1
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Kliver S, Houck ML, Perelman PL, Totikov A, Tomarovsky A, Dudchenko O, Omer AD, Colaric Z, Weisz D, Aiden EL, Chan S, Hastie A, Komissarov A, Ryder OA, Graphodatsky A, Johnson WE, Maldonado JE, Pukazhenthi BS, Marinari PE, Wildt DE, Koepfli KP. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). J Hered 2023; 114:539-548. [PMID: 37249392 PMCID: PMC10848218 DOI: 10.1093/jhered/esad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/27/2023] [Indexed: 05/31/2023] Open
Abstract
The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.
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Affiliation(s)
- Sergei Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, Copenhagen, Denmark
| | - Marlys L Houck
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Polina L Perelman
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Azamat Totikov
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Andrey Tomarovsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, United States
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Saki Chan
- Department of Research and Development, Bionano Genomics, San Diego, CA, United States
| | - Alex Hastie
- Department of Research and Development, Bionano Genomics, San Diego, CA, United States
| | - Aleksey Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, Saint Petersburg, Russia
| | - Oliver A Ryder
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Alexander Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Warren E Johnson
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, United States
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Loyola University Maryland, Baltimore, MD, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Paul E Marinari
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - David E Wildt
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, United States
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2
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Houck ML, Koepfli KP, Hains T, Khan R, Charter SJ, Fronczek JA, Misuraca AC, Kliver S, Perelman PL, Beklemisheva V, Graphodatsky A, Luo SJ, O'Brien SJ, Lim NTL, Chin JSC, Guerra V, Tamazian G, Omer A, Weisz D, Kaemmerer K, Sturgeon G, Gaspard J, Hahn A, McDonough M, Garcia-Treviño I, Gentry J, Coke RL, Janecka JE, Harrigan RJ, Tinsman J, Smith TB, Aiden EL, Dudchenko O. Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity. Chromosome Res 2023; 31:13. [PMID: 37043058 DOI: 10.1007/s10577-023-09722-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/27/2023] [Accepted: 03/04/2023] [Indexed: 04/13/2023]
Abstract
We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.
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Affiliation(s)
- Marlys L Houck
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA.
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, 22630, USA.
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA.
- Computer Technologies Laboratory, ITMO University, 197101, St. Petersburg, Russia.
| | - Taylor Hains
- Committee On Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suellen J Charter
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA
| | - Julie A Fronczek
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA
| | - Ann C Misuraca
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA
| | - Sergei Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, 5A, Oester Farimagsgade, 1353, Copenhagen, Denmark
| | - Polina L Perelman
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090, Novosibirsk, Russia
| | - Violetta Beklemisheva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090, Novosibirsk, Russia
| | - Alexander Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090, Novosibirsk, Russia
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Computer Technologies Laboratory, ITMO University, 197101, St. Petersburg, Russia
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33004, USA
| | - Norman T-L Lim
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, 637616, Singapore
| | - Jason S C Chin
- Taipei Zoo, No. 30 Sec. 2 Xinguang Rd., Taipei, 11656, Taiwan
| | - Vanessa Guerra
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Gaik Tamazian
- Centre for Computational Biology, Peter the Great Saint Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Arina Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | | | - Alicia Hahn
- Pittsburgh Zoo & Aquarium, PA, 15206, Pittsburgh, USA
| | | | | | - Jordan Gentry
- Center for Conservation and Research, San Antonio Zoo, San Antonio, TX, 78212, USA
| | - Rob L Coke
- Center for Conservation and Research, San Antonio Zoo, San Antonio, TX, 78212, USA
| | - Jan E Janecka
- Department of Biological Sciences, Bayer School of Natural and Environmental Sciences, Duquesne University, Pittsburgh, PA, 15282, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA
| | - Jen Tinsman
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX, 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX, 77030, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Center for Theoretical and Biological Physics, Rice University, Houston, TX, 77030, USA.
