Convergent Evolution in the Euarchontoglires
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A Phylogeny and Timescale for Marsupial Evolution Based on Sequences for Five Nuclear Genes
J Mammal Evol DOI 10.1007/s10914-007-9062-6 ORIGINAL PAPER A Phylogeny and Timescale for Marsupial Evolution Based on Sequences for Five Nuclear Genes Robert W. Meredith & Michael Westerman & Judd A. Case & Mark S. Springer # Springer Science + Business Media, LLC 2007 Abstract Even though marsupials are taxonomically less diverse than placentals, they exhibit comparable morphological and ecological diversity. However, much of their fossil record is thought to be missing, particularly for the Australasian groups. The more than 330 living species of marsupials are grouped into three American (Didelphimorphia, Microbiotheria, and Paucituberculata) and four Australasian (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelemorphia) orders. Interordinal relationships have been investigated using a wide range of methods that have often yielded contradictory results. Much of the controversy has focused on the placement of Dromiciops gliroides (Microbiotheria). Studies either support a sister-taxon relationship to a monophyletic Australasian clade or a nested position within the Australasian radiation. Familial relationships within the Diprotodontia have also proved difficult to resolve. Here, we examine higher-level marsupial relationships using a nuclear multigene molecular data set representing all living orders. Protein-coding portions of ApoB, BRCA1, IRBP, Rag1, and vWF were analyzed using maximum parsimony, maximum likelihood, and Bayesian methods. Two different Bayesian relaxed molecular clock methods were employed to construct a timescale for marsupial evolution and estimate the unrepresented basal branch length (UBBL). Maximum likelihood and Bayesian results suggest that the root of the marsupial tree is between Didelphimorphia and all other marsupials. All methods provide strong support for the monophyly of Australidelphia. Within Australidelphia, Dromiciops is the sister-taxon to a monophyletic Australasian clade. -
Convergent Evolution in the Euarchontoglires
This is a repository copy of Convergent evolution in the Euarchontoglires. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/133262/ Version: Published Version Article: Morris, Philip James Rencher, Cobb, Samuel Nicholas Frederick orcid.org/0000-0002- 8360-8024 and Cox, Philip Graham orcid.org/0000-0001-9782-2358 (2018) Convergent evolution in the Euarchontoglires. Biology letters. 2018036. ISSN 1744-957X https://doi.org/10.1098/rsbl.2018.0366 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Downloaded from http://rsbl.royalsocietypublishing.org/ on August 1, 2018 Evolutionary biology Convergent evolution in the rsbl.royalsocietypublishing.org Euarchontoglires Philip J. R. Morris1, Samuel N. F. Cobb2 and Philip G. Cox2 1Hull York Medical School, University of Hull, Hull HU6 7RX, UK Research 2Department of Archaeology and Hull York Medical School, University of York, York YO10 5DD, UK SNFC, 0000-0002-8360-8024; PGC, 0000-0001-9782-2358 Cite this article: Morris PJR, Cobb SNF, Cox PG. 2018 Convergent evolution in the Convergence—the independent evolution of similar phenotypes in distantly Euarchontoglires. -
Musculoskeletal Morphing from Human to Mouse
Procedia IUTAM Procedia IUTAM 00 (2011) 1–9 2011 Symposium on Human Body Dynamics Musculoskeletal Morphing from Human to Mouse Yoshihiko Nakamuraa,∗, Yosuke Ikegamia, Akihiro Yoshimatsua, Ko Ayusawaa, Hirotaka Imagawaa, and Satoshi Ootab aDepartment of Mechano-Informatics, Graduate School of Information and Science and Technology, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan bBioresource Center, Riken, 3-1-1 Takanodai, Tsukuba-shi, Ibaragi, Japan Abstract The analysis of movement provides various insights of human body such as biomechanical property of muscles, function of neural systems, physiology of sensory-motor system, skills of athletic movements, and more. Biomechan- ical modeling and robotics computation have been integrated to extend the applications of musculoskeletal analysis of human movements. The analysis would also provide valuable means for the other mammalian animals. One of current approaches of post-genomic research focuses to find connections between the phenotype and the genotype. The former means the visible morphological or behavioral expression of an animal, while the latter implies its genetic expression. Knockout mice allows to study the developmental pathway from the genetic disorders to the behavioral disorders. Would musculoskeletal analysis of mice also offer scientific means for such study? This paper reports our recent technological development to build the musculoskeletal model of a laboratory mouse. We propose mapping the musculoskeletal model of human to a laboratory mouse based on the morphological similarity between the two mammals. Although the model will need fine adjustment based on the CT data or else, we can still use the mapped musculoskeletal model as an approximate model of the mouse’s musculoskeletal system. -
Aspects of Tree Shrew Consolidated Sleep Structure Resemble Human Sleep
