DOCSLIB.ORG

Maximum Likelihood Tree of 11949529 Base Pair Exome Alignment

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

LCF_TUC_2060 (6) Black-tailed jackrabbit LCF_CAL_1954 LAM_Allab3_Bo (10) LAM_NBerg67_Rockies (12) Snowshoe hare LAM_A0604_WA (5) (14) LAM_A0965_WA LER_VIE_1639 (48) European hare LER_PYR_1546 LST_STA65 (9) (60) (47) Ethiopian highland hare 90 LST_STA89 (59) LHB_HAB35 (63) Abyssinian hare (51) LHB_HAB68 LCP_SAF_1903 (52) Cape hare LCP_TAN_3023 (53) (17) LFG_FAG114 (54) Ethiopian hare LFG_FAG96 LCR_ITA_1957 (20) Corsican hare LCR_ITA_1958 (19) (3) LCS_1894 (23) Broom hare LCS_1891 (18) 62 LGR_SEV_1163 (27) Iberian hare LGR_CRE_2553 LMS_PRI_2461 (26) (31) Manchurian hare LMS_PRI_2460 LTW_JRRK_3 (30) (35) White-tailed jackrabbit (2) LTW_MTA_3280 (34) LTM_CAT_2012 (39) LTM_AFR_3108 Mountain hare (38) LTM_MAG_1862 LOT_2110 (44) Alaskan hare LOT_2109 LCL_1956 White-sided jackrabbit (66) European rabbit Pygmy rabbit 0.002 Figure S1 – Maximum likelihood tree of 11,949,529 base pair exome alignment (positions with no missing data for any individual), generated using a simultaneous maximum likelihood (ML) search in RAxML and rapid bootstrapping run under the GTR+G model of sequence evolution (autoMRE option), and setting the European and pygmy rabbits as outgroups. We show branch supports for branches with support smaller than 100 in bold. Node labels in parenthesis correspond to node labels in the ancestral reconstruction output in Supplementary Table S6. OryCun European rabbit 31 a) BID_RC_444 Pygmy rabbit LCL_1956 White-sided jackrabbit LCF_CAL_1954 1: 0.69; 1.00 Black-tailed jackrabbit LCF_TUC_2060 31: 1.00; 1.00 LAM_Allab3_Bo 4: 0.77; 1.00 LAM_NBerg67_Rockies Snowshoe hare 3: 0.81; 1.00 LAM_A0965_WA 2: 0.81; 1.00 30: 0.43; 1.00 LAM_A0604_WA LER_PYR_1546 5: 0.71; 1.00 European hare LER_VIE_1639 LCP_SAF_1903 Cape hare 13: 0.41; 1.00 8: 0.51; 1.00 LCP_TAN_3023 29: 0.38; 1.00 7: 0.43; 1.00 LFG_FAG114 6: 0.84; 1.00 Ethiopian hare 12: 0.55; 1.00 LFG_FAG96 LST_STA65 9: 0.88; 1.00 Ethiopian highland hare LST_STA89 11: 0.60; 1.00 LHB_HAB35 10: 0.71; 1.00 Abyssinian hare LHB_HAB68 28: 0.61; 1.00 LMS_PRI_2461 14: 0.92; 1.00 Manchurian hare LMS_PRI_2460 LGR_CRE_2553 23: 0.46; 1.00 15: 0.87; 1.00 Iberian hare LGR_SEV_1163 22: 0.39; 0.89 LTW_JRRK_3 16: 0.64; 1.00 White-tailed jackrabbit LTW_MTA_3280 21: 0.67; 1.00 LTM_AFR_3108 27: 0.41; 1.00 20: 0.70; 1.00 LTM_CAT_2012 Mountain hare 19: 0.35; 0.79 LTM_MAG_1862 18: 0.35; 0.96 LOT_2109 17: 0.57; 1.00 Alaskan hare LOT_2110 LCS_1894 Broom hare 26: 0.92; 1.00 LCS_1891 25: 0.42; 1.00 LCR_ITA_1957 24: 0.42; 1.00 Corsican hare LCR_ITA_1958 2.0 White-sided jackrabbit b) Black-tailed jackrabbit 8: 1.00; 1.00 Snowshoe hare 9: 0.43; 1.00 Broom hare 2: 0.94; 1.00 Corsican hare 7: 0.41; 1.00 10: 0.38; 1.00 Manchurian hare 6: 0.46; 1.00 Iberian hare 5: 0.39; 0.89 White-tailed jackrabbit 4: 0.67; 1.00 11: 0.61; 1.00 Mountain hare 3: 0.71; 1.00 Alaskan hare European hare Ethiopian hare 12: 0.41; 1.00 1: 0.53; 1.00 Cape hare 13: 0.55; 1.00 Ethiopian highland hare 14: 0.71; 1.00 Abyssinian hare European rabbit 8: 1.00; 1.00 Pygmy rabbit 