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Granroth J, Laakkonen J. Comparison of chemical and enzymatic maceration processes for soft tissue removal from arterial silicone casts on skull scaffolds. Anat Histol Embryol 2024; 53:e12981. [PMID: 37838942 DOI: 10.1111/ahe.12981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/06/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
The various models used in gross anatomical studies to improve the visualization of blood vessels differ in the amount of manual labour, cost, equipment and time involved. This study aimed to compare chemical and enzymatic maceration processes for soft-tissue removal from arterial silicone casts on skull scaffolds using ringed seal (Pusa hispida) skull specimens. Both processes produced specimens that covered all anatomical aspects required to visualize the intracranial arterial arrangement on a bone scaffold. Overall, the enzyme maceration process was better for production of such specimens, as this process is easy and safe to perform, is less harmful to the bony parts of the specimen, and the resulting specimens are visually more appealing for display and teaching. Compared with previously published models, the end result varied in the amount of dissolved bone tissue and the visual presentation of the model.
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Affiliation(s)
- Janne Granroth
- Finnish Museum of Natural History (Luomus), University of Helsinki, Helsinki, Finland
| | - Juha Laakkonen
- Faculty of Veterinary Medicine, Department of Veterinary Biosciences, Division of Veterinary Anatomy and Developmental Biology, University of Helsinki, Helsinki, Finland
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2
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Valenzuela-Toro AM, Costa DP, Mehta R, Pyenson ND, Koch PL. Unexpected decadal density-dependent shifts in California sea lion size, morphology, and foraging niche. Curr Biol 2023; 33:2111-2119.e4. [PMID: 37116482 DOI: 10.1016/j.cub.2023.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/20/2023] [Accepted: 04/13/2023] [Indexed: 04/30/2023]
Abstract
Many marine mammal populations are recovering after long eras of exploitation.1,2 To what degree density-dependent body size declines in recovering species reflect a general response to increased resource competition is unknown. We examined skull size (as a proxy for body size), skull morphology, and foraging dynamics of the top marine predator, the California sea lion (Zalophus californianus), which have been steadily increasing over the last few decades and have approached or reached their carrying capacity in southern California.3 We show that, contrary to predictions, male California sea lions increased rather than decreased their average body size over a 46-year (1962-2008) recovery period. Larger males had proportionally longer oral cavities and more powerful bite strength, and their foraging niche expanded. Females between 1983 and 2007 maintained stable skull dimensions, but their isotopic niche was broader than contemporary males. Increased male body size is compatible with an intensification of density-dependent sexual selection for larger and more competitive individuals concurrent with an expanding foraging niche. High foraging variability among females would explain their body size stability during decades of population recovery. We demonstrate that body size reduction is not the universal response to population recovery in marine mammals and show that selective ecological dynamics could contribute to protecting populations against the increased density-dependent intraspecific competition. However, prey shifts associated with climate change will likely prevent California sea lions (and other marine mammals) from attaining these ecological dynamics, augmenting their vulnerability to resource competition and diminishing their capacity to overcome it.
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Affiliation(s)
- Ana M Valenzuela-Toro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA; Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th Street NW and Constitution Avenue NW, Washington, DC 20560, USA.
| | - Daniel P Costa
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA; Institute of Marine Sciences, University of California, Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95064, USA
| | - Rita Mehta
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Nicholas D Pyenson
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th Street NW and Constitution Avenue NW, Washington, DC 20560, USA; Department of Paleontology and Geology, Burke Museum of Natural History and Culture, 4303 Memorial Way Northeast, Seattle, WA 98105, USA
| | - Paul L Koch
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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3
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Blair ME, Cao GTH, López-Nandam EH, Veronese-Paniagua DA, Birchette MG, Kenyon M, Md-Zain BM, Munds RA, Nekaris KAI, Nijman V, Roos C, Thach HM, Sterling EJ, Le MD. Molecular Phylogenetic Relationships and Unveiling Novel Genetic Diversity among Slow and Pygmy Lorises, including Resurrection of Xanthonycticebus intermedius. Genes (Basel) 2023; 14:643. [PMID: 36980915 PMCID: PMC10048081 DOI: 10.3390/genes14030643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Genetic analysis of historical museum collections presents an opportunity to clarify the evolutionary history of understudied primate groups, improve taxonomic inferences, and inform conservation efforts. Among the most understudied primate groups, slow and pygmy lorises (genera Nycticebus and Xanthonycticebus) are nocturnal strepsirrhines found in South and Southeast Asia. Previous molecular studies have supported five species, but studies using morphological data suggest the existence of at least nine species. We sequenced four mitochondrial loci, CO1, cytb, d-loop, and ND4, for a total of 3324 aligned characters per sample from 41 historical museum specimens for the most comprehensive geographic coverage to date for these genera. We then combined these sequences with a larger dataset composed of samples collected in Vietnam as well as previously published sequences (total sample size N = 62). We inferred phylogenetic relationships using Bayesian inference and maximum likelihood methods based on data from each locus and on concatenated sequences. We also inferred divergence dates for the most recent common ancestors of major lineages using a BEAST analysis. Consistent with previous studies, we found support for Xanthonycticebus pygmaeus as a basal taxon to the others in the group. We also confirmed the separation between lineages of X. pygmaeus from northern Vietnam/Laos/China and southern Vietnam/Cambodia and included a taxonomic revision recognizing a second taxon of pygmy loris, X. intermedius. Our results found support for multiple reciprocally monophyletic taxa within Borneo and possibly Java. The study will help inform conservation management of these trade-targeted animals as part of a genetic reference database for determining the taxonomic unit and provenance of slow and pygmy lorises confiscated from illegal wildlife trade activities.
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Affiliation(s)
- Mary E. Blair
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - Giang T. H. Cao
- Department of Genetics, Vietnam National University, Hanoi 10000, Vietnam
| | - Elora H. López-Nandam
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- Institute for Biodiversity and Sustainability Science, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Daniel A. Veronese-Paniagua
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- The Division of Biology & Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mark G. Birchette
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- Department of Biology, Long Island University Brooklyn, Brooklyn, NY 11201, USA
| | - Marina Kenyon
- Dao Tien Endangered Primate Species Centre, Dong Nai 76000, Vietnam
| | - Badrul M. Md-Zain
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi Selangor 43600, Malaysia
| | - Rachel A. Munds
- Department of Anthropology & Archeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - K. Anne-Isola Nekaris
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
- School of Social Sciences and Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Vincent Nijman
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
- School of Social Sciences and Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Hoàng M. Thach
- Department of Anthropology, Vietnam National University, Hanoi 10000, Vietnam
- Department of Geography & Human Ecology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Eleanor J. Sterling
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - Minh D. Le
- Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 10000, Vietnam
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Heino MT, Nyman T, Palo JU, Harmoinen J, Valtonen M, Pilot M, Översti S, Salmela E, Kunnasranta M, Väinölä R, Hoelzel AR, Aspi J. Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections. Ecol Evol 2023; 13:e9720. [PMID: 36699566 PMCID: PMC9849707 DOI: 10.1002/ece3.9720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/20/2023] Open
Abstract
The Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to postglacial bedrock rebound around 9000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. We sequenced sections of the mitochondrial control region from 60 up to 125-years-old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies and how it is phylogenetically related to other ringed seal populations from the Baltic Sea, Lake Ladoga, North America, Svalbard, and the White Sea. We observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation also shows affinities to North American ringed seals. Our results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seal is not representative of the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.
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Affiliation(s)
- Matti T. Heino
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland,Department of Forensic MedicineUniversity of HelsinkiHelsinkiFinland
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Jukka U. Palo
- Department of Forensic MedicineUniversity of HelsinkiHelsinkiFinland,Forensic Chemistry Unit/Forensic GeneticsFinnish Institute for Health and WelfareHelsinkiFinland
| | - Jenni Harmoinen
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland,Wildlife Ecology GroupNatural Resources Institute FinlandHelsinkiFinland
| | - Mia Valtonen
- Wildlife Ecology GroupNatural Resources Institute FinlandHelsinkiFinland,Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland,Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | - Małgorzata Pilot
- School of Biological and Biomedical SciencesDurham UniversityDurhamUK,Museum and Institute of ZoologyPolish Academy of SciencesGdańskPoland,Faculty of BiologyUniversity of GdańskGdańskPoland
| | - Sanni Översti
- Transmission, Infection, Diversification and Evolution GroupMax‐Planck Institute for the Science of Human HistoryJenaGermany,Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Elina Salmela
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland,Department of Biology, Faculty of ScienceUniversity of TurkuTurkuFinland
| | - Mervi Kunnasranta
- University of Eastern FinlandJoensuuFinland,Natural Resources Institute FinlandJoensuuFinland
| | - Risto Väinölä
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | | | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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5
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Wood CL, Welicky RL, Preisser WC, Leslie KL, Mastick N, Greene C, Maslenikov KP, Tornabene L, Kinsella JM, Essington TE. A reconstruction of parasite burden reveals one century of climate-associated parasite decline. Proc Natl Acad Sci U S A 2023; 120:e2211903120. [PMID: 36623180 DOI: 10.1073/pnas.2211903120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Long-term data allow ecologists to assess trajectories of population abundance. Without this context, it is impossible to know whether a taxon is thriving or declining to extinction. For parasites of wildlife, there are few long-term data-a gap that creates an impediment to managing parasite biodiversity and infectious threats in a changing world. We produced a century-scale time series of metazoan parasite abundance and used it to test whether parasitism is changing in Puget Sound, United States, and, if so, why. We performed parasitological dissection of fluid-preserved specimens held in natural history collections for eight fish species collected between 1880 and 2019. We found that parasite taxa using three or more obligately required host species-a group that comprised 52% of the parasite taxa we detected-declined in abundance at a rate of 10.9% per decade, whereas no change in abundance was detected for parasites using one or two obligately required host species. We tested several potential mechanisms for the decline in 3+-host parasites and found that parasite abundance was negatively correlated with sea surface temperature, diminishing at a rate of 38% for every 1 °C increase. Although the temperature effect was strong, it did not explain all variability in parasite burden, suggesting that other factors may also have contributed to the long-term declines we observed. These data document one century of climate-associated parasite decline in Puget Sound-a massive loss of biodiversity, undetected until now.
