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Francesconi L, Conti M, Gheza G, Martellos S, Nimis PL, Vallese C, Nascimbene J. The Dolichens database: the lichen biota of the Dolomites. MycoKeys 2024; 103:25-35. [PMID: 38505537 PMCID: PMC10948996 DOI: 10.3897/mycokeys.103.115462] [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: 11/09/2023] [Accepted: 01/04/2024] [Indexed: 03/21/2024] Open
Abstract
The Dolichens project provides the first dynamic inventory of the lichens of the Dolomites (Eastern Alps, Italy). Occurrence records were retrieved from published and grey literature, reviewed herbaria, unpublished records collected by the authors, and new sampling campaigns, covering a period from 1820 to 2022. Currently, the dataset contains 56,251 records, referring to 1,719 infrageneric taxa, reported from 1820 to 2022, from hilly to nival belts, and corresponding to about half of the species known for the whole Alpine chain. Amongst them, 98% are georeferenced, although most of them were georeferenced a posteriori. The dataset is available through the Global Biodiversity Information Facility (GBIF; https://www.gbif.org/es/dataset/cea3ee2c-1ff1-4f8e-bb37-a99600cb4134) and through the Dolichens website (https://italic.units.it/dolichens/). We expect that this open floristic inventory will contribute to tracking the lichen diversity of the Dolomites over the past 200 years, and providing the basis for future taxonomic, biogeographical, and ecological studies.
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Affiliation(s)
- Luana Francesconi
- BIOME Lab, Alma Mater Studiorum - University of Bologna, Bologna, ItalyAlma Mater Studiorum - University of BolognaBolognaItaly
| | - Matteo Conti
- Department Of Life Sciences, University of Trieste, Trieste, ItalyUniversity of TriesteTriesteItaly
| | - Gabriele Gheza
- BIOME Lab, Alma Mater Studiorum - University of Bologna, Bologna, ItalyAlma Mater Studiorum - University of BolognaBolognaItaly
| | - Stefano Martellos
- Department Of Life Sciences, University of Trieste, Trieste, ItalyUniversity of TriesteTriesteItaly
| | - Pier Luigi Nimis
- Department Of Life Sciences, University of Trieste, Trieste, ItalyUniversity of TriesteTriesteItaly
| | - Chiara Vallese
- Department Of Earth, Environmental and Life Sciences, University of Genova, Genova, ItalyUniversity of GenovaGenovaItaly
| | - Juri Nascimbene
- BIOME Lab, Alma Mater Studiorum - University of Bologna, Bologna, ItalyAlma Mater Studiorum - University of BolognaBolognaItaly
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Mandrioli M. From Dormant Collections to Repositories for the Study of Habitat Changes: The Importance of Herbaria in Modern Life Sciences. Life (Basel) 2023; 13:2310. [PMID: 38137911 PMCID: PMC10744909 DOI: 10.3390/life13122310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/25/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In recent decades, the advent of new technologies for massive and automatized digitization, together with the availability of new methods for DNA sequencing, strongly increased the interest and relevance of herbarium collections for the study of plant biodiversity and evolution. These new approaches prompted new projects aimed at the creation of a large dataset of molecular and phenological data. This review discusses new challenges and opportunities for herbaria in the context of the numerous national projects that are currently ongoing, prompting the study of herbarium specimens for the understanding of biodiversity loss and habitat shifts as a consequence of climate changes and habitat destruction due to human activities. With regard to this, the National Biodiversity Future Center (active in Italy since 2022) started a large-scale digitization project of the Herbarium Centrale Italicum in Florence (Italy), which is the most important Italian botanical collection, consisting of more than 4 million samples at present.
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Affiliation(s)
- Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 213/D, 41125 Modena, Italy
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Pezzini FF, Ferrari G, Forrest LL, Hart ML, Nishii K, Kidner CA. Target capture and genome skimming for plant diversity studies. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11537. [PMID: 37601316 PMCID: PMC10439825 DOI: 10.1002/aps3.11537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.
