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Cryptic Phylogeographic History Sheds Light on the Generation of Species Diversity in Sky-Island Mountains
bioRxiv preprint doi: https://doi.org/10.1101/199786; this version posted October 7, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC-ND 4.0 International license. Cryptic phylogeographic history sheds light on the generation of species diversity in sky-island mountains Kai He1, 2, 3, #, Tao Wan 1, 4, Klaus-Peter Koepfli 5, 6, Wei Jin7, Shao-Ying Liu7, Xue-Long Jiang1, # 1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 2 Department of Biological Sciences, University of Manitoba, Winnipeg, MN R3T R3V, Canada 3 The Kyoto University Museum, Kyoto University, Kyoto 606-8501, Japan. 4 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China 5 Smithsonian Conservation Biology Institute, National Zoological Park, DC 20008, USA 6 Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199034, RUSSIA 7 Sichuan Academy of Forest, Chengdu 610081, Sichuan, China Keywords: allopatry, Approximate Bayesian Computation, cryptic corridor, interglacial refugia, niche modeling, species delimitation Running title: Cryptic sky-island phylogeography # Correspondence: Kai He and Xue-Long Jiang, Fax: 86 871 6512 5226; E-mails: [email protected], [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/199786; this version posted October 7, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Interglacial Refugia Preserved High Genetic Diversity of the Chinese Mole Shrew in the Mountains of Southwest China
Heredity (2016) 116, 23–32 & 2016 Macmillan Publishers Limited All rights reserved 0018-067X/16 www.nature.com/hdy ORIGINAL ARTICLE Interglacial refugia preserved high genetic diversity of the Chinese mole shrew in the mountains of southwest China KHe1,2, N-Q Hu1,3, X Chen4,5, J-T Li6 and X-L Jiang1 The mountains of southwest China (MSC) harbor extremely high species diversity; however, the mechanism behind this diversity is unknown. We investigated to what degree the topography and climate change shaped the genetic diversity and diversification in these mountains, and we also sought to identify the locations of microrefugia areas in these mountains. For these purposes, we sampled extensively to estimate the intraspecific phylogenetic pattern of the Chinese mole shrew (Anourosorex squamipes)in southwest China throughout its range of distribution. Two mitochondrial genes, namely, cytochrome b (CYT B) and NADH dehydrogenase subunit 2 (ND2), from 383 archived specimens from 43 localities were determined for phylogeographic and demographic analyses. We used the continuous-diffusion phylogeographic model, extensive Bayesian skyline plot species distribution modeling (SDM) and approximate Bayesian computation (ABC) to explore the changes in population size and distribution through time of the species. Two phylogenetic clades were identified, and significantly higher genetic diversity was preserved in the southern subregion of the mountains. The results of the SDM, continuous-diffusion phylogeographic model, extensive Bayesian skyline plot and ABC analyses were congruent and supported that the Last Interglacial Maximum (LIG) was an unfavorable period for the mole shrews because of a high degree of seasonality; A. squamipes survived in isolated interglacial refugia mainly located in the southern subregion during the LIG and rapidly expanded during the last glacial period. -
Wild Mammals of the Annapurna Conservation Area Cggk"0F{ ;+/If0f If]Qsf :Tgwf/L Jgohgt' Wild Mammals of the Annapurna Conservation Area - 2019
Wild Mammals of the Annapurna Conservation Area cGgk"0f{ ;+/If0f If]qsf :tgwf/L jGohGt' Wild Mammals of the Annapurna Conservation Area - 2019 ISBN 978-9937-8522-8-9978-9937-8522-8-9 9 789937 852289 National Trust for Nature Conservation Annapurna Conservation Area Project Khumaltar, Lalitpur, Nepal Hariyo Kharka, Pokhara, Kaski, Nepal National Trust for Nature Conservation P.O. Box: 3712, Kathmandu, Nepal P.O. Box: 183, Kaski, Nepal Tel: +977-1-5526571, 5526573, Fax: +977-1-5526570 Tel: +977-61-431102, 430802, Fax: +977-61-431203 Annapurna Conservation Area Project Email: [email protected] Email: [email protected] Website: www.ntnc.org.np Website: www.ntnc.org.np 2019 Wild Mammals of