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Meng H, Wang Y, Qiao GX, Chen J. Mitochondrial genome data provide insights into the phylogenetic relationships within Triplophysadalaica (Kessler, 1876) (Cypriniformes, Nemacheilidae). Zookeys 2024; 1197:43-55. [PMID: 38616923 PMCID: PMC11015090 DOI: 10.3897/zookeys.1197.116342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/14/2024] [Indexed: 04/16/2024] Open
Abstract
Due to the detrimental effect of formaldehyde on DNA, ethanol has replaced formalin as the primary preservative for animal specimens. However, short-term formalin fixation of specimens might be applied during field collection. In an increasing number of studies, DNA extraction and sequencing have been successfully conducted from formalin-fixed specimens. Here the DNA from five specimens of Triplophysadalaica (Kessler, 1876) were extracted and performed high-throughput sequencing. Four of the specimens underwent short-term fixation with formalin and were subsequently transferred to ethanol. One was continuously stored in ethanol. No significant difference of DNA quality and amount were observed among these samples. Followed by assembly and annotation, five mitochondrial genomes ranging in length from 16,569 to 16,572 bp were obtained. Additionally, previously published data of other individuals or species were included to perform phylogenetic analyses. In the reconstructed trees, all eight individuals of T.dalaica form a monophyletic group within the Triplophysa branch. The group is divided into three clades: (1) samples from the Yellow River, (2) those from the Yangtze River, and (3) those from the Haihe River, and the Lake Dali Nur. This study sheds initial light on the phylogeographic relationships among different populations of T.dalaica, and will support the research about its evolutionary history in the future.
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Affiliation(s)
- Hao Meng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Yingnan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Jun Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
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2
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Burroughs RW, Parham JF, Stuart BL, Smits PD, Angielczyk KD. Morphological Species Delimitation in The Western Pond Turtle ( Actinemys): Can Machine Learning Methods Aid in Cryptic Species Identification? Integr Org Biol 2024; 6:obae010. [PMID: 38689939 PMCID: PMC11058871 DOI: 10.1093/iob/obae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Indexed: 05/02/2024] Open
Abstract
As the discovery of cryptic species has increased in frequency, there has been an interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods (MLMs) to investigate whether plastron shape can differentiate two putative cryptic turtle species, Actinemys marmorata and Actinemys pallida. Actinemys has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, the other consisting of two subspecies of Trachemys (T. scripta scripta, T. scripta elegans). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via MLMs. In contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in Actinemys. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for Actinemys. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between A. marmorata and A. pallida specimens, lending tentative morphological support to the hypothesis of two Actinemys species. However, the machine learning results also underscore that Actinemys as a whole has lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.
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Affiliation(s)
- R W Burroughs
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Center for Inclusive Education, Stony Brook University, Stony Brook, NY 11794, USA
| | - J F Parham
- Department of Geological Sciences, California State University, Fullerton, CA 92834, USA
| | - B L Stuart
- Section of Research and Collections, NC Museum of Natural Sciences, Raleigh, NC 27601, USA
| | - P D Smits
- 952 NW 60th St., Seattle, Washington, WA 98107, USA
| | - K D Angielczyk
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
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Astudillo-Clavijo V, Mankis T, López-Fernández H. Opening the Museum's Vault: Historical Field Records Preserve Reliable Ecological Data. Am Nat 2024; 203:305-322. [PMID: 38358812 DOI: 10.1086/728422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractMuseum specimens have long served as foundational data sources for ecological, evolutionary, and environmental research. Continued reimagining of museum collections is now also generating new types of data associated with but beyond physical specimens, a concept known as "extended specimens." Field notes penned by generations of naturalists contain firsthand ecological observations associated with museum collections and comprise a form of extended specimens with the potential to provide novel ecological data spanning broad geographic and temporal scales. Despite their data-yielding potential, however, field notes remain underutilized in research because of their heterogeneous, unstandardized, and qualitative nature. We introduce an approach for transforming descriptive ecological notes into quantitative data suitable for statistical analysis. Tests with simulated and real-world published data show that field notes and our transformation approach retain reliable quantitative ecological information under a range of sample sizes and evolutionary scenarios. Unlocking the wealth of data contained within field records could facilitate investigations into the ecology of clades whose diversity, distribution, or other demographic features present challenges to traditional ecological studies, improve our understanding of long-term environmental and evolutionary change, and enhance predictions of future change.
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Hahn EE, Alexander M, Stiller J, Grewe PM, Holleley CE. Hot alkaline lysis gDNA extraction from formalin-fixed archival tissues. PLoS One 2024; 19:e0296491. [PMID: 38165968 PMCID: PMC10760679 DOI: 10.1371/journal.pone.0296491] [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: 09/12/2023] [Accepted: 12/14/2023] [Indexed: 01/04/2024] Open
Abstract
Formalin fixation of natural history specimens and histopathological material has historically been viewed as an impediment to successful genomic analysis. However, the development of extraction methods specifically tailored to contend with heavily crosslinked archival tissues, re-contextualises millions of previously overlooked specimens as viable molecular assets. Here, we present an easy-to-follow protocol for screening archival wet specimens for molecular viability and subsequent genomic DNA extraction suitable for sequencing. The protocol begins with non-destructive assessment of specimen degradation and preservation media conditions to allow both museum curators and researchers to select specimens most likely to yield an acceptable proportion (20-60%) of mappable endogenous DNA during short-read DNA sequencing. The extraction protocol uses hot alkaline lysis in buffer (0.1M NaOH, 1% SDS, pH 13) to simultaneously lyse and de-crosslink the tissue. To maximise DNA recovery, phenol:chloroform extraction is coupled with a small-fragment optimised SPRI bead clean up. Applied to well-preserved archival tissues, the protocol can yield 1-2 μg DNA per 50 mg of tissue with mean fragment sizes typically ranging from 50-150 bp, which is suitable to recover genomic DNA sufficient to reconstruct complete mitochondrial genomes and achieve up to 25X nuclear genome coverage. We provide guidance for read mapping to a reference genome and discuss the limitations of relying on small fragments for SNP genotyping and de novo genome assembly. This protocol opens the door to broader-scale genetic and phylogenetic analysis of historical specimens, contributing to a deeper understanding of evolutionary trends and adaptation in response to changing environments.