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Affiliation(s)
| | - Giada Ferrari
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | | | | | - Kanae Nishii
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | - Catherine A Kidner
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
- School of Biological Sciences University of Edinburgh Edinburgh United Kingdom
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Nizamani MM, Papeş M, Wang H, Harris AJ. How does spatial extent and environmental limits affect the accuracy of species richness estimates from ecological niche models? A case study with North American Pinaceae and Cactaceae. Ecol Evol 2023; 13:e10007. [PMID: 37091570 PMCID: PMC10121319 DOI: 10.1002/ece3.10007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Measuring species richness at varying spatial extents can be challenging, especially at large extents where exhaustive species surveys are difficult or impossible. Our work aimed at determining the reliability of species richness estimates from stacked ecological niche models at different spatial extents for taxonomic groups with vastly different environmental dependencies and interactions. To accomplish this, we generated ecological niche models for the species of Cactaceae and Pinaceae that occur within 180 published floras from North America north of Mexico. We overlaid or stacked the resulting species' potential distribution estimates over the bounding boxes representing each of the 180 floras to generate predictions of species richness. In general, our stacked models of Cactaceae and Pinaceae were poor predictors of species richness. The relationships between observed and predicted values improved noticeably with the size of spatial extents. However, the stacked models tended to overpredict the richness of Cactaceae and over- and underpredict the richness of Pinaceae. Cactaceae stacked models showed higher sensitivity and lower specificity than those for Pinaceae. We conclude that stacked ecological niche models may be somewhat poor predictors of species richness at smaller spatial extents and should be used with caution for this purpose. Perhaps more importantly, abilities to compensate for their limitations or apply corrections to their reliability may vary with taxonomic groups.
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Affiliation(s)
- Mir Muhammad Nizamani
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouChina
| | - Monica Papeş
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Hua‐Feng Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouChina
| | - AJ Harris
- South China Botanical Garden, Chinese Academy of ScienceGuangzhouChina
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Conti M, Nimis PL, Tretiach M, Muggia L, Moro A, Martellos S. The Italian lichens dataset from the TSB herbarium (University of Trieste). Biodivers Data J 2023; 11:e96466. [PMID: 38327327 PMCID: PMC10848505 DOI: 10.3897/bdj.11.e96466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Background The "Herbarium Universitatis Tergestinae" (TSB), with a total of ca. 50,000 specimens, includes the largest modern collection of lichens in Italy, with 25,796 samples collected from all over the country since 1984, representing 74% of all taxa known to occur in Italy. Almost all specimens have been georeferenced "a posteriori". The dataset is available through GBIF, as well as in ITALIC, the Information System of Italian Lichens. New information The TSB Herbarium hosts the largest modern lichen collection in Italy, with a total of ca. 50,000 specimens. This dataset contains all of the 25,796 specimens collected within the administrative borders of Italy. Amongst them, 98% are georeferenced and 87% have the date of collection. The dataset includes several type specimens (isotypes and holotypes) and exsiccata.
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Affiliation(s)
- Matteo Conti
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Pier Luigi Nimis
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Mauro Tretiach
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Lucia Muggia
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Andrea Moro
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Stefano Martellos
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
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Miller-Rushing AJ, Ellwood ER, Crimmins TM, Gallinat AS, Phillips M, Sandler RL, Primack RB. Conservation ethics in the time of the pandemic: Does increasing remote access advance social justice? BIOLOGICAL CONSERVATION 2022; 276:109788. [PMID: 36408461 PMCID: PMC9643013 DOI: 10.1016/j.biocon.2022.109788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
The COVID-19 pandemic is stimulating improvements in remote access and use of technology in conservation-related programs and research. In many cases, organizations have intended for remote engagement to benefit groups that have been marginalized in the sciences. But are they? It is important to consider how remote access affects social justice in conservation biology-i.e., the principle that all people should be equally respected and valued in conservation organizations, programs, projects, and practices. To support such consideration, we describe a typology of justice-oriented principles that can be used to examine social justice in a range of conservation activities. We apply this typology to three conservation areas: (1) remote access to US national park educational programs and data; (2) digitization of natural history specimens and their use in conservation research; and (3) remote engagement in conservation-oriented citizen science. We then address the questions: Which justice-oriented principles are salient in which conservation contexts or activities? How can those principles be best realized in those contexts or activities? In each of the three areas we examined, remote access increased participation, but access and benefits were not equally distributed and unanticipated consequences have not been adequately addressed. We identify steps that can and are being taken to advance social justice in conservation, such as assessing programs to determine if they are achieving their stated social justice-oriented aims and revising initiatives as needed. The framework that we present could be used to assess the social justice dimensions of many conservation programs, institutions, practices, and policies.