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3
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Nursyifa C, Brüniche-Olsen A, Garcia-Erill G, Heller R, Albrechtsen A. Joint identification of sex and sex-linked scaffolds in non-model organisms using low depth sequencing data. Mol Ecol Resour 2021; 22:458-467. [PMID: 34431216 DOI: 10.1111/1755-0998.13491] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/23/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022]
Abstract
Being able to assign sex to individuals and identify autosomal and sex-linked scaffolds are essential in most population genomic analyses. Non-model organisms often have genome assemblies at scaffold-level and lack characterization of sex-linked scaffolds. Previous methods to identify sex and sex-linked scaffolds have relied on synteny between the non-model organism and a closely related species or prior knowledge about the sex of the samples to identify sex-linked scaffolds. In the latter case, the difference in depth of coverage between the autosomes and the sex chromosomes are used. Here, we present "sex assignment through coverage" (SATC), a method to assign sex to samples and identify sex-linked scaffolds from next generation sequencing (NGS) data. The method works for species with a homogametic/heterogametic sex determination system and only requires a scaffold-level reference assembly and sampling of both sexes with whole genome sequencing (WGS) data. We use the sequencing depth distribution across scaffolds to jointly identify: (i) male and female individuals, and (ii) sex-linked scaffolds. This is achieved through projecting the scaffold depths into a low-dimensional space using principal component analysis (PCA) and subsequent Gaussian mixture clustering. We demonstrate the applicability of our method using data from five mammal species and a bird species complex. The method is freely available at https://github.com/popgenDK/SATC as R code and a graphical user interface (GUI).
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Affiliation(s)
- Casia Nursyifa
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anna Brüniche-Olsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Genis Garcia-Erill
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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4
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Jowers MJ, Queirós J, Resende Pinto R, Ali AH, Mutinda M, Angelone S, Alves PC, Godinho R. Genetic diversity in natural range remnants of the critically endangered hirola antelope. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe hirola antelope (Beatragus hunteri) is considered to be the most endangered antelope in the world. In the ex situ translocated population at Tsavo East National Park, calf mortality and the critically low population numbers might suggest low genetic diversity and inbreeding depression. Consequently, a genetic study of the wild population is pivotal to gain an understanding of diversity and differentiation within its range before designing future translocation plans to increase the genetic diversity of the ex situ population. For that purpose, we assessed 55 individuals collected across five localities in eastern Kenya, covering its entire natural range. We used the complete mitochondrial DNA control region and microsatellite genotyping to estimate genetic diversity and differentiation across its range. Nuclear genetic diversity was moderate in comparison to other endangered African antelopes, with no signals of inbreeding. However, the mitochondrial data showed low nucleotide diversity, few haplotypes and low haplotypic differentiation. Overall, the inferred low degree of genetic differentiation and population structure suggests a single population of hirola across the natural range. An overall stable population size was inferred over the recent history of the species, although signals of a recent genetic bottleneck were found. Our results show hope for ongoing conservation management programmes and that there is a future for the hirola in Kenya.
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Affiliation(s)
- Michael Joseph Jowers
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - João Queirós
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Rui Resende Pinto
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Abdullahi H Ali
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
- National Museums of Kenya, Nairobi, Kenya
- Hirola Conservation Programme, Garissa, Kenya
| | - Mathew Mutinda
- Department of Veterinary and Capture Services, Kenya Wildlife Service, Nairobi, Kenya
| | - Samer Angelone
- Institute of Evolutionary Biology and Environmental Studies (IEU), University of Zurich, Zurich, Switzerland
| | - Paulo Célio Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, University of Johannesburg, South Africa
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5
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Hassanin A, Houck ML, Tshikung D, Kadjo B, Davis H, Ropiquet A. Multi-locus phylogeny of the tribe Tragelaphini (Mammalia, Bovidae) and species delimitation in bushbuck: Evidence for chromosomal speciation mediated by interspecific hybridization. Mol Phylogenet Evol 2018; 129:96-105. [PMID: 30121341 DOI: 10.1016/j.ympev.2018.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/06/2018] [Accepted: 08/06/2018] [Indexed: 10/28/2022]
Abstract
The bushbuck is the most widespread bovid species in Africa. Previous mitochondrial studies have revealed a polyphyletic pattern suggesting the possible existence of two distinct species. To assess this issue, we have sequenced 16 nuclear genes and one mitochondrial fragment (cytochrome b gene + control region) for most species of the tribe Tragelaphini, including seven bushbuck individuals belonging to the two divergent mtDNA haplogroups, Scriptus and Sylvaticus. Our phylogenetic analyses show that the Scriptus lineage is a sister-group of Sylvaticus in the nuclear tree, whereas it is related to Tragelaphus angasii in the mitochondrial tree. This mito-nuclear discordance indicates that the mitochondrial genome of Scriptus was acquired by introgression after one or several past events of hybridization between bushbuck and an extinct species closely related to T. angasii. The division into two bushbuck species is supported by the analyses of nuclear markers and by the karyotype here described for T. scriptus (2n = 57 M/58F), which is strikingly distinct from the one previously found for T. sylvaticus (2n = 33 M/34F). Molecular dating estimates suggest that the two species separated during the Early Pleistocene after an event of interspecific hybridization, which may have mediated massive chromosomal rearrangements in the common ancestor of T. scriptus.
