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1.
BMC Genomics ; 25(1): 500, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38773374

ABSTRACT

BACKGROUND: The ricefield eel Monopterus albus undergoes a natural sex change from female to male during its life cycle, and previous studies have shown the potential mechanisms of this transition at the transcriptional and protein levels. However, the changes in protein levels have not been fully explored, especially in the intersexual stage. RESULTS: In the present study, the protein expression patterns in the gonadal tissues from five different periods, the ovary (OV), early intersexual stage gonad (IE), middle intersexual stage gonad (IM), late intersexual stage gonad (IL), and testis (TE), were determined by untargeted proteomics sequencing. A total of 5125 proteins and 394 differentially expressed proteins (DEPs) were detected in the gonadal tissues. Of the 394 DEPs, there were 136 between the OV and IE groups, 20 between the IM and IE groups, 179 between the IL and IM groups, and 59 between the TE and IL groups. Three candidate proteins, insulin-like growth factor 2 mRNA-binding protein 3 isoform X1 (Igf2bp3), triosephosphate isomerase (Tpi), and Cu-Zn superoxide dismutase isoform X1 [(Cu-Zn) Sod1], were validated by western blotting to verify the reliability of the data. Furthermore, metal metabolite-related proteins were enriched in the IL vs. IM groups and TE vs. IL groups, which had close relationships with sex change, including Cu2+-, Ca2+-, Zn2+- and Fe2+/Fe3+-related proteins. Analysis of the combined transcriptome data revealed consistent protein/mRNA expression trends for two metal metabolite-related proteins/genes [LOC109953912 and calcium Binding Protein 39 Like (cab39l)]. Notably, we detected significantly higher levels of Cu2+ during the sex change process, suggesting that Cu2+ is a male-related metal metabolite that may have an important function in male reproductive development. CONCLUSIONS: In summary, we analyzed the protein profiles of ricefield eel gonadal tissues in five sexual stages (OV, IE, IM, IL, and TE) and verified the plausibility of the data. After preforming the functional enrichment of metal metabolite-related DEPs, we detected the contents of the metal metabolites Zn2+, Cu2+, Ca2+, and Fe2+/Fe3+ at these five stages and screened for (Cu-Zn) Sod1 and Mmp-9 as possible key proteins in the sex reversal process.


Subject(s)
Metals , Animals , Male , Female , Metals/metabolism , Eels/metabolism , Eels/genetics , Proteomics , Fish Proteins/metabolism , Fish Proteins/genetics , Smegmamorpha/metabolism , Smegmamorpha/genetics , Hermaphroditic Organisms/metabolism , Hermaphroditic Organisms/genetics , Gene Expression Profiling , Testis/metabolism
2.
Environ Monit Assess ; 196(6): 496, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38693437

ABSTRACT

This study examined the presence of two heavy metals (Cd and Pb) in the sediments and Asian swamp eels (Monopterus albus) in the downstream area of Cisadane River. The average concentrations of Cd and Pb in the sediments from all sampling locations were 0.594 ± 0.230 mg/kg and 34.677 ± 24.406 mg/kg, respectively. These concentrations were above the natural background concentration and the recommended value of interim sediment quality guidelines (ISQG), suggesting an enrichment process and potential ecological risk of studied metals to the ecosystem of Cisadane River. The increase in contamination within this region may be attributed to point sources such as landfill areas, as well as the industrial and agricultural land activities in surrounding area, and experienced an increasing level leading towards the estuary of Cisadane River. Meanwhile, the average concentrations of Cd and Pb in the eels from all sampling locations were 0.775 ± 0.528 µg/g and 28.940 ± 12.921 µg/g, respectively. This study also discovered that gill tissues contained higher levels of Cd and Pb than the digestive organ and flesh of Asian swamp eels. These concentrations were higher than Indonesian and international standards, suggesting a potential human health risk and therefore the needs of limitations in the consumption of the eels. Based on the human health risk assessment, the eels from the downstream of Cisadane River are still considered safe to be consumed as long as they comply with the specified maximum consumption limits.


