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Adaptation of mammalian myosin II sequences to body mass Mark N Wass*1, Sarah T Jeanfavre*1,2, Michael P Coghlan*1, Martin Ridout#, Anthony J Baines*3 and Michael A Geeves*3 School of Biosciences*, and School of Mathematics#, Statistics and Actuarial Science, University of Kent, Canterbury, UK 1. Equal contribution 2. Current address: Broad Institute, 415 Main Street, 7029-K, Cambridge MA 02142 3. Joint corresponding authors Key words: selection, muscle contraction, mammalian physiology, heart rate Address for correspondence: Prof M.A.Geeves School of Biosciences, University of Kent, Canterbury CT1 7NJ UK [email protected] tel 44 1227827597 Dr A J Baines School of Biosciences, University of Kent, Canterbury CT1 7NJ UK [email protected] tel 44 1227 823462 SUPPLEMENTARY MATERIAL Supplementary Table 1. Source of Myosin sequences and the mass of each species used in the analysis of Fig 1 & 2 Species Isoform Mass Skeletal Skeletal Embryonic Skeletal α- β-cardiac Perinatal Non- Non- Smooth Extraocular Slow (kg) 2d/x 2a 2b cardiac muscle A muscle B Muscle Tonic Human P12882 Q9UKX2 251757455 Q9Y623 P13533 P12883 P13535 P35579 219841954 13432177 110624781 599045671 68a Bonobo 675746236 397494570 675746242 675746226 397473260 397473262 675746209 675764569 675746138 675746206 675798456 45.5a Macaque 544497116 544497114 544497126 109113269 544446347 544446351 544497122 383408157 384940798 387541766 544497107 544465262 6.55b Tarsier 640786419 640786435 640786417 640818214 640818212 640786413 640796733 640805785 640786411 640822915 0.1315c Rat 205830438 G3V6E1 6981234 Q29RW1 P02563 P02564 F1M8F6 Q62812 Q9JLT0 282158051 F1M789 211938461 0.325b Mouse Q5SX40 G3UW82 153792649 Q5SX39 Q02566 Q91Z83 P13542 Q8VDD5 Q61879 20070691 124486959 145864471 0.017b Guinea pig 348560933 D6N3E0 524926861 348577524 348577522 348560930 348569442 514454472 H0VCX1 348560928 514456949 0.9a Hamster 348560937 514454246 P13539 P13540 524926859 524925525 524926815 524926855 0.1125a Cow Q9BE40 Q9BE41 156120319 E1BP87 O97496 Q9BE39 F1N775 F1MQ37 554569298 151554905 741963173 741948777 755a Brandt’s Bat 554569234 554569240 554569232 554581513 554581511 554569226 G1PWB8 Q27991 554569314 554572455 0.0069b Minke 594653830 511880634 594665031 594653837 594622148 594623548 594681427 594692255 9200d Whale Opossum 126308741 126308745 126308751 126308737 611969297 126277437 126308731 126339824 611994225 126334598 611994046 F7GF97 0.048b 1 2 3 4 6 7 8 9 10 11 13 7b Myosin Heavy Chain - MyHC a = Animal Diversity Web: animaldiversity.org b = ARKive: Arkive.org c = Primatology.net d= National Oceanic and Atmospheric Administration Fisheries: nmfs.noaa.gov Sequence identifiers beginning with an upper case letter are from Uniprot. Identifiers consisting solely of numbers are NCBI GI numbers for Refseq Protein database entries. Table S2 Source of Myosin sequences and the mass of each species used in the analysis of Figs 3-5 MyHC3 MyHC7 MyHC9 Weight Animal Organism (kg) Clade Accession Accession Accession Aardvark Orycteropus afer afer 61 Afrotheria XP_007949396.1| XP_007952162.1 African Elephant Loxodonta africana 4800 Afrotheria XP_010597690.1 Alpaca Vicugna pacos 60 Laurasiatheria XP_006216239.1 XP_006207100.1 American Pika Ochotona princeps 0.1485 Euarchontoglires XP_004589604.1 Armadillo Dasypus novemcinctus 5.5 Metaferia XP_004483195.1 Bactrian Camel Camelus bactrianus 475 Laurasiatheria XP_010964285.1 XP_010958676.1 Big Brown Bat Eptesicus fuscus 0.023 Laurasiatheria XP_008151670.1 XP_008142904.1 Bison Bison bison bison 600 Laurasiatheria XP_010841308.1 Black Flying Fox Pteropus alecto 0.74 Laurasiatheria XP_006922456.1 XP_006913644.1 XP_006914548.1 Bolivian Squirrel Monkey Saimiri boliviensis boliviensis 0.75 Euarchontoglires XP_010341809.1 Bonobo Pan paniscus 44 Euarchontoglires XP_008969597.1 XP_003808134.1 