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Wood CL, Leslie KL, Claar D, Mastick N, Preisser W, Vanhove MPM, Welicky R. How to use natural history collections to resurrect information on historical parasite abundances. J Helminthol 2023; 97:e6. [PMID: 36633512 DOI: 10.1017/S0022149X2200075X] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many of the most contentious questions that concern the ecology of helminths could be resolved with data on helminth abundance over the past few decades or centuries, but unfortunately these data are rare. A new sub-discipline - the historical ecology of parasitism - is resurrecting long-term data on the abundance of parasites, an advancement facilitated by the use of biological natural history collections. Because the world's museums hold billions of suitable specimens collected over more than a century, these potential parasitological datasets are broad in scope and finely resolved in taxonomic, temporal and spatial dimensions. Here, we set out best practices for the extraction of parasitological information from natural history collections, including how to conceive of a project, how to select specimens, how to engage curators and receive permission for proposed projects, standard operating protocols for dissections and how to manage data. Our hope is that other helminthologists will use this paper as a reference to expand their own research programmes along the dimension of time.
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7
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Stuart KC, Sherwin WB, Edwards RJ, Rollins LA. Evolutionary genomics: Insights from the invasive European starlings. Front Genet 2023; 13:1010456. [PMID: 36685843 PMCID: PMC9845568 DOI: 10.3389/fgene.2022.1010456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/23/2022] [Indexed: 01/06/2023] Open
Abstract
Two fundamental questions for evolutionary studies are the speed at which evolution occurs, and the way that this evolution may present itself within an organism's genome. Evolutionary studies on invasive populations are poised to tackle some of these pressing questions, including understanding the mechanisms behind rapid adaptation, and how it facilitates population persistence within a novel environment. Investigation of these questions are assisted through recent developments in experimental, sequencing, and analytical protocols; in particular, the growing accessibility of next generation sequencing has enabled a broader range of taxa to be characterised. In this perspective, we discuss recent genetic findings within the invasive European starlings in Australia, and outline some critical next steps within this research system. Further, we use discoveries within this study system to guide discussion of pressing future research directions more generally within the fields of population and evolutionary genetics, including the use of historic specimens, phenotypic data, non-SNP genetic variants (e.g., structural variants), and pan-genomes. In particular, we emphasise the need for exploratory genomics studies across a range of invasive taxa so we can begin understanding broad mechanisms that underpin rapid adaptation in these systems. Understanding how genetic diversity arises and is maintained in a population, and how this contributes to adaptability, requires a deep understanding of how evolution functions at the molecular level, and is of fundamental importance for the future studies and preservation of biodiversity across the globe.
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Affiliation(s)
- Katarina C. Stuart
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia,*Correspondence: Katarina C. Stuart,
| | - William B. Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Richard J. Edwards
- Evolution & Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Lee A Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
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Moraitou M, Forsythe A, Fellows Yates JA, Brealey JC, Warinner C, Guschanski K. Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species. Mol Biol Evol 2022; 39:6874787. [PMID: 36472532 PMCID: PMC9778846 DOI: 10.1093/molbev/msac263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.
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Affiliation(s)
| | | | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany
| | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany,Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
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9
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Swank S, Elazegui E, Janidlo S, Sanger TJ, Bell MA, Stuart YE. Attempting genetic inference from directional asymmetry during convergent hindlimb reduction in squamates. Ecol Evol 2022; 12:e9088. [PMID: 35845359 PMCID: PMC9280442 DOI: 10.1002/ece3.9088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/22/2022] [Accepted: 06/14/2022] [Indexed: 11/06/2022] Open
Abstract
Loss and reduction in paired appendages are common in vertebrate evolution. How often does such convergent evolution depend on similar developmental and genetic pathways? For example, many populations of the threespine stickleback and ninespine stickleback (Gasterosteidae) have independently evolved pelvic reduction, usually based on independent mutations that caused reduced Pitx1 expression. Reduced Pitx1 expression has also been implicated in pelvic reduction in manatees. Thus, hindlimb reduction stemming from reduced Pitx1 expression has arisen independently in groups that diverged tens to hundreds of millions of years ago, suggesting a potential for repeated use of Pitx1 across vertebrates. Notably, hindlimb reduction based on the reduction in Pitx1 expression produces left-larger directional asymmetry in the vestiges. We used this phenotypic signature as a genetic proxy, testing for hindlimb directional asymmetry in six genera of squamate reptiles that independently evolved hindlimb reduction and for which genetic and developmental tools are not yet developed: Agamodon anguliceps, Bachia intermedia, Chalcides sepsoides, Indotyphlops braminus, Ophisaurus attenuatuas and O. ventralis, and Teius teyou. Significant asymmetry occurred in one taxon, Chalcides sepsoides, whose left-side pelvis and femur vestiges were 18% and 64% larger than right-side vestiges, respectively, suggesting modification in Pitx1 expression in that species. However, there was either right-larger asymmetry or no directional asymmetry in the other five taxa, suggesting multiple developmental genetic pathways to hindlimb reduction in squamates and the vertebrates more generally.
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Affiliation(s)
- Samantha Swank
- Department of Biology Loyola University Chicago Chicago Illinois USA.,Committee on Development, Regeneration, and Stem Cell Biology University of Chicago Chicago Illinois USA
| | - Ethan Elazegui
- Department of Biology Loyola University Chicago Chicago Illinois USA
| | - Sophia Janidlo
- Department of Biology Loyola University Chicago Chicago Illinois USA
| | - Thomas J Sanger
- Department of Biology Loyola University Chicago Chicago Illinois USA
| | - Michael A Bell
- UC Museum of Paleontology University of California Berkeley California USA
| | - Yoel E Stuart
- Department of Biology Loyola University Chicago Chicago Illinois USA
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10
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Straube N, Preick M, Naylor GJP, Hofreiter M. Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae). R Soc Open Sci 2021; 8:210474. [PMID: 34540250 PMCID: PMC8441122 DOI: 10.1098/rsos.210474] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy.
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Affiliation(s)
- Nicolas Straube
- Department of Natural History, University Museum of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Michaela Preick
- Evolutionary and Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Gavin J. P. Naylor
- Florida Museum of Natural History, University of Florida, Cultural Plaza, 3215 Hull Road, Gainesville, FL 32611-2710, USA
| | - Michael Hofreiter
- Evolutionary and Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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11
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Puckett EE, Murphy SM, Bradburd G. Phylogeographic analysis delimits three evolutionary significant units of least chipmunks in North America and identifies unique genetic diversity within the imperiled Peñasco population. Ecol Evol 2021; 11:12114-12128. [PMID: 34522364 PMCID: PMC8427584 DOI: 10.1002/ece3.7975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/10/2022] Open
Abstract
Although least chipmunks (Neotamias minimus) are a widely distributed North American species of least concern, the southernmost population, N. m. atristriatus (Peñasco least chipmunk), is imperiled and a candidate for federal listing as a subspecies. We conducted a phylogeographic analysis across the N. minimus range to assess genomic differentiation and distinctiveness of the N. m. atristriatus population. Additionally, we leveraged the historical component of sampling to conduct a temporal analysis of N. minimus genetic diversity and also considered climate change effects on range persistence probability by projecting a species distribution model into the IPCC5 RCP 2.6 and 8.5 scenarios. We identified three geographically structured groups (West, North, and South) that were supported by both mitochondrial and nuclear data. N. m. atristriatus grouped within a unique South subclade but were not reciprocally monophyletic from N. m. operarius, and nuclear genome analyses did not separate N. m. atristriatus, N. m. caryi, and N. m. operarius. Thus, while least chipmunks in the Southwest represent an evolutionary significant unit, subspecies distinctions were not supported and listing of the Peñasco population as a Distinct Population Segment of N. m. operarius may be warranted. Our results also support consideration of populations with North and West mitogenomes as two additional evolutionary significant units. We found that N. minimus genetic diversity declined by ~87% over the last century, and our models predicted substantial future habitat contraction, including the loss of the full contemporary ranges of N. m. atristriatus, N. m. arizonensis, and N. m. chuskaensis.
