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Kryukov K, Nakahama N, Kuraku S. Genome assembly catalog for species in the Japanese Red List: unlocking endangered biodiversity through genomic inventory. F1000Res 2024; 13:583. [PMID: 39050029 PMCID: PMC11267146 DOI: 10.12688/f1000research.149793.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
Improvements in DNA sequencing technology are allowing the dramatic increase of whole genome data for a wide variety of species. Such genome sequence data can assist the monitoring of intraspecific genetic diversity, but is often lacking for threatened species. In this project, we focused on the national Red List, a catalog of extinct and threatened species, issued by the Japanese government. We combined the data included in it with the record of genome assembly in NCBI and tabulated the assembly availability of the species in the list. The combined data shows a low percentage (2.1%) of the availability of whole genome sequence data for the taxa ranked on the Japanese Red List as well as a strong bias towards mammals and birds in Animalia and vascular plants in Plantae. Our data presentation highlights potential systematic limitations in genome sequencing (e.g., budget for sequencing large genomes of amphibians) and instructs future policies including which taxon needs more effort for genome sequencing. The resultant tables are available in the original website https://treethinkers.nig.ac.jp/redlist/ and are regularly updated.
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Affiliation(s)
- Kirill Kryukov
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, 411-8540, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Naoyuki Nakahama
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, 669-1546, Japan
- Division of Ecological Restoration, Museum of Nature and Human Activities, Hyogo, Sanda, Hyogo, 669-1546, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Department of Genetics, Sokendai Graduate University for Advanced Studies, Mishima, Shizuoka, 411-8540, Japan
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2
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Bezerra AMR, Di Russo E, Castiglia R. Disseminating "hidden" scientific collections: the medium and large-sized terrestrial mammals at the Museo di Anatomia Comparata "Giovanni Battista Grassi", Roma, Italy. Biodivers Data J 2024; 12:e124810. [PMID: 39015796 PMCID: PMC11250177 DOI: 10.3897/bdj.12.e124810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/03/2024] [Indexed: 07/18/2024] Open
Abstract
The dissemination of specimen data in scientific collections is a crucial step in making them available to the scientific community. However, even today, especially in some countries, little or nothing is known about the contents of the naturalistic collections of some museums. This is regrettable, especially in cases where the collections include historic specimens and endangered species. The Museum of Comparative Anatomy "Giovanni Battista Grassi", situated in Rome, Italy, houses historical anatomical and didactic collections, with specimens gathered from 1600s and almost worldwide. The collection holds 444 specimens of medium and large-sized terrestrial mammals, comprising 25 fossils, 40 skins, 186 skulls, 70 skeletons and 123 anatomical pieces, representing 63% of recent mammal orders, mainly from localities of Africa and Europe. A list of this material, indexed by the orders and families, is provided, as well as comments on the conservation status of the species. Remarkable data are summarised, including new data on a hippopotamus specimen from an extinct population and the record of three rhinoceros species from 1600s. Besides comparative anatomical studies, the Museum of Comparative Anatomy of Sapienza University emerges as a source of important material for biodiversity genomics.
