Playfish Playfish
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
1 Exon Probe Sets and Bioinformatics Pipelines for All Levels of Fish Phylogenomics
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics 2 3 Lily C. Hughes1,2,3,*, Guillermo Ortí1,3, Hadeel Saad1, Chenhong Li4, William T. White5, Carole 4 C. Baldwin3, Keith A. Crandall1,2, Dahiana Arcila3,6,7, and Ricardo Betancur-R.7 5 6 1 Department of Biological Sciences, George Washington University, Washington, D.C., U.S.A. 7 2 Computational Biology Institute, Milken Institute of Public Health, George Washington 8 University, Washington, D.C., U.S.A. 9 3 Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian 10 Institution, Washington, D.C., U.S.A. 11 4 College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China 12 5 CSIRO Australian National Fish Collection, National Research Collections of Australia, 13 Hobart, TAS, Australia 14 6 Sam Noble Oklahoma Museum of Natural History, Norman, O.K., U.S.A. 15 7 Department of Biology, University of Oklahoma, Norman, O.K., U.S.A. 16 17 *Corresponding author: Lily C. Hughes, [email protected]. 18 Current address: Department of Organismal Biology and Anatomy, University of Chicago, 19 Chicago, IL. 20 21 Keywords: Actinopterygii, Protein coding, Systematics, Phylogenetics, Evolution, Target 22 capture 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. -
Automated Measurement of Long-Term Bower Behaviors in Lake Malawi
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.27.968511; this version posted February 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 1 Automated measurement of long-term bower behaviors in Lake Malawi cichlids using 2 depth sensing and action recognition 3 4 Zachary V Johnson1, Lijiang Long1,2, Junyu Li1, Manu Tej Sharma Arrojwala1, Vineeth Aljapur1, 5 Tyrone Lee1, Mark C Lowder1, Karen Gu1, Tucker J Lancaster1,2, Joseph I Stockert1, Jean M 6 Moorman3, Rachel L Lecesne4, Jeffrey T Streelman# 1,2,3, and Patrick T McGrath# 1,2,3,5 7 8 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA 9 2Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, 10 Atlanta, GA 30332, USA 11 3Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, 12 Atlanta, GA 30332, USA 13 4School of Computer Science, Georgia Institute of Technology, Atlanta, GA 30332, USA 14 5School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA 15 16 #Co-corresponding authors: [email protected] (P.T.M.), 17 [email protected] (J.T.S.) 18 19 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.27.968511; this version posted February 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Supplemental Methods
Supplemental Methods Collection and Preparation After extraction, the DNA samples were sheared with a 1.5 blunt end needles (Jensen Global, Santa Barbara, CA, USA) and run through pulse field gel electrophoresis, in order to separate large DNA molecules, for 16 hours. Samples were checked with a spectrophotometer (Synergy H1 Hybrid Reader, BioTek Instruments Inc., Winooski, VT) and Qubit® fluorometer for quantification of our genomic DNA. Illumina and Pacbio Hybrid Assembly, Genome Size Estimation, and Quality Assessment All computational and bioinformatics analyses were conducted on the High Performance Computing (HPC) Cluster located that University of California, Irvine. Sequence data generated from two lanes of Illumina HiSeq 2500 were concatenated and raw sequence reads were assembled through PLATANUS v1.2.1 (1), which accounts for heterozygous diploid sequence data. Parameters used for PLATANUS was -m 256 (memory) and -t 48 (threads) for this initial assembly. Afterwards, contigs assembled from PLATANUS and reads from 40 SMRT cells of PacBio sequencing were assembled with a hybrid assembler DBG2OLC v1.0 (2). We used the following parameters in DBG2OLC: k 17 KmerCovTh 2 MinOverlap 20 AdaptiveTh 0.01 LD1 0 and RemoveChimera 1 and ran pbdagcon with default parameters. Without Illumina sequence reads, we also conducted a PacBio reads only assembly with FALCON v0.3.0 (https://github.com/PacificBiosciences/FALCON) with default parameters in order to assemble PacBio reads into contiguous sequences. The parameters we used were input type = raw, length_cutoff = 4000, length_cutoff_pr = 8000, with different cluster settings 32, 16, 32, 8, 64, and 32 cores, concurrency setting jobs were 32, and the remaining were default parameters. -
Checklist of the Cichlid Fishes of Lake Malawi (Lake Nyasa)