XP_008973255.1 Brandts Bat Myotis brandtii 0.0069 Laurasiatheria XP_005878881.1 XP_005882279.1 XP_005883308.1 Camel Camelus ferus 800 Laurasiatheria XP_006181417.1 XP_006172852.1 XP_006194713.1 Cape Elephant Shrew Elephantulus edwardii 0.0695 Afrotheria XP_006890222.1 Cape Golden Mole Chrysochloris asiatica 0.042 Afrotheria XP_006865288.1 Cattle Bos taurus 755 Laurasiatheria NP_001095305.1 NP_777152.1 NP_001179691.1 Chinchilla Chinchilla lanigera 0.65 Euarchontoglires XP_005399419.1 XP_013366946.1 Chinese Hamster Cricetulus griseus 0.02235 Euarchontoglires XP_007630255.1* XP_007609272.1 XP_007622799.1 Chinese Tree Shrew Tupaia chinensis 0.16 Euarchontoglires XP_006156482.1 Colobus Colobus angolensis palliatus 8.9 Euarchontoglires XP_011788651.1 XP_011786220.1 XP_011819709.1 Common Shrew Sorex araneus 0.0095 Laurasiatheria XP_004603954.1 Coquerels Mouse Lemur Propithecus coquereli 0.305 Euarchontoglires XP_012509396.1 XP_012493546.1 Crab-Eating Macaque Macaca fascicularis 6.55 Euarchontoglires XP_005582959.1 XP_005560929.1 XP_005567470.1 Damaraland Mole- Rat Fukomys damarensis 0.144 Euarchontoglires XP_010613296.1 XP_010612194.1 David's Myotis Myotis davidii 0.0085 Laurasiatheria XP_006757501.1 Degu Octodon degus 0.235 Euarchontoglires XP_004645229.1 XP_004646724.1 XP_004634632.1 Dog Canis lupus familiaris 35.5 Laurasiatheria XP_005619582.1 NP_001107183.1 NP_001104237.1 Dolphin Lipotes vexillifer 104.5 Laurasiatheria XP_007457908.1 XP_007449624.1 XP_007446800.1 Domestic Cat Felis catus 4.75 Laurasiatheria XP_011287146.1 XP_011281445.1 Drill Mandrillus leucophaeus 18.25 Euarchontoglires XP_011828556.1 XP_011834336.1 Dromedary Camelus dromedarius 495 Laurasiatheria XP_010986392.1 XP_010997289.1 Ferret Mustela putorius furo 1.5 Laurasiatheria XP_004760220.1 Flying Lemur Galeopterus variegatus 1.45 Euarchontoglires XP_008564810.1 XP_008585579.1 Galago Otolemur garnettii 0.1025 Euarchontoglires XP_012661460.1 XP_012656616.1 Giant Panda Ailuropoda melanoleuca 102.5 Laurasiatheria XP_002921226.1 XP_011217103.1 Gibbon Nomascus leucogenys 5.7 Euarchontoglires XP_012356893.1 Goat Capra hircus 45 Laurasiatheria XP_005680817.1 Golden Hamster Mesocricetus auratus 0.099 Euarchontoglires *P13540.2 Golden Snub-nosed Monkey Rhinopithecus roxellana 16.4 Euarchontoglires XP_010387470.1 Gray Mouse Lemur Microcebus murinus 0.06 Euarchontoglires XP_012642489.1 Green Monkey Chlorocebus sabaeus 5 Euarchontoglires XP_008008568.1 XP_007989071.1 XP_007973837.1 Ground Squirrel Ictidomys tridecemlineatus 0.125 Euarchontoglires XP_005332936.1 XP_005322354.1 Guinea Pig Cavia porcellus 0.9 Euarchontoglires XP_003466269.1 XP_003474533.1 XP_003470507.1 Hedgehog Erinaceus europaeus 0.6 Laurasiatheria XP_007522826.1 XP_007519425.1 Horse Equus caballus 563.5 Laurasiatheria XP_001504905.2 NP_001075227.1 Human Homo sapiens 68 Euarchontoglires NP_002461.2 NP_000248.2 NP_002464.1 Jerboa Jaculus jaculus 0.6 Euarchontoglires XP_004663184.1 XP_004650327.1 Kangaroo Rat Dipodomys ordii 0.0755 Euarchontoglires XP_012868629.1 XP_012880785.1 XP_012880308.1 Killer Whale Orcinus orca 7200 Laurasiatheria XP_004266884.1 XP_004283261.1* XP_004279478.1 Large Fruit Bat Pteropus vampyrus 0.85 Laurasiatheria XP_011357263.1 XP_011371126.1 XP_011385610.1 Little Brown Bat Myotis lucifugus 0.008 Laurasiatheria XP_006099793.1 XP_006100103.1 Trichechus manatus Manatee latirostris 480 Afrotheria XP_004390599.1 Mangabey Cercocebus atys 9.5 Euarchontoglires XP_011943848.1 Marmoset Callithrix jacchus 0.33 Euarchontoglires XP_002806839.1 XP_002753688.1 XP_009008395.1 Balaenoptera acutorostrata Minke Whale scammoni 9200 Laurasiatheria XP_007175343.1 XP_007180640.1 XP_007165739.1 Mole-Rat Nannospalax galili 0.375 Euarchontoglires XP_008853933.1 XP_008838094.1 XP_008853014.1 Mouse Mus musculus 0.017 Euarchontoglires NP_001093105.1 NP_542766.1 NP_071855.2 Night monkey Aotus nancymaae 0.75 