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327 results on '"Crawford, Andrew J."'

1. The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Author

Kosch, Tiffany A., Torres-Sánchez, María, Liedtke, H. Christoph, Summers, Kyle, Yun, Maximina H., Crawford, Andrew J., Maddock, Simon T., Ahammed, Md. Sabbir, Araújo, Victor L. N., Bertola, Lorenzo V., Bucciarelli, Gary M., Carné, Albert, Carneiro, Céline M., Chan, Kin O., Chen, Ying, Crottini, Angelica, da Silva, Jessica M., Denton, Robert D., Dittrich, Carolin, Espregueira Themudo, Gonçalo, Farquharson, Katherine A., Forsdick, Natalie J., Gilbert, Edward, Che, Jing, Katzenback, Barbara A., Kotharambath, Ramachandran, Levis, Nicholas A., Márquez, Roberto, Mazepa, Glib, Mulder, Kevin P., Müller, Hendrik, O’Connell, Mary J., Orozco-terWengel, Pablo, Palomar, Gemma, Petzold, Alice, Pfennig, David W., Pfennig, Karin S., Reichert, Michael S., Robert, Jacques, Scherz, Mark D., Siu-Ting, Karen, Snead, Anthony A., Stöck, Matthias, Stuckert, Adam M. M., Stynoski, Jennifer L., Tarvin, Rebecca D., and Wollenberg Valero, Katharina C.

Published
2024
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4. Global urban environmental change drives adaptation in white clover

Author

Santangelo, James S, Ness, Rob W, Cohan, Beata, Fitzpatrick, Connor R, Innes, Simon G, Koch, Sophie, Miles, Lindsay S, Munim, Samreen, Peres-Neto, Pedro R, Prashad, Cindy, Tong, Alex T, Aguirre, Windsor E, Akinwole, Philips O, Alberti, Marina, Álvarez, Jackie, Anderson, Jill T, Anderson, Joseph J, Ando, Yoshino, Andrew, Nigel R, Angeoletto, Fabio, Anstett, Daniel N, Anstett, Julia, Aoki-Gonçalves, Felipe, Arietta, AZ Andis, Arroyo, Mary TK, Austen, Emily J, Baena-Díaz, Fernanda, Barker, Cory A, Baylis, Howard A, Beliz, Julia M, Benitez-Mora, Alfonso, Bickford, David, Biedebach, Gabriela, Blackburn, Gwylim S, Boehm, Mannfred MA, Bonser, Stephen P, Bonte, Dries, Bragger, Jesse R, Branquinho, Cristina, Brans, Kristien I, Bresciano, Jorge C, Brom, Peta D, Bucharova, Anna, Burt, Briana, Cahill, James F, Campbell, Katelyn D, Carlen, Elizabeth J, Carmona, Diego, Castellanos, Maria Clara, Centenaro, Giada, Chalen, Izan, Chaves, Jaime A, Chávez-Pesqueira, Mariana, Chen, Xiao-Yong, Chilton, Angela M, Chomiak, Kristina M, Cisneros-Heredia, Diego F, Cisse, Ibrahim K, Classen, Aimée T, Comerford, Mattheau S, Fradinger, Camila Cordoba, Corney, Hannah, Crawford, Andrew J, Crawford, Kerri M, Dahirel, Maxime, David, Santiago, De Haan, Robert, Deacon, Nicholas J, Dean, Clare, del-Val, Ek, Deligiannis, Eleftherios K, Denney, Derek, Dettlaff, Margarete A, DiLeo, Michelle F, Ding, Yuan-Yuan, Domínguez-López, Moisés E, Dominoni, Davide M, Draud, Savannah L, Dyson, Karen, Ellers, Jacintha, Espinosa, Carlos I, Essi, Liliana, Falahati-Anbaran, Mohsen, Falcão, Jéssica CF, Fargo, Hayden T, Fellowes, Mark DE, Fitzpatrick, Raina M, Flaherty, Leah E, Flood, Pádraic J, Flores, María F, Fornoni, Juan, Foster, Amy G, Frost, Christopher J, Fuentes, Tracy L, Fulkerson, Justin R, Gagnon, Edeline, Garbsch, Frauke, Garroway, Colin J, Gerstein, Aleeza C, and Giasson, Mischa M

Subjects
Adaptation, Physiological, Biological Evolution, Cities, Ecosystem, Genes, Plant, Genome, Plant, Hydrogen Cyanide, Rural Population, Trifolium, Urbanization, General Science & Technology
Abstract

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.

Published
2022

5. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara KN, Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M, Baker, William J, Belov, Katherine, Blaxter, Mark L, Bonet, Tomas Marques, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Crawford, Andrew J, Davey, Robert P, Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J, Howe, Kerstin, Jarvis, Erich D, Johnson, Warren E, Johnson, Rebecca N, Kersey, Paul J, Liu, Xin, Lopez, Jose Victor, Myers, Eugene W, Pettersson, Olga Vinnere, Phillippy, Adam M, Poelchau, Monica F, Pruitt, Kim D, Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A, Soltis, Pamela S, Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L, Zhang, Guojie, Zhang, He, Lewin, Harris A, and Richards, Stephen

Subjects
Human Genome, Genetics, Animals, Base Sequence, Biodiversity, Eukaryota, Genomics, Humans, Reference Standards, Reference Values, Sequence Analysis, DNA, Earth BioGenome Project, genomics, ethics, genome assembly
Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

6. Using Prescription Drug Monitoring Program Data to Assess Likelihood of Incident Long-Term Opioid Use: a Statewide Cohort Study.

Author

Henry, Stephen G, Stewart, Susan L, Murphy, Eryn, Tseregounis, Iraklis Erik, Crawford, Andrew J, Shev, Aaron B, Gasper, James J, Tancredi, Daniel J, Cerdá, Magdalena, Marshall, Brandon DL, and Wintemute, Garen J

Subjects
Humans, Opioid-Related Disorders, Analgesics, Opioid, Odds Ratio, Cohort Studies, Child, Drug Prescriptions, Practice Patterns, Physicians', Prescription Drug Monitoring Programs, health policy, long-term opioid use, opioid analgesics, pain, prescription drug monitoring programs, Substance Misuse, Prescription Drug Abuse, Clinical Research, Patient Safety, Drug Abuse (NIDA only), Good Health and Well Being, Clinical Sciences, General & Internal Medicine
Abstract

BackgroundLimiting the incidence of opioid-naïve patients who transition to long-term opioid use (i.e., continual use for > 90 days) is a key strategy for reducing opioid-related harms.ObjectiveTo identify variables constructed from data routinely collected by prescription drug monitoring programs that are associated with opioid-naïve patients' likelihood of transitioning to long-term use after an initial opioid prescription.DesignStatewide cohort study using prescription drug monitoring program data PARTICIPANTS: All opioid-naïve patients in California (no opioid prescriptions within the prior 2 years) age ≥ 12 years prescribed an initial oral opioid analgesic from 2010 to 2017.Methods and main measuresMultiple logistic regression models using variables constructed from prescription drug monitoring program data through the day of each patient's initial opioid prescription, and, alternatively, data available up to 30 and 60 days after the initial prescription were constructed to identify probability of transition to long-term use. Model fit was determined by the area under the receiver operating characteristic curve (C-statistic).Key resultsAmong 30,569,125 episodes of patients receiving new opioid prescriptions, 1,809,750 (5.9%) resulted in long-term use. Variables with the highest adjusted odds ratios included concurrent benzodiazepine use, ≥ 2 unique prescribers, and receipt of non-pill, non-liquid formulations. C-statistics for the day 0, day 30, and day 60 models were 0.81, 0.88, and 0.94, respectively. Models assessing opioid dose using the number of pills prescribed had greater discriminative capacity than those using milligram morphine equivalents.ConclusionsData routinely collected by prescription drug monitoring programs can be used to identify patients who are likely to develop long-term use. Guidelines for new opioid prescriptions based on pill counts may be simpler and more clinically useful than guidelines based on days' supply or milligram morphine equivalents.