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Affiliation(s)
- Alexandra M. R. Bezerra
- Museu Paraense Emilio Goeldi, Belém, BrazilMuseu Paraense Emilio GoeldiBelémBrazil
- Fiocruz/IOC, Rio de janeiro, BrazilFiocruz/IOCRio de janeiroBrazil
- Dipartimento Biologia e Biotecnologie "Charles Darwin", Università di Roma "La Sapienza", Rome, ItalyDipartimento Biologia e Biotecnologie "Charles Darwin", Università di Roma "La Sapienza"RomeItaly
| | - Edoardo Di Russo
- Dipartimento Biologia e Biotecnologie "Charles Darwin", Università di Roma "La Sapienza", Rome, ItalyDipartimento Biologia e Biotecnologie "Charles Darwin", Università di Roma "La Sapienza"RomeItaly
- Istituto Scienze Marine ISMAR, Consiglio Nazionale delle Ricerche CNR, Venice, ItalyIstituto Scienze Marine ISMAR, Consiglio Nazionale delle Ricerche CNRVeniceItaly
| | - Riccardo Castiglia
- Dipartimento Biologia e Biotecnologie "Charles Darwin", Università di Roma "La Sapienza", Rome, ItalyDipartimento Biologia e Biotecnologie "Charles Darwin", Università di Roma "La Sapienza"RomeItaly
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3
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Goossens PL. Bacillus anthracis, "la maladie du charbon", Toxins, and Institut Pasteur. Toxins (Basel) 2024; 16:66. [PMID: 38393144 PMCID: PMC10891547 DOI: 10.3390/toxins16020066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/25/2023] [Accepted: 12/30/2023] [Indexed: 02/25/2024] Open
Abstract
Institut Pasteur and Bacillus anthracis have enjoyed a relationship lasting almost 120 years, starting from its foundation and the pioneering work of Louis Pasteur in the nascent fields of microbiology and vaccination, and blooming after 1986 following the molecular biology/genetic revolution. This contribution will give a historical overview of these two research eras, taking advantage of the archives conserved at Institut Pasteur. The first era mainly focused on the production, characterisation, surveillance and improvement of veterinary anthrax vaccines; the concepts and technologies with which to reach a deep understanding of this research field were not yet available. The second period saw a new era of B. anthracis research at Institut Pasteur, with the anthrax laboratory developing a multi-disciplinary approach, ranging from structural analysis, biochemistry, genetic expression, and regulation to bacterial-host cell interactions, in vivo pathogenicity, and therapy development; this led to the comprehensive unravelling of many facets of this toxi-infection. B. anthracis may exemplify some general points on how science is performed in a given society at a given time and how a scientific research domain evolves. A striking illustration can be seen in the additive layers of regulations that were implemented from the beginning of the 21st century and their impact on B. anthracis research. B. anthracis and anthrax are complex systems that raise many valuable questions regarding basic research. One may hope that B. anthracis research will be re-initiated under favourable circumstances later at Institut Pasteur.
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Tinsman JC, Gruppi C, Bossu CM, Prigge TL, Harrigan RJ, Zaunbrecher V, Koepfli KP, LeBreton M, Njabo K, Wenda C, Xing S, Abernethy K, Ades G, Akeredolu E, Andrew IB, Barrett TA, Bernáthová I, Černá Bolfíková B, Diffo JL, Difouo Fopa G, Ebong LE, Godwill I, Koumba Pambo AF, Labuschagne K, Nwobegahay Mbekem J, Momboua BR, Mousset Moumbolou CL, Ntie S, Rose-Jeffreys E, Simo FT, Sundar K, Swiacká M, Takuo JM, Talla VNK, Tamoufe U, Dingle C, Ruegg K, Bonebrake TC, Smith TB. Genomic analyses reveal poaching hotspots and illegal trade in pangolins from Africa to Asia. Science 2023; 382:1282-1286. [PMID: 38096373 DOI: 10.1126/science.adi5066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
The white-bellied pangolin (Phataginus tricuspis) is the world's most trafficked mammal and is at risk of extinction. Reducing the illegal wildlife trade requires an understanding of its origins. Using a genomic approach for tracing confiscations and analyzing 111 samples collected from known geographic localities in Africa and 643 seized scales from Asia between 2012 and 2018, we found that poaching pressures shifted over time from West to Central Africa. Recently, Cameroon's southern border has emerged as a site of intense poaching. Using data from seizures representing nearly 1 million African pangolins, we identified Nigeria as one important hub for trafficking, where scales are amassed and transshipped to markets in Asia. This origin-to-destination approach offers new opportunities to disrupt the illegal wildlife trade and to guide anti-trafficking measures.