1.0 Figure S2 – ASTRAL species tree obtained with 8889 gene trees without a) or with b) assigning individuals to species. Nodes in both trees are numbered and annotated with quartet scores and posterior probabilities. Further information for each node can be found in Supplementary Tables S7 and S8. a) BID_RC_444 Pygmy rabbit OryCuN European rabbit LAM_A0604_WA LAM_A0965_WA Snowshoe hare LAM_NBerg67_Rockies LAM_Allab3_Bo LCP_SAF_1903 Cape hare LCP_TAN_3023 99,9 LFG_FAG114 Ethiopian hare LFG_FAG96 LHB_HAB35 Abyssinian hare LHB_HAB68 79,7 LST_STA65 Ethiopian highland hare LST_STA89 LER_PYR_1546 98,7 European hare LER_VIE_1639 LCR_ITA_1957 Corsican hare LCR_ITA_1958 LCS_1891 98,6 Broom hare LCS_1894 LGR_CRE_2553 Iberian hare 99,5 LGR_SEV_1163 81,1 LOT_2109 Alaskan hare LOT_2110 60,3 53,8 48,9 LTM_MAG_1862 LTM_CAT_2012 Mountain hare LTM_AFR_3108 LTW_JRRK_3 White-tailed jackrabbit LTW_MTA_3280 LMS_PRI_2460 Manchurian hare LMS_PRI_2461 LCF_CAL_1954 Black-tailed jackrabbit LCF_TUC_2060 LCL_1956 White-sided jackrabbit 2.0 b) Pygmy rabbit European rabbit Cape hare Ethiopian hare Abyssinian hare 49,5 Ethiopian highland hare European hare Corsican hare Broom hare Iberian hare 97,7 65,2 Alaskan hare 99,8 Mountain hare White-tailed jackrabbit Manchurian hare Snowshoe hare Black-tailed jackrabbit White-sided jackrabbit 1.1 Figure S3 – SVDquartets species tree generated with 45,779 unlinked SNPs without a) or with b) assigning individuals to species. For both trees, we show branch supports for branches with support lower than 100% of 1000 bootstrap rounds. a) 27 Mountain hare and Alaskan hare 22 26 White-tailed jackrabbit 21 20 25 Iberian hare 19 24 Manchurian hare 23 Corsican hare and Broom hare 18 13 Abyssinian hare 9 12 Ethiopian highland hare 10 17 11 8 Cape hare and Ethiopian hare 7 European hare 16 6 Snowshoe hare 15 5 Black-tailed jackrabbit 2 4 White-sided jackrabbit 3 Pygmy rabbit 2 European rabbit b) 9 10 11 15 1.00 0.75 0.50 0.25 0.00 11,7 | 8,9 11,8 | 7,9 11,9 | 7,8 16,4 | 2,3 16,3 | 2,4 16,2 | 3,4 10,8 | 12,13 10,13 | 12,8 10,12 | 13,8 10,7 | 18,19 10,18 | 19,7 10,19 | 18,7 16 17 18 19 1.00 Topology 0.75 t1 e freq. 0.50 v t2 0.25 relati t3 0.00 15,4 | 17,5 15,17 | 4,5 15,5 | 17,4 16,5 | 18,6 16,18 | 5,6 16,6 | 18,5 11,19 | 17,6 11,17 | 19,6 11,6 | 17,19 11,18 | 20,23 11,23 | 18,20 11,20 | 18,23 20 21 22 1.00 0.75 0.50 0.25 0.00 21,25 | 26,27 21,26 | 25,27 21,27 | 25,26 19,23 | 21,24 19,24 | 21,23 19,21 | 23,24 20,24 | 22,25 20,25 | 22,24 20,22 | 24,25 Figure S4 – Frequencies of the three main topologies around focal branches of the ASTRAL species tree (Fig. 1b). For each internal branch of the tree in (a), the frequency of the three possible topologies connecting the four neighboring branches is shown in (b). The title of each bar plot in (b) corresponds to labeled internal branches in the tree in (a). The most frequent topology is shown in red, and the two alternative topologies are shown in blue. On the x-axis of each bar plot, the topology of each quartet is represented using the neighboring branch labels. The branches leading to Mountain hares and Alaskan hares, Cape and