Subject(s)
Cadmium , Environmental Monitoring , Geologic Sediments , Lead , Rivers , Smegmamorpha , Water Pollutants, Chemical , Animals , Geologic Sediments/chemistry , Water Pollutants, Chemical/analysis , Water Pollutants, Chemical/metabolism , Rivers/chemistry , Indonesia , Cadmium/analysis , Lead/analysis , Lead/metabolism , Smegmamorpha/metabolism
3.
An Acad Bras Cienc ; 96(1): e20230238, 2024.
Article in English | MEDLINE | ID: mdl-38629657

ABSTRACT

Fish consumption is the main path of human exposure to Hg and may represent a risk to public health, even with low Hg concentrations in fish, if consumption rates are high. This study quantifies, for the first time, the Hg concentrations in nine most commercialized species in the São Luís (MA) fish market, where fish consumption is high, and estimates human exposure. Average Hg concentrations were highest in carnivorous species, yellow hake (Cynoscion acoupa) (0.296 mg kg-1), the Atlantic croaker (Micropogonias undulatus) (0.263 mg kg-1), whereas lowest concentrations were recorded in iliophagous Mullets (Mugil curema) (0.021 mg kg-1) and the Shorthead drum Larimus breviceps (0.025 mg kg-1). Significant correlations were observed between Hg concentrations and fish length in two species: the Coco-Sea catfish (Bagre bagre) and the Atlantic bumper (Chloroscombrus crysurus), but not in the other species, since they presented relatively uniform size of individuals and/or a small number of samples. Risk coefficients, despite the relatively low Hg concentrations, suggest that consumers should limit their consumption of Yellow hake and Atlantic croaker, as they can present some risk to human health (EDI > RfD and THQ > 1), depending on the frequency of their consumption and the consumer's body weight.


Subject(s)
Catfishes , Mercury , Smegmamorpha , Water Pollutants, Chemical , Animals , Humans , Mercury/analysis , Water Pollutants, Chemical/analysis , Fishes , Seafood/analysis , Environmental Monitoring , Food Contamination
4.
Am Nat ; 203(5): 590-603, 2024 May.
Article in English | MEDLINE | ID: mdl-38635363

ABSTRACT

AbstractThe mechanisms underlying the divergence of reproductive strategies between closely related species are still poorly understood. Additionally, it is unclear which selective factors drive the evolution of reproductive behavioral variation and how these traits coevolve, particularly during early divergence. To address these questions, we quantified behavioral differences in a recently diverged pair of Nova Scotian three-spined stickleback (Gasterosteus aculeatus) populations, which vary in parental care, with one population displaying paternal care and the other lacking this. We compared both populations, and a full reciprocal F1 hybrid cross, across four major reproductive stages: territoriality, nesting, courtship, and parenting. We identified significant divergence in a suite of heritable behaviors. Importantly, F1 hybrids exhibited a mix of behavioral patterns, some of which suggest sex linkage. This system offers fresh insights into the coevolutionary dynamics of reproductive behaviors during early divergence and offers support for the hypothesis that coevolutionary feedback between sexual selection and parental care can drive rapid evolution of reproductive strategies.


Subject(s)
Reproduction , Smegmamorpha , Animals , Territoriality , Smegmamorpha/genetics , Sexual Selection
5.
Proc Biol Sci ; 291(2020): 20232617, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38593844

ABSTRACT

When populations repeatedly adapt to similar environments they can evolve similar phenotypes based on shared genetic mechanisms (parallel evolution). The likelihood of parallel evolution is affected by demographic history, as it depends on the standing genetic variation of the source population. The three-spined stickleback (Gasterosteus aculeatus) repeatedly colonized and adapted to brackish and freshwater. Most parallel evolution studies in G. aculeatus were conducted at high latitudes, where freshwater populations maintain connectivity to the source marine populations. Here, we analysed southern and northern European marine and freshwater populations to test two hypotheses. First, that southern European freshwater populations (which currently lack connection to marine populations) lost genetic diversity due to bottlenecks and inbreeding compared to their northern counterparts. Second, that the degree of genetic parallelism is higher among northern than southern European freshwater populations, as the latter have been subjected to strong drift due to isolation. The results show that southern populations exhibit lower genetic diversity but a higher degree of genetic parallelism than northern populations. Hence, they confirm the hypothesis that southern populations have lost genetic diversity, but this loss probably happened after they had already adapted to freshwater conditions, explaining the high degree of genetic parallelism in the south.


