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Wu R, Liu L, Zhang L, Bogan AE, Niu G, Jin D, Wu X, Liu X. Taxonomic revision of two species in the genus Ptychorhynchus Simpson, 1900 (Bivalvia: Unionidae: Gonideinae), with description of a new species. INVERTEBR SYST 2024; 38:IS24014. [PMID: 38963889 DOI: 10.1071/is24014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/04/2024] [Indexed: 07/06/2024]
Abstract
Accurate identification and precise classification of freshwater mussel species that are among the most threatened freshwater taxa in the world, play a crucial role in informing conservation and management efforts for these organisms. However, due to the variability in shell morphology, relying solely on shell characteristics for species taxonomy poses significant challenges, thereby impeding effective conservation planning and management. The freshwater mussel genus Ptychorhynchus Simpson, 1900 is one such group in need of study. We integrate molecular phylogeny, shell morphology and soft-body anatomy to examine the classification of Ptychorhynchus denserugata (Haas, 1910) and Ptychorhynchus resupinatus (von Martens, 1902). The COI barcoding data support the clustering of P. denserugata and Nodularia douglasiae within a single clade, and P. denserugata shares the diagnostic feature of the genus Nodularia , i.e. knobs or bumps on the inner mantle surface in the excurrent aperture. Therefore, by integrating molecular data and anatomical characteristics, we confirm that the nominal species P. denserugata syn. nov. is a new synonym for N. douglasiae . The multi-locus (COI + ND1 + 16S rRNA + 18S rRNA + 28S rRNA ) phylogeny and mitochondrial phylogenomics support the transfer of P. resupinatus from Ptychorhynchus to the newly elevated genus Cosmopseudodon stat. rev., as Cosmopseudodon resupinatus stat. rev. that is still considered the designated type species. We also describe a new species based on integrative taxonomy, i.e. Cosmopseudodon wenshanensis sp. nov. The comprehensive understanding of the taxonomy and diversity of the revised Cosmopseudodon species, and shell heteromorphism of N. douglasiae (=P. denserugata syn. nov.), will serve as a crucial foundation for further scientific assessment and conservation strategies pertaining to these taxa. ZooBank: urn:lsid:zoobank.org:pub:E48968B1-DF0F-42AD-8F31-B8C95F23CE57.
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Affiliation(s)
- Ruiwen Wu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, PR China
| | - Lili Liu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, PR China
| | - Liping Zhang
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, PR China
| | - Arthur E Bogan
- North Carolina Museum of Natural Sciences and Department of Applied Ecology, North Carolina State University, Raleigh, NC 27601, USA
| | - Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Dandong Jin
- Datian High School, Linhai, 317004, PR China
| | - Xiaoping Wu
- School of Life Sciences, Nanchang University, Nanchang, 330031, PR China
| | - Xiongjun Liu
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, School of Life Sciences, Jiaying University, Meizhou, 514000, PR China
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2
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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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3
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Johnson NA, Henderson AR, Jones JW, Beaver CE, Ahlstedt SA, Dinkins GR, Eckert NL, Endries MJ, Garner JT, Harris JL, Hartfield PD, Hubbs DW, Lane TW, McGregor MA, Moles KR, Morrison CL, Wagner MD, Williams JD, Smith CH. Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex. J Hered 2024; 115:72-85. [PMID: 38015800 DOI: 10.1093/jhered/esad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/16/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023] Open
Abstract
Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America's Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia-a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species (Erimystax dissimilis) confirmed to serve as a parasitic larval host for P. sintoxia. Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.
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Affiliation(s)
- Nathan A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Andrew R Henderson
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jess W Jones
- U.S. Fish and Wildlife Service, Virginia Tech University, Blacksburg, VA, United States
| | - Caitlin E Beaver
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Steven A Ahlstedt
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Gerald R Dinkins
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Nathan L Eckert
- U.S. Fish and Wildlife Service, Neosho National Fish Hatchery, Neosho, MO, United States
| | - Mark J Endries
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jeffrey T Garner
- Alabama Division of Wildlife and Freshwater Fisheries, Florence, AL, United States
| | - John L Harris
- Arkansas State University Museum of Zoology, Jonesboro, AR, United States
| | - Paul D Hartfield
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - Don W Hubbs
- DJH Environmental Services, Camden, TN, United States
| | - Timothy W Lane
- Virginia Department of Wildlife Resources, Marion, VA, United States
| | - Monte A McGregor
- Kentucky Department of Fish and Wildlife Resources, Frankfort, KY, United States
| | - Kendall R Moles
- Arkansas Game and Fish Commission, Benton, AR, United States
| | - Cheryl L Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Kearneysville, WV, United States
| | - Matthew D Wagner
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - James D Williams
- Florida Museum, University of Florida, Gainesville, FL, United States
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
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4
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Varney R. The Genomics in Emerging Marine Systems Checklist for Clear and Reproducible Genomics in Emerging, Marine Systems. Integr Comp Biol 2023; 63:1010-1016. [PMID: 37381586 DOI: 10.1093/icb/icad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/24/2023] [Accepted: 06/11/2023] [Indexed: 06/30/2023] Open
Abstract
Genome sequencing becomes more accessible and powerful every year, but there is a lack of consensus on what information should be provided in publications that include genomic data. The result is a flood of sequencing data without a framework to evaluate its quality and completeness, hindering reproducibility. In non-model taxa in marine systems, a lack of detail in methods sections often hinders future researchers from adopting improved techniques, leaving them to repeat costly protocols and take up computational (wall) time with programs that are already known to fail. Here, I present a set of guidelines tailored for marine taxa (emerging model organisms) to promote consistency between publications, increase transparency of sequencing projects, and preserve the value of sequence data as sequencing technologies advance. Included is a checklist to (1) guide authors toward including more detailed information in their manuscripts, (2) expand data availability, and (3) assist reviewers to thoroughly vet methods and results of future 'omic publications. This set of guidelines will support the usefulness of 'omic data in future analyses by providing a framework to document and evaluate these data, leading to transparent and reproducible genomics research on emerging marine systems.