Ethiopian hares, and Corsican and Broom hares were collapsed given the non-monophyly of the individuals of these species (Supplementary Figs. S2a and S3a). Figure S5 - Divergence time tree of Lepus, estimated from alignments of 9015 protein coding ortholog genes (10,863,822 bp alignment), with three partitions (1st, 2nd and 3rd codon positions) using (a) molecular-based dates extrapolated from deep fossil calibrations in the lagomorphs or (b) fossil calibrations for the divergence of the genus Lepus and the Lepus species (see Materials and Methods). Node labels in bold black are divergence time estimations in millions of years. Numbers in parenthesis in each node represent node numbers in Supplementary Table S5. Distance to species tree 1.0 0.8 0.6 ed RF distance z 0.4 mali r No 0.2 0.0 Chromosome Autosomes Gene tree X pairwise distance Figure S6 – Box plots of the normalized Robinson-Foulds distance between chromosome X and autosomes gene trees and the genome-wide species tree (Supplementary Fig. S2a), and pairwise distance among all gene trees. BID_RC_444 Pygmy rabbit [0.99,0.99] OryCun European rabbit LCL_1956 White-sided jackrabbit LTM_MAG_1862 Mountain hare [0.00,0.00] LOT_2109 [0.34,0.22] Alaskan hare [0.59,0.59] LOT_2110 LTM_CAT_2012 [0.00,0.00] Mountain hare [0.49,0.49] LTM_AFR_3108 LTW_JRRK_3 [0.00,0.06] [0.42,0.40] White-tailed jackrabbit LTW_MTA_3280 LMS_PRI_2461 [0.02,0.02] [0.91,0.91] Manchurian hare LMS_PRI_2460 LGR_CRE_2553 [0.89,0.89] Iberian hare [0.00,0.00] LGR_SEV_1163 LCS_1894 Broom hare [0.99,0.99] [0.94,0.94] LCS_1891 [0.01,0.05] LCR_ITA_1957 [0.06,0.11] Corsican hare LCR_ITA_1958 LCP_SAF_1903 [0.51,0.51] Cape hare [0.15,0.15] LCP_TAN_3023 [0.02,0.06] LFG_FAG114 [0.75,0.75] Ethiopian hare [0.13,0.13] LFG_FAG96 LST_STA65 [0.77,0.77] Abyssinian hare LST_STA89 [0.00,0.04] [0.34,0.34] [0.03,0.03] LHB_HAB35 [0.46,0.40] Ethiopian highland hare LHB_HAB68 LER_PYR_1546 [0.70,0.70] European hare LER_VIE_1639 [0.06,0.11] LAM_Allab3_Bo [0.73,0.73] LAM_NBerg67_Rockies Snowshoe hare [0.56,0.50] LAM_A0965_WA [0.54,0.47] LAM_A0604_WA LCF_CAL_1954 [0.51,0.51] Black-tailed jackrabbit LCF_TUC_2060 2.0 Figure S7 – Majority Rule Consensus Tree constructed from 8889 maximum likelihood gene trees. Tree nodes are annotated with the Internode Certainty (IC) and Internode Certainty All (ICA). a) White-sided jackrabbit Black-tailed jackrabbit 7 8 Snowshoe hare Manchurian hare 6 Iberian hare 9 5 White-tailed jackrabbit 4 Mountain hare 3 10 Alaskan hare Broom hare 2 Corsican hare 11 European hare Ethiopian hare 12 1 Cape hare 13 Ethiopian highland hare 14 Abyssinian hare European rabbit 8 Pygmy rabbit 0.7 Pygmy rabbit b) 94,1 European rabbit Snowshoe hare Cape hare 79,8 Ethiopian hare 60,5 European hare 94,1 56,3 Abyssinian hare 62,9 100 Ethiopian highland hare 70,2 Manchurian hare Corsican hare 100 100 Broom hare 99,4 Iberian hare 98,4 Alaskan hare 100 Mountain hare 94,1 99,9 White-tailed jackrabbit Black-tailed jackrabbit White-sided jackrabbit 1.1 Figure S8 – Chromosome X species trees.
Recommended publications
  • European Rabbits in Chile: the History of a Biological Invasion