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Affiliation(s)
- Erin E. Hahn
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Marina Alexander
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Jiri Stiller
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, St Lucia, Queensland, Australia
| | - Peter M. Grewe
- Environment, Commonwealth Scientific Industrial Research Organisation, Hobart, Tasmania, Australia
| | - Clare E. Holleley
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
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5
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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Sampaio FL, Day JJ, Mendis Wickramasinghe LJ, Cyriac VP, Papadopoulou A, Brace S, Rajendran A, Simon-Nutbrown C, Flouris T, Kapli P, Ranga Vidanapathirana D, Kotharambath R, Kodandaramaiah U, Gower DJ. A near-complete species-level phylogeny of uropeltid snakes harnessing historical museum collections as a DNA source. Mol Phylogenet Evol 2023; 178:107651. [PMID: 36306995 DOI: 10.1016/j.ympev.2022.107651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Uropeltidae is a clade of small fossorial snakes (ca. 64 extant species) endemic to peninsular India and Sri Lanka. Uropeltid taxonomy has been confusing, and the status of some species has not been revised for over a century. Attempts to revise uropeltid systematics and undertake evolutionary studies have been hampered by incompletely sampled and incompletely resolved phylogenies. To address this issue, we take advantage of historical museum collections, including type specimens, and apply genome-wide shotgun (GWS) sequencing, along with recent field sampling (using Sanger sequencing) to establish a near-complete multilocus species-level phylogeny (ca. 87% complete at species level). This results in a phylogeny that supports the monophyly of all genera (if Brachyophidium is considered a junior synonym of Teretrurus), and provides a firm platform for future taxonomic revision. Sri Lankan uropeltids are probably monophyletic, indicating a single colonisation event of this island from Indian ancestors. However, the position of Rhinophis goweri (endemic to Eastern Ghats, southern India) is unclear and warrants further investigation, and evidence that it may nest within the Sri Lankan radiation indicates a possible recolonisation event. DNA sequence data and morphology suggest that currently recognised uropeltid species diversity is substantially underestimated. Our study highlights the benefits of integrating museum collections in molecular genetic analyses and their role in understanding the systematics and evolutionary history of understudied organismal groups.
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Affiliation(s)
- Filipa L Sampaio
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | - Julia J Day
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Vivek P Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695 551, India
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
| | - Selina Brace
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Albert Rajendran
- Research Department of Zoology, St. John's College, Tirunelveli, Tamil Nadu, India
| | - Cornelia Simon-Nutbrown
- The Lyell Centre for Earth and Marine Science and Technology, Heriot-Watt University, Edinburgh EH14 4BA, UK; Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Tomas Flouris
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Ramachandran Kotharambath
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695 551, India
| | - David J Gower
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India.
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7
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León-Tapia MÁ, Rico Y, Fernández JA, Espinosa de los Monteros A. Molecular, morphometric, and spatial data analyses provide new insights into the evolutionary history of the Peromyscus boylii species complex (Rodentia: Cricetidae) in the mountains of Mexico. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2127966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- M. Ángel León-Tapia
- Laboratorio de Sistemática Filogenética, Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, Xalapa, 91073, Veracruz, México
| | - Yessica Rico
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología, A. C., Av. Lázaro Cárdenas, Pátzcuaro, 61600, Michoacán, México
| | - Jesús A. Fernández
- Departamento de Recursos Naturales, Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Periférico Francisco R. Almada Km 1, Chihuahua, 31453, México
| | - Alejandro Espinosa de los Monteros
- Laboratorio de Sistemática Filogenética, Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, Xalapa, 91073, Veracruz, México
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8
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Snead AA, Alda F. Time-Series Sequences for Evolutionary Inferences. Integr Comp Biol 2022; 62:1771-1783. [PMID: 36104153 DOI: 10.1093/icb/icac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023] Open
Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
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9
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Roberts JR, Iova B, Austin CC. A new species of New Guinea Worm-Eating Snake (Serpentes, Elapidae, Toxicocalamus Boulenger, 1896) from Western Highlands Province, Papua New Guinea. ZOOSYST EVOL 2022. [DOI: 10.3897/zse.98.90520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe a new species of New Guinea Worm-Eating Snake (Elapidae: Toxicocalamus) from a specimen in the reptile collection of the Papua New Guinea National Museum and Art Gallery. Toxicocalamus longhagensp. nov. can be easily distinguished from other species of this genus by the presence of paired subcaudals, a preocular scale unfused from the prefrontal scale, a prefrontal distinct from the internasal scale that contacts the supralabials, a single large posterior temporal and two postocular scales. The new taxon is currently known only from one specimen, which was collected from Mt. Hagen Town in Western Highlands Province, Papua New Guinea in 1967. The new species was originally identified as T. loriae, but the unique head scalation and postfrontal bone morphology revealed through micro-computed tomography scanning easily distinguish the new species from T. loriaesensu stricto. This is the first species of this genus described from Western Highlands Province.
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10
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Roycroft E, Moritz C, Rowe KC, Moussalli A, Eldridge MDB, Portela Miguez R, Piggott MP, Potter S. Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.931644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.
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11
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Ren X, Ma X, Allen E, Fang Y, Wen S. DNA Barcoding Technology Used to Successfully Sub-Classify a Museum Whale Specimen as Balaenoptera edeni edeni. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.921106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding technology is becoming an increasingly powerful tool in resolving issues of detailed species identification based on morphology, as commonly employed by museums. In the present study, we aimed to identify a stranded Bryde’s whale on Hainan Island, China by extracting DNA from a vertebra pre-treated by physical and/or chemical processes. Based on morphological characteristics, this Bryde’s whale was initially determined as Balaenoptera edeni. Then, DNA was efficiently extracted using ancient DNA techniques. The mitochondrial gene (COI) phylogenetic analysis further revealed that this museum whale specimen belonged to the sub-species B. e. edeni. This study provides a testable and rapid method for museum species verification, by using ancient DNA extraction methods to compensate the disadvantage of traditional DNA extraction methods that are difficult to extract valid DNA.
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12
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Abreu EF, Pavan SE, Tsuchiya MTN, McLean BS, Wilson DE, Percequillo AR, Maldonado JE. Old specimens for old branches: Assessing effects of sample age in resolving a rapid Neotropical radiation of squirrels. Mol Phylogenet Evol 2022; 175:107576. [PMID: 35809853 DOI: 10.1016/j.ympev.2022.107576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022]
Abstract
Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear. Furthermore, there is an ongoing debate on how to curate, filter, and properly analyze UCE data when locus recovery is uneven across sample age and quality. In the present study we address these questions with an empirical dataset composed of over 3800 UCE loci from 219 historical and modern samples of Sciuridae, a globally distributed and ecologically important family of rodents. We provide a genome-scale phylogeny of two squirrel subfamilies (Sciurillinae and Sciurinae: Sciurini) and investigate their placement within Sciuridae. For historical specimens, recovery of UCE loci and mean length per locus were inversely related to sample age; deeper sequencing improved the number of UCE loci recovered but not locus length. Most of our phylogenetic inferences-performed on six datasets with alternative data-filtering strategies, and using three distinct optimality criteria-resulted in distinct topologies. Datasets containing more loci (40% and 50% taxa representativeness matrices) yielded more concordant topologies and higher support values than strictly filtered datasets (60% matrices) particularly with IQ-Tree and SVDquartets, while filtering based on information content provided better topological resolution for inferences with the coalescent gene-tree based approach in ASTRAL-III. We resolved deep relationships in Sciuridae (including among the five currently recognized subfamilies) and relationships among the deepest branches of Sciurini, but conflicting relationships remain at both genus- and species-levels for the rapid Neotropical tree squirrel radiation. Our results suggest that phylogenomic consensus can be difficult and heavily influenced by the age of available samples and the filtering steps used to optimize dataset properties.