Euarchontoglires XP_012322603.1 XP_012331782.1 Olive Baboon Papio anubis 19.5 Euarchontoglires XP_009187946.1 XP_009215489.1 Opossum Monodelphis domestica 0.048 Metatheria XP_001371653.1 XP_001369357.1 XP_001376000.1 Pig Sus scrofa 169 Laurasiatheria NP_999020.1 Pig-tailed macaque Macaca nemestrina 6.55 Euarchontoglires XP_011770587.1 XP_011710795.1 Platypus Ornithorhynchus anatinus 1.65 ** XP_003430622.1 Peromyscus maniculatus Prairie Deer Mouse bairdii 0.017 Euarchontoglires XP_006973571.1 XP_006991969.1 Prairie Vole Microtus ochrogaster 0.05 Euarchontoglires XP_005349905.1 XP_013204243.1 Przewalskis Horse Equus przewalskii 250 Laurasiatheria XP_008527759.1 Rabbit Oryctolagus cuniculus 2 Euarchontoglires NP_001182585.1 XP_002718130.1 XP_008255309.1 Rat Rattus norvegicus 0.325 Euarchontoglires NP_036736.1 XP_006252013.1 NP_001292806.1 Rhesus Macaque Macaca mulatta 8 Euarchontoglires XP_001114005.2* Sheep Ovis aries 110 Laurasiatheria XP_004010374.1 XP_012004193.1 Siberian Tiger Panthera tigris altaica 176.4 Laurasiatheria XP_007086007.1 XP_007098159.1 Sooty Mangabey Cercocebus atys 9.5 Euarchontoglires XP_011906114.1 XP_011893491.1 Star Nosed Mole Condylura cristata 0.055 Laurasiatheria XP_004684642.1 Sumatran Orangutan Pongo abelii 60 Euarchontoglires XP_009232594.1 Tarsier Tarsius syrichta 0.1315 Euarchontoglires XP_008048958.1 XP_008065968.1 Tibetan Antelope Pantholops hodgsonii 33 Laurasiatheria XP_005959866.1 Odobenus rosmarus Walrus divergens 1050 Laurasiatheria XP_004398481.1 XP_004417395.1 Water Buffalo Bubalus bubalis 725 Laurasiatheria XP_006055107.1 XP_006080999.1 XP_006057029.1 Weddell Seal Leptonychotes weddellii 500 Laurasiatheria XP_006744844.1 Ceratotherium simum White Rhino simum 2520 Laurasiatheria XP_004433113.1 XP_004418151.1 Yak Bos mutus 562.5 Laurasiatheria XP_005907260.1 XP_005909865.1 * The sequence for the Golden hamster
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    What the American Society of Mammalogists has in the images library LIST OF 28 ORDERS, 129 FAMILIES, 598 GENERA AND 1121 SPECIES IN MAMMAL IMAGES LIBRARY 31 DECEMBER 2013 AFROSORICIDA (5 genera, 5 species) – golden moles and tenrecs CHRYSOCHLORIDAE - golden moles Chrysospalax villosus - Rough-haired Golden Mole TENRECIDAE - tenrecs 1. Echinops telfairi - Lesser Hedgehog Tenrec 2. Hemicentetes semispinosus – Lowland Streaked Tenrec 3. Microgale dobsoni - Dobson’s Shrew Tenrec 4. Tenrec ecaudatus – Tailless Tenrec ARTIODACTYLA (83 genera, 142 species) – paraxonic (mostly even-toed) ungulates ANTILOCAPRIDAE - pronghorns Antilocapra americana - Pronghorn BOVIDAE (46 genera) - cattle, sheep, goats, and antelopes 1. Addax nasomaculatus - Addax 2. Aepyceros melampus - Impala 3. Alcelaphus buselaphus - Hartebeest 4. Alcelaphus caama – Red Hartebeest 5. Ammotragus lervia - Barbary Sheep 6. Antidorcas marsupialis - Springbok 7. Antilope cervicapra – Blackbuck 8. Beatragus hunter – Hunter’s Hartebeest 9. Bison bison - American Bison 10. Bison bonasus - European Bison 11. Bos frontalis - Gaur 12. Bos javanicus - Banteng 13. Bos taurus -Auroch 14. Boselaphus tragocamelus - Nilgai 15. Bubalus bubalis - Water Buffalo 16. Bubalus depressicornis - Anoa 17. Bubalus quarlesi - Mountain Anoa 18. Budorcas taxicolor - Takin 19. Capra caucasica - Tur 20. Capra falconeri - Markhor 21. Capra hircus - Goat 22. Capra nubiana – Nubian Ibex 23. Capra pyrenaica – Spanish Ibex 24. Capricornis crispus – Japanese Serow 25. Cephalophus jentinki - Jentink's Duiker 26. Cephalophus natalensis – Red Duiker 1 What the American Society of Mammalogists has in the images library 27. Cephalophus niger – Black Duiker 28. Cephalophus rufilatus – Red-flanked Duiker 29. Cephalophus silvicultor - Yellow-backed Duiker 30. Cephalophus zebra - Zebra Duiker 31. Connochaetes gnou - Black Wildebeest 32. Connochaetes taurinus - Blue Wildebeest 33. Damaliscus korrigum – Topi 34.