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Rodriguez D, Harding SF, Sirsi S, McNichols-O’Rourke K, Morris T, Forstner MRJ, Schwalb AN. Mitochondrial sequence data reveal population structure within Pustulosa pustulosa. PeerJ 2023; 11:e15974. [PMID: 37810794 PMCID: PMC10552767 DOI: 10.7717/peerj.15974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/06/2023] [Indexed: 10/10/2023] Open
Abstract
Unionid mussels are among the most imperiled group of organisms in North America, and Pustulosa pustulosa is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus Pustulosa (formerly Cyclonaias) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing C. aurea, C. houstonensis, C. mortoni, and C. refulgens with C. pustulosa (currently P. pustulosa). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of P. pustulosa using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise ΦST measures based on ND1 data suggested there may be up to five major geographic groups present within P. pustulosa. Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels via the P. pustulosa system.
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Affiliation(s)
- David Rodriguez
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Stephen F. Harding
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Shashwat Sirsi
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Kelly McNichols-O’Rourke
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, ON, Canada
| | - Todd Morris
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, ON, Canada
| | | | - Astrid N. Schwalb
- Department of Biology, Texas State University, San Marcos, TX, United States
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Aldridge DC, Ollard IS, Bespalaya YV, Bolotov IN, Douda K, Geist J, Haag WR, Klunzinger MW, Lopes‐Lima M, Mlambo MC, Riccardi N, Sousa R, Strayer DL, Torres SH, Vaughn CC, Zając T, Zieritz A. Freshwater mussel conservation: A global horizon scan of emerging threats and opportunities. GLOBAL CHANGE BIOLOGY 2023; 29:575-589. [PMID: 36444494 PMCID: PMC10100069 DOI: 10.1111/gcb.16510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/27/2022] [Accepted: 10/15/2022] [Indexed: 06/16/2023]
Abstract
We identified 14 emerging and poorly understood threats and opportunities for addressing the global conservation of freshwater mussels over the next decade. A panel of 17 researchers and stakeholders from six continents submitted a total of 56 topics that were ranked and prioritized using a consensus-building Delphi technique. Our 14 priority topics fell into five broad themes (autecology, population dynamics, global stressors, global diversity, and ecosystem services) and included understanding diets throughout mussel life history; identifying the drivers of population declines; defining metrics for quantifying mussel health; assessing the role of predators, parasites, and disease; informed guidance on the risks and opportunities for captive breeding and translocations; the loss of mussel-fish co-evolutionary relationships; assessing the effects of increasing surface water changes; understanding the effects of sand and aggregate mining; understanding the effects of drug pollution and other emerging contaminants such as nanomaterials; appreciating the threats and opportunities arising from river restoration; conserving understudied hotspots by building local capacity through the principles of decolonization; identifying appropriate taxonomic units for conservation; improved quantification of the ecosystem services provided by mussels; and understanding how many mussels are enough to provide these services. Solutions for addressing the topics ranged from ecological studies to technological advances and socio-political engagement. Prioritization of our topics can help to drive a proactive approach to the conservation of this declining group which provides a multitude of important ecosystem services.