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Affiliation(s)
| | - Elizabeth R Ellwood
- iDigBio, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Natural History Museum of Los Angeles County, Los Angeles, CA, USA
| | - Theresa M Crimmins
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Amanda S Gallinat
- Department of Geography, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Molly Phillips
- iDigBio, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Ronald L Sandler
- Department of Philosophy and Religion, Northeastern University, Boston, MA, USA
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Teixeira‐Costa L, Heberling JM, Wilson CA, Davis CC. Parasitic flowering plant collections embody the extended specimen. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Luiza Teixeira‐Costa
- Harvard University Herbaria Cambridge MA USA
- Hanse‐Wissenschaftskolleg – Institute for Advanced Study, Lehmkuhlenbusch 4, 27753 Delmenhorst Germany
| | | | - Carol A. Wilson
- University and Jepson Herbaria University of California, Berkeley, 1001 Valley Life Sciences Building Berkeley CA USA
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Walker BE, Tucker A, Nicolson N. Harnessing Large-Scale Herbarium Image Datasets Through Representation Learning. FRONTIERS IN PLANT SCIENCE 2022; 12:806407. [PMID: 35095977 PMCID: PMC8794728 DOI: 10.3389/fpls.2021.806407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/06/2021] [Indexed: 05/10/2023]
Abstract
The mobilization of large-scale datasets of specimen images and metadata through herbarium digitization provide a rich environment for the application and development of machine learning techniques. However, limited access to computational resources and uneven progress in digitization, especially for small herbaria, still present barriers to the wide adoption of these new technologies. Using deep learning to extract representations of herbarium specimens useful for a wide variety of applications, so-called "representation learning," could help remove these barriers. Despite its recent popularity for camera trap and natural world images, representation learning is not yet as popular for herbarium specimen images. We investigated the potential of representation learning with specimen images by building three neural networks using a publicly available dataset of over 2 million specimen images spanning multiple continents and institutions. We compared the extracted representations and tested their performance in application tasks relevant to research carried out with herbarium specimens. We found a triplet network, a type of neural network that learns distances between images, produced representations that transferred the best across all applications investigated. Our results demonstrate that it is possible to learn representations of specimen images useful in different applications, and we identify some further steps that we believe are necessary for representation learning to harness the rich information held in the worlds' herbaria.
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Affiliation(s)
| | - Allan Tucker
- Department of Computer Science, Brunel University London, Uxbridge, United Kingdom
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9
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Monfils AK, Krimmel ER, Bates JM, Bauer JE, Belitz MW, Cahill BC, Caywood AM, Cobb NS, Colby JB, Ellis SA, Krejsa DM, Levine TD, Marsico TD, Mayfield-Meyer TJ, Miller-Camp JA, Nelson RM(G, Phillips MA, Revelez MA, Roberts DR, Singer RA, Zaspel JM. Regional Collections Are an Essential Component of Biodiversity Research Infrastructure. Bioscience 2020. [DOI: 10.1093/biosci/biaa102] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Anna K Monfils
- Department of Biology and the Institute for Great Lakes Research, Central Michigan University, Mount Pleasant
| | - Erica R Krimmel
- iDigBio, Institute for Digital Information and Scientific Communication, Florida State University, Tallahassee
| | - John M Bates
- Natural Science Collections Alliance and curator of birds and head of life sciences, Field Museum, in Chicago, Illinois
| | - Jennifer E Bauer
- Florida Museum of Natural History, University of Florida, Gainesville, and is currently, Museum of Paleontology, University of Michigan, Ann Arbor
| | - Michael W Belitz
- Florida Museum of Natural History, University of Florida, Gainesville
| | - Blake C Cahill
- Department of Biology and the Institute for Great Lakes Research, Central Michigan University, Mount Pleasant
| | - Alyssa M Caywood
- Department of Zoology, Milwaukee Public Museum, Milwaukee, Wisconsin
| | - Neil S Cobb
- Biodiversity Outreach Network, Phoenix, Arizona, and with Northern Arizona University, Flagstaff
| | - Julia B Colby
- Department of Zoology, Milwaukee Public Museum, Milwaukee, Wisconsin
| | - Shari A Ellis
- Florida Museum of Natural History, University of Florida, Gainesville
| | - Dianna M Krejsa
- Angelo State Natural History Collections, Angelo State University, San Angelo, Texas
| | - Todd D Levine
- Department of Life Sciences at Carroll University, Waukesha, Wisconsin
| | - Travis D Marsico
- Department of Biological Sciences, Arkansas State University, Jonesboro
| | | | - Jess A Miller-Camp
- Dept. of Earth and Atmospheric Sciencese, Indiana University, Bloomington
| | - Roy M (Gil) Nelson
- iDigBio, Florida Museum of Natural History, University of Florida, Gainesville
| | - Molly A Phillips
- iDigBio, Florida Museum of Natural History, University of Florida, Gainesville
| | - Marcia A Revelez
- Natural Science Research Laboratory, Texas Tech University, Lubbock
| | - Dawn R Roberts
- Chicago Academy of Sciences and the Peggy Notebaert Nature Museum, Chicago, Illinois
| | | | - Jennifer M Zaspel
- Natural Science Collections Alliance and is affiliated with the Department of Zoology, Milwaukee Public Museum, Milwaukee, Wisconsin
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