Published
2021

7. Testing effects of Pleistocene climate change on the altitudinal and horizontal distributions of frogs from the Colombian Andes: a species distribution modeling approach

Author

Paz, Andrea, González, Angélica, and Crawford, Andrew J.

Subjects
Amphibian, Climate change, Elevational range, Last Glacial Maximum, Refugia, Species distribution modeling
Abstract

Recent climatic models suggest the late Pleistocene was colder and had different precipitation regimes from the present. If this climatic shift occurred more rapidly than species could adapt, species likely shifted their ranges as populations moved in concert with suitable environmental conditions. We examined changes in altitudinal and horizontal distribution in response to past climate change of amphibian species from different elevational zones and habitat requirements in the Eastern Cordillera of the Colombian Andes. We used environmental information and species occurrence data to model the distribution of 14 amphibian species (seven highland and seven lowland) which we projected to the Last Glacial Maximum (LGM) using two past climatic reconstructions. For these 14 species, we studied the predicted elevational and areal shifts. In agreement with palynological-derived models for Andean flora, we predicted that the elevation of montane amphibians shifted downwards increasing their total altitudinal range. We did not detect any evidence of compression related to drier lowlands. In some cases, the wider distribution areas of high-elevation amphibians during the LGM overlapped with contemporary distributions implying that these areas are present-day refugia for some species. Lowland species showed little or no elevational changes across time, but their areal distributions changed depending on habitat requirements. Four lowland frog species occurring in present-day xeric environments showed substantial range expansion across the lowlands during the LGM, while two species occurring in humid habitats likely expanded their ranges since the LGM. Since the LGM ended, ranges of mid‐ to high-elevation species shrank and shifted to higher elevation. Lowland species in xeric or open habitats have also experienced shrinking ranges, with some evidence that they have been moving upwards. Thus, low- and high-elevation species may be at risk under predicted anthropogenic climate change. Our results generate spatial hypotheses about amphibian responses to climate change that can be tested with phylogeographic data.

Published
2019

8. Comparative analysis of amphibian genomes: An emerging resource for basic and applied research.

Author

Kosch, Tiffany A., Crawford, Andrew J., Lockridge Mueller, Rachel, Wollenberg Valero, Katharina C., Power, Megan L., Rodríguez, Ariel, O'Connell, Lauren A., Young, Neil D., and Skerratt, Lee F.

Abstract

Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex determination and in some lineages, the ability to regenerate limbs and organs. Although genomic approaches would shed light on these unique traits and aid conservation, sequencing and assembly of amphibian genomes has lagged behind other taxa due to their comparatively large genome sizes. Fortunately, the development of long‐read sequencing technologies and initiatives has led to a recent burst of new amphibian genome assemblies. Although growing, the field of amphibian genomics suffers from the lack of annotation resources, tools for working with challenging genomes and lack of high‐quality assemblies in multiple clades of amphibians. Here, we analyse 51 publicly available amphibian genomes to evaluate their usefulness for functional genomics research. We report considerable variation in genome assembly quality and completeness and report some of the highest transposable element and repeat contents of any vertebrate. Additionally, we detected an association between transposable element content and climatic variables. Our analysis provides evidence of conserved genome synteny despite the long divergence times of this group, but we also highlight inconsistencies in chromosome naming and orientation across genome assemblies. We discuss sequencing gaps in the phylogeny and suggest key targets for future sequencing endeavours. Finally, we propose increased investment in amphibian genomics research to promote their conservation. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Towards complete and error-free genome assemblies of all vertebrate species

Author

Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C., Lama, Tanya M., Grutzner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich, III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E., Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Diekhans, Mark, Nassar, Luis, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marques-Bonet, Tomas, Teeling, Emma C., Warnow, Tandy, Graves, Jennifer Marshall, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., and Jarvis, Erich D.

Published
2021
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15. Impact of 30-day prescribed opioid dose trajectory on fatal overdose risk: A population-based, statewide cohort study

Author

Henry, Stephen G., primary, Fang, Shao-You, additional, Crawford, Andrew J., additional, Wintemute, Garen J., additional, Tseregounis, Iraklis Erik, additional, Gasper, James J., additional, Shev, Aaron, additional, Cartus, Abigail R., additional, Marshall, Brandon D.L., additional, Tancredi, Daniel J., additional, Cerdá, Magdalena, additional, and Stewart, Susan L., additional

Published
2023
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17. Current and predicted distribution of the pathogenic fungus Batrachochytrium dendrobatidis in Colombia, a hotspot of amphibian biodiversity

Author

Flechas, Sandra V., Paz, Andrea, Crawford, Andrew J., Sarmiento, Carolina, Acevedo, Aldemar A., Arboleda, Alejandro, Bolívar-García, Wilmar, Echeverry-Sandoval, Claudia L., Franco, Rosmery, Mojica, Cindy, Muñoz, Amanda, Palacios-Rodríguez, Pablo, Posso-Terranova, Andrés M., Quintero-Marín, Paulina, Rueda-Solano, Luis A., Castro-Herrera, Fernando, and Amézquita, Adolfo

Published
2017

19. The feasibility, acceptability, and usability of telehealth visits

Author

Sinha Gregory, Naina, primary, Shukla, Alpana P., additional, Noel, Jahi J., additional, Alonso, Laura C., additional, Moxley, Jerad, additional, Crawford, Andrew J., additional, Martin, Peter, additional, Kumar, Sonal, additional, Leonard, John P., additional, and Czaja, Sara J., additional

Published
2023
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20. Taxonomic inflation and a reconsideration of speciation in the Andes: the case of the high-elevation tree frog Dendropsophus molitor (Anura: Hylidae).

Author

Arias-Cárdenas, Alexandra, Barrientos, Lucas S, Pardo-Diaz, Carolina, Paz, Andrea, Crawford, Andrew J, and Salazar, Camilo

Subjects
HYLIDAE, ANURA, GENETIC speciation, POPULATION differentiation, BIOLOGICAL classification, MORPHOMETRICS, MOLECULAR phylogeny
Abstract

Dendropsophus molitor is a hylid frog endemic to the Eastern Cordillera of the Colombian Andes, where it exhibits extensive geographic variation in size and colour pattern. Previous multivariate analyses of acoustic and genetic data suggested that northern and southern populations of D. molitor were distinct lineages, and consequently, the northern populations were described as Dendropsophus luddeckei. In this study, we conducted morphometric and genetic analyses of populations of D. molitor and D. luddeckei to test the validity of this recent taxonomic split. We sequenced the mitochondrial genes 12S, 16S, and COI , and the nuclear marker POMC , and also tested whether variation in the MC1R gene was associated with colour polymorphism in these frogs. Phylogenetic analyses recovered D. molitor and D. luddeckei as polyphyletic and species delimitation tests failed to recover them as separate lineages. Genetic differentiation between populations was mostly explained by high intra- and interpopulation variation in the absence of a north-south split, and we found no differences in morphometry between northern and southern populations. In addition, the coding region of MC1R is not associated with colour polymorphism. Thus, multiple lines of evidence suggest that D. luddeckei is not a valid species and D. molitor should be considered a single species. Our study highlights the danger of taxonomic inflation in the face of limited geographic sampling and a lack of clear diagnostic characters. [ABSTRACT FROM AUTHOR]

Published
2024
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24. Epistatic Effects Between Amino Acid Insertions and Substitutions Mediate Toxin resistance of Vertebrate Na+,K+-ATPases

Author

Mohammadi, Shabnam, primary, Özdemir, Halil İbrahim, additional, Ozbek, Pemra, additional, Sumbul, Fidan, additional, Stiller, Josefin, additional, Deng, Yuan, additional, Crawford, Andrew J, additional, Rowland, Hannah M, additional, Storz, Jay F, additional, Andolfatto, Peter, additional, and Dobler, Susanne, additional