    European Rabbits in Chile: the History of a Biological Invasion

    Historia. vol.4 no.se Santiago 2008 EUROPEAN RABBITS IN CHILE: THE HISTORY OF A BIOLOGICAL INVASION * ** *** PABLO C AMUS SERGIO C ASTRO FABIÁN J AKSIC * Centro de Estudios Avanzados en Ecología y Biodiversidad (CASEB) . email: [email protected] ** Departamento de Biología, Facultad de Química y Biología; Universidad de Santiago de Chile. Centro de Estudios Avanzados en Ecología y Biodiversidad (CASEB). email: [email protected] *** Departamento de Ecología, Pontificia Universidad Católica de Chile. Centro de Estudios Avanzados en Ecología y Biodiversidad (CASEB). email: [email protected] ABSTRACT This work analyses the relationship between human beings and their environment taking into consideration the adjustment and eventual invasion of rabbits in Chile. It argues that in the long run, human actions have unsuspected effects upon the environment. In fact rabbits were seen initially as an opportunity for economic development because of the exploitation of their meat and skin. Later, rabbits became a plague in different areas of Central Chile, Tierra del Fuego and Juan Fernández islands, which was difficult to control. Over the years rabbits became unwelcome guests in Chile. Key words: Environmental History, biological invasions, European rabbit, ecology and environment. RESUMEN Este trabajo analiza las relaciones entre los seres humanos y su ambiente, a partir de la historia de la aclimatación y posterior invasión de conejos en Chile, constatando que, en el largo plazo, las acciones humanas tienen efectos e impactos insospechados sobre el medio natural. En efecto, si bien inicialmente los conejos fueron vistos como una oportunidad de desarrollo económico a partir del aprovechamiento de su piel y su carne, pronto esta especie se convirtió en una plaga difícil de controlar en diversas regiones del país, como Chile central, Tierra del Fuego e islas Juan Fernández.
  • Behavior and Ecology of the Riparian Brush Rabbit at the San Joaquin

    Behavior and Ecology of the Riparian Brush Rabbit at the San Joaquin

    BEHAVIOR AND ECOLOGY OF THE RIPARIAN BRUSH RABBIT AT THE SAN JOAQUIN RIVER NATIONAL WILDLIFE REFUGE AS DETERMINED BY CAMERA TRAPS A Thesis Presented to the Faculty of California State University, Stanislaus In Partial Fulfillment of the Requirements for the Degree of Master of Ecology and Sustainability By Celia M. Tarcha May 2020 CERTIFICATION OF APPROVAL BEHAVIOR AND ECOLOGY OF THE RIPARIAN BRUSH RABBIT AT THE SAN JOAQUIN RIVER NATIONAL WILDLIFE REFUGE AS DETERMINED BY CAMERA TRAPS By Celia M. Tarcha Signed Certification of Approval page is on file with the University Library Dr. Patrick A. Kelly Date Professor of Zoology Dr. Michael P. Fleming Date Associate Professor of Biology Education Dr. Marina M. Gerson Date Professor of Zoology Matthew R. Lloyd Date U.S. Fish and Wildlife Service © 2020 Celia M. Tarcha ALL RIGHTS RESERVED DEDICATION For my family, living and departed, who first introduced me to wildlife and appreciating inconspicuous beauty. iv ACKNOWLEDGEMENTS I wish to express my deepest gratitude to my committee members, Matt Lloyd, Dr. Fleming, Dr. Gerson, and Dr. Kelly, for their time and effort towards perfecting this project. I would also like to thank Eric Hopson, refuge manager of San Joaquin River National Wildlife Refuge for his insight and field support. Thank you as well to refuge biologists Fumika Takahashi and Kathryn Heffernan for their field surveys and reports. Additional thanks to Camera Bits Inc. for their donation of the Photomechanic license. I would like to thank the CSU Stanislaus Department of Biological Sciences for their help and support. Thank you to Bernadette Paul of the Endangered Species Recovery Program for her equipment management and support.
  • The Status and Distribution of Mediterranean Mammals

    The Status and Distribution of Mediterranean Mammals

    THE STATUS AND DISTRIBUTION OF MEDITERRANEAN MAMMALS Compiled by Helen J. Temple and Annabelle Cuttelod AN E AN R R E IT MED The IUCN Red List of Threatened Species™ – Regional Assessment THE STATUS AND DISTRIBUTION OF MEDITERRANEAN MAMMALS Compiled by Helen J. Temple and Annabelle Cuttelod The IUCN Red List of Threatened Species™ – Regional Assessment The designation of geographical entities in this book, and the presentation of material, do not imply the expression of any opinion whatsoever on the part of IUCN or other participating organizations, concerning the legal status of any country, territory, or area, or of its authorities, or concerning the delimitation of its frontiers or boundaries. The views expressed in this publication do not necessarily reflect those of IUCN or other participating organizations. Published by: IUCN, Gland, Switzerland and Cambridge, UK Copyright: © 2009 International Union for Conservation of Nature and Natural Resources Reproduction of this publication for educational or other non-commercial purposes is authorized without prior written permission from the copyright holder provided the source is fully acknowledged. Reproduction of this publication for resale or other commercial purposes is prohibited without prior written permission of the copyright holder. Red List logo: © 2008 Citation: Temple, H.J. and Cuttelod, A. (Compilers). 2009. The Status and Distribution of Mediterranean Mammals. Gland, Switzerland and Cambridge, UK : IUCN. vii+32pp. ISBN: 978-2-8317-1163-8 Cover design: Cambridge Publishers Cover photo: Iberian lynx Lynx pardinus © Antonio Rivas/P. Ex-situ Lince Ibérico All photographs used in this publication remain the property of the original copyright holder (see individual captions for details).
  • 2011 COLUMBIA BASIN PYGMY RABBIT REINTRODUCTION and GENETIC MANAGEMENT PLAN Washington Department of Fish and Wildlife

