| 1. |
- Enault, Sébastien, et al.
(författare)
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Molecular footprinting of skeletal tissues in the catshark Scyliorhinus canicula and the clawed frog Xenopus tropicalis identifies conserved and derived features of vertebrate calcification.
- 2015
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the evolutionary emergence and subsequent diversification of the vertebrate skeleton requires a comprehensive view of the diverse skeletal cell types found in distinct developmental contexts, tissues, and species. To date, our knowledge of the molecular nature of the shark calcified extracellular matrix, and its relationships with osteichthyan skeletal tissues, remain scarce. Here, based on specific combinations of expression patterns of the Col1a1, Col1a2, and Col2a1 fibrillar collagen genes, we compare the molecular footprint of endoskeletal elements from the chondrichthyan Scyliorhinus canicula and the tetrapod Xenopus tropicalis. We find that, depending on the anatomical location, Scyliorhinus skeletal calcification is associated to cell types expressing different subsets of fibrillar collagen genes, such as high levels of Col1a1 and Col1a2 in the neural arches, high levels of Col2a1 in the tesserae, or associated to a drastic Col2a1 downregulation in the centrum. We detect low Col2a1 levels in Xenopus osteoblasts, thereby revealing that the osteoblastic expression of this gene was significantly reduced in the tetrapod lineage. Finally, we uncover a striking parallel, from a molecular and histological perspective, between the vertebral cartilage calcification of both species and discuss the evolutionary origin of endochondral ossification.
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| 2. |
- Infantes, Eduardo, et al.
(författare)
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An automated work-flow for pinniped surveys: A new tool for monitoring population dynamics
- 2022
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Detecting changes in population trends depends on the accuracy of estimated mean population growth rates and thus the quality of input data. However, monitoring wildlife populations poses economic and logistic challenges especially in complex and remote habitats. Declines in wildlife populations can remain undetected for years unless effective monitoring techniques are developed, guiding appropriate management actions. We developed an automated survey workflow using unmanned aerial vehicles (drones) to quantify the number and size of individual animals, using the well-studied Scandinavian harbour seal (Phoca vitulina) as a model species. We compared ground-based counts using telescopes with manual flights, using a zoom photo/video, and pre-programmed flights producing orthomosaic photo maps. We used machine learning to identify and count both pups and older seals and we present a new method for measuring body size automatically. We evaluate the population’s reproductive success using drone data, historical counts and predictions from a Leslie matrix population model. The most accurate and time-efficient results were achieved by performing pre-programmed flights where individual seals are identified by machine learning and their body sizes are measured automatically. The accuracy of the machine learning detector was 95–97% and the classification error was 4.6 ± 2.9 for pups and 3.1 ± 2.1 for older seals during good light conditions. There was a clear distinction between the body sizes of pups and older seals during breeding time. We estimated 320 pups in the breeding season 2021 with the drone, which is well beyond the expected number, based on historical data on pup production. The new high quality data from the drone survey confirms earlier indications of a deteriorating reproductive rate in this important harbour seal colony. We show that aerial drones and machine learning are powerful tools for monitoring wildlife in inaccessible areas which can be used to assess annual recruitment and seasonal variations in body condition.
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| 3. |
- Joffard, Nina, et al.
(författare)
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Digest : The role of postzygotic isolation in Mimulus speciation
- 2021
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Ingår i: Evolution: international journal of organic evolution. - : Wiley. - 1558-5646 .- 0014-3820. ; 75:3, s. 756-758
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Tidskriftsartikel (refereegranskat)abstract
- Recently diverged species often show incomplete reproductive isolation and subsequently experience hybridization and introgression. The plant genus Mimulus includes many such examples of closely related taxa that prove useful for studying incipient speciation. However, Sandstedt et al. show that in contrast to other Mimulus species, species of the M. tilingii complex are characterized by strong postzygotic isolation mediated by multiple barriers. This finding highlights the diverse speciation histories of related plant groups.
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| 4. |
- Sáez-Espinosa, Paula, et al.
