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118 results for “vertebrate evolution”
Alignments from "Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in vertebrates"
<p>Compressed file containing the alignments at both nucleotide and amino acid level for the manuscript "Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in vertebrates" </p>
The hagfish genome and the evolution of vertebrates
<p><strong>Genomic datasets for the hagfish </strong><i><strong>Eptatretus atami</strong></i></p><p><strong>Pata_MYAQb.rep.bed.gz:</strong> bed file with position of repeats masked by repeat masker</p><p><strong>Pata_ah2p.pep.fa</strong>: proteins from genome annotation </p><p><strong>Pata_MYAQb_rnm_ah2p.gtf</strong>: genome annotation performed using mikado, augustus and refined with Pasa (see methods). </p><p><strong>Pata_MYAQb_rnm.fa.gz: </strong>genome assembly in fasta format. </p><p> </p><p> </p>
Fig. 8 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 8. Comparison of centrum length/centrum height across Phocoenidae. A. Extinct species: Numataphocoena yamashitai, NFL 7, NMV-5; Pterophocaena nishinoi, NMV-7; Piscolithax longirostris, MNHN SAS 940. B. Extant species: Neophocaena phocaenoides, NMNS M 21382; Phocoenoides dalli, NMNS M 21382; Phocoena phocoena, NMNS M 27393; Phocoena dioptrica, USNM 571486; Phocoena spinipinnis, USNM 550782; Phocoena sinus, NHMUK 69678 (from Noble and Fraser 1971).
Fig. 7. Vertebral character trait evolution across phocoenids and related delphinoids. A. Character 2, thoracic vertebral counts. B. Character 8 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 7. Vertebral character trait evolution across phocoenids and related delphinoids. A. Character 2, thoracic vertebral counts. B. Character 8, ratio of centrum length/centrum height of lumbar vertebrae. C. Character 12, height of neural spine. D. Character 14, regional anterior inclination of neural arches. See Table 2 for detailed character descriptions.
Fig. 5 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 5. The phylogeny and vertebral morphology of Phocoenidae. The phylogenetic analysis is based on the data matrix of Murakami et al. (2012b), excluding character 220, 221, 222, 224, and 227. Quotations added to taxa which are paraphyly or polyphyly in the present cladistic analysis.
Fig. 4 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 4. Vertebrae (A–E) and ribs (F, G) of the porpoise Phocoenidae gen. et sp. indet., NMV-5, early Pliocene of Teshio, Hokkaido, Japan. Cervical (1–7), thoracic (1, 3, 5, 7, X, XX, XXX, last-1, last), and lumbar vertebrae (1–3) in lateral (A) and dorsal (B) views; atlas (C), axis (D), first lumbar (E), left rib fragment (F), and anterior to central right ribs (G) in anterior view.
Fig. 2 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 2. The rostrum (A–D) and mandible (E, F) of the porpoise Phocoenidae gen. et sp. indet., NMV-5, early Pliocene of Teshio, Hokkaido, Japan; in dorsal (A, F), lateral (B, E), ventral (C), and anterior (D) views.
Fig. 3 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 3. Isolated teeth of the porpoise Phocoenidae gen. et sp. indet., NMV-5, early Pliocene of Teshio, Hokkaido, Japan; in buccal view (A, B); longitudinal cross section of B (C); cross section from C stained with Mayer's haematoxylin (D). GLG, growth layer group.
Fig. 1 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 1. The locality of a small porpoise NMV-5. A. The Japanese islands. B. The locality of NMV-5. C. Detailed locality of NMV-5 near the Teshionakagawa area.
Fig. 6 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 6. Comparisons of the vertebral column of living and extinct phocoenids in lateral view. A. Pterophocaena nishinoi Murakami, Shimada, Hikida, and Hirano, 2012a, late Miocene of Hokkaido, Japan, NMV-7. B. Numataphocoena yamashitai Ichishima and Kimura, 2000, early Pliocene of Hokkaido, Japan, NFL 7. C. Piscolithax aenigmaticus Pilleri and Siber, 1989, late Miocene of Aguada de Lomas of Peru, SMNK-PAL 6660. D. Piscolithax longirostris Muizon, 1983, late Miocene of Sud-Sacaco, → Peru, MNHN SAS 934. E. Neophocaena phocaenoides Cuvier, 1829, Holocene of Japan?, NMNS M 24659. F. Phocoena sinus Norris and McFarland, 1958, Holocene of Baja California, Mexico, LACM 28259. G. Phocoena spinipinnis Burmeister, 1865, Holocene of Peru, USNM 550782. H. Phocoena dioptrica Lahille, 1912, Holocene of Tierra del Fuego, Argentina, LACM 86042. I. Phocoena phocoena Linnaeus, 1758, Holocene of Hokkaido, Japan, NMNS M 27393. J. Phocoenoides dalli True, 1885, Holocene of Iwate, Japan, NMNS M 21382. Not to scale.