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Affiliation(s)
- Emily E. Puckett
- Department of Biological SciencesUniversity of MemphisMemphisTennesseeUSA
| | - Sean M. Murphy
- Wildlife Management DivisionNew Mexico Department of Game & FishSanta FeNew MexicoUSA
- Present address:
Department of Forestry and Natural ResourcesUniversity of KentuckyLexingtonKentuckyUSA
| | - Gideon Bradburd
- Department of Integrative BiologyEcology, Evolution, and Behavior GroupMichigan State UniversityEast LansingMichiganUSA
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López-Aliste M, Flores-Prado L, Ruz L, Sepúlveda Y, Rodríguez S, Saraiva AM, Fontúrbel FE. Wild bees of Chile: a database on taxonomy, sociality, and ecology. Ecology 2021; 102:e03377. [PMID: 33937987 DOI: 10.1002/ecy.3377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/26/2021] [Accepted: 03/16/2021] [Indexed: 11/11/2022]
Abstract
Bees are a diverse group of insects that have tremendous importance as pollinators. In recent decades, there has been a global decline in bee populations because of land-use change, intensive agriculture, and climate change. Unfortunately, our knowledge of native bees' ecology is rather scarce, and such knowledge gaps are also a major threat to its conservation. In this sense, biological collections are a priceless natural history legacy and an information source for new research and decision making. Chile has a remarkable bee diversity, with 464 species currently known from Chile and a high incidence of endemism and a variety of habitats (including the Mediterranean biodiversity hotspot). The largest wild bee collection in Chile is held at the Pontificia Universidad Católica de Valparaíso (comprising a century of data). This collection has been recently included in GBIF. Here we present a database with 36,010 records, including information on sociality and ecology (including information on floral visitation range, the resource collected, and nesting substrates) for 160 out of the 167 bee species included (36% of the Chilean bee diversity, including 49 genera and five families). All records have the taxonomy resolved, and 83% of them have geographic coordinates, covering a latitudinal range between 18° S and 53° S from the continental and insular territories. This data set is released for noncommercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA).
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Affiliation(s)
- Manuel López-Aliste
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Luis Flores-Prado
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
| | - Luisa Ruz
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Yanet Sepúlveda
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | | | | | - Francisco E Fontúrbel
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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Wood TJ, Ghisbain G, Rasmont P, Kleijn D, Raemakers I, Praz C, Killewald M, Gibbs J, Bobiwash K, Boustani M, Martinet B, Michez D. Global patterns in bumble bee pollen collection show phylogenetic conservation of diet. J Anim Ecol 2021; 90:2421-2430. [PMID: 34096055 DOI: 10.1111/1365-2656.13553] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/01/2021] [Indexed: 11/30/2022]
Abstract
Bumble bees (Bombus) are a group of eusocial bees with a strongly generalised feeding pattern, collecting pollen from many different botanical families. Though predominantly generalists, some bumble bee species seem to have restricted dietary choices. It is unclear whether restricted diets in bumble bees are inherent or a function of local conditions due to a lack of data for many species across different regions. The objective of this study was to determine whether bumble bee species displayed specific patterns of pollen collection, and whether patterns were influenced by phylogenetic relatedness or tongue length, a trait known to be associated with structuring floral visitation. Bumble bee pollen collection patterns were quantified from 4,132 pollen loads taken from 58 bumble bee species, representing 24% of the pollen-collecting diversity of this genus. Phylogenetic trait mapping showed a conserved pattern of dietary dissimilarity across species, but not for dietary breadth. Dietary dissimilarity was driven by collection of Fabaceae, with the most similar species collecting around 50%-60% of their diet from this botanical family. The proportion of the diet collected from Fabaceae also showed a conserved phylogenetic signal. Greater collection of Fabaceae was associated with longer tongue lengths, with shorter tongued species focusing on alternative botanical families. However, this result was largely driven by phylogenetic relatedness, not tongue length per se. These results demonstrate that, though generalists, bumble bees are still subject to dietary restrictions that constrain their foraging choices. These dietary constraints have implications for their persistence should their core resources decline in abundance.
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Affiliation(s)
- Thomas J Wood
- Laboratory of Zoology, University of Mons, Mons, Belgium
| | | | - Pierre Rasmont
- Laboratory of Zoology, University of Mons, Mons, Belgium
| | - David Kleijn
- Plant Ecology and Nature Conservation Group, Wageningen University, Wageningen, The Netherlands
| | - Ivo Raemakers
- Van Caldenborghstraat 26, Gronsveld, The Netherlands
| | - Christophe Praz
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.,InfoFauna, Swiss Zoological Records Centre, Neuchâtel, Switzerland
| | | | - Jason Gibbs
- Department of Entomology, University of Manitoba, Winnipeg, Canada
| | - Kyle Bobiwash
- Department of Entomology, University of Manitoba, Winnipeg, Canada
| | - Mira Boustani
- Laboratory of Zoology, University of Mons, Mons, Belgium
| | - Baptiste Martinet
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Denis Michez
- Laboratory of Zoology, University of Mons, Mons, Belgium
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14
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Alminas OSV, Heffelfinger JR, Statham MJ, Latch EK. Phylogeography of Cedros and Tiburón Island Mule Deer in North America's Desert Southwest. J Hered 2021; 112:260-275. [PMID: 33755178 DOI: 10.1093/jhered/esab013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/22/2021] [Indexed: 11/14/2022] Open
Abstract
Though mule deer (Odocoileus hemionus) persist in robust populations throughout most of their North American distribution, habitat loss, unregulated hunting, and other factors have reduced their historical range in México. Two of the 6 putative subspecies inhabiting México's deserts and Baja California peninsula are of conservation concern, occupying islands in the Pacific Ocean (Odocoileus hemionus cerrosensis on Cedros Island: endangered) and Sea of Cortés (Odocoileus hemionus sheldoni on Tiburón Island: threatened). Focusing on the desert southwest (n = 448), we sampled Tiburón (n = 22) and Cedros (n = 15) Island mule deer using contemporary samples and natural history museum specimens to complete a phylogeographic evaluation of the species complex, and assess the phylogeography of these insular subspecies. Both insular subspecies formed endemic haplotype lineages, consistent with island biogeographic theory. Bayesian skyline plots were consistent with Holocene demographic expansion. Cedros Island deer were genetically most similar to adjacent mainland Baja California deer, but exhibited a suite of unique haplotypes and reduced genetic variation. Tiburón Island deer haplotypes unexpectedly nested within a mainland lineage found in distant New Mexico, rather than the adjacent mainland Sonoran lineage. Such findings suggest the importance of postglacial climate fluctuations and biotic community turnover in the phylogeographic history of mule deer in the desert southwest. Our genetic data corroborates cultural, archaeological, and phenotypic evidence supporting Cedros and Tiburón deer endemicity and subspecies status. Reduced genetic variation, divergence from mainland populations, and demographic trends on both islands indicate that conservation, monitoring, and management are critical to ensure persistence of these endemic insular subspecies.
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Affiliation(s)
- Ona S V Alminas
- California Department of Fish and Wildlife, 715 P Street, Sacramento, CA.,the Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | | | - Mark J Statham
- the Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue/Old Davis Road, Davis, CA 95616-8744
| | - Emily K Latch
- the Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
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15
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Porter LM, de la Torre S, Pérez-Peña P, Cortés-Ortiz L. Taxonomic diversity of Cebuella in the western Amazon: Molecular, morphological and pelage diversity of museum and free-ranging specimens. Am J Phys Anthropol 2021; 175:251-267. [PMID: 33751563 DOI: 10.1002/ajpa.24266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/01/2021] [Accepted: 02/24/2021] [Indexed: 11/11/2022]
Abstract
OBJECTIVES We investigated the diversity of the pygmy marmoset, Cebuella pygmaea, by comparing genetic, morphological and pelage traits of animals from Peru and Ecuador. MATERIALS AND METHODS We extracted DNA from museum specimen osteocrusts and from fecal samples collected from free-ranging individuals. We sequenced the mtDNA cytochrome b gene and the control region from samples collected at 13 different sites and used Bayesian inference and Maximum Likelihood to identify distinct clades. We took measurements of the crania of a subset of these specimens (n = 26) and ran a logistic regression to determine if any of the cranial measurements (n = 22) could predict a specimen's clade. In addition, we examined the pelage patterns of the museum specimens and photographs taken of free-ranging individuals and divided them into pelage types based on coloration of the underbelly. RESULTS We identified two divergent clades, and two distinct groups with clear geographic boundaries within one of those clades. Two measurements of the zygomatic bone perfectly predicted a given individual's mtDNA clade. We found four distinct pelage patterns in our samples, but these patterns are variable within clades and among individuals within the same population. CONCLUSION These analyses indicate that the two recognized subspecies of pygmy marmoset should be elevated to the species level (C. pygmaea and C. niveiventris) based on molecular and cranial differences but not on pelage patterns. We provide evidence on the geographic limits of the two clades and identify regions where additional sampling is required to better define the geographic distribution of the two clades.