the Annapurna Conservation Area cGgk"0f{ ;+/If0f If]qsf :tgwf/L jGohGt' National Trust for Nature Conservation Annapurna Conservation Area Project 2019 Wild Mammals of the Annapurna Conservation Area cGgk"0f{ ;+/If0f If]qsf :tgwf/L jGohGt' Published by © NTNC-ACAP, 2019 All rights reserved Any reproduction in full or in part must mention the title and credit NTNC-ACAP. Reviewers Prof. Karan Bahadur Shah (Himalayan Nature), Dr. Naresh Subedi (NTNC, Khumaltar), Dr. Will Duckworth (IUCN) and Yadav Ghimirey (Friends of Nature, Nepal). Compilers Rishi Baral, Ashok Subedi and Shailendra Kumar Yadav Suggested Citation Baral R., Subedi A. & Yadav S.K. (Compilers), 2019. Wild Mammals of the Annapurna Conservation Area. National Trust for Nature Conservation, Annapurna Conservation Area Project, Pokhara, Nepal. First Edition : 700 Copies ISBN : 978-9937-8522-8-9 Front Cover : Yellow-bellied Weasel (Mustela kathiah), back cover: Orange- bellied Himalayan Squirrel (Dremomys lokriah). -
Influence of Common Eland (Taurotragus Oryx) Meat Composition on Its Further Technological Processing
CZECH UNIVERSITY OF LIFE SCIENCES PRAGUE Faculty of Tropical AgriSciences Department of Animal Science and Food Processing Influence of Common Eland (Taurotragus oryx) Meat Composition on its further Technological Processing DISSERTATION THESIS Prague 2018 Author: Supervisor: Ing. et Ing. Petr Kolbábek prof. MVDr. Daniela Lukešová, CSc. Co-supervisors: Ing. Radim Kotrba, Ph.D. Ing. Ludmila Prokůpková, Ph.D. Declaration I hereby declare that I have done this thesis entitled “Influence of Common Eland (Taurotragus oryx) Meat Composition on its further Technological Processing” independently, all texts in this thesis are original, and all the sources have been quoted and acknowledged by means of complete references and according to Citation rules of the FTA. In Prague 5th October 2018 ………..………………… Acknowledgements I would like to express my deep gratitude to prof. MVDr. Daniela Lukešová CSc., Ing. Radim Kotrba, Ph.D. and Ing. Ludmila Prokůpková, Ph.D., and doc. Ing. Lenka Kouřimská, Ph.D., my research supervisors, for their patient guidance, enthusiastic encouragement and useful critiques of this research work. I am very gratefull to Ing. Petra Maxová and Ing. Eva Kůtová for their valuable help during the research. I am also gratefull to Mr. Petr Beluš, who works as a keeper of elands in Lány, Mrs. Blanka Dvořáková, technician in the laboratory of meat science. My deep acknowledgement belongs to Ing. Radek Stibor and Mr. Josef Hora, skilled butchers from the slaughterhouse in Prague – Uhříněves and to JUDr. Pavel Jirkovský, expert marksman, who shot the animals. I am very gratefull to the experts from the Natura Food Additives, joint-stock company and from the Alimpex-maso, Inc. -
Etruscan Shrew Muscle: the Consequences of Being Small Klaus D
The Journal of Experimental Biology 205, 2161–2166 (2002) 2161 Printed in Great Britain © The Company of Biologists Limited 2002 JEB3932 Review Etruscan shrew muscle: the consequences of being small Klaus D. Jürgens* Zentrum Physiologie, Medizinische Hochschule, D-30623 Hannover, Germany *e-mail: [email protected] Accepted 13 May 2002 Summary The skeletal muscles of the smallest mammal, the oxidative metabolism: they have a small diameter, their Etruscan shrew Suncus etruscus, are functionally and citrate synthase activity is higher and their lactate structurally adapted to the requirements of an enormously dehydrogenase activity is lower than in the muscles of any high energy turnover. Isometric twitch contractions of the other mammal and they have a rapid shortening velocity. extensor digitorum longus (EDL) and soleus muscles are Differences in isometric twitch contraction times between shorter than in any other mammal, allowing these muscles different muscles are, at least in part, probably due to to contract at outstandingly high frequencies. The skeletal differences in cytosolic creatine kinase activities. muscles of S. etruscus contract at up to 900 min–1 for respiration, up to 780 min–1 for running and up to 3500 min–1 for shivering. All skeletal muscles investigated Key words: Etruscan shrew, Suncus etruscus, skeletal muscle, lack slow-twitch type I fibres and consist only of fast- extensor digitorum longus, soleus, fibre composition, myosin heavy twitch type IID fibres. These fibres are optimally equipped chain, myosin light chain, lactate dehydrogenase, citrate synthase, with properties enabling a high rate of almost purely creatine kinase, myoglobin, Ca2+ transient, contraction, relaxation. Introduction The Etruscan shrew Suncus etruscus (Savi) and the heart muscle mass, 1.2 % of its body mass (Bartels et al., 1979), bumblebee bat (Craseonycteris thonglongyai), both weighing a value twice as high as expected from allometry, and a heart on average less than 2 g, are the smallest extant mammals. -