Subject(s)
Fresh Water , Smegmamorpha , Animals , Smegmamorpha/genetics , Inbreeding , Genetic Variation
6.
Aquat Toxicol ; 271: 106910, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38631122

ABSTRACT

This study investigates the impact of varying concentrations of stevioside in the presence of lead (Pb) exposure on multiple aspects of thinlip mullet (Liza ramada) juveniles. Over 60 days, a total of 540 juvenile L. ramada with an initial weight of 3.5 ± 0.13 g were evenly distributed into six groups, each consisting of three replicates. The experimental diet consisted of varying levels of stevioside (150, 250, 350, and 450 mg/kg diet), with a consistent concentration of lead (Pb) set at 100 µg/kg diet. Stevioside demonstrated a positive influence on growth parameters, with the 450 mg/kg +Pb treatment showing the highest values. Biochemical parameters remained stable, but lead-exposed fish without stevioside displayed signs of potential liver damage and metabolic issues. Stevioside supplementation, especially at higher doses (≥250 mg/kg), reversed these negative effects, restoring biochemical markers to healthy control levels. Lead exposure significantly suppressed antioxidant enzyme activities, but co-administration of stevioside exhibited a dose-dependent protective effect, with 250, 350, and 450 mg/kg groups showing activities comparable to the healthy control. Lead-exposed fish without stevioside demonstrated attenuation of the immune response, but stevioside supplementation reversed these effects, particularly at ≥250 mg/kg. Stev (≥250 mg/kg) reduced IL-1ß and hepcidin expression, contrasting dose-dependent upregulation in lower dosages and lead-only group. Histological examinations of the intestine and liver supported these findings. In conclusion, stevioside, especially at 450 mg, positively impacted growth, biochemical parameters, antioxidant activity, immune response, and gene expression in L. ramada exposed to lead, suggesting its potential to mitigate lead toxicity in aquaculture. Additional research is warranted to investigate the long-term impacts of stevioside supplementation and its prospective implementation in aquaculture.


Subject(s)
Diterpenes, Kaurane , Glucosides , Lead , Water Pollutants, Chemical , Animals , Lead/toxicity , Water Pollutants, Chemical/toxicity , Smegmamorpha , Liver/drug effects , Liver/metabolism , Antioxidants/metabolism
7.
Fish Shellfish Immunol ; 149: 109580, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38663464

ABSTRACT

Wild organisms are regularly exposed to a wide range of parasites, requiring the management of an effective immune response while avoiding immunopathology. Currently, our knowledge of immunoparasitology primarily derives from controlled laboratory studies, neglecting the genetic and environmental diversity that contribute to immune phenotypes observed in wild populations. To gain insight into the immunologic variability in natural settings, we examined differences in immune gene expression of two Alaskan stickleback (Gasterosteus aculeatus) populations with varying susceptibility to infection by the cestode Schistocephalus solidus. Between these two populations, we found distinct immune gene expression patterns at the population level in response to infection with fish from the high-infection population displaying signs of parasite-driven immune manipulation. Further, we found significant differences in baseline immune gene profiles between the populations, with uninfected low-infection population fish showing signatures of inflammation compared to uninfected high-infection population fish. These results shed light on divergent responses of wild populations to the same parasite, providing valuable insights into host-parasite interactions in natural ecosystems.


Subject(s)
Cestoda , Cestode Infections , Fish Diseases , Smegmamorpha , Animals , Smegmamorpha/immunology , Smegmamorpha/genetics , Smegmamorpha/parasitology , Fish Diseases/immunology , Fish Diseases/parasitology , Cestode Infections/veterinary , Cestode Infections/immunology , Cestode Infections/parasitology , Cestoda/immunology , Cestoda/physiology , Host-Parasite Interactions/immunology , Alaska , Immunity, Innate/genetics
8.
Proc Biol Sci ; 291(2021): 20240337, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38628124

ABSTRACT

Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish, Gasterosteus doryssus. This lineage appeared and, over approximately 8000 generations, evolved significant reduction of 12 of 16 traits related to armour, swimming and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reproductively isolated, benthic-limnetic ecotypes of extant Gasterosteus aculeatus. Therefore, we infer that reproductive isolation was evolving. However, local extinction of G. doryssus lineages shows how young, isolated, speciating populations often disappear, supporting Darwin's explanation for missing evidence and revealing a mechanism behind morphological stasis. Extinction may also account for limited sustained divergence within the stickleback species complex and help reconcile speciation rate variation observed across time scales.