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Affiliation(s)
- Leila M Porter
- Department of Anthropology, Northern Illinois University, DeKalb, Illinois, USA
| | - Stella de la Torre
- School of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
| | - Pedro Pérez-Peña
- Instituto de Investigaciones de la Amazonía Peruana, Iquitos, Peru
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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16
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Benham PM, Bowie RCK. The influence of spatially heterogeneous anthropogenic change on bill size evolution in a coastal songbird. Evol Appl 2021; 14:607-624. [PMID: 33664798 PMCID: PMC7896719 DOI: 10.1111/eva.13144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 12/25/2022] Open
Abstract
Natural history collections provide an unparalleled resource for documenting population responses to past anthropogenic change. However, in many cases, traits measured on specimens may vary temporally in response to a number of different anthropogenic pressures or demographic processes. While teasing apart these different drivers is challenging, approaches that integrate analyses of spatial and temporal series of specimens can provide a robust framework for examining whether traits exhibit common responses to ecological variation in space and time. We applied this approach to analyze bill morphology variation in California Savannah Sparrows (Passerculus sandwichensis). We found that bill surface area increased in birds from higher salinity tidal marshes that are hotter and drier. Only the coastal subspecies, alaudinus, exhibited a significant increase in bill size through time. As with patterns of spatial variation, alaudinus populations occupying higher salinity tidal marshes that have become warmer and drier over the past century exhibited the greatest increases in bill surface area. We also found a significant negative correlation between bill surface area and total evaporative water loss (TEWL) and estimated that observed increases in bill size could result in a reduction of up to 16.2% in daily water losses. Together, these patterns of spatial and temporal variation in bill size were consistent with the hypothesis that larger bills are favored in freshwater-limited environments as a mechanism of dissipating heat, reducing reliance on evaporative cooling, and increasing water conservation. With museum collections increasingly being leveraged to understand past responses to global change, this work highlights the importance of considering the influence of many different axes of anthropogenic change and of integrating spatial and temporal analyses to better understand the influence of specific human impacts on population change over time.
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Affiliation(s)
- Phred M. Benham
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeley, BerkeleyCAUSA
| | - Rauri C. K. Bowie
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeley, BerkeleyCAUSA
- Department of Integrative BiologyUniversity of CaliforniaBerkeley, BerkeleyCAUSA
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17
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Ocampo D, Borja-Acosta KG, Lozano-Flórez J, Cifuentes-Acevedo S, Arbeláez-Cortés E, Bayly NJ, Caguazango Á, Coral-Jaramillo B, Cueva D, Forero F, Gómez JP, Gómez C, Loaiza-Muñoz MA, Londoño GA, Losada-Prado S, Pérez-Peña S, Ramírez-Chaves HE, Rodríguez-Posada ME, Sanabria-Mejía J, Sánchez-Martínez M, Serrano-Cardozo VH, Sierra-Buitrago MS, Soto-Patiño J, Acevedo-Charry O. Body mass data set for 1,317 bird and 270 mammal species from Colombia. Ecology 2020; 102:e03273. [PMID: 33368188 DOI: 10.1002/ecy.3273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/05/2020] [Accepted: 10/30/2020] [Indexed: 11/09/2022]
Abstract
Body mass is one of the most important phenotypic attributes in animal ecology and life history. This trait is widely used in the fields of ecology and macroevolution, since it influences physiology, morphological functions, and a myriad of ecological and social interactions. In this data set, our aim was to gather a comprehensive bird and mammal body mass data set from northern South America. We report body mass, discriminated by sex, for 42,022 individual birds and 7,441 mammals representing 1,317 bird species (69% of Colombia's avifauna) and 270 mammal species (51% of Colombian mammals) from the Neotropics. The data were sourced from vouchers collected between 1942 and 2020 and from individuals captured and released at banding stations over the last two decades for birds (2000-2020) and the last decade for mammals (2010-2020), by 10 research groups and institutions in Colombia. This data set fills gaps identified in other similar databases, as it focuses on northern South America, a highly diverse Neotropical region often underrepresented in morphological data sets. We provide wide taxonomic coverage for studies interested in information both at regional and local scales. There are no copyright restrictions; the present data paper should be appropriately cited when data are used for publication. The authors would appreciate learning about research projects, teaching exercises, and other uses given to this data set and are open to contribute in further collaborations using these data.
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Affiliation(s)
- David Ocampo
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia
| | - Kevin G Borja-Acosta
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia
| | - Julián Lozano-Flórez
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia
| | - Sebastián Cifuentes-Acevedo
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia.,Colección de Teriológica, Universidad de Antioquia, Cl. 67 ##53-108, Medellín, Antioquia, Colombia
| | - Enrique Arbeláez-Cortés
- Colección de Ornitología, Grupo de Estudios en Biodiversidad, Escuela de Biología, Universidad Industrial de Santander, Cl. 9 #Cra 27, Bucaramanga, Santander, Colombia
| | - Nicholas J Bayly
- SELVA: Investigación para la Conservación en el Neotrópico, Dg. 42a #20 - 37, Bogotá, D.C., Colombia
| | - Ángela Caguazango
- SELVA: Investigación para la Conservación en el Neotrópico, Dg. 42a #20 - 37, Bogotá, D.C., Colombia
| | - Brayan Coral-Jaramillo
- Jardín Botánico Tabanok and Grupo de Observadores de Aves del Valle de Sibundoy, Calle 16 # 19-24, Sibundoy, Putumayo, Colombia
| | - Diego Cueva
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia
| | - Fernando Forero
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia.,Reserva Natural Los Yátaros, Gachantiva, Boyacá, Colombia
| | - Juan P Gómez
- Departamento de Química y Biología, Universidad del Norte, Km 5 Vía Puerto Colombia, Barranquilla, Atlántico, Colombia
| | - Camila Gómez
- SELVA: Investigación para la Conservación en el Neotrópico, Dg. 42a #20 - 37, Bogotá, D.C., Colombia.,Cornell Lab of Ornithology, 159 Sapsucker Woods Rd, Ithaca, New York, USA
| | - Mario A Loaiza-Muñoz
- Departamento de Ciencias Biológicas, Universidad ICESI, Cl. 18 #122-135, Cali, Valle del Cauca, Colombia
| | - Gustavo A Londoño
- Departamento de Ciencias Biológicas, Universidad ICESI, Cl. 18 #122-135, Cali, Valle del Cauca, Colombia
| | - Sergio Losada-Prado
- Grupo de Investigación en Zoología, Facultad de Ciencias, Universidad del Tolima, Cl. 42 # 1b-1, Ibagué, Tolima, Colombia
| | - Sebastián Pérez-Peña
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia
| | - Héctor E Ramírez-Chaves
- Departamento de Ciencias Biológicas and Centro de Museos, Museo de Historia Natural, Universidad de Caldas, Calle 65 # 26-10, Manizales, Caldas, Colombia
| | - Miguel E Rodríguez-Posada
- Fundación Reserva Natural La Palmita, Centro de Investigación, Grupo de investigaciones territoriales para el uso y conservación de la biodiversidad, Cra. 4 ## 58-59, Bogotá, D. C., Colombia
| | - Jeyson Sanabria-Mejía
- SELVA: Investigación para la Conservación en el Neotrópico, Dg. 42a #20 - 37, Bogotá, D.C., Colombia
| | - Manuel Sánchez-Martínez
- Departamento de Ciencias Biológicas, Universidad ICESI, Cl. 18 #122-135, Cali, Valle del Cauca, Colombia
| | - Víctor Hugo Serrano-Cardozo
- Colección de Mastozoología y Laboratorio de Ecología, Grupo de Estudios en Biodiversidad, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - M Socorro Sierra-Buitrago
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia
| | - Juliana Soto-Patiño
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia
| | - Orlando Acevedo-Charry
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Carrera 8 No. 15-08, Villa de Leyva, Boyacá, Colombia.,Asociación Colombiana de Ornitología, Bogotá, D.C., Colombia
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Kelemen EP, Rehan SM. Opposing pressures of climate and land-use change on a native bee. Glob Chang Biol 2020; 27:1017-1026. [PMID: 33274535 DOI: 10.1111/gcb.15468] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023]
Abstract
Anthropogenic activities are rapidly changing the environment, and species that do not respond face a higher risk of extinction. Species may respond to environmental changes by modifying their behaviors, shifting their distributions, or changing their morphology. Recent morphological responses are often measured by changes in body size. Changes in body size are often attributed to climate change, but may instead be due to differences in available resources associated with changes in local land-use. The effects of temperature and land-use can be uncoupled in populations of the small carpenter bee Ceratina calcarata, which have experienced changes in agricultural and urban cover independent of climate change. We studied how the morphology of this bee has changed over the past 118 years (1902-2019) in relation to climate change and the past 45 years (1974-2019) in relation to agricultural and urban cover. Over this time, summer temperatures increased. We found that male and female size decreased with increasing temperature. Male size also decreased with agricultural expansion. Female size, however, increased with agricultural expansion. These results suggest that rising temperatures correlate with a decrease in female body size, while, opposite to predicted, agricultural land-use may select for increased female body size. These opposing pressures act concurrently and may result in bee extirpation from agricultural habitats if selection for large sizes is unsustainable as temperatures continue to increase. Furthermore, this study emphasizes the need to consider multiple environmental stressors when examining the effects of climate change due to their interactions.