Checklist of the Cichlid Fishes of Lake Malawi (Lake Nyasa/Niassa) by M.K. Oliver, Ph.D. ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– Checklist of the Cichlid Fishes of Lake Malawi (Lake Nyasa/Niassa) by Michael K. Oliver, Ph.D. Peabody Museum of Natural History, Yale University Updated 24 June 2020 First posted June 1999 The cichlids of Lake Malawi constitute the largest vertebrate species flock and largest lacustrine fish fauna on earth. This list includes all cichlid species, and the few subspecies, that have been formally described and named. Many–several hundred–additional endemic cichlid species are known but still undescribed, and this fact must be considered in assessing the biodiversity of the lake. Recent estimates of the total size of the lake’s cichlid fauna, counting both described and known but undescribed species, range from 700–843 species (Turner et al., 2001; Snoeks, 2001; Konings, 2007) or even 1000 species (Konings 2016). Additional undescribed species are still frequently being discovered, particularly in previously unexplored isolated locations and in deep water. The entire Lake Malawi cichlid metaflock is composed of two, possibly separate, endemic assemblages, the “Hap” group and the Mbuna group. Neither has been convincingly shown to be monophyletic. Membership in one or the other, or nonendemic status, is indicated in the checklist below for each genus, as is the type species of each endemic genus. The classification and synonymies are primarily based on the Catalog of Fishes with a few deviations. All synonymized genera and species should now be listed under their senior synonym. Nearly all species are endemic to L. Malawi, in some cases extending also into the upper Shiré River including Lake Malombe and even into the middle Shiré. -
Behavioral Evolution Contributes to Hindbrain Diversification Among Lake Malawi Cichlid Fish
www.nature.com/scientificreports OPEN Behavioral evolution contributes to hindbrain diversifcation among Lake Malawi cichlid fsh Ryan A. York1,2*, Allie Byrne1, Kawther Abdilleh3, Chinar Patil3, Todd Streelman3, Thomas E. Finger4,5 & Russell D. Fernald1,6 The evolutionary diversifcation of animal behavior is often associated with changes in the structure and function of nervous systems. Such evolutionary changes arise either through alterations of individual neural components (“mosaically”) or through scaling of the whole brain (“concertedly”). Here we show that the evolution of a courtship behavior in Malawi cichlid fsh is associated with rapid, extensive, and specifc diversifcation of orosensory, gustatory centers in the hindbrain. We fnd that hindbrain volume varies signifcantly between species that build pit (depression) compared to castle (mound) type bowers and that this trait is evolving rapidly among castle-building species. Molecular analyses of neural activity via immediate early gene expression indicate a functional role for hindbrain structures during bower building. Finally, comparisons of bower building species in neighboring Lake Tanganyika suggest parallel patterns of neural diversifcation to those in Lake Malawi. Our results suggest that mosaic brain evolution via alterations to individual brain structures is more extensive and predictable than previously appreciated. Animal behaviors vary widely, as do their neural phenotypes1. Evolutionary neuroscience identifes how the brain diversifes over time and space in response to selective pressures2. A key goal of evolutionary neuroscience has been to identify whether brain structures evolve independently (“mosaically”) or in tandem with each other as they refect key life history traits, especially behavior3–6. While a number of studies have linked variation in brain structure with other traits across evolutionary time2,7–9, it remains unclear whether or not this variation is predict- able. -
Genome-Wide Microrna Screening in Nile Tilapia Reveals
www.nature.com/scientificreports OPEN Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs’ transcription, sex-biased Received: 7 November 2016 Accepted: 15 May 2018 arm switching and increasing Published: xx xx xxxx complexity of expression throughout development Danillo Pinhal 1, Luiz A. Bovolenta2, Simon Moxon3, Arthur C. Oliveira1, Pedro G. Nachtigall1, Marcio L. Acencio4, James G. Patton5, Alexandre W. S. Hilsdorf6, Ney Lemke2 & Cesar Martins 7 MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identifcation and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fshes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identifed, many of which seem to be teleost-specifc, cichlid-specifc or tilapia-specifc. Abundant miRNA isoforms (isomiRs) were identifed with modifcations in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable diferential ratio of miRNA arms and isoforms infuenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs. -
Evolutionary History and Whole Genome Sequence of Pejerrey (Odontesthes Bonariensis): New Insights Into Sex Determination in Fishes
