense genetics‐based conservation and management efforts owing to the important ecological and cultural roles these fish play. To address this gap, we generated a homology guide for six species ofOncorhynchuswith available genomes and used this guide to describe patterns of ohnolog retention and resolution. Overall, we find that ohnologs comprise approximately half of each species modern gene repertoires, which are functionally enriched for genes involved in DNA binding, while the less numerous singleton genes are heavily enriched in dosage‐sensitive processes such as mitochondrial metabolism. Additionally, by reanalyzing published expression data from locally adapted strains ofO. mykiss, we show that numerous ohnologs exhibit adaptive expression profiles; however, ohnologs are not more likely to display adaptive signatures than either paralogs or singletons. Finally, we demonstrate the utility of our homology guide by investigating the evolutionary relationship among genes highlighted as playing a role in salmonid life‐history traits or gene editing targets.more » « less
-
Knowledge of crustacean vision is lacking compared to the more well-studied vertebrates and insects. While crustacean visual systems are typically conserved morphologically, the molecular components (i.e. opsins) remain understudied. This review aims to characterize opsin diversity across crustacean lineages for an integrated view of visual system evolution. Using publicly available data from 95 species, we identified opsin sequences and classified them by clade. Our analysis produced 485 putative visual opsins and 141 non-visual opsins. The visual opsins were separated into six clades: long wavelength sensitive (LWS), middle wavelength sensitive (MWS) 1 and 2, short wavelength or ultraviolet sensitive (SWS/UVS) and a clade of thecostracan opsins, with multiple LWS and MWS opsin copies observed. The SWS/UVS opsins were relatively conserved in most species. The crustacean classes Cephalocarida, Remipedia and Hexanauplia exhibited reduced visual opsin diversity compared to others, with the malacostracan decapods having the highest opsin diversity. Non-visual opsins were identified from all investigated classes except Cephalocarida. Additionally, a novel clade of non-visual crustacean-specific, R-type opsins (Rc) was discovered. This review aims to provide a framework for future research on crustacean vision, with an emphasis on the need for more work in spectral characterization and molecular analysis. This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.more » « less
-
ABSTRACT Warming associated with climate change is driving poleward shifts in the marine habitat of anadromous Pacific salmon (Oncorhynchusspp.). Yet the spawning locations for salmon to establish self‐sustaining populations and the consequences for the ecosystem if they should do so are unclear. Here, we explore the role of temperature‐dependent incubation survival and developmental phenology of coho salmon (Oncorhynchus kisutch) as a potential early life history barrier to establishment in an Arctic stream. We exposed embryos to temperatures previously recorded in the substrate of an Arctic groundwater spring‐fed spawning environment. Using a common garden experimental design, coho salmon embryos were exposed to treatments that thermally mimicked four spawning dates from August 1 to October 1 (AUG1, SEPT1, SEPT15, and OCT1). Spawning temperatures were 6°C at the warmest (AUG1) and 1.25°C at the coldest (OCT1). We observed low survival rates in SEPT1 (41%) and OCT1 (34%) and near complete mortality in the other treatments. While far below what is considered normal in benign hatchery‐like conditions, these rates suggest that temperatures experienced at these spawning dates are survivable. We detected differences in developmental rates across treatments; embryos developed 1.9 times faster in the warmest treatment (AUG1, 120 days) compared to the coldest (OCT1, 231 days). Differences in accumulated thermal units (ATUs) needed for hatching ranged from 392 ATUs in AUG1 to 270 ATUs in OCT1, revealing compensation in developmental requirements. Given these findings, the most thermally suitable spawning dates within our study are between September 15 and October 1, which facilitates hatching and projected nest emergence to occur in spring warming conditions (March–September). Broadly, our findings suggest that spawning sites within thermal tolerances that can support the survival and development of coho salmon exist in the North American Arctic. Whether the habitat is otherwise suitable for transitions through other life stages remains unknown.more » « less
-
The short-chain dehydrogenases/reductases (SDR) superfamily is involved in multiple physiological processes. In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases. Overall, the number of SDR genes in animals increased with whole genome duplication (WGD), suggesting the expansion of SDRs during evolution, especially in 3R-WGD and polyploidization of teleosts. Phylogenetic analysis indicated that vertebrates SDRs were clustered into five categories: classical, extended, undefined, atypical, and complex. Moreover, tandem duplication of hpgd-a, rdh8b and dhrs13 was observed in teleosts analyzed. Additionally, tandem duplications of dhrs11-a, dhrs7a, hsd11b1b, and cbr1-a were observed in all cichlids analyzed, and tandem duplication of rdh10-b was observed in tilapiines. Transcriptome analysis of adult fish revealed that 93 SDRs were expressed in more than one tissue and 5 in one tissue only. Transcriptome analysis of gonads from different developmental stages showed that expression of 17 SDRs were sexually dimorphic with 11 higher in ovary and 6 higher in testis. The sexually dimorphic expressions of these SDRs were confirmed by in situ hybridization (ISH) and qPCR, indicating their possible roles in steroidogenesis and gonadal differentiation. Taken together, the identification and the expression data obtained in this study contribute to a better understanding of SDR superfamily evolution and functions in teleosts.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/fnana.2022.945344