    2011 COLUMBIA BASIN PYGMY RABBIT REINTRODUCTION and GENETIC MANAGEMENT PLAN Washington Department of Fish and Wildlife

    2011 COLUMBIA BASIN PYGMY RABBIT REINTRODUCTION AND GENETIC MANAGEMENT PLAN Washington Department of Fish and Wildlife Addendum to Washington State Recovery Plan for the Pygmy Rabbit (1995) Penny A. Becker, David W. Hays & Rodney D. Sayler EXECUTIVE SUMMARY This plan addresses the recovery strategy for the federal and state endangered Columbia Basin pygmy rabbit (Brachylagus idahoensis) in shrub-steppe habitat of central Washington. It is a consolidated update of the 2010 genetic management plan and the 2007 reintroduction plan for the pygmy rabbit. Technical background for the plan, covering the history, biology, and ecology of pygmy rabbits, has been reviewed extensively in a 5-Year Status Review (USFWS 2010) and an amendment to the federal Draft Recovery Plan (USFWS 2011) for the Columbia Basin distinct population segment of the pygmy rabbit. Currently, there are no wild pygmy rabbit populations known to occur in Washington’s Columbia Basin. As a result, the recovery strategy relies on the reintroduction of captive-bred pygmy rabbits originating from the joint captive population maintained since 2001 at Northwest Trek, Oregon Zoo, and Washington State University, in conjunction with the release of wild pygmy rabbits captured from other populations within the species’ historic distribution. The reintroduction plan was formulated with information gleaned from studies of pygmy rabbits in the wild, results of the 2002-04 pilot-scale reintroductions in southeastern Idaho, results of a trial 2007 release of animals into Washington, and comparable reintroduction efforts for other endangered species. Beginning in the spring of 2011, pygmy rabbits were reintroduced at Washington Department of Fish and Wildlife’s Sagebrush Flat Wildlife Area.
  • The State of Lagomorphs Today

    The State of Lagomorphs Today

    HOUSE RABBIT JOURNAL The publication for members of the international House Rabbit Society Winter 2016 The State of Lagomorphs Today by Margo DeMello, PhD Make Mine Chocolate™ Turns 15 by Susan Mangold and Terri Cook Advocating For Rabbits by Iris Klimczuk Fly Strike (Myiasis) in Rabbits by Stacie Grannum, DVM $4.99 CONTENTS HOUSE RABBIT JOURNAL Winter 2016 Contributing Editors Amy Bremers Shana Abé Maureen O’Neill Nancy Montgomery Linda Cook The State of Lagomorphs Today p. 4 Sandi Martin by Margo DeMello, PhD Rebecca Clawson Designer/Editor Sandy Parshall Veterinary Review Linda Siperstein, DVM Executive Director Anne Martin, PhD Board of Directors Marinell Harriman, Founder and Chair Margo DeMello, President Mary Cotter, Vice President Joy Gioia, Treasurer Beth Woolbright, Secretary Dana Krempels Laurie Gigous Kathleen Wilsbach Dawn Sailer Bill Velasquez Judith Pierce Edie Sayeg Nancy Ainsworth House Rabbit Society is a 501c3 and its publication, House Rabbit Journal, is published at 148 Broadway, Richmond, CA 94804. Photograph by Tom Young HRJ is copyright protected and its contents may not be republished without written permission. The Bunny Who Started It All p. 7 by Nareeya Nalivka Goldie is adoptable at House Rabbit Society International Headquarters in Richmond, CA. rabbitcenter.org/adopt Make Mine Chocolate™ Turns 15 p. 8 by Susan Mangold and Terri Cook Cover photo by Sandy Parshall, HRS Program Manager Bella’s Wish p. 9 by Maurice Liang Advocating For Rabbits p. 10 by Iris Klimczuk From Grief to Grace: Maurice, Miss Bean, and Bella p. 12 by Chelsea Eng Fly Strike (Myiasis) in Rabbits p. 13 by Stacie Grannum, DVM The Transpacifi c Bunny p.
  • Revised Distribution of an Alaskan Endemic, the Alaska Hare (Lepus Othus), with Implications for Taxonomy, Biogeography, and Climate Change