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Affiliation(s)
- Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE; 57 rue Cuvier, CP 51, 75005 Paris, France.
| | - Marlys L Houck
- San Diego Zoo Institute for Conservation Research; 15600 San Pasqual Valley Road, Escondido, CA 92027, USA
| | - Didier Tshikung
- Faculté de médicine vétérinaire; Université de Lubumbashi, 243 BP 1825, The Democratic Republic of the Congo
| | - Blaise Kadjo
- Université Félix-Houphouët-Boigny, UFR Biosciences; 22 BP 582, Abidjan 22, Cote d'Ivoire
| | - Heidi Davis
- San Diego Zoo Institute for Conservation Research; 15600 San Pasqual Valley Road, Escondido, CA 92027, USA
| | - Anne Ropiquet
- Middlesex University, Department of Natural Sciences, Faculty of Science and Technology, The Burroughs, Hendon, London NW4 4BT, United Kingdom
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6
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Steiner CC, Charter SJ, Goddard N, Davis H, Brandt M, Houck ML, Ryder OA. Chromosomal variation and perinatal mortality in San Diego zoo Soemmerring's gazelles. Zoo Biol 2015; 34:374-84. [DOI: 10.1002/zoo.21223] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/24/2015] [Accepted: 05/04/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Cynthia C. Steiner
- San Diego Zoo Institute for Conservation Research; San Diego Zoo Global; 15600 San Pasqual Valley Road, Escondido California
| | - Suellen J. Charter
- San Diego Zoo Institute for Conservation Research; San Diego Zoo Global; 15600 San Pasqual Valley Road, Escondido California
| | - Natalie Goddard
- San Diego State University; 5500 Campanile Drive, San Diego California
| | - Heidi Davis
- San Diego Zoo Institute for Conservation Research; San Diego Zoo Global; 15600 San Pasqual Valley Road, Escondido California
| | - Margot Brandt
- New York Genome Center; Columbia University; 101 Avenue of the Americas, New York New York
| | - Marlys L. Houck
- San Diego Zoo Institute for Conservation Research; San Diego Zoo Global; 15600 San Pasqual Valley Road, Escondido California
| | - Oliver A. Ryder
- San Diego Zoo Institute for Conservation Research; San Diego Zoo Global; 15600 San Pasqual Valley Road, Escondido California
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7
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Steiner CC, Charter SJ, Houck ML, Ryder OA. Molecular phylogeny and chromosomal evolution of Alcelaphini (Antilopinae). ACTA ACUST UNITED AC 2014; 105:324-33. [PMID: 24516191 DOI: 10.1093/jhered/esu004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Robertsonian (Rb) translocations, in particular centric fusions, are thought to play a primary role in evolution and speciation of the Bovidae family. However, Rb fusions are often polymorphic within species, being suggested as phylogenetically uninformative characters. This work studies chromosome variation in 72 captive individuals of 6 species of Alcelaphini (Antilopinae): The hartebeest (genus Alcelaphus), hirola (Beatragus), black and blue wildebeests (Connochaetes), and the topi and bontebok (Damaliscus). We infer the phylogenic relationships among Alcelaphini species and determine patterns of chromosomal evolution using G-banded karyotypes and complete mitochondrial genome sequences. The molecular phylogeny showed an early divergence of Connochaetes, followed by the split of Alcelaphus plus Beatragus + Damaliscus as sister taxa. Mitochondrial and chromosomal phylogenies only differed in the position of the critically endangered Beatragus, likely due to homoplasic chromosome characters. Patterns of chromosome evolution, reconstructed using a probabilistic approach, suggest that chromosome changes leading to speciation in Alcelaphini do not exclusively involve consecutive reduction of diploid number through centric fusion but also the losses and reversions of Rb translocations in Beatragus and Damaliscus lineages. Our results provide evidence that complex scenarios of chromosomal rearrangements can be detected in relatively recent-diverged bovids, as in this group of antelopes.