Evolutionary History and Whole Genome Sequence of Pejerrey (Odontesthes bonariensis): New Insights into Sex Determination in Fishes by Daniela Campanella B.Sc. in Biology, July 2009, Universidad Nacional de La Plata, Argentina A Dissertation submitted to The Faculty of The Columbian College of Arts and Sciences of The George Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy January 31, 2015 Dissertation co-directed by Guillermo Ortí Louis Weintraub Professor of Biology Elisabet Caler Program Director at National Heart, Lung and Blood Institute, NIH The Columbian College of Arts and Sciences of The George Washington University certifies that Daniela Campanella has passed the Final Examination for the degree of Doctor of Philosophy as of December 12th, 2014. This is the final and approved form of the dissertation. Evolutionary History and Whole Genome Sequence of Pejerrey (Odontesthes bonariensis): New Insights into Sex Determination in Fishes Daniela Campanella Dissertation Research Committee: Guillermo Ortí, Louis Weintraub Professor of Biology, Dissertation Co-Director Elisabet Caler, Program Director at National Heart, Lung and Blood Institute, NIH, Dissertation Co-Director Hernán Lorenzi, Assistant Professor in Bioinformatics Department, J. Craig Venter Institute Rockville Maryland, Committee Member Jeremy Goecks, Assistant Professor of Computational Biology, Committee Member ! ""! ! Copyright 2015 by Daniela Campanella All rights reserved ! """! Dedication The author wishes to dedicate this dissertation to: My love, Ford, for his unconditional support and inspiration. For teaching me that admiration towards each other’s work is the fundamental fuel to go anywhere. My family and friends, for being there, meaning “there” everywhere and whenever. My grandpa Hugo, a pejerrey lover who knew how to fish, cook and enjoy the “silver arrows”. -
Receptor Evolution, Neuronal Circuits and Behavior in the Model Organism Zebrafish Inaugur
Amine detection in aquatic organisms: receptor evolution, neuronal circuits and behavior in the model organism zebrafish Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Milan Dieris aus Berlin Köln, 2018 Berichterstatter: Prof. Dr. Sigrun Korsching Prof. Dr. Peter Kloppenburg Tag der mündlichen Prüfung: 11.12.2017 ABSTRACT Olfactory cues are responsible for the generation of diverse behaviors in the animal kingdom. Olfactory receptors are expressed by specialized sensory neurons (OSNs) in the olfactory epithelium. Upon odorant binding to the olfactory receptor, these neurons are activated. The information is transferred to the olfactory bulb glomeruli, which represent the first relay station for olfactory processing in the brain. Most olfactory receptors are G-protein coupled receptors and form large gene families. One type of olfactory receptors is the trace amine-associated receptor family (TAAR). TAARs generally recognize amines. One particular member of the zebrafish TAAR family, TAAR13c, is a high- affinity receptor for the death-associated odor cadaverine, which induces aversive behavior. Here, we identified the cell type of amine-sensitive OSNs in the zebrafish nose, which show typical properties of ciliated neurons. We used OSN type-specific markers to unambiguously characterize zebrafish TAAR13c OSNs. Using the neuronal activity marker pERK we could show that low concentrations of cadaverine activate a specific, invariant glomerulus in the dorso- lateral cluster of glomeruli (dlG) in the olfactory bulb of zebrafish. This cluster was also shown to process amine stimuli in general, a feature that is conserved in the neoteleost stickleback. Apart from developing a technique to measure neuronal activity in the adult olfactory epithelium, we also established the use of GCaMP6-expressing zebrafish to measure neuronal activity in the larval brain. -
Genomic Basis of Evolutionary Radiation in Lake Malawi Cichlids
GENOMIC BASIS OF EVOLUTIONARY RADIATION IN LAKE MALAWI CICHLIDS A Dissertation Presented to The Academic Faculty by Chinar Patil In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in Biology in the School of Biological Sciences Georgia Institute of Technology December 2018 COPYRIGHT © 2018 BY CHINAR PATIL GENOMIC BASIS OF ADAPTIVE RADIATION IN LAKE MALAWI CICHLIDS Approved by: Dr. J T Streelman, Advisor Dr. Michael Goodisman School of Biological Sciences School of Biological Sciences Georgia Institute of Technology Georgia Institute of Technology Dr. Soojin Yi Dr. Fredrik O. Vannberg School of Biological Sciences School of Biological Sciences Georgia Institute of Technology Georgia Institute of Technology Dr. Reade B. Roberts W. M. Keck Center for Behavioral Biology Comparative Medicine Institute North Carolina State University Date Approved: [October 31, 2018 ] Dedicated to Neha Ahirrao and Palvi Patil. One for the past, one for the future. ACKNOWLEDGEMENTS I would like to begin by thanking my advisor Todd Streelman for standing by me through thick and thin, teaching me valuable lessons and doing a lot of the heavy lifting required to make me the scientist I am today. I would also like to thank past and present members of the Streelman Lab, too many to name all, but in no particular order, Nick Parnell, Kawther Abdilleh, Jon Sylvester, Karen Pottin, Amanda Ballard, Natalie Haddad, Paula Lavantucksin, Zack Johnson, Teresa Fowler and many others. Beyond just the Streelman lab, I have had the privilege of collaborating with other labs, learning from professors at Georgia Tech . I would like to thank Ryan York, Soojin Yi, Michael Goodisman, Patrick McGrath, Fred Vannberg, Reade Roberts, Joe Lachance among others. -
