51
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Lyra ML, Lourenço ACC, Pinheiro PDP, Pezzuti TL, Baêta D, Barlow A, Hofreiter M, Pombal JP, Haddad CFB, Faivovich J. High-throughput DNA sequencing of museum specimens sheds light on the long-missing species of the Bokermannohyla claresignata group (Anura: Hylidae: Cophomantini). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The two species of the Bokermannohyla claresignata species group (Anura: Hylidae) have not been collected for the last four decades. It is the only species group of the hyline tribe Cophomantini that has not yet been analysed genetically. Its phylogenetic position is thus uncertain, and it has a combination of adult and larval character states that make this group a crucial missing piece that hinders our understanding of Cophomantini phylogenetics and character evolution. We obtained DNA sequences from a museum larval specimen of Bok. claresignata, using specialized extraction methods and high-throughput DNA sequencing, and combined the molecular phylogenetic results with available phenotypic information to provide new insights into the taxonomy and phylogenetic relationships of its species group. Our phylogenetic results place Bok. claresignata as sister to the Boana pulchella group, supporting its inclusion in Boana, together with Bokermannohyla clepsydra. In light of this new finding, we recognize a newly defined Boana claresignata group to accommodate these species, thus resolving both the polyphyly of Bokermannohyla and the paraphyly of Boana. Considering the phylogenetic relationships of the Boana claresignata group, we also discuss the evolution of suctorial tadpoles and mature oocyte/egg pigmentation in Cophomantini.
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Affiliation(s)
- Mariana L Lyra
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, CEP, Brazil
| | - Ana Carolina C Lourenço
- Departamento de Ciências Biológicas, Universidade do Estado de Minas Gerais, Campus Ubá, Avenida Olegário Maciel, Ubá, Minas Gerais, CEP, Brazil
| | - Paulo D P Pinheiro
- Laboratório de Anfíbios, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa, Sala, Cidade Universitária, São Paulo, São Paulo, CEP, Brazil
| | - Tiago L Pezzuti
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antônio Carlos, Pampulha, Belo Horizonte, Minas Gerais, CEP, Brazil
| | - Délio Baêta
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, CEP, Brazil
- Setor de Herpetologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista,, Rio de Janeiro, Rio de Janeiro, CEP, Brazil
| | - Axel Barlow
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Straße, Potsdam, Germany
- School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Straße, Potsdam, Germany
| | - José P Pombal
- Setor de Herpetologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista,, Rio de Janeiro, Rio de Janeiro, CEP, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, CEP, Brazil
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’-CONICET, Ángel Gallardo, Buenos Aires, Argentina
- Departamento de Biodiversidad y Biologia Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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52
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Bell RC, Mulcahy DG, Gotte SW, Maley AJ, Mendoza C, Steffensen G, Barron II JC, Hyman O, Flint W, Wynn A, Mcdiarmid RW, Mcleod DS. The Type Locality Project: collecting genomic-quality, topotypic vouchers and training the next generation of specimen-based researchers. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1769224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Rayna C. Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Daniel G. Mulcahy
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Steve W. Gotte
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - Abigail J. Maley
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
- Division of Integrated Sciences, Wilson College, Chambersburg, PA 17201, USA
| | - Cerrie Mendoza
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
| | - Gregory Steffensen
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Joseph C. Barron II
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24060, USA
| | - Oliver Hyman
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - William Flint
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Addison Wynn
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Roy W. Mcdiarmid
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - David S. Mcleod
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
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53
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Rancilhac L, Bruy T, Scherz MD, Pereira EA, Preick M, Straube N, Lyra ML, Ohler A, Streicher JW, Andreone F, Crottini A, Hutter CR, Randrianantoandro JC, Rakotoarison A, Glaw F, Hofreiter M, Vences M. Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus). J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1748243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Loïs Rancilhac
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Teddy Bruy
- Sektion Herpetologie, Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Paris, France
| | - Mark D. Scherz
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
- Sektion Herpetologie, Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
| | - Elvis Almeida Pereira
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
- Programa de Pós-Graduação em Biologia Animal, Departamento de Biologia Animal, Laboratório de Herpetologia, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - Michaela Preick
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nicolas Straube
- Department of Natural History, University Museum of Bergen, Bergen, Norway
| | - Mariana L. Lyra
- Depto de Zoologia, Instituto de Biologia, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil
| | - Annemarie Ohler
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Paris, France
| | - Jeffrey W. Streicher
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK
| | - Franco Andreone
- Sezione zoologia, Museo Regionale di Scienze Naturali, Torino, Italy
| | - Angelica Crottini
- Cibio, Research Centre in Biodiversity, Genetics and Evolution, InBio, Universidade do Porto, Vairão, Portugal
| | - Carl R. Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Andolalao Rakotoarison
- Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, Antananarivo, Madagascar
| | - Frank Glaw
- Sektion Herpetologie, Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
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54
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Léon-Tapia MÁ, Fernández JA, Rico Y, Cervantes FA, Espinosa de los Monteros A. A new mouse of the Peromyscus maniculatus species complex (Cricetidae) from the highlands of central Mexico. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract
The Peromyscus maniculatus species complex is one of the most widespread group of small mammals in North America. However, the taxonomy and phylogenetic relationships among its constituent taxa remain unclear. As part of a revision of Peromyscus specimens from the highlands of the Trans-Mexican Volcanic Belt in central Mexico, we identified five individuals collected in 1968 that differed externally from other Peromyscus specimens, although morphologically similar to P. labecula and P. melanotis, both latter in the P. maniculatus species complex. Based on cranial measurements and mitochondrial DNA sequences, we aimed to more accurately determine the phylogenetic relationships and the taxonomic status of these individuals. Molecular phylogenetic analyses showed that the specimens formed a monophyletic clade sister to the P. maniculatus species complex. Pairwise genetic distances between those specimens and other species within the P. maniculatus species complex were greater than 7.91%. In addition, morphological analyses clearly distinguished the test specimens from P. melanotis and P. labecula. Based on the results of our molecular and morphological analyses, we conclude that these specimens represent an undescribed species of the P. maniculatus species complex, which we describe herein.