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Affiliation(s)
- Cynthia C Steiner
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, 15600 San Pasqual Valley Road, Escondido, CA 92027
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8
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HEKKALA EVON, SHIRLEY MATTHEWH, AMATO GEORGE, AUSTIN JAMESD, CHARTER SUELLEN, THORBJARNARSON JOHN, VLIET KENTA, HOUCK MARLYSL, DESALLE ROB, BLUM MICHAELJ. An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile. Mol Ecol 2011; 20:4199-215. [DOI: 10.1111/j.1365-294x.2011.05245.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Robinson TJ, Ropiquet A. Examination of Hemiplasy, Homoplasy and Phylogenetic Discordance in Chromosomal Evolution of the Bovidae. Syst Biol 2011; 60:439-50. [DOI: 10.1093/sysbio/syr045] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Terence J. Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
| | - Anne Ropiquet
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
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10
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Huang L, Jing M, Nie W, Robinson TJ, Yang F. Chromosome homologies between tsessebe (Damaliscus lunatus) and Chinese muntjac (Muntiacus reevesi) facilitate tracing the evolutionary history of Damaliscus (Bovidae, Antilopinae, Alcelaphini). Cytogenet Genome Res 2010; 132:264-70. [PMID: 21178333 DOI: 10.1159/000322821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2010] [Indexed: 11/19/2022] Open
Abstract
Genome-wide homologies between the tsessebe (Damaliscus lunatus, 2n = 36) and Chinese muntjac (Muntiacus reevesi, 2n = 46) have been established by cross-species painting with Chinese muntjac chromosome paints. Twenty-two autosomal painting probes detected 35 orthologous segments in the tsessebe. Hybridization results confirmed that: (i) D. lunatus carries the (9;14) reciprocal translocation that has been proposed to be a derived chromosomal landmark shared by all species of the Antilopinae; (ii) the karyotype of D. lunatus can be derived almost exclusively from the bovid ancestral karyotype through 12 Robertsonian translocations involving 24 ancestral acrocentric autosomes; (iii) in addition to the Rb fusions, pericentric heterochromatic amplification has shaped the morphology of several of the D. lunatus chromosomes. Integrated analysis of these and published cytogenetic data on pecorans has allowed us to accurately discern the karyotype history of Damaliscus (D. lunatus; D. pygargus, 2n = 38; D. hunteri, 2n = 44). The phylogenomic relationships of 3 species reflected by specific chromosomal rearrangements were consistent with published phylogenies based on morphology, suggesting that chromosomal rearrangements have played an important role in speciation within the Alcelaphini, and that karyotype characters are valuable phylogenetic markers in this group.
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Affiliation(s)
- L Huang
- College of Life Sciences, Ludong University, Yantai, PR China.
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11
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Steiner CC, Houck ML, Ryder OA. Species identification and chromosome variation of captive two-toed sloths. Zoo Biol 2010; 30:623-35. [PMID: 22147591 DOI: 10.1002/zoo.20360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 09/22/2010] [Accepted: 09/30/2010] [Indexed: 11/06/2022]
Abstract
Two-toed sloth species, Linnaeus's and Hoffmman's, are frequent residents of zoo collections in North America. However, species identification has always been problematic because of their large overlap in external morphology, which represents an obstacle to the captive breeding program. We describe here a PCR-based technique that allows species identification of two-toed sloths without requiring sequencing, by using a mitochondrial marker (COI gene) and restriction enzyme assay. We also report intra- and inter-specific patterns of chromosome variation in captive two-toed sloths. Molecularly, we identified 22 samples of Linnaeus's and Hoffmman's two-toed sloths corresponding to 14 and 8 individuals, respectively. One animal was identified as a hybrid using the nuclear gene Enam having alleles derived from both species. The chromosome number in Hoffman's two-toed sloths showed low variation ranging only between 50 and 51. In contrast, Linnaeus's two-toed sloths appeared to vary widely, with diploid numbers ranging from 53 to 67, suggesting distinct geographic groups. The species identification method presented here represents a low-cost easy-to-use tool that will help to improve management of the captive population of two-toed sloths.
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Affiliation(s)
- Cynthia C Steiner
- San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA.
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Nsubuga AM, Holzman J, Chemnick LG, Ryder OA. The cryptic genetic structure of the North American captive gorilla population. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-0015-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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14
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Pitra C, Kock RA, Hofmann RR, Lieckfeldt D. Molecular phylogeny of the critically endangered Hunter's antelope (Beatragus hunteri Sclater 1889). J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.1998.tb00840.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Chaves R, Frönicke L, Guedes-Pinto H, Wienberg J. Multidirectional chromosome painting between the Hirola antelope (Damaliscus hunteri, Alcelaphini, Bovidae), sheep and human. Chromosome Res 2005; 12:495-503. [PMID: 15252245 DOI: 10.1023/b:chro.0000034751.84769.4c] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Chromosome specific painting probes of human, sheep and the Hirola antelope ( Damaliscus hunteri ) derived by flow sorting of chromosomes were used in multi directional chromosome painting experiments to better define the karyological relationship within Bovidae species (specifically, Caprini and Alcelaphini tribes) and humans. Although not all chromosomes of Damaliscus hunteri could be resolved into single peaks by flow-sorting we managed to present a complete homology map for chromosomes between the three species. When comparing the karyotype of Damaliscus hunteri with human all of the main known motives in mammalian chromosome evolution are present (i.e. associations of human homologous chromosomes 3-21, 4-8, 7-16, 14-15, 16-19 and two forms of 12-22) which were also confirmed with the sheep paint probes. Further, we observed those patterns that have been described as common derived traits for artiodactyls (i.e. associations of human homologous chromosomes 5/19 and a complex alternating pattern of hybridizations with human chromosome 14 and 15 probes). As known from classical karyotyping some of the Damaliscus chromosomes are biarmed and were supposedly involved in Robertsonian translocations frequently found in karyotype evolution of bovids. We refined these rearrangements with the molecular probes and also delineated a chromosome painting pattern that should be the result of a paracentric inversion in the Damaliscus hunteri karyotype. This study demonstrates that multidirectional chromosome painting will be a valuable tool for the investigation of the dynamics of chromosome evolution in exotic bovid species.
