Species Examined.Xlsx 8:17 PM 5/31/2011

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8:17 PM 5/31/2011 Names Accepted Binomial Name, Family Page Binomial Name, Page Common Name as of 2011, as given in Sperber if different than in Sperber Monotremata 264 Duckbilled Platypus Ornithorhynchus anatinus 264 Marsupialia 266 Slender‐tailed Dunnart Sminthopsis murina 266 Kultarr Antechinomys laniger 268 Gray Four‐eyed Opossum Philander opossum Didelphys opossum 269 (or possibly Virginia Opossum) ( or Didelphis virginiana) Eastern Grey Kangaroo Macropus giganteus 269 Insectivora 272 Elephant Shrew Macroscelides sp. 272 Hedgehog Erinaceus europaeus 273 Eurasian Pygmy Shrew Sorex minutus 274 Eurasian Water Shrew Neomys fodiens 279 Pygmy White Toothed Suncus etruscus Pachyura etrusca 280 (or Etruscan ) Shrew Russian Desman Desmana moschata 280 Chiroptera 281 Greater Flying Fox Pteropus vampyrus Pteropus edulis 281 (Kalong, Kalang) Northern Bat Eptesicus nilssonii Pipistrellus nilssoni 283 Particoloured Bat Vespertilio murinus 285 Xenarthra 287 and Pholidota Armadillos, anteaters and pangolins: Review of the literature only Rodentia 288 European Rabbit Oryctolagus cuniculus 288 Eurasian Red Squirrel Sciurus vulgaris 293 Eurasian Beaver Castor fiber 294 Agile Kangaroo Rats Dipodomys agilis Perodipus agilis 296 Fresno Kangaroo Rat Dipodomys nitratoides exilis Dipodomys meriami exilis 297 Lesser Egyptian Jerboa Jaculus jaculus 298 Field (or Short‐tailed) Vole Microtus agrestis 299 Bank Vole Myodes glareolus Evotomys glareolus 303 European (or Northern) Water Arvicola terrestris 303 Vole Black Rat Rattus Rattus Epimys rattus 303 House Mouse Mus musculus 304 Yellow‐necked Mouse Apodemus flavicollis Mus flavicollis 306 Wood Mouse Apodemus sylvaticus Mus sylvaticus 312 Rakali or Water Rrat Hydromys chrysogaster 313 Fat Sand Rat Psammomys obesus 313 Crested Porcupine Hystrix cristata Hystris cristata 315 Carnivora fissipedia 318 Domestic Cat Felis catus 318 Binturong or Asian Bearcat Arctictis binturong 324 Dog Canis lupus familiaris Canis familiaris 325 Brown Bear Ursus arctos 327 Stoat , Ermine or Mustela erminea 329 Short‐tailed Weasel American Mink Neovison vison Lutreola vison 330 European Otter Lutra lutra 331 Carnivora pinnipedia 335 C:\Users\Terry\Documents\UMMC\Kidney\Literature\Sperber\Species Examined\Species Examined.xlsx 8:17 PM 5/31/2011 Ringed Seal Pusa hispida Phoca hispida 335 Bearded Seal Erignathus barbatus Phoca barbata 337 Cetacea 338 Harbour Porpoise Phocoena phocoena Phocaena phocaena 338 Blue Whale Balaenoptera musculus 340 Hyracoidea 341 Rock Hyrax Procavia capensis 341 Proboscidea 342 Asian Elephant Elephas maximus 342 Sirenia 346 West Indian Manatee Trichechus manatus 346 Artiodactyla 347 Hippopotamus Hippopotamus amphibius 347 Domestic Pig Sus scrofa domestica 349 Bactrian Camel Camelus bactrianus 351 Fallow Deer Dama dama 352 Moose Alces alces 353 Reindeer Rangifer tarandus 354 Sheep Ovis aries 355 Cattle Bos taurus 356 Perissodactyla 363 Horse Equus caballus 363 Primates 366 Daubentonia Aye‐Aye Chiromys madagascariensis 366 madagascarensis C:\Users\Terry\Documents\UMMC\Kidney\Literature\Sperber\Species Examined\Species Examined.xlsx.

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The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads
www.nature.com/scientificreports OPEN The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads Liliya Doronina1,*, Andreas Matzke1,*, Gennady Churakov1,2, Monika Stoll3, Andreas Huge3 & Jürgen Schmitz1 Received: 13 October 2016 Solving problematic phylogenetic relationships often requires high quality genome data. However, Accepted: 25 January 2017 for many organisms such data are still not available. Among rodents, the phylogenetic position of the Published: 03 March 2017 beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy- free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data). Most of an organism’s phylogenetic history is fossilized in their heritable genomic material. Using data from genome sequencing projects, particularly informative regions of this material can be extracted in sufficient num- bers to resolve the deepest history of speciation.
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