ARTICLE https://doi.org/10.1038/s42003-021-02234-7 OPEN Aspects of tree shrew consolidated sleep structure resemble human sleep Marta M. Dimanico1,4, Arndt-Lukas Klaassen1,2,4, Jing Wang1,3, Melanie Kaeser1, Michael Harvey1, ✉ Björn Rasch 2 & Gregor Rainer 1 Understanding human sleep requires appropriate animal models. Sleep has been extensively studied in rodents, although rodent sleep differs substantially from human sleep. Here we investigate sleep in tree shrews, small diurnal mammals phylogenetically close to primates, and compare it to sleep in rats and humans using electrophysiological recordings from frontal cortex of each species. Tree shrews exhibited consolidated sleep, with a sleep bout duration 1234567890():,; parameter, τ, uncharacteristically high for a small mammal, and differing substantially from the sleep of rodents that is often punctuated by wakefulness. Two NREM sleep stages were observed in tree shrews: NREM, characterized by high delta waves and spindles, and an intermediate stage (IS-NREM) occurring on NREM to REM transitions and consisting of intermediate delta waves with concomitant theta-alpha activity. While IS-NREM activity was reliable in tree shrews, we could also detect it in human EEG data, on a subset of transitions. Finally, coupling events between sleep spindles and slow waves clustered near the beginning of the sleep period in tree shrews, paralleling humans, whereas they were more evenly distributed in rats. Our results suggest considerable homology of sleep structure between humans and tree shrews despite the large difference in body mass between these species. 1 Department of Neuroscience and Movement Sciences, Section of Medicine, University of Fribourg, Fribourg, Switzerland. -
The Phylogenetic Roots of Human Lethal Violence José María Gómez1,2, Miguel Verdú3, Adela González-Megías4 & Marcos Méndez5
LETTER doi:10.1038/nature19758 The phylogenetic roots of human lethal violence José María Gómez1,2, Miguel Verdú3, Adela González-Megías4 & Marcos Méndez5 The psychological, sociological and evolutionary roots of 600 human populations, ranging from the Palaeolithic era to the present conspecific violence in humans are still debated, despite attracting (Supplementary Information section 9c). The level of lethal violence the attention of intellectuals for over two millennia1–11. Here we was defined as the probability of dying from intraspecific violence propose a conceptual approach towards understanding these roots compared to all other causes. More specifically, we calculated the level based on the assumption that aggression in mammals, including of lethal violence as the percentage, with respect to all documented humans, has a significant phylogenetic component. By compiling sources of mortality, of total deaths due to conspecifics (these sources of mortality from a comprehensive sample of mammals, were infanticide, cannibalism, inter-group aggression and any other we assessed the percentage of deaths due to conspecifics and, type of intraspecific killings in non-human mammals; war, homicide, using phylogenetic comparative tools, predicted this value for infanticide, execution, and any other kind of intentional conspecific humans. The proportion of human deaths phylogenetically killing in humans). predicted to be caused by interpersonal violence stood at 2%. Lethal violence is reported for almost 40% of the studied mammal This value was similar to the one phylogenetically inferred for species (Supplementary Information section 9a). This is probably the evolutionary ancestor of primates and apes, indicating that a an underestimation, because information is not available for many certain level of lethal violence arises owing to our position within species. -
Sectional Geometry in a Simulated Fine Branch Niche
JOURNAL OF MORPHOLOGY 276:759–765 (2015) Mouse Hallucal Metatarsal Cross-Sectional Geometry in a Simulated Fine Branch Niche Craig D. Byron,1* Anthony Herrel,2,3 Elin Pauwels,4 Amelie De Muynck,4 and Biren A. Patel5,6 1Department of Biology, Mercer University, Macon, Georgia 2Departement d’Ecologie et de Gestion de la Biodiversite, CNRS/MNHN, Paris, France 3Department of Vertebrate Evolutionary Morphology, Ghent University, Gent, Belgium 4Department of Physics and Astronomy, Ghent University, UGCT, Ghent, Belgium 5Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, California 6Human and Evolutionary Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California ABSTRACT Mice raised in experimental habitats con- arboreal substrates (Le Gros Clark, 1959; Cart- taining an artificial network of narrow “arboreal” sup- mill, 1972; Szalay and Drawhorn, 1980; Sussman, ports frequently use hallucal grasps during locomotion. 1991; Schmitt and Lemelin, 2002; Bloch et al., Therefore, mice in these experiments can be used to 2007; Sargis et al., 2007). There are also examples model a rudimentary form of arboreal locomotion in an of rodent (Orkin and Pontzer, 2011), carnivoran animal without other morphological specializations for using a fine branch niche. This model would prove use- (Fabre et al., 2013), marsupial (Lemelin and ful to better understand the origins of arboreal behav- Schmitt, 2007; Shapiro et al., 2014), and nonmam- iors in mammals like primates. In this study, we malian vertebrates including frogs, lizards, and examined if locomotion on these substrates influences birds (Herrel et al., 2013; Sustaita et al., 2013) the mid-diaphyseal cross-sectional geometry of mouse that are effective in this niche without primate- metatarsals. -
Creating Animal Models, Why Not Use the Chinese Tree Shrew (Tupaia Belangeri Chinensis)?