    Revised Distribution of an Alaskan Endemic, the Alaska Hare (Lepus Othus), with Implications for Taxonomy, Biogeography, and Climate Change

    50 ARTICLE Revised distribution of an Alaskan endemic, the Alaska Hare (Lepus othus), with implications for taxonomy, biogeography, and climate change Michelle M. Cason, Andrew P. Baltensperger, Travis L. Booms, John J. Burns, and Link E. Olson Abstract: The Alaska Hare (Lepus othus Merriam 1900) is the largest lagomorph in North America but remains one of the most poorly studied terrestrial mammals on the con- tinent. Its current distribution is restricted to western Alaska south of the Brooks Range, but historical accounts from north of the Brooks Range (the North Slope) have led to confusion over its past, present, and predicted future distributions. To determine if L. othus occurs or historically occurred on the North Slope, we surveyed museum collections, vetted observa- tional accounts, and produced a spatial distribution model based on the resulting georefer- enced records. We located a historic specimen long presumed lost that suggests the occurrence of L. othus on the North Slope as recently as the late 1800s. We also uncovered evidence of L. othus and (or) Mountain Hare (Lepus timidus Linnaeus 1758) on several islands in the Bering Sea, raising the possibility of recurring gene flow between these closely related species across seasonal ice connecting Asia and North America. While our results paint a more complete picture of the current distribution of L. othus, persistent uncertainties surrounding its taxonomic status and potential northward range shift onto lands reserved for oil and gas development call for additional study. For personal use only. Key words: Alaska Hare, Arctic Hare, Lepus othus, Mountain Hare, North Slope. Résumé : Le lièvre d’Alaska (Lepus othus Merriam 1900) est le plus grand lagomorphe en Amérique du Nord mais il demeure un des mammifères terrestres du continent qui n’a aiment pas fait l’objet d’études.
  • Raising Hares

    Raising Hares

    Raising Hares Photographs by Andy Rouse/naturepl.com The agility and grace of the European hare (Lepus europaeus) is a familiar sight in the British countryside, and their spirited springtime antics mark the end of winter in the minds of many. Despite their similarities in appearance to the European rabbit, the life history and behaviour of the European hare differs significantly from that of their smaller cousins. We join photographer Andy Rouse as he captures the story of the hare and discovers the true meaning of ‘Mad as a March hare’. Brown hares are widespread throughout central and west- ern Europe, including most of the UK, where they were thought to be introduced by the Romans. “I’ve been passionate about watching and photographing hares for years”, says Rouse. “They are always a challenge because they’re so wary and elusive. Getting decent images usually requires hours of lying quietly in a ditch! So I was de- lighted when I found a unique site in Southern England that has a thriving population of hares”. “Hares are wonderful to work with”, says Rouse. “Concentrating on one population opens up much greater opportunities than photo- graphing at a multitude of sites. It has been such a pleasure getting to know individuals on this project”. “I took these images at a former WWI airfield”, says Rouse. “It is the oldest in the world and still in use, with grass runways. The alternation of cut and long grass provides ideal habitat for hares, which are traditionally found along field margins”. “The hares here are used to people so it’s easier to observe them and predict their behaviour”, says Rouse.
  • World Distribution of the European Rabbit (Oryctolagus Cuniculus)

    World Distribution of the European Rabbit (Oryctolagus Cuniculus)