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Affiliation(s)
- Jen C Tinsman
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- National Fish and Wildlife Forensic Laboratory, US Fish and Wildlife Service, Ashland, OR, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
| | - Cristian Gruppi
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christen M Bossu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Tracey-Leigh Prigge
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Virginia Zaunbrecher
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Matthew LeBreton
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Mosaic, Yaoundé, Cameroon
- International Institute for Tropical Agriculture, Yaoundé, Cameroon
| | - Kevin Njabo
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cheng Wenda
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shuang Xing
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Katharine Abernethy
- Institut de Recherche en Ecologie Tropicale, Centre National de la Recherche Scientifique et Technologique, Libreville, Gabon
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Gary Ades
- Fauna Conservation Department, Kadoorie Farm and Botanic Garden, Hong Kong, China
| | | | - Imuzei B Andrew
- Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Taneisha A Barrett
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Iva Bernáthová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | | | - Ghislain Difouo Fopa
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- Department of Biology and Animal Physiology, University of Yaoundé I, Yaoundé, Cameroon
| | - Lionel Esong Ebong
- Department of Ecology and Nature Management, School of Earth Sciences and Environmental Engineering, National Research Tomsk Polytechnic University, Tomsk, Russia
| | - Ichu Godwill
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Starkville, MS, USA
| | | | - Kim Labuschagne
- South African National Biodiversity Institute, Pretoria, South Africa
| | | | - Brice R Momboua
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Carla L Mousset Moumbolou
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
- Pangolin Conservation Network, Libreville, Gabon
| | - Stephan Ntie
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | | | - Franklin T Simo
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- Department of Biology and Animal Physiology, University of Yaoundé I, Yaoundé, Cameroon
| | - Keerthana Sundar
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
| | - Markéta Swiacká
- Department of Spatial Sciences, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jean Michel Takuo
- International Institute for Tropical Agriculture, Yaoundé, Cameroon
- Metabiota Cameroon Ltd, Yaoundé, Cameroon
| | - Valery N K Talla
- Département de Biologie des Organismes, Université Libre de Bruxelles, Brussels, Belgium
- Laboratory of Applied Biology and Ecology, Faculty of Science, University of Dschang, Dschang, Cameroon
| | | | - Caroline Dingle
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Kristen Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Timothy C Bonebrake
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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5
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Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
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Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
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Kersten O, Star B, Krabberød AK, Atmore LM, Tørresen OK, Anker-Nilssen T, Descamps S, Strøm H, Johansson US, Sweet PR, Jakobsen KS, Boessenkool S. Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. SCIENCE ADVANCES 2023; 9:eadh1407. [PMID: 37801495 PMCID: PMC10558128 DOI: 10.1126/sciadv.adh1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.
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Affiliation(s)
- Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders K. Krabberød
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Hallvard Strøm
- Norwegian Polar Institute, Fram Centre, Langnes, Tromsø, Norway
| | | | - Paul R. Sweet
- American Museum of Natural History, New York, NY, USA
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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Madison JD, LaBumbard BC, Woodhams DC. Shotgun metagenomics captures more microbial diversity than targeted 16S rRNA gene sequencing for field specimens and preserved museum specimens. PLoS One 2023; 18:e0291540. [PMID: 37725594 PMCID: PMC10508626 DOI: 10.1371/journal.pone.0291540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023] Open
Abstract
The use of museum specimens for research in microbial evolutionary ecology remains an under-utilized investigative dimension with important potential. Despite this potential, there remain barriers in methodology and analysis to the wide-spread adoption of museum specimens for such studies. Here, we hypothesized that there would be significant differences in taxonomic prediction and related diversity among sample type (museum or fresh) and sequencing strategy (medium-depth shotgun metagenomic or 16S rRNA gene). We found dramatically higher predicted diversity from shotgun metagenomics when compared to 16S rRNA gene sequencing in museum and fresh samples, with this differential being larger in museum specimens. Broadly confirming these hypotheses, the highest diversity found in fresh samples was with shotgun sequencing using the Rep200 reference inclusive of viruses and microeukaryotes, followed by the WoL reference database. In museum-specimens, community diversity metrics also differed significantly between sequencing strategies, with the alpha-diversity ACE differential being significantly greater than the same comparisons made for fresh specimens. Beta diversity results were more variable, with significance dependent on reference databases used. Taken together, these findings demonstrate important differences in diversity results and prompt important considerations for future experiments and downstream analyses aiming to incorporate microbiome datasets from museum specimens.