Small Carnivores in Tinjure-Milke-Jaljale, Eastern Nepal
SMALL CARNIVORES IN TINJURE-MILKE-JALJALE, EASTERN NEPAL The content of this booklet can be used freely with permission for any conservation and education purpose. However we would be extremely happy to get a hard copy or soft copy of the document you have used it for. For further information: Friends of Nature Kathmandu, Nepal P.O. Box: 23491 Email: [email protected], Website: www.fonnepal.org Facebook: www.facebook.com/fonnepal2005 First Published: April, 2018 Photographs: Friends of Nature (FON), Jeevan Rai, Zaharil Dzulkafly, www.pixabay/ werner22brigitte Design: Roshan Bhandari Financial support: Rufford Small Grants, UK Authors: Jeevan Rai, Kaushal Yadav, Yadav Ghimirey, Som GC, Raju Acharya, Kamal Thapa, Laxman Prasad Poudyal and Nitesh Singh ISBN: 978-9937-0-4059-4 Acknowledgements: We are grateful to Zaharil Dzulkafly for his photographs of Marbled Cat, and Andrew Hamilton and Wildscreen for helping us get them. We are grateful to www.pixabay/werner22brigitte for giving us Binturong’s photograph. We thank Bidhan Adhikary, Thomas Robertson, and Humayra Mahmud for reviewing and providing their valuable suggestions. Preferred Citation: Rai, J., Yadav, K., Ghimirey, Y., GC, S., Acharya, R., Thapa, K., Poudyal, L.P., and Singh, N. 2018. Small Carnivores in Tinjure-Milke-Jaljale, Eastern Nepal. Friends of Nature, Nepal and Rufford Small Grants, UK. Small Carnivores in Tinjure-Milke-Jaljale, Eastern Nepal Why Protect Small Carnivores! Small carnivores are an integral part of our ecosystem. Except for a few charismatic species such as Red Panda, a general lack of research and conservation has created an information gap about them. I am optimistic that this booklet will, in a small way, be the starting journey of filling these gaps in our knowledge bank of small carnivore in Nepal. -
Mammals of Jordan
© Biologiezentrum Linz/Austria; download unter www.biologiezentrum.at Mammals of Jordan Z. AMR, M. ABU BAKER & L. RIFAI Abstract: A total of 78 species of mammals belonging to seven orders (Insectivora, Chiroptera, Carni- vora, Hyracoidea, Artiodactyla, Lagomorpha and Rodentia) have been recorded from Jordan. Bats and rodents represent the highest diversity of recorded species. Notes on systematics and ecology for the re- corded species were given. Key words: Mammals, Jordan, ecology, systematics, zoogeography, arid environment. Introduction In this account we list the surviving mammals of Jordan, including some reintro- The mammalian diversity of Jordan is duced species. remarkable considering its location at the meeting point of three different faunal ele- Table 1: Summary to the mammalian taxa occurring ments; the African, Oriental and Palaearc- in Jordan tic. This diversity is a combination of these Order No. of Families No. of Species elements in addition to the occurrence of Insectivora 2 5 few endemic forms. Jordan's location result- Chiroptera 8 24 ed in a huge faunal diversity compared to Carnivora 5 16 the surrounding countries. It shelters a huge Hyracoidea >1 1 assembly of mammals of different zoogeo- Artiodactyla 2 5 graphical affinities. Most remarkably, Jordan Lagomorpha 1 1 represents biogeographic boundaries for the Rodentia 7 26 extreme distribution limit of several African Total 26 78 (e.g. Procavia capensis and Rousettus aegypti- acus) and Palaearctic mammals (e. g. Eri- Order Insectivora naceus concolor, Sciurus anomalus, Apodemus Order Insectivora contains the most mystacinus, Lutra lutra and Meles meles). primitive placental mammals. A pointed snout and a small brain case characterises Our knowledge on the diversity and members of this order. -