(författare)
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Morphological and ultrastructural alterations of zebrafish (Danio rerio) spermatozoa after motility activation
- 2022
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Ingår i: Theriogenology. - : Elsevier BV. - 0093-691X. ; 188, s. 108-115
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Tidskriftsartikel (refereegranskat)abstract
- Spermatozoa motility in freshwater and marine fish is mainly controlled by the difference in osmotic pressure. Specifically, zebrafish (Danio rerio) spermatozoa undergo hypoosmotic shock due to the decrease in extracellular potassium, which leads to membrane hyperpolarization and activation of flagellar motility. Previous studies have concluded that motility activation has a negative effect on the spermatozoa structure. However, no evidence exists about ultrastructural changes in zebrafish spermatozoa after motility activation. In this study, spermatozoa samples were obtained from ten adult zebrafish individuals before and 60 s after motility activation and analyzed using Scanning and Transmission Electron Microscopy. Results showed dramatic morphological and ultrastructural alterations of the zebrafish spermatozoa after activation. In particular, the spermatozoa head underwent severe morphological distortion, including swelling of the nucleus, the bursting of the plasma membrane, and the alteration of the genetic material. Midpieces were also affected after activation since rupture of the cell membrane and lysis of mitochondria occurred. Furthermore, after the hypoosmotic shock, most spermatozoa showed a coiled flagellum and a disaggregated plasma membrane. Overall, our findings show that the activation of motility leads to substantial zebrafish spermatozoa morphological and ultrastructural changes, which could modify their physiology and decrease the fertilizing potential.
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| 5. |
- Silva, Willian T.A.F.
(författare)
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Digest : A synergistic approach explains the evolutionary connection between brain size and longevity*
- 2020
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 74:12, s. 2743-2745
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Tidskriftsartikel (refereegranskat)abstract
- The cognitive buffer hypothesis poses that brain size evolves to buffer individuals from environmental changes, increasing survival. Jiménez-Ortega et al. (2020) explored this hypothesis using a phylogenetic path analysis and showed that there is a direct causal link between brain size and longevity in birds, even when allometric effects are taken into account. Furthermore, a synergistic model was better supported than models that included independent effects of brain size and body size.
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| 6. |
- Silva, Willian T. A. F., 1987-, et al.
(författare)
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Evolution of plasticity in production and transgenerational inheritance of small RNAs under dynamic environmental conditions
- 2021
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Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 17:5
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Tidskriftsartikel (refereegranskat)abstract
- In a changing environment, small RNAs (sRNAs) play an important role in the post-transcriptional regulation of gene expression and can vary in abundance depending on the conditions experienced by an individual (phenotypic plasticity) and its parents (non-genetic inheritance). Many sRNAs are unusual in that they can be produced in two ways, either using genomic DNA as the template (primary sRNAs) or existing sRNAs as the template (secondary sRNAs). Thus, organisms can evolve rapid plastic responses to their current environment by adjusting the amplification rate of sRNA templates. sRNA levels can also be transmitted transgenerationally by the direct transfer of either sRNAs or the proteins involved in amplification. Theory is needed to describe the selective forces acting on sRNA levels, accounting for the dual nature of sRNAs as regulatory elements and templates for amplification and for the potential to transmit sRNAs and their amplification agents to offspring. Here, we develop a model to study the dynamics of sRNA production and inheritance in a fluctuating environment. We tested the selective advantage of mutants capable of sRNA-mediated phenotypic plasticity within resident populations with fixed levels of sRNA transcription. Even when the resident was allowed to evolve an optimal constant rate of sRNA production, plastic amplification rates capable of responding to environmental conditions were favored. Mechanisms allowing sRNA transcripts or amplification agents to be inherited were favored primarily when parents and offspring face similar environments and when selection acts before the optimal level of sRNA can be reached within the organism. Our study provides a clear set of testable predictions for the evolution of sRNA-related mechanisms of phenotypic plasticity and transgenerational inheritance.Author summarySmall RNAs (sRNA) are produced by a wide range of organisms, from bacteria to plants and animals. These molecules are involved in the response to environmental stress (e.g., temperature, pathogens) and can be transmitted across generations. We developed a model to explore the dynamics of sRNA production (phenotypic plasticity) and inheritance in a fluctuating environment. We tested whether different sRNA mutants can invade a population where individuals produce sRNA at a constant optimal transcription rate. In our simulations, plastic amplification rates capable of responding to environmental conditions were favored and the transmission of sRNA transcripts or amplification agents across generations was particularly advantageous when parents and offspring faced similar environments. sRNA amplification alone is not favored except when optimal sRNA levels are not reached within a generation. Our model provides novel predictions for the molecular mechanisms of sRNA production and guidance for future empirical studies on mutations that impair the mechanisms of sRNA production and their fitness consequences.
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| 7. |
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| 8. |
- Silva, Willian T. A. F.