Published
2022
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28. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Author

Dahn, Hollis A, Mountcastle, Jacquelyn, Balacco, Jennifer, Winkler, Sylke, Bista, Iliana, Schmitt, Anthony D, Pettersson, Olga Vinnere, Formenti, Giulio, Oliver, Karen, Smith, Michelle, Tan, Wenhua, Kraus, Anne, Mac, Stephen, Komoroske, Lisa M, Lama, Tanya, Crawford, Andrew J, Murphy, Robert W, Brown, Samara, Scott, Alan F, Morin, Phillip A, Jarvis, Erich D, Fedrigo, Olivier, Dahn, Hollis A [0000-0001-9777-2303], Mountcastle, Jacquelyn [0000-0003-1078-4905], Balacco, Jennifer [0000-0001-7102-1632], Winkler, Sylke [0000-0002-0915-3316], Bista, Iliana [0000-0002-6155-3093], Pettersson, Olga Vinnere [0000-0002-5597-1870], Formenti, Giulio [0000-0002-7554-5991], Smith, Michelle [0000-0001-5288-0001], Tan, Wenhua [0000-0002-5208-8126], Komoroske, Lisa M [0000-0003-0676-7053], Lama, Tanya [0000-0002-7372-8081], Crawford, Andrew J [0000-0003-3153-6898], Murphy, Robert W [0000-0001-8555-2338], Brown, Samara [0000-0003-0391-2016], Scott, Alan F [0000-0002-9706-7839], Morin, Phillip A [0000-0002-3279-1519], Jarvis, Erich D [0000-0001-8931-5049], Fedrigo, Olivier [0000-0002-6450-7551], and Apollo - University of Cambridge Repository

Subjects
High-Throughput Nucleotide Sequencing, Health Informatics, DNA, Sequence Analysis, DNA, HMW DNA extraction, Computer Science Applications, Molecular Weight, Benchmarking, long-read sequencing, Genetics, genome assembly, Animals, Dimethyl Sulfoxide, Genetik, tissue preservation, Edetic Acid
Abstract

Background Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. Results We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20–25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20–25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. Conclusion We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.

Published
2021

29. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, and Zhang, Guojie

Published
2022

30. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

31. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Author

Dahn, Hollis A., Mountcastle, Jacquelyn, Balacco, Jennifer, Winkler, Sylke, Bista, Iliana, Schmitt, Anthony D., Vinnere, Olga, Formenti, Giulio, Oliver, Karen, Smith, Michelle, Tan, Wenhua, Kraus, Anne, Mac, Stephen, Komoroske, Lisa M., Lama, Tanya, Crawford, Andrew J., Murphy, Robert W., Brown, Samara, Scott, Alan F., Morin, Phillip A., Jarvis, Erich D., Fedrigo, Olivier, Dahn, Hollis A., Mountcastle, Jacquelyn, Balacco, Jennifer, Winkler, Sylke, Bista, Iliana, Schmitt, Anthony D., Vinnere, Olga, Formenti, Giulio, Oliver, Karen, Smith, Michelle, Tan, Wenhua, Kraus, Anne, Mac, Stephen, Komoroske, Lisa M., Lama, Tanya, Crawford, Andrew J., Murphy, Robert W., Brown, Samara, Scott, Alan F., Morin, Phillip A., Jarvis, Erich D., and Fedrigo, Olivier

Abstract

Background: Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. Results: We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4 degrees C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4 degrees C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. Conclusion: We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all similar to 70,000 extant vertebrate species.

Published
2022
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32. Global urban environmental change drives adaptation in white clover