Corynorhinus Townsendii): a Technical Conservation Assessment
Townsend’s Big-eared Bat (Corynorhinus townsendii): A Technical Conservation Assessment Prepared for the USDA Forest Service, Rocky Mountain Region, Species Conservation Project October 25, 2006 Jeffery C. Gruver1 and Douglas A. Keinath2 with life cycle model by Dave McDonald3 and Takeshi Ise3 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada 2Wyoming Natural Diversity Database, Old Biochemistry Bldg, University of Wyoming, Laramie, WY 82070 3Department of Zoology and Physiology, University of Wyoming, P.O. Box 3166, Laramie, WY 82071 Peer Review Administered by Society for Conservation Biology Gruver, J.C. and D.A. Keinath (2006, October 25). Townsend’s Big-eared Bat (Corynorhinus townsendii): a technical conservation assessment. [Online]. USDA Forest Service, Rocky Mountain Region. Available: http:// www.fs.fed.us/r2/projects/scp/assessments/townsendsbigearedbat.pdf [date of access]. ACKNOWLEDGMENTS The authors would like to acknowledge the modeling expertise of Dr. Dave McDonald and Takeshi Ise, who constructed the life-cycle analysis. Additional thanks are extended to the staff of the Wyoming Natural Diversity Database for technical assistance with GIS and general support. Finally, we extend sincere thanks to Gary Patton for his editorial guidance and patience. AUTHORS’ BIOGRAPHIES Jeff Gruver, formerly with the Wyoming Natural Diversity Database, is currently a Ph.D. candidate in the Biological Sciences program at the University of Calgary where he is investigating the physiological ecology of bats in northern arid climates. He has been involved in bat research for over 8 years in the Pacific Northwest, the Rocky Mountains, and the Badlands of southern Alberta. He earned a B.S. in Economics (1993) from Penn State University and an M.S. -
Wild Animal, Birds and Reptiles Rescues from Unprotected Open Wells, Bore Wells and Water Tanks for Last Three Years by Animal Rahat
JOURNAL OF WILDLIFE RESEARCH Journal homepage: www.jakraya.com/journal/jwr STUDY REPORT Wild Animal, Birds and Reptiles Rescues from Unprotected Open Wells, Bore Wells and Water Tanks for Last Three Years by Animal Rahat 1* Chittora R.K., 2Upreti N.C., 3Jadhav A.S., 4Yadav C.D., 5Bhise P.R., 6Naik K.P. and 7Pol K.K. 1Senior Veterinary Trainer, 2Chief Operating Officer, 3Veterinary Field Officer, 4Clinical Quality Assurance Manager, 5Veterinary Field Officer, 6Community Facilitator and Animal Rescue Officer, 7Animal Welfare Inspector, Animal Rahat, Post Box No-30 Pin 416416, Maharashtra, India. Abstract The open wells, bore wells and water tanks (storage of water in big ponds on ground in advance system of agriculture) are the means of irrigation in most part of India but on the other hand these open wells, bore wells and water tanks are unprotected from top, while guidelines for *Corresponding Author: protecting of these structures are in the system. These unprotected open wells, bore wells and water tanks are nightmare for wild animals, they fall Chittora R. K. down into these structures accidentally when they are chased by other Email: [email protected] predator species or while playing or fighting with each other. Animal Rahat has rescued 43 wild animals, birds and reptiles including 10 species; namely Indian foxes, Jackals, Civets, Wolf, Indian spectacled cobra, Received: 11/05/2020 Russell’s viper, Indian rat snakes, Monitor lizard, Crocodile, Pea fowls Accepted: 25/05/2020 from these unprotected structures in last 3 years’ period i.e. from April 2017 to March 2020. Appropriate equipment’s, trained persons, and veterinarians along with rapid actions are necessary for rescue of these wild species without harming them as well as humans. -
Kopi Luwak Coffee