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Affiliation(s)
- David C. Aldridge
- Aquatic Ecology Group, Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Isobel S. Ollard
- Aquatic Ecology Group, Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Yulia V. Bespalaya
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of SciencesArkhangelskRussia
| | - Ivan N. Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of SciencesArkhangelskRussia
- Northern Arctic Federal UniversityArkhangelskRussia
| | - Karel Douda
- Department of Zoology and FisheriesCzech University of Life Sciences PraguePragueCzech Republic
| | - Juergen Geist
- Aquatic Systems Biology UnitTechnical University of MunichFreisingGermany
| | - Wendell R. Haag
- Southern Research Station, Center for Bottomland Hardwoods ResearchU.S. Forest ServiceFrankfortKentuckyUSA
| | - Michael W. Klunzinger
- Australian Rivers InstituteGriffith UniversityNathanQueenslandAustralia
- Department of Aquatic ZoologyWestern Australian MuseumWelshpoolWestern AustralianAustralia
| | - Manuel Lopes‐Lima
- CIBIO/InBIO/BIOPOLIS—Research Center in Biodiversity and Genetic ResourcesUniversity of PortoVairãoPortugal
| | - Musa C. Mlambo
- Department of Freshwater InvertebratesAlbany MuseumMakhandaSouth Africa
- Department of Zoology and EntomologyRhodes UniversityMakhandaSouth Africa
| | | | - Ronaldo Sousa
- CBMA—Centre of Molecular and Environmental Biology, Department of BiologyUniversity of MinhoBragaPortugal
| | - David L. Strayer
- Cary Institute of Ecosystem StudiesMillbrookNew YorkUSA
- Graham Sustainability InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Santiago H. Torres
- Centro de Investigaciones y Transferencia Santa Cruz (CONICET, UNPA, UTN), Unidad Académica San JuliánUniversidad Nacional de la Patagonia AustralSanta CruzArgentina
| | - Caryn C. Vaughn
- Oklahoma Biological Survey and Department of BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Tadeusz Zając
- Institute of Nature ConservationPolish Academy of SciencesKrakówPoland
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Klunzinger MW, Whisson C, Zieritz A, Benson JA, Stewart BA, Kirkendale L. Integrated taxonomy reveals new threatened freshwater mussels (Bivalvia: Hyriidae: Westralunio) from southwestern Australia. Sci Rep 2022; 12:20385. [PMID: 36437370 PMCID: PMC9701689 DOI: 10.1038/s41598-022-24767-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The freshwater mussel Westralunio carteri (Iredale, 1934) has long been considered the sole Westralunio species in Australia, limited to the Southwest and listed as vulnerable on the IUCN Red List and under Australian legislation. Here, we used species delimitation models based on COI mtDNA sequences to confirm existence of three evolutionarily significant units (ESUs) within this taxon and conducted morphometric analyses to investigate whether shell shape differed significantly among these ESUs. "W. carteri" I was found to be significantly larger and more elongated than "W. carteri" II and "W. carteri" II + III combined, but not different from "W. carteri" III alone. We recognise and redescribe "W. carteri" I as Westralunio carteri (Iredale, 1934) from western coastal drainages and describe "W. carteri" II and "W. carteri" III as Westralunio inbisi sp. nov. from southern and lower southwestern drainages. Two subspecies are further delineated: "W. carteri" II is formally described as Westralunio inbisi inbisi subsp. nov. from southern coastal drainages, and "W. carteri" III as Westralunio inbisi meridiemus subsp. nov. from the southwestern corner. Because this study profoundly compresses the range of Westralunio carteri northward and introduces additional southern and southwestern taxa with restricted distributions, new threatened species nominations are necessary.
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Affiliation(s)
- Michael W Klunzinger
- Australian Rivers Institute, Griffith University, Nathan, QLD, 6111, Australia.
- Mollusc Section, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA, 6163, Australia.
| | - Corey Whisson
- Mollusc Section, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA, 6163, Australia
| | - Alexandra Zieritz
- School of Geography, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Justin A Benson
- Centre for Natural Resource Management, UWA School of Agriculture and the Environment, The University of Western Australia, Albany, WA, 6330, Australia
| | - Barbara A Stewart
- Centre for Natural Resource Management, UWA School of Agriculture and the Environment, The University of Western Australia, Albany, WA, 6330, Australia
| | - Lisa Kirkendale
- Mollusc Section, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA, 6163, Australia
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8
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Figurskey AC, Hollingsworth B, Doyle MS, Reiskind MH. Effectiveness of autocidal gravid trapping and chemical control in altering abundance and age structure of Aedes albopictus. PEST MANAGEMENT SCIENCE 2022; 78:2931-2939. [PMID: 35417621 PMCID: PMC9321977 DOI: 10.1002/ps.6917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/01/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Aedes albopictus is a nuisance pest mosquito of public health importance commonly managed with adulticides and larvicides. We investigated whether adding Gravid Aedes Traps (GATs), Autocidal Gravid Ovitraps (AGOs) or In2Care traps would extend the effectiveness of chemical control methods in Wake County, North Carolina, USA, by combining barrier sprays and larval habitat management (LHM) with each trap type at suburban households. We compared these three treatment groups to untreated controls and to backyards treated only with barrier sprays and LHM. Once a week, for ten weeks, we collected adult mosquitoes at each house using lure-baited surveillance traps and dissected a portion of Ae. albopictus females to determine parity. RESULTS Barrier sprays and LHM alone or combined with any supplemental autocidal ovitrap significantly reduced female Ae. albopictus through Week 3 post-treatment. GATs significantly extended chemical control effectiveness for the duration of the study. Compared to the untreated control, the AGO and GAT treatment groups had significant overall female Ae. albopictus reductions of 74% and 80.4%, respectively, with populations aging significantly slower at houses treated with AGOs. CONCLUSION This household-level study, though limited in size, observed significant reductions in nuisance Ae. albopictus when combining AGOs and GATs with chemical controls for an eight-week period. Delayed population aging in AGO-treated yards suggests that traps also could mitigate disease transmission risk. Future studies should test these control methods at the neighborhood level to evaluate large-scale effectiveness as well as assess the effect of autocidal ovitraps without chemical intervention. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