Author

Santangelo, James S., Ness, Rob W., Cohan, Beata, Fitzpatrick, Connor R., Innes, Simon G., Koch, Sophie, Miles, Lindsay S., Munim, Samreen, Peres-Neto, Pedro R., Prashad, Cindy, Tong, Alex T., Aguirre, Windsor E., Akinwole, Philips O., Alberti, Marina, Alvarez, Jackie, Anderson, Jill T., Anderson, Joseph J., Ando, Yoshino, Andrew, Nigel R., Angeoletto, Fabio, Anstett, Daniel N., Anstett, Julia, Aoki-Goncalves, Felipe, Arietta, A. Z. Andis, Arroyo, Mary T. K., Austen, Emily J., Baena-Diaz, Fernanda, Barker, Cory A., Baylis, Howard A., Beliz, Julia M., Benitez-Mora, Alfonso, Bickford, David, Biedebach, Gabriela, Blackburn, Gwylim S., Boehm, Mannfred M. A., Bonser, Stephen P., Bonte, Dries, Bragger, Jesse R., Branquinho, Cristina, Brans, Kristien, I, Bresciano, Jorge C., Brom, Peta D., Bucharova, Anna, Burt, Briana, Cahill, James F., Campbell, Katelyn D., Carlen, Elizabeth J., Carmona, Diego, Castellanos, Maria Clara, Centenaro, Giada, Chalen, Izan, Chaves, Jaime A., Chavez-Pesqueira, Mariana, Chen, Xiao-Yong, Chilton, Angela M., Chomiak, Kristina M., Cisneros-Heredia, Diego F., Cisse, Ibrahim K., Classen, Aimee T., Comerford, Mattheau S., Fradinger, Camila Cordoba, Corney, Hannah, Crawford, Andrew J., Crawford, Kerri M., Dahirel, Maxime, David, Santiago, De Haan, Robert, Deacon, Nicholas J., Dean, Clare, Del-Val, Ek, Deligiannis, Eleftherios K., Denney, Derek, Dettlaff, Margarete A., DiLeo, Michelle F., Ding, Yuan-Yuan, Dominguez-Lopez, Moises E., Dominoni, Davide M., Draud, Savannah L., Dyson, Karen, Ellers, Jacintha, Espinosa, Carlos, I, Essi, Liliana, Falahati-Anbaran, Mohsen, Falcao, Jessica C. F., Fargo, Hayden T., Fellowes, Mark D. E., Fitzpatrick, Raina M., Flaherty, Leah E., Flood, Padraic J., Flores, Maria F., Fornoni, Juan, Foster, Amy G., Frost, Christopher J., Fuentes, Tracy L., Fulkerson, Justin R., Gagnon, Edeline, Garbsch, Frauke, Garroway, Colin J., Gerstein, Aleeza C., Giasson, Mischa M., Girdler, E. Binney, Gkelis, Spyros, Godsoe, William, Golemiec, Anneke M., Golemiec, Mireille, Gonzalez-Lagos, Cesar, Gorton, Amanda J., Gotanda, Kiyoko M., Granath, Gustaf, Greiner, Stephan, Griffiths, Joanna S., Grilo, Filipa, Gundel, Pedro E., Hamilton, Benjamin, Hardin, Joyce M., He, Tianhua, Heard, Stephen B., Henriques, Andre F., Hernandez-Poveda, Melissa, Hetherington-Rauth, Molly C., Hill, Sarah J., Hochuli, Dieter F., Hodgins, Kathryn A., Hood, Glen R., Hopkins, Gareth R., Hovanes, Katherine A., Howard, Ava R., Hubbard, Sierra C., Ibarra-Cerdena, Carlos N., Iniguez-Armijos, Carlos, Jara-Arancio, Paola, Jarrett, Benjamin J. M., Jeannot, Manon, Jimenez-Lobato, Vania, Johnson, Mae, Johnson, Oscar, Johnson, Philip P., Johnson, Reagan, Josephson, Matthew P., Jung, Meen Chel, Just, Michael G., Kahilainen, Aapo, Kailing, Otto S., Karinho-Betancourt, Eunice, Karousou, Regina, Kirn, Lauren A., Kirschbaum, Anna, Laine, Anna-Liisa, LaMontagne, Jalene M., Lampei, Christian, Lara, Carlos, Larson, Erica L., Lazaro-Lobo, Adrian, Le, Jennifer H., Leandro, Deleon S., Lee, Christopher, Lei, Yunting, Leon, Carolina A., Tamara, Manuel E. Lequerica, Levesque, Danica C., Liao, Wan-Jin, Ljubotina, Megan, Locke, Hannah, Lockett, Martin T., Longo, Tiffany C., Lundholm, Jeremy T., MacGillavry, Thomas, Mackin, Christopher R., Mahmoud, Alex R., Manju, Isaac A., Marien, Janine, Martinez, D. Nayeli, Martinez-Bartolome, Marina, Meineke, Emily K., Mendoza-Arroyo, Wendy, Merritt, Thomas J. S., Merritt, Lila Elizabeth L., Migiani, Giuditta, Minor, Emily S., Mitchell, Nora, Bazargani, Mitra Mohammadi, Moles, Angela T., Monk, Julia D., Moore, Christopher M., Morales-Morales, Paula A., Moyers, Brook T., Munoz-Rojas, Miriam, Munshi-South, Jason, Murphy, Shannon M., Murua, Maureen M., Neila, Melisa, Nikolaidis, Ourania, Njunji, Iva, Nosko, Peter, Nunez-Farfan, Juan, Ohgushi, Takayuki, Olsen, Kenneth M., Opedal, Oystein H., Ornelas, Cristina, Parachnowitsch, Amy L., Paratore, Aaron S., Parody-Merino, Angela M., Paule, Juraj, Paulo, Octavio S., Pena, Joao Carlos, Pfeiffer, Vera W., Pinho, Pedro, Piot, Anthony, Porth, Ilga M., Poulos, Nicholas, Puentes, Adriana, Qu, Jiao, Quintero-Vallejo, Estela, Raciti, Steve M., Raeymaekers, Joost A. M., Raveala, Krista M., Rennison, Diana J., Ribeiro, Milton C., Richardson, Jonathan L., Rivas-Torres, Gonzalo, Rivera, Benjamin J., Roddy, Adam B., Rodriguez-Munoz, Erika, Roman, Jose Raul, Rossi, Laura S., Rowntree, Jennifer K., Ryan, Travis J., Salinas, Santiago, Sanders, Nathan J., Santiago-Rosario, Luis Y., Savage, Amy M., Scheepens, J. F., Schilthuizen, Menno, Schneider, Adam C., Scholier, Tiffany, Scott, Jared L., Shaheed, Summer A., Shefferson, Richard P., Shepard, Caralee A., Shykoff, Jacqui A., Silveira, Georgianna, Smith, Alexis D., Solis-Gabriel, Lizet, Soro, Antonella, Spellman, Katie, V, Whitney, Kaitlin Stack, Starke-Ottich, Indra, Stephan, Jorg G., Stephens, Jessica D., Szulc, Justyna, Szulkin, Marta, Tack, Ayco J. M., Tamburrino, Italo, Tate, Tayler D., Tergemina, Emmanuel, Theodorou, Panagiotis, Thompson, Ken A., Threlfall, Caragh G., Tinghitella, Robin M., Toledo-Chelala, Lilibeth, Tong, Xin, Uroy, Lea, Utsumi, Shunsuke, Vandegehuchte, Martijn L., VanWallendael, Acer, Vidal, Paula M., Wadgymar, Susana M., Wang, Ai-Ying, Wang, Nian, Warbrick, Montana L., Whitney, Kenneth D., Wiesmeier, Miriam, Wiles, J. Tristian, Wu, Jianqiang, Xirocostas, Zoe A., Yan, Zhaogui, Yao, Jiahe, Yoder, Jeremy B., Yoshida, Owen, Zhang, Jingxiong, Zhao, Zhigang, Ziter, Carly D., Zuellig, Matthew P., Zufall, Rebecca A., Zurita, Juan E., Zytynska, Sharon E., Johnson, Marc T. J., Santangelo, James S., Ness, Rob W., Cohan, Beata, Fitzpatrick, Connor R., Innes, Simon G., Koch, Sophie, Miles, Lindsay S., Munim, Samreen, Peres-Neto, Pedro R., Prashad, Cindy, Tong, Alex T., Aguirre, Windsor E., Akinwole, Philips O., Alberti, Marina, Alvarez, Jackie, Anderson, Jill T., Anderson, Joseph J., Ando, Yoshino, Andrew, Nigel R., Angeoletto, Fabio, Anstett, Daniel N., Anstett, Julia, Aoki-Goncalves, Felipe, Arietta, A. Z. Andis, Arroyo, Mary T. K., Austen, Emily J., Baena-Diaz, Fernanda, Barker, Cory A., Baylis, Howard A., Beliz, Julia M., Benitez-Mora, Alfonso, Bickford, David, Biedebach, Gabriela, Blackburn, Gwylim S., Boehm, Mannfred M. A., Bonser, Stephen P., Bonte, Dries, Bragger, Jesse R., Branquinho, Cristina, Brans, Kristien, I, Bresciano, Jorge C., Brom, Peta D., Bucharova, Anna, Burt, Briana, Cahill, James F., Campbell, Katelyn D., Carlen, Elizabeth J., Carmona, Diego, Castellanos, Maria Clara, Centenaro, Giada, Chalen, Izan, Chaves, Jaime A., Chavez-Pesqueira, Mariana, Chen, Xiao-Yong, Chilton, Angela M., Chomiak, Kristina M., Cisneros-Heredia, Diego F., Cisse, Ibrahim K., Classen, Aimee T., Comerford, Mattheau S., Fradinger, Camila Cordoba, Corney, Hannah, Crawford, Andrew J., Crawford, Kerri M., Dahirel, Maxime, David, Santiago, De Haan, Robert, Deacon, Nicholas J., Dean, Clare, Del-Val, Ek, Deligiannis, Eleftherios K., Denney, Derek, Dettlaff, Margarete A., DiLeo, Michelle F., Ding, Yuan-Yuan, Dominguez-Lopez, Moises E., Dominoni, Davide M., Draud, Savannah L., Dyson, Karen, Ellers, Jacintha, Espinosa, Carlos, I, Essi, Liliana, Falahati-Anbaran, Mohsen, Falcao, Jessica C. F., Fargo, Hayden T., Fellowes, Mark D. E., Fitzpatrick, Raina M., Flaherty, Leah E., Flood, Padraic J., Flores, Maria F., Fornoni, Juan, Foster, Amy G., Frost, Christopher J., Fuentes, Tracy L., Fulkerson, Justin R., Gagnon, Edeline, Garbsch, Frauke, Garroway, Colin J., Gerstein, Aleeza C., Giasson, Mischa M., Girdler, E. Binney, Gkelis, Spyros, Godsoe, William, Golemiec, Anneke M., Golemiec, Mireille, Gonzalez-Lagos, Cesar, Gorton, Amanda J., Gotanda, Kiyoko M., Granath, Gustaf, Greiner, Stephan, Griffiths, Joanna S., Grilo, Filipa, Gundel, Pedro E., Hamilton, Benjamin, Hardin, Joyce M., He, Tianhua, Heard, Stephen B., Henriques, Andre F., Hernandez-Poveda, Melissa, Hetherington-Rauth, Molly C., Hill, Sarah J., Hochuli, Dieter F., Hodgins, Kathryn A., Hood, Glen R., Hopkins, Gareth R., Hovanes, Katherine A., Howard, Ava R., Hubbard, Sierra C., Ibarra-Cerdena, Carlos N., Iniguez-Armijos, Carlos, Jara-Arancio, Paola, Jarrett, Benjamin J. M., Jeannot, Manon, Jimenez-Lobato, Vania, Johnson, Mae, Johnson, Oscar, Johnson, Philip P., Johnson, Reagan, Josephson, Matthew P., Jung, Meen Chel, Just, Michael G., Kahilainen, Aapo, Kailing, Otto S., Karinho-Betancourt, Eunice, Karousou, Regina, Kirn, Lauren A., Kirschbaum, Anna, Laine, Anna-Liisa, LaMontagne, Jalene M., Lampei, Christian, Lara, Carlos, Larson, Erica L., Lazaro-Lobo, Adrian, Le, Jennifer H., Leandro, Deleon S., Lee, Christopher, Lei, Yunting, Leon, Carolina A., Tamara, Manuel E. Lequerica, Levesque, Danica C., Liao, Wan-Jin, Ljubotina, Megan, Locke, Hannah, Lockett, Martin T., Longo, Tiffany C., Lundholm, Jeremy T., MacGillavry, Thomas, Mackin, Christopher R., Mahmoud, Alex R., Manju, Isaac A., Marien, Janine, Martinez, D. Nayeli, Martinez-Bartolome, Marina, Meineke, Emily K., Mendoza-Arroyo, Wendy, Merritt, Thomas J. S., Merritt, Lila Elizabeth L., Migiani, Giuditta, Minor, Emily S., Mitchell, Nora, Bazargani, Mitra Mohammadi, Moles, Angela T., Monk, Julia D., Moore, Christopher M., Morales-Morales, Paula A., Moyers, Brook T., Munoz-Rojas, Miriam, Munshi-South, Jason, Murphy, Shannon M., Murua, Maureen M., Neila, Melisa, Nikolaidis, Ourania, Njunji, Iva, Nosko, Peter, Nunez-Farfan, Juan, Ohgushi, Takayuki, Olsen, Kenneth M., Opedal, Oystein H., Ornelas, Cristina, Parachnowitsch, Amy L., Paratore, Aaron S., Parody-Merino, Angela M., Paule, Juraj, Paulo, Octavio S., Pena, Joao Carlos, Pfeiffer, Vera W., Pinho, Pedro, Piot, Anthony, Porth, Ilga M., Poulos, Nicholas, Puentes, Adriana, Qu, Jiao, Quintero-Vallejo, Estela, Raciti, Steve M., Raeymaekers, Joost A. M., Raveala, Krista M., Rennison, Diana J., Ribeiro, Milton C., Richardson, Jonathan L., Rivas-Torres, Gonzalo, Rivera, Benjamin J., Roddy, Adam B., Rodriguez-Munoz, Erika, Roman, Jose Raul, Rossi, Laura S., Rowntree, Jennifer K., Ryan, Travis J., Salinas, Santiago, Sanders, Nathan J., Santiago-Rosario, Luis Y., Savage, Amy M., Scheepens, J. F., Schilthuizen, Menno, Schneider, Adam C., Scholier, Tiffany, Scott, Jared L., Shaheed, Summer A., Shefferson, Richard P., Shepard, Caralee A., Shykoff, Jacqui A., Silveira, Georgianna, Smith, Alexis D., Solis-Gabriel, Lizet, Soro, Antonella, Spellman, Katie, V, Whitney, Kaitlin Stack, Starke-Ottich, Indra, Stephan, Jorg G., Stephens, Jessica D., Szulc, Justyna, Szulkin, Marta, Tack, Ayco J. M., Tamburrino, Italo, Tate, Tayler D., Tergemina, Emmanuel, Theodorou, Panagiotis, Thompson, Ken A., Threlfall, Caragh G., Tinghitella, Robin M., Toledo-Chelala, Lilibeth, Tong, Xin, Uroy, Lea, Utsumi, Shunsuke, Vandegehuchte, Martijn L., VanWallendael, Acer, Vidal, Paula M., Wadgymar, Susana M., Wang, Ai-Ying, Wang, Nian, Warbrick, Montana L., Whitney, Kenneth D., Wiesmeier, Miriam, Wiles, J. Tristian, Wu, Jianqiang, Xirocostas, Zoe A., Yan, Zhaogui, Yao, Jiahe, Yoder, Jeremy B., Yoshida, Owen, Zhang, Jingxiong, Zhao, Zhigang, Ziter, Carly D., Zuellig, Matthew P., Zufall, Rebecca A., Zurita, Juan E., Zytynska, Sharon E., and Johnson, Marc T. J.

