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30 results for “plethodontid salamanders”
Data from: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders
Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ∼14 Gb to ∼120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of LTR retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.
Figure 2 from: Gladstone NS, Carter ET, Niemiller KDK, Hayter LE, Niemiller ML (2018) A new maximum body size record for the Berry Cave Salamander (Gyrinophilus gulolineatus) and genus Gyrinophilus (Caudata, Plethodontidae) with a comment on body size in plethodontid salamanders. Subterranean Biology 28: 29-38. https://doi.org/10.3897/subtbiol.28.30506
Figure 2 Dorsal view of the Gyrinophilusgulolineatus captured at Berry Cave. Photo credit: Matthew L. Niemiller.
Figure 1 from: Gladstone NS, Carter ET, Niemiller KDK, Hayter LE, Niemiller ML (2018) A new maximum body size record for the Berry Cave Salamander (Gyrinophilus gulolineatus) and genus Gyrinophilus (Caudata, Plethodontidae) with a comment on body size in plethodontid salamanders. Subterranean Biology 28: 29-38. https://doi.org/10.3897/subtbiol.28.30506
Figure 1 Geographic distribution of the Berry Cave Salamander (Gyrinophilusgulolineatus) in relation to karst adapted from Weary and Doctor (2014). Blue circles represent cave localities from which the species has been reported, and the red star represents the location of Berry Cave. The top right image shows the main stream passage near the entrance of Berry Cave that continues throughout the entirety of our sampling area. The bottom right image shows the large individual captured on 12 August 2018. Photo credits: Matthew L. Niemiller.
Data from: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders
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Vastly underestimated radiation of Amazonian salamanders (Plethodontidae: Bolitoglossa) and implications about plethodontid diversification
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Data from: Genetic data reveal fine-scale ecological segregation between larval plethodontid salamanders in replicate contact zones
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Data from: Morphological polymorphism associated with alternative reproductive tactics in a plethodontid salamander
Understanding polymorphism is a central problem in evolution and ecology, and alternative reproductive tactics (ARTs) provide compelling examples for studying the origin and maintenance of behavioral and morphological variation. Much attention has been given to examples where "parasitic" individuals exploit the reproductive investment of "bourgeois" individuals, but some ARTs are instead maintained by environmental heterogeneity, with alternative tactics exhibiting differential fitness in discontinuous reproductive niches. We use genomic, behavioral, karyological, and field observational data to demonstrate one such example in plethodontid salamanders. These ARTs ("searching" and "guarding" males) are associated with different reproductive niches and, unlike most other examples in amphibians, demonstrate substantial morphological differences and inflexibility within a reproductive season. Evidence suggests the existence of these ARTs within three putative species in the two-lined salamander (Eurycea bislineata) species complex, with other members of this clade fixed for one of the two tactics. We highlight directions for future research in this system, including the relationship between these ARTs and parental care.
Data from: Morphological polymorphism associated with alternative reproductive tactics in a plethodontid salamander
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FIG. 7 in The Evolution of Courtship Behavior in Plethodontid Salamanders, Contrasting Patterns of Stasis and Diversification
FIG. 7.—The evolutionary origin and loss of key courtship traits in Ensatina, Aneides, and Plethodon. Character origins are shown with solid rectangles; loss is shown with open rectangles: TSW ¼ tail-straddling walk module, c-TSW ¼ circular tail-straddling walk, tbf ¼ turning back towards the female during TSW, tpd ¼ transdermal pheromone delivery (tpd1 and tpd2), opd ¼ olfactory pheromone delivery, fd ¼ foot dance, ps ¼ pulling and snapping, tw ¼ tail wagging, and mgr ¼ mouth grasping. The time of origin or loss for each trait is bounded by the times at the ends of the branch on which it resides. Timecalibrated phylogeny based on Kozak et al. (2009); time scale shown in millions of years.
FIG. 2 in The Evolution of Courtship Behavior in Plethodontid Salamanders, Contrasting Patterns of Stasis and Diversification
FIG. 2.—Inventory of behavior patterns used in descriptions of plethodontid and rhyacotritonid courtship, showing their assignments to modules and submodules. Module abbreviations: AP ¼ approach, HC ¼ head contact, TSW ¼ tail-straddling walk, SD ¼ spermatophore deposition, POS ¼ positioning. Submodule abbreviations: pur ¼ male pursuit of female, pd ¼ preliminary display, con ¼ contact, tpd1 ¼ transdermal pheromone delivery Type 1, walk ¼ progress aspect of TSW, tpd2 ¼ transdermal pheromone delivery Type 2, oph ¼ olfactory pheromone delivery. Behaviors shown in the same colors occur in the same temporal context. Behaviors shown in shades of the same color occur in the sequence: lighter shade earlier, darker shade later. References for behavioral descriptions: 1 ¼ this study; 2 ¼ Arnold (1972); 3 ¼ Verrell and Mabry (2003); 4 ¼ Kiemnec-Tyburczy and Sapp (2017); 5 ¼ Doten et al. (in press); 6 ¼ Picard (2005); 7 ¼ Organ (1960b); 8 ¼ Organ (1960a); 9 ¼ Organ (1961); 10 ¼ Verrell (1999); 11 ¼ Sapp and Kiemnec-Tyburczy (2011).
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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.
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DANDI Archive for NWB datasets
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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.