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Affiliation(s)
- Raquel Chaves
- Department of Genetics and Biotechnology, Centre of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro-CGB/UTAD, P-5000-911 Vila Real, Portugal.
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Dahiye YM, Aman RA. Population size and seasonal distribution of the hirola antelope (Beatragus hunteri,
Sclater 1889) in southern Garissa, Kenya. Afr J Ecol 2002. [DOI: 10.1046/j.1365-2028.2002.00370.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Chaves R, Heslop-Harrsion JS, Guedes-Pinto H. Centromeric heterochromatin in the cattle rob(1;29) translocation: alpha-satellite I sequences, in-situ MspI digestion patterns, chromomycin staining and C-bands. Chromosome Res 2001; 8:621-6. [PMID: 11117358 DOI: 10.1023/a:1009290125305] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The centromeric regions and alpha-satellite I sequence were studied on chromosomes 1, 29 and the rob(1;29) translocation in a Portuguese breed of cattle, Barrosa, carrying the translocation. Rob(1;29) centromeric regions showed heterochromatic bands with propidium iodide but, unlike the acrocentric autosomes, no strong centromeric bands were revealed with chromomycin A3. An alpha-satellite I sequence was not found at the centromeres of the X, Y and rob(1;29) chromosomes in the breed, although it was present at the centromeres of all acrocentric chromosomes including 1 and 29. Restriction enzyme banding with MspI revealed polymorphisms between different rob(1;29) chromosomes in both centromeric and intercalary regions. The data show that the centromeric region of the rob(1;29) chromosome has lost the alpha-satellite I sequences, while retaining other heterochromatin, and suggest that this important and widespread translocation has occurred multiple times.
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Affiliation(s)
- R Chaves
- Department of Genetics and Biotechnology, ICETA-UTAD, University of Trás-os-Montes and Alto Douro,Vila Real, Portugal
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Gallagher DS, Davis SK, De Donato M, Burzlaff JD, Womack JE, Taylor JF, Kumamoto AT. A karyotypic analysis of nilgai, Boselaphus tragocamelus (Artiodactyla: Bovidae). Chromosome Res 1998; 6:505-13. [PMID: 9886771 DOI: 10.1023/a:1009268917856] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A combination of chromosomal banding and fluorescence in situ hybridization (FISH) was used to characterize the karyotype of Boselaphus tragocamelus (nilgai) relative to the domestic cattle standard karyotype. G-, Q- and C-band karyotypes of nilgai are presented, and the chromosomal complement of nilgai is determined to be 2n=46 (female FN=60, male FN=59; NAA=56), consistent with previous reports for the species. Comparisons with cattle identified extensive monobrachial homologies with some noteworthy exceptions. Chromosome 25 is centrically fused to 24, and chromosome 16 is acrocentric. Both appear to have additional pericentromeric material not seen in the equivalent cattle acrocentrics. This pericentromeric chromatin may be the result of de novo additions or translocation of pericentromeric material from chromosome 6, which is shown to be centrically fused to 13 but is only about two-thirds the length of cattle 6. Comparisons with cattle demonstrated that nilgai chromosome 17 has undergone a paracentric inversion and that chromosome 20 has two blocks of interstitial constitutive heterochromatin. The identities of both chromosomes were confirmed by chromosomal FISH. Furthermore, chromosomal banding and FISH were used to determine that autosome 14 has been fused to the ancestral X and Y of nilgai to form compound neo-X and -Y chromosomes. Additional FISH analyses were conducted to confirm other proposed chromosome homologies and to identify nucleolar organizing regions within the nilgai complement.
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Affiliation(s)
- D S Gallagher
- Department of Animal Science, Texas A&M University, College Station 77843, USA.
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