| | | | - Michael S. Doyle
- Division of Public HealthNorth Carolina Department of Health and Human ServicesRaleighNCUSA
| | - Michael H. Reiskind
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
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9
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Speciation with gene flow in a narrow endemic West Virginia cave salamander (Gyrinophilus subterraneus). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01445-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Moulpied M, Smith CH, Robertson CR, Johnson NA, Lopez R, Randklev CR. Biogeography of freshwater mussels (Bivalvia: Unionida) in Texas and implications on conservation biology. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Michael Moulpied
- Texas A&M Natural Resources Institute Texas A&M AgriLife Research Center at Dallas Dallas Texas USA
| | - Chase H. Smith
- Department of Integrative Biology University of Texas at Austin Austin Texas USA
| | - Clinton R. Robertson
- Inland Fisheries – Management and Conservation Branch Texas Parks & Wildlife Department San Marcos Texas USA
| | - Nathan A. Johnson
- U.S. Geological Survey Wetland and Aquatic Research Center Florida USA
| | - Roel Lopez
- Texas A&M Natural Resources Institute Texas A&M AgriLife Research Center at Dallas Dallas Texas USA
| | - Charles R. Randklev
- Texas A&M Natural Resources Institute Texas A&M AgriLife Research Center at Dallas Dallas Texas USA
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11
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Nardi F, Pezzella L, Drago R, Rita AD, Simoncelli M, Marotta G, Gozzetti A, Bocchia M, Kabanova A. Assessing gene function in human B cells: CRISPR/Cas9‐based gene editing and mRNA‐based gene expression in healthy and tumour cells. Eur J Immunol 2022; 52:1362-1365. [DOI: 10.1002/eji.202149784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/07/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Federica Nardi
- Toscana Life Sciences Foundation Siena 53100 Italy
- Department of Medicine Surgery and Neuroscience University of Siena Siena 53100 Italy
| | | | - Roberta Drago
- Toscana Life Sciences Foundation Siena 53100 Italy
- Department of Medicine Surgery and Neuroscience University of Siena Siena 53100 Italy
| | - Anthea Di Rita
- Toscana Life Sciences Foundation Siena 53100 Italy
- Department of Life Sciences University of Siena Siena 53100 Italy
| | | | - Giuseppe Marotta
- Stem Cell Transplant and Cellular Therapy Unit University Hospital of Siena Siena 53100 Italy
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12
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Wardyn JD, Chan ASY, Jeyasekharan AD. A Robust Protocol for CRISPR-Cas9 Gene Editing in Human Suspension Cell Lines. Curr Protoc 2021; 1:e286. [PMID: 34748280 DOI: 10.1002/cpz1.286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The implementation of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 systems in mammalian cells has sparked an exciting new era in targeted gene editing. CRISPR-Cas9 technologies allow gene function to be interrogated by gene deletions, mutations, and truncations, and by epitope tagging and promoter activity modulation. Many robust protocols have been published to date on CRISPR-Cas9 techniques, however, most of these focus on adherent cell lines. Suspension cell lines, typically of hematolymphoid origin, such as Jurkat, Daudi, and TOLEDO, pose unique challenges to the setup of CRISPR experiments. Here, using B cell lymphoma cells as a primary model, we describe a comprehensive protocol for targeted gene manipulations using the CRISPR-Cas9 system in suspension cells. We also highlight necessary optimization steps to make this approach universal to other suspension cell lines. We first describe a detailed protocol for transient expression of the Cas9 nuclease and guide RNAs. We then suggest workflows for obtaining single-cell clones and for screening for successful homozygous knockout (KO) clones in suspension lines. This protocol aims to serve as a comprehensive resource to facilitate gene editing experiments for users starting CRISPR-Cas9 gene editing protocols on suspension cell lines or those looking to optimize their current workflows. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Transient CRISPR Cas9-gRNA delivery for gene knockout by NeonTM electroporation Support Protocol 1: Designing and preparing gene-specific gRNA Support Protocol 2: Preparation of conditioned medium and culture vessels for single-cell FACS Alternate Protocol 1: Transient CRISPR Cas9-gRNA delivery for gene knockout by Nepagene electroporator Basic Protocol 2: FACS and single-cell clone generation Alternate Protocol 2: Manual cell dilution to obtain single-cell clones Basic Protocol 3: Confirming indels status in single-cell clones by PCR on genomic DNA and Sanger sequencing.
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Affiliation(s)
- Joanna D Wardyn
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- MSD Singapore, Quantitative Biosciences, MSD, Singapore
| | - Allison S Y Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore
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13
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Morrison CL, Johnson NA, Jones JW, Eackles MS, Aunins AW, Fitzgerald DB, Hallerman EM, King TL. Genetic and morphological characterization of the freshwater mussel clubshell species complex ( Pleurobema clava and Pleurobema oviforme) to inform conservation planning. Ecol Evol 2021; 11:15325-15350. [PMID: 34765181 PMCID: PMC8571583 DOI: 10.1002/ece3.8219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/14/2021] [Accepted: 08/26/2021] [Indexed: 11/09/2022] Open
Abstract
The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding.