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Affiliation(s)
- Edson F Abreu
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil; Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA.
| | - Silvia E Pavan
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Mirian T N Tsuchiya
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
| | - Bryan S McLean
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Don E Wilson
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alexandre R Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
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13
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Salter JF, Hosner PA, Tsai WLE, McCormack JE, Braun EL, Kimball RT, Brumfield RT, Faircloth BC. Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae). Mol Phylogenet Evol 2022; 175:107559. [PMID: 35803448 DOI: 10.1016/j.ympev.2022.107559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 01/22/2023]
Abstract
As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.
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Affiliation(s)
- Jessie F Salter
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
| | - Peter A Hosner
- Natural History Museum of Denmark, Center for Global Mountain Biodiversity, and Center for Macroecology, Evolution, and Climate, University of Copenhagen, Copenhagen, Denmark; Department of Biology, University of Florida, Gainesville, FL, USA
| | - Whitney L E Tsai
- Moore Laboratory of Biology, Occidental College, Los Angeles, CA, USA
| | - John E McCormack
- Moore Laboratory of Biology, Occidental College, Los Angeles, CA, USA; Biology Department, Occidental College, Los Angeles, CA, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | | | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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14
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Verry AJF, Lubbe P, Mitchell KJ, Rawlence NJ. Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2093227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alexander J. F. Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Pascale Lubbe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kieren J. Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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15
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Bernstein JM, Ruane S. Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.893088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops. Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount results entirely, we used mapping methods with references and pseudoreferences, along with phylogenetic analyses, to maximize any usable molecular data from our sequencing efforts, identify the taxonomic affinity of H. periops, and compare sequencing success between fresh and degraded tissue samples. This resulted in largely complete mitochondrial genomes for five specimens and hundreds to thousands of nuclear loci (ultra-conserved loci, anchored-hybrid enrichment loci, and a variety of loci frequently used in squamate phylogenetic studies) from fluid-preserved snakes, including a specimen of H. periops from the Field Museum of Natural History collection. We combined our H. periops data with previously published genomic and Sanger-sequenced datasets to confirm the familial designation of this taxon, reject previous taxonomic hypotheses, and make biogeographic inferences for Hydrablabes. A second H. periops specimen, despite being seemingly similar for initial raw sequencing results and after being put through the same protocols, resulted in little usable molecular data. We discuss the successes and failures of using different pipelines and methods to maximize the products from these data and provide expectations for others who are looking to use DNA sequencing efforts on specimens that likely have degraded DNA.Life Science Identifier (Hydrablabes periops)urn:lsid:zoobank.org:pub:F2AA44 E2-D2EF-4747-972A-652C34C2C09D.
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16
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Clewing C, Kehlmaier C, Stelbrink B, Albrecht C, Wilke T. Poor hDNA-Derived NGS Data May Provide Sufficient Phylogenetic Information of Potentially Extinct Taxa. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.907889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Museum material is an important source of metadata for past and recent biological events. With current sequencing technologies, it is possible to obtain historical DNA (hDNA) from older material and/or endangered species to answer taxonomic, systematic, and biogeographical questions. However, hDNA from museum collections is often highly degraded, making it difficult to assess relationships at or above the species level. We therefore studied two probably extinct gastropod species of the genus Laevicaspia, which were collected ∼140 years ago in the Caspian Sea, to map “standard” mitochondrial and nuclear markers and assess both the sequencing depth and the proportion of ambiguous sites as an indicator for the phylogenetic quality of the NGS data. Our study resulted in the first phylogenetically informative mitochondrial and nuclear markers for L. caspia. Assessment of both sequencing depth (mean coverage) and proportion of ambiguous sites suggests that our assembled consensus sequences are reliable for this species. In contrast, no informative gastropod-specific DNA was obtained for L. conus, likely due to a high degree of tissue digestion and contamination with non-gastropod DNA. Nevertheless, our results show that hDNA may in principle yield high-quality sequences for species-level phylogenetic analyses, which underlines the importance of museum collections as valuable archives of the biological past.
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17
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Zamani A, Dal Pos D, Fric ZF, Orfinger AB, Scherz MD, Bartoňová AS, Gante HF. The future of zoological taxonomy is integrative, not minimalist. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2063964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alireza Zamani
- Zoological Museum, Biodiversity Unit, University of Turku, 20500 Turku, Finland
| | - Davide Dal Pos
- Department of Biology, University of Central Florida, 4110 Libra dr. Rm 442, Orlando, FL 32816, USA
| | - Zdenek Faltýnek Fric
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Alexander B. Orfinger
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
- Center for Water Resources, Florida A&M University, Tallahassee, FL 32301, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Alena Sucháčková Bartoňová
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Hugo F. Gante
- cE3c—Center for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisboa, Portugal
- Department of Biology, KU Leuven, Section Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 32 box 2439, Leuven, B-3000, Belgium
- Royal Museum for Central Africa, Leuvensesteenweg 17, Tervuren, 3080, Belgium
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18
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Van Dam AR, Covas Orizondo JO, Lam AW, McKenna DD, Van Dam MH. Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens. Ecol Evol 2022; 12:e8625. [PMID: 35342556 PMCID: PMC8932080 DOI: 10.1002/ece3.8625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/03/2022] [Accepted: 01/17/2022] [Indexed: 11/30/2022] Open
Abstract
Phylogenomics via ultraconserved elements (UCEs) has led to improved phylogenetic reconstructions across the tree of life. However, inadvertently incorporating non‐targeted DNA into the UCE marker design will lead to misinformation being incorporated into subsequent analyses. To date, the effectiveness of basic metagenomic filtering strategies has not been assessed in arthropods. Designing markers from museum specimens requires careful consideration of methods due to the high levels of microbial contamination typically found in such specimens. We investigate if contaminant sequences are carried forward into a UCE marker set we developed from insect museum specimens using a standard bioinformatics pipeline. We find that the methods currently employed by most researchers do not exclude contamination from the final set of targets. Lastly, we highlight several paths forward for reducing contamination in UCE marker design.