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Affiliation(s)
- Evan P Kelemen
- Department of Biology, York University, Toronto, ON, Canada
| | - Sandra M Rehan
- Department of Biology, York University, Toronto, ON, Canada
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19
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Potash AD, Greene DU, Foursa GA, Mathis VL, Conner LM, McCleery RA. A comparison of animal color measurements using a commercially available digital color sensor and photograph analysis. Curr Zool 2020; 66:601-606. [PMID: 33391358 PMCID: PMC7769579 DOI: 10.1093/cz/zoaa016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/21/2020] [Indexed: 11/14/2022] Open
Abstract
An animal's pelage, feather, or skin color can serve a variety of functions, so it is important to have multiple standardized methods for measuring color. One of the most common and reliable methods for measuring animal coloration is the use of standardized digital photographs of animals. New technology in the form of a commercially available handheld digital color sensor could provide an alternative to photography-based animal color measurements. To determine whether a digital color sensor could be used to measure animal coloration, we tested the ability of a digital color sensor to measure coloration of mammalian, avian, and lepidopteran museums specimens. We compared results from the sensor to measurements taken using traditional photography methods. Our study yielded significant differences between photography-based and digital color sensor measurements of brightness (light to dark) and colors along the green to red spectrum. There was no difference between photographs and the digital color sensor measurements for colors along the blue to yellow spectrum. The average difference in recorded color (ΔE) by the 2 methods was above the threshold at which humans can perceive a difference. There were significant correlations between the sensor and photographs for all measurements indicating that the sensor is an effective animal coloration measuring tool. However, the sensor's small aperture and narrow light spectrum range designed for human-vision limit its value for ecological research. We discuss the conditions in which a digital color sensor can be an effective tool for measuring animal coloration in both laboratory settings and in the field.
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Affiliation(s)
- Alex D Potash
- Department of Wildlife Ecology and Conservation, University of Florida Institute of Food and Agricultural Science, Gainesville, FL 32611, USA
| | - Daniel U Greene
- Weyerhaeuser Company, Environmental Research South, Columbus, MS 39701, USA
| | - Gabrielle A Foursa
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Verity L Mathis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Robert A McCleery
- Department of Wildlife Ecology and Conservation, University of Florida Institute of Food and Agricultural Science, Gainesville, FL 32611, USA
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20
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Ferrari G, Neukamm J, Baalsrud HT, Breidenstein AM, Ravinet M, Phillips C, Rühli F, Bouwman A, Schuenemann VJ. Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190572. [PMID: 33012235 PMCID: PMC7702794 DOI: 10.1098/rstb.2019.0572] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2020] [Indexed: 12/15/2022] Open
Abstract
Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Helle T. Baalsrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
| | - Abagail M. Breidenstein
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Carina Phillips
- The Royal College of Surgeons of England, 35-43 Lincoln's Inn Fields, London WC2A 3PE, UK
| | - Frank Rühli
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Abigail Bouwman
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Verena J. Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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21
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Shin Y, Jang Y, Allain SJR, Borzée A. Catalogue of herpetological specimens of the Ewha Womans University Natural History Museum (EWNHM), Republic of Korea. Zookeys 2020; 965:103-139. [PMID: 32973383 PMCID: PMC7483326 DOI: 10.3897/zookeys.965.52976] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/16/2020] [Indexed: 11/25/2022] Open
Abstract
The herpetology collection of the Ewha Womans University Natural History Museum (EWNHM) represents one of the oldest and largest institutional collections in the Republic of Korea. The specimens deposited in the EWNHM represent a major historical collection of the native herpetofauna, both in species diversity and time span. However, the full inventory of the herpetology collection has never been conducted and thus the collection has received little attention from researchers. Here, the first full account of the herpetology specimens held at the EWNHM is provided, with voucher information for all documented specimens to make the collection accessible for future studies.
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Affiliation(s)
- Yucheol Shin
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China.,Division of EcoScience and Department of Life Sciences, Ewha Womans University, Seoul 03760, South Korea Ewha Womans University Seoul South Korea.,Department of Biological Sciences, College of Natural Science, Kangwon National University, Chuncheon 24341, South Korea Kangwon National University Chuncheon South Korea
| | - Yikweon Jang
- Division of EcoScience and Department of Life Sciences, Ewha Womans University, Seoul 03760, South Korea Ewha Womans University Seoul South Korea
| | - Steven J R Allain
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, United Kingdom University of Kent Canterbury United Kingdom
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
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22
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Catarino D, Jakobsen K, Jakobsen J, Giacomello E, Menezes GM, Diogo H, Canha Â, Porteiro FM, Melo O, Stefanni S. First record of the opal chimaera, Chimaera opalescens (Holocephali: Chimaeridae) and revision of the occurrence of the rabbitfish Chimaera monstrosa in the Azores waters. J Fish Biol 2020; 97:763-775. [PMID: 32520391 DOI: 10.1111/jfb.14432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
The presence of the opal chimaera, Chimaera opalescens, is reported for the first time in the deep waters of the Azores, with the capture of four specimens by fishermen and the video recording of an additional five individuals. Species identification was supported by the 646 bp sequenced fragment of the mitochondrial gene cytochrome oxidase subunit I. Because C. opalescens is a recently recognised species that had been recurrently misidentified as rabbitfish, Chimaera monstrosa, the historical data of C. monstrosa in the Azores were reviewed to assess the possible presence of both Chimaera species in the region. Although several authors have reported the occurrence of C. monstrosa in the Azorean waters since the 1800s, the majority of these are based on only three specimens caught during the late 1800s. The investigation performed using literature and examination of the museum specimens still available concluded that the most likely scenario is that C. monstrosa is absent from the Azores and past records of that species in the region are most likely misidentifications of C. opalescens.
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Affiliation(s)
- Diana Catarino
- MARE, Marine and Environmental Sciences Centre, Horta, Portugal
- OKEANOS Centre, University of the Azores, Horta, Portugal
- IMAR-Instituto do Mar, Horta, Portugal
- Department of Natural Sciences, Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | | | | | - Eva Giacomello
- MARE, Marine and Environmental Sciences Centre, Horta, Portugal
- OKEANOS Centre, University of the Azores, Horta, Portugal
- IMAR-Instituto do Mar, Horta, Portugal
| | - Gui M Menezes
- Regional Directorate of Fisheries, Secretariat of Sea, Science and Technology, Azores Regional Government, Horta, Portugal
- Department of Oceanography and Fisheries (DOP), University of the Azores, Horta, Portugal
| | - Hugo Diogo
- OKEANOS Centre, University of the Azores, Horta, Portugal
- Regional Directorate of Fisheries, Secretariat of Sea, Science and Technology, Azores Regional Government, Horta, Portugal
| | - Ângela Canha
- OKEANOS Centre, University of the Azores, Horta, Portugal
- Regional Directorate of Fisheries, Secretariat of Sea, Science and Technology, Azores Regional Government, Horta, Portugal
| | - Filipe M Porteiro
- Department of Oceanography and Fisheries (DOP), University of the Azores, Horta, Portugal
- Regional Directorate of Sea Affairs, Secretariat of Sea, Science and Technology, Azores Regional Government, Horta, Portugal
| | - Octávio Melo
- OKEANOS Centre, University of the Azores, Horta, Portugal
- IMAR-Instituto do Mar, Horta, Portugal
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23
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McElroy K, Black A, Dolman G, Horton P, Pedler L, Campbell CD, Drew A, Joseph L. Robbery in progress: Historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the Copperback Quail-thrush Cinclosoma clarum. Ecol Evol 2020; 10:6785-6793. [PMID: 32724551 PMCID: PMC7381587 DOI: 10.1002/ece3.6403] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 01/01/2023] Open
Abstract
We surveyed mitochondrial, autosomal, and Z chromosome diversity within and between the Copperback Quail-thrush Cinclosoma clarum and Chestnut Quail-thrush C. castanotum, which together span the arid and semi-arid zones of southern Australia, and primarily from specimens held in museum collections. We affirm the recent taxonomic separation of the two species and then focus on diversity within the more widespread of the two species, C. clarum. To guide further study of the system and what it offers to understanding the genomics of the differentiation and speciation processes, we develop and present a hypothesis to explain mitonuclear discordance that emerged in ourdata. Following a period of historical allopatry, secondary contact has resulted in an eastern mitochondrial genome replacing the western mitochondrial genome in western populations. This is predicted under a population-level invasion in the opposite direction, that of the western population invading the range of the eastern one. Mitochondrial captures can be driven by neutral, demographic processes, or adaptive mechanisms, and we favor the hypothesized capture being driven by neutral means. We cannot fully reject the adaptive process but suggest how these alternatives may be further tested. We acknowledge an alternative hypothesis, which finds some support in phenotypic data published elsewhere, namely that outcomes of secondary contact have been more complex than our current genomic data suggest. Discriminating and reconciling these two alternative hypotheses, which may not be mutually exclusive, could be tested with closer sampling at levels of population, individual, and nucleotide than has so far been possible. This would be further aided by knowledge of the genetic basis to phenotypic variation described elsewhere.