Abstract

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural dines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.

Published
2022
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33. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022
Full Text
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34. Standards recommendations for the Earth BioGenome Project

Author

National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

35. Epistatic Effects Between Amino Acid Insertions and Substitutions Mediate Toxin resistance of Vertebrate Na+, K+-ATPases

Author

Mohammadi, Shabnam, Özdemir, Halil İbrahim, Ozbek, Pemra, Sumbul, Fidan, Stiller, Josefin, Deng, Yuan, Crawford, Andrew J, Rowland, Hannah, Storz, Jay, Andolfatto, Peter, Dobler, Susanne, Mohammadi, Shabnam, Özdemir, Halil İbrahim, Ozbek, Pemra, Sumbul, Fidan, Stiller, Josefin, Deng, Yuan, Crawford, Andrew J, Rowland, Hannah, Storz, Jay, Andolfatto, Peter, and Dobler, Susanne

Abstract

The recurrent evolution of resistance to cardiotonic steroids (CTS) across diverse animals most frequently involves convergent amino-acid substitutions in the H1-H2 extracellular loop of Na+, K + -ATPase (NKA). Previous work revealed that hystricognath rodents (e.g. chinchilla) and pterocliform birds (sandgrouse) have convergently evolved amino-acid insertions in the H1-H2 loop, but their functional significance was not known. Using protein engineering, we show that these insertions have distinct effects on CTS resistance in homologs of each of the two species that strongly depend on intramolecular interactions with other residues. Removing the insertion in the chinchilla NKA unexpectedly increases CTS resistance and decreases NKA activity. In the sandgrouse NKA, the amino acid insertion and substitution Q111R both contribute to an augmented CTS resistance without compromising ATPase activity levels. Molecular docking simulations provide additional insight into the biophysical mechanisms responsible for the context-specific mutational effects on CTS insensitivity of the enzyme. Our results highlight the diversity of genetic substrates that underlie CTS insensitivity in vertebrate NKA and reveal how amino-acid insertions can alter the phenotypic effects of point mutations at key sites in the same protein domain.

Published
2022

36. The Earth BioGenome Project 2020:Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., and Zhang, Guojie

Published
2022

38. Landscape Genetics and Species Delimitation in the Andean Palm Rocket Frog (Aromobatidae, Rheobates)

Author

Genty, Gabrielle, Guarnizo, Carlos E., Ramírez, Juan P., Barrientos, Lucas S., and Crawford, Andrew J.

Subjects
Article Subject, Colombia, genetic distance, historical demography, isolation by distance, isolation by environment, phylogeography, Genetics, Animal Science and Zoology, Molecular Biology, Ecology, Evolution, Behavior and Systematics
Abstract

The complex topography of the species-rich northern Andes creates heterogeneous environmental landscapes that are hypothesized to have promoted population fragmentation and diversification by processes such as vicariance or local adaptation. Previous phylogenetic work on the palm rocket frog (Anura: Aromobatidae: Rheobates spp.), endemic to midelevation forests of Colombia, suggested that valleys were important in promoting divergence between lineages. In this study, we first evaluated previous hypotheses of species-level diversity, then fitted an isolation-with-migration (IM) historical demographic model, and tested two landscape genetic models to explain genetic divergence within Rheobates: isolation by distance and isolation by environment. The data consisted of two mitochondrial and four nuclear genes from 24 samples covering most of the geographic range of the genus. Species delimitation by Bayesian Phylogenetics and Phylogeography recovered five highly divergent genetic lineages within Rheobates, among which few to no migrants are exchanged according to IM. We found that isolation by environment provided the only variable significantly correlated with genetic distances for both mitochondrial and nuclear genes, suggesting that local adaptation may have a role in driving the genetic divergence within this frog genus. Thus, genetic divergence in Rheobates may be driven more by variation among the local environments where these frogs live rather than by geographic distance.