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Affiliation(s)
- Alex R. Van Dam
- Department of Biology University of Puerto Rico Mayagüez Mayagüez Puerto Rico
| | | | - Athena W. Lam
- Department of Entomology California Academy of Sciences San Francisco California USA
| | - Duane D. McKenna
- Department of Biological Sciences University of Memphis Memphis Tennessee USA
- Center for Biodiversity Research University of Memphis Memphis Tennessee USA
| | - Matthew H. Van Dam
- Department of Entomology California Academy of Sciences San Francisco California USA
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19
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Hockney R, Orr CH, Waring GJ, Christiaens I, Taylor G, Cummings SP, Robson SC, Nelson A. Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research. PLoS One 2022; 17:e0265441. [PMID: 35298530 PMCID: PMC8929612 DOI: 10.1371/journal.pone.0265441] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Formalin-Fixed Paraffin-Embedded (FFPE) tissues are routinely collected, archived, and used for clinical diagnosis, including maternal and neonatal health. Applying FFPE samples to microbiota research would be beneficial to reduce preparation, storage and costs associated with limited available frozen samples. This research aims to understand if FFPE fetal membrane samples are comparable to frozen tissues, which are the current gold standard for DNA microbiota analysis. Extracted DNA from nine matched paired patients were sequenced by Illumina sequencing of the V4 16S rRNA gene region. This included duplicate frozen amnion and chorion fetal membrane rolls or FFPE combined amniochorionic samples. Negative controls of surrounding wax blocks and DNA extraction reagents were processed alongside samples using identical methods. DNA quality and quantity was assessed by NanoDrop, agarose gel electrophoresis and Bioanalyzer. Decontam and SourceTracker were integrated into microbiota analysis to identify the presence of contaminating sources. The bacterial profile and nine genera differed between FFPE and frozen fetal membranes. There were no differences in bacterial profiles between FFPE samples and corresponding wax negative controls, with 49% of bacteria in FFPE fetal membrane samples matched to the source origin of paraffin wax, and 40% originating from DNA extraction reagent sources. FFPE samples displayed high fragmentation and low quantity of extracted DNA compared to frozen samples. The microbiota of FFPE fetal membrane samples is influenced by processing methods, with the inability to differentiate between the microbiota of the tissue sample and the surrounding wax block. Illumina sequencing results of FFPE and frozen fetal membrane samples should not be compared using the methods employed here. Variation could be influenced by limitations including storage time, DNA extraction and purification methods. To utilise FFPE fetal membrane samples in microbiota research then contamination prevention and detection methods must be included into optimised and standardised protocols, with recommendations presented here.
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Affiliation(s)
- Rochelle Hockney
- School of Health, Leeds Beckett University, Leeds, United Kingdom
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
- * E-mail:
| | - Caroline H. Orr
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Gareth J. Waring
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Inge Christiaens
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Gillian Taylor
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Stephen P. Cummings
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Stephen C. Robson
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
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20
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Contextualizing enigmatic extinctions using genomic DNA from fluid-preserved museum specimens of Desmognathus salamanders. CONSERV GENET 2022. [DOI: 10.1007/s10592-021-01424-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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21
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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22
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Reyes-Velasco J, Goutte* S, Freilich X, Boissinot S. Mitogenomics of historical type specimens clarifies the taxonomy of Ethiopian Ptychadena Boulenger, 1917 (Anura, Ptychadenidae). Zookeys 2021; 1070:135-149. [PMID: 34819775 PMCID: PMC8604866 DOI: 10.3897/zookeys.1070.66598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/07/2021] [Indexed: 11/12/2022] Open
Abstract
The taxonomy of the Ptychadenaneumanni species complex, a radiation of grass frogs inhabiting the Ethiopian highlands, has puzzled scientists for decades because of the morphological resemblance among its members. Whilst molecular phylogenetic methods allowed the discovery of several species in recent years, assigning pre-existing and new names to clades was challenged by the unavailability of molecular data for century-old type specimens. We used Illumina short reads to sequence the mitochondrial DNA of type specimens in this group, as well as ddRAD-seq analyses to resolve taxonomic uncertainties surrounding the P.neumanni species complex. The phylogenetic reconstruction revealed recurrent confusion between Ptychadenaerlangeri (Ahl, 1924) and P.neumanni (Ahl, 1924) in the literature. The phylogeny also established that P.largeni Perret, 1994 represents a junior synonym of P.erlangeri (Ahl, 1924) and distinguished between two small species, P.nana Perret, 1994, restricted to the Arussi Plateau, and P.robeensis Goutte, Reyes-Velasco, Freilich, Kassie & Boissinot, 2021, which inhabits the Bale Mountains. The phylogenetic analyses of mitochondrial DNA from type specimens also corroborate the validity of seven recently described species within the group. Our study shows how modern molecular tools applied to historical type specimens can help resolve long-standing taxonomic issues in cryptic species complexes.
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Affiliation(s)
- Jacobo Reyes-Velasco
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAENew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Sandra Goutte*
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAENew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Xenia Freilich
- Department of Biology, Queens College, City University of New York, Flushing, NY, USACity University of New YorkFlushingUnited States of America
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAENew York University Abu DhabiAbu DhabiUnited Arab Emirates
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23
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León‐Tapia MÁ, Rico Y, Fernández JA, Arellano E, Espinosa de los Monteros A. Role of Pleistocene climatic oscillations on genetic differentiation and evolutionary history of the Transvolcanic deer mouse
Peromyscus hylocetes
(Rodentia: Cricetidae) throughout the Mexican central highlands. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- M. Ángel León‐Tapia
- Laboratorio de Sistemática Filogenética, Biología Evolutiva Instituto de Ecología A.C Xalapa Mexico
| | - Yessica Rico
- Red de Diversidad Biológica del Occidente Mexicano Instituto de Ecología, A.C. Pátzcuaro Mexico
| | - Jesús A. Fernández
- Departamento de Recursos Naturales Facultad de Zootecnia y Ecología Universidad Autónoma de Chihuahua Chihuahua Mexico
| | - Elizabeth Arellano
- Centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de Morelos Cuernavaca Morelos Mexico
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24
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Houston DD, Satler JD, Stack TK, Carroll HM, Bevan AM, Moya AL, Alexander KD. A phylogenomic perspective on the evolutionary history of the stonefly genus Suwallia (Plecoptera: Chloroperlidae) revealed by ultraconserved genomic elements. Mol Phylogenet Evol 2021; 166:107320. [PMID: 34626810 DOI: 10.1016/j.ympev.2021.107320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 09/20/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022]
Abstract
Evolutionary biologists have long sought to disentangle phylogenetic relationships among taxa spanning the tree of life, an increasingly important task as anthropogenic influences accelerate population declines and species extinctions, particularly in insects. Phylogenetic analyses are commonly used to identify unique evolutionary lineages, to clarify taxonomic designations of the focal taxa, and to inform conservation decisions. Advances in DNA sequencing techniques have increasingly facilitated the ability of researchers to apply genomic methods to phylogenetic analyses, even for non-model organisms. Stoneflies are non-model insects that are important bioindicators of the quality of freshwater habitats and landscape disturbance as they spend the immature stages of their life cycles in fresh water, and the adult stages in terrestrial environments. Phylogenetic relationships within the stonefly genus Suwallia (Insecta: Plecoptera: Chloroperlidae) are poorly understood, and have never been assessed using molecular data. We used DNA sequence data from genome-wide ultraconserved element loci to generate the first molecular phylogeny for the group and assess its monophyly. We found that Palearctic and Nearctic Suwallia do not form reciprocally monophyletic clades, and that a biogeographic history including dispersal, vicariance, and founder event speciation via jump dispersal best explains the geographic distribution of this group. Our results also strongly suggest that Neaviperla forcipata (Neave, 1929) is nested within Suwallia, and the concept of the genus Suwallia should be revised to include it. Thus, we formally propose a new taxonomic combination wherein Neaviperla forcipata (Neave, 1929) is reclassified as Suwallia forcipata (Neave, 1929). Moreover, some Suwallia species (e.g., S. amoenacolens, S. kerzhneri, S. marginata, S. pallidula, and S. starki) exhibit pronounced cryptic diversity that is worthy of further investigation. These findings provide a first glimpse into the evolutionary history of Suwallia, improve our understanding of stonefly diversity in the tribe Suwallini, and highlight areas where additional research is needed.