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Affiliation(s)
- Kerensa McElroy
- Australian National Wildlife CollectionCSIRO National Research Collections AustraliaCanberraACTAustralia
| | | | - Gaynor Dolman
- Molecular Systematics UnitWestern Australian MuseumWAAustralia
- University of AdelaideAdelaideSAAustralia
| | | | - Lynn Pedler
- South Australian MuseumAdelaideSAAustralia
- KoolungaSAAustralia
| | - Catriona D. Campbell
- Australian National Wildlife CollectionCSIRO National Research Collections AustraliaCanberraACTAustralia
| | - Alex Drew
- Australian National Wildlife CollectionCSIRO National Research Collections AustraliaCanberraACTAustralia
| | - Leo Joseph
- Australian National Wildlife CollectionCSIRO National Research Collections AustraliaCanberraACTAustralia
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24
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Cardona-Salazar LJ, Benavides-Ossa YA, Vargas-Daza ÁM, Betancurt-Grisales JF, Bohada-Murillo M, Martínez-Sánchez ET, Cardona-Romero M, Busi A, Tobón-Escobar WD, Ortíz-Giraldo M, Gómez Castillo D, Alvarez-Londoño J, Molina-Marin DA, Rodas-Rua JC, Grisales-Muñoz LD, Velásquez-Trujillo V, Salazar-Ramírez LF, Pineda-Gómez DM, Hoyos-Jaramillo A, Santisteban-Arenas RR, Salazar-Ramírez JG, Orozco-Montoya GP, Ramos-Valencia SA, Gómez-Londoño G, Ospina-Bautista F, Estévez-Varón JV, Ossa-López PA, Rivera-Páez FA, Pérez Cárdenas JE, Fontúrbel FE, Castaño-Villa GJ. A morphological, reproductive, and molt phenology database for 379 bird species from the Colombian Tropical Andes. Ecology 2020; 101:e03016. [PMID: 32083734 DOI: 10.1002/ecy.3016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/07/2020] [Accepted: 01/29/2020] [Indexed: 11/12/2022]
Abstract
The Colombian Tropical Andes are one of the regions with highest bird diversity on Earth. However, information on bird morphology, reproductive phenology, and molt is particularly scarce in this region. Also, this region is heavily impacted by deforestation, and it is vulnerable to climate change. Hence, providing baseline information on life history and morphological traits will be essential to support future research on functional diversity, climate change effects, conservation, evolution, and phenology. To fill this gap, we have compiled information on bird distribution, morphology, molt, and reproductive phenology at 52 localities of the Department of Caldas, covering an elevation range between 148 and 3845 m. This compilation comprises a wide range of habitats, including native forests, forestry plantations, croplands, and paramo. Our database presents information for 3,398 records belonging to 379 bird species (representing 23 orders, 53 families, and 258 genera). From those records, 2,843 correspond to information collected in the field between 2008 and 2019, and the remaining 555 records correspond to specimens deposited in the Natural History Museum of the Caldas University, collected between 1969 and 2014. We measured nine morphological traits from all specimens: total culmen, gape, bill width, bill depth, tarsus, wing length, tail length, total length, and mass. We also have reproductive condition information for 257 species and molt information available for 378 species. The information contained in this data set represents ~20% of the Colombian avifauna and ~11% of the bird species richness in South America. This data set is released for non-commercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA).
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Affiliation(s)
- Leydy J Cardona-Salazar
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia
| | - Yeny A Benavides-Ossa
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia
| | - Ángela M Vargas-Daza
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia
| | | | - Mauricio Bohada-Murillo
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia
| | - Estefani T Martínez-Sánchez
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia
| | - Marelid Cardona-Romero
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia
| | - Ana Busi
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia
| | - William D Tobón-Escobar
- Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia
| | - Mateo Ortíz-Giraldo
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia
| | - Daniela Gómez Castillo
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia
| | - Johnathan Alvarez-Londoño
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia
| | - Dimas A Molina-Marin
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia
| | - Juan C Rodas-Rua
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia
| | - Laura D Grisales-Muñoz
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia
| | | | - Luisa F Salazar-Ramírez
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia
| | - Diana M Pineda-Gómez
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia
| | | | | | - Juan G Salazar-Ramírez
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia
| | | | | | - Germán Gómez-Londoño
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Departamento de Producción Agropecuaria, Facultad de Ciencias Agropecuarias, Universidad de Caldas, Manizales, Colombia
| | - Fabiola Ospina-Bautista
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Jaime V Estévez-Varón
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Paula A Ossa-López
- Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia.,Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Fredy A Rivera-Páez
- Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia.,Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Jorge E Pérez Cárdenas
- Grupo de Investigación Biosalud, Universidad de Caldas, Manizales, Colombia.,Departamento de Ciencias Básicas para la Salud, Facultad de Ciencias para la Salud, Universidad de Caldas, Manizales, Colombia
| | - Francisco E Fontúrbel
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Gabriel J Castaño-Villa
- Grupo de Investigación en Ecosistemas Tropicales, Universidad de Caldas, Manizales, Colombia.,Genética, Biodiversidad y Manejo de Ecosistemas-GEBIOME, Universidad de Caldas, Manizales, Colombia.,Departamento de Desarrollo Rural y Recursos Naturales, Facultad de Ciencias Agropecuarias, Universidad de Caldas, Manizales, Colombia
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25
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Scott MF, Botigué LR, Brace S, Stevens CJ, Mullin VE, Stevenson A, Thomas MG, Fuller DQ, Mott R. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Nat Plants 2019; 5:1120-1128. [PMID: 31685951 PMCID: PMC6858886 DOI: 10.1038/s41477-019-0534-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/22/2019] [Indexed: 05/05/2023]
Abstract
Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.
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Affiliation(s)
- Michael F Scott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Laura R Botigué
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris J Stevens
- Institute of Archaeology, University College London, London, UK
| | | | - Alice Stevenson
- Institute of Archaeology, University College London, London, UK
| | - Mark G Thomas
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Dorian Q Fuller
- Institute of Archaeology, University College London, London, UK
| | - Richard Mott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
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26
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Cooper N, Bond AL, Davis JL, Portela Miguez R, Tomsett L, Helgen KM. Sex biases in bird and mammal natural history collections. Proc Biol Sci 2019; 286:20192025. [PMID: 31640514 PMCID: PMC6834056 DOI: 10.1098/rspb.2019.2025] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/30/2019] [Indexed: 01/18/2023] Open
Abstract
Natural history specimens are widely used across ecology, evolutionary biology and conservation. Although biological sex may influence all of these areas, it is often overlooked in large-scale studies using museum specimens. If collections are biased towards one sex, studies may not be representative of the species. Here, we investigate sex ratios in over two million bird and mammal specimen records from five large international museums. We found a slight bias towards males in birds (40% females) and mammals (48% females), but this varied among orders. The proportion of female specimens has not significantly changed in 130 years, but has decreased in species with showy male traits like colourful plumage and horns. Body size had little effect. Male bias was strongest in name-bearing types; only 27% of bird and 39% of mammal types were female. These results imply that previous studies may be impacted by undetected male bias, and vigilance is required when using specimen data, collecting new specimens and designating types.
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Affiliation(s)
- Natalie Cooper
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alexander L. Bond
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Bird Group, Department of Life Sciences, Natural History Museum, Akeman Street, Tring, Hertfordshire, HP23 6AP, UK
| | - Joshua L. Davis
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Roberto Portela Miguez
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Mammal Group, Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Louise Tomsett
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Mammal Group, Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Kristofer M. Helgen
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Mammal Group, Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
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27
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Ewart KM, Johnson RN, Ogden R, Joseph L, Frankham GJ, Lo N. Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species. Mol Ecol Resour 2019; 19:1578-1592. [PMID: 31484222 DOI: 10.1111/1755-0998.13082] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq™ ). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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28
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Schmitt CJ, Cook JA, Zamudio KR, Edwards SV. Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170387. [PMID: 30455205 PMCID: PMC6282080 DOI: 10.1098/rstb.2017.0387] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 11/12/2022] Open
Abstract
Natural history museums and the specimen collections they curate are vital scientific infrastructure, a fact as true today as it was when biologists began collecting and preserving specimens over 200 years ago. The importance of museum specimens in studies of taxonomy, systematics, ecology and evolutionary biology is evidenced by a rich and abundant literature, yet creative and novel uses of specimens are constantly broadening the impact of natural history collections on biodiversity science and global sustainability. Excellent examples of the critical importance of specimens come from their use in documenting the consequences of environmental change, which is particularly relevant considering the alarming rate at which we now modify our planet in the Anthropocene. In this review, we highlight the important role of bird, mammal and amphibian specimens in documenting the Anthropocene and provide examples that underscore the need for continued collection of museum specimens.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- C Jonathan Schmitt
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joseph A Cook
- Museum of Southwestern Biology & Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
| | - Kelly R Zamudio
- Museum of Vertebrates and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Scott V Edwards
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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29
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Chatfield-Taylor W, Cole JA. Living rain gauges: cumulative precipitation explains the emergence schedules of California protoperiodical cicadas. Ecology 2018; 98:2521-2527. [PMID: 28779534 DOI: 10.1002/ecy.1980] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 11/06/2022]
Abstract
Mass multi-species cicada emergences (broods) occur in California with variable periodicity. Here we present the first rule set that predicts the emergence of protoperiodical cicada communities. We tested two hypotheses with a dataset consisting of direct observations and georeferenced museum specimen records: first, that cicada broods are triggered to emerge by periodic ENSO events and second, that brood emergences occur after precipitation accumulates above a threshold value. The period of ENSO events does not explain the observed pattern of cicada brood emergence. Rather, broods emerged given two conditions: (1) that total precipitation exceeded a threshold of 1,181 mm, and (2) that a minimum 3-yr period lapsed. The precipitation threshold is obeyed over an 800 km north-south distance in California and across a variety of habitats. We predict the next brood emergence at one study site in arid Los Angeles County desert foothills to occur in 2020 or, if drought conditions continue, in 2021.