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Affiliation(s)
- M Ángel Léon-Tapia
- Laboratorio de Sistemática Filogenética, Biología Evolutiva, Instituto de Ecología A.C., El Haya, Xalapa, Veracruz, México
| | - Jesús A Fernández
- Departamento de Recursos Naturales, Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Yessica Rico
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología, Pátzcuaro, Michoacán, México
- CONACYT, Avenida Insurgentes Sur 1582, Ciudad de México, México
| | - F A Cervantes
- Colección Nacional de Mamíferos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
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55
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Li JN, Liang D, Wang YY, Guo P, Huang S, Zhang P. A large-scale systematic framework of Chinese snakes based on a unified multilocus marker system. Mol Phylogenet Evol 2020; 148:106807. [PMID: 32268200 DOI: 10.1016/j.ympev.2020.106807] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 01/05/2020] [Accepted: 03/23/2020] [Indexed: 01/04/2023]
Abstract
Snakes are one of the most diverse groups of terrestrial vertebrates, with approximately 3500 extant species. A robust phylogeny and taxonomy of snakes is crucial for us to know, study and protect them. For a large group such as snakes, broad-scale phylogenetic reconstructions largely rely on data integration. Increasing the compatibility of the data from different researches is thus important, which can be facilitated by standardization of the loci used in systematic analyses. In this study, we proposed a unified multilocus marker system for snake systematics by conflating 5 mitochondrial markers, 19 vertebrate-universal nuclear protein coding (NPC) markers and 72 snake-specific noncoding intron markers. This marker system is an addition to the large squamate conserved locus set (SqCL) for studies preferring a medium-scale data set. We applied this marker system to over 440 snake samples and constructed the currently most comprehensive systematic framework of the snakes in China. Robust snake phylogenetic relationships were recovered at both deep and shallow evolutionary depths, demonstrating the usefulness of this multilocus marker system. Discordance was revealed by a parallel comparison between the snake tree based on the multilocus marker system and that based on only the mitochondrial loci, highlighting the necessity of using multiple types of markers to better understand the snake evolutionary histories. The divergence times of different snake groups were estimated with the nuclear data set. Our comprehensive snake tree not only confirms many important nodes inferred in previous studies but also contributes new insights into many snake phylogenetic relationships. Suggestions are made for the current Chinese snake taxonomy.
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Affiliation(s)
- Jiang-Ni Li
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying-Yong Wang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peng Guo
- College of Life Sciences and Food Engineering, Yibin University, Yibin, China
| | - Song Huang
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China.
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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56
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Lim HC, Shakya SB, Harvey MG, Moyle RG, Fleischer RC, Braun MJ, Sheldon FH. Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA. Ecol Evol 2020; 10:3222-3247. [PMID: 32273983 PMCID: PMC7141000 DOI: 10.1002/ece3.5964] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/02/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Indochina and Sundaland are biologically diverse, interconnected regions of Southeast Asia with complex geographic histories. Few studies have examined phylogeography of bird species that span the two regions because of inadequate population sampling. To determine how geographic barriers/events and disparate dispersal potential have influenced the population structure, gene flow, and demographics of species that occupy the entire area, we studied five largely codistributed rainforest bird species: Arachnothera longirostra, Irena puella, Brachypodius atriceps, Niltava grandis, and Stachyris nigriceps. We accomplished relatively thorough sampling and data collection by sequencing ultraconserved elements (UCEs) using DNA extracted from modern and older (historical) specimens. We obtained a genome-wide set of 753-4,501 variable loci and 3,919-18,472 single nucleotide polymorphisms. The formation of major within-species lineages occurred within a similar span of time (0.5-1.5 mya). Major patterns in population genetic structure are largely consistent with the dispersal potential and habitat requirements of the study species. A population break across the Isthmus of Kra was shared only by the two hill/submontane insectivores (N. grandis and S. nigriceps). Across Sundaland, there is little structure in B. atriceps, which is a eurytopic and partially frugivorous species that often utilizes forest edges. Two other eurytopic species, A. longirostra and I. puella, possess highly divergent populations in peripheral Sunda Islands (Java and/or Palawan) and India. These species probably possess intermediate dispersal abilities that allowed them to colonize new areas, and then remained largely isolated subsequently. We also observed an east-west break in Indochina that was shared by B. atriceps and S. nigriceps, species with very different habitat requirements and dispersal potential. By analyzing high-throughput DNA data, our study provides an unprecedented comparative perspective on the process of avian population divergence across Southeast Asia, a process that is determined by geography, species characteristics, and the stochastic nature of dispersal and vicariance events.
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Affiliation(s)
- Haw Chuan Lim
- Department of BiologyGeorge Mason UniversityFairfaxVirginia
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
| | - Subir B. Shakya
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
| | - Michael G. Harvey
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennessee
| | - Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas
| | - Robert C. Fleischer
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
| | - Michael J. Braun
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
| | - Frederick H. Sheldon
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
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57
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Šmíd J, Mazuch T, Nováková L, Modrý D, Malonza PK, Abdirahman Elmi HS, Carranza S, Moravec J. Phylogeny and Systematic Revision of the Gecko Genus Hemidactylus from the Horn of Africa (Squamata: Gekkonidae). HERPETOLOGICAL MONOGRAPHS 2020. [DOI: 10.1655/herpmonographs-d-19-00010.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jiří Šmíd
- Department of Zoology, National Museum, Cirkusová 1740, 19300, Prague, Czech Republic
| | | | - Lucie Nováková
- Department of Zoology, National Museum, Cirkusová 1740, 19300, Prague, Czech Republic
| | - David Modrý
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1/3, Brno 62142, Czech Republic
| | - Patrick K. Malonza
- Section of Herpetology, National Museums of Kenya, P.O. Box 40658-00100, Museum Hill Road, Nairobi, Kenya
| | | | - Salvador Carranza
- Institute of Evolutionary Biology (CSICut i-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37–49, Barcelona, Spain
| | - Jiří Moravec
- Department of Zoology, National Museum, Cirkusová 1740, 19300, Prague, Czech Republic
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58
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Preservation-Induced Morphological Change in Salamanders and Failed DNA Extraction from a Decades-Old Museum Specimen: Implications for Plethodon ainsworthi. J HERPETOL 2020. [DOI: 10.1670/19-012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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59
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McGaughran A. Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time? BMC Genomics 2020; 21:188. [PMID: 32111157 PMCID: PMC7048091 DOI: 10.1186/s12864-020-6594-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/19/2020] [Indexed: 01/04/2023] Open
Abstract
Background Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet-lab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of ~ 1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years. Results I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing. Conclusions Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.
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Affiliation(s)
- Angela McGaughran
- Australian National University, Research School of Biology, Division of Ecology and Evolution, Acton, Canberra, ACT, 2600, Australia. .,CSIRO Land and Water, Integrated Omics Team, Black Mountain Laboratories, Canberra, ACT, 2600, Australia.