Subject(s)
Reproductive Isolation , Smegmamorpha , Animals , Fossils , Ecosystem , Smegmamorpha/anatomy & histology , Phenotype
9.
Methods Mol Biol ; 2783: 335-347, 2024.
Article in English | MEDLINE | ID: mdl-38478245

ABSTRACT

Bioenergetic and biosynthetic processes are key indicators regulating adipose-derived stromal/stem cell (ADSC) function, health, and differentiation. A common method used to metabolically profile cells is the Seahorse XF Analyzer. This live-cell assay can be used to define key metabolic pathways, including glycolysis and oxidative phosphorylation. Here, we share optimized protocols to characterize metabolism of ADSCs under basal conditions and provide insight into further assays defining metabolic changes and/or dependency during ADSC differentiation.


Subject(s)
Smegmamorpha , Animals , Smegmamorpha/metabolism , Adipocytes , Energy Metabolism , Oxidative Phosphorylation , Glycolysis , Adipose Tissue/metabolism
10.
PLoS One ; 19(3): e0298213, 2024.
Article in English | MEDLINE | ID: mdl-38478568

ABSTRACT

Freshwater salinization poses global challenges for aquatic organisms inhabiting urban streams, impacting their physiology and ecology. However, current salinization research predominantly focuses on mortality endpoints in limited model species, overlooking the sublethal effects on a broader spectrum of organisms and the exploration of adaptive mechanisms and pathways under natural field conditions. To address these gaps, we conducted high-throughput sequencing transcriptomic analysis on the gill tissue of the euryhaline fish Gasterosteus aculeatus, investigating its molecular response to salinity stress in the highly urbanized river Boye, Germany. We found that in stream sections with sublethal concentrations of chloride costly osmoregulatory systems were activated, evidenced by the differential expression of genes related to osmoregulation. Our enrichment analysis revealed differentially expressed genes (DEGs) related to transmembrane transport and regulation of transport and other osmoregulation pathways, which aligns with the crucial role of these pathways in maintaining biological homeostasis. Notably, we identified candidate genes involved in increased osmoregulatory activity under salinity stress, including those responsible for moving ions across membranes: ion channels, ion pumps, and ion transporters. Particularly, genes from the solute carrier family SLC, aquaporin AQP1, chloride channel CLC7, ATP-binding cassette transporter ABCE1, and ATPases member ATAD2 exhibited prominent differential expression. These findings provide insights into the potential molecular mechanisms underlying the adaptive response of euryhaline fish to salinity stress and have implications for their conservation and management in the face of freshwater salinization.


Subject(s)
Rivers , Smegmamorpha , Animals , Salinity , Gene Expression Profiling , Osmoregulation/genetics , Fresh Water , Fishes/genetics , Smegmamorpha/genetics , Gills/metabolism
11.
Mar Environ Res ; 196: 106438, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38479294

ABSTRACT

Monitoring microplastics (MPs) in the marine environment is an ongoing process, and our understanding of their impact on marine organisms is limited. The present study evaluates the effects of ingested MPs on the marine MP pollution bioindicator fish species Mullus surmuletus. The study follows a three-fold approach to assess the impact of MPs on marine organisms by investigating: 1) the ingestion of MPs, 2) the bioaccumulation of phthalate compounds as plastic additives, and 3) the evaluation of toxicological biochemical and cellular biomarkers. Striped red mullets were sampled in the marine protected area (MPA) of the National Marine Park of Zakynthos and coastal sites with high touristic pressure in Zakynthos Island in the Ionian Sea, Greece. Fewer ingested MPs and lower phthalate concentrations were found in fish inside the MPA compared to those sampled outside the marine park. However, no relationship was found between either phthalate concentrations or biomarker levels with the ingested MPs in the red striped mullets. Biomarker levels were influenced by season and site, but no effect could be attributed to the ingested MPs. The lack of association of biomarker responses and plasticizer bioaccumulation to MP ingestion can be explained by the low number of ingested MPs in the fish from Zakynthos coastal area as MP abundance ranged from 0.15 to 0.55 items per individual fish.