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Affiliation(s)
- Joseph D. Madison
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Brandon C. LaBumbard
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Douglas C. Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
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8
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Ilechukwu I, Das RR, Reimer JD. Review of microplastics in museum specimens: An under-utilized tool to better understand the Plasticene. MARINE POLLUTION BULLETIN 2023; 191:114922. [PMID: 37068343 DOI: 10.1016/j.marpolbul.2023.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/25/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
This study summarises the status of microplastic research in marine and freshwater specimens in natural museum collections around the world. Abundances, distributions, and types of microplastics in the archived collections are discussed. Museum collections can fill knowledge gaps on evolution of microplastic pollution before and during the Plasticene era. The specimens in these studies, ranging from plankton to vertebrates, were collected and archived between 1900 and 2019, and are dominated by specimens from marine ecosystems. All the specimens included in this review were preserved by freezing or in ethanol/formaldehyde except for specimens in one study that were preserved via cryomilling. Microfibers were the most common microplastics in the reviewed studies. We recommend more microplastic studies over a wider taxonomic range of species and across a longer span of years utilizing archival specimen collections around the world in order to establish reference points and develop temporal trends for microplastic pollution of the environment.
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Affiliation(s)
- Ifenna Ilechukwu
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan; Department of Industrial Chemistry, Madonna University, Elele Campus, Rivers State, Nigeria.
| | - Rocktim Ramen Das
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan; Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
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9
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Snead AA, Alda F. Time-Series Sequences for Evolutionary Inferences. Integr Comp Biol 2022; 62:1771-1783. [PMID: 36104153 DOI: 10.1093/icb/icac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023] Open
Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
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10
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Salnitska M, Solodovnikov A, Orlov I. Sampling and curation of rove beetles (Insecta, Coleoptera, Staphylinidae) for comprehensive and DNA-grade collections to enhance biodiversity exploration in Northern Eurasia. Biodivers Data J 2022; 10:e96080. [PMID: 36761535 PMCID: PMC9836449 DOI: 10.3897/bdj.10.e96080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
Staphylinidae beetles form a major portion of terrestrial biodiversity globally and, in particular, in Northern Eurasia, a large area with a historically better known north temperate, subarctic and arctic biota. However, even here, rove beetles remain amongst the so-called "dark taxa" with a high fraction of taxonomically unknown lineage diversity. The propagation of DNA-based technologies in systematic entomology in recent decades has brought new opportunities for biodiversity exploration, true also for Staphylinidae. Simultaneously, new methods have revealed limitations of specimens sampled and curated by traditional practices, as existing legacy collections, whether institutional or private, unfortunately do not always qualify as a source of DNA-grade material. In addition, both legacy and newly-collected DNA-grade material of Staphylinidae remain highly biased towards Central Europe, a region with a traditionally well-developed scientific infrastructure and long-established culture for the maintenance of entomological collections. To increase the degree of biodiversity knowledge for our target organismal group across the globe, efficient sampling of DNA-grade material and, in particular, the development of comprehensive local collections in under-studied regions is highly desirable. To facilitate that, here we provide a practical guide for collecting and curation of Staphylinidae with a focus on capacity building for DNA-grade collections in Siberia and elsewhere in Northern Eurasia.