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Affiliation(s)
- Derek D Houston
- Department of Natural and Environmental Sciences, Western Colorado University, Gunnison, CO, USA.
| | - Jordan D Satler
- Department of Ecology Evolution and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Taylor K Stack
- Department of Natural and Environmental Sciences, Western Colorado University, Gunnison, CO, USA.
| | - Hannah M Carroll
- Department of Ecology Evolution and Organismal Biology, Iowa State University, Ames, IA, USA; Department of Earth Planetary and Space Sciences, University of California-Los Angeles, CA, USA.
| | - Alissa M Bevan
- Department of Natural and Environmental Sciences, Western Colorado University, Gunnison, CO, USA.
| | - Autumn L Moya
- Department of Natural and Environmental Sciences, Western Colorado University, Gunnison, CO, USA.
| | - Kevin D Alexander
- Department of Natural and Environmental Sciences, Western Colorado University, Gunnison, CO, USA.
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25
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Hahn EE, Alexander MR, Grealy A, Stiller J, Gardiner DM, Holleley CE. Unlocking inaccessible historical genomes preserved in formalin. Mol Ecol Resour 2021; 22:2130-2147. [PMID: 34549888 DOI: 10.1111/1755-0998.13505] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/27/2022]
Abstract
Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine sample processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically diverse specimens collected between 1962 and 2006 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3× nuclear genome coverage from formalin-preserved tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out-performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. Here, we demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and nondestructive assessment criteria. Sequencing of formalin-preserved specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.
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Affiliation(s)
- Erin E Hahn
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Marina R Alexander
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Alicia Grealy
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Jiri Stiller
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, St Lucia, Qld, Australia
| | - Donald M Gardiner
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, St Lucia, Qld, Australia
| | - Clare E Holleley
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
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26
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Mining museums for historical DNA: advances and challenges in museomics. Trends Ecol Evol 2021; 36:1049-1060. [PMID: 34456066 DOI: 10.1016/j.tree.2021.07.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/22/2023]
Abstract
Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.
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27
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Zacho CM, Bager MA, Margaryan A, Gravlund P, Galatius A, Rasmussen AR, Allentoft ME. Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes. PLoS One 2021; 16:e0256353. [PMID: 34424926 PMCID: PMC8382189 DOI: 10.1371/journal.pone.0256353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/04/2021] [Indexed: 11/19/2022] Open
Abstract
Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.
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Affiliation(s)
- Claus M. Zacho
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martina A. Bager
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Anders Galatius
- Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Arne R. Rasmussen
- Institute of Conservation, Royal Danish Academy—Architecture, Design, Conservation, Copenhagen, Denmark
| | - Morten E. Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Australia
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28
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O'Connell KA, Mulder KP, Wynn A, de Queiroz K, Bell RC. Genomic library preparation and hybridization capture of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based single nucleotide polymorphism data sets. Mol Ecol Resour 2021; 22:487-502. [PMID: 34329532 DOI: 10.1111/1755-0998.13481] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/10/2021] [Accepted: 07/14/2021] [Indexed: 12/17/2022]
Abstract
Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.
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Affiliation(s)
- Kyle A O'Connell
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA.,Biomedical Data Science Lab, Deloitte Consulting LLP, Arlington, Virginia, USA
| | - Kevin P Mulder
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Addison Wynn
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Department of Herpetology, California Academy of Sciences, San Francisco, California, USA
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29
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Smith BT, Mauck WM, Benz BW, Andersen MJ. Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets. Genome Biol Evol 2021; 12:1131-1147. [PMID: 32470111 PMCID: PMC7486955 DOI: 10.1093/gbe/evaa113] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2020] [Indexed: 01/21/2023] Open
Abstract
The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded, which presents various challenges. In this study, we evaluated how the coverage at variant sites and missing data among historical and modern samples impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage characters had several clades where relationships appeared to be influenced by whether the sample came from historical or modern specimens, which were not observed when more stringent filtering was applied. To assess if the topologies were affected by missing data, we performed an outlier analysis of sites and loci, and a data reduction approach where we excluded sites based on data completeness. Depending on the outlier test, 0.15% of total sites or 38% of loci were driving the topological differences among trees, and at these sites, historical samples had 10.9× more missing data than modern ones. In contrast, 70% data completeness was necessary to avoid spurious relationships. Predictive modeling found that outlier analysis scores were correlated with parsimony informative sites in the clades whose topologies changed the most by filtering. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, New York
| | - William M Mauck
- Department of Ornithology, American Museum of Natural History, New York, New York.,New York Genome Center, New York, New York
| | - Brett W Benz
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico
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31
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Straube N, Lyra ML, Paijmans JLA, Preick M, Basler N, Penner J, Rödel MO, Westbury MV, Haddad CFB, Barlow A, Hofreiter M. Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Mol Ecol Resour 2021; 21:2299-2315. [PMID: 34036732 DOI: 10.1111/1755-0998.13433] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023]
Abstract
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.
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Affiliation(s)
- Nicolas Straube
- University Museum of Bergen, Bergen, Norway.,SNSB Bavarian State Collection of Zoology, München, Germany
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.,Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Johanna L A Paijmans
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michaela Preick
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nikolas Basler
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johannes Penner
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Chair of Wildlife Ecology and Management, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Célio F B Haddad
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil
| | - Axel Barlow
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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32
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Toussaint EFA, Gauthier J, Bilat J, Gillett CPDT, Gough HM, Lundkvist H, Blanc M, Muñoz-Ramírez CP, Alvarez N. HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution. Genome Biol Evol 2021; 13:6275686. [PMID: 33988685 PMCID: PMC8480185 DOI: 10.1093/gbe/evab112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/27/2022] Open
Abstract
Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.