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Affiliation(s)
- Cheryl L. Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research CenterGainesvilleFloridaUSA
| | - Jess W. Jones
- U.S. Fish and Wildlife Service, Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Michael S. Eackles
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Aaron W. Aunins
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Daniel B. Fitzgerald
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Eric M. Hallerman
- Department of Fish and Wildlife ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Tim L. King
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
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14
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Smith CH, Johnson NA, Robertson CR, Doyle RD, Randklev CR. Establishing conservation units to promote recovery of two threatened freshwater mussel species (Bivalvia: Unionida: Potamilus). Ecol Evol 2021; 11:11102-11122. [PMID: 34429906 PMCID: PMC8366875 DOI: 10.1002/ece3.7897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 05/11/2021] [Accepted: 06/28/2021] [Indexed: 11/09/2022] Open
Abstract
Population genomics has significantly increased our ability to make inferences about microevolutionary processes and demographic histories, which have the potential to improve protection and recovery of imperiled species. Freshwater mussels (Bivalvia: Unionida) represent one of the most imperiled groups of organisms globally. Despite systemic decline of mussel abundance and diversity, studies evaluating spatiotemporal changes in distribution, demographic histories, and ecological factors that threaten long-term persistence of imperiled species remain lacking. In this study, we use genotype-by-sequencing (GBS) and mitochondrial sequence data (mtDNA) to define conservation units (CUs) for two highly imperiled freshwater mussel species, Potamilus amphichaenus and Potamilus streckersoni. We then synthesize our molecular findings with details from field collections spanning from 1901 to 2019 to further elucidate distributional trends, contemporary status, and other factors that may be contributing to population declines for our focal species. We collected GBS and mtDNA data for individuals of P. amphichaenus and P. streckersoni from freshwater mussel collections in the Brazos, Neches, Sabine, and Trinity drainages ranging from 2012 to 2019. Molecular analyses resolved disputing number of genetic clusters within P. amphichaenus and P. streckersoni; however, we find defensible support for four CUs, each corresponding to an independent river basin. Evaluations of historical and recent occurrence data illuminated a generally increasing trend of occurrence in each of the four CUs, which were correlated with recent increases in sampling effort. Taken together, these findings suggest that P. amphichaenus and P. streckersoni are likely rare throughout their respective ranges. Because of this, the establishment of CUs will facilitate evidence-based recovery planning and ensure potential captive propagation and translocation efforts are beneficial. Our synthesis represents a case study for conservation genomic assessments in freshwater mussels and provides a model for future studies aimed at recovery planning for these highly imperiled organisms.
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Affiliation(s)
- Chase H. Smith
- Department of Integrative BiologyUniversity of TexasAustinTexasUSA
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at DallasDallasTexasUSA
- Biology DepartmentBaylor UniversityWacoTexasUSA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research CenterGainesvilleFloridaUSA
| | | | | | - Charles R. Randklev
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at DallasDallasTexasUSA
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15
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Gardiner MM, Perry KI, Riley CB, Turo KJ, Delgado de la flor YA, Sivakoff FS. Community science data suggests that urbanization and forest habitat loss threaten aphidophagous native lady beetles. Ecol Evol 2021; 11:2761-2774. [PMID: 33767834 PMCID: PMC7981222 DOI: 10.1002/ece3.7229] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 11/27/2022] Open
Abstract
Community scientists have illustrated rapid declines of several aphidophagous lady beetle (Coccinellidae) species. These declines coincide with the establishment of alien coccinellids. We established the Buckeye Lady Beetle Blitz program to measure the seasonal occupancy of coccinellids within gardens across a wide range of landscape contexts. Following the Habitat Compression Hypothesis, we predicted that gardens within agricultural landscapes would be alien-dominated, whereas captures of natives would be higher within landscapes encompassing a high concentration of natural habitat.Within the state of Ohio, USA, community scientists collected lady beetles for a 7-day period across 4 years in June and August using yellow sticky card traps. All identifications were verified by professional scientists and beetles were classified by three traits: status (alien or native), mean body length, and primary diet. We compared the relative abundance and diversity of coccinellids seasonally and determined if the distribution of beetles by size, status, and diet was related to landscape features.Alien species dominated the aphidophagous fauna. Native aphidophagous coccinellid abundance was positively correlated with forest habitat while alien species were more common when gardens were embedded within agricultural landscapes. Urbanization was negatively associated with both aphidophagous alien and native coccinellids. Synthesis and Applications: Our census of native coccinellid species within residential gardens-a widespread and understudied habitat-was enabled by volunteers. These data will serve as an important baseline to track future changes within coccinellid communities within this region. We found that native coccinellid species richness and native aphidophagous coccinellid abundance in gardens were positively associated with forest habitat at a landscape scale of 2 km. However, our understanding of when and why (overwintering, summer foraging, or both) forest habitats are important remains unclear. Our findings highlight the need to understand how declining aphidophagous native species utilize forest habitats as a conservation priority.