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60
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Bakker FT, Antonelli A, Clarke JA, Cook JA, Edwards SV, Ericson PGP, Faurby S, Ferrand N, Gelang M, Gillespie RG, Irestedt M, Lundin K, Larsson E, Matos-Maraví P, Müller J, von Proschwitz T, Roderick GK, Schliep A, Wahlberg N, Wiedenhoeft J, Källersjö M. The Global Museum: natural history collections and the future of evolutionary science and public education. PeerJ 2020; 8:e8225. [PMID: 32025365 PMCID: PMC6993751 DOI: 10.7717/peerj.8225] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/15/2019] [Indexed: 12/27/2022] Open
Abstract
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.
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Affiliation(s)
- Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Julia A Clarke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, United States of America
| | - Joseph A Cook
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America.,Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Nuno Ferrand
- Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Magnus Gelang
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Rosemary G Gillespie
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Kennet Lundin
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Ellen Larsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Pável Matos-Maraví
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Johannes Müller
- Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Ted von Proschwitz
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - George K Roderick
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alexander Schliep
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | | | - John Wiedenhoeft
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | - Mari Källersjö
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Botanical Garden, Göteborg, Sweden
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61
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Vershinina AO, Kapp JD, Baryshnikov GF, Shapiro B. The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections. Mol Ecol Resour 2020; 20:1182-1190. [DOI: 10.1111/1755-0998.13130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Alisa O. Vershinina
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
| | - Joshua D. Kapp
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
| | - Gennady F. Baryshnikov
- Laboratory of Theriology Zoological Institute of the Russian Academy of Sciences St. Petersburg Russia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
- Howard Hughes Medical InstituteUniversity of California Santa Cruz Santa Cruz CA USA
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Esselstyn JA, Achmadi AS, Handika H, Giarla TC, Rowe KC. A new climbing shrew from Sulawesi highlights the tangled taxonomy of an endemic radiation. J Mammal 2019. [DOI: 10.1093/jmammal/gyz077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
We describe a new species of Crocidura (Soricidae) from Sulawesi Island, Indonesia, documenting its novelty with both genetic and morphological characters. The new species is widespread on the island, with vouchered records from nine general localities distributed among five of the island’s areas of endemism. Morphologically, the new species is readily distinguished from all other described Sulawesi Crocidura by its intermediate body size, gray pelage, and long, hairy tail. The new species was mainly captured in pitfalls placed in the ground, but we also obtained evidence that it readily climbs trees and may be scansorial in its locomotor habits. Populations of the new species sampled from across the island are closely related, separated by < 0.02 uncorrected mitochondrial p-distances. The new species is one member of an endemic radiation of shrews on Sulawesi now known to contain six valid species and several undescribed species, all within the genus Crocidura. Resolution of species limits and phylogenetic relationships in this radiation is hindered by habitat loss at type localities, historical designation of new species using very small sample sizes, and a lack of genetic data from type specimens.
Kami mendeskripsikan spesies baru Crocidura (Soricidae) dari Pulau Sulawesi, Indonesia, sekaligus mendokumentasikan keunikan karakter secara genetik maupun morfologi dari spesies tersebut. Spesies baru ini tersebar luas di Pulau Sulawesi, diketahui berdasarkan spesimen yang berasal dari sembilan lokasi umum yang tersebar di lima kawasan endemik di pulau tersebut. Secara morfologi, spesies baru ini dapat dibedakan dari spesies Crocidura lainnya dari Sulawesi berdasarkan ukuran tubuh yang sedang, rambut tubuh berwarna abu-abu, dan ekor yang panjang dan berambut. Spesies baru ini sebagian besar diperoleh dari perangkap sumuran yang ditanam didalam tanah, selain itu kami juga mendapatkan bukti bahwa spesies ini mampu memanjat pohon dan kemungkinan memiliki perilaku sebagai pemanjat. Beberapa populasi spesies yang dikoleksi dari Sulawesi ini mempunyai kekerabatan yang dekat, hanya dipisahkan oleh jarak proporsi DNA mitokondria (tidak terkoreksi) sebesar < 0.02. Spesies baru ini merupakan salah satu anggota dari suatu kelompok radiasi endemik cecurut di Sulawesi yang sampai saat ini diketahui terdiri atas enam spesies yang valid, dan beberapa spesies yang belum dideskripsikan, semuanya termasuk didalam genus Crocidura. Kepastian dalam menetapkan batasan jarak antar spesies dan hubungan kekerabatan genetik dari radiasi kelompok cecurut di Sulawesi terkendala oleh kerusakan habitat pada lokasi spesimen tipe, sejarah penamaan spesies yang hanya berdasarkan sampel yang sedikit, dan keterbatasan data molekuler dari spesimen tipe.
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Affiliation(s)
- Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, USA
| | - Anang S Achmadi
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Km. 46 Jl. Raya Jakarta–Bogor, Cibinong, Indonesia
| | - Heru Handika
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, USA
- Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Melbourne, Victoria, Australia
| | | | - Kevin C Rowe
- Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Melbourne, Victoria, Australia
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63
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Kulkarni S, Wood H, Lloyd M, Hormiga G. Spider-specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae). Mol Ecol Resour 2019; 20:185-203. [PMID: 31599100 DOI: 10.1111/1755-0998.13099] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/11/2019] [Accepted: 09/24/2019] [Indexed: 11/29/2022]
Abstract
Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target-capture methods, using the previously designed arachnid-specific probe set, can target a maximum of about 1,000 loci. Here, we develop a specialized target-capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. We designed the 'spider-specific' probe set using three spider genomes (Loxosceles, Parasteatoda and Stegodyphus) and ensured that the newly designed probe set includes UCEs from the previously designed Arachnida probe set. The new 'spider-specific' probes were used to sequence UCE loci in 51 specimens. The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. The 'spider-specific' probes were also used to gather loci from a total of 84 representative taxa across Araneae. On mapping these 84 taxa to the Arachnida probe set, we captured at most 710 UCE loci, while the spider-specific probe set captured up to 1,547 UCE loci from the same taxon sample. Phylogenetic analyses using maximum likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g. UCE data suggest monophyly of 'symphytognathoids'). Our preferred hypothesis based on topology tests, suggests monophyly of the 'symphytognathoids' (the miniature orb weavers), which in previous studies has only been supported by a combination of morphological and behavioural characters.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Hannah Wood
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Michael Lloyd
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA.,The Jackson Laboratory, Bar Harbor, ME, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
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64
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Tsai WLE, Schedl ME, Maley JM, McCormack JE. More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens. Mol Ecol Resour 2019; 20:1220-1227. [PMID: 31478338 DOI: 10.1111/1755-0998.13077] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/11/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022]
Abstract
Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.