Subject(s)
Phthalic Acids , Smegmamorpha , Water Pollutants, Chemical , Animals , Microplastics , Plastics , Environmental Monitoring , Water Pollutants, Chemical/toxicity , Water Pollutants, Chemical/analysis , Fishes , Aquatic Organisms , Eating , Biomarkers
12.
Am Nat ; 203(2): 284-291, 2024 02.
Article in English | MEDLINE | ID: mdl-38306277

ABSTRACT

AbstractOrganismal divergence can be driven by differential resource use and adaptation to different trophic niches. Variation in diet is a major factor shaping the gut microbiota, which is crucial for many aspects of their hosts' biology. However, it remains largely unknown how host diet diversity affects the gut microbiota, and it could be hypothesized that trophic niche width is positively associated with gut microbiota diversity. To test this idea, we sequenced the 16S ribosomal RNA gene from intestinal tissue of 14 threespine stickleback populations from lakes of varying size on Vancouver Island, Canada, that have been shown to differ in trophic niche width. Using lake size as a proxy for trophic ecology, we found evidence for higher gut microbiota uniqueness among individuals from populations with broader trophic niches. While these results suggest that diet diversity might promote gut microbiota diversity, additional work investigating diet and gut microbiota variation of the same host organisms will be necessary. Yet our results motivate the question of how host population diversity (e.g., ecological, morphological, genetic) might interact with the gut microbiota during the adaptation to ecological niches.


Subject(s)
Gastrointestinal Microbiome , Smegmamorpha , Animals , Gastrointestinal Microbiome/genetics , Smegmamorpha/genetics , Lakes , Fishes/genetics , Diet , RNA, Ribosomal, 16S/genetics
13.
Ecol Lett ; 27(2): e14382, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38361474

ABSTRACT

Differentiation of foraging traits among predator populations may help explain observed variation in the structure of prey communities. However, few studies have investigated the phenotypic effects of predators on their prey in natural communities. Here, we use a comparative analysis of 78 Greenlandic lakes to examine how foraging trait variation among threespine stickleback populations can help explain variation in zooplankton community composition among lakes. We find that landscape-scale variation in zooplankton composition was jointly explained by lake properties, such as size and water chemistry, and the presence and absence of both stickleback and arctic char. Additional variation in zooplankton community structure can be explained by stickleback jaw protrusion, a trait with known utility for foraging on zooplankton, but only in lakes where stickleback co-occur with arctic char. Overall, our results illustrate how trait variation of predators, alongside other ecosystem properties, can influence the composition of prey communities in nature.


Subject(s)
Ecosystem , Smegmamorpha , Animals , Zooplankton , Fishes , Lakes , Predatory Behavior
14.
Proc Biol Sci ; 291(2016): 20232036, 2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38320611

ABSTRACT

Early life microbial colonizers shape and support the immature vertebrate immune system. Microbial colonization relies on the vertical route via parental provisioning and the horizontal route via environmental contribution. Vertical transmission is mostly a maternal trait making it hard to determine the source of microbial colonization in order to gain insight into the establishment of the microbial community during crucial development stages. The evolution of unique male pregnancy in pipefishes and seahorses enables the disentanglement of both horizontal and vertical transmission, but also facilitates the differentiation of maternal versus paternal provisioning ranging from egg development, to male pregnancy and early juvenile development. Using 16S rRNA amplicon sequencing and source-tracker analyses, we revealed how the distinct origins of transmission (maternal, paternal and horizontal) shaped the juvenile internal and external microbiome establishment in the broad-nosed pipefish Syngnathus typhle. Our data suggest that transovarial maternal microbial contribution influences the establishment of the juvenile gut microbiome whereas paternal provisioning mainly shapes the juvenile external microbiome. The identification of juvenile key microbes reveals crucial temporal shifts in microbial development and enhances our understanding of microbial transmission routes, colonization dynamics and their impact on lifestyle evolution.