Vertebrate Genome Evolution in the Light of Fish Cytogenomics and Rdnaomics
G C A T T A C G G C A T genes Review Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics Radka Symonová 1,* ID and W. Mike Howell 2 1 Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic 2 Department of Biological and Environmental Sciences, Samford University, Birmingham, AL 35229, USA; [email protected] * Correspondence: [email protected]; Tel.: +420-776-121-054 Received: 30 November 2017; Accepted: 29 January 2018; Published: 14 February 2018 Abstract: To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal ‘rDNAome’ consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. -
Body Depth and Pectoral Fin Ecomorphology Coevolve in Lake Malawi Cichlid Fishes
Erschienen in: Ecology and Evolution ; 8 (2018), 23. - S. 11945-11953 Received: 1 July 2018 | Revised: 22 September 2018 | Accepted: 1 October 2018 https://dx.doi.org/10.1002/ece3.4651 DOI: 10.1002/ece3.4651 ORIGINAL RESEARCH Dissecting a potential spandrel of adaptive radiation: Body depth and pectoral fin ecomorphology coevolve in Lake Malawi cichlid fishes Christopher D. Hulsey1 | Roi Holzman2 | Axel Meyer1 1Department of Biology, University of Konstanz, Konstanz, Germany Abstract 2School of Zoology, Faculty of Life The evolution of body shape reflects both the ecological factors structuring organis‐ science, Tel Aviv University, Tel Aviv, Israel mal diversity as well as an organism’s underlying anatomy. For instance, body depth and The Inter‐University Institute for Marine Sciences, Eilat, Israel in fishes is thought to determine their susceptibility to predators, attractiveness to mates, as well as swimming performance. However, the internal anatomy influencing Correspondence Christopher D. Hulsey, Department of diversification of body depth has not been extensively examined, and changes in Biology, University of Konstanz, Konstanz, body depth could arise as a by‐product of functional changes in other anatomical Germany. Email: darrin.hulsey@uni‐konstanz.de structures. Using an improved phylogenetic hypothesis for a diverse set of Lake Malawi cichlid fishes, we tested the evolutionary association between body depth Funding information National Science Foundation, Grant/Award and the height of the pectoral girdle. To refine the functional importance of the ob‐ Number: IOS‐0919459; United States–Israel served substantial correlation, we also tested the coevolution of pectoral girdle Bi‐National Science Foundation, Grant/ Award Number: 2011067 height and pectoral fin area. -
Automated Measurement of Long-Term Bower Behaviors in Lake Malawi
www.nature.com/scientificreports OPEN Automated measurement of long‑term bower behaviors in Lake Malawi cichlids using depth sensing and action recognition Zachary V. Johnson1, Manu Tej Sharma Arrojwala1, Vineeth Aljapur1, Tyrone Lee1, Tucker J. Lancaster1,2, Mark C. Lowder1, Karen Gu1, Joseph I. Stockert1, Rachel L. Lecesne3, Jean M. Moorman3, Jefrey T. Streelman1,2* & Patrick T. McGrath1,2,4,5* In the wild, behaviors are often expressed over long time periods in complex and dynamic environments, and many behaviors include direct interaction with the environment itself. However, measuring behavior in naturalistic settings is difcult, and this has limited progress in understanding the mechanisms underlying many naturally evolved behaviors that are critical for survival and reproduction. Here we describe an automated system for measuring long‑term bower construction behaviors in Lake Malawi cichlid fshes, in which males use their mouths to sculpt sand into large species‑specifc structures for courtship and mating. We integrate two orthogonal methods, depth sensing and action recognition, to simultaneously track the developing bower structure and the thousands of individual sand manipulation behaviors performed throughout construction. By registering these two data streams, we show that behaviors can be topographically mapped onto a dynamic 3D sand surface through time. The system runs reliably in multiple species, across many aquariums simultaneously, and for up to weeks at a time. Using this system, we show strong diferences in construction behavior and bower form that refect species diferences in nature, and we gain new insights into spatial, temporal, social dimensions of bower construction, feeding, and quivering behaviors. Taken together, our work highlights how low‑cost tools can automatically quantify behavior in naturalistic and social environments over long timescales in the lab.