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Affiliation(s)
- Whitney L E Tsai
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - Margaret E Schedl
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - James M Maley
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California.,Biology Department, Occidental College, Los Angeles, California
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65
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Derkarabetian S, Benavides LR, Giribet G. Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault. Mol Ecol Resour 2019; 19:1531-1544. [DOI: 10.1111/1755-0998.13072] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Shahan Derkarabetian
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Ligia R. Benavides
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
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66
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Hamilton CA, St Laurent RA, Dexter K, Kitching IJ, Breinholt JW, Zwick A, Timmermans MJTN, Barber JR, Kawahara AY. Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives. BMC Evol Biol 2019; 19:182. [PMID: 31533606 PMCID: PMC6751749 DOI: 10.1186/s12862-019-1505-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/29/2019] [Indexed: 03/13/2023] Open
Abstract
BACKGROUND Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. RESULTS The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). CONCLUSIONS Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth "arms race". Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
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Affiliation(s)
- C A Hamilton
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
- Department of Entomology, Plant Pathology & Nematology, University of Idaho, Moscow, ID, 83844, USA.
| | - R A St Laurent
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - K Dexter
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - I J Kitching
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - J W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- RAPiD Genomics, 747 SW 2nd Avenue #314, Gainesville, FL, 32601, USA
| | - A Zwick
- Australian National Insect Collection, CSIRO, Clunies Ross St, Acton, ACT, Canberra, 2601, Australia
| | - M J T N Timmermans
- Department of Natural Sciences, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - J R Barber
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - A Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
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67
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Scherz MD, Glaw F, Hutter CR, Bletz MC, Rakotoarison A, Köhler J, Vences M. Species complexes and the importance of Data Deficient classification in Red List assessments: The case of Hylobatrachus frogs. PLoS One 2019; 14:e0219437. [PMID: 31412043 PMCID: PMC6693689 DOI: 10.1371/journal.pone.0219437] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 06/19/2019] [Indexed: 12/22/2022] Open
Abstract
Taxonomy is the cornerstone of extinction risk assessments. Currently, the IUCN Red List treats species complexes either under a single overarching species name—resulting in an unhelpfully broad circumscription and underestimated threat assessment that does not apply to any one species lineage—or omits them altogether—resulting in the omission of species that should be assessed. We argue that taxonomic uncertainty alone, as in species complexes, should be grounds for assessment as Data Deficient (DD). Yet, use of the DD category is currently discouraged, resulting in assessments based on poor data quality and dismissal of the importance of taxonomic confidence in conservation. This policy may be leading to volatile and unwarranted assessments of hundreds of species across the world, and needs to be revised. To illustrate this point, we here present a partial taxonomic revision of torrent frogs from eastern Madagascar in the Mantidactylus subgenus Hylobatrachus. Two named species, Mantidactylus (Hylobatrachus) lugubris and M. (H.) cowanii, and several undescribed candidate species are recognised, but the application of the available names has been somewhat ambiguous. In a recent re-assessment of its conservation status, M. (H.) lugubris was assessed including all complex members except M. (H.) cowanii within its distribution, giving it a status of Least Concern and distribution over most of eastern Madagascar. After describing two of the unnamed lineages as Mantidactylus (Hylobatrachus) atsimo sp. nov. (from southeastern Madagascar) and Mantidactylus (Hylobatrachus) petakorona sp. nov. (from the Marojejy Massif in northeastern Madagascar), we show that Mantidactylus (Hylobatrachus) lugubris is restricted to the central east of Madagascar, highlighting the inaccuracy of its current Red List assessment. We propose to re-assess its status under a more restrictive definition that omits well-defined candidate species, thus representing the actual species to which its assessment refers, to the best of current knowledge. We recommend that for species complexes in general, (1) nominal lineages that can be confidently restricted should be assessed under the strict definition, (2) non-nominal species-level lineages and ambiguous names should be prioritised for taxonomic research, and (3) ambiguous names should be assessed as DD to highlight the deficiency in data on their taxonomic status, which is an impediment to their conservation. This would reduce ambiguity and underestimation of threats involved in assessing species complexes, and place the appropriate emphasis on the importance of taxonomy in anchoring conservation.
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Affiliation(s)
- Mark D. Scherz
- Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
- * E-mail:
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
| | - Carl R. Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
| | - Molly C. Bletz
- Department of Biology, University of Massachusetts Boston, Boston, MA, United States of America
| | | | - Jörn Köhler
- Hessisches Landesmuseum Darmstadt, Darmstadt, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
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68
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Bowman LL, MacGuigan DJ, Gorchels ME, Cahillane MM, Moore MV. Revealing paraphyly and placement of extinct species within Epischura (Copepoda: Calanoida) using molecular data and quantitative morphometrics. Mol Phylogenet Evol 2019; 140:106578. [PMID: 31401068 DOI: 10.1016/j.ympev.2019.106578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/02/2019] [Accepted: 08/07/2019] [Indexed: 10/26/2022]
Abstract
Epischura (Calanoida: Temoridae) is a Holarctic group of copepods serving important ecological roles, but it is difficult to study because of small range sizes of individual species and widespread distribution of the genus. This genus includes Tertiary relicts, some endemic to single, isolated lakes and can play major roles in unique ecosystems like Lakes Baikal and Tahoe. We present the first molecular and morphological analysis of Epischura that reveals their spatio-temporal evolutionary history. Morphological measurements of mandibles and genetics estimated phylogenetic relationships among all species represented in Epischura, including E. massachusettsensis, whose extinction status is of concern. Analyses used three gene regions for six previously unsequenced species to infer highly-resolved and well-supported phylogenies confirming a split between Siberian and North American species. Previously published age estimates and sequence data from broad taxonomic sampling of calanoid copepods estimated divergence times between the two Epischura groups. Divergence time estimates for Epischura were consistent with earlier molecular clock estimates and late-Miocene cooling events. Additionally, we provide the first taxonomically broad estimates of divergence times within Calanoida. The paraphyletic nature of the genus Epischura (and the family Temoridae) is apparent and requires the resurrection of the genus Epischurella (Smirnov, 1936) to describe the Siberian species.