(författare)
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Methylation dynamics during the maternal-to-zygotic genome transition in dioecious species
- 2018
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 13:7
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Tidskriftsartikel (refereegranskat)abstract
- The starting point of a new generation in sexually reproducing species is fertilization. In many species, fertilization is followed by cell divisions controlled primarily by maternal transcripts, with little to no zygotic transcription. The activation of the zygotic genome (ZGA) is part of a process called maternal-to-zygotic transition (MZT), during which transcripts from the zygotic genome take control of development, setting the conditions for cellular specialization. While we know that epigenetic processes (e.g. methylation) are involved in the MZT, their roles and interplay in the transition are largely unknown. I developed a model and used simulations to elucidate the interaction between possible epigenetic processes, namely methylation processes, involved in the MZT. The model focuses on the dynamics of global methylation levels and how these interact with factors such as a parental repressor and the nucleocytoplasmic ratio to trigger the ZGA, followed by development from fertilization to adulthood. In addition, I included transgenerational effects transmitted to the zygote from both parents through their gametes to show that these may set the stage for plastic developmental processes. I demonstrate that the rates of maintenance methylation and demethylation, which are important for the achievement of the final methylation levels of an individual, exhibit a certain level of flexibility in terms of parameter values. I find that high final methylation levels require more restricted combinations of parameter values. The model is discussed in the context of the current empirical knowledge and provide suggestions for directions of future empirical and theoretical studies.
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| 9. |
- Silva, Willian T. A. F., 1987-
(författare)
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Non-genetic processes in development and heredity
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- There is a swiftly increasing amount of empirical evidence that non-genetic factors, such as DNA methylation and small RNAs, play an important role not only in development but also in heredity and, therefore, evolutionary dynamics. One of the most interesting aspects of non-genetic processes is their responsiveness to environmental conditions, which has been shown to affect not only the phenotype and fitness of the individuals directly exposed to the stimulus, but also their offspring even when the stimulus is no longer present, indicating that the transmission of non-genetic factors across generations might work analogously to immunization against recurring conditions. In this thesis, I explored the effects and consequences of non-genetic processes in development and heredity, from both theoretical and experimental perspectives. In Article I, I created a mathematical model of DNA methylation dynamics during the maternal-to-zygotic transition, leading to the zygotic genome activation. I found that there is a developmental constraint on the transition between different cell lineages, with an increasing flexibility of active methylation and decreasing flexibility of maintenance (de-)methylation. In Article II, we explored the dynamics of small RNA production throughout development, including their amplification, transgenerational transmission and responsiveness to environmental conditions. Responsiveness of small RNA production resulted in greater benefits when soma and germline are both responsive, especially in highly correlated environmental conditions. In Article III, I carried out experiments on zebrafish to explore the effects of the male social environment on sperm production in terms of sperm morphology and DNA quality. Males exposed to different social treatments produced sperm with different morphologies and DNA integrity levels. In Article IV, we used the same experimental design to look at the effects of the male social environment on offspring development in terms of differential gene expression patterns. Males exposed to different social treatments sired offspring that showed different expression patterns of genes involved in post-transcriptional processes of gene expression regulation. Our findings shed light on the importance of non-genetic processes in development and heredity and contributes to the current knowledge about which and how non-genetic mechanisms can potentially affect evolutionary dynamics.
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| 10. |
- Silva, Willian T.A.F., et al.
(författare)
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Phenological evolution in annual plants under light competition, changes in the growth season and mass loss
- 2024
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Ingår i: Ecology and Evolution. - 2045-7758. ; 14:4
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Tidskriftsartikel (refereegranskat)abstract
- Flowering time is an important phenological trait in plants and a critical determinant of the success of pollination and fruit or seed development, with immense significance for agriculture as it directly affects crop yield and overall food production. Shifts in the growth season, changes in the growth season duration and changes in the production rate are environmental processes (potentially linked to climate change) that can lead to changes in flowering time in the long-term due to selection. In contrast, biomass loss (due to, for example, herbivory or diseases) can have profound consequences for plant mass production and food security. We model the effects of these environmental processes on the flowering time evolutionarily stable strategy (ESS) of annual plants and the potential consequences for reproductive output. Our model recapitulates previous theoretical results linked to climate change and light competition and makes novel predictions about the effects of biomass loss on the evolution of flowering time. Our analysis elucidates how both the magnitude and direction of the evolutionary response can depend on whether biomass loss occurs during the earlier vegetative phase or during the later reproductive phase and on whether or not plants are adapted to grow in dense, competitive environments. Specifically, light competition generates an asymetric effect of mass loss on flowering time even when loss is indiscriminate (equal rates), with vegetative mass loss having a stronger effect on flowering time (resulting in greater ESS change) and final reproductive output.