    1 The Evolution, Domestication and World Distribution of the European Rabbit (Oryctolagus cuniculus) Luca Fontanesi1*, Valerio Joe Utzeri1 and Anisa Ribani1 1Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Italy 1.1 The Order Lagomorpha to assure essential vitamin uptake, the digestion of the vegetarian diet and water reintroduction The European rabbit (Oryctolagus cuniculus, (Hörnicke, 1981). Linnaeus 1758) is a mammal belonging to the The order Lagomorpha was recognized as a order Lagomorpha. distinct order within the class Mammalia in Lagomorphs are such a distinct group of 1912, separated from the order Rodentia within mammalian herbivores that the very word ‘lago- which lagomorphs were originally placed (Gidely, morph’ is a circular reference meaning ‘hare- 1912; Landry, 1999). Lagomorphs are, however, shaped’ (Chapman and Flux, 1990; Fontanesi considered to be closely related to the rodents et al., 2016). A unique anatomical feature that from which they diverged about 62–100 million characterizes lagomorphs is the presence of years ago (Mya), and together they constitute small peg-like teeth immediately behind the up- the clade Glires (Chuan-Kuei et al., 1987; Benton per-front incisors. For this feature, lagomorphs and Donoghue, 2007). Lagomorphs, rodents and are also known as Duplicidentata. Therefore, primates are placed in the major mammalian instead of four incisor teeth characteristic of clade of the Euarchontoglires (O’Leary et al., 2013). rodents (also known as Simplicidentata), lago- Modern lagomorphs might be evolved from morphs have six. The additional pair is reduced the ancestral lineage from which derived the in size. Another anatomical characteristic of the †Mimotonidae and †Eurymilydae sister taxa, animals of this order is the presence of an elong- following the Cretaceous-Paleogene (K-Pg) bound- ated rostrum of the skull, reinforced by a lattice- ary around 65 Mya (Averianov, 1994; Meng et al., work of bone, which is a fenestration to reduce 2003; Asher et al., 2005; López-Martínez, 2008).
  • Pygmy Rabbit Brachylagus Idahoensis

    Pygmy Rabbit Brachylagus Idahoensis

    Pygmy Rabbit Brachylagus idahoensis Mammalia — Lagomorpha — Leporidae CONSERVATION STATUS / CLASSIFICATION Rangewide: Apparently secure (G4) Statewide: Imperiled (S2) ESA: No status USFS: Region 1: No status; Region 4: Sensitive BLM: Rangewide/Globally imperiled (Type 2) IDFG: Upland game animal BASIS FOR INCLUSION Regional population abundance and trend data are lacking; habitat threats. TAXONOMY The pygmy rabbit is within the monotypic genus Brachylagus. DISTRIBUTION AND ABUNDANCE This species occurs in the Great Basin and adjoining intermountain regions. Populations are widely scattered across this landscape in association with tall, dense sagebrush aggregations with deep, loose soils of alluvial origin that allow burrowing. In Idaho, pygmy rabbits occur across the southern half of the state. The species is considered rare in Idaho, though data on abundance and population trends are generally lacking. Recent surveys for presence of pygmy rabbits have augmented statewide distribution data and documented relatively abundant populations in localized areas (Waterbury, in prep; Roberts 2001). POPULATION TREND There are no trend data for Idaho populations. HABITAT AND ECOLOGY The pygmy rabbit is a sagebrush obligate inhabiting areas characterized by cold winters, warm summers, scant precipitation. Elevations range from 900-2380 m (2800- 7800 ft). Habitat comprises dense, tall stands of big sagebrush growing on deep, friable soils that allow the rabbits to dig rather extensive burrow systems (Janson 2002). Landscape features includes alluvial fans and hillsides, swales within rolling topography, floodplains, brushy draws, riparian channels, edges of rock and lava outcroppings, and mima mounds (low, circular mounds of loose, unstratified soils that support distinctly taller patches of sagebrush). Big sagebrush is the primary food item of pygmy rabbits and may comprise up to 99% of the winter diet (Green and Flinders 1980).
  • Response of Wildlife to Bush Thinning on the North Central Freehold Farmlands of Namibia T

    Response of Wildlife to Bush Thinning on the North Central Freehold Farmlands of Namibia T

    Forest Ecology and Management 473 (2020) 118330 Contents lists available at ScienceDirect Forest Ecology and Management journal homepage: www.elsevier.com/locate/foreco Response of wildlife to bush thinning on the north central freehold farmlands of Namibia T Matti T. Nghikembuaa,b,c, Laurie L. Markera,b, Bruce Brewera,b, Lauri Mehtätaloc, Mark Appiahc,d, ⁎ Ari Pappinenc, a Cheetah Conservation Fund, Otjiwarongo, Namibia b CCF Bush PTY Ltd, Otijwarongo, Namibia c University of Eastern Finland, School of Forest Sciences, Joensuu Campus, Yliopistokatu 7, 80101 Joensuu, Finland d Forestry Research Institute of Ghana (CSIR-FORIG), Kumasi, Ghana ARTICLE INFO ABSTRACT Keywords: Agriculture is considered the backbone of the Namibian economy. However, bush encroachment affects ap- Bush encroachment proximately 45 million hectares of Namibian farmland and in the absence of appropriate restoration measures, Biodiversity negatively affects local biodiversity and the national economy. Bush thinning operations on three freehold farms Restoration were assessed to examine the response of local ungulates (small, medium, large) and predators (meso, large). Carrying capacity Camera traps were used to capture wildlife in bush encroached and previously thinned habitats. We hy- Overgrazing pothesized that thinning would increase the activity of small, medium, and large ungulates, meso and large Bush thinning predators, and that the magnitude of the increase in activity at thinned sites would differ among animal types. Our results revealed that the expected animal captures were not equal – small, medium, and large ungulates were common, large predators were least common; thinned areas had more expected animal captures and overall animal-treatment interactions were almost significant (p = 0.051).
  • The Cape, 2017

