Browsing by Autor "Andrew J. Crawford"

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    Characterization of the First Batrachochytrium dendrobatidis Isolate from the Colombian Andes, an Amphibian Biodiversity Hotspot
    (Springer Science+Business Media, 2013) Sandra V. Flechas; Edgar M. Medina; Andrew J. Crawford; Carolina Sarmiento; Martha Cárdenas; Adolfo Amézquita; Silvia Restrepo
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    Genome assembly of the endangered Santa Marta Harlequin Toad, <i>Atelopus laetissimus</i> , endemic to the Sierra Nevada de Santa Marta of Colombia
    (Oxford University Press, 2025) Victor Araújo; José Horacio Grau; Luis Alberto Rueda‐Solano; José D Barros-Castañeda; Sandra V. Flechas; Andrew J. Crawford
    Despite the critical conservation status of many harlequin toads (Anura: Bufonidae: Atelopus) and their significance in elucidating the impacts of emerging diseases on amphibians, genomic data for this genus are scarce. Here, we present a de novo genome assembly of the Santa Marta Harlequin Toad, Atelopus laetissimus, using PacBio HiFi sequencing data, representing the first published Atelopus genome assembly and only the second amphibian genome assembly from Colombia. The assembly consists of 1,487 contigs at 35× coverage with an N50 of 31 Mb and a total length of 3.5 Gb. A Tetrapoda BUSCO score of 92% suggests our assembly is very nearly complete. Analysis revealed a high repeat content, with 70% of the genome consisting of interspersed repeats. This high-contiguity draft assembly will drive the search for a possible genetic basis of pathogen resistance in these endangered toads of the Sierra Nevada de Santa Marta, as well as facilitate ongoing evolutionary studies.
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    Landscape genetics and species delimitation in the Andean Palm Rocket Frog (Aromobatidae, Rheobates).
    (European Organization for Nuclear Research, 2020) Gabrielle Genty; Carlos E. Guarnizo; Juan P. Ramírez; Lucas S. Barrientos; Andrew J. Crawford
    These contain all supporting data generated in the paper, entitled 'Landscape genetics and species delimitation in the Andean Palm Rocket Frog (Aromobatidae, Rheobates).' It includes DNA sequence alignments, phylogenetic trees, geographic coordinates, haplotype networks, and R script.
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    Landscape genetics and species delimitation in the Andean Palm Rocket Frog (Aromobatidae, Rheobates).
    (European Organization for Nuclear Research, 2020) Gabrielle Genty; Carlos E. Guarnizo; Juan P. Ramírez; Lucas S. Barrientos; Andrew J. Crawford
    These contain all supporting data generated in the paper, entitled 'Landscape genetics and species delimitation in the Andean Palm Rocket Frog (Aromobatidae, Rheobates).' It includes DNA sequence alignments, phylogenetic trees, geographic coordinates, haplotype networks, and R script.
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    Untangling relationships among terraranan frogs: a phylogenomic approach based on 2,665 loci
    (2019) Lucas S. Barrientos; Jeffrey W. Streicher; Elizabeth Christina Miller; Márcio R. Pie; John J. Wiens; Andrew J. Crawford
    <title>Abstract</title> Background: Terraranae is a large clade of New World direct-developing frogs that includes 3–5 families and &gt;1,000 described species, encompassing ~15% of all named frog species. The relationships among major groups of terraranan frogs have been highly contentious, including conflicts among three recent phylogenomic studies utilizing 95, 389, and 2,214 nuclear loci, respectively. In this paper, we re-evaluate relationships within Terraranae using a novel genomic dataset for 16 ingroup species representing most terraranan families and subfamilies. Results: The preferred data matrix consisted of 2,665 nuclear loci from ultraconserved elements (UCEs), with a total of 743,419 aligned base pairs and 57% missing data. Concatenated likelihood analyses and coalescent-based species-tree analyses both recovered strong statistical support for the following relationships among terraranan families: (Brachycephalidae, (Eleutherodactylidae, (Craugastoridae + “Strabomantidae”))). Our placement of Brachycephalidae agrees with two previous phylogenomic studies but conflicts with another. Our results place Strabomantis (of the Strabomantidae) with (or within) Craugastor (Craugastoridae) rather than with other strabomantid genera, rendering Strabomantidae paraphyletic with respect to Craugastoridae. Conclusions: Our results suggest that Strabomantidae should be placed in the synonymy of the older Craugastoridae. Furthermore, our results suggest that Pristimantinae is paraphyletic with respect to Holoadeninae and should be subsumed into the older Holoadeninae. We also found that using matrices of UCE loci with less missing data (and concomitantly fewer loci) generally decreased support for most nodes on the tree. Overall, our results help resolve controversial relationships within one of the largest clades of frogs, with a dataset containing ~7 times more loci than previous studies focused on this clade.