Published
2022
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42. DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age

Author

Mulcahy, Daniel G., primary, Ibáñez, Roberto, additional, Jaramillo, Cesar A., additional, Crawford, Andrew J., additional, Ray, Julie M., additional, Gotte, Steve W., additional, Jacobs, Jeremy F., additional, Wynn, Addison H., additional, Gonzalez-Porter, Gracia P., additional, McDiarmid, Roy W., additional, Crombie, Ronald I., additional, Zug, George R., additional, and de Queiroz, Kevin, additional

Published
2022
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44. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., primary, Richards, Stephen, additional, Lieberman Aiden, Erez, additional, Allende, Miguel L., additional, Archibald, John M., additional, Bálint, Miklós, additional, Barker, Katharine B., additional, Baumgartner, Bridget, additional, Belov, Katherine, additional, Bertorelle, Giorgio, additional, Blaxter, Mark L., additional, Cai, Jing, additional, Caperello, Nicolette D., additional, Carlson, Keith, additional, Castilla-Rubio, Juan Carlos, additional, Chaw, Shu-Miaw, additional, Chen, Lei, additional, Childers, Anna K., additional, Coddington, Jonathan A., additional, Conde, Dalia A., additional, Corominas, Montserrat, additional, Crandall, Keith A., additional, Crawford, Andrew J., additional, DiPalma, Federica, additional, Durbin, Richard, additional, Ebenezer, ThankGod E., additional, Edwards, Scott V., additional, Fedrigo, Olivier, additional, Flicek, Paul, additional, Formenti, Giulio, additional, Gibbs, Richard A., additional, Gilbert, M. Thomas P., additional, Goldstein, Melissa M., additional, Graves, Jennifer Marshall, additional, Greely, Henry T., additional, Grigoriev, Igor V., additional, Hackett, Kevin J., additional, Hall, Neil, additional, Haussler, David, additional, Helgen, Kristofer M., additional, Hogg, Carolyn J., additional, Isobe, Sachiko, additional, Jakobsen, Kjetill Sigurd, additional, Janke, Axel, additional, Jarvis, Erich D., additional, Johnson, Warren E., additional, Jones, Steven J. M., additional, Karlsson, Elinor K., additional, Kersey, Paul J., additional, Kim, Jin-Hyoung, additional, Kress, W. John, additional, Kuraku, Shigehiro, additional, Lawniczak, Mara K. N., additional, Leebens-Mack, James H., additional, Li, Xueyan, additional, Lindblad-Toh, Kerstin, additional, Liu, Xin, additional, Lopez, Jose V., additional, Marques-Bonet, Tomas, additional, Mazard, Sophie, additional, Mazet, Jonna A. K., additional, Mazzoni, Camila J., additional, Myers, Eugene W., additional, O’Neill, Rachel J., additional, Paez, Sadye, additional, Park, Hyun, additional, Robinson, Gene E., additional, Roquet, Cristina, additional, Ryder, Oliver A., additional, Sabir, Jamal S. M., additional, Shaffer, H. Bradley, additional, Shank, Timothy M., additional, Sherkow, Jacob S., additional, Soltis, Pamela S., additional, Tang, Boping, additional, Tedersoo, Leho, additional, Uliano-Silva, Marcela, additional, Wang, Kun, additional, Wei, Xiaofeng, additional, Wetzer, Regina, additional, Wilson, Julia L., additional, Xu, Xun, additional, Yang, Huanming, additional, Yoder, Anne D., additional, and Zhang, Guojie, additional

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2022
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45. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Author

Dahn, Hollis A, primary, Mountcastle, Jacquelyn, additional, Balacco, Jennifer, additional, Winkler, Sylke, additional, Bista, Iliana, additional, Schmitt, Anthony D, additional, Pettersson, Olga Vinnere, additional, Formenti, Giulio, additional, Oliver, Karen, additional, Smith, Michelle, additional, Tan, Wenhua, additional, Kraus, Anne, additional, Mac, Stephen, additional, Komoroske, Lisa M, additional, Lama, Tanya, additional, Crawford, Andrew J, additional, Murphy, Robert W, additional, Brown, Samara, additional, Scott, Alan F, additional, Morin, Phillip A, additional, Jarvis, Erich D, additional, and Fedrigo, Olivier, additional

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2022
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47. Comentario sobre el artículo EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity conservation and sustainable development de Joseph E. A. Huddart, Andrew J. Crawford, Arturo L. Luna-Tapia, Silvia Restrepo y Federica Di Palma

Author

J Crawford, Andrew J, Restrepo, Silvia, and Academia Colombiana de Ciencias Exactas, Físicas y Naturales

Subjects
General Energy, History and Philosophy of Science, General Mathematics, General Earth and Planetary Sciences, General Physics and Astronomy, General Chemistry, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology
Abstract

PNAS 2022. Vol. 119 (4)e2115641119.https://doi.org/10.1073/pnas.2115641119

Published
2022
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48. Boana platanera Escalona & Marca & Castellanos & Fouquet & Crawford & Rojas-Runjaic & Giaretta & Señaris & Castroviejo-Fisher 2021, sp. nov

Author

Escalona, Moisés, Marca, Enrique La, Castellanos, Michelle, Fouquet, Antoine, Crawford, Andrew J., Rojas-Runjaic, Fernando J. M., Giaretta, Ariovaldo A., Señaris, J. Celsa, and Castroviejo-Fisher, Santiago

Subjects
Amphibia, Hylidae, Boana platanera, Animalia, Biodiversity, Boana, Anura, Chordata, Taxonomy
Abstract