Subject(s)
Gastrointestinal Microbiome , Microbiota , Smegmamorpha , Animals , Male , RNA, Ribosomal, 16S/genetics , Immune System , Smegmamorpha/genetics
15.
Front Cell Infect Microbiol ; 14: 1348973, 2024.
Article in English | MEDLINE | ID: mdl-38371296

ABSTRACT

Introduction: Aeromonas hydrophila and methicillin-resistant Staphylococcus aureus (MRSA) are potent bacterial pathogens posing major hazards to human health via consuming fish harboring these pathogens or by cross-contamination beyond the contaminated environment. The aim of this study was to determine risk variables associated with the presence of certain pathogenic bacteria from Mugil cephalus fish in retail markets in Egypt. The virulence genes of A. hydrophila and S. aureus were also studied. Furthermore, the antibiotic sensitivity and multidrug resistance of the microorganisms were evaluated. Methods: In a cross-sectional investigation, 370 samples were collected from mullet skin and muscle samples, washing water, fish handlers, knives, and chopping boards. Furthermore, fish handlers' public health implications were assessed via their response to a descriptive questionnaire. Results: S. aureus and Aeromonas species dominated the investigated samples with percentages of 26.76% and 30.81%, respectively. Furthermore, A. hydrophila and MRSA were the predominant recovered bacterial pathogens among washing water and knives (53.85% and 46.66%, respectively). The virulence markers aerA and hlyA were found in 90.7% and 46.5% of A. hydrophila isolates, respectively. Moreover, the virulence genes nuc and mec were prevalent in 80% and 60% of S. aureus isolates, respectively. Antimicrobial susceptibility results revealed that all A. hydrophila isolates were resistant to amoxicillin and all MRSA isolates were resistant to amoxicillin and ampicillin. Remarkably, multiple drug resistance (MDR) patterns were detected in high proportions in A. hydrophila (88.37%) and MRSA (100%) isolates. The prevalence of Aeromonas spp. and S. aureus had a positive significant correlation with the frequency of handwashing and use of sanitizer in cleaning of instruments. MRSA showed the highest significant prevalence rate in the oldest age category. Conclusion: The pathogenic bacteria recovered in this study were virulent and had a significant correlation with risk factors associated with improper fish handling. Furthermore, a high frequency of MDR was detected in these pathogenic bacteria, posing a significant risk to food safety and public health.


Subject(s)
Aeromonas , Methicillin-Resistant Staphylococcus aureus , Smegmamorpha , Staphylococcal Infections , Animals , Humans , Methicillin-Resistant Staphylococcus aureus/genetics , Staphylococcus aureus/genetics , Aeromonas hydrophila/genetics , Cross-Sectional Studies , Anti-Bacterial Agents/pharmacology , Fishes , Amoxicillin , Risk Factors , Water , Microbial Sensitivity Tests , Staphylococcal Infections/epidemiology , Staphylococcal Infections/veterinary , Staphylococcal Infections/microbiology
16.
Curr Biol ; 34(5): 1142-1147.e6, 2024 Mar 11.
Article in English | MEDLINE | ID: mdl-38350445

ABSTRACT

Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.


Subject(s)
Ecosystem , Smegmamorpha , Animals , Adaptation, Physiological/genetics , Smegmamorpha/genetics , Retrospective Studies , Lakes
17.
Reproduction ; 167(4)2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38377683

ABSTRACT

In brief: Seahorses exhibit male pregnancy and are thus valuable comparative models for the study of the physiology and evolution of pregnancy. This study shows that protein is transported from fathers to developing embryos during gestation, and provides new knowledge about paternal contributions to embryonic development. Abstract: Syngnathid embryos (seahorses, pipefishes and seadragons) develop on or in the male in a specialised brooding structure (brood pouch). Seahorse brood pouches supply nutrients, including lipids, to developing embryos (patrotrophy). We tested the hypothesis that proteins, vital for gene regulation and tissue growth during embryogenesis, are also transported from father to embryos, using the Australian pot-bellied seahorse, Hippocampus abdominalis. We used dry masses and total nitrogen content to estimate the total protein content of newly fertilised egg and neonate H. abdominalis. Neonates contained significantly greater protein mass than newly fertilised eggs. This result indicates that paternal protein transport to developing embryos occurs during H. abdominalis pregnancy. This study is the first to show paternal protein transport during pregnancy in seahorses, and furthers our understanding of paternal influence on embryonic development in male pregnant vertebrates.