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Affiliation(s)
| | | | - Julia Bilat
- Natural History Museum of Geneva, Switzerland
| | - Conrad P D T Gillett
- University of Hawai'i Insect Museum, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Harlan M Gough
- Florida Natural History Museum, University of Florida, Gainesville, Florida, USA
| | | | | | - Carlos P Muñoz-Ramírez
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile.,Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Chile
| | - Nadir Alvarez
- Natural History Museum of Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Switzerland
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33
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Hardy BM, Pope KL, Latch EK. Genomic signatures of demographic declines in an imperiled amphibian inform conservation action. Anim Conserv 2021. [DOI: 10.1111/acv.12695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- B. M. Hardy
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - K. L. Pope
- United States Forest Service Pacific Southwest Research Station Arcata CA USA
| | - E. K. Latch
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
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34
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Martínez-Vargas J, Roqué L, Del Canto I, Carrillo-Ortiz J, Orta C, Quesada J. The impact of prolonged frozen storage on the preparation quality of bird skins and skeletons in zoological collections. Naturwissenschaften 2021; 108:18. [PMID: 33877435 DOI: 10.1007/s00114-021-01726-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 11/27/2022]
Abstract
Specimens from zoological collections play a pivotal role in improving scientific knowledge in many natural science disciplines. To guarantee an optimum state of conservation and ensure their usefulness, the preparation process employed is crucial. Skins and skeletons are key elements in vertebrate scientific collections and, ideally, are prepared from recently deceased animals; however, specimens are often stored in a frozen state for a long time (years) prior to preparation. Whether the duration of this frozen state has a deleterious effect on preparation quality has rarely been studied. The main objective of this study was thus to contribute towards research into zoological preparation by testing to see whether prolonged frozen storage hinders the preparation of bird skins and skeletons. We used the common buzzard (Buteo buteo) and the barn owl (Tyto alba) as biological models. Our results showed that long-term frozen storage led to weight loss, bone marrow acidification and solidification, and hampered skin preparation. The necropsy affected weight loss and decreased the skin tear resistance, probably due to tissue dehydration. Thus, prolonged frozen storage appears to have a harmful effect on the preparation quality of vertebrate specimens. Since frozen storage could ultimately have an impact on the conservation and scientific use of museum specimens, practices should be implemented to minimise the amount of time specimens are frozen or to mitigate any detrimental effects. More importance should be attached to research on zoological preparation since it is fundamental for optimising the quality, conservation status, and value of museum collections.
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Affiliation(s)
- Jessica Martínez-Vargas
- Department of Vertebrates, Museu de Ciències Naturals de Barcelona - Natural Science Museum of Barcelona, Passeig Picasso s/n, 08003, Barcelona, Catalonia, Spain
- Myrmex. Serveis Tècnics a les Ciències Naturals S.L., Carrer de Bailèn 148 3r 1a, 08037, Barcelona, Catalonia, Spain
| | - Laura Roqué
- Department of Vertebrates, Museu de Ciències Naturals de Barcelona - Natural Science Museum of Barcelona, Passeig Picasso s/n, 08003, Barcelona, Catalonia, Spain
- Ulnae Bones, Carrer de la Canal 22, 17869 Vilallonga de Ter, Catalonia, Spain
| | - Irene Del Canto
- Department of Vertebrates, Museu de Ciències Naturals de Barcelona - Natural Science Museum of Barcelona, Passeig Picasso s/n, 08003, Barcelona, Catalonia, Spain
| | - José Carrillo-Ortiz
- Department of Vertebrates, Museu de Ciències Naturals de Barcelona - Natural Science Museum of Barcelona, Passeig Picasso s/n, 08003, Barcelona, Catalonia, Spain
| | - Carles Orta
- Department of Vertebrates, Museu de Ciències Naturals de Barcelona - Natural Science Museum of Barcelona, Passeig Picasso s/n, 08003, Barcelona, Catalonia, Spain
| | - Javier Quesada
- Department of Vertebrates, Museu de Ciències Naturals de Barcelona - Natural Science Museum of Barcelona, Passeig Picasso s/n, 08003, Barcelona, Catalonia, Spain.
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35
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Narayanan S, Mohapatra PP, Balan A, Das S, Gower DJ. A new species of Xylophis Beddome, 1878 (Serpentes: Pareidae) from the southern Western Ghats of India. VERTEBRATE ZOOLOGY 2021. [DOI: 10.3897/vz.71.e63986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We reassess the taxonomy of the Indian endemic snake Xylophis captaini and describe a new species of Xylophis based on a type series of three specimens from the southernmost part of mainland India. Xylophis deepakisp. nov. is most similar phenotypically to X. captaini, with which it was previously confused. The new species differs from X. captaini by having a broader, more regular and ventrally extensive off-white collar, more ventral scales (117–125 versus 102–113), and by lack of flounces on the body and proximal lobes of the hemipenis. Phylogenetic analysis of mitochondrial 16S DNA sequences strongly indicates that the new species is most closely related to X. captaini, differing from it by an uncorrected pairwise genetic distance of 4.2%. A revised key to the species of Xylophis is provided.
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36
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García NC, Robinson WD. Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.
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37
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Phylogenetics of mud snakes (Squamata: Serpentes: Homalopsidae): A paradox of both undescribed diversity and taxonomic inflation. Mol Phylogenet Evol 2021; 160:107109. [PMID: 33609712 DOI: 10.1016/j.ympev.2021.107109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/20/2020] [Accepted: 02/05/2021] [Indexed: 12/30/2022]
Abstract
Mud snakes (Serpentes: Homalopsidae) are a family of 55 described, mainly aquatic, species primarily distributed throughout mainland Southeast Asia and the Indo-Australian Archipelago. Although they have been the focus of prior research, the basic relationships amongst genera and species remain poorly known. We used a combined mitochondrial and nuclear gene dataset to infer their phylogenetic relationships, using the highest levels of taxon and geographic sampling for any homalopsid phylogeny to date (62% generic and 62% species coverage; 140 individuals). Our results recover two reciprocally monophyletic groups: the fangless Brachyorrhos and its sister clade comprised of all rear-fanged homalopsids. Most genera and interspecific relationships were monophyletic and strongly supported, but intergeneric relationships and intraspecific population structure lack support. We find evidence of both undescribed diversity as well as cases of taxonomic inflation within several species. Tree-based species delimitation approaches (mPTP) support potential new candidate species as distinct from their conspecifics and also suggest that many named taxa may not be distinct species. Divergence date estimation and lineage-through-time analyses indicate lower levels of speciation in the Eocene, with a subsequent burst in diversification in the Miocene. Homalopsids may have diversified most rapidly during the Pliocene and Pleistocene, possibly in relation to tectonic shifts and sea-level fluctuations that took place in Sundaland and the Sahul Shelf. Our analyses provide new insights on homalopsid taxonomy, a baseline phylogeny for the family, and further biogeographic implications demonstrating how dynamic tectonics and Quaternary sea level changes may have shaped a widespread, diverse family of snakes.