KOPI LUWAK KOPI LUWAK “THE WORLD’S MOST EXPENSIVE COFFEE” “THE WORLD’S MOST EXPENSIVE COFFEE” An Asian palm civet eating the red berries of an Indonesian coffee plant. An Asian palm civet eating the red berries of an Indonesian coffee plant. Most expensive coffee in the world? Maybe. Kopi Luwak, or Civet Coffee, is really expensive. Most expensive coffee in the world? Maybe. Kopi Luwak, or Civet Coffee, is really expensive. We’re talking $60 for 4 ounces, or in some Indonesian coffee shops, $10 per cup. It is We’re talking $60 for 4 ounces, or in some Indonesian coffee shops, $10 per cup. It is undoubtedly a very rare cup of coffee. undoubtedly a very rare cup of coffee. Tasting notes: vegetabley, tea-like and earthy Tasting notes: vegetabley, tea-like and earthy *We sourced these beans from a small coffee farmer in Bali, Indonesia *We sourced these beans from a small coffee farmer in Bali, Indonesia and the roasting is done here in the states. and the roasting is done here in the states. So, what is Kopi Luwak? So, what is Kopi Luwak? Coffee beans are actually seeds found in the pit of cherry-sized fruits on the coffee plant. Coffee beans are actually seeds found in the pit of cherry-sized fruits on the coffee plant. Before coffee beans are ready to be sold to the consumer, they are separated from the flesh of Before coffee beans are ready to be sold to the consumer, they are separated from the flesh of the fruit, fermented, and roasted. -
Whole-Genome Sequencing of Wild Siberian Musk
Yi et al. BMC Genomics (2020) 21:108 https://doi.org/10.1186/s12864-020-6495-2 RESEARCH ARTICLE Open Access Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features Li Yi1†, Menggen Dalai2*†, Rina Su1†, Weili Lin3, Myagmarsuren Erdenedalai4, Batkhuu Luvsantseren4, Chimedragchaa Chimedtseren4*, Zhen Wang3* and Surong Hasi1* Abstract Background: Siberian musk deer, one of the seven species, is distributed in coniferous forests of Asia. Worldwide, the population size of Siberian musk deer is threatened by severe illegal poaching for commercially valuable musk and meat, habitat losses, and forest fire. At present, this species is categorized as Vulnerable on the IUCN Red List. However, the genetic information of Siberian musk deer is largely unexplored. Results: Here, we produced 3.10 Gb draft assembly of wild Siberian musk deer with a contig N50 of 29,145 bp and a scaffold N50 of 7,955,248 bp. We annotated 19,363 protein-coding genes and estimated 44.44% of the genome to be repetitive. Our phylogenetic analysis reveals that wild Siberian musk deer is closer to Bovidae than to Cervidae. Comparative analyses showed that the genetic features of Siberian musk deer adapted in cold and high-altitude environments. We sequenced two additional genomes of Siberian musk deer constructed demographic history indicated that changes in effective population size corresponded with recent glacial epochs. Finally, we identified several candidate genes that may play a role in the musk secretion based on transcriptome analysis. Conclusions: Here, we present a high-quality draft genome of wild Siberian musk deer, which will provide a valuable genetic resource for further investigations of this economically important musk deer. -
A Cryptic Species of the Tylonycteris Pachypus Complex (Chiroptera
Int. J. Biol. Sci. 2014, Vol. 10 200 Ivyspring International Publisher International Journal of Biological Sciences 2014; 10(2):200-211. doi: 10.7150/ijbs.7301 Research Paper A Cryptic Species of the Tylonycteris pachypus Complex (Chiroptera: Vespertilionidae) and Its Population Genetic Structure in Southern China and nearby Regions Chujing HUANG1*, Wenhua YU1*, Zhongxian XU1, Yuanxiong QIU1, Miao CHEN1, Bing QIU1, Masaharu MOTOKAWA2, Masashi HARADA3, Yuchun LI4 and Yi WU1 1. College of Life Sciences, Guangzhou University, Guangzhou 510006, China. 2. The Kyoto University Museum, Kyoto 606-8501, Japan. 3. Laboratory Animal Center, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan. 4. Marine College, Shandong University (Weihai), Weihai 264209, China. * These authors contribute to this work equally. Corresponding authors: E-mail: [email protected] or [email protected]. © Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/ licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. Received: 2013.07.30; Accepted: 2014.01.09; Published: 2014.02.05 Abstract Three distinct bamboo bat species (Tylonycteris) are known to inhabit tropical and subtropical areas of Asia, i.e., T. pachypus, T. robustula, and T. pygmaeus. This study performed karyotypic examina- tions of 4 specimens from southern Chinese T. p. fulvidus populations and one specimen from Thai T. p. fulvidus population, which detected distinct karyotypes (2n=30) compared with previous karyotypic descriptions of T. p. pachypus (2n=46) and T. robustula (2n=32) from Malaysia.