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Affiliation(s)
- Larry L Bowman
- Department of Ecology and Evolutionary Biology, Yale University, Osborn Memorial Laboratories, 165 Prospect St., New Haven, CT 06511, USA.
| | - Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology, Yale University, Osborn Memorial Laboratories, 165 Prospect St., New Haven, CT 06511, USA
| | - Madeline E Gorchels
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481-0832, USA
| | - Madeline M Cahillane
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481-0832, USA
| | - Marianne V Moore
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481-0832, USA
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69
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Abstract
It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.
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70
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Gustafson GT, Alexander A, Sproul JS, Pflug JM, Maddison DR, Short AEZ. Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization. Ecol Evol 2019; 9:6933-6948. [PMID: 31312430 PMCID: PMC6617817 DOI: 10.1002/ece3.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 01/10/2023] Open
Abstract
Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open‐source UCE probe set for beetles of the suborder Adephaga.
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Affiliation(s)
- Grey T Gustafson
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas.,Biodiversity Institute University of Kansas Lawrence Kansas
| | - Alana Alexander
- Biodiversity Institute University of Kansas Lawrence Kansas.,Department of Anatomy, School of Biomedical Sciences University of Otago Dunedin New Zealand
| | - John S Sproul
- Department of Integrative Biology Oregon State University Corvallis Oregon.,Department of Biology University of Rochester Rochester New York
| | - James M Pflug
- Department of Integrative Biology Oregon State University Corvallis Oregon
| | - David R Maddison
- Department of Integrative Biology Oregon State University Corvallis Oregon
| | - Andrew E Z Short
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas.,Biodiversity Institute University of Kansas Lawrence Kansas
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71
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Zaher H, Murphy RW, Arredondo JC, Graboski R, Machado-Filho PR, Mahlow K, Montingelli GG, Quadros AB, Orlov NL, Wilkinson M, Zhang YP, Grazziotin FG. Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes). PLoS One 2019; 14:e0216148. [PMID: 31075128 PMCID: PMC6512042 DOI: 10.1371/journal.pone.0216148] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/15/2019] [Indexed: 11/29/2022] Open
Abstract
Caenophidian snakes include the file snake genus Acrochordus and advanced colubroidean snakes that radiated mainly during the Neogene. Although caenophidian snakes are a well-supported clade, their inferred affinities, based either on molecular or morphological data, remain poorly known or controversial. Here, we provide an expanded molecular phylogenetic analysis of Caenophidia and use three non-parametric measures of support-Shimodaira-Hasegawa-Like test (SHL), Felsentein (FBP) and transfer (TBE) bootstrap measures-to evaluate the robustness of each clade in the molecular tree. That very different alternative support values are common suggests that results based on only one support value should be viewed with caution. Using a scheme to combine support values, we find 20.9% of the 1265 clades comprising the inferred caenophidian tree are unambiguously supported by both SHL and FBP values, while almost 37% are unsupported or ambiguously supported, revealing the substantial extent of phylogenetic problems within Caenophidia. Combined FBP/TBE support values show similar results, while SHL/TBE result in slightly higher combined values. We consider key morphological attributes of colubroidean cranial, vertebral and hemipenial anatomy and provide additional morphological evidence supporting the clades Colubroides, Colubriformes, and Endoglyptodonta. We review and revise the relevant caenophidian fossil record and provide a time-calibrated tree derived from our molecular data to discuss the main cladogenetic events that resulted in present-day patterns of caenophidian diversification. Our results suggest that all extant families of Colubroidea and Elapoidea composing the present-day endoglyptodont fauna originated rapidly within the early Oligocene-between approximately 33 and 28 Mya-following the major terrestrial faunal turnover known as the "Grande Coupure" and associated with the overall climate shift at the Eocene-Oligocene boundary. Our results further suggest that the caenophidian radiation originated within the Caenozoic, with the divergence between Colubroides and Acrochordidae occurring in the early Eocene, at ~ 56 Mya.
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Affiliation(s)
- Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, São Paulo, São Paulo,
Brazil
- CR2P –Centre de Recherche en Paléontologie – Muséum national d’Histoire
naturelle – Sorbonne Université, Paris, France
| | - Robert W. Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, Ontario,
Canada
- State Key Laboratory of Genetic Resources and Evolution, Kunming
Institute of Zoology, Kunming, China
| | | | - Roberta Graboski
- Museu de Zoologia, Universidade de São Paulo, São Paulo, São Paulo,
Brazil
- Laboratório de Herpetologia, Museu Paraense Emílio Goeldi, Belém, Pará,
Brazil
| | | | - Kristin Mahlow
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity
Science, Berlin, Germany
| | | | - Ana Bottallo Quadros
- Museu de Zoologia, Universidade de São Paulo, São Paulo, São Paulo,
Brazil
- CR2P –Centre de Recherche en Paléontologie – Muséum national d’Histoire
naturelle – Sorbonne Université, Paris, France
| | - Nikolai L. Orlov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg,
Russia
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London, United
Kingdom
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming
Institute of Zoology, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan
University, Kunming, China
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo, São
Paulo, Brazil
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72
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Matos-Maraví P, Duarte Ritter C, Barnes CJ, Nielsen M, Olsson U, Wahlberg N, Marquina D, Sääksjärvi I, Antonelli A. Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies. PeerJ 2019; 7:e6727. [PMID: 31106048 PMCID: PMC6499058 DOI: 10.7717/peerj.6727] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.
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Affiliation(s)
- Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Camila Duarte Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | | | - Martin Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Urban Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanical Garden, Kew, Richmond, Surrey, UK
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73
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Smith CT, Von Bargen J, DeHaan PW, Scheerer P, Meeuwig MH. Genetic structure and the history of chub in the Alvord Basin. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01148-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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74
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Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
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75
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Sun Z, Liu Y, Wilson JJ, Chen Z, Song F, Cai W, Li H. Mitochondrial genome of Phalantus geniculatus (Hemiptera: Reduviidae): trnT duplication and phylogenetic implications. Int J Biol Macromol 2019; 129:110-115. [PMID: 30711565 DOI: 10.1016/j.ijbiomac.2019.01.205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 01/05/2023]
Abstract
Reduviidae is the second largest family of Heteroptera and most of them are important natural enemies of agricultural and forest pests. Most of the sequenced mitochondrial (mt) genomes in this family have the typical gene arrangement of insects and encode 37 coding genes (13 protein-coding genes, 22 tRNA genes and two rRNA genes). In the present study, we sequenced the mt genome of Phalantus geniculatus from the subfamily Peiratinae through high-throughput sequencing and encountered the duplication of tRNA genes for the first time in this subfamily. We identified 23 tRNA genes, including 22 tRNAs commonly found in insect mt genomes and an extra trnT (trnT2), which has high sequence similarity (96.9%) to trnT1. The presence of a "pseudo-trnP" in the non-coding region between trnT1 and trnT2 supports the hypothesis that the presence of an extra trnT can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic results inferred from mt genome sequences supported a sister relationship between Phymatinae and the remaining sampled subfamilies, as well as a paraphyletic Reduviinae. The present study highlights the utility of mt genomes in the phylogenetic study of Reduviidae based on the large scale taxon sampling in the future.