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Shiozaki T, Itoh F, Hirose Y, Onodera J, Kuwata A, Harada N. A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin. PLoS One 2021; 16:e0245936. [PMID: 33596231 PMCID: PMC7888612 DOI: 10.1371/journal.pone.0245936] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/08/2021] [Indexed: 01/04/2023] Open
Abstract
Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure.
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Affiliation(s)
- Takuhei Shiozaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- * E-mail:
| | - Fumihiro Itoh
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Jonaotaro Onodera
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Naomi Harada
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
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39
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Lebedev VS, Kovalskaya Y, Solovyeva EN, Zemlemerova ED, Bannikova AA, Rusin MY, Matrosova VA. Molecular systematics of the Sicista tianschanica species complex: a contribution from historical DNA analysis. PeerJ 2021; 9:e10759. [PMID: 33520475 PMCID: PMC7810041 DOI: 10.7717/peerj.10759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
The Tianshan birch mouse Sicista tianschanica is an endemic of the Central Asian mountains and has previously been shown to include several karyomorphs (“Terskey”, “Talgar”, “Dzungar”); however, the taxonomic status of these forms has remained uncertain. We examined the genetic variation in S. tianschanica based on historical DNA samples from museum collections, including the type series. Mitochondrial and nuclear data indicated that the species complex includes two major clades: Northern (N) and Southern (S) (cytb distance 13%). The N clade corresponds to the “Dzungar” karyomorph (Dzungar Alatau, Tarbagatay). The S clade is comprised of four lineages (S1–S4) divergent at 6–8%; the relationships among which are resolved incompletely. The S1 lineage is found in eastern Tianshan and corresponds to the nominal taxon. The S2 is distributed in central and northern Tianshan and corresponds to the “Terskey” karyomorph. The S3 is restricted to Trans-Ili Alatau and belongs to the “Talgar” karyomorph. The S4 is represented by a single specimen from southeastern Dzungar Alatau with "Talgar" karyotype. No interlineage gene flow was revealed. The validity of S. zhetysuica (equivalent to the N clade) is supported. Based on genetic and karyotypic evidence, lineages S2 and S3 are described as distinct species. The status of the S4 requires further investigation.
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Affiliation(s)
| | - Yulia Kovalskaya
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | | | - Elena D Zemlemerova
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Bannikova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail Yu Rusin
- Research and International Cooperation Department, Kiev Zoo, Kiev, Ukraine.,Schmalhausen Institute of Zoology, Kiev, Ukraine
| | - Vera A Matrosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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40
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Gould AL, Fritts-Penniman A, Gaisiner A. Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish. Front Ecol Evol 2021; 9:630207. [PMID: 34485316 PMCID: PMC8412414 DOI: 10.3389/fevo.2021.630207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Symbiotic relationships between bioluminescent bacteria and fishes have evolved multiple times across hundreds of fish taxa, but relatively little is known about the specificity of these associations and how stable they are over host generations. This study describes the degree of specificity of a bioluminescent symbiosis between cardinalfishes in the genus Siphamia and luminous bacteria in the Vibrio family. Primarily using museum specimens, we investigated the codivergence of host and symbiont and test for patterns of divergence that correlate with both biogeography and time. Contrary to expectations, we determined that the light organ symbionts of all 14 Siphamia species examined belong to one genetic clade of Photobacterium mandapamensis (Clade II), indicating that the association is highly specific and conserved throughout the host genus. Thus, we did not find evidence of codivergence among hosts and symbionts. We did observe that symbionts hosted by individuals sampled from colder water regions were more divergent, containing more than three times as many single nucleotide polymorphisms than the rest of the symbionts examined. Overall, our findings indicate that the symbiosis between Siphamia fishes and P. mandapamensis Clade II has been highly conserved across host taxa and over a broad geographic range despite the facultative nature of the bacterial symbiont. We also present a new approach to simultaneously recover genetic information from a bacterial symbiont and its vertebrate host from formalin-fixed specimens, enhancing the utility of museum collections.
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Affiliation(s)
- Alison L. Gould
- California Academy of Sciences, San Francisco, CA, United States
| | | | - Ana Gaisiner
- California Academy of Sciences, San Francisco, CA, United States
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41
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Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, Gelang M, Khan FAA, Paul DL, Reeder DM, Simmons NB, Vanhove MPM, Webala PW, Weksler M, Kilpatrick CW. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. mBio 2021; 12:e02698-20. [PMID: 33436435 PMCID: PMC7844540 DOI: 10.1128/mbio.02698-20] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.
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Affiliation(s)
- Cody W Thompson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marc W Allard
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA
| | - Joseph A Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Adam W Ferguson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Magnus Gelang
- Gothenburg Natural History Museum, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Deborah L Paul
- Florida State University, Tallahassee, Florida, USA
- Species File Group, University of Illinois, Urbana-Champaign, Illinois, USA
| | | | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Maarten P M Vanhove
- Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Orr RJS, Sannum MM, Boessenkool S, Di Martino E, Gordon DP, Mello HL, Obst M, Ramsfjell MH, Smith AM, Liow LH. A molecular phylogeny of historical and contemporary specimens of an under-studied micro-invertebrate group. Ecol Evol 2021; 11:309-320. [PMID: 33437431 PMCID: PMC7790615 DOI: 10.1002/ece3.7042] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/08/2020] [Accepted: 10/28/2020] [Indexed: 11/06/2022] Open
Abstract
Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under-studied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer the sequencing of air-dried cheilostomes, utilizing a recently developed library preparation method for low DNA input. We evaluate a de novo mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and/or congenerics have been sequenced verifies the appropriateness of our workflow and gives confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced. The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species.
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Affiliation(s)
| | | | - Sanne Boessenkool
- Department of BiosciencesCentre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | | | - Dennis P. Gordon
- National Institute of Water and Atmospheric ResearchWellingtonNew Zealand
| | - Hannah L. Mello
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Matthias Obst
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | | | - Abigail M. Smith
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Lee Hsiang Liow
- Natural History MuseumUniversity of OsloOsloNorway
- Department of BiosciencesCentre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
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43
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Shultz AJ, Adams BJ, Bell KC, Ludt WB, Pauly GB, Vendetti JE. Natural history collections are critical resources for contemporary and future studies of urban evolution. Evol Appl 2021; 14:233-247. [PMID: 33519967 PMCID: PMC7819571 DOI: 10.1111/eva.13045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/30/2022] Open
Abstract
Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.
