736 research outputs found

    Ecological and morphological correlates of visual acuity in birds

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    This is the author accepted manuscript. The final version is available on open access from the Company of Biologists via the DOI in this record Data Availability: All data, codes, phylogenetic trees, and other files necessary to reproduce the analyses in this paper have been uploaded to the Dryad data repository: https://doi.org/10.5061/dryad.bzkh189g3Birds use their visual systems for important tasks, such as foraging and predator detection, that require them to resolve an image. However, visual acuity (the ability to perceive spatial detail) varies by two orders of magnitude across birds. Prior studies indicate that eye size and aspects of a species' ecology may drive variation in acuity, but these studies have been restricted to small numbers of species. We used a literature review to gather data on acuity measured either behaviorally or anatomically for 94 species from 38 families. We then examined how acuity varies in relation to (1) eye size, (2) habitat spatial complexity, (3) habitat light level, (4) diet composition, (5) prey mobility, and (6) foraging mode. A phylogenetically-controlled model including all of the above factors as predictors indicated that eye size and foraging mode are significant predictors of acuity. Examining each ecological variable in turn revealed that acuity is higher in species whose diet comprises vertebrates or scavenged food and whose foraging modes require resolving prey from farther away. Additionally, species that live in spatially-complex, vegetative habitats have lower acuity than expected for their eye sizes. Together, our results suggest that the need to detect important objects from far away-such as predators for species that live in open habitats, and food items for species that forage on vertebrate and scavenged prey-has likely been a key driver of higher acuity in some species, helping to elucidate how visual capabilities may be adapted to an animal's visual needs.European Union Horizon 2020Royal Societ

    The skeletal completeness of the Palaeozoic chondrichthyan fossil record

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    Chondrichthyes (sharks, rays, ratfish and their extinct relatives) originated and diversified in the Palaeozoic but are rarely preserved as articulated or partly articulated remains because of their predominantly cartilaginous endoskeletons. Consequently, their evolutionary history is perceived to be documented predominantly by isolated teeth, scales and fin spines. Here, we aim to capture and analyse the quality of the Palaeozoic chondrichthyan fossil record by using a variation of the skeletal completeness metric, which calculates how complete the skeletons of individuals are compared to estimates of their original entirety. Notably, chondrichthyan completeness is significantly lower than any published vertebrate group: low throughout the Silurian and Permian but peaking in the Devonian and Carboniferous. Scores increase to a range similar to pelycosaurs and parareptiles only when taxa identified solely from isolated teeth, scales and spines are excluded. We argue that environmental influences probably played an important role in chondrichthyan completeness. Sea level significantly negatively correlates with chondrichthyan completeness records and resembles patterns already evident in records of ichthyosaurs, plesiosaurs and sauropodomorphs. Such observed variations in completeness highlight the impact of different sampling biases on the chondrichthyan fossil record and the need to acknowledge these when inferring patterns of chondrichthyan macroevolution

    The influence of transposable elements on animal colouration

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    This is the final version. Available on open access from Cell Press via the DOI in this recordTransposable elements (TEs) are mobile genetic sequences present within host genomes. TEs can contribute to the evolution of host traits, since transposition is mutagenic and TEs often contain host regulatory and protein coding sequences. We review cases where TEs influence animal colouration, reporting major patterns and outstanding questions. TE-induced colouration phenotypes typically arise via introduction of novel regulatory sequences and splice sites, affecting pigment cell development or pigment synthesis. We discuss if particular TE types may be more frequently involved in the evolution of colour variation in animals, given that examples involving long terminal repeat (LTR) elements appear to dominate. Currently, examples of TE-induced colouration phenotypes in animals mainly concern model and domesticated insect and mammal species. However, several influential recent examples, coupled with increases in genome sequencing, suggest cases reported from wild species will increase considerably.Biotechnology and Biological Sciences Research Council (BBSRC

    Immunohistochemistry of the gut-associated lymphoid tissue (GALT) in African bonytongue (Heterotis niloticus, Cuvier 1829)

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    Heterotis niloticus is a basal teleost, belonging to the Osteoglossidae family, which is widespread in many parts of Africa. The digestive tract of H. niloticus presents similar characteristics to those of higher vertebrates, exhibiting a gizzard-like stomach and lymphoid aggregates in the intestinal lamina propria. The adaptive immune system of teleost fish is linked with each of their mucosal body surfaces. In fish, the gut-associated lymphoid tissue (GALT) is generally a diffuse immune system that represents an important line of defense against those pathogens inhabiting the external environment that can enter through food. The GALT comprises intraepithelial lymphocytes, which reside in the epithelial layer, and lamina propria leukocytes, which consist of lymphocytes, macrophages, granulocytes, and dendritic-like cells. This study aims to characterize, for the first time, the leukocytes present in the GALT of H. niloticus, by confocal immuno- fluorescence techniques, using specific antibodies: toll-like receptor 2, major histocompatibility complex class II, S100 protein, serotonin, CD4, langerin, and inducible nitric oxide synthetase. Our results show massive aggregates of immune cells in the thickness of the submucosa, arranged in circumscribed oval-shaped structures that are morphologically similar to the isolated lymphoid follicles present in birds and mammals, thus expanding our knowledge about the intestinal immunity shown by this fish

    Genomics of cold adaptations in the Antarctic notothenioid fish radiation

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    Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes

    Unlocking the genome of perch - From genes to ecology and back again

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    Eurasian perch Perca fluviatilis has been a popular model species for decades in the fields of aquatic ecology, community dynamics, behaviour, physiology and ecotoxicology. Yet, despite extensive research, the progress of integrating genomic perspective into existing ecological knowledge in perch has been relatively modest. Meanwhile, the emergence of high-throughput sequencing technologies has completely changed the methods for genetic variation assessment and conducting biodiversity and evolutionary research. During the last 5 years, three genome assemblies of P. fluviatilis have been generated, allowing substantial advancement of our understanding of the interactions between ecological and evolutionary processes at the whole-genome level. We review the past progress, current status and potential future impact of the genomic resources and tools for ecological research in Eurasian perch focusing on the utility of recent whole-genome assemblies. Furthermore, we demonstrate the power of genome-wide approaches and newly developed tools and outline recent cases where genomics have contributed to new ecological and evolutionary knowledge. We explore how the availability of reference assembly enables the efficient application of various statistical tools, and how genomic approaches can provide novel insights into resource polymorphism, host-parasite interactions and to genetic and phenotypic changes associated with climate change and harvesting-induced evolution. In summary, we call for increased integration of genomic tools into ecological research for perch, as well as for other fish species, which is likely to yield novel insights into processes linking the adaptation and plasticity to ecosystem functioning and environmental change

    Molecular immune responses of lumpfish (Cyclopterus lumpus) to aeromonas salmonicida

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    Lumpfish (Cyclopterus lumpus) have been utilized to biocontrol sea-lice (e.g., Lepeophtheirus salmonis) infestations in Atlantic salmon (Salmo salar) farms in the North Atlantic region. Aeromonas salmonicida subsp. salmonicida is a Gram-negative facultative intracellular pathogen infecting several fish species, including lumpfish. Here, I established an A. salmonicida systemic infection model in lumpfish. Juvenile lumpfish were intraperitoneally (ip) injected with different doses of A. salmonicida strain J223. A. salmonicida median lethal dose (LD50) was calculated at 102 colony-forming units (CFU)/dose. Samples from blood, head kidney, spleen, and liver were collected at different time points to determine the infection kinetics. Triplicated RNA samples from the head kidney, spleen, and liver of non-infected and infected (104 CFU/dose) lumpfish at 3 and 10 days post-infection (dpi) were utilized for RNA sequencing (RNA-Seq). Analysis of RNA-Seq data suggested that A. salmonicida could induce lethal infection in lumpfish by septic-like shock, suppression of the adaptive immune system, impairment of the DNA repair system, and disruption of cytoskeleton structure. Thus, an effective vaccine for lumpfish against A. salmonicida is highly needed. Here, I evaluated the immune protective effect of A. salmonicida bacterins and outer membrane proteins (OMPs) expressing iron-regulated outer membrane proteins (IROMPs) in lumpfish. However, my results demonstrate that vaccines do not confer protection to lumpfish against A. salmonicida J223. Additionally, I observed that formalin-killed A. salmonicida J223 bacterins do not increase IgM titers in lumpfish serum. Instead, the bacterins downregulate genes encoding IgM, MHC-II, and CD4, which indicates immune suppression and vaccine’s inability to trigger humoral and cell-mediated immune responses. Furthermore, different post-transcriptional factors (e.g., microRNAs (miRNAs)) that significantly determine an organism’s disease state are not explored yet in lumpfish. Therefore, I characterized miRNA encoding genes in lumpfish from three developmental stages (adult, embryos, and larvae) in this study, providing the reference miRNAome for future functional studies. Altogether, 443 unique mature miRNAs were identified in lumpfish. Transcriptomics analysis suggested organ-specific and age-specific expression of miRNAs. This thesis contributes significantly to understanding lumpfish- A. salmonicida interactions and provides guidelines for future host-pathogen interaction and vaccine studies

    Mesopelagic fishes of the North-West African Upwelling from the Discovery Collections

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    Mesopelagic fish specimens from two stations in the NW African Upwelling were identified and catalogued to produce a Darwin Core-aligned dataset. A total of 9655 individual fishes were identified, with 9017 specimens identified at least to genus level and 3124 specimens identified to species level. This dataset comprises specimens collected from the 1990 RRS Discovery (III) Cruise D195 and was used to investigate depth-related trends in diversity and community composition alongside species-specific migratory behaviour. The finalised dataset was published on OBIS through the Deep-Sea node

    Chromosome-level genome assembly of Patagonian moray cod (Muraenolepis orangiensis) and immune deficiency of major histocompatibility complex (MHC) class II

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    The Patagonian moray cod, Muraenolepis orangiensis, belongs to the family Muraenolepididae and is the sole order of Gadiformes that inhabits the temperate and cold waters of the southern hemisphere. One of the features of the Gadiformes order is that they have a remarkably unique immune gene repertoire that influences innate and adaptive immunity, and they lack major histocompatibility complex (MHC) class II, invariant chains (CD74), and CD4 genes. In this study, a high-quality chromosome-level genome assembly was constructed, resulting in a final assembled genome of 893.75 Mb, with an N50 scaffold length of 30.07 Mb and the longest scaffold being 39.77 Mb. Twenty-five high-quality pseudochromosomes were assembled, and the complete BUSCO rate was 93.4%. A total of 34,553 genes were structurally annotated, and 27,691 genes were functionally annotated. Among the 10 primary genes involved in MHC class II, only two ERAP1 genes and one AIRE gene were identified through the genome study. Although no specific reason for the MHC class II deficiency has been identified, it has been shown that the toll-like receptors (TLRs), which are significant to the innate immune response, are significantly expanded in M. orangiensis. A total of 44 TLRs have been identified, with 32 TLR13 genes distributed evenly on six different pseudochromosomes. This study is the first to reveal the whole genome of a Muraenolepididae family and provides valuable insights into the potential rationale for the MHC class II deficiency in a Gadiformes fish species
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