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Affiliation(s)
- Ziqiang Sun
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yingqi Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - John-James Wilson
- Vertebrate Zoology at World Museum, National Museums Liverpool, Liverpool L3 8EN, United Kingdom; Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Zhuo Chen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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76
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Deepak V, Ruane S, Gower DJ. A new subfamily of fossorial colubroid snakes from the Western Ghats of peninsular India. J NAT HIST 2019. [DOI: 10.1080/00222933.2018.1557756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- V. Deepak
- Department of Life Sciences, The Natural History Museum, London, UK
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Sara Ruane
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ, USA
| | - David J. Gower
- Department of Life Sciences, The Natural History Museum, London, UK
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77
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Schmitt CJ, Cook JA, Zamudio KR, Edwards SV. Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170387. [PMID: 30455205 PMCID: PMC6282080 DOI: 10.1098/rstb.2017.0387] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 11/12/2022] Open
Abstract
Natural history museums and the specimen collections they curate are vital scientific infrastructure, a fact as true today as it was when biologists began collecting and preserving specimens over 200 years ago. The importance of museum specimens in studies of taxonomy, systematics, ecology and evolutionary biology is evidenced by a rich and abundant literature, yet creative and novel uses of specimens are constantly broadening the impact of natural history collections on biodiversity science and global sustainability. Excellent examples of the critical importance of specimens come from their use in documenting the consequences of environmental change, which is particularly relevant considering the alarming rate at which we now modify our planet in the Anthropocene. In this review, we highlight the important role of bird, mammal and amphibian specimens in documenting the Anthropocene and provide examples that underscore the need for continued collection of museum specimens.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- C Jonathan Schmitt
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joseph A Cook
- Museum of Southwestern Biology & Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
| | - Kelly R Zamudio
- Museum of Vertebrates and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Scott V Edwards
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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78
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Bossert S, Murray EA, Almeida EAB, Brady SG, Blaimer BB, Danforth BN. Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae. Mol Phylogenet Evol 2018; 130:121-131. [PMID: 30326287 DOI: 10.1016/j.ympev.2018.10.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023]
Abstract
Two increasingly popular approaches to reconstruct the Tree of Life involve whole transcriptome sequencing and the target capture of ultraconserved elements (UCEs). Both methods can be used to generate large, multigene datasets for analysis of phylogenetic relationships in non-model organisms. While targeted exon sequencing across divergent lineages is now a standard method, it is still not clear if UCE data can be readily combined with published transcriptomes. In this study, we evaluate the combination of UCEs and transcriptomes in a single analysis using genome-, transcriptome-, and UCE data for 79 bees in the largest and most biologically diverse bee family, Apidae. Using existing tools, we first developed a workflow to assemble phylogenomic data from different sources and produced two large nucleotide matrices of combined data. We then reconstructed the phylogeny of the Apidae using concatenation- and coalescent-based methods, and critically evaluated the resulting phylogenies in the context of previously published genetic, genomic, and morphological data sets. Our estimated phylogenetic trees are robustly supported and largely congruent with previous molecular hypotheses, from deep nodes to shallow species-level phylogenies. Moreover, the combined approach allows us to resolve controversial nodes of the apid Tree of Life, by clarifying the relationships among the genera of orchid bees (Euglossini) and the monophyly of the Centridini. Additionally, we present novel phylogenetic evidence supporting the monophyly of the diverse clade of cleptoparasitic Apidae and the placement of two enigmatic, oil-collecting genera (Ctenoplectra and Tetrapedia). Lastly, we propose a revised classification of the family Apidae that reflects our improved understanding of apid higher-level relationships.
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Affiliation(s)
- Silas Bossert
- Department of Entomology, Cornell University, Ithaca, NY, USA.
| | | | - Eduardo A B Almeida
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bonnie B Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA
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79
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Wood HM, González VL, Lloyd M, Coddington J, Scharff N. Next-generation museum genomics: Phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea). Mol Phylogenet Evol 2018; 127:907-918. [DOI: 10.1016/j.ympev.2018.06.038] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/14/2018] [Accepted: 06/22/2018] [Indexed: 10/28/2022]
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80
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Boas of the World (Superfamily Booidae): A Checklist With Systematic, Taxonomic, and Conservation Assessments. ACTA ACUST UNITED AC 2018. [DOI: 10.3099/mcz48.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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81
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McCartney-Melstad E, Gidiş M, Shaffer HB. Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog. Heredity (Edinb) 2018; 121:112-125. [PMID: 29941996 PMCID: PMC6039490 DOI: 10.1038/s41437-018-0097-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/17/2018] [Accepted: 05/13/2018] [Indexed: 12/25/2022] Open
Abstract
Genomic data have the potential to inform high resolution landscape genetic and biological conservation studies that go far beyond recent mitochondrial and microsatellite analyses. We characterize the relationships of populations of the foothill yellow-legged frog, Rana boylii, a declining, "sentinel" species for stream ecosystems throughout its range in California and Oregon. We generated RADseq data and applied phylogenetic methods, hierarchical Bayesian clustering, PCA and population differentiation with admixture analyses to characterize spatial genetic structure across the species range. To facilitate direct comparison with previous analyses, we included many localities and individuals from our earlier work based on mitochondrial DNA. The results are striking, and emphasize the power of our landscape genomic approach. We recovered five extremely differentiated primary clades that indicate that R. boylii may be the most genetically differentiated anuran yet studied. Our results provide better resolution and more spatially consistent patterns than our earlier work, confirming the increased resolving power of genomic data compared to single-locus studies. Genomic structure is not equal across the species distribution. Approximately half the range of R. boylii consists of a single, relatively uniform population, while Sierra Nevada and coastal California clades are deeply, hierarchically substructured with biogeographic breaks observed in other codistributed taxa. Our results indicate that clades should serve as management units for R. boylii rather than previously suggested watershed boundaries, and that the near-extinct population from southwestern California is particularly diverged, exhibits the lowest genetic diversity, and is a critical conservation target for species recovery.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA.
| | - Müge Gidiş
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Kütahya School of Health, Dumlupınar University, Kütahya, Turkey
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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82
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Förster DW, Bull JK, Lenz D, Autenrieth M, Paijmans JLA, Kraus RHS, Nowak C, Bayerl H, Kuehn R, Saveljev AP, Sindičić M, Hofreiter M, Schmidt K, Fickel J. Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species. Mol Ecol Resour 2018; 18:1356-1373. [PMID: 29978939 DOI: 10.1111/1755-0998.12924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/28/2018] [Accepted: 06/05/2018] [Indexed: 11/29/2022]
Abstract
Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.