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Affiliation(s)
| | - Kayla I. Perry
- Department of EntomologyThe Ohio State UniversityColumbusOHUSA
| | - Christopher B. Riley
- Department of EntomologyThe Ohio State UniversityColumbusOHUSA
- Bartlett Tree Research LaboratoriesCharlotteNCUSA
| | | | - Yvan A. Delgado de la flor
- Department of EntomologyThe Ohio State UniversityColumbusOHUSA
- California Department of Pesticide RegulationSacramentoCAUSA
| | - Frances S. Sivakoff
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State UniversityMarionOHUSA
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16
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Rogers RL, Grizzard SL, Titus-McQuillan JE, Bockrath K, Patel S, Wares JP, Garner JT, Moore CC. Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa. Mol Ecol 2021; 30:1155-1173. [PMID: 33382161 DOI: 10.1111/mec.15786] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 01/05/2023]
Abstract
Freshwater unionid bivalves currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways and overfishing. These species are notable for their unusual life history strategy, parasite-host co-evolution and biparental mitochondrial inheritance. Among this clade, the washboard mussel Megalonaias nervosa is one species that remains prevalent across the Southeastern United States, with robust population sizes. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe dynamic changes in genome content, with a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Birth-death models suggest rapid expansions among gene families, with a mutation rate of 1.16 × 10-8 duplications per gene per generation. Cytochrome P450 gene families have experienced exceptional recent amplification beyond expectations based on genome-wide birth-death processes. These genes are associated with increased rates of amino acid changes, a signature of selection driving evolution of detox genes. Fitting evolutionary models of adaptation from standing genetic variation, we can compare adaptive potential across species and mutation types. The large population size in M. nervosa suggests a 4.7-fold advantage in the ability to adapt from standing genetic variation compared with a low diversity endemic E. hopetonensis. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv = 0.185 compared with Psgv = 0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of 'hopeful monsters' within the genome that may facilitate adaptation when selective pressures shift. These results suggest that gene family expansion is a key driver of adaptive evolution in this key species of freshwater Unionidae that is currently facing widespread environmental challenges. This work has clear implications for conservation genomics on freshwater bivalves as well as evolutionary theory. This genome represents a first step to facilitate reverse ecological genomics in Unionidae and identify the genetic underpinnings of phenotypic diversity.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
| | - Stephanie L Grizzard
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | | | - Katherine Bockrath
- Department of Genetics, University of Georgia, Athens, GA, USA.,U.S. Fish and Wildlife Service, Midwest Fisheries Center Whitney Genetics Lab, Onalaska, WI, USA
| | - Sagar Patel
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - John P Wares
- Department of Genetics, University of Georgia, Athens, GA, USA.,Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Jeffrey T Garner
- Division of Wildlife and Freshwater Fisheries, Alabama Department of Conservation and Natural Resources, Florence, AL, USA
| | - Cathy C Moore
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
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17
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Paz-Sedano S, Wilson NG, Carmona L, Gosliner TM, Pola M. An ocean yet to be discovered: increasing systematic knowledge of Indo-Pacific Okenia Menke, 1830 (Nudibranchia:Goniodorididae). INVERTEBR SYST 2021. [DOI: 10.1071/is20088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Numerous faunistic and ecological studies have been conducted throughout the Indo-Pacific Ocean to assess its biodiversity. Despite the abundance of research, studies on the species that inhabit the Indo-Pacific are still necessary due to its extent and high species richness. The major species richness of the genus Okenia Menke, 1830 (Nudibranchia, Goniodorididae) is found in the Indo-Pacific Ocean, including 38 of 60 valid species. Nevertheless, this number does not represent the real biodiversity, since at least 20 more species are already reported in field-guides as undescribed species belonging to this genus. The systematics of the genus Okenia are still unclear since it has been the subject of only a few and incomplete studies. In the present paper, we describe five new Okenia species from the coastlines of Japan, Mozambique and Australia: Okenia aurorapapillata sp. nov., Okenia elisae sp. nov., Okenia nakanoae sp. nov., Okenia siderata sp. nov. and Okenia tenuifibrata sp. nov. Moreover, anatomical details not previously described of Okenia atkinsonorum, Okenia barnardi, Okenia cf. echinata, Okenia hallucigenia, Okenia hiroi, Okenia japonica, Okenia pellucida, Okenia pilosa and Okenia rhinorma are provided. New partial sequences of standard markers (COI, 16S rRNA and H3) were obtained and a phylogenetic analysis that included all species with available data was performed.