Boana platanera sp. nov. La Marca, Escalona, Castellanos, Rojas-Runjaic, Crawford, Señaris, Fouquet, Giaretta, and Castroviejo-Fisher (Figs. 2, 4–6, 8J, 10) Suggested common name: Banana tree dwelling frog (rana platanera, in Spanish). Boana xerophylla —populations north of the Orinoco River, Dubois (2017); Rojas-Runjaic & Infante-Rivero (2018); populations north of the Orinoco River, Barrio-Amorós et al. (2019); populations north of the Orinoco River, Escalona et al. (2019a); Cañizales (2020). Hypsiboas xerophyllus —populations north of the Orinoco River, Orrico et al. (2017). Hypsiboas crepitans —populations north of the Orinoco River, Faivovich et al. (2005); populations north of the Orinoco River, Köhler (2010); Lehtinen (2014); Guarnizo et al. (2015). Hyla crepitans — Lutz (1927); Shreve (1947); Alemán (1953); Ginés (1959); Röhl (1959); Rivero (1961); Fouquette (1966); Solano de Chacín (1968); Kenny (1969); populations north of the Orinoco River, Duellman (1970, 1997, 2001); populations north of the Orinoco River, Cochran & Goin (1970); Donoso-Barros & León (1972); Yústiz (1976); Kluge (1979); La Marca (1992); Kime et al. (2000); Lynch & Vargas Ramírez (2000); Lynch & Suárez-Mayorga (2001); Bernal et al. (2004); Nava (2005); populations from Colombia and Panama, Vanzolini & Myers (2015). Holotype. Adult male, ULABG 7758 (field number MES 018; Figs. 2, 4), from 2 km of La Soledad, on the road from Barinitas to Santo Domingo, Barinas state, Venezuela (08º48’26’’ N, 70º30’46’’ W [datum: WGS 84]; 947 m asl; Fig. 7A), collected by Enrique La Marca, Moisés Escalona, and Iván Mendoza, on June 13, 2012. Paratypes. Three adult male specimens, ULABG 7759–7761, topotypes, same data as holotype (Fig. 5). Three adult male specimens, ULABG 7762–7764, from La Soledad, Barinas state, Venezuela (08º48’35’’ N, 70º31’31’’ W [datum: WGS 84] 980 m asl), collected by Enrique La Marca, Moisés Escalona, and Iván Mendoza, on June 13, 2012. Referred specimens. Up to 497 specimens were used to assess the genetic and phenotypic variation, although they are not included in the type series. In addition, we analyzed the calls of eleven non-vouchered specimens. See Appendices 1–3 for details. Generic placement. The new species is assigned to Boana, within the B. faber group (sensu Faivovich et al. 2005), based on the results of the phylogenetic analyses (Fig. 1). Definition. The new species is defined by the combination of the following characters: (1) moderately large size, snout-vent length (SVL) 54.33–74.74 mm in females (n = 76) and 46.57–63.34 mm in males (n = 195); (2) head narrower than body, flat in dorsal view; (3) snout truncated (slightly rounded in some individuals) in dorsal and lateral view; nostrils protuberant; (4) horizontal pupil; first half of palpebral membrane densely pigmented with black dots; (5) supratympanic fold extents posteriorly from posterior eye corner and slopes downward to a point above arm insertion; (6) distance between tympanum and eye equal to or shorter than half tympanum diameter; (7) forearm relatively more robust than arm; fingers moderately long and slender with large rounded discs; (8) adult males with prepollical spine, protruding through distal end in some cases; (9) hand-web formula I 0–0 II (1–1 +)– (1–1 +) III 1.5–(2 - –2 +) IV; (10) foot-web formula I 1.5–1 + II (2 - –2 +)–(2–3 -) III 3–(2 - –3 -) IV (3–3 -)–(3 - –3 +) V; (11) cloacal opening at thighs upper level, with supracloacal fold directed posteriorly; pericloacal region dark-brown with a white-colored crenulated supracloacal fold; (12) skin areolate on throat, chest, belly, and ventral surfaces of thighs; (13) dorsal skin smooth, slightly granulated on flanks; (14) poorly developed ulnar fold extending along finger IV external side; (15) tarsal fold poorly evident; (16) calcars absent; (17) adult males with vocal sac single, median, subgular, and moderately distensible (Fig. 6H); (18) dorsal coloration is variable at night, from almost uniform pale yellowish ocher, reddish brown, to conspicuously marbled with more or less well-defined dark-brown marks, and an irregular or broad X-shaped on the mid dorsum (Fig. 6); (19) in preservative, palms and soles pale cream-colored, hand and foot webs cream with dark brown flecks, especially on foot. Diagnosis. Character states of compared species are given in parentheses. Boana platanera is sister of B. xerophylla (Fig. 1) and it can be diagnosed from the latter by the following combination of adult male characters: a pale orange-yellow or light brown coloration on dorsum (dark brown to green tones; Fig. 8I, J); presence of black or dark brown speckles in the anterior half of the palpebral membrane (absent; Fig. 9); pericloacal region dark brown (cream); advertisement call with shorter, 28−71 ms, first note length (79–124 ms in call type I and 85−110 ms in call type II), composed of five notes (one note in call type I). Although not diagnostic, the following characters may help to differentiate both species: the new species has a statistically significant larger body (46.57–63.34 mm) than B. xerophylla (45.13–56.71 mm) (Table 2 in Escalona et al. 2019a); in preservative, the gular region is cream with dark brown or black flecks near to the jaw border (cream and sometimes with few dark brown speckles on the border of the jaw; Fig. 9); advertisement call with statistically significant longer pulse interval (11−23 ms) than B. xerophylla (12–14 ms in call type I and 11−14 ms in call type II); statistically significant longer second phase length (137−312 ms) than B. xerophylla (73−150 ms in call type II). Boana platanera is sympatric with B. pugnax in lowland western and central Venezuela, as well as some regions in Colombia and Panama. The new species is distinguished from B. pugnax by having a pale orange-yellow or light brown coloration on dorsum (dark-brown to dark-grey tones; Fig. 8G, J); the anterior half of the palpebral membrane densely pigmented (poorly pigmented); dorsal surfaces of finger and toe discs usually cream, when pigmented, pale gray (dark); calcar absent (poorly developed); a complex advertisement call composed of five notes (simple call of one note). Although not diagnostic, B. platanera is distinguished from B. pugnax by having a statistically significant smaller body (males: B. platanera: 46.57–63.34 mm; B. pugnax: 55.85–74.80 mm [sample from western Venezuela]; Table 4); and a statistically significant longer advertisement call (B. platanera: 200−451 ms; B. pugnax: 156–258 ms). The new species differs from Boana crepitans by having a pale orange-yellow or light brown coloration on dorsum (gray-cream tones to dark brown; Fig. 8H, J); advertisement call composed of five notes (two notes). Although not diagnostic, the new species has a statistically significant shorter ETD (eye to tympanum distance; B. platanera: 0.96–2.78 mm) than B. crepitans (1.99–3.29 mm) (Tables 1–2 in Escalona et al. 2019a); statistically significant shorter advertisement call (B. platanera: 200−451 ms; B. crepitans: 368−473 ms), with a statistically significant shorter second phase (B. platanera: 137−312 ms; B. crepitans: 278−367 ms) (Tables 2, 3 in Escalona et al. 2019a). Boana platanera differs from B. rosenbergi by having a smooth dorsum, thighs, and flanks (rough or with tubercles in at least one of these regions; Fig. 8F, J); smaller body size (males: B. platanera: 46.57–63.34 mm; B. rosenbergi: 75.55–83.98 mm); presence of black dots on anterior half of the palpebral membrane (absent); ulnar fold smooth (slightly crenulated); and a complex advertisement call (simple in B. rosenbergi) with shorter duration (B. platanera: 200−451 ms; B. rosenbergi: 551–759 ms) (Table 2). The new species differs from Boana exastis by having a smooth dorsum, thighs, and flanks (rough or with tubercles in at least one of these regions; Fig. 8D, J); smaller body size (males: B. platanera: 46.57–63.34 mm; B. exastis: 81.1–99.0 mm); presence of black dots on anterior half of the palpebral membrane (absent); poorly-defined dermal fringes on limbs (crenulated dermal fringes), less webbing in hands and feet (more extensive webbing in hands and feet), absence of cloacal plate (presence); absence of calcars (presence); complex advertisement call (simple in B. exastis), with shorter duration (B. platanera: 200−451 ms; B. exastis: 807–1229 ms) (Table 2). Boana platanera differs from B. lundii by having a smooth dorsum, thighs, and flanks (rough or with tubercles in at least one of these regions; Fig. 8E, J); presence of black dots on anterior half of the palpebral membrane (absence); poorly-defined dermal fringes on limbs (well defined); less webbing in hands and feet (more webbing in hands and feet); absence of calcars (presence); complex advertisement call (simple), with shorter duration (B. platanera: 200−451 ms; B. lundii: 834–1228 ms) (Table 2). The new species differs from Boana pardalis by having a smooth dorsum, thighs, and flanks (rough or with tubercles in at least one these regions; Fig. 8C, J); presence of black dots on first half of the palpebral membrane (absence); poorly-defined dermal fringes on limbs (crenulated); less webbing in hands and feet (more webbing in hands and feet); absence of cloacal plate (presence); absence of calcars (presence); complex advertisement call (simple), with longer duration (B. platanera: 200−451 ms; B. pardalis: 117–143 ms), composed of 4–6 notes (one) (Table 2). Boana platanera differs from B. faber by having a smaller body size (males: