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Jean-nicolas Volff - One of the best experts on this subject based on the ideXlab platform.
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Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths.
PloS one, 2014Co-Authors: Magali Naville, Domitille Chalopin, Jean-nicolas VolffAbstract:Coelacanths are Lobe-Finned Fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned Fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.
Per E. Ahlberg - One of the best experts on this subject based on the ideXlab platform.
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Unique pelvic fin in a tetrapod-like fossil Fish, and the evolution of limb patterning
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: Jonathan E. Jeffery, Clifford J Tabin, Glenn W. Storrs, Timothy Holland, Per E. AhlbergAbstract:All living tetrapods have a one-to-two branching pattern in the embryonic proximal limb skeleton, with a single element at the base of the limb (the humerus or femur) that articulates distally with two parallel radials (the ulna and radius or the tibia and fibula). This pattern is also seen in the fossilized remains of stem-tetrapods, including the Fishlike members of the group, in which despite the absence of digits, the proximal parts of the fin skeleton clearly resemble those of later tetrapods. However, little is known about the developmental mechanisms that establish and canalize this highly conserved pattern. We describe the well-preserved pelvic fin skeleton of Rhizodus hibberti, a Carboniferous sarcopterygian (Lobe-Finned) Fish, and member of the tetrapod stem group. In this specimen, three parallel radials, each robust with a distinct morphology, articulate with the femur. We review this unexpected morphology in a phylogenetic and developmental context. It implies that the developmental patterning mechanisms seen in living tetrapods, now highly constrained, evolved from mechanisms flexible enough to accommodate variation in the zeugopod (even between pectoral and pelvic fins), while also allowing each element to have a unique morphology.
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neurocranial anatomy of an enigmatic early devonian Fish sheds light on early osteichthyan evolution
eLife, 2018Co-Authors: Per E. Ahlberg, Alice M Clement, Benedict King, Sam Giles, Brian Choo, Gavin C YoungAbstract:All animals can be classified as either vertebrate (those that have a spine) or invertebrate (those that do not). About 98% of all living vertebrate species belong to a group called Osteichthyes, otherwise known as bony Fish. Despite the name, this group also includes all four-limbed vertebrates – amphibians, reptiles, birds and mammals – since they evolved from prehistoric bony Fish millions of years ago. The oldest known bony Fish can be traced back to around 425 million years. These ancient bony Fish are all part of a sub-group called Lobe-Finned Fish. Most modern bony Fish, however, are part of a different sub-group called ray-finned Fish, which can only be confidently traced back about 390 million years. A species called Ligulalepis was once thought to represent the oldest ray-finned Fish. Scientists worked this out by examining a single Ligulalepis skull fossil from around 400 million years ago. However, subsequent studies have disputed its position in the evolutionary tree. So, the early evolution of bony Fish remains poorly understood. To address this, Clement, King, Giles et al. re-examined the original Ligulalepis skull fossil, alongside a newly discovered second skull fossil of the same species. Modern x-ray scanning techniques were used to produce detailed 3D models of both skulls and compare them to other prehistoric bony Fish. This allowed Clement, King, Giles et al. to find Ligulalepis’s exact place in the evolutionary family tree. The experiments identified many previously unknown features of the Ligulalepis skull. These features suggest that this species was not a ray-finned Fish; rather, it existed just before bony Fish split into two sub-groups (Lobe-Finned and ray-finned). The analysis also suggests that Ligulalepis was the species most closely related to another group of Fish called psarolepids. Overall, these findings clarify our understanding of the evolutionary tree of all vertebrates, including humans. Future research should continue using modern scanning techniques to uncover new information from old fossils and give further insights into the early evolution of vertebrates.
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the pectoral fin of panderichthys and the origin of digits
Nature, 2008Co-Authors: Catherine A Boisvert, Elga Markkurik, Per E. AhlbergAbstract:One of the identifying characteristics of tetrapods (limbed vertebrates) is the presence of fingers and toes. Whereas the proximal part of the tetrapod limb skeleton can easily be homologized with the paired fin skeletons of sarcopterygian (Lobe-Finned) Fish, there has been much debate about the origin of digits. Early hypotheses interpreted digits as derivatives of fin radials, but during the 1990s the idea gained acceptance that digits are evolutionary novelties without direct equivalents in Fish fin skeletons. This was partly based on developmental genetic data, but also substantially on the pectoral fin skeleton of the elpistostegid (transitional Fish/tetrapod) Panderichthys, which appeared to lack distal digit-like radials. Here we present a CT scan study of an undisturbed pectoral fin of Panderichthys demonstrating that the plate-like 'ulnare' of previous reconstructions is an artefact and that distal radials are in fact present. This distal portion is more tetrapod-like than that found in Tiktaalik and, in combination with new data about fin development in basal actinopterygians, sharks and lungFish, makes a strong case for fingers not being a novelty of tetrapods but derived from pre-existing distal radials present in all sarcopterygian Fish.