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Affiliation(s)
- Allison J. Shultz
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Ornithology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Benjamin J. Adams
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Entomology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Department of Biological SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Kayce C. Bell
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Mammalogy DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - William B. Ludt
- Ichthyology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Gregory B. Pauly
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Herpetology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Jann E. Vendetti
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Malacology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
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A New Species of New Guinea Worm-Eating Snake (Elapidae: Toxicocalamus Boulenger, 1896), with Comments on Postfrontal Bone Variation Based on Micro-computed Tomography. J HERPETOL 2020. [DOI: 10.1670/20-043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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O'Toole B, Simmons NB, Hekkala E. Reconstructing the Genomic Diversity of a Widespread Sub-Saharan Bat (Pteropodidae: Eidolon helvum) Using Archival Museum Collections. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.2.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Brian O'Toole
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Evon Hekkala
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
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46
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'Barcode fishing' for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species. Sci Rep 2020; 10:19109. [PMID: 33154397 PMCID: PMC7644772 DOI: 10.1038/s41598-020-75431-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/28/2020] [Indexed: 11/08/2022] Open
Abstract
Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne d'Ambre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d'Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this 'barcode fishing' approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.
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47
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Chakona A, Gouws G, Kadye WT, Mpopetsi PP, Skelton PH. Probing hidden diversity to enhance conservation of the endangered narrow-range endemic Eastern Cape rocky, Sandelia bainsii (Castelnau 1861). KOEDOE: AFRICAN PROTECTED AREA CONSERVATION AND SCIENCE 2020. [DOI: 10.4102/koedoe.v62i1.1627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Torres-Roig E, Mitchell KJ, Alcover JA, Martínez-Freiría F, Bailón S, Heiniger H, Williams M, Cooper A, Pons J, Bover P. Origin, extinction and ancient DNA of a new fossil insular viper: molecular clues of overseas immigration. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Viperinae is a subfamily of viperid snakes whose fossil record in the Mediterranean islands is, until now, restricted to 12 palaeontological deposits on seven islands. Revision of the material excavated 30 years ago from the Middle/Late Pleistocene–Holocene deposit of Es Pouàs [Eivissa (= Ibiza), Balearic Islands, western Mediterranean] revealed about 6000 bones of a small-sized viper across different stratigraphic levels. Its morphological characteristics are different enough to known species of Vipera to warrant the description of a new species, but the nearly complete mitochondrial genome obtained from this snake based on a sample dated to 16 130 ± 45 bp, suggested it belonged to a new insular population of Lataste’s viper (Vipera latastei), Vipera latastei ebusitana subsp. nov. Phylogenetic analysis indicates that the dispersal of the ancestors of V. l. ebusitana to Eivissa, most probably from a north-east Iberian population, occurred via overwater colonization < 1.5 Mya, well after the Messinian Salinity Crisis (5.97–5.32 Mya) when land bridges allowed terrestrial colonization of the Balearic Islands by mainland faunas. The morphological differences between V. l. ebusitana and the Iberian populations suggest that it is a new dwarf taxon resulting from insular evolutionary processes, becoming extinct shortly after the first human arrival to this island about 4000 years ago.
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Affiliation(s)
- Enric Torres-Roig
- Departament de Dinàmica de la Terra i de l’Oceà, Facultat de Ciències de la Terra, Universitat de Barcelona, Barcelona, Spain
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Josep Antoni Alcover
- Departament de Biodiversitat Animal i Microbiana. Institut Mediterrani d’Estudis Avançats (UIB-CSIC), Esporles, Mallorca, Spain
| | - Fernando Martínez-Freiría
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
| | - Salvador Bailón
- Histoire Naturelle de l’Homme Préhistorique, UMR 7194, Sorbonne Universités, MNHN, CNRS, Paris, France
- Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements, UMR 7209, Sorbonne Universités, MNHN, CNRS, Paris, France
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew Williams
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Joan Pons
- Departament de Biodiversitat Animal i Microbiana. Institut Mediterrani d’Estudis Avançats (UIB-CSIC), Esporles, Mallorca, Spain
| | - Pere Bover
- Aragonese Foundation for Research & Development (ARAID), Zaragoza, Spain
- IUCA, Instituto Universitario de Investigación en Ciencias Ambientales-Grupo Aragosaurus. Universidad de Zaragoza, Zaragoza, Spain
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49
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Erickson KL, Pentico A, Quattrini AM, McFadden CS. New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons. Mol Ecol Resour 2020; 21:78-92. [PMID: 32786110 DOI: 10.1111/1755-0998.13241] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/04/2020] [Indexed: 01/06/2023]
Abstract
As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,181 baits) to target-capture 3,023 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered single nucleotide polymorphisms delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using restriction site associated DNA sequencing. Both case studies demonstrate the utility of target-enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow timescales in corals.
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Affiliation(s)
| | - Alicia Pentico
- Department of Biology, Harvey Mudd College, Claremont, CA, USA
| | - Andrea M Quattrini
- Department of Biology, Harvey Mudd College, Claremont, CA, USA.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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50
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Miller SE, Barrow LN, Ehlman SM, Goodheart JA, Greiman SE, Lutz HL, Misiewicz TM, Smith SM, Tan M, Thawley CJ, Cook JA, Light JE. Building Natural History Collections for the Twenty-First Century and Beyond. Bioscience 2020. [DOI: 10.1093/biosci/biaa069] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Natural history collections (NHCs) are important resources for a diverse array of scientific fields. Recent digitization initiatives have broadened the user base of NHCs, and new technological innovations are using materials generated from collections to address novel scientific questions. Simultaneously, NHCs are increasingly imperiled by reductions in funding and resources. Ensuring that NHCs continue to serve as a valuable resource for future generations will require the scientific community to increase their contribution to and acknowledgement of collections. We provide recommendations and guidelines for scientists to support NHCs, focusing particularly on new users that may be unfamiliar with collections. We hope that this perspective will motivate debate on the future of NHCs and the role of the scientific community in maintaining and improving biological collections.
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Affiliation(s)
- Sara E Miller
- Cornell University Department of Neurobiology and Behavior, Ithaca, New York
| | - Lisa N Barrow
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Sean M Ehlman
- Ecology, Evolution, and Behavior Department, University of Minnesota—Twin Cities, Saint Paul
| | - Jessica A Goodheart
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, in Santa Barbara, California
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
| | - Stephen E Greiman
- Department of Biology, Georgia Southern University, Statesboro Georgia
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Tracy M Misiewicz
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman
| | - Stephanie M Smith
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Urbana–Champaign, Champaign
| | - Christopher J Thawley
- Department of Biological Sciences, University of Rhode Island, Kingston
- Department of Mathematics and Sciences, Neumann University, Aston, Pennsylvania
| | - Joseph A Cook
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Jessica E Light
- Department of Ecology and Conservation Biology, Texas A&M University, College Station
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