ZOOLOGICAL RESEARCH Creating animal models, why not use the Chinese tree shrew (Tupaia belangeri chinensis)? Yong-Gang Yao1,2,* 1 Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China 2 Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China ABSTRACT the spot light as a viable animal model for investigating the basis of many different human diseases. The Chinese tree shrew (Tupaia belangeri chinensis), a squirrel-like and rat-sized mammal, has a wide Keywords: Chinese tree shrew; Genome biology; distribution in Southeast Asia, South and Southwest Animal model; Gene editing; Innate immunity China and has many unique characteristics that 1 make it suitable for use as an experimental animal. INTRODUCTION There have been many studies using the tree shrew (Tupaia belangeri) aimed at increasing our As human beings, our knowledge about ourselves, especially understanding of fundamental biological mechanisms about how our brain works, how a disease develops, and the and for the modeling of human diseases and discovery of many efficient therapeutic agents, has largely therapeutic responses. The recent release of a come from studies using animals. The higher the similarity publicly available annotated genome sequence of between an animal species and the human, the more we can the Chinese tree shrew and its genome database obtain helpful and precise information concerning the (www.treeshrewdb.org) has offered a solid base fundamental biology, disease mechanism, and safety, efficiency from which it is possible to elucidate the basic and predictability of therapeutic agents (Franco, 2013; biological properties and create animal models using McGonigle & Ruggeri, 2014). -
Elaborate Expansion of Syntenic V1R Hotspots Correlates with High Species
bioRxiv preprint doi: https://doi.org/10.1101/637348; this version posted May 22, 2019. 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. 1 Working Title: Elaborate expansion of syntenic V1R hotspots correlates with high species 2 diversity in nocturnal mouse and dwarf lemurs 3 Authors: Kelsie E. Hunnicutt1,8†, George P. Tiley1†, Rachel C. Williams1,2, Peter A. Larsen1, 9, Marina B. Blanco2, Rodin M. Rasoloarison3,4, C. Ryan Campbell1, Kevin Zhu5, David W. Weisrock8, Hiroaki Matsunami5,7 & Anne D. Yoder1* Affiliations: 1Department of Biology, Duke University, Durham, NC 27708, USA 2Duke Lemur Center, Duke University, Durham, NC 27705 3Behavioral Ecology and Sociobiology Unit, German Primate Centre, 37077 Göttingen, Germany 4Département de Biologie Animale, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar 5Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 6Department of Biology, University of Kentucky, Lexington, KY 40506 7Department of Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC 27710 8Current address: Department of Biological Sciences, University of Denver, Denver, CO 80208 9Current address: Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108 †Equal contributors 1 bioRxiv preprint doi: https://doi.org/10.1101/637348; this version posted May 22, 2019. 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. -
Colugos: Obscure Mammals Glide Into the Evolutionary Limelight Robert D Martin
BioMed Central Minireview Colugos: obscure mammals glide into the evolutionary limelight Robert D Martin Address: Department of Anthropology, The Field Museum, Chicago, IL 60605-2496, USA. Email: [email protected] Published: 1 May 2008 Journal of Biology 2008, 7:13 (doi:10.1186/jbiol74) The electronic version of this article is the complete one and can be found online at http://jbiol.com/content/7/4/13 © 2008 BioMed Central Ltd Abstract Substantial molecular evidence indicates that tree-shrews, colugos and primates cluster together on the mammalian phylogenetic tree. Previously, a sister-group relationship between colugos and primates seemed likely. A new study of colugo chromosomes indicates instead an affinity between colugos and tree-shrews. Colugos, constituting the obscure and tiny order Dermop- shrews, tree-shrews, colugos, bats and primates. However, tera, are gliding mammals confined to evergreen tropical Simpson’s ensuing influential classification of mammals [1] rainforests of South-East Asia. There are two extant species, rejected this assemblage. Subsequently, prompted by Butler now placed in separate genera: Galeopterus variegatus [4], the superorder Archonta was progressively resuscitated, (Malayan colugo, formerly known as Cynocephalus variegatus) although most authors emphatically excluded elephant- and Cynocephalus volans (Philippine colugo). Their most shrews (for example [5,6]). A quite recent major classifi- obvious hallmark is a gliding membrane (patagium) cation of mammals [7] united tree-shrews, colugos, bats surrounding almost the entire body margin. Colugos are and primates in the grand order Archonta. also called ‘flying lemurs’, but - as Simpson aptly noted [1] - they “are not lemurs and cannot fly”. They differ from other This whole topic has been reinvigorated by molecular gliding mammals (certain rodents and marsupials) in that evidence indicating that tree-shrews, colugos and primates, the patagium also extends between the hind limbs and the at least, may be quite closely related. -