ZOOBANK urn:lsid:zoobank.org:pub:28AE2536-A264–4194–8AE3-C430620572E7
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18
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Pernat N, Kampen H, Jeschke JM, Werner D. Citizen science versus professional data collection: Comparison of approaches to mosquito monitoring in Germany. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13767] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Nadja Pernat
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Department of Biology, Chemistry, Pharmacy Institute of BiologyFreie Universität Berlin Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - Helge Kampen
- Friedrich‐Loeffler‐Institut Federal Research Institute for Animal Health Greifswald, Insel Riems Germany
| | - Jonathan M. Jeschke
- Department of Biology, Chemistry, Pharmacy Institute of BiologyFreie Universität Berlin Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
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19
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Smith CH, Johnson NA, Havlik K, Doyle RD, Randklev CR. Resolving species boundaries in the critically imperiled freshwater mussel species,
Fusconaia mitchelli
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chase H. Smith
- Biology Department Baylor University Waco TX USA
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
- Department of Integrative Biology University of Texas Austin TX USA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville FL USA
| | | | | | - Charles R. Randklev
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
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20
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Novel Molecular Resources to Facilitate Future Genetics Research on Freshwater Mussels (Bivalvia: Unionidae). DATA 2020. [DOI: 10.3390/data5030065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Molecular data have been an integral tool in the resolution of the evolutionary relationships and systematics of freshwater mussels, despite the limited number of nuclear markers available for Sanger sequencing. To facilitate future studies, we evaluated the phylogenetic informativeness of loci from the recently published anchored hybrid enrichment (AHE) probe set Unioverse and developed novel Sanger primer sets to amplify two protein-coding nuclear loci with high net phylogenetic informativeness scores: fem-1 homolog C (FEM1) and UbiA prenyltransferase domain-containing protein 1 (UbiA). We report the methods used for marker development, along with the primer sequences and optimized PCR and thermal cycling conditions. To demonstrate the utility of these markers, we provide haplotype networks, DNA alignments, and summary statistics regarding the sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA). Additionally, we compare the DNA sequence variation of FEM1 and UbiA to three loci commonly used in freshwater mussel genetic studies: the mitochondrial genes cytochrome c oxidase subunit 1 (CO1) and NADH dehydrogenase subunit 1 (ND1), and the nuclear internal transcribed spacer 1 (ITS1). All five loci distinguish among the three focal species (Potamilus fragilis, Potamilus inflatus, and Potamilus purpuratus), and the sequence variation was highest for ND1, followed by CO1, ITS1, UbiA, and FEM1, respectively. The newly developed Sanger PCR primers and methodologies for extracting additional loci from AHE probe sets have great potential to facilitate molecular investigations targeting supraspecific relationships in freshwater mussels, but may be of limited utility at shallow taxonomic scales.
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21
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Randklev CR, Wolverton S, Johnson NA, Smith CH, DuBose TP, Robertson CR, Conley J. The utility of zooarchaeological data to guide listing efforts for an imperiled mussel species (Bivalvia: Unionidae:
Pleurobema riddellii
). CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Charles R. Randklev
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas Texas USA
| | - Steve Wolverton
- Department of Geography and the Environment & the Advanced Environmental Research InstituteUniversity of North Texas Denton Texas USA
| | - Nathan A. Johnson
- US Geological Survey, Wetland and Aquatic Research Center Gainesville Florida USA
| | - Chase H. Smith
- Department of Integrative BiologyUniversity of Texas Austin Texas USA
| | - Traci P. DuBose
- Oklahoma Biological Survey, Department of Biology, and Ecology and Evolutionary Biology Graduate ProgramUniversity of Oklahoma Norman Oklahoma USA
| | | | - Julian Conley
- Department of GeosciencesEast Tennessee State University Johnson City Tennessee USA
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22
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Smith CH, Pfeiffer JM, Johnson NA. Comparative phylogenomics reveal complex evolution of life history strategies in a clade of bivalves with parasitic larvae (Bivalvia: Unionoida: Ambleminae). Cladistics 2020; 36:505-520. [DOI: 10.1111/cla.12423] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 01/27/2023] Open
Affiliation(s)
| | - John M. Pfeiffer
- National Museum of Natural History Smithsonian Institution Washington DC USA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL32653 USA
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23
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Inoue K, Harris JL, Robertson CR, Johnson NA, Randklev CR. A comprehensive approach uncovers hidden diversity in freshwater mussels (Bivalvia: Unionidae) with the description of a novel species. Cladistics 2020; 36:88-113. [PMID: 34618970 DOI: 10.1111/cla.12386] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2019] [Indexed: 11/30/2022] Open
Abstract
Major geological processes have shaped biogeographical patterns of riverine biota. The Edwards Plateau of central Texas, USA, exhibits unique aquatic communities and endemism, including several species of freshwater mussels. Lampsilis bracteata (Gould, 1855) is endemic to the Edwards Plateau region; however, its phylogenetic relationship with other species in the Gulf coastal rivers and Mississippi River basin is unknown. We evaluated phylogenetic relationships, shell morphologies and soft anatomy characters of L. bracteata and a closely related congener, Lampsilis hydiana (Lea, 1838) throughout their ranges. Our results showed the presence of an undescribed species: Lampsilis bergmanni sp.n. Lampsilis bracteata and L. bergmanni sp.n. share similar shell morphologies and soft anatomy characters; however, they are genetically distinct. Geological processes, such as faulting and sea-level changes during the Miocene to Pliocene, are likely to have facilitated diversification of Lampsilis species, resulting in isolation of L. bracteata on the Edwards Plateau and diversification between L. bergmanni sp.n. and L. hydiana. We conclude that L. bracteata range is restricted to the Colorado River basin, whereas L. bergmanni sp.n. occurs only in upstream reaches of the Guadalupe River basin. Conservation actions are warranted for both species due to their restricted distributions and potential anthropogenic threats.