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Affiliation(s)
- Daniel W Förster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - James K Bull
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marijke Autenrieth
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Helmut Bayerl
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany
| | - Ralph Kuehn
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany.,Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, New Mexico
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | - Magda Sindičić
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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83
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Hedin M, Derkarabetian S, Blair J, Paquin P. Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). Zookeys 2018:49-76. [PMID: 29988790 PMCID: PMC6030207 DOI: 10.3897/zookeys.769.25814] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/27/2018] [Indexed: 01/21/2023] Open
Abstract
Morphological, mitochondrial, and nuclear phylogenomic data were combined to address phylogenetic and species delimitation questions in cave-limited Cicurina spiders from central Texas. Special effort was focused on specimens and cave locations in the San Antonio region (Bexar County), home to four eyeless species listed as US Federally Endangered. Sequence capture experiments resulted in the recovery of ~200–400 homologous ultra-conserved element (UCE) nuclear loci across taxa, and nearly complete COI mitochondrial DNA sequences from the same set of individuals. Some of these nuclear and mitochondrial sequences were recovered from “standard” museum specimens without special preservation of DNA material, including museum specimens preserved in the 1990s. Multiple phylogenetic analyses of the UCE data agree in the recovery of two major lineages of eyeless Cicurina in Texas. These lineages also differ in mitochondrial clade membership, female genitalic morphology, degree of troglomorphy (as measured by relative leg length), and are mostly allopatric across much of Texas. Rare sympatry was confirmed in Bexar County, where members of the two major clades sometimes co-exist in the same karst feature. Both nuclear phylogenomic and mitochondrial data indicate the existence of undescribed species from the San Antonio region, although further sampling and collection of adult specimens is needed to explicitly test these hypotheses. Our data support the two following species synonymies (Cicurinavenii Gertsch, 1992 = Cicurinamadla Gertsch, 1992; Cicurinaloftini Cokendolpher, 2004 = Cicurinavespera Gertsch, 1992), formally proposed here. Overall, our taxonomy-focused research has many important conservation implications, and again highlights the fundamental importance of robust taxonomy in conservation research.
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Affiliation(s)
- Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego CA, 92182, USA
| | - Shahan Derkarabetian
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego CA, 92182, USA.,Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge MA, 02138, USA
| | - Jennifer Blair
- Blair Wildlife Consulting, 3815 Dacy Lane, Kyle TX, 78640, USA
| | - Pierre Paquin
- Scienceinfuse Inc, 12 Saxby Sud, Shefford, QC, J2M 1S2, Canada
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84
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Dupuis JR, Bremer FT, Kauwe A, San Jose M, Leblanc L, Rubinoff D, Geib SM. HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing. Mol Ecol Resour 2018. [PMID: 29633537 DOI: 10.1101/213454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.
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Affiliation(s)
- Julian R Dupuis
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Forest T Bremer
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Angela Kauwe
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
| | - Michael San Jose
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho
| | - Daniel Rubinoff
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
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85
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Dupuis JR, Bremer FT, Kauwe A, San Jose M, Leblanc L, Rubinoff D, Geib SM. HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing. Mol Ecol Resour 2018; 18:1000-1019. [PMID: 29633537 DOI: 10.1111/1755-0998.12783] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 01/22/2023]
Abstract
High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.
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Affiliation(s)
- Julian R Dupuis
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Forest T Bremer
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Angela Kauwe
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
| | - Michael San Jose
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho
| | - Daniel Rubinoff
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
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86
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McGuire JA, Cotoras DD, O'Connell B, Lawalata SZS, Wang-Claypool CY, Stubbs A, Huang X, Wogan GOU, Hykin SM, Reilly SB, Bi K, Riyanto A, Arida E, Smith LL, Milne H, Streicher JW, Iskandar DT. Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards. PeerJ 2018; 6:e4470. [PMID: 29576952 PMCID: PMC5865465 DOI: 10.7717/peerj.4470] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/16/2018] [Indexed: 11/20/2022] Open
Abstract
We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (721 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.