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Affiliation(s)
- Maria Salnitska
- The Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, RussiaThe Institute of Environmental and Agricultural Biology (X-BIO), University of TyumenTyumenRussia
| | - Alexey Solodovnikov
- The Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, RussiaThe Institute of Environmental and Agricultural Biology (X-BIO), University of TyumenTyumenRussia,Natural History Museum of Denmark, Copenhagen, DenmarkNatural History Museum of DenmarkCopenhagenDenmark
| | - Igor Orlov
- The Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, RussiaThe Institute of Environmental and Agricultural Biology (X-BIO), University of TyumenTyumenRussia
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Roycroft E, Moritz C, Rowe KC, Moussalli A, Eldridge MDB, Portela Miguez R, Piggott MP, Potter S. Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.931644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.
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Kearns AM, Campana MG, Slikas B, Berry L, Saitoh T, Cibois A, Fleischer RC. Conservation genomics and systematics of a near-extinct island radiation. Mol Ecol 2022; 31:1995-2012. [PMID: 35119154 DOI: 10.1111/mec.16382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/16/2022] [Accepted: 01/24/2022] [Indexed: 11/27/2022]
Abstract
Conservation benefits from incorporating genomics to explore the impacts of population declines, inbreeding, loss of genetic variation and hybridization. Here we use the near-extinct Mariana Islands reedwarbler radiation to showcase how ancient DNA approaches can allow insights into the population dynamics of extinct species and threatened populations for which historical museum specimens or material with low DNA yield (e.g., scats, feathers) are the only sources for DNA. Despite their having paraphyletic mtDNA, nuclear SNPs support the distinctiveness of critically endangered Acrocephalus hiwae and the other three species in the radiation that went extinct between the 1960s and 1990s. Two extinct species, A. yamashinae and A. luscinius, were deeply divergent from each other and from a third less differentiated lineage containing A. hiwae and extinct A. nijoi. Both mtDNA and SNPs suggest that the two isolated populations of A. hiwae from Saipan and Alamagan Islands are sufficiently distinct to warrant subspecies recognition and separate conservation management. We detected no significant differences in genetic diversity or inbreeding between Saipan and Alamagan, nor strong signatures of geographic structuring within either island. However, the implications of possible signatures of inbreeding in both Saipan and Alamagan, and long-term population declines in A. hiwae that predate modern anthropogenic threats require further study with denser population sampling. Our study highlights the value conservation genomics studies of island radiations have as windows onto the possible future for the world's biota as climate change and habitat destruction increasingly fragments their ranges and contributes to rapid declines in population abundances.
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Affiliation(s)
- Anna M Kearns
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Beth Slikas
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA.,Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Lainie Berry
- Department of Lands and Natural Resources, Commonwealth of the Northern Mariana Islands, Saipan, MP, 96950, USA.,Hawaii Department of Land and Natural Resources-Division of Forestry and Wildlife, Honolulu, HI, 96813, USA
| | - Takema Saitoh
- Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba, 270-1145, Japan
| | - Alice Cibois
- Natural History Museum of Geneva, CP, 6434, 1211, Geneva, Switzerland
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
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Contextualizing enigmatic extinctions using genomic DNA from fluid-preserved museum specimens of Desmognathus salamanders. CONSERV GENET 2022. [DOI: 10.1007/s10592-021-01424-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Conservation Genomics of Two Threatened Subspecies of Northern Giraffe: The West African and the Kordofan Giraffe. Genes (Basel) 2022; 13:genes13020221. [PMID: 35205265 PMCID: PMC8872558 DOI: 10.3390/genes13020221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 11/17/2022] Open
Abstract
Three of the four species of giraffe are threatened, particularly the northern giraffe (Giraffa camelopardalis), which collectively have the smallest known wild population estimates. Among the three subspecies of the northern giraffe, the West African giraffe (Giraffa camelopardalis peralta) had declined to 49 individuals by 1996 and only recovered due to conservation efforts undertaken in the past 25 years, while the Kordofan giraffe (Giraffa camelopardalis antiquorum) remains at <2300 individuals distributed in small, isolated populations over a large geographical range in Central Africa. These combined factors could lead to genetically depauperated populations. We analyzed 119 mitochondrial sequences and 26 whole genomes of northern giraffe individuals to investigate their population structure and assess the recent demographic history and current genomic diversity of West African and Kordofan giraffe. Phylogenetic and population structure analyses separate the three subspecies of northern giraffe and suggest genetic differentiation between populations from eastern and western areas of the Kordofan giraffe’s range. Both West African and Kordofan giraffe show a gradual decline in effective population size over the last 10 ka and have moderate genome-wide heterozygosity compared to other giraffe species. Recent inbreeding levels are higher in the West African giraffe and in Kordofan giraffe from Garamba National Park, Democratic Republic of Congo. Although numbers for both West African and some populations of Kordofan giraffe have increased in recent years, the threat of habitat loss, climate change impacts, and illegal hunting persists. Thus, future conservation actions should consider close genetic monitoring of populations to detect and, where practical, counteract negative trends that might develop.