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Affiliation(s)
- Kentaro Inoue
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA.,Daniel P. Haerther Center for Research and Conservation, John G. Shedd Aquarium, 1200 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - John L Harris
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72467, USA
| | - Clinton R Robertson
- River Studies Program, Texas Parks and Wildlife Department, San Marcos, TX, 78667, USA
| | - Nathan A Johnson
- Wetland and Aquatic Research Center, U.S. Geological Survey, Gainesville, FL, 32653, USA
| | - Charles R Randklev
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA
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24
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Abstract
The use of the "integrative approach" for classification of organisms since its formal establishment in 2005 has become a recurrent theme of zoosystematics. A bibliometric survey of the publications on integrative taxonomy of animals, which is aimed at exploring the most popular areas of research and characterizing the practical systematists' attitudes to this new approach, is presented. An analysis of 582 papers, which appeared between 2005 and 2017 in journals indexed by Scopus and the Web of Science Core Collection, has illustrated the gradual growth of the popularity of integrative taxonomy as well as some biases in the representation of higher taxa in "integrated" studies. It has been shown that the "integrative" papers have more chance of appearing in a top-ranking journal and gain relatively more citations as compared with non-integrative papers. The obtained results are discussed in the context of the "taxonomic impediment" problem thought to be a consequence of the institutional crisis of traditional taxonomy, which has been vividly debated over the past decades.
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Affiliation(s)
- Maxim V Vinarski
- Laboratory of Macroecology and Biogeography of Invertebrates, Saint-Petersburg State University, Saint-Petersburg, Russia
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25
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Smith CH, Johnson NA, Inoue K, Doyle RD, Randklev CR. Integrative taxonomy reveals a new species of freshwater mussel, Potamilus streckersoni sp. nov. (Bivalvia: Unionidae): implications for conservation and management. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1607615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Chase H. Smith
- Biology Department, Baylor University, Waco, TX, 76798, USA
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Nathan A. Johnson
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Kentaro Inoue
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA
| | | | - Charles R. Randklev
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA
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26
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Keogh SM, Simons AM. Molecules and morphology reveal 'new' widespread North American freshwater mussel species (Bivalvia: Unionidae). Mol Phylogenet Evol 2019; 138:182-192. [PMID: 31129350 DOI: 10.1016/j.ympev.2019.05.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/10/2019] [Accepted: 05/22/2019] [Indexed: 10/26/2022]
Abstract
In the Family Unionidae, the greatest radiation of freshwater mussels, malacologists have been misled by extreme intraspecific shell variation and conversely interspecific conchological stasis or convergence. We characterized the genetic and morphological diversity of two phenotypes of Lampsilis teres from specimens (n = 108) collected across its distribution using geometric and traditional morphometrics and multilocus molecular phylogenetics to test the hypothesis that phenotypes represent separate species. Results from our morphometric and molecular phylogenetic analyses unanimously indicate that L. teres sensu lato is made up of two divergent, widespread species with overlapping distributions. We describe a new species and provide a revised description of L. teres sensu stricto. We use morphometrics and machine-learning classification algorithms to test if shell morphology alone can be used to discriminate between these species. Classification percentages of 97.02% and 93.86% demonstrate that shell morphology is highly informative for species identification. This study highlights our lack of understanding of species diversity of freshwater mussels and the importance of multiple characters and quantitative approaches to species delimitation.
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Affiliation(s)
- Sean M Keogh
- Conservation Sciences Graduate Program, University of Minnesota, 135B Skok Hall, 2003 Upper Buford Circle, St Paul, MN 55108, USA; Bell Museum of Natural History, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Andrew M Simons
- Bell Museum of Natural History, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St. Paul, MN 55108, USA; Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, 135B Skok Hall, 2003 Upper Buford Circle, St Paul, MN 55108, USA
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27
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Lopes‐Lima M, Burlakova L, Karatayev A, Gomes‐dos‐Santos A, Zieritz A, Froufe E, Bogan AE. Revisiting the North American freshwater mussel genus
Quadrula
sensu lato (Bivalvia Unionidae): Phylogeny, taxonomy and species delineation. ZOOL SCR 2019. [DOI: 10.1111/zsc.12344] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Manuel Lopes‐Lima
- CIBIO/InBIO ‐ Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | | | | | - André Gomes‐dos‐Santos
- CIIMAR/CIMAR ‐ Interdisciplinary Centre of Marine and Environmental Research University of Porto, Terminal de Cruzeiros do Porto de Leixões Matosinhos Portugal
| | - Alexandra Zieritz
- School of Environmental and Geographical Sciences University of Nottingham Malaysia Campus Semenyih Malaysia
| | - Elsa Froufe
- CIIMAR/CIMAR ‐ Interdisciplinary Centre of Marine and Environmental Research University of Porto, Terminal de Cruzeiros do Porto de Leixões Matosinhos Portugal
| | - Arthur E. Bogan
- Research Laboratory North Carolina Museum of Natural Sciences Raleigh North Carolina
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