B. platanera: 46.57–63.34 mm; B. faber: 77.90–97.08 mm); presence of black dots on anterior half of the palpebral membrane (absence); ulnar fold present (absent); cream gular coloration with dark-brown flecks near to the jaw border (dark); complex advertisement call (simple), longer advertisement call (B. platanera: 200−451 ms; B. faber: 75–121 ms), composed of 4–6 notes (one note), with higher fundamental frequency (B. platanera: 542.7−1125.0 Hz; B. faber: 344.5–447.9 Hz) (Table 2). Boana platanera is readily distinguishable from B. albomarginata by having a smooth dorsal skin (slightly granular in B. albomarginata), a pale orange-yellow coloration with dark-brown marks, irregular or broad X-shaped on the dorsum and dark-brown bars on flanks and thighs (green with some white spots on the dorsum; Fig. 8A, J); supratympanic fold slopes downward to a point above arm insertion (supratympanic extends posteriorly until half of the laterodorsal region); absence of calcar (presence); complex advertisement call (simple), with longer duration (B. platanera: 200−451 ms; B. albomarginata: 166–185 ms), with 4–6 notes (one note), and lower fundamental frequency (B. platanera: 542.7−1125.0 Hz; B. albomarginata: 1136.9–1231.7 Hz) (Table 2).Although not diagnostic, the new species is larger bodied (males: B. platanera: 51.97–59.08 mm; B. albomarginata: 44.68–53.6 mm). Holotype description. Adult male in a good state of preservation (Fig. 4), with a piece of tissue sampled from the right thigh. Morphometric measurements of the holotype are presented in Table 5. Body slender; head wider than long (HW/HeL = 1.06); snout truncated in lateral and dorsal views; nostrils protuberant, oblique and directed dorsolaterally; internarial distance smaller (66 %) than eye-to-nostril distance; eye diameter, upper eyelid width and interorbital distance approximately equal to tympanum diameter; canthus rostralis rounded, almost indistinct; loreal region concave; lips not flared; eyes large (ED/HeL = 0.28), protruding; interorbital region and dorsal surface of snout slightly concave. Tympanum conspicuous, nearly circular; tympanic membrane differentiated; tympanic annulus well-defined, with upper border concealed by the tympanic membrane. Vocal sac single, subgular; vocal slits large, located at the posterolateral edge of the mouth floor. Tongue wider than long, cordiform, slightly notched behind; almost completely attached to mouth floor. Choanae elliptical, widely separate. Vomerine teeth massive; vomerine processes arched, slightly separate and between choanae. Arms slender; forearms more robust than upper arms; an inconspicuous crenulated fringe along forearm ventroexternal surface and prolateral side finger IV (more conspicuous on right forearm). Hand with an elliptical and flat palmar tubercle and an inconspicuous thenar tubercle; prepollex well-developed, with a single curved spine (Fig. 4); numerous small supernumerary tubercles scattered on the palm; relative fingers length: III>IV>II>I; subarticular tubercles single, rounded to conical and prominent; fingers discs large, expanded and nearly circular; disc on first finger slightly smaller than those of other fingers; third finger disc diameter about 50 % of eye diameter and approximately 60 % of tympanum diameter; hand-webbing formula: I 0–0 II 1 + –1 III 1.5–2 + IV. Legs long and slender; thigh length slightly longer than shank length (FL/TL = 1.01); without calcars—the protrusion of the skin fold on the right heel, which resembles a calcar, is caused by the fixation position of the hind limbs, with the feet oriented posteriorly; tarsal fringe not evident; foot with an elliptical inner metatarsal tubercle; outer metatarsal tubercle not evident; subarticular tubercles single, rounded and prominent; supernumerary tubercles scarce, small, and flat; toes extensively webbed, with rounded and expanded disks; foot-web formula: I 1.5–1 + II 2 + –2 III 3–3 - IV 3–3 + V. Skin on dorsal surfaces smooth; throat, chest, belly and ventral surface of thighs areolate; supracloacal fold crenulated; pericloacal region tuberculate. Color of euthanized holotype. The holotype was photographed two minutes after anesthesia and the following description was based in those photographs. Dorsum with a large dark brown irregular blotch over an olive background; flanks olive with vertical narrow brown bands; groin and postero-ventral part of flank orange; throat and chest dark gray; chin olive with dark brown markings; upper part of venter gray; middle and lower part of venter reddish orange, with gray tubercles; upper parts of extremities gray to olive, with brown bands or markings; foot web reddish; iris light greenish gray with fine dark venation. Color of holotype in preservative. Dorsum pale brown with dark-brown irregular blotches without a defined pattern, darker on dorsum than on head (Fig. 4); upper surface of arms pale brown, with one dark-brown incomplete band on forearm, wider on the external edge; dorsal surface of hands with one dark-brown incomplete band (more evident on the right hand); third and fourth fingers with the same coloration of arms; first and second fingers pale cream colored; dorsal surface of thighs pale brown with dark brown bars that form an irregular reticular pattern; dorsal surface of shanks, metatarsus and toes pale brown with dark brown blotches without a defined pattern; webbing on hands cream colored with dark brown flecks. Flanks cream with dark-brown vertical lines. Pericloacal region dark brown surrounded by white. Ventral surfaces of arms, forearms and hand palms pale cream; pattern on dorsal surface of thigh partially extended to ventral surface; lower edge of thighs pale cream; shanks pale brown with dark brown blotches; metatarsus, feet and foot-web cream with numerous dark brown flecks; throat cream with dark brown flecks, mostly in borders of the mouth; chest and belly pale cream. Variation in morphology. The variation of external measurements, as well as hand and foot webbing formula of some type specimens and from all the specimens examined is shown in Table 5. There is sexual dimorphism in body size, with males generally smaller than females (males: 46.57–63.34 mm; females: 54.33–74.74 mm), and by the presence of a prominent prepollical spine in males (Figs. 5, 6). Color variation in life. When active at night, adult specimens have a yellow, tan, to light brown coloration, with brown patterns (irregular in shape or with a broad X-shaped blotch near the head; some specimens have a brown vertebral line) on dorsum (Figs. 6A, 7C). Brown dots are spread on the flanks, above the upper lip, on the limbs, and on the webbings. Some specimens have a brown line delimiting the supratympanic fold. Some specimens have apparent scars on the dorsum. There is a brown blotch with a white line on the upper margin on heels and cloacal region. There are several vertical brown bars on flanks and transversal brown bars on the thighs. White coloration predominates along all the ventral surfaces, with strong orange or pinkish tones on the belly, arms, and thighs. In some specimens, the dorsal brown bars of the thighs are projected on the internal portion. The tarsus has two colorations delimited by the tarsal fold. The outer portion of the tarsus has a brown coloration with orange tones, while the internal portion has orange coloration. Some specimens have some brown spots around the mandible, on the upper portion of the thigh, and/or the webbing at the hands and foots. During the day, when normally are inactive, they have a pale cream coloration (Fig. 6E). The brown patterns and spots, when visible, are pale gray, and the bars on the flanks and thighs are dark brown almost black. Juvenile specimens have a pale green coloration with black diffuse dots on the dorsum (Fig. 6F). During the night, the iris around the pupil is metallic gray color and the outer area is pale emerald (Fig. 6A, C, D). Color variation in preservative. Coloration pattern of paratopotypes in preservative is depicted in Fig. 5. Specimens from localities other than the type locality show some color variation, as follows: dorsum occasionally may be uniformly pale-brown (e.g., ULABG 2950, 2951, 7755, 7803), sometimes bearing two scapular dark brown spots (e.g., ULABG 5338), or few scattered small dots on sacral region (e.g., ULABG 5337, 5338) or dorsum (e.g., ULABG 7745). Some specimens tend to have an ashy background with irregular markings (e.g., ULABG 5060, 6902, 7753) and, very rarely, have a lichen aspect (e.g., ULABG 7756, 7757). More often, dorsum bears large blotches that may be irregular

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2021
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50. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Author

Dahn, Hollis A., primary, Mountcastle, Jacquelyn, additional, Balacco, Jennifer, additional, Winkler, Sylke, additional, Bista, Iliana, additional, Schmitt, Anthony D., additional, Pettersson, Olga Vinnere, additional, Formenti, Giulio, additional, Oliver, Karen, additional, Smith, Michelle, additional, Tan, Wenhua, additional, Kraus, Anne, additional, Mac, Stephen, additional, Komoroske, Lisa M., additional, Lama, Tanya, additional, Crawford, Andrew J., additional, Murphy, Robert W., additional, Brown, Samara, additional, Scott, Alan F., additional, Morin, Phillip A., additional, Jarvis, Erich D., additional, and Fedrigo, Olivier, additional

Published
2021
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