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Yamashita Y, Ogura‐Tsujita Y, Nagata N, Kurosawa T, Yukawa T. Molecular identification of seed‐feeding flies dissected from herbarium specimens clarifies the 100‐year history of parasitism by
Japanagromyza tokunagai
in Japan. Ecol Res 2021. [DOI: 10.1111/1440-1703.12283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yumi Yamashita
- Graduate School of Symbiotic Systems Science and Technology Fukushima University 1 Kanayagawa, Fukushima Fukushima Japan
- Tsukuba Botanical Garden National Museum of Nature and Science Tsukuba, Ibaraki Japan
| | - Yuki Ogura‐Tsujita
- Faculty of Agriculture Saga University, 1 Honjyo Saga Japan
- United Graduate School of Agricultural Sciences Kagoshima University Kagoshima Japan
| | - Nobuaki Nagata
- Department of Anthropology National Museum of Nature and Science Tsukuba, Ibaraki Japan
| | - Takahide Kurosawa
- Faculty of Symbiotic Systems Science Fukushima University Fukushima Fukushima Japan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden National Museum of Nature and Science Tsukuba, Ibaraki Japan
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Pohjoismäki J, Haarto A. Scenopinusjerei, a new species of window fly (Diptera, Scenopinidae) from Finland. Zookeys 2021; 1059:135-156. [PMID: 34611455 PMCID: PMC8448723 DOI: 10.3897/zookeys.1059.70085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/10/2021] [Indexed: 11/22/2022] Open
Abstract
A new species of window fly (Diptera: Scenopinidae), Scenopinusjereisp. nov., with characteristic bicoloured legs and completely black halteres, is described from Finland. To exclude potential previously named species, a survey of the relevant type specimens as well as original descriptions of the Palearctic and Nearctic Scenopinus species has been conducted, including old Scenopinusfenestralis (Linnaeus) synonyms. Scenopinusjereisp. nov. is likely to be an overlooked, boreal forest specialist living in the nests of cavity-nesting birds. An identification key to the European species is provided.
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Affiliation(s)
- Jaakko Pohjoismäki
- University of Eastern Finland, Department of Biology, P.O. Box 111, FI-80101 Joensuu, Finland University of Eastern Finland Joensuu Finland
| | - Antti Haarto
- Zoological Museum, Biodiversity Unit, University of Turku, FI-20014 Turku, Finland University of Turku Turku Finland
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Edwards SV, Robin V, Ferrand N, Moritz C. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 2021; 14:6339579. [PMID: 34347070 PMCID: PMC8743039 DOI: 10.1093/gbe/evab176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Vv Robin
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati, Andhra Pradesh, 517507, India
| | - Nuno Ferrand
- CIBIO/InBIO, Laboratório Associado, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Portugal
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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