    The Cape, 2017

    The Cape August 2017 Wildlife Travel 1 10th August Early arrival Cape Town. Afternoon wander around Scarborough o/n Scarborough 11th Cape Point Nature Reserve: Buffel’s Beach, Cape of Good Hope, Circular Drive, Gifkomnetjie. Night drive from Scarborough to Cape Point entry gate, to Simonstown and back to Scarobourgh. o/n Scarborough 12th Rooiels (am), Scarborough (pm) o/n Scarborough 13th Kirstenbosch Botanic Gardens o/n Pinelands, Cape Town 14th Cape Point Nature Reserve: Cape Point and Oliphants Bay Rondevlei Nature Reserve, Strandfontein o/n Pinelands, Cape Town 15th Travel up the west coast to Langebaan o/n Langebaan 16th West Coast National Park o/n Langebaan 17th Langebaan to Nieuwoudtville, via Quaggaskop, Knersvlakte o/n Nieuwoudtville 18th Nieuwoudtville o/n Nieuwoudtville 19th Nieuwoudtville to Ceres, via Tanqwa Karoo NP o/n Ceres 20th Ceres to De Hoop Nature Reserve o/n De Hoop 21st De Hoop Nature Reserve o/n De Hoop 22nd De Hoop to Hermanus o/n Hermanus 23rd Betty’s Bay: Stony Point and Harold Porter Botanic Garden o/n Hermanus 24th Hermanus to Cape Town Return to UK 2 th th th th th th th th th th th st nd rd th 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Order Primates (Apes & Monkeys) Chacma Baboon X X X X X X X X X Papio ursinus Order Tubulidentata (Aardvark) Aardvark S S Orycteropus afer Burrows and termite diggings around Nieuwoudtville and in the Tanqwa Karoo Order Lagomorpha (Hares) Cape Hare X X Lepus capensis Scrub Hare X X Lepus saxatilis Hares were identified on the (probably dodgy) basis of habitat preference (Cape Hare being in open agricultural fields and more barren, open habitats, Scrub Hare being in more vegetated bush) and the presence of a rusty nape patch seen well on the animals in De Hoop.
  • Appendix Lagomorph Species: Geographical Distribution and Conservation Status

    Appendix Lagomorph Species: Geographical Distribution and Conservation Status

    Appendix Lagomorph Species: Geographical Distribution and Conservation Status PAULO C. ALVES1* AND KLAUS HACKLÄNDER2 Lagomorph taxonomy is traditionally controversy, and as a consequence the number of species varies according to different publications. Although this can be due to the conservative characteristic of some morphological and genetic traits, like general shape and number of chromosomes, the scarce knowledge on several species is probably the main reason for this controversy. Also, some species have been discovered only recently, and from others we miss any information since they have been first described (mainly in pikas). We struggled with this difficulty during the work on this book, and decide to include a list of lagomorph species (Table 1). As a reference, we used the recent list published by Hoffmann and Smith (2005) in the “Mammals of the world” (Wilson and Reeder, 2005). However, to make an updated list, we include some significant published data (Friedmann and Daly 2004) and the contribu- tions and comments of some lagomorph specialist, namely Andrew Smith, John Litvaitis, Terrence Robinson, Andrew Smith, Franz Suchentrunk, and from the Mexican lagomorph association, AMCELA. We also include sum- mary information about the geographical range of all species and the current IUCN conservation status. Inevitably, this list still contains some incorrect information. However, a permanently updated lagomorph list will be pro- vided via the World Lagomorph Society (www.worldlagomorphsociety.org). 1 CIBIO, Centro de Investigaça˜o em Biodiversidade e Recursos Genéticos and Faculdade de Ciˆencias, Universidade do Porto, Campus Agrário de Vaira˜o 4485-661 – Vaira˜o, Portugal 2 Institute of Wildlife Biology and Game Management, University of Natural Resources and Applied Life Sciences, Gregor-Mendel-Str.