Subject(s)
Smegmamorpha , Animals , Humans , Infant, Newborn , Male , Smegmamorpha/genetics , Australia , Embryonic Development , Fathers
18.
Mol Biol Evol ; 41(2)2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38366566

ABSTRACT

Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.


Subject(s)
Genetic Introgression , Smegmamorpha , Animals , Smegmamorpha/genetics , Genome , Genomics , Hybridization, Genetic
19.
Mol Biol Evol ; 41(2)2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38306314

ABSTRACT

Allele-specific gene expression evolves rapidly on heteromorphic sex chromosomes. Over time, the accumulation of mutations on the Y chromosome leads to widespread loss of gametolog expression, relative to the X chromosome. It remains unclear if expression evolution on degrading Y chromosomes is primarily driven by mutations that accumulate through processes of selective interference, or if positive selection can also favor the down-regulation of coding regions on the Y chromosome that contain deleterious mutations. Identifying the relative rates of cis-regulatory sequence evolution across Y chromosomes has been challenging due to the limited number of reference assemblies. The threespine stickleback (Gasterosteus aculeatus) Y chromosome is an excellent model to identify how regulatory mutations accumulate on Y chromosomes due to its intermediate state of divergence from the X chromosome. A large number of Y-linked gametologs still exist across 3 differently aged evolutionary strata to test these hypotheses. We found that putative enhancer regions on the Y chromosome exhibited elevated substitution rates and decreased polymorphism when compared to nonfunctional sites, like intergenic regions and synonymous sites. This suggests that many cis-regulatory regions are under positive selection on the Y chromosome. This divergence was correlated with X-biased gametolog expression, indicating the loss of expression from the Y chromosome may be favored by selection. Our findings provide evidence that Y-linked cis-regulatory regions exhibit signs of positive selection quickly after the suppression of recombination and allow comparisons with recent theoretical models that suggest the rapid divergence of regulatory regions may be favored to mask deleterious mutations on the Y chromosome.


Subject(s)
Evolution, Molecular , Smegmamorpha , Humans , Animals , Y Chromosome/genetics , Sex Chromosomes , Chromosomes, Human, Y , Chromosomes, Human, X , Smegmamorpha/genetics
20.
J Fish Biol ; 104(5): 1548-1565, 2024 May.
Article in English | MEDLINE | ID: mdl-38408838

ABSTRACT

Marine community science presents an important route to gather valuable scientific information while also influencing local management and policy, thus contributing to marine conservation efforts. Because seahorses are cryptic but charismatic species, they are good candidates for engaging diverse people to help overcome the many gaps in biological knowledge. We have synthesized information contributed to the community science project iSeahorse from October 2013 to April 2022 for 35 of 46 known seahorse species. We then compared the obtained results with information in existing IUCN Red List assessments, executed from 2014 to 2017, to explore the potential of iSeahorse in expanding seahorse knowledge. Our results show updated geographic ranges for 7 seahorse species, new habitats described for 24 species, observations outside the previously recorded depth range for 14 species, and new information on sex ratio for 15 species and on pregnancy seasonality for 11 species. As one example of the power of iSeahorse, contributed observations on Coleman's pygmy seahorse (Hippocampus colemani) indicated that its geographic range is thousands of square kilometers larger, its habitat more diverse, and its depth range shallower than previously known. It is clear that iSeahorse is expanding knowledge on seahorses to a level that will help improve IUCN Red List assessments. The power of community science for marine conservation in general needs to be fully explored.


Subject(s)
Conservation of Natural Resources , Ecosystem , Smegmamorpha , Animals , Female , Male , Sex Ratio , Endangered Species
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