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Affiliation(s)
| | - Jeffrey A Cole
- Natural Sciences Division, Pasadena City College, 1570 East Colorado Boulevard, Pasadena, California, 91106, USA.,Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California, 90007, USA
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30
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Kingston AK. Longitudinal study of rat volar fat pad fixation and ethanol storage: implications for the use of fluid-preserved specimens in morphological studies. J Anat 2018; 233:607-617. [PMID: 30155995 DOI: 10.1111/joa.12875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2018] [Indexed: 11/29/2022] Open
Abstract
Museum fluid collections preserve important biological specimens for study. Tissues are often fixed in 10% buffered formalin to halt metabolic activities and transferred to a solution of ethanol for long-term storage. This process, however, forces water from the tissues and has been shown to alter the morphology of preserved specimens in ways that may influence the biological interpretation of results. The degree to which fluid preservation alters morphology is linked to multiple biological factors, such as tissue size and composition, and should therefore be examined prior to functional analysis. This study is undertaken as part of a more inclusive examination of mammalian volar morphology. A sample of five adult male and five adult female rats (Rattus norvegicus) was utilized to evaluate longitudinal changes in the dimensions of the volar pads across fixation in 10% buffered formalin and preservation in 70% ethanol for 1 year. No significant changes to the measured dimensions of the rat volar pads were present across stages of fixation and preservation, and no significant interactions of specimen size or sex were noted. These findings indicate that small mammalian volar pads that have been fixed in 10% buffered formalin and stored in 70% ethanol are appropriate for morphological study using the measurements described here without corrective algorithms. This finding is rare among preservation studies but highlights the variability of tissue behavior during chemical preservation and the necessity of preliminary investigations of preservation artifacts. Concurrence here between the preserved and unpreserved samples is likely related to the anhydrous nature of the volar pads and the supporting skeletal structure, and their confined position between major joints of the hands and feet.
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Affiliation(s)
- Amanda K Kingston
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona, USA
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Dufresnes C, Miquel C, Remollino N, Biollaz F, Salamin N, Taberlet P, Fumagalli L. Howling from the past: historical phylogeography and diversity losses in European grey wolves. Proc Biol Sci 2018; 285:rspb.2018.1148. [PMID: 30068681 DOI: 10.1098/rspb.2018.1148] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf (Canis lupus) is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Christian Miquel
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Nadège Remollino
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - François Biollaz
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Route Pra de Louetse 32, 1968 Mase, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Computational Biology University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Pierre Taberlet
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
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Barnsley JE, Tay EJ, Gordon KC, Thomas DB. Frequency dispersion reveals chromophore diversity and colour-tuning mechanism in parrot feathers. R Soc Open Sci 2018; 5:172010. [PMID: 30109049 PMCID: PMC6083696 DOI: 10.1098/rsos.172010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Variation in animal coloration is often viewed as the result of chemically distinct pigments conferring different hues. The role of molecular environment on hue tends to be overlooked as analyses are mostly performed on free pigments extracted from the integument. Here we analysed psittacofulvin pigments within parrot feathers to explore whether the in situ organization of pigments may have an effect on hue. Resonance Raman spectra from a red region of a yellow-naped amazon Amazona auropalliata tail feather show frequency dispersion, a phenomenon that is related to the presence of a range of molecular conformations (and multiple chromophores) in the pigment, whereas spectra from a yellow region on the same feather do not show the same evidence for multiple chromophores. Our findings are consistent with non-isomeric psittacofulvin pigments behaving as a single chromophore in yellow feather barbs, which implies that psittacofulvins are dispersed into a structurally disordered mixture in yellow feathers compared with red feathers. Frequency dispersion in red barbs may instead indicate that pigments are structurally organized through molecule-molecule interactions. Major differences in the hues of parrot feathers are thus associated with differences in the organization of pigments within feathers.
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Affiliation(s)
- Jonathan E. Barnsley
- Department of Chemistry, University of Otago, Dunedin, New Zealand
- The Dodd-Walls Centre, University of Otago, Dunedin, New Zealand
| | - Elliot J. Tay
- Department of Chemistry, University of Otago, Dunedin, New Zealand
- The Dodd-Walls Centre, University of Otago, Dunedin, New Zealand
| | - Keith C. Gordon
- Department of Chemistry, University of Otago, Dunedin, New Zealand
- The Dodd-Walls Centre, University of Otago, Dunedin, New Zealand
| | - Daniel B. Thomas
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
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Cross EL, Harper EM, Peck LS. A 120-year record of resilience to environmental change in brachiopods. Glob Chang Biol 2018; 24:2262-2271. [PMID: 29536586 PMCID: PMC6850138 DOI: 10.1111/gcb.14085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 12/25/2017] [Accepted: 01/17/2018] [Indexed: 06/01/2023]
Abstract
The inability of organisms to cope in changing environments poses a major threat to their survival. Rising carbon dioxide concentrations, recently exceeding 400 μatm, are rapidly warming and acidifying our oceans. Current understanding of organism responses to this environmental phenomenon is based mainly on relatively short- to medium-term laboratory and field experiments, which cannot evaluate the potential for long-term acclimation and adaptation, the processes identified as most important to confer resistance. Here, we present data from a novel approach that assesses responses over a centennial timescale showing remarkable resilience to change in a species predicted to be vulnerable. Utilising museum collections allows the assessment of how organisms have coped with past environmental change. It also provides a historical reference for future climate change responses. We evaluated a unique specimen collection of a single species of brachiopod (Calloria inconspicua) collected every decade from 1900 to 2014 from one sampling site. The majority of brachiopod shell characteristics remained unchanged over the past century. One response, however, appears to reinforce their shell by constructing narrower punctae (shell perforations) and laying down more shell. This study indicates one of the most calcium-carbonate-dependent species globally to be highly resilient to environmental change over the last 120 years and provides a new insight for how similar species might react and possibly adapt to future change.
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Affiliation(s)
- Emma L. Cross
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
- British Antarctic SurveyNatural Environment Research CouncilCambridgeUK
| | | | - Lloyd S. Peck
- British Antarctic SurveyNatural Environment Research CouncilCambridgeUK
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Tiee MS, Harrigan RJ, Thomassen HA, Smith TB. Ghosts of infections past: using archival samples to understand a century of monkeypox virus prevalence among host communities across space and time. R Soc Open Sci 2018; 5:171089. [PMID: 29410823 PMCID: PMC5792900 DOI: 10.1098/rsos.171089] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/15/2017] [Indexed: 06/08/2023]
Abstract
Infectious diseases that originate from multiple wildlife hosts can be complex and problematic to manage. A full understanding is further limited by large temporal and spatial gaps in sampling. However, these limitations can be overcome, in part, by using historical samples, such as those derived from museum collections. Here, we screened over 1000 museum specimens collected over the past 120 years to examine the historical distribution and prevalence of monkeypox virus (MPXV) in five species of African rope squirrel (Funisciurus sp.) collected across Central Africa. We found evidence of MPXV infections in host species as early as 1899, half a century earlier than the first recognized case of MPXV in 1958, supporting the suggestion that historic pox-like outbreaks in humans and non-human primates may have been caused by MPXV rather than smallpox as originally thought. MPX viral DNA was found in 93 of 1038 (9.0%) specimens from five Funisciurus species (F. anerythrus, F. carruthersi, F. congicus, F. lemniscatus and F. pyrropus), of which F. carruthersi and pyrropus had not previously been identified as potential MPXV hosts. We additionally documented relative prevalence rates of infection in museum specimens of Funisciurus and examined the spatial and temporal distribution of MPXV in these potential host species across nearly a hundred years (1899-1993).
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Affiliation(s)
- Madeline S. Tiee
- Department of Ecology and Evolutionary Biology, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Henri A. Thomassen
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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Cleland TP, Schroeter ER, Feranec RS, Vashishth D. Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics. Proc Biol Sci 2017; 283:rspb.2016.0593. [PMID: 27306052 DOI: 10.1098/rspb.2016.0593] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 11/12/2022] Open
Abstract
Vertebrate fossils have been collected for hundreds of years and are stored in museum collections around the world. These remains provide a readily available resource to search for preserved proteins; however, the vast majority of palaeoproteomic studies have focused on relatively recently collected bones with a well-known handling history. Here, we characterize proteins from the nasal turbinates of the first Castoroides ohioensis skull ever discovered. Collected in 1845, this is the oldest museum-curated specimen characterized using palaeoproteomic tools. Our mass spectrometry analysis detected many collagen I peptides, a peptide from haemoglobin beta, and in vivo and diagenetic post-translational modifications. Additionally, the identified collagen I sequences provide enough resolution to place C. ohioensis within Rodentia. This study illustrates the utility of archived museum specimens for both the recovery of preserved proteins and phylogenetic analyses.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Deepak Vashishth
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Peacock MM, Hekkala ER, Kirchoff VS, Heki LG. Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct. R Soc Open Sci 2017; 4:171253. [PMID: 29291110 PMCID: PMC5717685 DOI: 10.1098/rsos.171253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/13/2017] [Indexed: 05/05/2023]
Abstract
Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.