  • The Genome 10K Project: a Way Forward

    The Genome 10K Project: a Way Forward

    The Genome 10K Project: A Way Forward Klaus-Peter Koepfli,1 Benedict Paten,2 the Genome 10K Community of Scientists,Ã and Stephen J. O’Brien1,3 1Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russian Federation; email: [email protected] 2Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064 3Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida 33004 Annu. Rev. Anim. Biosci. 2015. 3:57–111 Keywords The Annual Review of Animal Biosciences is online mammal, amphibian, reptile, bird, fish, genome at animal.annualreviews.org This article’sdoi: Abstract 10.1146/annurev-animal-090414-014900 The Genome 10K Project was established in 2009 by a consortium of Copyright © 2015 by Annual Reviews. biologists and genome scientists determined to facilitate the sequencing All rights reserved and analysis of the complete genomes of10,000vertebratespecies.Since Access provided by Rockefeller University on 01/10/18. For personal use only. ÃContributing authors and affiliations are listed then the number of selected and initiated species has risen from ∼26 Annu. Rev. Anim. Biosci. 2015.3:57-111. Downloaded from www.annualreviews.org at the end of the article. An unabridged list of G10KCOS is available at the Genome 10K website: to 277 sequenced or ongoing with funding, an approximately tenfold http://genome10k.org. increase in five years. Here we summarize the advances and commit- ments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and futurevision of the landscape of Genome 10K.
  • Phylogeography of Moose in Western North America

    Phylogeography of Moose in Western North America

    Journal of Mammalogy, 101(1):10–23, 2020 DOI:10.1093/jmammal/gyz163 Published online November 30, 2019 Phylogeography of moose in western North America Nicholas J. DeCesare,* Byron V. Weckworth, Kristine L. Pilgrim, Andrew B. D. Walker, Eric J. Bergman, Kassidy E. Colson, Rob Corrigan, Richard B. Harris, Mark Hebblewhite, Brett R. Jesmer, Jesse R. Newby, Jason R. Smith, Rob B. Tether, Timothy P. Thomas, and Michael K. Schwartz Montana Fish, Wildlife and Parks, Missoula, MT 59804, USA (NJD) Panthera, New York, NY 10018, USA (BVW) Rocky Mountain Research Station, United States Forest Service, Missoula, MT 59801, USA (KLP, MKS) British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Penticton, British Columbia V2A 7C8, Canada (ABDW) Colorado Parks and Wildlife, Fort Collins, CO 80526, USA (EJB) Alaska Department of Fish and Game, Palmer, AK 99645, USA (KEC) Alberta Environment and Parks, Edmonton, Alberta T5K 2M4, Canada (RC) Washington Department of Fish and Wildlife, Olympia, WA 98501, USA (RBH) University of Montana, Missoula, MT 59812, USA (MH) University of Wyoming, Laramie, WY 82071, USA (BRJ) Montana Fish, Wildlife and Parks, Kalispell, MT 59901, USA (JRN) North Dakota Game and Fish Department, Jamestown, ND 58401, USA (JRS) Saskatchewan Ministry of Environment, Meadow Lake, Saskatchewan S9X 1Y5, Canada (RBT) Wyoming Game and Fish Department, Sheridan, WY 82801, USA (TPT) * Correspondent: [email protected] Subspecies designations within temperate species’ ranges often reflect populations that were isolated by past continental glaciation, and glacial vicariance is believed to be a primary mechanism behind the diversification of several subspecies of North American cervids.