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Affiliation(s)
- Jimmy A McGuire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Darko D Cotoras
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States of America.,Entomology Department, California Academy of Sciences, San Francisco, CA, United States of America.,Current affiliation: Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
| | - Brendan O'Connell
- Department of Biomolecular Engineering and Bioinformatics, Baskin School of Engineering, University of California, Santa Cruz, CA, United States of America.,Current affiliation: Department of Medical & Molecular Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States of America
| | - Shobi Z S Lawalata
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America.,Jalan Hayam Wuruk, United in Diversity Foundation, Jakarta, Indonesia
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Alexander Stubbs
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Guinevere O U Wogan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, United States of America
| | - Sarah M Hykin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Sean B Reilly
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Ke Bi
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, United States of America
| | - Awal Riyanto
- Museum Zoologicum Bogoriense, Research Center for Biology-The Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Evy Arida
- Museum Zoologicum Bogoriense, Research Center for Biology-The Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Lydia L Smith
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Heather Milne
- Department of Biomolecular Engineering and Bioinformatics, Baskin School of Engineering, University of California, Santa Cruz, CA, United States of America
| | - Jeffrey W Streicher
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institute of Technology Bandung, Bandung, West Java, Indonesia
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87
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Bossert S, Danforth BN. On the universality of target‐enrichment baits for phylogenomic research. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.12988] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Silas Bossert
- Department of Entomology Cornell University Ithaca NY USA
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88
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Centuries-Old DNA from an Extinct Population of Aesculapian Snake (Zamenis longissimus) Offers New Phylogeographic Insight. DIVERSITY 2018. [DOI: 10.3390/d10010014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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89
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Ceríaco LMP, Bauer AM. An integrative approach to the nomenclature and taxonomic status of the genus Blanus Wagler, 1830 (Squamata: Blanidae) from the Iberian Peninsula. J NAT HIST 2018. [DOI: 10.1080/00222933.2017.1422283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Luis M. P. Ceríaco
- Department of Biology, Villanova University, Villanova, PA USA
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Lisboa, Portugal
| | - Aaron M. Bauer
- Department of Biology, Villanova University, Villanova, PA USA
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90
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Hedin M, Derkarabetian S, Ramírez MJ, Vink C, Bond JE. Phylogenomic reclassification of the world's most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution. Sci Rep 2018; 8:1636. [PMID: 29374214 PMCID: PMC5785998 DOI: 10.1038/s41598-018-19946-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/10/2018] [Indexed: 12/27/2022] Open
Abstract
Here we show that the most venomous spiders in the world are phylogenetically misplaced. Australian atracine spiders (family Hexathelidae), including the notorious Sydney funnel-web spider Atrax robustus, produce venom peptides that can kill people. Intriguingly, eastern Australian mouse spiders (family Actinopodidae) are also medically dangerous, possessing venom peptides strikingly similar to Atrax hexatoxins. Based on the standing morphology-based classification, mouse spiders are hypothesized distant relatives of atracines, having diverged over 200 million years ago. Using sequence-capture phylogenomics, we instead show convincingly that hexathelids are non-monophyletic, and that atracines are sister to actinopodids. Three new mygalomorph lineages are elevated to the family level, and a revised circumscription of Hexathelidae is presented. Re-writing this phylogenetic story has major implications for how we study venom evolution in these spiders, and potentially genuine consequences for antivenom development and bite treatment research. More generally, our research provides a textbook example of the applied importance of modern phylogenomic research.
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Affiliation(s)
- Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA, 92182-4614, USA.
| | - Shahan Derkarabetian
- Department of Biology, San Diego State University, San Diego, CA, 92182-4614, USA
- Department of Biology, University of California Riverside, Riverside, California, 92521, USA
| | - Martín J Ramírez
- Division of Arachnology Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Cor Vink
- Canterbury Museum Christchurch, Christchurch, 8013, New Zealand
| | - Jason E Bond
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
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91
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Cornetti L, Girardi M, Ghielmi S, Vernesi C. Museum specimens indicate genetic erosion in an endangered lizard. AMPHIBIA-REPTILIA 2018. [DOI: 10.1163/15685381-17000198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Abstract
Genetic variability, one of the main factors that guarantees species persistence, and species’ conservation status are generally evaluated with indices calculated at the present time. Natural history collections might help compare historical and current genetic diversity so to identify major trends. Here we analysed museum specimens of the lizard Zootoca vivipara carniolica, with a specific and stringent protocol for degraded DNA, in order to contrast its past and current genetic variability, using fragments of one mitochondrial DNA gene. Part of the distributional range of Z. v. carniolica (Po Plain, Italy), heavily impacted by human activities, was investigated. We found two previously unknown haplotypes in populations that are extinct today, suggesting the loss of these haplotypes and thus an overall shrinking of genetic variability. We argue that these results, together with the increasing threats posed by climate and land use changes, suggest that specific conservation measures for the persistence of Z. v. carniolica in Northern Italian lowlands have to be considered.
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Affiliation(s)
- Luca Cornetti
- 1Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige (TN)
- 2Zoological Institute, University of Basel, Vesalgasse 1, Basel CH-4051, Switzerland
| | - Matteo Girardi
- 1Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige (TN)
| | - Samuele Ghielmi
- 3Tropical Biodiversity Section, MUSE-Science Museum of Trento, Corso del Lavoro e della Scienza 3, 38122, Trento, Italy
| | - Cristiano Vernesi
- 1Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige (TN)
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92
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Quattrini AM, Faircloth BC, Dueñas LF, Bridge TCL, Brugler MR, Calixto‐Botía IF, DeLeo DM, Forêt S, Herrera S, Lee SMY, Miller DJ, Prada C, Rádis‐Baptista G, Ramírez‐Portilla C, Sánchez JA, Rodríguez E, McFadden CS. Universal target‐enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long‐standing problems. Mol Ecol Resour 2017; 18:281-295. [DOI: 10.1111/1755-0998.12736] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/28/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA USA
| | - Luisa F. Dueñas
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
| | - Tom C. L. Bridge
- Queensland Museum Network Townsville QLD Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD Australia
| | - Mercer R. Brugler
- Division of Invertebrate Zoology American Museum of Natural History New York NY USA
- Biological Sciences Department NYC College of Technology City University of New York Brooklyn NY USA
| | - Iván F. Calixto‐Botía
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
- Department of Animal Ecology and Systematics Justus Liebig Universität Giessen Germany
| | - Danielle M. DeLeo
- Department of Biological Sciences Florida International University North Miami FL USA
- Biology Department Temple University Philadelphia PA USA
| | - Sylvain Forêt
- Research School of Biology Australian National University Canberra ACT Australia
| | - Santiago Herrera
- Department of Biological Sciences Lehigh University Bethlehem PA USA
| | - Simon M. Y. Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences University of Macau Macao China
| | - David J. Miller
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD Australia
| | - Carlos Prada
- Department of Biological Sciences University of Rhode Island Kingston RI USA
| | | | - Catalina Ramírez‐Portilla
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
- Department of Animal Ecology and Systematics Justus Liebig Universität Giessen Germany
| | - Juan A. Sánchez
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology American Museum of Natural History New York NY USA
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93
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Peacock MM, Hekkala ER, Kirchoff VS, Heki LG. Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171253. [PMID: 29291110 PMCID: PMC5717685 DOI: 10.1098/rsos.171253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/13/2017] [Indexed: 05/05/2023]
Abstract
Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.
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Affiliation(s)
- Mary M. Peacock
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Ecology, Evolution, and Conservation Biology Interdisciplinary Program, University of Nevada, Reno, NV 89557, USA
| | - Evon R. Hekkala
- Department of Biological Sciences, Fordham University, New York, NY 10458, USA
| | - Veronica S. Kirchoff
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- United States Department of Agriculture, Agricultural Research Service, Reno, NV 89512, USA
| | - Lisa G. Heki
- United States Fish and Wildlife Service, Lahontan National Fish Hatchery Complex, 1340 Financial Blvd, Suite 234, Reno, NV 89502, USA
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94
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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