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Affiliation(s)
- Mary M. Peacock
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Ecology, Evolution, and Conservation Biology Interdisciplinary Program, University of Nevada, Reno, NV 89557, USA
| | - Evon R. Hekkala
- Department of Biological Sciences, Fordham University, New York, NY 10458, USA
| | - Veronica S. Kirchoff
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- United States Department of Agriculture, Agricultural Research Service, Reno, NV 89512, USA
| | - Lisa G. Heki
- United States Fish and Wildlife Service, Lahontan National Fish Hatchery Complex, 1340 Financial Blvd, Suite 234, Reno, NV 89502, USA
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Roberts DL, Jarić I, Solow AR. On the functional extinction of the Passenger Pigeon. Conserv Biol 2017; 31:1192-1195. [PMID: 28233409 DOI: 10.1111/cobi.12914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 02/10/2017] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
The Passenger Pigeon (Ectopistes migratorius) was a social breeder, and it has been suggested that the species experienced functional extinction, defined as a total reproductive failure, prior to its actual extinction in the early years of the 20th century. We applied a novel randomization test based on the relative times of the most recent egg- and skin-specimen sightings (i.e., recorded date of specimen collection) to test for functional extinction. For a total of 6 eggs and 27 skins, the observed significance level was 0.38, which indicated that the species did not become functionally extinct. Thus, proposals to reverse its rapid decline in the late 19th century could have been successful.
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Affiliation(s)
- David L Roberts
- Durrell Institute of Conservation and Ecology, School of Anthropology & Conservation, Marlowe Building, University of Kent, Canterbury, Kent, CT2 7NR, U.K
| | - Ivan Jarić
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
- Institute for Multidisciplinary Research, University of Belgrade, KnezaViseslava 1, 11000, Belgrade, Serbia
| | - Andrew R Solow
- Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, U.S.A
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Thomas JE, Carvalho GR, Haile J, Martin MD, Castruita JAS, Niemann J, Sinding MS, Sandoval-Velasco M, Rawlence NJ, Fuller E, Fjeldså J, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M. An ‛Aukward' Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks. Genes (Basel) 2017; 8:E164. [PMID: 28617333 DOI: 10.3390/genes8060164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 06/09/2017] [Indexed: 11/16/2022] Open
Abstract
One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller’s candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars’ minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.
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Poquita-Du RC, Ng CSL, Loo JB, Afiq-Rosli L, Tay YC, Todd PA, Chou LM, Huang D. New evidence shows that Pocillopora ' Pocilloporadamicornis-like' corals in Singapore are actually Pocillopora acuta (Scleractinia: Pocilloporidae). Biodivers Data J 2017:e11407. [PMID: 28325983 PMCID: PMC5345112 DOI: 10.3897/bdj.5.e11407] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/07/2017] [Indexed: 12/03/2022] Open
Affiliation(s)
- Rosa Celia Poquita-Du
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Chin Soon Lionel Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Jun Bin Loo
- School of Chemical and Life Sciences, Singapore Polytechnic, Singapore, Singapore
| | - Lutfi Afiq-Rosli
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Ywee Chieh Tay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Peter A Todd
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Loke Ming Chou
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
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Li C, Corrigan S, Yang L, Straube N, Harris M, Hofreiter M, White WT, Naylor GJ. DNA capture reveals transoceanic gene flow in endangered river sharks. Proc Natl Acad Sci U S A 2015; 112:13302-7. [PMID: 26460025 DOI: 10.1073/pnas.1508735112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.
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Hernández-Triana LM, Prosser SW, Rodríguez-Perez MA, Chaverri LG, Hebert PDN, Gregory TR. Recovery of DNA barcodes from blackfly museum specimens (Diptera: Simuliidae) using primer sets that target a variety of sequence lengths. Mol Ecol Resour 2013; 14:508-18. [PMID: 24299419 DOI: 10.1111/1755-0998.12208] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/20/2013] [Accepted: 11/22/2013] [Indexed: 11/29/2022]
Abstract
In this study, we evaluated the efficacy of various primers for the purpose of DNA barcoding old, pinned museum specimens of blackflies (Diptera: Simuliidae). We analysed 271 pinned specimens representing two genera and at least 36 species. Due to the age of our material, we targeted overlapping DNA fragments ranging in size from 94 to 407 bp. We were able to recover valid sequences from 215 specimens, of which 18% had 500- to 658-bp barcodes, 36% had 201- to 499-bp barcodes and 46% had 65- to 200-bp barcodes. Our study demonstrates the importance of choosing suitable primers when dealing with older specimens and shows that even very short sequences can be diagnostically informative provided that an appropriate gene region is used. Our study also highlights the lack of knowledge surrounding blackfly taxonomy, and we briefly discuss the need for further phylogenetic studies in this socioeconomically important family of insects.
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Affiliation(s)
- L M Hernández-Triana
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Hoffmann D, Geller-Grimm F. A catalog of bird specimens associated with Prince Maximilian of Wied-Neuwied and potential type material in the natural history collection in Wiesbaden. Zookeys 2013:81-93. [PMID: 24294100 PMCID: PMC3837487 DOI: 10.3897/zookeys.353.4198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 11/12/2013] [Indexed: 11/25/2022] Open
Abstract
Bird specimens collected by 19th century explorer and ornithologist Prince Maximilian of Wied-Neuwied form one of the foundation collections of the American Museum of Natural History in New York. However, parts of his collection remained in Germany and came to the Museum Wiesbaden. Since Wied described numerous new species without designating types, some of these specimens might be type material. Here we present a catalog of the 30 Wiesbaden specimens associated with him and discuss their potential type status. We conclude that 17 individuals in 11 species are potential type specimens that should be considered in future taxonomic work.
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Affiliation(s)
- Dorothee Hoffmann
- Museum Wiesbaden - Hessisches Landesmuseum für Kunst und Natur, Naturhistorische Sammlungen, Friedrich-Ebert-Allee 2, 65185 Wiesbaden, Germany
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Niland EE, McGuire A, Cox MH, Sandusky GE. High quality DNA obtained with an automated DNA extraction method with 70+ year old formalin-fixed celloidin-embedded (FFCE) blocks from the indiana medical history museum. Am J Transl Res 2012; 4:198-205. [PMID: 22611472 PMCID: PMC3353536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 01/19/2012] [Indexed: 06/01/2023]
Abstract
DNA and RNA have been used as markers of tissue quality and integrity throughout the last few decades. In this research study, genomic quality DNA of kidney, liver, heart, lung, spleen, and brain were analyzed in tissues from post-mortem patients and surgical cancer cases spanning the past century. DNA extraction was performed on over 180 samples from: 70+ year old formalin-fixed celloidin-embedded (FFCE) tissues, formalin-fixed paraffin-embedded (FFPE) tissue samples from surgical cases and post-mortem cases from the 1970's, 1980's, 1990's, and 2000's, tissues fixed in 10% neutral buffered formalin/stored in 70% ethanol from the 1990's, 70+ year old tissues fixed in unbuffered formalin of various concentrations, and fresh tissue as a control. To extract DNA from FFCE samples and ethanol-soaked samples, a modified standard operating procedure was used in which all tissues were homogenized, digested with a proteinase K solution for a long period of time (24-48 hours), and DNA was extracted using the Autogen Flexstar automated extraction machine. To extract DNA from FFPE, all tissues were soaked in xylene to remove the paraffin from the tissue prior to digestion, and FFPE tissues were not homogenized. The results were as follows: celloidin-embedded and paraffin-embedded tissues yielded the highest DNA concentration and greatest DNA quality, while the formalin in various concentrations, and long term formalin/ethanol-stored tissue yielded both the lowest DNA concentration and quality of the tissues tested. The average DNA yield for the various fixatives was: 367.77 μg/ mL FFCE, 590.7 μg/mL FFPE, 53.74 μg/mL formalin-fixed/70% ethanol-stored and 33.2 μg/mL unbuffered formalin tissues. The average OD readings for FFCE, FFPE, formalin-fixed/70% ethanol-stored tissues, and tissues fixed in unbuffered formalin were 1.86, 1.87, 1.43, and 1.48 respectively. The results show that usable DNA can be extracted from tissue fixed in formalin and embedded in celloidin or paraffin from the early 1900's to present, and may be amplified through PCR and used for clinical and experimental studies.
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Hajibabaei M, deWaard JR, Ivanova NV, Ratnasingham S, Dooh RT, Kirk SL, Mackie PM, Hebert PDN. Critical factors for assembling a high volume of DNA barcodes. Philos Trans R Soc Lond B Biol Sci 2005; 360:1959-67. [PMID: 16214753 PMCID: PMC1609220 DOI: 10.1098/rstb.2005.1727] [Citation(s) in RCA: 281] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Large-scale DNA barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. To satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. In this paper we discuss the prospects for establishing high volume DNA barcoding facilities by evaluating key steps in the analytical chain from specimens to barcodes. Alliances with members of the taxonomic community represent the most effective strategy for provisioning the analytical chain with specimens. The optimal protocols for DNA extraction and subsequent PCR amplification of the barcode region depend strongly on their condition, but production targets of 100K barcode records per year are now feasible for facilities working with compliant specimens. The analysis of museum collections is currently challenging, but PCR cocktails that combine polymerases with repair enzyme(s) promise future success. Barcode analysis is already a cost-effective option for species identification in some situations and this will increasingly be the case as reference libraries are assembled and analytical protocols are simplified.
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Affiliation(s)
- Mehrdad Hajibabaei
- Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, ON, Canada N1G 2W1.
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