Eutheria (Placental Mammals) Thought of As More Primitive
Eutheria (Placental Introductory article Mammals) Article Contents . Introduction J David Archibald, San Diego State University, San Diego, California, USA . Basic Design . Taxonomic and Ecological Diversity Eutheria includes one of three major clades of mammals, the extant members of which are . Fossil History and Distribution referred to as placentals. Phylogeny Introduction doi: 10.1038/npg.els.0004123 Eutheria (or Placentalia) is the most taxonomically diverse each. Except for placentals that have supernumerary teeth of three branches or clades of mammals, the other two (e.g. some whales, armadillos, etc.), in extant placentals, the being Metatheria (or Marsupialia) and Prototheria (or number of teeth is at most three upper and lower incisors, Monotremata). When named by Gill in 1872, Eutheria in- one upper and lower canine, four upper and lower premo- cluded both marsupials and placentals. It was Huxley in lars and three upper and lower molars. Pigs retain this pat- 1880 who recognized Eutheria basically as used today to tern, and except for one fewer upper molar, a domestic dog include only placentals. McKenna and Bell in their Clas- does as well. Compared to reptiles, mammals have fewer sification of Mammals published in 1997, chose to use Pla- skull bones through fusion and loss, although bones are centalia rather than Eutheria to avoid the confusion of variously emphasized in each of the three major mammalian what taxa should be included in Eutheria. Others such as taxa. See also: Digestive system of mammals; Ingestion in Rougier have used Eutheria and Placentalia in the sense mammals; Mesozoic mammals; Reptilia (reptiles) used here. Placentalia includes all extant placentals and Physiologically, mammals are all endotherms with var- their most recent common ancestor. -
Evaluating the Phylogenetic Position of Chinese Tree Shrew
Available online at www.sciencedirect.com JGG Journal of Genetics and Genomics 39 (2012) 131e137 ORIGINAL RESEARCH Evaluating the Phylogenetic Position of Chinese Tree Shrew (Tupaia belangeri chinensis) Based on Complete Mitochondrial Genome: Implication for Using Tree Shrew as an Alternative Experimental Animal to Primates in Biomedical Research Ling Xu a,b, Shi-Yi Chen c, Wen-Hui Nie d, Xue-Long Jiang d, Yong-Gang Yao a,* a Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China b Graduate School of the Chinese Academy of Sciences, Beijing 100039, China c Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Ya’an, Sichuan 625014, China d State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China Received 13 October 2011; revised 25 December 2011; accepted 5 January 2012 Available online 18 February 2012 ABSTRACT Tree shrew (Tupaia belangeri) is currently placed in Order Scandentia and has a wide distribution in Southeast Asia and Southwest China. Due to its unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low-cost of maintenance, tree shrew has been proposed to be an alternative experimental animal to primates in biomedical research. However, there are some debates regarding the exact phylogenetic affinity of tree shrew to primates. In this study, we determined the mtDNA entire genomes of three Chinese tree shrews (T. belangeri chinensis) and one Malayan flying lemur (Galeopterus variegatus). -
The Wide Distribution and Horizontal Transfers of Beta Satellite DNA in Eukaryotes
bioRxiv preprint doi: https://doi.org/10.1101/772921; this version posted September 18, 2019. 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. The wide distribution and horizontal transfers of beta satellite DNA in eukaryotes One-sentence summary: Beta satDNAs in Opimoda could be result of HT from Diaphoretickes and those in primates might have originated in common ancestor of Primatomorpha. Jiawen Yang1, Bin Yuan2, Yu Wu3, Meiyu Li4, Jian Li1, Donglin Xu5, Zeng-hong Gao1, Guangwei Ma1,Yiting Zhou1, Yachao Zuo1, Jin Wang1 and Yabin Guo1* 1Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China. 2Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences Wuhan China. 3Department of Parasitology, Zhongshan School Of Medicine, Sun Yat-sen university. 4Key Laboratory of Tropical Disease Control, Sun Yat-Sen University; Ministry of Education Experimental Teaching Center,Zhongshan School Of Medicine,Sun Yat-sen University. 5Guangzhou Academy of Agricultural Sciences, Guangzhou, China. *Correspondence: [email protected] Keywords: Beta satellite DNA, Sau3A sequences, Horizontal gene transfer, Primates, Eukaryotes, bioRxiv preprint doi: https://doi.org/10.1101/772921; this version posted September 18, 2019. 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.