UMD Data Collection

Permanent URI for this collectionhttp://hdl.handle.net/1903/27670

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Author: search.filters.author.Wilkinson, Gerald

Search Results

Now showing 1 - 6 of 6
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    Transposable element annotation for a Genome Assembly of the stalk-eyed fly, Teleopsis dalmanni
    (2020-09-21) Wilkinson, Gerald; Baker, Richard; Reinhardt, Josephine
    Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio meiotic drive (SR) and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long-reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the sex ratio haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, i.e. either recent duplicates or lacking a dipteran ortholog, including an X-linked duplicate of maelstrom, which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species.
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    Gene Annotation for a Genome Assembly of the stalk-eyed fly, Teleopsis dalmanni
    (2020-09-14) Wilkinson, Gerald; Baker, Richard; Reinhardt, Josephine
    Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio meiotic drive (SR) and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long-reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the sex ratio haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, i.e. either recent duplicates or lacking a dipteran ortholog, including an X-linked duplicate of maelstrom, which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species.
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    Gene annotations for the Horvath37K_DNAMethylation array for 10 bat genomes
    (2020-09) Wilkinson, Gerald; Haghani, Amin; Horvath, Steve
    This submission contain gene annotations for an Illumina microarray (HorvathMammalMethylChip40) for 10 species of bats. The array design is available from the Gene Expression Omnibus (GEO) at NCBI as platform GPL28271. This array was used to generate DNA methylation data for nearly 700 known-aged individuals representing 26 species of bats. The resulting data were then used to predict age and species lifespan, and identify genomic regions that influence both of those traits.
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    Genotype data and linkage map for Teleopsis dalmanni, described in “Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome
    (2020) Wilkinson, Gerald; Reinhardt, Josephine; Baker, Richard; Paczolt, Kimberly
    These files contain genotype matrices used to create a linkage map for the stalk-eyed fly, Teleopsis dalmanni. They were created from individuals derived from a backcross between two populations of flies derived from collections made in peninsular Malaysia and northern Sumatra. These linkage map was used to validate a chromosomal genome assembly, as described in a paper titled, “Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome," which is being submitted for publication.
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    Data for "Recurrent evolution of extreme longevity in bats"
    (2018) Adams, Danielle; Wilkinson, Gerald
    This dataset was used in a comparative analysis of longevity in bats. Bats live longer than similar-sized mammals, but the number of lineages that have independently evolved extreme longevity has not previously been determined. Here we reconstruct the evolution of size-corrected longevity on a recent phylogeny and find that at least four lineages of bats have lifespans more than four-fold those of similar-sized placental mammals with the ancestral bat projected to live 2.5 times as long. We then use an information theoretic approach to evaluate a series of phylogenetic generalized least squares (PGLS) models containing up to eight variables hypothesized to influence extrinsic mortality. The PLGS analyses reveal that body mass and hibernation predict longevity. Among hibernators, longevity is predicted by median latitude of the species range, while cave roosting and lack of sexual dimorphism predict longevity among nonhibernators. The importance of torpor in extending lifespan is further supported by the one lineage with extreme longevity that does not hibernate but does exhibit flexible thermoregulation, the common vampire bat. We propose a number of potential mechanisms that may enable bats to live so long, and suggest that the ability to tolerate a wide range of body temperatures could be particularly important for surviving viral or other pathogen infections.
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    Data for "Dynamic sex-specific responses to synthetic songs in a duetting suboscine passerine"
    (2018) Fishbein, Adam; Löschner, Julia; Mallon, Julie; Wilkinson, Gerald
    Many bird species produce temporally coordinated duets and choruses, requiring the rapid integration of auditory perception and motor production. While males and females of some species are known to participate in these displays for sex-specific purposes, few studies have identified perceptual features that trigger sex-specific contributions of coordinated song. Especially little is known about perception and production in duetting suboscine passerines which are thought to have innate songs and largely static, rather than dynamic, vocal behavior. Here, we used synthetic stimuli in a playback experiment on chestnut-backed antbirds (Myrmeciza exsul) to (1) test if differences in song frequency (Hz) can trigger sex-specific vocal behavior in a suboscine passerine (2) test for the functions of duetting in males and females of this species, and (3) determine if these suboscines can dynamically adjust the temporal and spectral features of their songs. We found sex-specific responses to synthetic playback differing in song frequency, providing evidence that in this context males sing in duets for general territory defense and females join in for mate guarding purposes. In addition, we found that the birds altered the frequency, duration, and timing of their songs depending on the frequency of the playback songs. Thus, we show that these birds integrate spectral and temporal information about conspecific songs and actively modulate their responses in sex-specific ways.