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tetrapod like middle ear architecture in a devonian Fish
Nature, 2006Co-Authors: Martin D Brazeau, Per E. AhlbergAbstract:Detailed study of Panderichthys, a Lobe-Finned Fish closely related to the first amphibians, suggests that the early stages in the evolution of the vertebrate middle ear were related to breathing, rather than detecting sound. Our middle ear corresponds to a reduced gill slit called the ‘spiracle’ in Fishes. In a well preserved Panderichthys fossil specimen held in the Latvian Natural History Museum in Riga, this gill slit is much larger than in other ancient Fish species and has vertebrate-like architecture, yet was probably used to inhale water or air. It seems that a rudimentary auditory role for the stapes and other middle-ear components first developed in primitive land vertebrates. Few fossils show the incipient stages of complex morphological transformations1. For example, the earliest stages in the remodelling of the spiracular tract and suspensorium (jaw suspension) of osteolepiform Fishes2,3,4 into the middle ear of tetrapods have remained elusive3. The most primitive known tetrapods show a middle ear architecture that is very different from osteolepiforms such as Eusthenopteron3, with little indication of how this transformation took place. Here we present an analysis of tetrapod middle ear origins that is based on a detailed study of Panderichthys, the immediate sister taxon of tetrapods. We show that the spiracular region is radically transformed from osteolepiforms and represents the earliest stages in the origin of the tetrapod middle ear architecture. The posterior palatoquadrate of Panderichthys is completely tetrapod-like and defines a similarly tetrapod-like spiracular tract. The hyomandibula has lost its distal portion, representing a previously unrecognized advance towards a stapes-like morphology. This spiracular specialization suggests that the middle ear of early tetrapods evolved initially as part of a spiracular breathing apparatus5,6.
Magali Naville - One of the best experts on this subject based on the ideXlab platform.
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Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths.
PloS one, 2014Co-Authors: Magali Naville, Domitille Chalopin, Jean-nicolas VolffAbstract:Coelacanths are Lobe-Finned Fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned Fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.
Gyri Teien Haugland - One of the best experts on this subject based on the ideXlab platform.
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interleukin 1 ligands and receptors in lumpFish cyclopterus lumpus l molecular characterization phylogeny gene expression and transcriptome analyses
Frontiers in Immunology, 2020Co-Authors: Havard Oritsland Eggestol, Harald S Lunde, Tim Martin Knutsen, Gyri Teien HauglandAbstract:The interleukin (IL)-1 family play a fundamental role as immune system modulators. Our previous transcriptome-analyses of leukocytes from lumpFish (Cyclopterus lumpus L.) showed that IL-1β was among the most highly upregulated genes following bacterial exposure. In the present study, we characterized IL-1 signaling pathways, identified and characterized four ligands of the IL-1 family in lumpFish; IL-1β type I and type II, IL-18, and the novel IL-1 family members (nIL-1F), both at mRNA and gene levels. The two IL-1β in lumpFish is termed IL-1β1 (type II) and IL-1β2 (type I). Furthermore, a comprehensive phylogenetic analysis of 277 IL-1 ligands showed that nIL-1F, in common with IL-1β, likely represents an ancestral gene, as representatives for nIL-1F were found in cartilaginous and Lobe-Finned Fish, in addition to teleosts. This shows that nIL-1F is not exclusively present in teleosts as previously suggested. Our analyses of exon-intron structures, intron phases, phylogeny and synteny clearly show the separation of IL-1β into groups; type I and type II, which likely is a result of the third whole genome duplication (3R WGD). The phylogenetic analysis shows that most teleosts have both type I and type II. Furthermore, we have determined transcription levels of the IL-1 ligands in leukocytes and 16 different tissues, and their responses upon in vitro stimulation with seven different ligands. In addition, we have identified the IL-1 receptors IL-1R1, IL-1R2, IL-1R4 (ST2/IL-33 receptor/IL-1RL), IL-1R5 (IL-18R1), and partial sequences of DIGIRR and IL-1R3 (IL-RAcP). Identification of immune molecules and description of innate responses in lumpFish is interesting for comparative and evolutionary studies and our study constitutes a solid basis for further functional analyses of IL-1 ligands and receptors in lumpFish. Furthermore, since lumpFish are now farmed in large numbers to be used as cleaner Fish for removal of sea lice on farmed salmon, in-depth knowledge of key immune molecules, signaling pathways and innate immune responses is needed, as the basis for design of efficient immune prophylactic measures such as vaccination.
Axel Meyer - One of the best experts on this subject based on the ideXlab platform.
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the complete dna sequence of the mitochondrial genome of a living fossil the coelacanth latimeria chalumnae
Genetics, 1997Co-Authors: Rafael Zardoya, Axel MeyerAbstract:The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned Fishes, the lungFish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3' end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNAs, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a Lobe-Finned Fish; it is more closely related to tetrapods than to ray-finned Fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant Lobe-Finned Fishes, the lungFishes and the tetrapods. Maximum parsimony favored a lungFish/coelacanth or a lungFish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungFish/tetrapod sistergroup relationship.
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The complete mitochondrial DNA sequence of the bichir (Polypterus ornatipinnis), a basal ray-finned Fish: ancient establishment of the consensus vertebrate gene order.
Genetics, 1996Co-Authors: Katharina Noack, Rafael Zardoya, Axel MeyerAbstract:The evolutionary position of bichirs is disputed, and they have been variously aligned with ray-finned Fish (Actinopterygii) or Lobe-Finned Fish (Sarcopterygii), which also include tetrapods. Alternatively, they have been placed into their own group, the Brachiopterygii. The phylogenetic position of bichirs as possibly the most primitive living bony Fish (Osteichthyes) made knowledge about their mitochondrial genome of considerable evolutionary interest. We determined the complete nucleotide sequence (16,624 bp) of the mitochondrial genome of a bichir, Polypterus ornutipinnis. Its genome contains 13 proteincoding genes, 22 WAS, two rRNAs and one major noncoding region. The genome’s structure and organization show that this is the most basal vertebrate that conforms to the consensus vertebrate mtDNA gene order. Bichir mitochondrial protein-coding and ribosomal RNA genes have greater sequence similarity to ray-finned Fish than to either lamprey or lungFish. Phylogenetic analyses suggest the bichir’s placement as the most basal living member of the ray-finned Fish and rule out its classification as a lobefinned Fish. Hence, its lobe-fins are probably not a shared-derived trait with those of Lobe-Finned Fish (Sarcopterygii).