Phylogenomic resolution of lampreys reveals the recent evolution of an ancient vertebrate lineage
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Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis-causing fly of warm-blooded vertebrates
<p><em>Wohlfahrtia magnifica</em> is a pest fly species, invading livestock in many European, African and Asian countries, and causing heavy agro-economic losses. In the life cycle of this obligatory parasite, adult flies infect the host by depositing the first-stage larvae into body cavities or open wounds. The feeding larvae cause severe (skin) tissue damage and potentially fatal infections if untreated. Despite serious health detriments and agro-economic concerns, genomic resources for understanding the biology of <em>W. magnifica</em> have so far been lacking. Here, we present a complete genome assembly from a single adult female <em>W. magnifica</em> using a Low-DNA Input workflow for PacBio HiFi library preparation. The <em>de novo</em> assembled genome is 753.99 Mb in length, with a scaffold N50 of 5.00 Mb, consisting of 16,718 predicted protein-encoding genes. Comparative genomic analysis revealed that <em>W. magnifica</em> has the closest phylogenetic relationship to <em>Sarcophaga bullata</em> followed by <em>Lucilia cuprina</em>. Evolutionary analysis of gene families showed expansions of 173 gene families in <em>W. magnifica</em> that were enriched for gene ontology (GO) categories related to immunity, insecticide-resistance mechanisms, heat stress response and cuticle development. In addition, 45 positively selected genes displaying various functions were identified. This new genomic resource contributes to the evolutionary and comparative analysis of dipterous flies and an in-depth understanding of many aspects of <em>W. magnifica </em>biology. Furthermore, it will facilitate the development of novel tools for controlling <em>W. magnifica</em> infection in livestock.</p>
Data from: Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade
While specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators. This supports the existence of pollination syndromes in centropogonids, an idea corroborated by ecological studies. We further demonstrate that hummingbird pollination is ancestral, and that bat pollination has evolved ∼13 times independently, with ∼11 reversals. This convergence is associated with correlated evolution of floral traits within selective regimes corresponding to pollination syndrome. Collectively, our results suggest that floral morphological diversity is extremely labile, likely resulting from selection imposed by pollinators. Finally, even though this clade's rapid diversification is partially attributed to their association with vertebrate pollinators, we detect no difference in diversification rates between hummingbird- and bat-pollinated lineages. Our study demonstrates the utility of pollination syndromes as a proxy for ecological relationships in macroevolutionary studies of certain species-rich clades.
Data from: Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas
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Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes
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Data from: Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade
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Data from: Contemporary evolution of the innate immune receptor gene TLR3 in an isolated vertebrate population
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Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis-causing fly of warm-blooded vertebrates
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Data from: Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation
Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fish that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability' – the capacity of organisms to evolve – shapes the dynamics of speciation through time at the largest phylogenetic scales.
Data from: The evolution of vertebrate eye size across an environmental gradient: phenotype does not predict genotype in a Trinidadian killifish
Vertebrates exhibit substantial variation in eye size. Eye size correlates positively with visual capacity and behaviors that enhance fitness, such as predator avoidance. This foreshadows a connection between predation and eye size evolution. Yet, the conditions that favor evolutionary shifts in eye size, besides the well-known role for light availability, are unclear. We tested the influence of predation on the evolution of eye size in Trinidadian killifish, Rivulus hartii. Rivulus are located across a series of communities where they coexist with visually oriented piscivores ('high predation' sites), and no predators ('Rivulus-only' sites). Wild-caught Rivulus from high predation sites generally exhibited a smaller relative eye size than communities that lack predators. Yet, such differences were inconsistent across rivers. Second-generation common garden reared fish revealed repeatable decreases in eye size in Rivulus from high predation sites. We performed additional experiments that tested the importance of light and resources on eye size evolution. Sites that differ in light or resource availability did not differ in eye size. Our results argue that differences in predator-induced mortality underlie genetically-based shifts in vertebrate eye size. We discuss the drivers of eye size evolution in light of the nonparallel trends between the phenotypic and common garden results.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.