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| 11. |
- Silva, Willian T.A.F., et al.
(författare)
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Risk for overexploiting a seemingly stable seal population: influence of multiple stressors and hunting
- 2021
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Ingår i: Ecosphere. - : Wiley. - 2150-8925. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Conservation efforts have mainly been focused on depleted species or populations, but many formerly reduced marine mammal populations have recovered to historical abundances. This calls for new management strategies and new models for ecological risk assessment that incorporate local density dependence and multiple environmental stressors. The harbor seal metapopulation in Swedish and Danish waters has increased from about 2500 to 25,000 over the past 40yr. Trend analysis based on aerial survey data and somatic growth curves indicates that the population is close to carrying capacity. We performed a population viability analysis based on realistic life history parameters and investigated a range of potential scenarios caused by future stressors. If the population is able to resume its high intrinsic rate of increase at about 11% annually, when pushed down below carrying capacity, it can also sustain additional mortality such as modest hunting and infrequent epizootics. However, if xenobiotics will cause even a slight reduction in average fecundity, the population becomes significantly more vulnerable. In the absence of epizootics, and given full reproductive capacity, hunting of a few hundred animals annually is not harmful to the long-term persistence of the population. Nevertheless, a slight decrease in growth potential, for example, caused by exposure to endocrine disruptors, makes even limited hunting risky. Our study shows how an apparently stable and abundant marine mammal population can be close to a point of rapid population decline. Thus, careful monitoring of population size, growth rate, health, and exposure to xenobiotics as well as recording of the age and sex structure of the hunt is required to avoid repeating the history of overexploitation and another population collapse.
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| 12. |
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| 13. |
- Silva, Willian T. A. F., 1987-, et al.
(författare)
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The effects of male social environment on sperm phenotype and genome integrity
- 2019
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Ingår i: Journal of Evolutionary Biology. - : John Wiley & Sons. - 1010-061X .- 1420-9101. ; 32:6, s. 535-544
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Tidskriftsartikel (refereegranskat)abstract
- Sperm function and quality are primary determinants of male reproductive performance and hence fitness. The presence of rival males has been shown to affect ejaculate and sperm traits in a wide range of taxa. However, male physiological conditions may not only affect sperm phenotypic traits but also their genetic and epigenetic signatures, affecting the fitness of the resulting offspring. We investigated the effects of male-male competition on sperm quality using TUNEL assays and geometric morphometrics in the zebrafish, Danio rerio. We found that the sperm produced by males exposed to high male-male competition had smaller heads but larger midpiece and flagellum than sperm produced by males under low competition. Head and flagella also appeared less sensitive to the osmotic stress induced by activation with water. In addition, more sperm showed signals of DNA damage in ejaculates of males under high competition. These findings suggest that the presence of a rival male may have positive effects on sperm phenotypic traits but negative effects on sperm DNA integrity. Overall, males facing the presence of rival males may produce faster swimming and more competitive sperm but this may come at a cost for the next generation.
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| 14. |
- Yazdi, Homa Papoli, et al.
(författare)
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Why Do Some Sex Chromosomes Degenerate More Slowly Than Others? : The Odd Case of Ratite Sex Chromosomes
- 2020
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 11:10
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Tidskriftsartikel (refereegranskat)abstract
- The hallmark of sex chromosome evolution is the progressive suppression of recombination which leads to subsequent degeneration of the non-recombining chromosome. In birds, species belonging to the two major clades, Palaeognathae (including tinamous and flightless ratites) and Neognathae (all remaining birds), show distinctive patterns of sex chromosome degeneration. Birds are female heterogametic, in which females have a Z and a W chromosome. In Neognathae, the highly-degenerated W chromosome seems to have followed the expected trajectory of sex chromosome evolution. In contrast, among Palaeognathae, sex chromosomes of ratite birds are largely recombining. The underlying reason for maintenance of recombination between sex chromosomes in ratites is not clear. Degeneration of the W chromosome might have halted or slowed down due to a multitude of reasons ranging from selective processes, such as a less pronounced effect of sexually antagonistic selection, to neutral processes, such as a slower rate of molecular evolution in ratites. The production of genome assemblies and gene expression data for species of Palaeognathae has made it possible, during recent years, to have a closer look at their sex chromosome evolution. Here, we critically evaluate the understanding of the maintenance of recombination in ratites in light of the current data. We conclude by highlighting certain aspects of sex chromosome evolution in ratites that require further research and can potentially increase power for the inference of the unique history of sex chromosome evolution in this lineage of birds.
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